diff --git a/.gitignore b/.gitignore index d10591ab..8076f8e3 100644 --- a/.gitignore +++ b/.gitignore @@ -21,7 +21,6 @@ dist/ js/src/inline.js coverage/ .nyc_output/ -py/escher/package.json # site files 1-0-0 @@ -32,3 +31,5 @@ package-lock.json node_modules/ .yarnclean .mypy_cache/ +/TODO.txt +/py/escher/package.json diff --git a/README.md b/README.md index b0145a45..3ed7c70f 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,7 @@ [![Travis](https://img.shields.io/travis/zakandrewking/escher/master.svg)](https://travis-ci.org/zakandrewking/escher) [![Coverage Status](https://img.shields.io/coveralls/zakandrewking/escher/master.svg)](https://coveralls.io/github/zakandrewking/escher?branch=master) -Escher -====== +# Escher Escher is a web-based tool to build, view, share, and embed metabolic maps. The easiest way to use Escher is to browse or build maps on the @@ -33,7 +32,116 @@ building, sharing, and embedding data-rich visualizations of biological pathways*, PLOS Computational Biology 11(8): e1004321. doi:[10.1371/journal.pcbi.1004321](http://dx.doi.org/10.1371/journal.pcbi.1004321) -Built at SBRG -============= +Escher was developed at [SBRG](http://systemsbiology.ucsd.edu/). Funding was +provided by [The National Science Foundation Graduate Research Fellowship](https://www.nsfgrfp.org) +under Grant no. DGE-1144086, The European Commission as part of a Marie Curie +International Outgoing Fellowship within the EU 7th Framework Program for +Research and Technological Development ([EU project AMBiCon, 332020](http://ec.europa.eu/research/mariecurieactions/node_en)), +and [The Novo Nordisk Foundation](http://novonordiskfonden.dk/) +through [The Center for Biosustainability](https://www.biosustain.dtu.dk/) +at the Technical University of Denmark (NNF10CC1016517) -[![SBRG](https://raw.githubusercontent.com/zakandrewking/escher/master/py/escher/static/img/sbrg-logo.png)](http://systemsbiology.ucsd.edu/) +# Building and testing Escher + +## JavaScript + +First, install dependencies with [npm](https://www.npmjs.com) (or you can use +[yarn](https://yarnpkg.com)): + +``` +npm install +``` + +Escher uses webpack to manage the build process. To run typical build steps, just run: + +``` +npm run build +``` + +You can run a development server with: + +``` +npm run start +# or for live updates when the source code changes: +npm run watch +``` + +To test the JavaScript files, run: + +``` +npm run test +``` + +## Python + +Escher has a Python package for generating Escher visualizations from within a +Python data anlaysis session. To learn more about using the features of the +Python package, check out the documentation: + +https://escher.readthedocs.io/en/latest/escher-python.html + +For development of the Python package, first build the JavaScript package and +copy it over to the `py` directory with these commands in the Escher root: + +``` +npm install +npm run build +npm run copy +``` + +Then in the `py` directory, install the Python package: + +``` +cd py +pip install -e . # installs escher in develop mode and dependencies +``` + +For Python testing, run this in the `py` directory: + +``` +cd py +pytest +``` + +## Jupyter extensions + +To develop the Jupyter notebook and Jupyter Lab extensions, you will need +install them with symlinks (the typical installation is describe in the +[docs](https://escher.readthedocs.io/en/latest/escher-python.html)). + +First, install the Python package for development as described above. + +For the Jupyter notebooks, run: + +``` +cd py +jupyter nbextension install --py --symlink --sys-prefix escher +jupyter nbextension enable --py --sys-prefix escher +``` + +When you make changes, you will need to `yarn copy` and refresh notebook browser +tab. + +For Jupyter Lab, run (in the root directory): + +``` +yarn watch # keep this running as a separate process +jupyter labextension install @jupyter-widgets/jupyterlab-manager +jupyter labextension link +jupyter lab --watch +``` + +If you don't see changes when you edit the code, try refreshing or restarting +`jupyter lab --watch`. + +## Docs + +Build and run the docs:: + +``` +cd docs +make html +cd _build/html +python -m SimpleHTTPServer # python 2 +python -m http.server # python 3 +``` diff --git a/docs/contribute_maps.rst b/docs/contribute_maps.rst index 6a74dd1c..4c5beec2 100644 --- a/docs/contribute_maps.rst +++ b/docs/contribute_maps.rst @@ -34,28 +34,6 @@ Once you have a COBRA model, you can follow these steps: iMM904.Amino acid biosynthesis.json -5. (Optional) Once you have a set of subsystem maps, you can set up a local - Escher server so that subsystem maps appear in the "quick jump" menu in the - bottom right corner of the screen (as seen here_ for iJO1366). To set this - up, you will need to start a local server as describe in - :ref:`local-server`. Next, find your local cache directory by running this - command in a terminal:: - - python -c "import escher; print(escher.get_cache_dir(name='maps'))" - - This will print the location of the local maps cache. Add your new subsystem - maps to cache folder. Now, when you run the server (described in - :ref:`local-server`), you should see that quick jump menu appear. - - NOTE: The cache directory is organized into folders for organisms. You can - use these folder for filtering by organism on the local launch page, or you - can place the maps in the top directory. - - NOTE 2: A similar approach can be used to access your models from the local - launch page. Place maps in the folder indicated by:: - - python -c "import escher; print(escher.get_cache_dir(name='models'))" - Building from an existing map for a similar organism ---------------------------------------------------- diff --git a/docs/development.rst b/docs/development.rst index 44cd7774..a56ff6e8 100644 --- a/docs/development.rst +++ b/docs/development.rst @@ -1,9 +1,15 @@ Developing with Escher ---------------------- -If you are interested in developing Escher or just want to try out the source -code, this is the place to start. You might also want to check out the the -`Gitter chat room`_ and the `Development Roadmap`_. +If you are interested in developing software using Escher as a dependency, this +is the place to start. If want contribute to development of Escher, then check +out the GitHub repository (instruction for building and testing the project are +in the README): + +https://github.com/zakandrewking/escher + +You might also want to check out the the `Gitter chat room`_ and the +`Development Roadmap`_. Using the static JavaScript and CSS files ========================================= @@ -49,41 +55,6 @@ If you are using JavaScript ES6 import syntax, the default export is Builder:: import * as escher from 'escher' console.log(Builder, escher.Builder, escher.libs.preact) -Building and testing Escher -=========================== - -First, install dependencies with npm:: - - npm install - -Escher uses grunt to manage the build process. To run typical build steps, just run:: - - npm run compile - -To test the JavaScript files, run:: - - npm run test - -For Python testing, run this in the ``py`` directory:: - - python setup.py test - -Build the static website:: - - python setup.py build_gh - -Clear static website files:: - - python setup.py clean - -Build and run the docs:: - - cd docs - make html - cd _build/html - python -m SimpleHTTPServer # python 2 - python -m http.server # python 3 - Generating and reading Escher and COBRA files ============================================= diff --git a/docs/escher-python.rst b/docs/escher-python.rst index ecb594c2..1a05deda 100644 --- a/docs/escher-python.rst +++ b/docs/escher-python.rst @@ -16,6 +16,15 @@ directly:: python setup.py install +To install the Jupyter notebook extension:: + + jupyter nbextension enable --py --sys-prefix escher # can be skipped for notebook 5.3 and above + +To install the Jupyter Lab extension:: + + jupyter labextension install @jupyter-widgets/jupyterlab-manager + jupyter labextension install escher + Dependencies should install automatically, but they are: - `Jinja2`_ @@ -58,20 +67,6 @@ Here are example notebooks to get started with: - `JavaScript development and offline maps`_ - `Generate JSON models in COBRApy`_ -.. _`local-server`: - -Running the local server -======================== - -You can run your own local server if you want to use Escher offline or explore -your own maps with the homepage browser. To get started, install the Python -package and run from any directory by calling:: - - python -m escher.server - -This starts a server at http://localhost:7778. You can also choose another port:: - - python -m escher.server --port=8005 .. _`source files`: https://github.com/zakandrewking/escher/releases diff --git a/docs/getting_started.rst b/docs/getting_started.rst index 986f8daf..cf811a5b 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -7,39 +7,6 @@ Introduction **Escher** is here to help you visualize pathway maps. But, if you have never heard of a pathway map, you might appreciate a quick introduction. -What are pathway maps? -^^^^^^^^^^^^^^^^^^^^^^ - -To understand pathway maps, it is useful to think about the general organization -of a cell. At the smallest level, molecules in a cell are arranged in -three-dimensional structures, and these structures determine many of the -functions that take place in a cell. For example, the 3D structure of an enzyme -determines the biochemical reactions that it can catalyze. These structures can -be visualized in 3D using tools like `Jmol`_ (as in this `example structure`_). - -The DNA sequence is a second fundamental level of biological organization. DNA -sequences are the blueprints for all the machinery of the cell, and they can be -visualized as a one-dimensional series of bases (ATCG) using tools like the -`UCSC genome browser`_. - -To use a football analogy, the 3D molecular structures are akin to the players -on the field, and the information in the DNA sequence is like the playbook on -the sidelines. But, football would not be very interesting if the players never -took to the field and executed those plays. So, we are missing this level of -detail: *the execution of biological plans by the molecular players*. - -What we are missing is the biochemical reaction network. Proteins in the cell -catalyze the conversion of substrate molecules into product molecules, and these -*reactions* are responsible for generating energy, constructing cellular machinery -and structures, detecting molecules in the environment, signaling, and -more. Biochemical reactions can be grouped into pathways when they work in -concert to carry out a function. (If a reaction is a football play, then the -pathway is a `drive`_). And Escher can be used to visualize these reactions and -pathways. Together, we call these visualizations **pathway maps**. - -Escher to the rescue -^^^^^^^^^^^^^^^^^^^^ - Many Escher maps represent *metabolic* pathways, and Escher was developed at the `Systems Biology Research Group`_ where we have been building genome-scale models of metabolism over the past fifteen years. However, Escher is not limited to diff --git a/docs/javascript_api.rst b/docs/javascript_api.rst index 8c517ea0..8c5d706c 100644 --- a/docs/javascript_api.rst +++ b/docs/javascript_api.rst @@ -42,11 +42,10 @@ JavaScript API .. js:attribute:: options.use_3d_transform - (Default: Chooses a good option by testing the browser) If true, then - use CSS3 3D transforms to speed up panning and zooming. This feature - will only work on browsers that `support the 3D transforms`_. It works - best in the latest versions of Chrome, Firefox and Internet - Explorer. Safari works better with this turned off. + (Default: false) If true, then use CSS3 3D transforms to speed up + panning and zooming. This feature will only work on browsers that + `support the 3D transforms`_. In general, this is no longer necessary + for modern browsers and hardware with small to medium sized maps. .. js:attribute:: options.enable_editing @@ -292,30 +291,35 @@ JavaScript API .. js:attribute:: options.tooltip_component - (Default: ``escher.Tooltip.DefaultTooltip``) A function or `tinier`_ - component to show when hoving over reactions, metabolites, and - genes. If a function is passed, the function will be called with a - single object as an argument with two attributes: state - containing - the data associated with that reaction, metabolite or gene; and el - a - HTML node that you can render content in. If you need to manage state - for your tooltip, you can alternatively pass a tinier component. See + (Default: ``escher.Tooltip.DefaultTooltip``) A `Preact`_ Component to + show when hoving over reactions, metabolites, and genes. See ``escher.Tooltip.DefaultTooltip`` in the source code for an example of - a tinier component that defines the default tooltips. + a Preact component that defines the default tooltips. And see the + :doc:`Tooltip Tutorial ` for more tips on + getting started with custom tooltips. .. js:attribute:: options.enable_tooltips - (Default: `[`label`]`) Determines the mouseover or touch event required - to show the related tooltip.['label'] will show tooltips upon mouseover - or touch of the reaction or metabolite labels whereas ['object'] will - show the the tooltips over the reaction line segments and metabolite - circles. Can be set as an empty array to disable tooltips or can have - both options passed in to enable tooltips over both labels and objects. + (Default: ``['label']``) Determines the mouseover or touch + event required to show the related tooltip.['label'] will show + tooltips upon mouseover or touch of the reaction or metabolite labels + whereas ['object'] will show the the tooltips over the reaction line + segments and metabolite circles. Can be set as an empty array to + disable tooltips or can have both options passed in to enable tooltips + over both labels and objects. + + .. js:attribute:: options.enable_keys_with_tooltip + + (Default: ``true``) Set this to ``false`` to disallow non-prefixed + (i.e. not starting with ctrl or cmd) keyboard shortcuts when the + tooltip is visible. This is useful if your tooltip has text inputs. **Callbacks** .. js:attribute:: options.first_load_callback - A function to run after loading the Builder. + A function to run after loading the Builder. The Builder instance is + passed as a single argument to the callback. .. **Callbacks** @@ -397,4 +401,4 @@ JavaScript API turn of the gene_reaction_rules. .. _`support the 3D transforms`: http://caniuse.com/#feat=transforms3d -.. _`tinier`: https://github.com/zakandrewking/tinier +.. _`Preact`: https://preactjs.com/ diff --git a/docs/notebooks/Escher Widget Example.ipynb b/docs/notebooks/Escher Widget Example.ipynb new file mode 100644 index 00000000..ce12acd7 --- /dev/null +++ b/docs/notebooks/Escher Widget Example.ipynb @@ -0,0 +1,161 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [], + "source": [ + "from escher import Builder" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [], + "source": [ + "import cobra" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [], + "source": [ + "core = cobra.io.load_json_model('/Users/zaking/Downloads/e_coli_core.json')" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [], + "source": [ + "builder = Builder(height=600, map_name=None, model_name='iJO1366', model_json='https://escher.github.io/1-0-0/5/models/Escherichia%20coli/e_coli_core.json')" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "d6adebc2155f456d9bf24f45910a2d0c", + "version_major": 2, + "version_minor": 0 + }, + "text/html": [ + "

Failed to display Jupyter Widget of type Builder.

\n", + "

\n", + " If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n", + " that the widgets JavaScript is still loading. If this message persists, it\n", + " likely means that the widgets JavaScript library is either not installed or\n", + " not enabled. See the Jupyter\n", + " Widgets Documentation for setup instructions.\n", + "

\n", + "

\n", + " If you're reading this message in another frontend (for example, a static\n", + " rendering on GitHub or NBViewer),\n", + " it may mean that your frontend doesn't currently support widgets.\n", + "

\n" + ], + "text/plain": [ + "Builder(height=600)" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "builder" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": {}, + "outputs": [], + "source": [ + "builder.map_json = 'https://escher.github.io/1-0-0/5/maps/Escherichia%20coli/e_coli_core.Core%20metabolism.json'" + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "metadata": {}, + "outputs": [], + "source": [ + "builder.model = core" + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "metadata": {}, + "outputs": [], + "source": [ + "builder.height = 500" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'[{\"map_name\": \"e_coli_core.Core metabolism\", \"map_id\": \"0df3827fde8464e80f455a773a52c274\", \"map_description\": \"E. coli core metabolic network\\\\nLast Modified Fri Dec 05 2014 16:39:44 GMT-0800 (PST)\", 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\"node_type\": \"midmarker\"}, \"1576961\": {\"y\": 4614.0, \"x\": 3257.0, \"node_type\": \"midmarker\"}, \"1576960\": {\"y\": 3341.0, \"x\": 2582.0, \"node_type\": \"multimarker\"}, \"1576969\": {\"y\": 3228.0, \"x\": 5032.0, \"node_type\": \"midmarker\"}, \"1576499\": {\"node_is_primary\": false, \"name\": \"H+\", \"label_x\": 3522.892333984375, \"node_type\": \"metabolite\", \"y\": 1080.287841796875, \"x\": 3510.0, \"bigg_id\": \"h_c\", \"label_y\": 1099.0072021484375}, \"1576999\": {\"y\": 1041.710205078125, \"x\": 1056.5867919921875, \"node_type\": \"multimarker\"}}, \"canvas\": {\"y\": 314.36893920898433, \"x\": 7.857062530517567, \"height\": 4860.457037353515, \"width\": 5894.515691375733}, \"text_labels\": {}}]'" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "builder._loaded_map_json" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.5" + }, + "widgets": { + "application/vnd.jupyter.widget-state+json": { + "state": {}, + "version_major": 2, + "version_minor": 0 + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/docs/python_api.rst b/docs/python_api.rst index 113df56c..b11a65b2 100644 --- a/docs/python_api.rst +++ b/docs/python_api.rst @@ -8,16 +8,8 @@ Python API .. _`cache`: -Cache ------ - -.. autofunction:: get_cache_dir - -.. autofunction:: clear_cache - -.. autofunction:: list_cached_maps - -.. autofunction:: list_cached_models +Map Server +---------- .. autofunction:: list_available_maps diff --git a/jupyter/lab-extension.js b/jupyter/lab-extension.js new file mode 100644 index 00000000..6fcdc28d --- /dev/null +++ b/jupyter/lab-extension.js @@ -0,0 +1,13 @@ +const escher = require('../dist/escher.min') +const base = require('@jupyter-widgets/base') + +module.exports = { + id: 'jupyter.extensions.jupyter-escher', + requires: [base.IJupyterWidgetRegistry], + activate: (app, widgets) => widgets.registerWidget({ + name: 'jupyter-escher', + version: escher.version, + exports: escher.initializeJupyterWidget() + }), + autoStart: true +} diff --git a/jupyter/notebook-extension.js b/jupyter/notebook-extension.js new file mode 100644 index 00000000..56cb2c58 --- /dev/null +++ b/jupyter/notebook-extension.js @@ -0,0 +1,34 @@ +// This file contains the javascript that is run when the notebook is loaded. +// It contains some requirejs configuration and the `load_ipython_extension` +// which is required for any notebook extension. +// +// Some static assets may be required by the custom widget javascript. The base +// url for the notebook is not known at build time and is therefore computed +// dynamically. +window.__webpack_public_path__ = document.querySelector('body').getAttribute('data-base-url') + 'nbextensions/jupyter-escher' + +// Pull jupyter object out when importing escher +window.define( + 'jupyter-escher-intercept', + ['escher'], + escher => escher.initializeJupyterWidget() +) + +// Configure requirejs +if (window.require) { + window.require.config({ + map: { + '*': { + 'jupyter-escher': 'jupyter-escher-intercept' + }, + 'jupyter-escher-intercept': { + escher: 'nbextensions/jupyter-escher/escher.min' + } + } + }) +} + +// Export the required load_ipython_extension +module.exports = { + load_ipython_extension: () => {} +} diff --git a/package.json b/package.json index 392c0939..86656961 100644 --- a/package.json +++ b/package.json @@ -19,7 +19,8 @@ "repository": "https://github.com/zakandrewking/escher", "bugs": "https://github.com/zakandrewking/escher/issues", "files": [ - "dist/*" + "dist/*", + "jupyter/*" ], "main": "/dist/escher.js", "engines": { @@ -53,6 +54,7 @@ "webpack-node-externals": "^1.6.0" }, "dependencies": { + "@jupyter-widgets/base": "^1.1.10", "baconjs": "^0.7.71", "d3-brush": "https://github.com/zakandrewking/d3-brush.git", "d3-drag": "^1.0.2", @@ -72,9 +74,9 @@ "build": "./node_modules/.bin/webpack --config webpack.prod.js", "watch": "./node_modules/.bin/webpack --config webpack.prod.js --watch", "start": "./node_modules/.bin/webpack-dev-server --config webpack.dev.js", - "clean": "rm -r dist/*", + "clean": "rm -r dist/* && rm py/escher/static/*", "test": "./node_modules/.bin/mocha-webpack --webpack-config webpack.test.js \"src/tests/*.js\"", - "copy": "cp package.json py/escher/ && cp dist/* py/escher/static/escher/ && cp jsonschema/* py/escher/static/jsonschema/", + "copy": "cp package.json py/escher/static/ && cp jupyter/notebook-extension.js py/escher/static/extension.js && cp dist/escher.min.* py/escher/static/ && cp jsonschema/* py/escher/static/", "coverage": "./node_modules/.bin/cross-env NODE_ENV=coverage ./node_modules/.bin/nyc --reporter=text-lcov npm run test | ./node_modules/.bin/coveralls" }, "nyc": { @@ -83,5 +85,8 @@ ], "instrument": false, "sourceMap": false + }, + "jupyterlab": { + "extension": "jupyter/lab-extension" } } diff --git a/py/MANIFEST.in b/py/MANIFEST.in new file mode 100644 index 00000000..aac14555 --- /dev/null +++ b/py/MANIFEST.in @@ -0,0 +1,2 @@ +recursive-include escher/static *.* +include jupyter-escher.json \ No newline at end of file diff --git a/py/README.md b/py/README.md index c1ba6b0d..31ce8b46 100644 --- a/py/README.md +++ b/py/README.md @@ -1,10 +1,3 @@ -Escher Python Package ---------------------- +For documentation on the Escher Python package, see: -To install from source, run: - -``` -python setup.py install -# or -python setup.py develop -``` +https://escher.readthedocs.io/en/stable/escher-python.html diff --git a/py/escher/__init__.py b/py/escher/__init__.py index 265f18fc..499509ae 100644 --- a/py/escher/__init__.py +++ b/py/escher/__init__.py @@ -1,6 +1,20 @@ -from escher.version import __version__, __schema_version__, __map_model_version__ +from escher.version import ( + __version__, + __schema_version__, + __map_model_version__, +) -from escher.plots import (Builder, get_cache_dir, clear_cache, list_cached_maps, - list_cached_models, list_available_maps, - list_available_models) +from escher.plots import ( + Builder, + list_available_maps, + list_available_models, +) + +def _jupyter_nbextension_paths(): + return [{ + 'section': 'notebook', + 'src': 'static', + 'dest': 'jupyter-escher', + 'require': 'jupyter-escher/extension' + }] diff --git a/py/escher/appdirs.py b/py/escher/appdirs.py deleted file mode 100644 index 94c592fc..00000000 --- a/py/escher/appdirs.py +++ /dev/null @@ -1,346 +0,0 @@ -#!/usr/bin/env python -# Copyright (c) 2005-2010 ActiveState Software Inc. - -"""Utilities for determining application-specific dirs. - -See for details and usage. -""" -# Dev Notes: -# - MSDN on where to store app data files: -# http://support.microsoft.com/default.aspx?scid=kb;en-us;310294#XSLTH3194121123120121120120 -# - Mac OS X: http://developer.apple.com/documentation/MacOSX/Conceptual/BPFileSystem/index.html -# - XDG spec for Un*x: http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html - -__version_info__ = (1, 2, 0) -__version__ = '.'.join(map(str, __version_info__)) - - -import sys -import os - -PY3 = sys.version_info[0] == 3 - -if PY3: - unicode = str - -class AppDirsError(Exception): - pass - - - -def user_data_dir(appname, appauthor=None, version=None, roaming=False): - r"""Return full path to the user-specific data dir for this application. - - "appname" is the name of application. - "appauthor" (only required and used on Windows) is the name of the - appauthor or distributing body for this application. Typically - it is the owning company name. - "version" is an optional version path element to append to the - path. You might want to use this if you want multiple versions - of your app to be able to run independently. If used, this - would typically be ".". - "roaming" (boolean, default False) can be set True to use the Windows - roaming appdata directory. That means that for users on a Windows - network setup for roaming profiles, this user data will be - sync'd on login. See - - for a discussion of issues. - - Typical user data directories are: - Mac OS X: ~/Library/Application Support/ - Unix: ~/.config/ # or in $XDG_CONFIG_HOME if defined - Win XP (not roaming): C:\Documents and Settings\\Application Data\\ - Win XP (roaming): C:\Documents and Settings\\Local Settings\Application Data\\ - Win 7 (not roaming): C:\Users\\AppData\Local\\ - Win 7 (roaming): C:\Users\\AppData\Roaming\\ - - For Unix, we follow the XDG spec and support $XDG_CONFIG_HOME. We don't - use $XDG_DATA_HOME as that data dir is mostly used at the time of - installation, instead of the application adding data during runtime. - Also, in practice, Linux apps tend to store their data in - "~/.config/" instead of "~/.local/share/". - """ - if sys.platform.startswith("win"): - if appauthor is None: - raise AppDirsError("must specify 'appauthor' on Windows") - const = roaming and "CSIDL_APPDATA" or "CSIDL_LOCAL_APPDATA" - path = os.path.join(_get_win_folder(const), appauthor, appname) - elif sys.platform == 'darwin': - path = os.path.join( - os.path.expanduser('~/Library/Application Support/'), - appname) - else: - path = os.path.join( - os.getenv('XDG_CONFIG_HOME', os.path.expanduser("~/.config")), - appname.lower()) - if version: - path = os.path.join(path, version) - return path - - -def site_data_dir(appname, appauthor=None, version=None): - """Return full path to the user-shared data dir for this application. - - "appname" is the name of application. - "appauthor" (only required and used on Windows) is the name of the - appauthor or distributing body for this application. Typically - it is the owning company name. - "version" is an optional version path element to append to the - path. You might want to use this if you want multiple versions - of your app to be able to run independently. If used, this - would typically be ".". - - Typical user data directories are: - Mac OS X: /Library/Application Support/ - Unix: /etc/xdg/ - Win XP: C:\Documents and Settings\All Users\Application Data\\ - Vista: (Fail! "C:\ProgramData" is a hidden *system* directory on Vista.) - Win 7: C:\ProgramData\\ # Hidden, but writeable on Win 7. - - For Unix, this is using the $XDG_CONFIG_DIRS[0] default. - - WARNING: Do not use this on Windows. See the Vista-Fail note above for why. - """ - if sys.platform.startswith("win"): - if appauthor is None: - raise AppDirsError("must specify 'appauthor' on Windows") - path = os.path.join(_get_win_folder("CSIDL_COMMON_APPDATA"), - appauthor, appname) - elif sys.platform == 'darwin': - path = os.path.join( - os.path.expanduser('/Library/Application Support'), - appname) - else: - # XDG default for $XDG_CONFIG_DIRS[0]. Perhaps should actually - # *use* that envvar, if defined. - path = "/etc/xdg/"+appname.lower() - if version: - path = os.path.join(path, version) - return path - - -def user_cache_dir(appname, appauthor=None, version=None, opinion=True): - r"""Return full path to the user-specific cache dir for this application. - - "appname" is the name of application. - "appauthor" (only required and used on Windows) is the name of the - appauthor or distributing body for this application. Typically - it is the owning company name. - "version" is an optional version path element to append to the - path. You might want to use this if you want multiple versions - of your app to be able to run independently. If used, this - would typically be ".". - "opinion" (boolean) can be False to disable the appending of - "Cache" to the base app data dir for Windows. See - discussion below. - - Typical user cache directories are: - Mac OS X: ~/Library/Caches/ - Unix: ~/.cache/ (XDG default) - Win XP: C:\Documents and Settings\\Local Settings\Application Data\\\Cache - Vista: C:\Users\\AppData\Local\\\Cache - - On Windows the only suggestion in the MSDN docs is that local settings go in - the `CSIDL_LOCAL_APPDATA` directory. This is identical to the non-roaming - app data dir (the default returned by `user_data_dir` above). Apps typically - put cache data somewhere *under* the given dir here. Some examples: - ...\Mozilla\Firefox\Profiles\\Cache - ...\Acme\SuperApp\Cache\1.0 - OPINION: This function appends "Cache" to the `CSIDL_LOCAL_APPDATA` value. - This can be disabled with the `opinion=False` option. - """ - if sys.platform.startswith("win"): - if appauthor is None: - raise AppDirsError("must specify 'appauthor' on Windows") - path = os.path.join(_get_win_folder("CSIDL_LOCAL_APPDATA"), - appauthor, appname) - if opinion: - path = os.path.join(path, "Cache") - elif sys.platform == 'darwin': - path = os.path.join( - os.path.expanduser('~/Library/Caches'), - appname) - else: - path = os.path.join( - os.getenv('XDG_CACHE_HOME', os.path.expanduser('~/.cache')), - appname.lower()) - if version: - path = os.path.join(path, version) - return path - -def user_log_dir(appname, appauthor=None, version=None, opinion=True): - r"""Return full path to the user-specific log dir for this application. - - "appname" is the name of application. - "appauthor" (only required and used on Windows) is the name of the - appauthor or distributing body for this application. Typically - it is the owning company name. - "version" is an optional version path element to append to the - path. You might want to use this if you want multiple versions - of your app to be able to run independently. If used, this - would typically be ".". - "opinion" (boolean) can be False to disable the appending of - "Logs" to the base app data dir for Windows, and "log" to the - base cache dir for Unix. See discussion below. - - Typical user cache directories are: - Mac OS X: ~/Library/Logs/ - Unix: ~/.cache//log # or under $XDG_CACHE_HOME if defined - Win XP: C:\Documents and Settings\\Local Settings\Application Data\\\Logs - Vista: C:\Users\\AppData\Local\\\Logs - - On Windows the only suggestion in the MSDN docs is that local settings - go in the `CSIDL_LOCAL_APPDATA` directory. (Note: I'm interested in - examples of what some windows apps use for a logs dir.) - - OPINION: This function appends "Logs" to the `CSIDL_LOCAL_APPDATA` - value for Windows and appends "log" to the user cache dir for Unix. - This can be disabled with the `opinion=False` option. - """ - if sys.platform == "darwin": - path = os.path.join( - os.path.expanduser('~/Library/Logs'), - appname) - elif sys.platform == "win32": - path = user_data_dir(appname, appauthor, version); version=False - if opinion: - path = os.path.join(path, "Logs") - else: - path = user_cache_dir(appname, appauthor, version); version=False - if opinion: - path = os.path.join(path, "log") - if version: - path = os.path.join(path, version) - return path - - -class AppDirs(object): - """Convenience wrapper for getting application dirs.""" - def __init__(self, appname, appauthor, version=None, roaming=False): - self.appname = appname - self.appauthor = appauthor - self.version = version - self.roaming = roaming - @property - def user_data_dir(self): - return user_data_dir(self.appname, self.appauthor, - version=self.version, roaming=self.roaming) - @property - def site_data_dir(self): - return site_data_dir(self.appname, self.appauthor, - version=self.version) - @property - def user_cache_dir(self): - return user_cache_dir(self.appname, self.appauthor, - version=self.version) - @property - def user_log_dir(self): - return user_log_dir(self.appname, self.appauthor, - version=self.version) - - - - -#---- internal support stuff - -def _get_win_folder_from_registry(csidl_name): - """This is a fallback technique at best. I'm not sure if using the - registry for this guarantees us the correct answer for all CSIDL_* - names. - """ - import _winreg - - shell_folder_name = { - "CSIDL_APPDATA": "AppData", - "CSIDL_COMMON_APPDATA": "Common AppData", - "CSIDL_LOCAL_APPDATA": "Local AppData", - }[csidl_name] - - key = _winreg.OpenKey(_winreg.HKEY_CURRENT_USER, - r"Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders") - dir, type = _winreg.QueryValueEx(key, shell_folder_name) - return dir - -def _get_win_folder_with_pywin32(csidl_name): - from win32com.shell import shellcon, shell - dir = shell.SHGetFolderPath(0, getattr(shellcon, csidl_name), 0, 0) - # Try to make this a unicode path because SHGetFolderPath does - # not return unicode strings when there is unicode data in the - # path. - try: - dir = unicode(dir) - - # Downgrade to short path name if have highbit chars. See - # . - has_high_char = False - for c in dir: - if ord(c) > 255: - has_high_char = True - break - if has_high_char: - try: - import win32api - dir = win32api.GetShortPathName(dir) - except ImportError: - pass - except UnicodeError: - pass - return dir - -def _get_win_folder_with_ctypes(csidl_name): - import ctypes - - csidl_const = { - "CSIDL_APPDATA": 26, - "CSIDL_COMMON_APPDATA": 35, - "CSIDL_LOCAL_APPDATA": 28, - }[csidl_name] - - buf = ctypes.create_unicode_buffer(1024) - ctypes.windll.shell32.SHGetFolderPathW(None, csidl_const, None, 0, buf) - - # Downgrade to short path name if have highbit chars. See - # . - has_high_char = False - for c in buf: - if ord(c) > 255: - has_high_char = True - break - if has_high_char: - buf2 = ctypes.create_unicode_buffer(1024) - if ctypes.windll.kernel32.GetShortPathNameW(buf.value, buf2, 1024): - buf = buf2 - - return buf.value - -if sys.platform == "win32": - try: - import win32com.shell - _get_win_folder = _get_win_folder_with_pywin32 - except ImportError: - try: - import ctypes - _get_win_folder = _get_win_folder_with_ctypes - except ImportError: - _get_win_folder = _get_win_folder_from_registry - - - -#---- self test code - -if __name__ == "__main__": - appname = "MyApp" - appauthor = "MyCompany" - - props = ("user_data_dir", "site_data_dir", "user_cache_dir", - "user_log_dir") - - print("-- app dirs (without optional 'version')") - dirs = AppDirs(appname, appauthor, version="1.0") - for prop in props: - print("%s: %s" % (prop, getattr(dirs, prop))) - - print("\n-- app dirs (with optional 'version')") - dirs = AppDirs(appname, appauthor) - for prop in props: - print("%s: %s" % (prop, getattr(dirs, prop))) diff --git a/py/escher/convert_map.py b/py/escher/convert_map.py deleted file mode 100755 index dd676e80..00000000 --- a/py/escher/convert_map.py +++ /dev/null @@ -1,876 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -"""This script has two purposes: - -1. Apply the attributes from a cobra model to an existing Escher -map. For instance, update modified reversibilities. - -2. Convert maps made with Escher beta versions to valid jsonschema/1-0-0 -maps. - -""" - - -from __future__ import print_function, unicode_literals - - -usage_string = """ -Usage: - -./convert_map.py {map path} {model path} - -OR - -python -m escher.convert_map {map path} {model path} -""" - - -try: - import cobra.io - import jsonschema -except ImportError: - raise Exception(('The Python packages jsonschema and COBRApy (0.3.0b3 or later) ' - 'are required for converting maps.')) -import sys -import json -import random -import string -import hashlib -from os.path import basename, join -import logging -try: - from urllib.request import urlopen -except ImportError: - from urllib import urlopen - -from escher.validate import validate_map, genes_for_gene_reaction_rule - -# configure logger -logging.basicConfig(stream=sys.stdout, level=logging.INFO) - - -def main(): - """Main entrypoint for convert_map. Instructions are at the top of this file.""" - # get the arguments - try: - in_file = sys.argv[1] - model_path = sys.argv[2] - except IndexError: - print(usage_string) - sys.exit() - - # load the cobra model - try: - model = cobra.io.load_json_model(model_path) - except (IOError, ValueError): - try: - model = cobra.io.read_sbml_model(model_path) - except IOError: - raise Exception('Could not load the model: %s' % model_path) - - # get the current map - with open(in_file, 'r') as f: - out = json.load(f) - - # convert the map - the_map = convert(out, model) - - # don't replace the file - out_file = in_file.replace('.json', '_converted.json') - logging.info('Saving validated map to %s' % out_file) - with open(out_file, 'w') as f: - json.dump(the_map, f, allow_nan=False) - -# ------------------------------------------------------------------------------ -# Functions for manipulating Escher maps as Python objects -# ------------------------------------------------------------------------------ - -class MissingDefaultAttribute(Exception): - pass - -def make_map(header, body): - return [header, body] - -def get_header(a_map): - return a_map[0] - -def set_header(a_map, value): - a_map[0] = value - -def get_body(a_map): - return a_map[1] - -def set_body(a_map, value): - a_map[1] = value - -def get_nodes(body): - return body['nodes'] - -def set_nodes(body, value): - body['nodes'] = value - -def get_reactions(body): - return body['reactions'] - -def set_reactions(body, value): - body['reactions'] = value - -def is_valid_header(val): - """Header must have these values.""" - return (isinstance(val, dict) and - all(x in val for x in - ['schema', 'homepage', 'map_name', 'map_id', 'map_description'])) - -def is_valid_body(val): - """Body must be a dictionary.""" - return isinstance(val, dict) - -def has_header_and_body(val): - """Check for header and body.""" - return (isinstance(val, list) and len(val) == 2 and - is_valid_header(get_header(val)) and is_valid_body(get_body(val))) - -# ------------------------------------------------------------------------------ -# Functions for fixing nested dictionaries & lists -# ------------------------------------------------------------------------------ - -def dict_with_required_elements(the_dict, required_attributes, get_default=None, - nullable=[], cast={}): - """Remove unsupported elements and provide defaults for missing - elements or elements with zero length (e.g. {}, []). - - Arguments - --------- - - the_dict: A dictionary. - - required_attributes: The attributes required in the dictionary. - - get_default: A function that takes the attribute name and the current - object, and returns a default value. If not function is provided, then - MissingDefaultAttribute is raised when an attribute is not present. - - nullable: A list of attributes that can be None. - - cast: A dictionary of attributes for keys and functions for values. - - """ - if type(the_dict) is not dict: - raise MissingDefaultAttribute('(Bad object)') - - def has_zero_length(o): - """Returns True if o has a length and it is zero.""" - try: - return len(o) == 0 - except TypeError: - return False - - def current_otherwise_default(name): - """Take the value in the current dict, or else provide a default.""" - if name not in the_dict or has_zero_length(the_dict[name]): - if get_default is not None: - default = get_default(name, the_dict) - the_dict[name] = default - else: - raise MissingDefaultAttribute(name) - elif the_dict[name] is None and name not in nullable: - raise MissingDefaultAttribute('%s (is None)' % name) - # casting - try: - new = cast[name](the_dict[name]) - except KeyError: - pass - else: - the_dict[name] = new - - # map over the dict - not_required = set(the_dict.keys()) - for name in required_attributes: - current_otherwise_default(name) - # remember the keys that are not required - try: - not_required.remove(name) - except KeyError: - pass - - # remove not required - for key in not_required: - del the_dict[key] - -def map_over_dict_with_deletions(the_dict, fix_function): - """Use this to map over dictionary. The fix function updates values, and returns - None to delete a value. - - Returns the dictionary. - - Arguments - --------- - - the_dict: A dictionary to fix. - - fix_function: A function that takes the dictionary key and value as - arguments, and that returns None if the key is deleted, otherwise - returns the updated value. - - """ - - # this will update the dictionary and return a set of deleted ids - deleted_keys = set() - for key, val in list(the_dict.items()): - updated_val = fix_function(key, val) - if updated_val is None: - # add to aggregation set - deleted_keys.add(key) - # delete the value - del the_dict[key] - else: - # set the new value - the_dict[key] = updated_val - - return the_dict - -def list_of_dicts_with_required_elements(a_list, required_attributes, - get_default=None, nullable=[], - cast={}): - """For a list (dictionary) of dictionaries with required attributes, check - each one. Returns the new list. - - Arguments - --------- - - a_list: A dictionary with values that are dictionaries. - - required_attributes: A list of required attributes for the internal - dictionaries. - - get_default: A function that takes the attribute name and the current - object, and returns a default value. If not function is provided, then - MissingDefaultAttribute is raised when an attribute is not present. - - """ - - def fix_a_value(val): - try: - dict_with_required_elements(val, required_attributes, - nullable=nullable, cast=cast) - return val - except MissingDefaultAttribute: - return None - - # fix each element in the list - return [y for y in (fix_a_value(x) for x in a_list) - if y is not None] - -def collection_of_dicts_with_required_elements(collection, required_attributes, - get_default=None, nullable=[], - cast={}): - """For a collection (dictionary) of dictionaries with required - attributes, check each one. Returns the new collection. - - Arguments - --------- - - collection: A dictionary with values that are dictionaries. - - required_attributes: A list of required attributes for the internal - dictionaries. - - get_default: A function that takes the attribute name and the current - object, and returns a default value. If not function is provided, then - MissingDefaultAttribute is raised when an attribute is not present. - - """ - - def fix_a_value(val): - try: - dict_with_required_elements(val, required_attributes, - nullable=nullable, cast=cast) - return val - except MissingDefaultAttribute: - return None - - # update the dictionary - for k, v in list(collection.items()): - new_value = fix_a_value(v) - if new_value is None: - del collection[k] - else: - collection[k] = new_value - - return collection - -# ------------------------------------------------------------------------------ -# Functions for cleaning up unconnected map elements -# ------------------------------------------------------------------------------ - -def remove_unconnected_nodes(nodes, reactions, node_ids_deleted=set()): - """Check for nodes with no connected segments in the reactions object, and - return a new nodes object with only connected nodes. - - Arguments - --------- - - nodes: A collection (dict) of nodes. - - reactions: A collection (dict) of reactions. - - node_ids_deleted: A set of previously deleted ids to update. - - """ - # update - def map_over_connected_node_ids(fn, reactions): - """Run fn with all node ids that have connected segments.""" - for reaction in reactions.values(): - for segment in reaction['segments'].values(): - fn(segment['from_node_id']) - fn(segment['to_node_id']) - - # use a set to keep track of connected nodes - nodes_with_segments = set() - add_node = nodes_with_segments.add - has_node = lambda x: x in nodes_with_segments - # update - map_over_connected_node_ids(add_node, reactions) - - # filter the nodes - def check_fn(key, value): - if has_node(key): - return value - else: - logging.debug('No segments for node %s. Deleting' % key) - return None - map_over_dict_with_deletions(nodes, check_fn) - -def remove_unconnected_segments(reactions, nodes): - """Check for segments with no connected nodes. - - Arguments - --------- - - reactions: A collection (dict) of reactions. - - nodes: A collection (dict) of nodes. - - """ - # use a set to keep track of connected nodes - node_ids = set(nodes.keys()) - is_node = lambda x: x in node_ids - - # filter the segments - def check_fn(key, value): - if is_node(value['from_node_id']) and is_node(value['to_node_id']): - return value - else: - logging.debug('Missing node for segment %s. Deleting' % key) - return None - for reaction in reactions.values(): - map_over_dict_with_deletions(reaction['segments'], check_fn) - -def remove_reactions_with_missing_metabolites(reactions, nodes): - """Check for reactions that do not have all of their metabolites. - - Arguments - --------- - - reactions: A collection (dict) of reactions. - - nodes: A collection (dict) of nodes. - - """ - # filter the reactions - def check_fn(reaction_id, reaction): - # get the metabolites - metabolite_ids = {x['bigg_id'] for x in reaction['metabolites']} - # look for matching segments - for segment_id, segment in reaction['segments'].items(): - # find node - for n in 'from_node_id', 'to_node_id': - node = nodes[segment[n]] - try: - metabolite_ids.remove(node['bigg_id']) - except KeyError: - pass - if len(metabolite_ids) > 0: - logging.info('Deleting reaction %s with missing metabolites %s' % (reaction['bigg_id'], - str(list(metabolite_ids)))) - return None - else: - return reaction - - map_over_dict_with_deletions(reactions, check_fn) - -# ------------------------------------------------------------------------------ -# Functions for converting maps -# ------------------------------------------------------------------------------ - -def old_map_to_new_schema(the_map, map_name=None, map_description=None): - """Convert any old map to match the latest schema. Returns a new map. - - Arguments - --------- - - the_map: An Escher map loaded as a Python object (e.g. json.load('my_map.json')). - - map_name: A name for the map. If a name is already present, this name - overrides it. - - map_description: A description for the map. If a name is already present, - this name overrides it. - - """ - - def add_default_header(body, name, description): - """Return a map with header and body.""" - - def check_for(var, name): - """Print a warning if var is None.""" - if var is None: - logging.warn('No {} for map'.format(name)) - return '' - return var - - new_id = hashlib.md5(json.dumps(body).encode('utf-8')).hexdigest() - default_header = { - "schema": "https://escher.github.io/escher/jsonschema/1-0-0#", - "homepage": "https://escher.github.io", - "map_name": check_for(name, 'name'), - "map_id": new_id, - "map_description": check_for(description, 'description') - } - logging.info('Map has the ID {}'.format(new_id)) - return make_map(default_header, body) - - def add_header_if_missing(a_map): - """Check for new, 2-level maps, and add the header.""" - - if has_header_and_body(a_map): - use_name = (get_header(a_map)['map_name'] if map_name is None else map_name) - use_description = (get_header(a_map)['map_description'] - if map_description is None else map_description) - return add_default_header(get_body(a_map), use_name, use_description) - elif is_valid_body(a_map): - return add_default_header(a_map, map_name, map_description) - else: - raise Exception('The map provided cannot be converted. It is not a valid Escher map.') - - def fix_body(body): - """Fill in necessary attributes for the body.""" - - def get_default(key, _): - """Get default value for key in body.""" - if key == 'canvas': - # default canvas - return {'x': -1440, 'y': -775, 'width': 4320, 'height': 2325} - else: - # other defaults - return {} - - def fix_canvas(canvas): - """Return a canvas with correct attributes.""" - canvas_keys = ['x', 'y', 'width', 'height'] - cast = {'x': float, 'y': float, 'width': float, 'height': float} - dict_with_required_elements(canvas, canvas_keys, cast=cast) - - def fix_text_labels(text_labels): - """Return a list of text_labels with correct attributes.""" - text_label_keys = ['x', 'y', 'text'] - cast = {'x': float, 'y': float} - collection_of_dicts_with_required_elements(text_labels, - text_label_keys, - cast=cast) - - # fix canvas before body so that a default canvas can be added if the - # canvas is invalid - try: - fix_canvas(body['canvas']) - except KeyError: - pass - except MissingDefaultAttribute: - del body['canvas'] - - # fix body - core_keys = ['nodes', 'reactions', 'text_labels', 'canvas'] - dict_with_required_elements(body, core_keys, get_default) - - # fix text labels - fix_text_labels(body['text_labels']) - - def fix_nodes(nodes): - """Fill in necessary attributes for the nodes. Returns nodes.""" - - def get_default_node_attr(name, obj): - """Return default values when possible. Otherwise, raise MissingDefaultAttribute.""" - if name == 'node_is_primary': - return False - elif name == 'name': - return '' - elif name == 'label_x' and 'x' in obj: - return obj['x'] - elif name == 'label_y' and 'y' in obj: - return obj['y'] - else: - raise MissingDefaultAttribute(name) - - def fix_a_node(node_id, node): - """Return an updated node, or None if the node is invalid.""" - - if not 'node_type' in node: - logging.debug('Deleting node %s with no node_type' % node_id) - return None - - elif node['node_type'] == 'metabolite': - met_keys = ['node_type', 'x', 'y', 'bigg_id', 'name', 'label_x', - 'label_y', 'node_is_primary'] - cast = {'x': float, 'y': float, 'label_x': float, 'label_y': float} - try: - dict_with_required_elements(node, met_keys, get_default_node_attr, cast=cast) - return node - except MissingDefaultAttribute as e: - logging.debug('Deleting node %s with missing attribute %s' % (node_id, e)) - return None - - elif node['node_type'] in ['multimarker', 'midmarker']: - marker_keys = ['node_type', 'x', 'y'] - cast = {'x': float, 'y': float} - try: - dict_with_required_elements(node, marker_keys, get_default_node_attr, cast=cast) - return node - except MissingDefaultAttribute as e: - logging.debug('Deleting node %s with missing attribute %s' % (node_id, e)) - return None - - else: - logging.debug('Deleting node %s with bad node_type %s' % (node_id, node['node_type'])) - return None - - # run fix functions - map_over_dict_with_deletions(nodes, fix_a_node) - - def fix_reactions(reactions): - """Fill in necessary attributes for the reactions. - - Returns reactions. - - """ - - def get_default_reaction_attr(name, obj): - """Return default values when possible. Otherwise, raise MissingDefaultAttribute.""" - if name in ['name', 'gene_reaction_rule']: - return '' - elif name == 'reversibility': - return True - elif name in ['genes', 'metabolites']: - return [] - else: - raise MissingDefaultAttribute(name) - - def fix_a_reaction(reaction_id, reaction): - """Return an updated reaction, or None if the reaction is invalid.""" - - def fix_segments(segments): - """Fix dictionary of segments with correct attributes.""" - def fix_a_segment(segment_id, segment): - segment_keys = ['from_node_id', 'to_node_id', 'b1', 'b2'] - def get_default_segment_attr(key, _): - if key in ['b1', 'b2']: - return None - else: - raise MissingDefaultAttribute(key) - try: - dict_with_required_elements(segment, segment_keys, - get_default_segment_attr, - nullable=['b1', 'b2']) - except MissingDefaultAttribute as e: - logging.debug('Deleting segment %s with missing attribute %s' % (segment_id, e)) - return None - - # check the beziers too - required_bezier_keys = ['x', 'y'] - cast = {'x': float, 'y': float} - for b in ['b1', 'b2']: - try: - dict_with_required_elements(segment[b], - required_bezier_keys, - cast=cast) - except MissingDefaultAttribute as e: - logging.debug('Deleting bezier %s with missing attribute %s in segment %s' % (b, e, segment_id)) - segment[b] = None - - return segment - - map_over_dict_with_deletions(segments, fix_a_segment) - - def fix_metabolites(metabolites): - """Return a list of metabolites with correct attributes.""" - metabolite_keys = ['coefficient', 'bigg_id'] - cast = {'coefficient': float} - return list_of_dicts_with_required_elements(metabolites, - metabolite_keys, - cast=cast) - - def fix_genes(genes): - """Return a list of genes with correct attributes.""" - gene_keys = ['bigg_id', 'name'] - def get_default_gene_attr(name, _): - if name == 'name': - return '' - else: - raise MissingDefaultAttribute(name) - return list_of_dicts_with_required_elements(genes, gene_keys, - get_default_gene_attr) - - # fix all the attributes - reaction_keys = ['name', 'bigg_id','reversibility', 'label_x', - 'label_y', 'gene_reaction_rule', 'genes', - 'metabolites', 'segments'] - cast = {'label_x': float, 'label_y': float} - try: - dict_with_required_elements(reaction, reaction_keys, - get_default_reaction_attr, - cast=cast) - except MissingDefaultAttribute as e: - logging.debug('Deleting reaction %s with missing attribute %s' % (reaction_id, e)) - return None - - # fix segments, metabolites, and genes - fix_segments(reaction['segments']) - # must have segments - if len(reaction['segments']) == 0: - logging.debug('Deleting reaction %s with no segments' % reaction_id) - return None - reaction['metabolites'] = fix_metabolites(reaction['metabolites']) - reaction['genes'] = fix_genes(reaction['genes']) - - return reaction - - # run the fix functions - map_over_dict_with_deletions(reactions, fix_a_reaction) - - - # make sure there is a body and a head - the_map = add_header_if_missing(the_map) - body = get_body(the_map) - - # add missing elements to body - fix_body(body) - - # fix the nodes - fix_nodes(get_nodes(body)) - - # fix the reactions - fix_reactions(get_reactions(body)) - - # delete any nodes with no segment - remove_unconnected_nodes(get_nodes(body), get_reactions(body)) - - # delete segments with no nodes - remove_unconnected_segments(get_reactions(body), get_nodes(body)) - - # delete reactions with missing metabolite segments - remove_reactions_with_missing_metabolites(get_reactions(body), get_nodes(body)) - - return the_map - - -def apply_id_mappings(the_map, reaction_id_mapping=None, - metabolite_id_mapping=None, gene_id_mapping=None): - """Convert bigg_ids in the map using the mappings dictionaries. - - Arguments - --------- - - the_map: The Escher map Python object. - - reaction_id_mapping: A dictionary with keys for existing bigg_ids and value for new bigg_ids. - - metabolite_id_mapping: A dictionary with keys for existing bigg_ids and value for new bigg_ids. - - gene_id_mapping: A dictionary with keys for existing bigg_ids and value for new bigg_ids. - - """ - - id_key = 'bigg_id' - - def check(a_dict, mapping): - """Try to change the value for id_key to a new value defined in mapping.""" - try: - new_id = mapping[a_dict[id_key]] - except KeyError: - pass - else: - a_dict[id_key] = new_id - return a_dict - - def apply_mapping_list(a_list, mapping): - """Use the mapping on each dict in the list. Returns a new list.""" - return [check(x, mapping) for x in a_list] - - def apply_mapping_dict(collection, mapping): - """Use the mapping on each dict in the collection (dict). Returns the dictionary.""" - for val in collection.values(): - check(val, mapping) - return collection - - body = get_body(the_map) - # reactions - if reaction_id_mapping is not None: - apply_mapping_dict(get_reactions(body), reaction_id_mapping) - # metabolites - if metabolite_id_mapping is not None: - apply_mapping_dict(get_nodes(body), metabolite_id_mapping) - # genes & metabolites in reactions - for reaction in get_reactions(body).values(): - if gene_id_mapping is not None: - reaction['genes'] = apply_mapping_list(reaction['genes'], gene_id_mapping) - if metabolite_id_mapping is not None: - reaction['metabolites'] = apply_mapping_list(reaction['metabolites'], metabolite_id_mapping) - - -def apply_cobra_model_to_map(the_map, model): - """Apply the COBRA model attributes (descriptive names, gene reaction rules, - reversibilities) to the map. - - Cleans up unconnected segments and nodes after deleting any nodes and - reactions not found in the cobra model. - - """ - - def apply_model_attributes(a_dict, dict_list, attribute_fns, collection_on='bigg_id'): - """For each attribute_fn, apply the values from the dict_list to given - dictionary, using the given IDs. Returns the dictionary, or None if a - matching object was not found in the DictList. - - """ - try: - on_id = a_dict[collection_on] - except KeyError: - return a_dict - try: - dl_object = dict_list.get_by_id(on_id) - except KeyError: - logging.info('Could not find %s in model. Deleting.' % on_id) - return None - else: - for attribute_fn in attribute_fns: - attribute_fn(a_dict, dl_object) - - return a_dict - - def apply_model_attributes_dict(collection, dict_list, attribute_fns, - collection_on='bigg_id'): - """For each attribute_fn, apply the values from the dict_list to the matching - results in the collection, using the given IDs. Returns the collection.""" - for key, val in list(collection.items()): - new_val = apply_model_attributes(val, dict_list, attribute_fns, - collection_on) - if new_val is None: - del collection[key] - - def apply_model_attributes_list(a_list, dict_list, attribute_fns, - collection_on='bigg_id'): - """For each attribute_fn, apply the values from the dict_list to the matching - results in the list of dicts, using the given IDs. Returns a new list.""" - return [y for y in (apply_model_attributes(x, dict_list, attribute_fns, collection_on) for x in a_list) - if y is not None] - - def get_attr_fn(attribute): - """Make a default attribute setting function.""" - def new_attr_fn(val, dl_object): - try: - val[attribute] = getattr(dl_object, attribute) - except AttributeError: - logging.debug('No %s found in DictList %s' % (attribute, on_id)) - return new_attr_fn - - def set_reversibility(reaction, cobra_reaction): - reaction['reversibility'] = (cobra_reaction.lower_bound < 0 and cobra_reaction.upper_bound > 0) - # reverse metabolites if reaction runs in reverse - rev_mult = (-1 if - (cobra_reaction.lower_bound < 0 and cobra_reaction.upper_bound <= 0) - else 1) - # use metabolites from reaction - reaction['metabolites'] = [{'bigg_id': met.id, 'coefficient': coeff * rev_mult} - for met, coeff in - cobra_reaction.metabolites.items()] - - def set_genes(reaction, cobra_reaction): - reaction['genes'] = [{'bigg_id': x.id, 'name': x.name} for x in cobra_reaction.genes] - - # vars - body = get_body(the_map) - - # compare reactions to model - reaction_attributes = [get_attr_fn('name'), get_attr_fn('gene_reaction_rule'), - set_reversibility, set_genes] - apply_model_attributes_dict(get_reactions(body), model.reactions, - reaction_attributes) - - # compare metabolites to model - metabolite_attributes = [get_attr_fn('name')] - apply_model_attributes_dict(get_nodes(body), model.metabolites, - metabolite_attributes) - - # delete any nodes with no segment - remove_unconnected_nodes(get_nodes(body), get_reactions(body)) - - # delete segments with no nodes - remove_unconnected_segments(get_reactions(body), get_nodes(body)) - - # delete reactions with missing metabolite segments - remove_reactions_with_missing_metabolites(get_reactions(body), get_nodes(body)) - - -def convert(the_map, model, map_name=None, map_description=None, - reaction_id_mapping=None, metabolite_id_mapping=None, - gene_id_mapping=None, debug=False): - """Convert an Escher map to the latest format using the COBRA model to update - content. Returns a new map. - - Arguments - --------- - - the_map: An Escher map loaded as a Python object (e.g. json.load('my_map.json')). - - model: A COBRA model. - - map_name: A name for the map. If a name is already present, this name - overrides it. - - map_description: A description for the map. If a name is already present, - this name overrides it. - - reaction_id_mapping: A dictionary with existing reaction IDs as keys and the - new reaction IDs as values. - - metabolite_id_mapping: A dictionary with existing metabolite IDs as keys and the - new metabolite IDs as values. - - gene_id_mapping: A dictionary with existing gene IDs as keys and the new - gene IDs as values. - - debug: Check the map against the schema at some intermediate steps. - - """ - - # make sure everything is up-to-date - new_map = old_map_to_new_schema(the_map, map_name=map_name, - map_description=map_description) - if debug: - validate_map(new_map) - - # apply the ids mappings - apply_id_mappings(new_map, reaction_id_mapping, metabolite_id_mapping, - gene_id_mapping) - if debug: - validate_map(new_map) - - # apply the new model - apply_cobra_model_to_map(new_map, model) - - validate_map(new_map) - return new_map - - -if __name__ == "__main__": - main() diff --git a/py/escher/generate_index.py b/py/escher/generate_index.py deleted file mode 100644 index de3a7a4f..00000000 --- a/py/escher/generate_index.py +++ /dev/null @@ -1,39 +0,0 @@ -from __future__ import print_function, unicode_literals - -import json -from os import listdir -from os.path import join, dirname, realpath, exists, isdir, relpath -import sys -from collections import defaultdict -from escher import __schema_version__, __map_model_version__ -from escher.urls import top_directory - -def generate_index(directory): - def list_cached(directory, kind): - l = [] - if isdir(directory): - for f in listdir(directory): - tf = join(directory, f) - if isdir(tf): - for f2 in listdir(tf): - if f2.endswith('.json'): - f2 = f2.replace('.json', '') - l.append({ 'organism': f, - kind + '_name': f2 }) - return l - return { 'maps': list_cached(join(directory, 'maps'), 'map'), - 'models': list_cached(join(directory, 'models'), 'model') } - -def main(): - directory = join(top_directory, __schema_version__, __map_model_version__) - if not exists(directory): - print('No directory to index') - sys.exit() - print('Indexing %s' % directory) - index = generate_index(directory) - with open(join(directory, 'index.json'), 'w') as f: - json.dump(index, f) - print('Saved index.json') - -if __name__=='__main__': - main() diff --git a/py/escher/plots.py b/py/escher/plots.py index b211da22..afbf3936 100644 --- a/py/escher/plots.py +++ b/py/escher/plots.py @@ -1,17 +1,16 @@ # -*- coding: utf-8 -*- - from __future__ import print_function, unicode_literals -from escher.quick_server import serve_and_open from escher.urls import get_url, root_directory -from escher.appdirs import user_cache_dir -from escher.generate_index import generate_index -from escher.version import __schema_version__, __map_model_version__ -from escher.util import query_yes_no, b64dump +from escher.util import b64dump +from escher.version import __version__ +import cobra +from cobra import Model +import ipywidgets as widgets +from traitlets import Unicode, Int, Instance, Dict, observe, validate import os -from os.path import (dirname, basename, abspath, join, isfile, isdir, exists, - expanduser) +from os.path import join, isfile, expanduser from warnings import warn try: from urllib.request import urlopen @@ -27,79 +26,16 @@ import string from tornado.escape import url_escape import shutil +from typing import Optional # set up jinja2 template location env = Environment(loader=PackageLoader('escher', 'templates')) -# cache management - -def get_cache_dir(versioned=True, name=None): - """Get the cache dir as a string, and make the directory if it does not already - exist. - - :param Boolean versioned: Whether to return the versioned path in the - cache. Escher maps for the latest version of - Escher are found in the versioned directory - (versioned = True), but maps for previous versions - of Escher can be found by visiting the parent - directory (versioned = False). - - :param string name: An optional subdirectory within the cache. If versioned - is False, then name is ignored. - - """ - cache_dir = user_cache_dir('escher', appauthor='Zachary King') - # add version - if versioned: - cache_dir = join(cache_dir, __schema_version__, __map_model_version__) - # add subdirectory - if name is not None: - cache_dir = join(cache_dir, name) - try: - os.makedirs(cache_dir) - except OSError: - pass - return cache_dir - -def clear_cache(different_cache_dir=None, ask=True): - """Empty the contents of the cache directory, including all versions of all maps - and models. - - :param string different_cache_dir: (Optional) The directory of another - cache. This is mainly for testing. - - :param Boolean ask: Whether to ask before deleting. - - """ - if ask and not query_yes_no('Are you sure you want to delete the contents of the cache?'): - return - - if different_cache_dir is None: - cache_dir = get_cache_dir(versioned=False) - else: - cache_dir = different_cache_dir - - for root, dirs, files in os.walk(cache_dir): - for f in files: - os.unlink(join(root, f)) - for d in dirs: - shutil.rmtree(join(root, d)) - -def local_index(cache_dir=get_cache_dir()): - return generate_index(cache_dir) - -def list_cached_maps(): - """Return a list of all cached maps.""" - return local_index()['maps'] - -def list_cached_models(): - """Return a list of all cached models.""" - return local_index()['models'] # server management def server_index(): - url = get_url('server_index', source='web', protocol='https') + url = get_url('server_index') try: download = urlopen(url) except URLError: @@ -108,76 +44,58 @@ def server_index(): index = json.loads(data) return index + def list_available_maps(): """Return a list of all maps available on the server""" return server_index()['maps'] + def list_available_models(): """Return a list of all models available on the server""" return server_index()['models'] + # download maps and models -def _json_for_name(name, kind, cache_dir): + +def _json_for_name(name: str, kind: str): # check the name name = name.replace('.json', '') def match_in_index(name, index, kind): - return [(obj['organism'], obj[kind + '_name']) for obj in index[kind + 's'] + return [(obj['organism'], obj[kind + '_name']) + for obj in index[kind + 's'] if obj[kind + '_name'] == name] - # first check the local index - match = match_in_index(name, local_index(cache_dir=cache_dir), kind) + try: + index = server_index() + except URLError: + raise Exception('Could not connect to the Escher server') + match = match_in_index(name, server_index(), kind) if len(match) == 0: - path = None - else: - org, name = match[0] - path = join(cache_dir, kind + 's', org, name + '.json') - - if path: - # load the file - with open(path, 'rb') as f: - return f.read().decode('utf-8') - # if the file is not present attempt to download - else: - try: - index = server_index() - except URLError: - raise Exception(('Could not find the %s %s in the cache, and could ' - 'not connect to the Escher server' % (kind, name))) - match = match_in_index(name, server_index(), kind) - if len(match) == 0: - raise Exception('Could not find the %s %s in the cache or on the server' % (kind, name)) - org, name = match[0] - url = (get_url(kind + '_download', source='web', protocol='https') + - '/'.join([url_escape(x, plus=False) for x in [org, name + '.json']])) - warn('%s not in cache. Attempting download from %s' % (kind.title(), url)) - try: - download = urlopen(url) - except URLError: - raise ValueError('No %s found in cache or at %s' % (kind, url)) - data = _decode_response(download) - # save the file - org_path = join(cache_dir, kind + 's', org) - try: - os.makedirs(org_path) - except OSError: - pass - with open(join(org_path, name + '.json'), 'w') as outfile: - outfile.write(data) - return data + raise Exception('Could not find the %s %s on the server' % (kind, name)) + org, name = match[0] + url = (get_url(kind + '_download') + + '/'.join([url_escape(x, plus=False) for x in [org, name + '.json']])) + print('Downloading %s from %s' % (kind.title(), url)) + try: + download = urlopen(url) + except URLError: + raise ValueError('No %s found in at %s' % (kind, url)) + data = _decode_response(download) + return data + -def model_json_for_name(model_name, cache_dir=get_cache_dir()): - return _json_for_name(model_name, 'model', cache_dir) +def model_json_for_name(model_name): + return _json_for_name(model_name, 'model') + + +def map_json_for_name(map_name): + return _json_for_name(map_name, 'map') -def map_json_for_name(map_name, cache_dir=get_cache_dir()): - return _json_for_name(map_name, 'map', cache_dir) # helper functions -def _get_an_id(): - return (''.join(random.choice(string.ascii_lowercase) - for _ in range(10))) def _decode_response(download): """Decode the urllib.response.addinfourl response.""" @@ -192,7 +110,8 @@ def _decode_response(download): data = data.decode('utf-8') return data -def _load_resource(resource, name, safe=False): + +def _load_resource(resource, name): """Load a resource that could be a file, URL, or json string.""" # if it's a url, download it if resource.startswith('http://') or resource.startswith('https://'): @@ -209,8 +128,6 @@ def _load_resource(resource, name, safe=False): # check for error with long filepath (or URL) on Windows is_file = False if is_file: - if (safe): - raise Exception('Cannot load resource from file with safe mode enabled.') try: with open(resource, 'rb') as f: loaded_resource = f.read().decode('utf-8') @@ -223,83 +140,80 @@ def _load_resource(resource, name, safe=False): try: _ = json.loads(resource) except ValueError as err: - raise ValueError('Could not load %s. Not valid json, url, or filepath' % name) + raise ValueError('Could not load %s. Not valid json, url, or filepath' + % name) else: return resource raise Exception('Could not load %s.' % name) -class Builder(object): - """A metabolic map that can be viewed, edited, and used to visualize data. +class Builder(widgets.DOMWidget): + """A Python wrapper for the Escher metabolic map. - This map will also show metabolic fluxes passed in during consruction. It - can be viewed as a standalone html inside a browswer. Alternately, the - respresentation inside an IPython notebook will also display the map. + This map will also show data on reactions, metabolites, or genes. - Maps are stored in json files and are stored in a cache directory. Maps - which are not found will be downloaded from a map repository if found. + The Builder is a Jupyter widget that can be viewed in a Jupyter notebook or + in Jupyter Lab. It can also be used to create a standalone HTML file for + the map with the save_html() function. - :param map_name: + Maps are downloaded from the Escher website if found by name. - A string specifying a map to be downloaded from the Escher web server, - or loaded from the cache. + :param int height: - :param map_json: + The height of the Escher Jupyter widget in pixels. - A JSON string, or a file path to a JSON file, or a URL specifying a JSON - file to be downloaded. + :param str map_name: - :param model: A Cobra model. + A string specifying a map to be downloaded from the Escher website. + + :param str map_json: + + A JSON string, or a file path to a JSON file, or a URL specifying a + JSON file to be downloaded. + + :param model: + + A COBRApy model. :param model_name: - A string specifying a model to be downloaded from the Escher web server, - or loaded from the cache. + A string specifying a model to be downloaded from the Escher web + server. :param model_json: - A JSON string, or a file path to a JSON file, or a URL specifying a JSON - file to be downloaded. + A JSON string, or a file path to a JSON file, or a URL specifying a + JSON file to be downloaded. :param embedded_css: - The CSS (as a string) to be embedded with the Escher SVG. + The CSS (as a string) to be embedded with the Escher SVG. In Jupyter, + if you change embedded_css on an existing builder instance, the Builder + must be restarted for this to take effect (e.g. by re-evaluating the + widget in a cell). You can use the default embedded css as a starting + point: + + https://github.com/zakandrewking/escher/blob/master/src/Builder-embed.css :param reaction_data: - A dictionary with keys that correspond to reaction ids and values that + A dictionary with keys that correspond to reaction IDs and values that will be mapped to reaction arrows and labels. :param metabolite_data: - A dictionary with keys that correspond to metabolite ids and values that - will be mapped to metabolite nodes and labels. + A dictionary with keys that correspond to metabolite IDs and values + that will be mapped to metabolite nodes and labels. :param gene_data: - A dictionary with keys that correspond to gene ids and values that will + A dictionary with keys that correspond to gene IDs and values that will be mapped to corresponding reactions. - :param local_host: - - A hostname that will be used for any local files. This is generally used - for using the notebook offline and for testing in the IPython Notebook - with modified Escher code. An example value for local_host is - 'http://localhost:7778/'. - - :param id: - - Specify an id to make the javascript data definitions unique. A random - id is chosen by default. - - :param safe: - - If True, then loading files from the filesytem is not allowed. This is - to ensure the safety of using Builder within a web server. - **Keyword Arguments** - These are defined in the Javascript API: + You can also pass in any of the following options as keyword arguments. The + details on each of these are provided in the JavaScript API documentation: - use_3d_transform - enable_search @@ -333,500 +247,269 @@ class Builder(object): - cofactors - enable_tooltips - All keyword arguments can also be set on an existing Builder object - using setter functions, e.g.: + All arguments can also be set by assigning the property of an an existing + Builder object, e.g.: .. code:: python - my_builder.set_reaction_styles(new_styles) + my_builder.map_name = 'iJO1366.Central metabolism' """ - def __init__(self, map_name=None, map_json=None, model=None, - model_name=None, model_json=None, embedded_css=None, - reaction_data=None, metabolite_data=None, gene_data=None, - local_host=None, id=None, safe=False, **kwargs): - - self.safe = safe - - # load the map - self.map_name = map_name - self.map_json = map_json - self.loaded_map_json = None - if map_name and map_json: - warn('map_json overrides map_name') - self._load_map() - # load the model - self.model = model - self.model_name = model_name - self.model_json = model_json - self.loaded_model_json = None - if sum([x is not None for x in (model, model_name, model_json)]) >= 2: - warn('model overrides model_json, and both override model_name') - self._load_model() - # set the args - self.reaction_data = reaction_data - self.metabolite_data = metabolite_data - self.gene_data = gene_data - self.local_host = local_host - - # remove illegal characters from css - try: - self.embedded_css = (embedded_css.replace('\n', '')) - except AttributeError: - self.embedded_css = None - # make the unique id - self.the_id = _get_an_id() if id is None else id - - # set up the options - self.options = [ - 'use_3d_transform', - 'enable_search', - 'fill_screen', - 'zoom_to_element', - 'full_screen_button', - 'starting_reaction', - 'unique_map_id', - 'primary_metabolite_radius', - 'secondary_metabolite_radius', - 'marker_radius', - 'gene_font_size', - 'hide_secondary_metabolites', - 'show_gene_reaction_rules', - 'hide_all_labels', - 'canvas_size_and_loc', - 'reaction_styles', - 'reaction_compare_style', - 'reaction_scale', - 'reaction_no_data_color', - 'reaction_no_data_size', - 'and_method_in_gene_reaction_rule', - 'metabolite_styles', - 'metabolite_compare_style', - 'metabolite_scale', - 'metabolite_no_data_color', - 'metabolite_no_data_size', - 'identifiers_on_map', - 'highlight_missing', - 'allow_building_duplicate_reactions', - 'cofactors', - 'enable_tooltips', - ] - def get_getter_setter(o): - """Use a closure.""" - # create local fget and fset functions - fget = lambda self: getattr(self, '_%s' % o) - fset = lambda self, value: setattr(self, '_%s' % o, value) - return fget, fset - for option in self.options: - fget, fset = get_getter_setter(option) - # make the setter - setattr(self.__class__, 'set_%s' % option, fset) - # add property to self - setattr(self.__class__, option, property(fget)) - # add corresponding local variable - setattr(self, '_%s' % option, None) - - # set the kwargs - for key, val in kwargs.items(): - try: - getattr(self, 'set_%s' % key)(val) - except AttributeError: - print('Unrecognized keywork argument %s' % key) - - - def _load_model(self): - """Load the model. - - Try first from self.model, second from self.model_json, and - third from from self.model_name. - - """ - if self.model is not None: - try: - import cobra.io - except ImportError: - raise Exception(('The COBRApy package must be available to load ' - 'a COBRA model object')) - self.loaded_model_json = cobra.io.to_json(self.model) - elif self.model_json is not None: - self.loaded_model_json = _load_resource(self.model_json, - 'model_json', - safe=self.safe) - elif self.model_name is not None: - self.loaded_model_json = model_json_for_name(self.model_name) - - - def _load_map(self): - """Load the map from input map_json using _load_resource, or, secondarily, - from map_name. - - """ - if self.map_json is not None: - self.loaded_map_json = _load_resource(self.map_json, - 'map_json', - safe=self.safe) - elif self.map_name is not None: - self.loaded_map_json = map_json_for_name(self.map_name) - - - def _get_html(self, js_source='web', menu='none', scroll_behavior='pan', - html_wrapper=False, enable_editing=False, enable_keys=False, - minified_js=True, fill_screen=False, height='800px', - never_ask_before_quit=False, static_site_index_json=None, - protocol=None, ignore_bootstrap=False): - """Generate the Escher HTML. - - Arguments - -------- - - js_source: Can be one of the following: - 'web' - (Default) use js files from unpkg. - 'local' - Use compiled js files in the local escher installation. Works offline. - 'dev' - No longer necessary with source maps. This now gives the - same behavior as 'local'. - - menu: Menu bar options include: - 'none' - (Default) No menu or buttons. - 'zoom' - Just zoom buttons (does not require bootstrap). - 'all' - Menu and button bar (requires bootstrap). - - scroll_behavior: Scroll behavior options: - 'pan' - (Default) Pan the map. - 'zoom' - Zoom the map. - 'none' - No scroll events. - - minified_js: If True, use the minified version of JavaScript files. - - html_wrapper: If True, return a standalone html file. - - enable_editing: Enable the editing modes (build, rotate, etc.). - - enable_keys: Enable keyboard shortcuts. - - height: The height of the HTML container. - - never_ask_before_quit: Never display an alert asking if you want to - leave the page. By default, this message is displayed if enable_editing - is True. - - static_site_index_json: The index, as a JSON string, for the static - site. Use javascript to parse the URL options. Used for - generating static pages (see static_site.py). - - protocol: The protocol can be 'http', 'https', or None which indicates a - 'protocol relative URL', as in //escher.github.io. Ignored if source is - local. - - ignore_bootstrap: Deprecated - - """ - - if js_source not in ['web', 'local', 'dev']: - raise Exception('Bad value for js_source: %s' % js_source) - - if menu not in ['none', 'zoom', 'all']: - raise Exception('Bad value for menu: %s' % menu) - - if scroll_behavior not in ['pan', 'zoom', 'none']: - raise Exception('Bad value for scroll_behavior: %s' % scroll_behavior) - - content = env.get_template('content.html') - - # if height is not a string - if type(height) is int: - height = "%dpx" % height - elif type(height) is float: - height = "%fpx" % height - elif type(height) is str: - height = str(height) - - # set the proper urls - url_source = 'local' if (js_source=='local' or js_source=='dev') else 'web' - local_host = self.local_host - - # get the urls - escher_url = get_url(('escher_min' if minified_js else 'escher'), - url_source, local_host, protocol) - favicon_url = get_url('favicon', url_source, local_host, protocol) - # for static site - map_download_url = get_url('map_download', url_source, local_host, protocol) - model_download_url = get_url('model_download', url_source, local_host, protocol) - - # local host - lh_string = ('' if local_host is None else - local_host.rstrip('/') + '/') - - # options - options = { - 'menu': menu, - 'enable_keys': enable_keys, - 'enable_editing': enable_editing, - 'scroll_behavior': scroll_behavior, - 'fill_screen': fill_screen, - 'never_ask_before_quit': never_ask_before_quit, - 'reaction_data': self.reaction_data, - 'metabolite_data': self.metabolite_data, - 'gene_data': self.gene_data, - } - # Add the specified options - for option in self.options: - val = getattr(self, option) - if val is None: - continue - options[option] = val - - html = content.render( - # standalone - title='Escher ' + ('Builder' if enable_editing else 'Viewer'), - favicon_url=favicon_url, - # content - wrapper=html_wrapper, - height=height, - id=self.the_id, - escher_url=escher_url, - # dump json - id_json=b64dump(self.the_id), - options_json=b64dump(options), - map_download_url_json=b64dump(map_download_url), - model_download_url_json=b64dump(model_download_url), - builder_embed_css_json=b64dump(self.embedded_css), - # alreay json - map_data_json=b64dump(self.loaded_map_json), - model_data_json=b64dump(self.loaded_model_json), - static_site_index_json=b64dump(static_site_index_json), - ) - - return html - - - def display_in_notebook(self, js_source='web', menu='zoom', scroll_behavior='none', - minified_js=True, height=500, enable_editing=False): - """Embed the Map within the current IPython Notebook. - - :param string js_source: - - Can be one of the following: - - - *web* (Default) - Use JavaScript files from escher.github.io. - - *local* - Use compiled JavaScript files in the local Escher installation. Works offline. - - *dev* - No longer necessary with source maps. This now gives the - same behavior as 'local'. - - :param string menu: Menu bar options include: - - - *none* - No menu or buttons. - - *zoom* - Just zoom buttons. - - Note: The *all* menu option does not work in an IPython notebook. - - :param string scroll_behavior: Scroll behavior options: - - - *pan* - Pan the map. - - *zoom* - Zoom the map. - - *none* - (Default) No scroll events. - - :param Boolean minified_js: - - If True, use the minified version of JavaScript and CSS files. - - :param height: Height of the HTML container. - - :param Boolean enable_editing: Enable the map editing modes. - - """ - if (enable_editing and menu == 'zoom'): - menu = 'all' - if enable_editing: - print('Some functions (e.g. saving maps) are not available in the notebook. Use ' - 'Builder.display_in_browser() for a full-featured Escher Builder.') - html = self._get_html(js_source=js_source, menu=menu, scroll_behavior=scroll_behavior, - html_wrapper=False, enable_editing=enable_editing, enable_keys=False, - minified_js=minified_js, fill_screen=False, height=height, - never_ask_before_quit=True, ignore_bootstrap=True) - # import here, in case users don't have requirements installed - try: - from IPython.display import HTML - except ImportError: - raise Exception('You need to be using the IPython notebook for this function to work') - return HTML(html) - - - def display_in_browser(self, ip='127.0.0.1', port=7655, n_retries=50, js_source='web', - menu='all', scroll_behavior='pan', enable_editing=True, enable_keys=True, - minified_js=True, never_ask_before_quit=False): - """Launch a web browser to view the map. - - :param ip: The IP address to serve the map on. - - :param port: - - The port to serve the map on. If specified the port is occupied, - then a random free port will be used. - - :param int n_retries: - - The number of times the server will try to find a port before - quitting. - - :param string js_source: - - Can be one of the following: - - - *web* (Default) - Use JavaScript files from escher.github.io. - - *local* - Use compiled JavaScript files in the local Escher installation. Works offline. - - *dev* - No longer necessary with source maps. This now gives the - same behavior as 'local'. - - :param string menu: Menu bar options include: - - - *none* - No menu or buttons. - - *zoom* - Just zoom buttons. - - *all* (Default) - Menu and button bar. - - :param string scroll_behavior: Scroll behavior options: - - - *pan* - Pan the map. - - *zoom* - Zoom the map. - - *none* (Default) - No scroll events. - - :param Boolean enable_editing: Enable the map editing modes. - - :param Boolean enable_keys: Enable keyboard shortcuts. - - :param Boolean minified_js: - - If True, use the minified version of JavaScript and CSS files. - - :param Boolean never_ask_before_quit: - - Never display an alert asking if you want to leave the page. By - default, this message is displayed if enable_editing is True. + # widget info traitlets - """ - html = self._get_html(js_source=js_source, menu=menu, scroll_behavior=scroll_behavior, - html_wrapper=True, enable_editing=enable_editing, enable_keys=enable_keys, - minified_js=minified_js, fill_screen=True, height="100%", - never_ask_before_quit=never_ask_before_quit) - serve_and_open(html, ip=ip, port=port, n_retries=n_retries) + _view_name = Unicode('EscherMapView').tag(sync=True) + _model_name = Unicode('EscherMapModel').tag(sync=True) + _view_module = Unicode('jupyter-escher').tag(sync=True) + _model_module = Unicode('jupyter-escher').tag(sync=True) + _view_module_version = Unicode(__version__).tag(sync=True) + _model_module_version = Unicode(__version__).tag(sync=True) + # editable attributes - def save_html(self, filepath=None, overwrite=False, js_source='web', - protocol='https', menu='all', scroll_behavior='pan', - enable_editing=True, enable_keys=True, minified_js=True, - never_ask_before_quit=False, static_site_index_json=None): - """Save an HTML file containing the map. + height = Int(500).tag(sync=True) + _loaded_map_json = Unicode(None, allow_none=True).tag(sync=True) - :param string filepath: + @observe('_loaded_map_json') + def _observe_loaded_map_json(self, change): + # if map is cleared, then clear these + if not change.new: + self.map_name = None + self.map_json = None - The HTML file will be saved to this location. When js_source is - 'local', then a new directory will be created with this name. + _loaded_model_json = Unicode(None, allow_none=True).tag(sync=True) - :param Boolean overwrite: + @observe('_loaded_model_json') + def _observe_loaded_model_json(self, change): + # if model is cleared, then clear these + if not change.new: + self.model = None + self.model_name = None + self.model_json = None - Overwrite existing files. + embedded_css = Unicode(None, allow_none=True).tag(sync=True) - :param string js_source: - - Can be one of the following: - - - *web* (Default) - Use JavaScript files from escher.github.io. - - *local* - Use compiled JavaScript files in the local Escher - installation. Works offline. To make the dependencies - available to the downloaded file, a new directory will - be made with the name specified by filepath. - - *dev* - No longer necessary with source maps. This now gives the - same behavior as 'local'. - - :param string protocol: - - The protocol can be 'http', 'https', or None which indicates a - 'protocol relative URL', as in //escher.github.io. Ignored if source - is local. - - :param string menu: Menu bar options include: - - - *none* - No menu or buttons. - - *zoom* - Just zoom buttons. - - *all* (Default) - Menu and button bar. - - :param string scroll_behavior: Scroll behavior options: - - - *pan* - Pan the map. - - *zoom* - Zoom the map. - - *none* (Default) - No scroll events. - - :param Boolean enable_editing: Enable the map editing modes. - - :param Boolean enable_keys: Enable keyboard shortcuts. - - :param Boolean minified_js: - - If True, use the minified version of JavaScript and CSS files. - - :param number height: Height of the HTML container. - - :param Boolean never_ask_before_quit: + @validate('embedded_css') + def _validate_embedded_css(self, proposal): + css = proposal['value'] + if css: + return css.replace('\n', '') + else: + return None - Never display an alert asking if you want to leave the page. By - default, this message is displayed if enable_editing is True. + reaction_data = Dict(None, allow_none=True).tag(sync=True) + metabolite_data = Dict(None, allow_none=True).tag(sync=True) + gene_data = Dict(None, allow_none=True).tag(sync=True) + scroll_behavior = Unicode('pan').tag(sync=True) - :param string static_site_index_json: + # builder traitlets that are indirectly synced to the widget - The index, as a JSON string, for the static site. Use javascript - to parse the URL options. Used for generating static pages (see - static_site.py). + map_name = Unicode(None, allow_none=True) + map_json = Unicode(None, allow_none=True) + model = Instance(Model, allow_none=True) + model_name = Unicode(None, allow_none=True) + model_json = Unicode(None, allow_none=True) - """ + @observe('map_name') + def _observe_map_name(self, change): + if change.new: + self._loaded_map_json = map_json_for_name(change.new) + else: + self._loaded_map_json = None - filepath = expanduser(filepath) + @observe('map_json') + def _observe_map_json(self, change): + if change.new: + self._loaded_map_json = _load_resource(change.new, 'map_json') + else: + self._loaded_map_json = None - if js_source in ['local', 'dev']: - if filepath is None: - raise Exception('Must provide a filepath when js_source is not "web"') + @observe('model') + def _observe_model(self, change): + if change.new: + self._loaded_model_json = cobra.io.to_json(change.new) + else: + self._loaded_model_json = None - # make a directory - directory = re.sub(r'\.html$', '', filepath) - if exists(directory): - if not overwrite: - raise Exception('Directory already exists: %s' % directory) - else: - os.makedirs(directory) - # add dependencies to the directory - escher = get_url('escher_min' if minified_js else 'escher', 'local') - favicon = get_url('favicon', 'local') + @observe('model_name') + def _observe_model_name(self, change): + if change.new: + self._loaded_model_json = model_json_for_name(change.new) + else: + self._loaded_model_json = None - for path in [escher, favicon]: - if path is None: - continue - src = join(root_directory, path) - dest = join(directory, path) - dest_dir = dirname(dest) - if not exists(dest_dir): - os.makedirs(dest_dir) - shutil.copy(src, dest) - filepath = join(directory, 'index.html') + @observe('model_json') + def _observe_model_json(self, change): + if change.new: + self._loaded_model_json = _load_resource(change.new, 'model_json') else: - if not filepath.endswith('.html'): - filepath += '.html' - if exists(filepath) and not overwrite: - raise Exception('File already exists: %s' % filepath) - - html = self._get_html(js_source=js_source, menu=menu, - scroll_behavior=scroll_behavior, - html_wrapper=True, enable_editing=enable_editing, - enable_keys=enable_keys, minified_js=minified_js, - fill_screen=True, height="100%", - never_ask_before_quit=never_ask_before_quit, - static_site_index_json=static_site_index_json, - protocol=protocol) - if filepath is not None: - with open(filepath, 'wb') as f: - f.write(html.encode('utf-8')) - return filepath + self._loaded_model_json = None + + def __init__( + self, + # + height: int = 500, + map_name: str = None, + map_json: str = None, + model: Model = None, + model_name: str = None, + model_json: str = None, + embedded_css: str = None, + reaction_data: dict = None, + metabolite_data: dict = None, + gene_data: dict = None, + scroll_behavior: str = 'pan', + # menu: str='zoom', + # enable_editing: bool=False, + # **kwargs, + ) -> None: + super().__init__() + + # set attributes + self.height = height + + if map_json: + if map_name: + warn('map_json overrides map_name') + self.map_json = map_json else: - from tempfile import mkstemp - from os import write, close - os_file, filename = mkstemp(suffix=".html", text=False) # binary - write(os_file, html.encode('utf-8')) - close(os_file) - return filename + self.map_name = map_name + + if model: + if model_name: + warn('model overrides model_name') + if model_json: + warn('model overrides model_json') + self.model = model + elif model_json: + if model_name: + warn('model_json overrides model_name') + self.model_json = model_json + else: + self.model_name = model_name + + self.embedded_css = embedded_css + + self.reaction_data = reaction_data + self.metabolite_data = metabolite_data + self.gene_data = gene_data + self.scroll_behavior = scroll_behavior + + # # set up the options + # self.options = [ + # 'use_3d_transform', + # 'enable_search', + # 'fill_screen', + # 'zoom_to_element', + # 'full_screen_button', + # 'starting_reaction', + # 'unique_map_id', + # 'primary_metabolite_radius', + # 'secondary_metabolite_radius', + # 'marker_radius', + # 'gene_font_size', + # 'hide_secondary_metabolites', + # 'show_gene_reaction_rules', + # 'hide_all_labels', + # 'canvas_size_and_loc', + # 'reaction_styles', + # 'reaction_compare_style', + # 'reaction_scale', + # 'reaction_no_data_color', + # 'reaction_no_data_size', + # 'and_method_in_gene_reaction_rule', + # 'metabolite_styles', + # 'metabolite_compare_style', + # 'metabolite_scale', + # 'metabolite_no_data_color', + # 'metabolite_no_data_size', + # 'identifiers_on_map', + # 'highlight_missing', + # 'allow_building_duplicate_reactions', + # 'cofactors', + # 'enable_tooltips', + # ] + + # def get_getter_setter(o): + # """Use a closure.""" + # # create local fget and fset functions + # fget = lambda self: getattr(self, '_%s' % o) + # fset = lambda self, value: setattr(self, '_%s' % o, value) + # return fget, fset + # for option in self.options: + # fget, fset = get_getter_setter(option) + # # make the setter + # setattr(self.__class__, 'set_%s' % option, fset) + # # add property to self + # setattr(self.__class__, option, property(fget)) + # # add corresponding local variable + # setattr(self, '_%s' % option, None) + + # # set the kwargs + # for key, val in kwargs.items(): + # try: + # getattr(self, 'set_%s' % key)(val) + # except AttributeError: + # print('Unrecognized keywork argument %s' % key) + + # def display_in_notebook(self): + # """Deprecated. + + # The Builder is now a Jupyter Widget, so you can return the Builder + # object from a cell to display it, or you can manually call the IPython + # display function: + + # from IPython.display import display + # from escher import Builder + # b = Builder(...) + # display(b) + + # """ + # raise Exception(('display_in_notebook is deprecated. The Builder is ' + # 'now a Jupyter Widget, so you can return the ' + # 'Builder in a cell to see it, or use the IPython ' + # 'display function (see Escher docs for details)')) + + # def display_in_browser(self, ip='127.0.0.1', port=7655, n_retries=50, + # js_source='web', menu='all', scroll_behavior='pan', + # enable_editing=True, enable_keys=True, + # minified_js=True, never_ask_before_quit=False): + # """Deprecated. + + # We recommend using the Jupyter Widget (which now supports all Escher + # features) or the save_html option to generate a standalone HTML file + # that loads the map. + + # """ + # raise Exception(('display_in_browser is deprecated. We recommend using' + # 'the Jupyter Widget (which now supports all Escher' + # 'features) or the save_html option to generate a' + # 'standalone HTML file that loads the map.')) + + # def save_html(self, filepath=None): + # """Save an HTML file containing the map. + + # :param string filepath: + + # The name of the HTML file. + + # """ + + # # TODO apply options from self + # options = tranform(self.options) + + # template = env.get_template('standalone.html') + # html = template.render( + # escher_url=get_url('escher_min'), + # # dump json + # options_json=b64dump(options), + # map_download_url_json=b64dump(get_url('map_download')), + # model_download_url_json=b64dump(get_url('model_download')), + # builder_embed_css_json=b64dump(self.embedded_css), + # # alreay json + # map_data_json=b64dump(self.loaded_map_json), + # model_data_json=b64dump(self.loaded_model_json), + # ) + + # with open(expanduser(filepath), 'wb') as f: + # f.write(html.encode('utf-8')) diff --git a/py/escher/quick_server.py b/py/escher/quick_server.py deleted file mode 100644 index a91e5e61..00000000 --- a/py/escher/quick_server.py +++ /dev/null @@ -1,133 +0,0 @@ -""" The following code has been adapted from mpld3. Modifications (c) 2014, -Zachary King. - -mpld3, http://mpld3.github.io/, A Simple server used to show mpld3 images. -Copyright (c) 2013, Jake Vanderplas -All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, -are permitted provided that the following conditions are met: - -* Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -* Redistributions in binary form must reproduce the above copyright notice, this - list of conditions and the following disclaimer in the documentation and/or - other materials provided with the distribution. - -* Neither the name of the {organization} nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -""" -import sys -import threading -import webbrowser -import socket -import itertools -import random - -IPYTHON_WARNING = """ -Note: You must interrupt the kernel to end this command -""" - -try: - # Python 2.x - import BaseHTTPServer as server -except ImportError: - # Python 3.x - from http import server - -def generate_handler(html, files=None): - if files is None: - files = {} - - class MyHandler(server.BaseHTTPRequestHandler): - def do_GET(self): - """Respond to a GET request.""" - if self.path == '/': - self.send_response(200) - self.send_header("Content-type", "text/html") - self.end_headers() - self.wfile.write(html.encode('utf-8')) - elif self.path in files: - content_type, content = files[self.path] - self.send_response(200) - self.send_header("Content-type", content_type) - self.end_headers() - self.wfile.write(content) - else: - self.send_error(404) - - return MyHandler - -def find_open_port(ip, port, n=50): - """Find an open port near the specified port""" - ports = itertools.chain((port + i for i in range(n)), - (port + random.randint(-2 * n, 2 * n))) - - for port in ports: - s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) - result = s.connect_ex((ip, port)) - s.close() - if result != 0: - return port - raise ValueError("no open ports found") - -def serve_and_open(html, ip='127.0.0.1', port=8888, n_retries=50, files=None, - ipython_warning=True): - """Start a server serving the given HTML, and open a browser - - Parameters - ---------- - html : string - HTML to serve - ip : string (default = '127.0.0.1') - ip address at which the HTML will be served. - port : int (default = 8888) - the port at which to serve the HTML - n_retries : int (default = 50) - the number of nearby ports to search if the specified port is in use. - files : dictionary (optional) - dictionary of extra content to serve - ipython_warning : bool (optional) - if True (default), then print a warning if this is used within IPython - """ - port = find_open_port(ip, port, n_retries) - Handler = generate_handler(html, files) - srvr = server.HTTPServer((ip, port), Handler) - - if ipython_warning: - try: - __IPYTHON__ - except: - pass - else: - print(IPYTHON_WARNING) - - # Start the server - print(("Serving to http://{0}:{1}/\n".format(ip, port) + - "[Ctrl-C to exit from terminal, or Ctrl-M i i to interrupt notebook kernel]")) - sys.stdout.flush() - - # Use a thread to open a web browser pointing to the server - b = lambda: webbrowser.open('http://{0}:{1}'.format(ip, port)) - threading.Thread(target=b).start() - - try: - srvr.serve_forever() - except (KeyboardInterrupt, SystemExit): - print("\nstopping Server...") - - srvr.server_close() diff --git a/py/escher/server.py b/py/escher/server.py deleted file mode 100644 index cd599bf2..00000000 --- a/py/escher/server.py +++ /dev/null @@ -1,198 +0,0 @@ -# -*- coding: utf-8 -*- - -from __future__ import print_function, unicode_literals - -from escher.plots import (Builder, local_index, model_json_for_name, - map_json_for_name) -from escher.urls import get_url, root_directory -from escher.util import b64dump - -import os, subprocess -from os.path import join -import tornado.ioloop -from tornado.web import RequestHandler, HTTPError, Application, asynchronous, StaticFileHandler -from tornado.httpclient import AsyncHTTPClient -from tornado import gen -import tornado.escape -from tornado.options import define, options, parse_command_line -import json -import re -from jinja2 import Environment, PackageLoader -from mimetypes import guess_type - -from escher.version import __version__, __schema_version__, __map_model_version__ - -# set up jinja2 template location -env = Environment(loader=PackageLoader('escher', 'templates')) - -# set directory to server -NO_CACHE = False -PORT = 7778 -PUBLIC = False - -def run(port=PORT, public=PUBLIC): - global PORT - global PUBLIC - PORT = port - PUBLIC = public - print('serving directory %s on port %d' % (root_directory, PORT)) - application.listen(port, None if public else "localhost") - try: - tornado.ioloop.IOLoop.instance().start() - except KeyboardInterrupt: - print("bye!") - -def stop(): - tornado.ioloop.IOLoop.instance().stop() - -class BaseHandler(RequestHandler): - def serve_path(self, path): - # make sure the path exists - if not os.path.isfile(path): - raise HTTPError(404) - # serve any raw file type - with open(path, "rb") as file: - data = file.read() - # set the mimetype - the_type = guess_type(path, strict=False)[0] - self.set_header("Content-Type", ("application/octet-stream" - if the_type is None - else the_type)) - self.serve(data) - - def serve(self, data): - if (NO_CACHE): - self.set_header('Cache-Control', 'no-store, no-cache, must-revalidate, max-age=0') - self.set_header('Access-Control-Allow-Origin', '*') - self.write(data) - self.finish() - -class IndexHandler(BaseHandler): - @asynchronous - @gen.coroutine - def get(self): - # get the organisms, maps, and models - response = yield gen.Task(AsyncHTTPClient().fetch, get_url('server_index', protocol='http')) - if response.code == 200 and response.body is not None: - server_index_json = response.body.decode('utf-8') - else: - server_index_json = None - - # get the cached maps and models - index = local_index() - - # render the template - template = env.get_template('homepage.html') - data = template.render(escher=get_url('escher_min', 'local'), - homepage_css=get_url('homepage_css', 'local'), - favicon=get_url('favicon', 'local'), - logo=get_url('logo', 'local'), - documentation=get_url('documentation', protocol='https'), - github=get_url('github'), - github_releases=get_url('github_releases'), - homepage_js=get_url('homepage_js', 'local'), - map_download_url=get_url('map_download', 'local'), - server_index_json=b64dump(server_index_json), - local_index_json=b64dump(index), - version=__version__, - web_version=False) - - self.set_header("Content-Type", "text/html") - self.serve(data) - -class BuilderHandler(BaseHandler): - @asynchronous - @gen.coroutine - def get(self): - # Builder options - builder_kwargs = {} - for a in ['starting_reaction', 'model_name', 'map_name', 'map_json', - 'reaction_no_data_color', 'reaction_no_data_size', - 'metabolite_no_data_color', 'metabolite_no_data_size', - 'hide_secondary_nodes']: - args = self.get_arguments(a) - if len(args)==1: - builder_kwargs[a] = (True if args[0].lower()=='true' else - (False if args[0].lower()=='false' else - args[0])) - # array args - for a in ['quick_jump', 'metabolite_size_range', 'metabolite_color_range', - 'reaction_size_range', 'reaction_color_range', 'gene_styles']: - args = self.get_arguments(a + '[]') - if len(args) > 0: - builder_kwargs[a] = args - - # js source - args = self.get_arguments('js_source') - js_source = args[0] if len(args) == 1 else 'web' - - # example data - def load_data_file(rel_path): - """Load a JSON file with relative path.""" - try: - with open(join(root_directory, rel_path), 'r') as f: - return json.load(f) - except: - logging.warn('Could not load testing_data file: %s' % rel_path) - if len(self.get_arguments('testing_data')) > 0: - r_filepath = 'escher/testing_data/reaction_data_iJO1366.json' - builder_kwargs['reaction_data'] = load_data_file(r_filepath) - m_filepath = 'escher/testing_data/metabolite_data_iJO1366.json' - builder_kwargs['metabolite_data'] = load_data_file(m_filepath) - - # display options - display_kwargs = {'minified_js': True, - 'scroll_behavior': 'pan', - 'menu': 'all'} - - # keyword - for a in ['menu', 'scroll_behavior', 'minified_js', - 'auto_set_data_domain', 'never_ask_before_quit', - 'enable_editing']: - args = self.get_arguments(a) - if len(args)==1: - display_kwargs[a] = (True if args[0].lower()=='true' else - (False if args[0].lower()=='false' else - args[0])) - - # make the builder - builder = Builder(safe=True, **builder_kwargs) - html = builder._get_html(js_source=js_source, enable_keys=True, - html_wrapper=True, fill_screen=True, - height='100%', **display_kwargs) - - self.set_header("Content-Type", "text/html") - self.serve(html) - -class MapModelHandler(BaseHandler): - def get(self, path): - try: - kind, organism, name = path.strip('/').split('/') - except (TypeError, ValueError): - raise Exception('invalid path %s' % path) - if kind == 'maps': - b = Builder(map_name=name) - self.set_header('Content-Type', 'application/json') - self.serve(b.loaded_map_json) - else: - b = Builder(model_name=name) - self.set_header('Content-Type', 'application/json') - self.serve(b.loaded_model_json) - -settings = {'debug': True} - -application = Application([ - (r'.*escher/static/(.*)', StaticFileHandler, {'path': join(root_directory, 'escher', 'static')}), - (r'/builder/index.html', BuilderHandler), - (r'/%s/%s(/.*)' % (__schema_version__, __map_model_version__), MapModelHandler), - (r'/', IndexHandler), -], **settings) - -if __name__ == '__main__': - # define port - define('port', default=PORT, type=int, help='Port to serve on.') - define('public', default=PUBLIC, type=bool, - help=('If False, listen only on localhost. If True, listen on ' - 'all available addresses.')) - parse_command_line() - run(port=options.port, public=options.public) diff --git a/py/escher/static/.gitignore b/py/escher/static/.gitignore new file mode 100644 index 00000000..c96a04f0 --- /dev/null +++ b/py/escher/static/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore \ No newline at end of file diff --git a/py/escher/static/escher/.gitignore b/py/escher/static/escher/.gitignore deleted file mode 100644 index 86d0cb27..00000000 --- a/py/escher/static/escher/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore \ No newline at end of file diff --git a/py/escher/static/homepage/main.css b/py/escher/static/homepage/main.css deleted file mode 100644 index c3c179c0..00000000 --- a/py/escher/static/homepage/main.css +++ /dev/null @@ -1,176 +0,0 @@ -html, -body { - height: 100%; - background-color: #FCFCFC; - /* The html and body elements cannot have any padding or margin. */ -} - -body { - font-size: 17px; - color: #585858; -} - -body, h2, h3, h4, h5, h6 { - font-family: "Helvetica Neue", Helvetica, Arial, sans-serif !important; -} - -h2 { - font-size: 30px !important; -} - -h3 { - font-size: 24px !important; -} - -.form-control { - font-size: 14px !important; -} - -h4 { - font-size: 18px !important; -} - -button { - font-size: 14px !important; -} - -#whats-new { - position: absolute; - top: 5px; - right: 20px; - font-style: italic; - font-size: 18px; - /* background-color: rgba(0, 0, 0, 0.05); */ - border-radius: 2px; - padding: 1px 5px; - border: 1px solid #CF6965; -} -@media (max-width: 768px) { - #whats-new { - font-size: 14px; - } -} - -/* Wrapper for page content to push down footer */ -main { - /* Negative indent footer by it's height */ - margin: 0px auto -60px auto; - max-width: 700px; - min-height: 100%; - height: auto !important; - height: 100%; -} - -/* Demos */ -.demo-title { - position: absolute; - margin: 5px 0 0 20px; - color: #5A5A5A; - font-style: italic; - font-size: 32px; - font-weight: bold; - z-index: 10; -} -.demo-img { - border: 3px solid #eee; - opacity: 0.7; -} - -/* Set the fixed height of the footer here */ -#push { - height: 80px; -} -footer { - height: 60px; - background-color: #291E1E; - color: #eee; -} -a, a:hover, a:focus, a:visited { - color: #CF6965; -} -footer a, footer a:hover, footer a:focus, footer a:visited { - color: #FFA09D; -} -@media (max-width: 768px) { - #footer { - margin-left: -20px; - margin-right: -20px; - padding-left: 20px; - padding-right: 20px; - } -} - -.container { - width: auto; - max-width: 700px; -} -.container .more { - margin: 20px 0; - float: left; -} -.container .version { - margin: 20px 0; - float: right; -} -.column-button { - width: 100%; - margin-top: 35px; -} -label { - font-weight: inherit; -} -#title-box { - display: inline-block; -} -#title { - color: #291E1E; - font-size: 160px; - font-family: tulpen-one, Futura, serif; - font-weight: 400; - margin-bottom: 0px; -} -#title-box p { - font-size: 22px; - font-style: italic; -} -#logo { - vertical-align: inherit; - margin-bottom: 60px; -} -#faq li { - padding-top: 5px; -} -@media (max-width: 768px) { - #title-box { - width: 100%; - text-align: center; - } - #logo { - display: none; - } -} -@media (min-width: 768px) { /*@screen-sm-min) { */ - .column-button { - margin-top: 56px; - } - header { - margin-bottom: 20px; - } - #title-box { - max-width: 400px; - overflow: hidden; - } - #title { - position: relative; - top: 45px; - left: -7px; - font-size: 230px; - text-align: left; - margin-bottom: 10px; - } - #logo { - width: 250px; - display: inline-block; - overflow: hidden; - } -} diff --git a/py/escher/static/homepage/main.js b/py/escher/static/homepage/main.js deleted file mode 100644 index 593da862..00000000 --- a/py/escher/static/homepage/main.js +++ /dev/null @@ -1,380 +0,0 @@ -/* global escher */ - -var MAP_DOWNLOAD -var SERVER_INDEX -var LOCAL_INDEX - -/** - * Get model from a map name. - */ -function get_model (name) { - var parts = name.split('.') - if (parts.length == 2) - return parts[0] - return null -} - -function select_model (model_name) { - var sel = escher.libs.d3_select('#models') - var ind = 0 - sel.selectAll('option') - .each(function (d, i) { - if (d && (d.model_name === model_name)) - ind = i - }) - sel.node().selectedIndex = ind -} - -/** - * Find maps with the same model. Returns null if no quick jump options could be - * found. - */ -function get_quick_jump (this_map, server_index, local_index) { - var model = get_model(this_map) - if (model === null) { - return null - } - - var quick_jump = {} - var all_maps = [] - if (server_index !== null) { - all_maps = all_maps.concat(server_index.maps) - } - if (local_index !== null) { - all_maps = all_maps.concat(local_index.maps) - } - all_maps.forEach(function (o) { - if (get_model(o.map_name) === model) { - quick_jump[o.map_name] = true - } - }) - quick_jump = Object.keys(quick_jump) - return quick_jump.length == 0 ? null : quick_jump -} - -function submit (server_index, local_index, map_download) { - // get the selections - var maps = escher.libs.d3_select('#maps') - var map_data = (maps.selectAll('option') - .filter(function(d, i) { - return i == maps.node().selectedIndex - }).node().__data__) - var map_name = map_data ? map_data.map_name : null - var organism = map_data ? map_data.organism : null - var model_name = escher.libs.d3_select('#models').node().value - var options_value = escher.libs.d3_select('#tools').node().value - var scroll_value = escher.libs.d3_select('#scroll').node().checked - var never_ask_value = escher.libs.d3_select('#never_ask').node().checked - var add = [] - var url - // only add model for builder - if (model_name !== 'none' && options_value === 'builder') { - add.push('model_name=' + model_name) - } - if (map_name !== null) { - add.push('map_name=' + map_name) - } - if (scroll_value) { - add.push('scroll_behavior=zoom') - } - if (never_ask_value) { - add.push('never_ask_before_quit=true') - } - if (options_value === 'viewer') { - add.push('enable_editing=false') - } else { - add.push('enable_editing=true') - } - - // choose the file - url = 'builder/index.html' - add.push('js_source=local') - - // set the quick jump maps - if (map_name) { - var quick_jump = get_quick_jump(map_name, server_index, local_index) - if (quick_jump !== null) { - quick_jump.forEach(function(o) { - add.push('quick_jump[]=' + o) - }) - add.push('quick_jump_path=' + map_download + encodeURIComponent(organism)) - } - } - - url += '?' - for (var i=0, l=add.length; i < l; i++) { - if (i > 0) url += '&' - url += add[i] - } - window.open(url, '_blank') -} - -/** - * Draw the models selector. - */ -function draw_models_select (server_index, local_index) { - // filter function - var filter_models = function(d) { - var org = escher.libs.d3_select('#organisms').node().value - if (org === 'all') { - return true - } - if (org === d.organism) { - return true - } - return false - } - - var web_sel - var local_sel - var select_sel = escher.libs.d3_select('#models') - if (local_index === null) { - // no cache - web_sel = select_sel - } else { - // local cache - var s = select_sel.selectAll('optgroup') - .data([ [ 'local', 'Cached' ], [ 'web', 'Web' ] ]) - s.enter() - .append('optgroup') - .merge(s) - .attr('label', function (d) { return d[1] }) - .attr('id', function (d) { return 'models-' + d[0] }) - web_sel = select_sel.select('#models-web') - local_sel = select_sel.select('#models-local') - } - - // cached - var local_model_names = [] - var model_data - var map_data - if (local_index !== null) { - model_data = local_index.models.filter(filter_models) - local_model_names = model_data.map(function(x) { return x.model_name; }) - - var models_sel = local_sel.selectAll('.model') - .data(model_data, function (d) { return d.model_name }) - models_sel.enter() - .append('option') - .classed('model', true) - .merge(models_sel) - .attr('value', function (d) { return d.model_name }) - .text(function(d) { - var parts = d.model_name.split('.') - if (parts.length==2) { - return d.model_name.split('.').slice(-1)[0] - } else { - return d.model_name - } - }) - models_sel.exit().remove() - } - - // web - if (server_index !== null) { - model_data = server_index.models - .filter(filter_models) - .filter(function(o) { return local_model_names.indexOf(o.model_name) == -1; }) - models_sel = web_sel.selectAll('.model') - .data(model_data, function(d) { return d.model_name; }) - models_sel.enter() - .append('option') - .classed('model', true) - .merge(models_sel) - .attr('value', function(d) { return d.model_name; }) - .text(function(d) { - return d.model_name.split('.').slice(-1)[0] - }) - models_sel.exit().remove() - } - -} - -/** - * Draw the models selector. - * @param {Object} server_index - The index for the server. - * @param {Object} local_index - The index of local maps and models - * @return {Boolean} True if there are maps, and false if no maps. - */ -function draw_maps_select (server_index, local_index) { - var filter_maps = function(d) { - var org = escher.libs.d3_select('#organisms').node().value - if (org === 'all') { - return true - } - if (org === d.organism) { - return true - } - return false - } - - var select_sel = escher.libs.d3_select('#maps') - if (local_index === null) { - // no cache - web_sel = select_sel - } else { - // local cache - var s = select_sel.selectAll('optgroup') - .data([ [ 'local', 'Cached' ], [ 'web', 'Web' ] ]) - s.enter() - .append('optgroup') - .merge(s) - .attr('label', function (d) { return d[1] }) - .attr('id', function (d) { return 'maps-' + d[0] }) - var web_sel = escher.libs.d3_select('#maps-web') - var local_sel = escher.libs.d3_select('#maps-local') - } - - // cached - var local_map_names = [] - var has_maps = false - var map_data - if (local_index !== null) { - map_data = local_index.maps.filter(filter_maps) - local_map_names = map_data.map(function(x) { return x.map_name; }) - if (map_data.length > 0) - has_maps = true - - var maps_sel = local_sel.selectAll('.map') - .data(map_data, function(d) { return d.map_name; }) - maps_sel.enter() - .append('option') - .classed('map', true) - .merge(maps_sel) - .text(function (d) { - var parts = d.map_name.split('.') - if (parts.length == 2) { - var map = d.map_name.split('.').slice(-1)[0] - var model = get_model(d.map_name) - return map + ' (' + model + ')' - } else { - return d.map_name - } - }) - maps_sel.exit().remove() - } - - // web - if (server_index !== null) { - map_data = server_index.maps - .filter(filter_maps) - .filter(function(o) { return local_map_names.indexOf(o.map_name) == -1; }) - if (map_data.length > 0) - has_maps = true - - maps_sel = web_sel.selectAll('.map') - .data(map_data, function (d) { return d.map_name }) - maps_sel.enter() - .append('option') - .classed('map', true) - .merge(maps_sel) - .text(function(d) { - var map = d.map_name.split('.').slice(-1)[0] - var model = get_model(d.map_name) - return map + ' (' + model + ')' - }) - maps_sel.exit().remove() - } - - // select the first map and model - if (has_maps && select_sel.node().selectedIndex == 0) { - select_sel.node().selectedIndex = 1 - select_sel - .selectAll('option') - .each(function(d, i) { - if (i == 1) select_model(get_model(d.map_name)) - }) - } - - return has_maps -} - -function draw_organisms_select (organisms) { - var org = escher.libs.d3_select('#organisms').selectAll('.organism') - .data(organisms, function (d) { return d }) - org.enter() - .append('option') - .classed('organism', true) - .merge(org) - .attr('value', function (d) { return d }) - .text(function (d) { return d }) -} - -function setup (server_index, local_index, map_download) { - // GO - var uniq = function (a) { - var seen = {} - return a.filter(function (item) { - return seen.hasOwnProperty(item) ? false : (seen[item] = true) - }) - } - var not_cached = function (web, local) { - if (local === null) return web - return web.filter(function (m) { - return local.indexOf(m) === -1 - }) - } - - // organisms - var organisms = {} - ;[ local_index, server_index ] - .filter(function (x) { return x !== null; }) - .forEach(function (i) { - ;[ 'maps', 'models' ].forEach(function (n) { - i[n].forEach(function (m) { - organisms[m.organism] = true - }) - }) - }) - organisms = Object.keys(organisms) - - // draw dropdown menus - draw_organisms_select(organisms) - draw_models_select(server_index, local_index) - var has_maps = draw_maps_select(server_index, local_index) - - // update filters - escher.libs.d3_select('#organisms') - .on('change', function() { - draw_models_select(server_index, local_index) - draw_maps_select(server_index, local_index) - }) - - // select an appropriate model for selected map - escher.libs.d3_select('#maps') - .on('change', function() { - var is_none = this.value === 'none' - var selectedIndex = this.selectedIndex - escher.libs.d3_select(this) - .selectAll('option') - .each(function (d, i) { - if (d && i == selectedIndex) - select_model(get_model(d.map_name)) - }) - }) - - // disable Model for viewer - escher.libs.d3_select('#tools') - .on('change', function() { - escher.libs.d3_select('#models') - .attr('disabled', this.value.indexOf('viewer') == -1 ? null : true) - }) - - // select the first map - var map_node = escher.libs.d3_select('#maps').node() - if (has_maps && map_node.selectedIndex == 0) - map_node.selectedIndex = 1 - - // submit button - escher.libs.d3_select('#submit') - .on('click', submit.bind(null, server_index, local_index, map_download)) - - // submit on enter - var selection = escher.libs.d3_select(window) - var kc = 13 - selection.on('keydown.' + kc, function () { - if (escher.libs.d3_selection.event.keyCode === kc) { - submit(server_index, local_index, map_download) - } - }) -} diff --git a/py/escher/static/img/escher-logo.png b/py/escher/static/img/escher-logo.png deleted file mode 100644 index 150f1818..00000000 Binary files a/py/escher/static/img/escher-logo.png and /dev/null differ diff --git a/py/escher/static/img/escher-logo@2x.png b/py/escher/static/img/escher-logo@2x.png deleted file mode 100644 index c84065cd..00000000 Binary files a/py/escher/static/img/escher-logo@2x.png and /dev/null differ diff --git a/py/escher/static/img/favicon.ico b/py/escher/static/img/favicon.ico deleted file mode 100644 index b79bc3d1..00000000 Binary files a/py/escher/static/img/favicon.ico and /dev/null differ diff --git a/py/escher/static/img/knockout-demo-screenshot.png b/py/escher/static/img/knockout-demo-screenshot.png deleted file mode 100644 index 4e022005..00000000 Binary files a/py/escher/static/img/knockout-demo-screenshot.png and /dev/null differ diff --git a/py/escher/static/img/sbrg-logo.png b/py/escher/static/img/sbrg-logo.png deleted file mode 100644 index 1613f98d..00000000 Binary files a/py/escher/static/img/sbrg-logo.png and /dev/null differ diff --git a/py/escher/static/img/structures-demo-screenshot.png b/py/escher/static/img/structures-demo-screenshot.png deleted file mode 100644 index da564046..00000000 Binary files a/py/escher/static/img/structures-demo-screenshot.png and /dev/null differ diff --git a/py/escher/static/jsonschema/.gitignore b/py/escher/static/jsonschema/.gitignore deleted file mode 100644 index 86d0cb27..00000000 --- a/py/escher/static/jsonschema/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore \ No newline at end of file diff --git a/py/escher/static_site.py b/py/escher/static_site.py deleted file mode 100644 index 05419de8..00000000 --- a/py/escher/static_site.py +++ /dev/null @@ -1,60 +0,0 @@ -from __future__ import print_function, unicode_literals - -from escher.plots import Builder -from escher.urls import get_url -from escher.version import __version__ -from escher.urls import top_directory, root_directory - -from os.path import join, dirname, realpath -from jinja2 import Environment, PackageLoader -import shutil - -# set up jinja2 template location -env = Environment(loader=PackageLoader('escher', 'templates')) - -def generate_static_site(): - print('Generating static site at %s' % top_directory) - - # index file - template = env.get_template('homepage.html') - - def static_rel(path): - return 'py/' + path - - data = template.render(escher=static_rel(get_url('escher_min', 'local')), - homepage_css=static_rel(get_url('homepage_css', 'local')), - favicon=static_rel(get_url('favicon', 'local')), - logo=static_rel(get_url('logo', 'local')), - documentation=get_url('documentation', protocol='https'), - github=get_url('github', protocol='https'), - github_releases=get_url('github_releases', protocol='https'), - homepage_js=static_rel(get_url('homepage_js', 'local')), - version=__version__, - map_download_url=get_url('map_download', 'local'), - web_version=True, - server_index_url=static_rel(get_url('server_index', 'local'))) - - with open(join(top_directory, 'index.html'), 'wb') as f: - f.write(data.encode('utf-8')) - - # viewer and builder - # make the builder - builder = Builder(safe=True, id='static_map') - - filepath = join(top_directory, 'builder') - with open(join(root_directory, get_url('server_index', source='local')), 'r') as f: - index_json = f.read() - html = builder.save_html(filepath=filepath, - overwrite=True, - js_source='local', - protocol=None, - minified_js=True, - static_site_index_json=index_json) - - # copy over the source map - escher_map = get_url('escher_min', 'local') + '.map' - shutil.copy(join(root_directory, escher_map), join(top_directory, 'builder', escher_map)) - - -if __name__ == '__main__': - generate_static_site() diff --git a/py/escher/templates/content.html b/py/escher/templates/content.html deleted file mode 100644 index a6b49e4a..00000000 --- a/py/escher/templates/content.html +++ /dev/null @@ -1,98 +0,0 @@ -{% if wrapper %}{% extends 'standalone.html' %}{% endif %} - -{% block content %} -
- - -{% endblock %} diff --git a/py/escher/templates/homepage.html b/py/escher/templates/homepage.html deleted file mode 100644 index 663bae6f..00000000 --- a/py/escher/templates/homepage.html +++ /dev/null @@ -1,210 +0,0 @@ -{% extends "standalone.html" %} - -{% block title %}Escher{% endblock %} - -{% block head %} - - - - - - - - - -{% endblock %} - -{% block content %} -
-
-
-
- - -
-

ESCHER

-

Build, share, and embed visualizations of biological pathways.

-
-
-
-
-
-

Filter by organism

- -
-
-
-
-

Map

- -
-
-

Model (Optional)

- -
-
-

Tool

- -
-
-
-
-

Options

-
- -
-
- -
-
-
- -
-
- -
- - {% if web_version %} - -
-
-

Demos

-
-
- -
-
- -
-
- -
- - - -
-
-

EscherConverter

-
-
-
-

EscherConverter is a standalone program that reads files - created with Escher and converts them to files in community - standard formats.

-

Learn more and download.

-
-
-
- -
- - {% endif %} - - -
-
-

FAQ

-
    -

  1. What is Escher?

    -

    Escher is a web-based tool for building, viewing, and sharing - visualizations of biological pathways. These 'pathway maps' are a - great way to contextualize data about metabolism. To get started, - load a map by clicking the Load Map button above, or visit - the documentation to learn more. -

    -
    2. -

  2. How do I cite Escher?

    -

    You can help support Escher by citing our publication when you - use Escher or EscherConverter:

    -

    Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus - Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson - (2015) Escher: A web application for building, sharing, and - embedding data-rich visualizations of biological pathways, - PLOS Computational Biology 11(8): e1004321. - doi:10.1371/journal.pcbi.1004321

    -

  3. Are there more maps available? Can I contribute maps?

    -

    We will be uploading maps for all of the organisms in the - BiGG database. If you - would like to contribute maps, there is a - guide - available in the documentation. -

    4. -

  4. How is Escher licensed?

    -

    Escher and EscherConverter are distributed under the - MIT license.

    -

  5. What browsers can I use?

    -

    We recommend using Google Chrome for optimal performance, but - Escher will also run in the latest versions of Firefox, Internet - Explorer, and Safari (including mobile Safari).

    -
    6. -

  6. I have more questions. Who do I ask?

    -

    Visit the documentation - to get started with Escher and explore the API, or ask - questions in the Gitter chat - room. If you find bugs or would like to contribute to - the project, feel free to submit an issue and or a pull - request on Github.

    -
    7. -
-
- -
-
-
-
- - - - -{% endblock %} diff --git a/py/escher/templates/standalone.html b/py/escher/templates/standalone.html index 98ea2066..796958e5 100644 --- a/py/escher/templates/standalone.html +++ b/py/escher/templates/standalone.html @@ -1,19 +1,41 @@ - {% block title %}{{ title }}{% endblock %} + Escher Builder - {% block head %}{% endblock %} - - {% if favicon_url %} - - {% endif %} + + initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui"/> - {% block content %}{% endblock %} +
+ + diff --git a/py/escher/tests/test_convert_map.py b/py/escher/tests/test_convert_map.py deleted file mode 100644 index ab7ca76d..00000000 --- a/py/escher/tests/test_convert_map.py +++ /dev/null @@ -1,249 +0,0 @@ -from __future__ import print_function, unicode_literals - -from escher.convert_map import * -from escher.urls import root_directory -import cobra.io -from os.path import join -from pytest import raises - -def get_old_map(): - # map - return {'reactions': {'1': {'bigg_id': 'GAPD', - 'label_x': '0', - 'label_y': 0, - "metabolites": [{ - "coefficient": -1, - "bigg_id": "g3p_c" - }], - 'segments': {'2': {'from_node_id': '0', - 'to_node_id': '1', - 'b1': None, - 'b2': {'x': None, 'y': None}}, - '10': {'from_node_id': '11', - 'to_node_id': '12'}}}, - '2': {'bigg_id': 'PDH'}, - '3': {'bigg_id': 'TTT', - 'label_x': 0, - 'label_y': 0, - "metabolites": [ - { - "coefficient": -1, - "bigg_id": "test_met_c" - }, - { - "coefficient": -1, - "bigg_id": "glc__D_c" - } - ], - 'segments': { - '10': {'from_node_id': '3', - 'to_node_id': '4'} - } - }}, - 'nodes': {'0': {'node_type': 'multimarker', - 'x': 1, - 'y': 2}, - '1': {'node_type': 'metabolite', - 'label_x': 10, - 'label_y': 12.2, - 'x': 1, - 'y': 2, - 'bigg_id': 'g3p_c', - 'name': 'glycerol-3-phosphate'}, - '3': {'node_type': 'metabolite', - 'x': 1, - 'y': 2, - 'bigg_id': 'glc__D_c', - 'name': 'D-Glucose'}, - '4': {'node_type': 'multimarker', - 'x': 9, - 'y': 9}, - }, - 'text_labels': []} # should be {} - -def get_new_map(): - return [ - {"schema": "https://escher.github.io/escher/jsonschema/1-0-0#", - "homepage": "https://escher.github.io", - "map_name": "", - "map_id": "", - "map_description": "my new map"}, - {"reactions": {"1576769": {"name": "glyceraldehyde-3-phosphate dehydrogenase", - "bigg_id": "GAPD", - "reversibility": True, - "label_x": 1065, - "label_y": 2385, - "gene_reaction_rule": "b1779", - "genes": [{"bigg_id": "b1779", "name": "b1779"}], - "metabolites": [ - {"coefficient": 1, "bigg_id": "nadh_c"}, - {"coefficient": 1, "bigg_id": "13dpg_c"}, - {"coefficient": -1, "bigg_id": "pi_c"}, - {"coefficient": 1, "bigg_id": "h_c"}, - {"coefficient": -1, "bigg_id": "nad_c"}, - {"coefficient": -1, "bigg_id": "g3p_c"} - ], - "segments": { - "217": {"from_node_id": "1577006", "to_node_id": "1577008", "b1": None, "b2": None}, - "218": {"from_node_id": "1577008", "to_node_id": "1577007", "b1": None, "b2": None}, - "219": {"from_node_id": "1576575", "to_node_id": "1577006", "b1": {"y": 2270, "x": 1055}, "b2": {"y": 2322.5, "x": 1055}}, - "220": {"from_node_id": "1576669", "to_node_id": "1577006", "b1": {"y": 2284.7920271060384, "x": 1055}, "b2": {"y": 2326.9376081318114, "x": 1055}}, - "221": {"from_node_id": "1576670", "to_node_id": "1577006", "b1": {"y": 2297.5658350974745, "x": 1055}, "b2": {"y": 2330.769750529242, "x": 1055}}, - "222": {"from_node_id": "1577007", "to_node_id": "1576487", "b1": {"y": 2454.5, "x": 1055}, "b2": {"y": 2500, "x": 1055}}, - "223": {"from_node_id": "1577007", "to_node_id": "1576671", "b1": {"y": 2453.0623918681886, "x": 1055}, "b2": {"y": 2495.2079728939616, "x": 1055}}, - "224": {"from_node_id": "1577007", "to_node_id": "1576672", "b1": {"y": 2449.230249470758, "x": 1055}, "b2": {"y": 2482.4341649025255, "x": 1055}} - } - } - }, - "nodes": { - "1577006": {"node_type": "multimarker", "x": 1055, "y": 2345}, - "1577007": {"node_type": "multimarker", "x": 1055, "y": 2435}, - "1577008": {"node_type": "midmarker", "x": 1055, "y": 2395}, - "1576575": {"node_type": "metabolite", "x": 1055, "y": 2195, "bigg_id": "g3p_c", "name": "Glyceraldehyde-3-phosphate", "label_x": 1085, "label_y": 2195, "node_is_primary": True}, - "1576487": {"node_type": "metabolite", "x": 1055, "y": 2565, "bigg_id": "13dpg_c", "name": "3-Phospho-D-glyceroyl-phosphate", "label_x": 1085, "label_y": 2565, "node_is_primary": True}, - "1576669": {"node_type": "metabolite", "x": 1145, "y": 2265, "bigg_id": "nad_c", "name": "Nicotinamide-adenine-dinucleotide", "label_x": 1165, "label_y": 2265, "node_is_primary": False}, - "1576670": {"node_type": "metabolite", "x": 1145, "y": 2315, "bigg_id": "pi_c", "name": "Phosphate", "label_x": 1165, "label_y": 2315, "node_is_primary": False}, - "1576671": {"node_type": "metabolite", "x": 1145, "y": 2515, "bigg_id": "nadh_c", "name": "Nicotinamide-adenine-dinucleotide-reduced", "label_x": 1165, "label_y": 2515, "node_is_primary": False}, - "1576672": {"node_type": "metabolite", "x": 1145, "y": 2465, "bigg_id": "h_c", "name": "H", "label_x": 1169, "label_y": 2465, "node_is_primary": False}, - } - } - ] - - -def test_get_header(): - assert get_header([1,2]) == 1 - -def test_get_body(): - assert get_body([1,2]) == 2 - -def test_is_valid_body(): - assert is_valid_body(get_old_map()) - -def test_dict_with_required_elements(): - out = {'my': 'dict', 'remove': 'me'} - dict_with_required_elements(out, ['my', 'also'], - get_default=lambda x, _: 'this' if x == 'also' else None) - assert out['also'] == 'this' - assert 'my' in out - assert out['my'] is out['my'] - assert 'remove' not in out - - with raises(MissingDefaultAttribute): - out = {'my': 'dict'} - dict_with_required_elements(out, ['also']) - - # nullable attributes - with raises(MissingDefaultAttribute): - out = {'my': None} - dict_with_required_elements(out, ['my']) - out = {'my': None} - dict_with_required_elements(out, ['my'], nullable=['my']) - - # casting - out = {'my': 0} - dict_with_required_elements(out, ['my'], cast={'my': float}) - assert out['my'] == 0 - -def test_old_map_to_new_schema(): - old_map = get_old_map() - new_map = old_map_to_new_schema(old_map) - assert len(new_map) == 2 - assert 'schema' in get_header(new_map) - assert 'reactions' in get_body(new_map) - assert old_map['reactions'] is get_reactions(get_body(new_map)) - # fixed bezier attribute - assert get_body(new_map)['reactions']['1']['segments']['2']['b2'] is None - assert get_body(new_map)['canvas']['x'] == -1440 - assert get_body(new_map)['text_labels'] == {} - # removed reaction with missing metabolite - assert '3' not in get_body(new_map)['reactions'] - -def test_old_map_to_new_schema__map_name(): - """Make sure the arguments are being used.""" - new_map = get_new_map() - converted = old_map_to_new_schema(new_map, map_name='Tosche', - map_description='Station') - assert converted[0]['map_name'] == 'Tosche' - assert converted[0]['map_description'] == 'Station' - new_map = get_new_map() - converted = old_map_to_new_schema(new_map, map_name='Tosche', - map_description=None) - assert converted[0]['map_name'] == 'Tosche' - assert converted[0]['map_description'] == 'my new map' - new_map = get_new_map() - converted = old_map_to_new_schema(new_map, map_name=None, - map_description='Station') - assert converted[0]['map_name'] == '' - assert converted[0]['map_description'] == 'Station' - -def test_apply_id_mappings(): - new_map = get_new_map() - reaction_id_mapping = {'GAPD': 'GAPD_1'} - metabolite_id_mapping = {'g3p_c': 'g3p_c_1'} - gene_id_mapping = {'b1779': 'gapA'} - apply_id_mappings(new_map, reaction_id_mapping, metabolite_id_mapping, gene_id_mapping) - assert list(get_reactions(get_body(new_map)).values())[0]['bigg_id'] == 'GAPD_1' - assert list(get_reactions(get_body(new_map)).values())[0]['genes'][0]['bigg_id'] == 'gapA' - assert 'g3p_c_1' in [x['bigg_id'] for x in list(get_reactions(get_body(new_map)).values())[0]['metabolites']] - assert 'g3p_c_1' in [x['bigg_id'] for x in get_nodes(get_body(new_map)).values() if 'bigg_id' in x] - -def test_apply_cobra_model_to_map(): - new_map = get_new_map() - model = cobra.io.load_json_model(join(root_directory, 'escher', 'testing_data', 'iJO1366.json')) - model.reactions.get_by_id('GAPD').gene_reaction_rule = '12345' - model.reactions.get_by_id('GAPD').name = '54321' - assert model.reactions.get_by_id('GAPD').lower_bound < 0 - model.reactions.get_by_id('GAPD').lower_bound = 0 - model.genes.get_by_id('12345').name = 'gonzo' - apply_cobra_model_to_map(new_map, model) - gapd_reaction = list(get_reactions(get_body(new_map)).values())[0] - assert gapd_reaction['gene_reaction_rule'] == model.reactions.get_by_id('GAPD').gene_reaction_rule - assert gapd_reaction['name'] == model.reactions.get_by_id('GAPD').name - assert gapd_reaction['reversibility'] is False - assert 'gonzo' in [x['name'] for x in gapd_reaction['genes']] - - -def test_convert(): - model = cobra.io.load_json_model(join(root_directory, 'escher', 'testing_data', 'iJO1366.json')) - - # reverse the reaction - model.reactions.get_by_id('GAPD').upper_bound = 0 - model.reactions.get_by_id('GAPD').lower_bound = -1000 - - new_map = convert(get_old_map(), model) - - # no segments: delete reaction - assert '2' not in new_map[1]['reactions'] - - # missing segments: delete reaction - assert '1' not in new_map[1]['reactions'] - - # now again with the correct number of segments - gapd = model.reactions.get_by_id('GAPD') - gapd.subtract_metabolites({k: v for k, v in gapd.metabolites.items() if k.id != 'g3p_c'}) - new_map = convert(get_old_map(), model) - - # reversed the map - for m in new_map[1]['reactions']['1']['metabolites']: - if m['bigg_id'] == 'g3p_c': - assert m['coefficient'] == 1 - elif m['bigg_id'] == 'nadh_c': - assert m['coefficient'] == -1 - assert new_map[1]['reactions']['1']['reversibility'] == False - - # Remove unconnected nodes. These do not make the map invalid, but they are - # annoying. - assert '3' not in new_map[1]['nodes'] - - # casting - assert type(new_map[1]['reactions']['1']['label_x']) is float - assert new_map[1]['reactions']['1']['segments']['2']['b1'] is None - - -def test_convert_2(): - model = cobra.io.load_json_model(join(root_directory, 'escher', 'testing_data', 'iJO1366.json')) - convert(get_new_map(), model) - - -def test_genes_for_gene_reaction_rule(): - assert genes_for_gene_reaction_rule('((G1 and G2)or G3and)') == ['G1', 'G2', 'G3and'] diff --git a/py/escher/tests/test_generate_index.py b/py/escher/tests/test_generate_index.py deleted file mode 100644 index b77fda82..00000000 --- a/py/escher/tests/test_generate_index.py +++ /dev/null @@ -1,23 +0,0 @@ -from __future__ import print_function, unicode_literals - -from escher.generate_index import generate_index -from os.path import join -from os import makedirs -from shutil import rmtree -import pytest - -@pytest.fixture() -def index_dir(request, tmpdir): - tmpdir.mkdir('maps').mkdir('Escherichia coli').join('iJO1366.central_metabolism.json').write('temp') - tmpdir.mkdir('models').mkdir('Escherichia coli').join('iJO1366.json').write('temp') - def fin(): - tmpdir.remove() - request.addfinalizer(fin) - return str(tmpdir) - -def test_generate_index(index_dir): - out = generate_index(index_dir) - assert out['models'] == [ { 'organism': 'Escherichia coli', - 'model_name': 'iJO1366' } ] - assert out['maps'] == [ { 'organism': 'Escherichia coli', - 'map_name': 'iJO1366.central_metabolism' } ] diff --git a/py/escher/tests/test_plots.py b/py/escher/tests/test_plots.py index 51433607..9a4f608e 100644 --- a/py/escher/tests/test_plots.py +++ b/py/escher/tests/test_plots.py @@ -1,11 +1,14 @@ +# -*- coding: utf-8 -*- from __future__ import print_function, unicode_literals from escher import __schema_version__, __map_model_version__ -import escher.server -from escher import Builder, get_cache_dir, clear_cache -from escher.plots import (_load_resource, local_index, server_index, - model_json_for_name, map_json_for_name) - +from escher import Builder +from escher.plots import ( + _load_resource, + server_index, + model_json_for_name, + map_json_for_name, +) from escher.urls import get_url import base64 @@ -24,46 +27,6 @@ else: unicode_type = str -# cache - -def test_get_cache_dir(): - d = get_cache_dir(versioned=False) - assert os.path.isdir(d) - assert basename(d) != __map_model_version__ - d = get_cache_dir() - assert os.path.isdir(d) - assert basename(d) == __map_model_version__ - assert __schema_version__ in d - d = get_cache_dir(name='maps') - assert os.path.isdir(d) - -def test_clear_cache(tmpdir, request): - (tmpdir.mkdir('2').mkdir('maps').mkdir('Escherichia coli') - .join('iJO1366.Central metabolism.json').write('temp')) - (tmpdir.join('2').mkdir('models').mkdir('Escherichia coli') - .join('iJO1366.json').write('temp')) - (tmpdir.mkdir('x').mkdir('y').mkdir('z')) - clear_cache(str(tmpdir), ask=False) - assert os.listdir(str(tmpdir)) == [] - def fin(): - tmpdir.remove() - request.addfinalizer(fin) - -def test_local_index(tmpdir, request): - maps = tmpdir.mkdir('maps') - maps.mkdir('Escherichia coli').join('iJO1366.Central metabolism.json').write('temp') - # ignore these - maps.join('ignore_md.json').write('ignore') - tmpdir.mkdir('models').mkdir('Escherichia coli').join('iJO1366.json').write('temp') - assert local_index(str(tmpdir)) == { 'maps': [ { 'organism': 'Escherichia coli', - 'map_name': 'iJO1366.Central metabolism' } ], - 'models': [ { 'organism': 'Escherichia coli', - 'model_name': 'iJO1366' } ] } - def fin(): - tmpdir.remove() - request.addfinalizer(fin) - -# server @mark.web def test_server_index(): @@ -75,47 +38,26 @@ def test_server_index(): assert 'organism' in model_0 assert 'model_name' in model_0 -# model and maps - -def test_model_json_for_name(tmpdir): - models = tmpdir.mkdir('models') - models.mkdir('Escherichia coli').join('iJO1366.json').write('"temp"') - json = model_json_for_name('iJO1366', cache_dir=str(tmpdir)) - assert json == '"temp"' - -@mark.web -def test_model_json_for_name_web(tmpdir): - data = model_json_for_name('iJO1366', cache_dir=str(tmpdir)) - assert 'reactions' in data - assert 'metabolites' in data - -def test_map_json_for_name(tmpdir): - maps = tmpdir.mkdir('maps') - maps.mkdir('Escherichia coli').join('iJO1366.Central metabolism.json').write('"temp"') - json = map_json_for_name('iJO1366.Central metabolism', cache_dir=str(tmpdir)) - assert json == '"temp"' - -@mark.web -def test_map_json_for_name_web(tmpdir): - data = map_json_for_name('iJO1366.Central metabolism', cache_dir=str(tmpdir)) - root = get_url('escher_root', protocol='https').rstrip('/') - assert json.loads(data)[0]['schema'] == '/'.join([root, 'escher', 'jsonschema', - __schema_version__ + '#']) # helper functions + def test_load_resource_json(tmpdir): test_json = '{"r": "val"}' assert _load_resource(test_json, 'name') == test_json + def test_load_resource_long_json(tmpdir): # this used to fail on Windows with Python 3 test_json = '{"r": "' + ('val' * 100000) + '"}' assert _load_resource(test_json, 'name') == test_json + def test_load_resource_directory(tmpdir): directory = os.path.abspath(os.path.dirname(__file__)) - assert _load_resource(join(directory, 'example.json'), 'name').strip() == '{"r": "val"}' + val = _load_resource(join(directory, 'example.json'), 'name').strip() + assert val == '{"r": "val"}' + def test_load_resource_invalid_file(tmpdir): with raises(ValueError) as err: @@ -125,62 +67,20 @@ def test_load_resource_invalid_file(tmpdir): _load_resource(p, 'name') assert 'not a valid json file' in err.value + @mark.web def test_load_resource_web(tmpdir): - url = '/'.join([get_url('map_download', protocol='https'), + url = '/'.join([get_url('map_download'), 'Escherichia%20coli/iJO1366.Central%20metabolism.json']) _ = json.loads(_load_resource(url, 'name')) -def test_Builder(tmpdir): - # ok with embedded_css arg - b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}', embedded_css='') - # b.display_in_notebook(js_source='local') - b.save_html(join(str(tmpdir), 'Builder.html'), js_source='local') - - # test options - with raises(Exception): - b._get_html(js_source='devv') - with raises(Exception): - b._get_html(menu='') - with raises(Exception): - b._get_html(scroll_behavior='asdf') - b._get_html(js_source='local') - b._get_html(menu='all') - b._get_html(scroll_behavior='zoom') - -@mark.web -def test_Builder_download(): - # download - b = Builder(map_name='iJO1366.Central metabolism', - model_name='iJO1366') - assert b.loaded_map_json is not None - assert b.loaded_model_json is not None - b._get_html(js_source='web') - # b.display_in_notebook(height=200) - - # data - b = Builder(map_name='iJO1366.Central metabolism', - model_name='iJO1366', - reaction_data=[{'GAPD': 123}, {'GAPD': 123}]) - b = Builder(map_name='iJO1366.Central metabolism', - model_name='iJO1366', - metabolite_data=[{'nadh_c': 123}, {'nadh_c': 123}]) - b = Builder(map_name='iJO1366.Central metabolism', - model_name='iJO1366', - gene_data=[{'gapA': 123}, {'adhE': 123}]) - - assert type(b.the_id) is unicode_type - assert len(b.the_id) == 10 - -def test_Builder_options(): - b = Builder(embedded_css='') - b.set_metabolite_no_data_color('white') - assert b.metabolite_no_data_color == 'white' - -def test__get_html(): +def test_save_html(tmpdir): + # ok with embedded_css arg b = Builder(map_json='"useless_map"', model_json='"useless_model"', embedded_css='') + filepath = join(str(tmpdir), 'builder.html') + b.save_html(filepath) def look_for_string(st, substring): """Look for the string in the substring. This solves a bug in py.test @@ -189,25 +89,28 @@ def look_for_string(st, substring): found = st.find(substring) assert found > -1 except AssertionError: - raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' % (substring, st)) + raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' % + (substring, st)) # no static parse, local - html = b._get_html(js_source='local') - look_for_string(html, 'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),') - look_for_string(html, 'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),') - look_for_string(html, 'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,') - - # static parse, not dev - static_index = '{"my": ["useless", "index"]}' + with open(filepath, 'r') as f: + html = f.read() + + look_for_string( + html, + 'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),', + ) + look_for_string( + html, + 'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),', + ) + look_for_string( + html, + 'escher.Builder(data.map_data, data.model_data, ', + ) - html = b._get_html(static_site_index_json=static_index, protocol='https') - look_for_string(html, 'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),') - look_for_string(html, 'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),') - map_download_url = base64.b64encode(("https://escher.github.io/%s/%s/maps/" % (__schema_version__, __map_model_version__)).encode('utf-8')).decode('utf-8') - look_for_string(html, 'map_download_url: b64DecodeUnicode(\'%s\'),' % map_download_url) - - model_download_url = base64.b64encode(("https://escher.github.io/%s/%s/models/" % (__schema_version__, __map_model_version__)).encode('utf-8')).decode('utf-8') - look_for_string(html, 'model_download_url: b64DecodeUnicode(\'%s\'),' % model_download_url) - look_for_string(html, 'eyJteSI6IFsidXNlbGVzcyIsICJpbmRleCJdfQ==') # static_index - look_for_string(html, 'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,') +def test_Builder_options(): + b = Builder(embedded_css='') + b.set_metabolite_no_data_color('white') + assert b.metabolite_no_data_color == 'white' diff --git a/py/escher/tests/test_server.py b/py/escher/tests/test_server.py deleted file mode 100644 index 20695adf..00000000 --- a/py/escher/tests/test_server.py +++ /dev/null @@ -1,32 +0,0 @@ -from __future__ import print_function, unicode_literals - -import escher.server -import tornado.ioloop -from tornado.testing import AsyncHTTPTestCase, gen_test - -from pytest import mark - -class TestBuilder(AsyncHTTPTestCase): - def get_app(self): - return escher.server.application - - def test_index(self): - escher.server.PORT = self.get_http_port() - response = self.fetch('/') - assert response.code==200 - - @mark.web - def test_builder_request(self): - escher.server.PORT = self.get_http_port() - response = self.fetch('/builder/index.html') - assert response.code==200 - - def test_local_builder_request(self): - escher.server.PORT = self.get_http_port() - response = self.fetch('/builder/index.html?js_source=local') - assert response.code==200 - -# def test_server(): -# tornado.ioloop.IOLoop.instance().add_timeout(100, escher.server.stop) -# escher.server.run(port = 8123) -# print('stopped') diff --git a/py/escher/tests/test_urls.py b/py/escher/tests/test_urls.py index 480651a9..1fd5806a 100644 --- a/py/escher/tests/test_urls.py +++ b/py/escher/tests/test_urls.py @@ -1,37 +1,38 @@ -from escher.urls import get_url, names, root_directory -from escher.version import __version__, __schema_version__, __map_model_version__ -import os +from escher.urls import ( + get_url, + get_filepath, + root_directory, +) +from escher.version import ( + __version__, + __schema_version__, + __map_model_version__, +) from os.path import join, exists - from pytest import raises + def test_online(): - url = get_url('escher', source='web', protocol='https') + url = get_url('escher') assert url == 'https://unpkg.com/escher@%s/dist/escher.js' % __version__ -def test_no_protocol(): - url = get_url('escher', 'web') - assert url == '//unpkg.com/escher@%s/dist/escher.js' % __version__ def test_local(): - url = get_url('escher_min', 'local') - assert url == 'escher/static/escher/escher.min.js' - assert exists(join(root_directory, url)) + assert exists(get_filepath('map_jsonschema')) + + +def test_index_url(): + url = get_url('server_index') + assert url == ('https://escher.github.io/%s/%s/index.json' % + (__schema_version__, __map_model_version__)) -def test_localhost(): - url = get_url('escher', source='local', local_host='http://localhost:7778/') - assert url == 'http://localhost:7778/escher/static/escher/escher.js' -def test_download(): - url = get_url('server_index', source='local') - assert url == '../' + __schema_version__ + '/' + __map_model_version__ + '/index.json' - url = get_url('map_download', protocol='https') - assert url == 'https://escher.github.io/%s/%s/maps/' % (__schema_version__, __map_model_version__) +def test_map_download_url(): + url = get_url('map_download') + assert url == ('https://escher.github.io/%s/%s/maps/' % + (__schema_version__, __map_model_version__)) + def test_bad_url(): with raises(Exception): get_url('bad-name') - with raises(Exception): - get_url('d3', source='bad-source') - with raises(Exception): - get_url('d3', protocol='bad-protocol') diff --git a/py/escher/tests/test_utils.py b/py/escher/tests/test_utils.py index e0263b12..61694a7a 100644 --- a/py/escher/tests/test_utils.py +++ b/py/escher/tests/test_utils.py @@ -1,14 +1,16 @@ # -*- coding: utf-8 -*- -from __future__ import unicode_literals +from __future__ import print_function, unicode_literals import base64 import json from escher.util import b64dump + def b64decode(str): return base64.b64decode(str.encode('utf-8')).decode('utf-8') + def test_b64dump(): assert b64decode(b64dump(None)) == 'null' accented_str = 'árvíztűrő tükörfúrógép' diff --git a/py/escher/urls.py b/py/escher/urls.py index bc655673..37a36c33 100644 --- a/py/escher/urls.py +++ b/py/escher/urls.py @@ -2,102 +2,61 @@ from __future__ import print_function, unicode_literals -from escher.version import __version__, __schema_version__, __map_model_version__ +from escher.version import ( + __version__, + __schema_version__, + __map_model_version__, +) import os import re from os.path import dirname, realpath, join root_directory = realpath(join(dirname(__file__), '..')) -top_directory = realpath(join(dirname(__file__), '..', '..')) +# relative to root_directory _escher_local = { - 'escher': 'escher/static/escher/escher.js', - 'escher_min': 'escher/static/escher/escher.min.js', - 'logo': 'escher/static/img/escher-logo@2x.png', - 'favicon': 'escher/static/img/favicon.ico', - 'homepage_js': 'escher/static/homepage/main.js', - 'homepage_css': 'escher/static/homepage/main.css', - 'server_index': '../%s/%s/index.json' % (__schema_version__, __map_model_version__), - 'map_download': '../%s/%s/maps/' % (__schema_version__, __map_model_version__), - 'model_download': '../%s/%s/models/' % (__schema_version__, __map_model_version__), + 'map_jsonschema': 'escher/static/jsonschema/1-0-0', } _escher_web = { - 'server_index': '%s/%s/index.json' % (__schema_version__, __map_model_version__), - 'map_download': '%s/%s/maps/' % (__schema_version__, __map_model_version__), - 'model_download': '%s/%s/models/' % (__schema_version__, __map_model_version__), - 'favicon': 'escher/static/img/favicon.ico', -} - -_dependencies = { + 'server_index': '%s/%s/index.json' % (__schema_version__, + __map_model_version__), + 'map_download': '%s/%s/maps/' % (__schema_version__, + __map_model_version__), + 'model_download': '%s/%s/models/' % (__schema_version__, + __map_model_version__), } _dependencies_cdn = { - 'escher': '//unpkg.com/escher@%s/dist/escher.js' % __version__, - 'escher_min': '//unpkg.com/escher@%s/dist/escher.min.js' % __version__, + 'escher': 'https://unpkg.com/escher@%s/dist/escher.js' % __version__, + 'escher_min': ('https://unpkg.com/escher@%s/dist/escher.min.js' % + __version__), } _links = { - 'escher_root': '//escher.github.io/', - 'github': '//github.com/zakandrewking/escher/', - 'github_releases': '//github.com/zakandrewking/escher/releases', - 'documentation': '//escher.readthedocs.org/', + 'escher_root': 'https://escher.github.io/', + 'github': 'https://github.com/zakandrewking/escher', + 'github_releases': 'https://github.com/zakandrewking/escher/releases', + 'documentation': 'https://escher.readthedocs.org/', } -# external dependencies -names = list(_escher_local.keys()) + list(_escher_web.keys()) + list(_dependencies.keys()) + list(_links.keys()) - -def get_url(name, source='web', local_host=None, protocol=None): - """Get a url. - - Arguments - --------- - - name: The name of the URL. Options are available in urls.names. - - source: Either 'web' or 'local'. Cannot be 'local' for external links. - - protocol: The protocol can be 'http', 'https', or None which indicates a - 'protocol relative URL', as in //escher.github.io. Ignored if source is - local. - local_host: A host url, including the protocol. e.g. http://localhost:7778. - - """ - if source not in ['web', 'local']: - raise Exception('Bad source: %s' % source) - - if protocol not in [None, 'http', 'https']: - raise Exception('Bad protocol: %s' % protocol) - - if protocol is None: - protocol = '' +def get_filepath(key): + """Get the filepath for the key""" + if key in _escher_local: + return join(root_directory, _escher_local[key]) else: - protocol = protocol + ':' + raise Exception('File key not recognized: %s' % key) - def apply_local_host(url): - return '/'.join([local_host.rstrip('/'), url.lstrip('/')]) - # escher - if name in _escher_local and source == 'local': - if local_host is not None: - return apply_local_host(_escher_local[name]) - return _escher_local[name] - elif name in _escher_web and source == 'web': - return protocol + '/'.join([_links['escher_root'].rstrip('/'), - _escher_web[name].lstrip('/')]) - # links - elif name in _links: - if source=='local': - raise Exception('Source cannot be "local" for external links') - return protocol + _links[name] - # local dependencies - elif name in _dependencies and source == 'local': - if local_host is not None: - return apply_local_host(_dependencies[name]) - return _dependencies[name] - # cdn dependencies - elif name in _dependencies_cdn and source == 'web': - return protocol + _dependencies_cdn[name] +def get_url(name): + """Get a url for the key""" - raise Exception('name not found') + if name in _escher_web: + return _links['escher_root'] + _escher_web[name] + elif name in _links: + return _links[name] + elif name in _dependencies_cdn: + return _dependencies_cdn[name] + else: + raise Exception('name not found') diff --git a/py/escher/util.py b/py/escher/util.py index 52332ac5..8db8d89e 100644 --- a/py/escher/util.py +++ b/py/escher/util.py @@ -1,40 +1,9 @@ +# -*- coding: utf-8 -*- +from __future__ import print_function, unicode_literals + import base64 import json -import sys - -# user input for python 2 and 3 -try: - import __builtin__ - input = getattr(__builtin__, 'raw_input') -except (ImportError, AttributeError): - pass - -def query_yes_no(question): - """Ask a yes/no question via input() and return their answer. - - Returns True for yes or False for no. - - Arguments - --------- - question: A string that is presented to the user. - - - Adapted from http://stackoverflow.com/questions/3041986/python-command-line-yes-no-input. - - """ - valid = {"yes": True, "y": True, "ye": True, - "no": False, "n": False} - prompt = " [y/n] " - - while True: - sys.stdout.write(question + prompt) - choice = input().lower() - try: - return valid[choice] - except KeyError: - sys.stdout.write("Please respond with 'yes' or 'no' " - "(or 'y' or 'n').\n") def b64dump(data): """Returns the base64 encoded dump of the input @@ -43,6 +12,7 @@ def b64dump(data): --------- data: Can be a dict, a (JSON or plain) string, or None + """ if isinstance(data, dict): data = json.dumps(data) diff --git a/py/escher/validate.py b/py/escher/validate.py index 9691209a..bf62d19d 100644 --- a/py/escher/validate.py +++ b/py/escher/validate.py @@ -3,7 +3,7 @@ from __future__ import print_function, unicode_literals from escher import __schema_version__ -from escher.urls import root_directory +from escher.urls import get_filepath from os.path import join import re import json @@ -20,6 +20,7 @@ """ + def main(): if len(sys.argv) < 2: print(usage_string) @@ -30,6 +31,7 @@ def main(): validate_map(map_data) print('Your map passed inspection and is free of infection.') + def validate_map(map_data): """Validate a map using the jsonschema, and some extra checks for consistency.""" import jsonschema @@ -56,11 +58,13 @@ def validate_map(map_data): if error != '': raise Exception(error) + def validate_schema(): import jsonschema schema = get_jsonschema() jsonschema.Draft4Validator.check_schema(schema) + def check_map(map_data): """Check reactions and metabolites. @@ -98,13 +102,15 @@ def check_map(map_data): missing_gene_names.append(found_gene) return bad_segments, missing_multimarkers, missing_stoich, missing_gene_names + def get_jsonschema(): """Get the local jsonschema. """ - with open(join(root_directory, 'escher', 'static', 'jsonschema', __schema_version__), 'r') as f: + with open(get_filepath('map_jsonschema'), 'r') as f: return json.load(f) + def genes_for_gene_reaction_rule(rule): """ Find genes in gene_reaction_rule string. diff --git a/py/escher/version.py b/py/escher/version.py index fec4ed4c..63633e27 100644 --- a/py/escher/version.py +++ b/py/escher/version.py @@ -16,7 +16,7 @@ def get_full_version(main_version, post_version=None): # to get autodoc going package = defaultdict(str) else: - with open(join(dirname(__file__), 'package.json'), 'r') as f: + with open(join(dirname(__file__), 'static', 'package.json'), 'r') as f: package = json.load(f) # software version diff --git a/py/jupyter-escher.json b/py/jupyter-escher.json new file mode 100644 index 00000000..76a26bff --- /dev/null +++ b/py/jupyter-escher.json @@ -0,0 +1,5 @@ +{ + "load_extensions": { + "jupyter-escher/extension": true + } +} diff --git a/py/setup.py b/py/setup.py index 4396f3c1..3ef61e96 100644 --- a/py/setup.py +++ b/py/setup.py @@ -1,4 +1,5 @@ # -*- coding: utf-8 -*- +from __future__ import print_function, unicode_literals import sys from sys import argv @@ -11,13 +12,7 @@ from glob import glob import re -try: - from setuptools import setup, Command - from setuptools.command.sdist import sdist as SDistCommand - from setuptools.command.bdist import bdist as BDistCommand - from setuptools.command.upload import upload as UploadCommand -except ImportError: - from distutils.core import setup, Command +from setuptools import setup, find_packages, Command directory = dirname(realpath(__file__)) sys.path.insert(0, join(directory, 'escher')) @@ -26,59 +21,6 @@ package = __import__('version').package port = 8789 -class CleanCommand(Command): - description = "Custom clean command that removes static site" - user_options = [] - def initialize_options(self): - pass - def finalize_options(self): - pass - def run(self): - def remove_if(x): - if exists(x): rmtree(x) - remove_if(join(directory, 'build')) - remove_if(join(directory, 'dist')) - # remove site files - remove_if(join(directory, '..', 'builder')) - for f in glob(join(directory, '..', 'index.html')): - os.remove(f) - print('done cleaning') - - -class BuildGHPagesCommand(Command): - description = "Custom build command that generates static site, and copies escher libs" - user_options = [] - def initialize_options(self): - pass - def finalize_options(self): - pass - def run(self): - # generate the static site - try: - from escher import generate_index, static_site - except ImportError: - raise Exception('Escher not installed') - generate_index.main() - static_site.generate_static_site() - print('Done building gh-pages') - - -class TestCommand(Command): - description = "Custom test command that runs pytest" - user_options = [('noweb', None, 'Skip run tests that require the Escher website')] - def initialize_options(self): - self.noweb = False - def finalize_options(self): - pass - def run(self): - import pytest - if self.noweb: - exit_code = pytest.main(['-m', 'not web']) - else: - exit_code = pytest.main([]) - sys.exit(exit_code) - - setup( name='Escher', version=full_version, @@ -97,26 +39,35 @@ def run(self): 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', 'Operating System :: OS Independent' ], - packages=['escher'], - package_data={'escher': ['package.json', 'static/escher/*', 'static/fonts/*', - 'static/jsonschema/*', 'static/homepage/*', - 'static/img/*', 'static/lib/*', 'templates/*']}, - install_requires=['Jinja2>=2.7.3', - 'tornado>=4.0.2', - 'pytest>=2.6.2', - 'cobra>=0.3.0', - 'jsonschema>=2.4.0'], - extras_require={'docs': ['sphinx>=1.2', - 'sphinx-rtd-theme>=0.1.6'], - 'all': ['sphinx>=1.2', - 'sphinx-rtd-theme>=0.1.6', - 'ipython>=4.0.2', - 'jupyter>=1.0.0', - 'wheel>=0.24.0', - 'twine>=1.5.0'] }, - cmdclass={'clean': CleanCommand, - 'build_gh': BuildGHPagesCommand, - 'test': TestCommand} + packages=find_packages(), + include_package_data=True, + data_files=[ + ( + 'share/jupyter/nbextensions/jupyter-escher', + [ + 'escher/static/extension.js', + 'escher/static/escher.min.js', + 'escher/static/escher.min.js.map', + ] + ), + ( + 'etc/jupyter/nbconfig/notebook.d', + ['jupyter-escher.json'], + ) + ], + install_requires=[ + 'Jinja2>=2.7.3,<3', + 'tornado>=4.0.2,<5', + 'pytest>=4.0.1,<5', + 'cobra>=0.5.0', + 'jsonschema>=2.4.0,<3', + 'ipywidgets>=7.1.0,<8', + ], + extras_require={ + 'docs': ['sphinx>=1.2', 'sphinx-rtd-theme>=0.1.6'], + }, ) diff --git a/src/Behavior.js b/src/Behavior.js index d3504125..784e7d22 100644 --- a/src/Behavior.js +++ b/src/Behavior.js @@ -1,1040 +1,990 @@ -/** - * Behavior. Defines the set of click and drag behaviors for the map, and keeps - * track of which behaviors are activated. - * - * A Behavior instance has the following attributes: - * - * my_behavior.rotation_drag, my_behavior.text_label_mousedown, - * my_behavior.text_label_click, my_behavior.selectable_mousedown, - * my_behavior.selectable_click, my_behavior.selectable_drag, - * my_behavior.node_mouseover, my_behavior.node_mouseout, - * my_behavior.label_mousedown, my_behavior.label_mouseover, - * my_behavior.label_mouseout, my_behavior.label_touch, - * my_behavior.bezier_drag, - * my_behavior.bezier_mouseover, my_behavior.bezier_mouseout, - * my_behavior.reaction_label_drag, my_behavior.node_label_drag, - * my_behavior.object_mouseover, my_behavior.object_touch, - * my_behavior.object_mouseout - * - */ +import utils from './utils' +import build from './build' +import { drag as d3Drag } from 'd3-drag' +import * as d3Selection from 'd3-selection' -var utils = require('./utils') -var build = require('./build') -var d3_drag = require('d3-drag').drag -var d3_select = require('d3-selection').select -var d3_mouse = require('d3-selection').mouse -var d3_selection = require('d3-selection') - -var Behavior = utils.make_class() -// methods -Behavior.prototype = { - init: init, - toggle_rotation_mode: toggle_rotation_mode, - turn_everything_on: turn_everything_on, - turn_everything_off: turn_everything_off, - // toggle - toggle_selectable_click: toggle_selectable_click, - toggle_text_label_edit: toggle_text_label_edit, - toggle_selectable_drag: toggle_selectable_drag, - toggle_label_drag: toggle_label_drag, - toggle_label_mouseover: toggle_label_mouseover, - toggle_label_touch: toggle_label_touch, - toggle_object_mouseover: toggle_object_mouseover, - toggle_object_touch: toggle_object_touch, - toggle_bezier_drag: toggle_bezier_drag, - // util - turn_off_drag: turn_off_drag, - // get drag behaviors - _get_selectable_drag: _get_selectable_drag, - _get_bezier_drag: _get_bezier_drag, - _get_reaction_label_drag: _get_reaction_label_drag, - _get_node_label_drag: _get_node_label_drag, - _get_generic_drag: _get_generic_drag, - _get_generic_angular_drag: _get_generic_angular_drag -} -module.exports = Behavior - - -// definitions -function init (map, undo_stack) { - this.map = map - this.undo_stack = undo_stack - - // make an empty function that can be called as a behavior and does nothing - this.empty_behavior = function () {} - - // rotation mode operates separately from the rest - this.rotation_mode_enabled = false - this.rotation_drag = d3_drag() - - // behaviors to be applied - this.selectable_mousedown = null - this.text_label_mousedown = null - this.text_label_click = null - this.selectable_drag = this.empty_behavior - this.node_mouseover = null - this.node_mouseout = null - this.label_mousedown = null - this.label_mouseover = null - this.label_mouseout = null - this.label_touch = null - this.object_mouseover = null - this.object_touch = null - this.object_mouseout = null - this.bezier_drag = this.empty_behavior - this.bezier_mouseover = null - this.bezier_mouseout = null - this.reaction_label_drag = this.empty_behavior - this.node_label_drag = this.empty_behavior - this.dragging = false - this.turn_everything_on() -} +const d3Select = d3Selection.select +const d3Mouse = d3Selection.mouse /** - * Toggle everything except rotation mode and text mode. - */ -function turn_everything_on () { - this.toggle_selectable_click(true) - this.toggle_selectable_drag(true) - this.toggle_label_drag(true) - this.toggle_label_mouseover(true) - this.toggle_label_touch(true) - this.toggle_object_mouseover(true) - this.toggle_object_touch(true) -} - -/** - * Toggle everything except rotation mode and text mode. - */ -function turn_everything_off () { - this.toggle_selectable_click(false) - this.toggle_selectable_drag(false) - this.toggle_label_drag(false) - this.toggle_label_mouseover(false) - this.toggle_label_touch(false) - this.toggle_object_mouseover(false) - this.toggle_object_touch(false) -} - -/** - * Listen for rotation, and rotate selected nodes. + * Behavior. Defines the set of click and drag behaviors for the map, and keeps + * track of which behaviors are activated. + * @param map {Map} - + * @param undoStack {UndoStack} - */ -function toggle_rotation_mode (on_off) { - if (on_off === undefined) { - this.rotation_mode_enabled = !this.rotation_mode_enabled - } else { - this.rotation_mode_enabled = on_off - } - - var selection_node = this.map.sel.selectAll('.node-circle') - var selection_background = this.map.sel.selectAll('#canvas') - - if (this.rotation_mode_enabled) { - this.map.callback_manager.run('start_rotation') - - var selected_nodes = this.map.get_selected_nodes() - if (Object.keys(selected_nodes).length === 0) { - console.warn('No selected nodes') - return - } - - // show center - this.center = average_location(selected_nodes) - show_center.call(this) - - // this.set_status('Drag to rotate.') - var map = this.map - var selected_node_ids = Object.keys(selected_nodes) - var reactions = this.map.reactions - var nodes = this.map.nodes - var beziers = this.map.beziers - - var start_fn = function (d) { - // silence other listeners - d3_selection.event.sourceEvent.stopPropagation() - } - var drag_fn = function (d, angle, total_angle, center) { - var updated = build.rotate_nodes(selected_nodes, reactions, - beziers, angle, center) - map.draw_these_nodes(updated.node_ids) - map.draw_these_reactions(updated.reaction_ids) +export default class Behavior { + constructor (map, undoStack) { + this.map = map + this.undoStack = undoStack + + // make an empty function that can be called as a behavior and does nothing + this.emptyBehavior = () => {} + + // rotation mode operates separately from the rest + this.rotationModeEnabled = false + this.rotationDrag = d3Drag() + + // behaviors to be applied + this.selectableMousedown = null + this.textLabelMousedown = null + this.textLabelClick = null + this.selectableDrag = this.emptyBehavior + this.nodeMouseover = null + this.nodeMouseout = null + this.labelMousedown = null + this.labelMouseover = this.emptyBehavior + this.labelMouseout = null + this.labelTouch = null + this.objectMouseover = this.emptyBehavior + this.objectTouch = null + this.objectMouseout = null + this.bezierDrag = this.emptyBehavior + this.bezierMouseover = null + this.bezierMouseout = null + this.reactionLabelDrag = this.emptyBehavior + this.nodeLabelDrag = this.emptyBehavior + this.dragging = false + this.turnEverythingOn() + } + + /** + * Toggle everything except rotation mode and text mode. + */ + turnEverythingOn () { + this.toggleSelectableClick(true) + this.toggleSelectableDrag(true) + this.toggleLabelDrag(true) + this.toggleLabelMouseover(true) + this.toggleLabelTouch(true) + this.toggleObjectMouseover(true) + this.toggleObjectTouch(true) + } + + /** + * Toggle everything except rotation mode and text mode. + */ + turnEverythingOff () { + this.toggleSelectableClick(false) + this.toggleSelectableDrag(false) + this.toggleLabelDrag(false) + this.toggleLabelMouseover(false) + this.toggleLabelTouch(false) + this.toggleObjectMouseover(false) + this.toggleObjectTouch(false) + } + + averageLocation (nodes) { + const xs = [] + const ys = [] + for (const nodeId in nodes) { + const node = nodes[nodeId] + if (node.x !== undefined) xs.push(node.x) + if (node.y !== undefined) ys.push(node.y) } - var end_fn = function (d) {} - var undo_fn = function (d, total_angle, center) { - // undo - var these_nodes = {} - selected_node_ids.forEach(function (id) { - these_nodes[id] = nodes[id] - }) - var updated = build.rotate_nodes(these_nodes, reactions, - beziers, -total_angle, - center) - map.draw_these_nodes(updated.node_ids) - map.draw_these_reactions(updated.reaction_ids) + return { + x: utils.mean(xs), + y: utils.mean(ys) } - var redo_fn = function (d, total_angle, center) { - // redo - var these_nodes = {} - selected_node_ids.forEach(function (id) { - these_nodes[id] = nodes[id] - }) - var updated = build.rotate_nodes(these_nodes, reactions, - beziers, total_angle, - center) - map.draw_these_nodes(updated.node_ids) - map.draw_these_reactions(updated.reaction_ids) } - var center_fn = function () { - return this.center - }.bind(this) - this.rotation_drag = this._get_generic_angular_drag(start_fn, drag_fn, - end_fn, undo_fn, - redo_fn, center_fn, - this.map.sel) - selection_background.call(this.rotation_drag) - this.selectable_drag = this.rotation_drag - } else { - // turn off all listeners - hide_center.call(this) - selection_node.on('mousedown.center', null) - selection_background.on('mousedown.center', null) - selection_background.on('mousedown.drag', null) - selection_background.on('touchstart.drag', null) - this.rotation_drag = null - this.selectable_drag = null } - // definitions - function show_center () { - var sel = this.map.sel.selectAll('#rotation-center').data([ 0 ]) - var enter_sel = sel.enter().append('g').attr('id', 'rotation-center') + showCenter () { + const sel = this.map.sel.selectAll('#rotation-center').data([ 0 ]) + const enterSel = sel.enter().append('g').attr('id', 'rotation-center') - enter_sel.append('path').attr('d', 'M-32 0 L32 0') + enterSel.append('path').attr('d', 'M-32 0 L32 0') .attr('class', 'rotation-center-line') - enter_sel.append('path').attr('d', 'M0 -32 L0 32') + enterSel.append('path').attr('d', 'M0 -32 L0 32') .attr('class', 'rotation-center-line') - var update_sel = enter_sel.merge(sel) + const updateSel = enterSel.merge(sel) - update_sel.attr('transform', - 'translate(' + this.center.x + ',' + this.center.y + ')') + updateSel.attr('transform', + 'translate(' + this.center.x + ',' + this.center.y + ')') .attr('visibility', 'visible') .on('mouseover', function () { - var current = parseFloat(update_sel.selectAll('path').style('stroke-width')) - update_sel.selectAll('path').style('stroke-width', current * 2 + 'px') + const current = parseFloat(updateSel.selectAll('path').style('stroke-width')) + updateSel.selectAll('path').style('stroke-width', current * 2 + 'px') }) .on('mouseout', function () { - update_sel.selectAll('path').style('stroke-width', null) + updateSel.selectAll('path').style('stroke-width', null) }) - .call(d3_drag().on('drag', function () { - var cur = utils.d3_transform_catch(update_sel.attr('transform')) - var new_loc = [ - d3_selection.event.dx + cur.translate[0], - d3_selection.event.dy + cur.translate[1] + .call(d3Drag().on('drag', () => { + const cur = utils.d3_transform_catch(updateSel.attr('transform')) + const newLoc = [ + d3Selection.event.dx + cur.translate[0], + d3Selection.event.dy + cur.translate[1] ] - update_sel.attr('transform', 'translate(' + new_loc + ')') - this.center = { x: new_loc[0], y: new_loc[1] } - }.bind(this))) + updateSel.attr('transform', 'translate(' + newLoc + ')') + this.center = { x: newLoc[0], y: newLoc[1] } + })) } - function hide_center(sel) { + + hideCenter () { this.map.sel.select('#rotation-center') .attr('visibility', 'hidden') } - function average_location(nodes) { - var xs = [] - var ys = [] - for (var node_id in nodes) { - var node = nodes[node_id] - if (node.x !== undefined) - xs.push(node.x) - if (node.y !== undefined) - ys.push(node.y) - } - return { x: utils.mean(xs), - y: utils.mean(ys) } - } -} -/** - * With no argument, toggle the node click on or off. Pass in a boolean argument - * to set the on/off state. - */ -function toggle_selectable_click (on_off) { - if (on_off === undefined) { - on_off = this.selectable_mousedown === null - } - if (on_off) { - var map = this.map - this.selectable_mousedown = function (d) { - // stop propogation for the buildinput to work right - d3_selection.event.stopPropagation() - // this.parentNode.__data__.was_selected = d3_select(this.parentNode).classed('selected') - // d3_select(this.parentNode).classed('selected', true) - } - this.selectable_click = function (d) { - // stop propogation for the buildinput to work right - d3_selection.event.stopPropagation() - // click suppressed. This DOES have en effect. - if (d3_selection.event.defaultPrevented) return - // turn off the temporary selection so select_selectable - // works. This is a bit of a hack. - // if (!this.parentNode.__data__.was_selected) - // d3_select(this.parentNode).classed('selected', false) - map.select_selectable(this, d, d3_selection.event.shiftKey) - // this.parentNode.__data__.was_selected = false - } - this.node_mouseover = function (d) { - d3_select(this).style('stroke-width', null) - var current = parseFloat(d3_select(this).style('stroke-width')) - if (!d3_select(this.parentNode).classed('selected')) - d3_select(this).style('stroke-width', current * 3 + 'px') - } - this.node_mouseout = function (d) { - d3_select(this).style('stroke-width', null) + /** + * Listen for rotation, and rotate selected nodes. + */ + toggleRotationMode (onOff) { + if (onOff === undefined) { + this.rotationModeEnabled = !this.rotationModeEnabled + } else { + this.rotationModeEnabled = onOff } - } else { - this.selectable_mousedown = null - this.selectable_click = null - this.node_mouseover = null - this.node_mouseout = null - this.map.sel.select('#nodes') - .selectAll('.node-circle').style('stroke-width', null) - } -} -/** - * With no argument, toggle the text edit on mousedown on/off. Pass in a boolean - * argument to set the on/off state. The backup state is equal to - * selectable_mousedown. - */ -function toggle_text_label_edit (on_off) { - if (on_off === undefined) { - on_off = this.text_edit_mousedown == null - } - if (on_off) { - var map = this.map - var selection = this.selection - this.text_label_mousedown = function () { - if (d3_selection.event.defaultPrevented) { - return // mousedown suppressed - } - // run the callback - var coords_a = utils.d3_transform_catch(d3_select(this).attr('transform')) - .translate - var coords = { x: coords_a[0], y: coords_a[1] } - map.callback_manager.run('edit_text_label', null, d3_select(this), coords) - d3_selection.event.stopPropagation() - } - this.text_label_click = null - this.map.sel.select('#text-labels') - .selectAll('.label') - .classed('edit-text-cursor', true) - // add the new-label listener - this.map.sel.on('mousedown.new_text_label', function (node) { - // silence other listeners - d3_selection.event.preventDefault() - var coords = { - x: d3_mouse(node)[0], - y: d3_mouse(node)[1], - } - this.map.callback_manager.run('new_text_label', null, coords) - }.bind(this, this.map.sel.node())) - } else { - this.text_label_mousedown = this.selectable_mousedown - this.text_label_click = this.selectable_click - this.map.sel.select('#text-labels') - .selectAll('.label') - .classed('edit-text-cursor', false) - // remove the new-label listener - this.map.sel.on('mousedown.new_text_label', null) - this.map.callback_manager.run('hide_text_label_editor') - } -} + const selectionNode = this.map.sel.selectAll('.node-circle') + const selectionBackground = this.map.sel.selectAll('#canvas') -/** - * With no argument, toggle the node drag & bezier drag on or off. Pass in a - * boolean argument to set the on/off state. - */ -function toggle_selectable_drag (on_off) { - if (on_off === undefined) { - on_off = this.selectable_drag === this.empty_behavior - } - if (on_off) { - this.selectable_drag = this._get_selectable_drag(this.map, this.undo_stack) - this.bezier_drag = this._get_bezier_drag(this.map, this.undo_stack) - } else { - this.selectable_drag = this.empty_behavior - this.bezier_drag = this.empty_behavior - } -} + if (this.rotationModeEnabled) { + this.map.callback_manager.run('start_rotation') -/** - * With no argument, toggle the label drag on or off. Pass in a boolean argument - * to set the on/off state. - * @param {Boolean} on_off - The new on/off state. - */ -function toggle_label_drag (on_off) { - if (on_off === undefined) { - on_off = this.label_drag === this.empty_behavior - } - if (on_off) { - this.reaction_label_drag = this._get_reaction_label_drag(this.map) - this.node_label_drag = this._get_node_label_drag(this.map) - } else { - this.reaction_label_drag = this.empty_behavior - this.node_label_drag = this.empty_behavior - } -} + const selectedNodes = this.map.getSelectedNodes() + if (Object.keys(selectedNodes).length === 0) { + console.warn('No selected nodes') + return + } -/** - * With no argument, toggle the tooltips on mouseover labels. - * @param {Boolean} on_off - The new on/off state. - */ -function toggle_label_mouseover (on_off) { - if (on_off === undefined) { - on_off = this.label_mouseover === null - } + // show center + this.center = this.averageLocation(selectedNodes) + this.showCenter() - if (on_off) { + // this.setStatus('Drag to rotate.') + const map = this.map + const selectedNodeIds = Object.keys(selectedNodes) + const reactions = this.map.reactions + const nodes = this.map.nodes + const beziers = this.map.beziers - // Show/hide tooltip. - // @param {String} type - 'reaction_label' or 'node_label' - // @param {Object} d - D3 data for DOM element - this.label_mouseover = function (type, d) { - if (!this.dragging) { - this.map.callback_manager.run('show_tooltip', null, type, d) + const startFn = d => { + // silence other listeners + d3Selection.event.sourceEvent.stopPropagation() } - }.bind(this) - - this.label_mouseout = function () { - this.map.callback_manager.run('delay_hide_tooltip') - }.bind(this) - - } else { - this.label_mouseover = null + const dragFn = (d, angle, totalAngle, center) => { + const updated = build.rotate_nodes(selectedNodes, reactions, + beziers, angle, center) + map.draw_these_nodes(updated.node_ids) + map.draw_these_reactions(updated.reaction_ids) + } + const endFn = d => {} + const undoFn = (d, totalAngle, center) => { + // undo + const theseNodes = {} + selectedNodeIds.forEach(function (id) { + theseNodes[id] = nodes[id] + }) + const updated = build.rotate_nodes(theseNodes, reactions, + beziers, -totalAngle, + center) + map.draw_these_nodes(updated.node_ids) + map.draw_these_reactions(updated.reaction_ids) + } + const redoFn = (d, totalAngle, center) => { + // redo + const theseNodes = {} + selectedNodeIds.forEach(id => { + theseNodes[id] = nodes[id] + }) + const updated = build.rotate_nodes(theseNodes, reactions, + beziers, totalAngle, + center) + map.draw_these_nodes(updated.node_ids) + map.draw_these_reactions(updated.reaction_ids) + } + const centerFn = () => this.center + this.rotationDrag = this.getGenericAngularDrag(startFn, dragFn, + endFn, undoFn, + redoFn, centerFn, + this.map.sel) + selectionBackground.call(this.rotationDrag) + this.selectableDrag = this.rotationDrag + } else { + // turn off all listeners + this.hideCenter() + selectionNode.on('mousedown.center', null) + selectionBackground.on('mousedown.center', null) + selectionBackground.on('mousedown.drag', null) + selectionBackground.on('touchstart.drag', null) + this.rotationDrag = null + this.selectableDrag = null + } } -} -/** - * With no argument, toggle the tooltips upon touching of labels. - * @param {Boolean} on_off - The new on/off state. If this argument is not provided, then toggle the state. - */ -function toggle_label_touch (on_off) { - if (on_off === undefined) { - on_off = this.label_touch === null + /** + * With no argument, toggle the node click on or off. Pass in a boolean argument + * to set the on/off state. + */ + toggleSelectableClick (onOff) { + if (onOff === undefined) { + onOff = this.selectableMousedown === null + } + if (onOff) { + const map = this.map + this.selectableMousedown = d => { + // stop propogation for the buildinput to work right + d3Selection.event.stopPropagation() + // this.parentNode.__data__.wasSelected = d3Select(this.parentNode).classed('selected') + // d3Select(this.parentNode).classed('selected', true) + } + this.selectableClick = function (d) { + // stop propogation for the buildinput to work right + d3Selection.event.stopPropagation() + // click suppressed. This DOES have en effect. + if (d3Selection.event.defaultPrevented) return + // turn off the temporary selection so select_selectable + // works. This is a bit of a hack. + // if (!this.parentNode.__data__.wasSelected) + // d3Select(this.parentNode).classed('selected', false) + map.select_selectable(this, d, d3Selection.event.shiftKey) + // this.parentNode.__data__.wasSelected = false + } + this.nodeMouseover = function (d) { + d3Select(this).style('stroke-width', null) + const current = parseFloat(d3Select(this).style('stroke-width')) + if (!d3Select(this.parentNode).classed('selected')) { + d3Select(this).style('stroke-width', current * 3 + 'px') + } + } + this.nodeMouseout = function (d) { + d3Select(this).style('stroke-width', null) + } + } else { + this.selectableMousedown = null + this.selectableClick = null + this.nodeMouseover = null + this.nodeMouseout = null + this.map.sel.select('#nodes') + .selectAll('.node-circle').style('stroke-width', null) + } } - if (on_off) { - // Show/hide tooltip. - // @param {String} type - 'reaction_label' or 'node_label' - // @param {Object} d - D3 data for DOM element - this.label_touch = (type, d) => { - if (!this.dragging) { - this.map.callback_manager.run('show_tooltip', null, type, d) + /** + * With no argument, toggle the text edit on mousedown on/off. Pass in a boolean + * argument to set the on/off state. The backup state is equal to + * selectableMousedown. + */ + toggleTextLabelEdit (onOff) { + if (onOff === undefined) { + onOff = this.textEditMousedown == null + } + if (onOff) { + const map = this.map + this.textLabelMousedown = function () { + if (d3Selection.event.defaultPrevented) { + return // mousedown suppressed + } + // run the callback + const coordsA = utils.d3_transform_catch(d3Select(this).attr('transform')).translate + const coords = { x: coordsA[0], y: coordsA[1] } + map.callback_manager.run('edit_text_label', null, d3Select(this), coords) + d3Selection.event.stopPropagation() } + this.textLabelClick = null + this.map.sel.select('#text-labels') + .selectAll('.label') + .classed('edit-text-cursor', true) + // add the new-label listener + this.map.sel.on('mousedown.new_text_label', function (node) { + // silence other listeners + d3Selection.event.preventDefault() + const coords = { + x: d3Mouse(node)[0], + y: d3Mouse(node)[1] + } + this.map.callback_manager.run('new_text_label', null, coords) + }.bind(this, this.map.sel.node())) + } else { + this.textLabelMousedown = this.selectableMousedown + this.textLabelClick = this.selectableClick + this.map.sel.select('#text-labels') + .selectAll('.label') + .classed('edit-text-cursor', false) + // remove the new-label listener + this.map.sel.on('mousedown.new_text_label', null) + this.map.callback_manager.run('hide_text_label_editor') } - } else { - this.label_touch = null } -} -/** - * With no argument, toggle the tooltips on mouseover of nodes or arrows. - * @param {Boolean} on_off - The new on/off state. - */ -function toggle_object_mouseover (on_off) { - if (on_off === undefined) { - on_off = this.label_mouseover === null + /** + * With no argument, toggle the node drag & bezier drag on or off. Pass in a + * boolean argument to set the on/off state. + */ + toggleSelectableDrag (onOff) { + if (onOff === undefined) { + onOff = this.selectableDrag === this.emptyBehavior + } + if (onOff) { + this.selectableDrag = this.getSelectableDrag(this.map, this.undoStack) + this.bezierDrag = this.getBezierDrag(this.map, this.undoStack) + } else { + this.selectableDrag = this.emptyBehavior + this.bezierDrag = this.emptyBehavior + } } - if (on_off) { + /** + * With no argument, toggle the label drag on or off. Pass in a boolean argument + * to set the on/off state. + * @param {Boolean} onOff - The new on/off state. + */ + toggleLabelDrag (onOff) { + if (onOff === undefined) { + onOff = this.labelDrag === this.emptyBehavior + } + if (onOff) { + this.reactionLabelDrag = this.getReactionLabelDrag(this.map) + this.nodeLabelDrag = this.getNodeLabelDrag(this.map) + } else { + this.reactionLabelDrag = this.emptyBehavior + this.nodeLabelDrag = this.emptyBehavior + } + } - // Show/hide tooltip. - // @param {String} type - 'reaction_object' or 'node_object' - // @param {Object} d - D3 data for DOM element - this.object_mouseover = function (type, d) { - if (!this.dragging) { - this.map.callback_manager.run('show_tooltip', null, type, d) - } - }.bind(this) + /** + * With no argument, toggle the tooltips on mouseover labels. + * @param {Boolean} onOff - The new on/off state. + */ + toggleLabelMouseover (onOff) { + if (onOff === undefined) { + onOff = this.labelMouseover === this.emptyBehavior + } - this.object_mouseout = function () { - this.map.callback_manager.run('delay_hide_tooltip') - }.bind(this) + if (onOff) { + // Show/hide tooltip. + // @param {String} type - 'reactionLabel' or 'nodeLabel' + // @param {Object} d - D3 data for DOM element + this.labelMouseover = (type, d) => { + if (!this.dragging) { + this.map.callback_manager.run('show_tooltip', null, type, d) + } + } - } else { - this.object_mouseover = null + this.labelMouseout = () => { + this.map.callback_manager.run('delay_hide_tooltip') + } + } else { + this.labelMouseover = this.emptyBehavior + } } -} -/** - * With no argument, toggle the tooltips upon touching of nodes or arrows. - * @param {Boolean} on_off - The new on/off state. If this argument is not provided, then toggle the state. - */ -function toggle_object_touch (on_off) { - if (on_off === undefined) { - on_off = this.label_touch === null - } + /** + * With no argument, toggle the tooltips upon touching of labels. + * @param {Boolean} onOff - The new on/off state. If this argument is not + * provided, then toggle the state. + */ + toggleLabelTouch (onOff) { + if (onOff === undefined) { + onOff = this.labelTouch === null + } - if (on_off) { - this.object_touch = (type, d) => { - if (!this.dragging) { - this.map.callback_manager.run('show_tooltip', null, type, d) + if (onOff) { + // Show/hide tooltip. + // @param {String} type - 'reactionLabel' or 'nodeLabel' + // @param {Object} d - D3 data for DOM element + this.labelTouch = (type, d) => { + if (!this.dragging) { + this.map.callback_manager.run('show_tooltip', null, type, d) + } } + } else { + this.labelTouch = null } - } else { - this.object_touch = null } -} -/** - * With no argument, toggle the bezier drag on or off. Pass in a boolean - * argument to set the on/off state. - */ -function toggle_bezier_drag (on_off) { - if (on_off === undefined) { - on_off = this.bezier_drag === this.empty_behavior - } - if (on_off) { - this.bezier_drag = this._get_bezier_drag(this.map) - this.bezier_mouseover = function (d) { - d3_select(this).style('stroke-width', String(3)+'px') - } - this.bezier_mouseout = function (d) { - d3_select(this).style('stroke-width', String(1)+'px') + /** + * With no argument, toggle the tooltips on mouseover of nodes or arrows. + * @param {Boolean} onOff - The new on/off state. + */ + toggleObjectMouseover (onOff) { + if (onOff === undefined) { + onOff = this.objectMouseover === this.emptyBehavior } - } else { - this.bezier_drag = this.empty_behavior - this.bezier_mouseover = null - this.bezier_mouseout = null - } -} -function turn_off_drag (sel) { - sel.on('mousedown.drag', null) - sel.on('touchstart.drag', null) -} + if (onOff) { + // Show/hide tooltip. + // @param {String} type - 'reaction_object' or 'node_object' + // @param {Object} d - D3 data for DOM element + this.objectMouseover = (type, d) => { + if (!this.dragging) { + this.map.callback_manager.run('show_tooltip', null, type, d) + } + } -/** - * Drag the selected nodes and text labels. - * @param {} map - - * @param {} undo_stack - - */ -function _get_selectable_drag (map, undo_stack) { - // define some variables - var behavior = d3_drag() - var the_timeout = null - var total_displacement = null - // for nodes - var node_ids_to_drag = null - var reaction_ids = null - // for text labels - var text_label_ids_to_drag = null - var move_label = function (text_label_id, displacement) { - var text_label = map.text_labels[text_label_id] - text_label.x = text_label.x + displacement.x - text_label.y = text_label.y + displacement.y - } - var set_dragging = function (on_off) { - this.dragging = on_off - }.bind(this) - - behavior.on('start', function (d) { - set_dragging(true) - - // silence other listeners (e.g. nodes BELOW this one) - d3_selection.event.sourceEvent.stopPropagation() - // remember the total displacement for later - total_displacement = { x: 0, y: 0 } - - // If a text label is selected, the rest is not necessary - if (d3_select(this).attr('class').indexOf('label') === -1) { - // Note that drag start is called even for a click event - var data = this.parentNode.__data__, - bigg_id = data.bigg_id, - node_group = this.parentNode - // Move element to back (for the next step to work). Wait 200ms - // before making the move, becuase otherwise the element will be - // deleted before the click event gets called, and selection - // will stop working. - the_timeout = setTimeout(function () { - node_group.parentNode.insertBefore(node_group, - node_group.parentNode.firstChild) - }, 200) - // prepare to combine metabolites - map.sel.selectAll('.metabolite-circle') - .on('mouseover.combine', function (d) { - if (d.bigg_id === bigg_id && d.node_id !== data.node_id) { - d3_select(this).style('stroke-width', String(12) + 'px') - .classed('node-to-combine', true) - } - }) - .on('mouseout.combine', function (d) { - if (d.bigg_id === bigg_id) { - map.sel.selectAll('.node-to-combine') - .style('stroke-width', String(2) + 'px') - .classed('node-to-combine', false) - } - }) + this.objectMouseout = () => { + this.map.callback_manager.run('delay_hide_tooltip') + } + } else { + this.objectMouseover = this.emptyBehavior } - }) + } - behavior.on('drag', function (d) { - // if this node is not already selected, then select this one and - // deselect all other nodes. Otherwise, leave the selection alone. - if (!d3_select(this.parentNode).classed('selected')) { - map.select_selectable(this, d) + /** + * With no argument, toggle the tooltips upon touching of nodes or arrows. + * @param {Boolean} onOff - The new on/off state. If this argument is not provided, then toggle the state. + */ + toggleObjectTouch (onOff){ + if (onOff === undefined) { + onOff = this.labelTouch === null } - // get the grabbed id - var grabbed = {} - if (d3_select(this).attr('class').indexOf('label') === -1) { - // if it is a node - grabbed['type'] = 'node' - grabbed['id'] = this.parentNode.__data__.node_id + if (onOff) { + this.objectTouch = (type, d) => { + if (!this.dragging) { + this.map.callback_manager.run('show_tooltip', null, type, d) + } + } } else { - // if it is a text label - grabbed['type'] = 'label' - grabbed['id'] = this.__data__.text_label_id + this.objectTouch = null } + } - var selected_node_ids = map.get_selected_node_ids() - var selected_text_label_ids = map.get_selected_text_label_ids() - node_ids_to_drag = []; text_label_ids_to_drag = [] - // choose the nodes and text labels to drag - if (grabbed['type']=='node' && - selected_node_ids.indexOf(grabbed['id']) === -1) { - node_ids_to_drag.push(grabbed['id']) - } else if (grabbed['type'] === 'label' && - selected_text_label_ids.indexOf(grabbed['id']) === -1) { - text_label_ids_to_drag.push(grabbed['id']) - } else { - node_ids_to_drag = selected_node_ids - text_label_ids_to_drag = selected_text_label_ids - } - reaction_ids = [] - var displacement = { - x: d3_selection.event.dx, - y: d3_selection.event.dy, - } - total_displacement = utils.c_plus_c(total_displacement, displacement) - node_ids_to_drag.forEach(function (node_id) { - // update data - var node = map.nodes[node_id], - updated = build.move_node_and_dependents(node, node_id, - map.reactions, - map.beziers, - displacement) - reaction_ids = utils.unique_concat([ reaction_ids, updated.reaction_ids ]) - // remember the displacements - // if (!(node_id in total_displacement)) total_displacement[node_id] = { x: 0, y: 0 } - // total_displacement[node_id] = utils.c_plus_c(total_displacement[node_id], displacement) - }) - text_label_ids_to_drag.forEach(function (text_label_id) { - move_label(text_label_id, displacement) - // remember the displacements - // if (!(node_id in total_displacement)) total_displacement[node_id] = { x: 0, y: 0 } - // total_displacement[node_id] = utils.c_plus_c(total_displacement[node_id], displacement) - }) - // draw - map.draw_these_nodes(node_ids_to_drag) - map.draw_these_reactions(reaction_ids) - map.draw_these_text_labels(text_label_ids_to_drag) - }) - - behavior.on('end', function () { - set_dragging(false) - - if (node_ids_to_drag === null) { - // Drag end can be called when drag has not been called. In this, case, do - // nothing. - total_displacement = null - node_ids_to_drag = null - text_label_ids_to_drag = null - reaction_ids = null - the_timeout = null - return + /** + * With no argument, toggle the bezier drag on or off. Pass in a boolean + * argument to set the on/off state. + */ + toggleBezierDrag (onOff) { + if (onOff === undefined) { + onOff = this.bezierDrag === this.emptyBehavior } - // look for mets to combine - var node_to_combine_array = [] - map.sel.selectAll('.node-to-combine').each(function (d) { - node_to_combine_array.push(d.node_id) - }) - if (node_to_combine_array.length === 1) { - // If a node is ready for it, combine nodes - var fixed_node_id = node_to_combine_array[0], - dragged_node_id = this.parentNode.__data__.node_id, - saved_dragged_node = utils.clone(map.nodes[dragged_node_id]), - segment_objs_moved_to_combine = combine_nodes_and_draw(fixed_node_id, - dragged_node_id) - undo_stack.push(function () { - // undo - // put the old node back - map.nodes[dragged_node_id] = saved_dragged_node - var fixed_node = map.nodes[fixed_node_id], - updated_reactions = [] - segment_objs_moved_to_combine.forEach(function (segment_obj) { - var segment = map.reactions[segment_obj.reaction_id].segments[segment_obj.segment_id] - if (segment.from_node_id==fixed_node_id) { - segment.from_node_id = dragged_node_id - } else if (segment.to_node_id==fixed_node_id) { - segment.to_node_id = dragged_node_id - } else { - console.error('Segment does not connect to fixed node') - } - // removed this segment_obj from the fixed node - fixed_node.connected_segments = fixed_node.connected_segments.filter(function (x) { - return !(x.reaction_id==segment_obj.reaction_id && x.segment_id==segment_obj.segment_id) - }) - if (updated_reactions.indexOf(segment_obj.reaction_id)==-1) - updated_reactions.push(segment_obj.reaction_id) - }) - map.draw_these_nodes([dragged_node_id]) - map.draw_these_reactions(updated_reactions) - }, function () { - // redo - combine_nodes_and_draw(fixed_node_id, dragged_node_id) - }) - + if (onOff) { + this.bezierDrag = this.getBezierDrag(this.map) + this.bezierMouseover = function (d) { + d3Select(this).style('stroke-width', String(3)+'px') + } + this.bezierMouseout = function (d) { + d3Select(this).style('stroke-width', String(1)+'px') + } } else { - // otherwise, drag node - - // add to undo/redo stack - // remember the displacement, dragged nodes, and reactions - var saved_displacement = utils.clone(total_displacement), - // BUG TODO this variable disappears! - // Happens sometimes when you drag a node, then delete it, then undo twice - saved_node_ids = utils.clone(node_ids_to_drag), - saved_text_label_ids = utils.clone(text_label_ids_to_drag), - saved_reaction_ids = utils.clone(reaction_ids) - undo_stack.push(function () { - // undo - saved_node_ids.forEach(function (node_id) { - var node = map.nodes[node_id] - build.move_node_and_dependents(node, node_id, map.reactions, - map.beziers, - utils.c_times_scalar(saved_displacement, -1)) - }) - saved_text_label_ids.forEach(function (text_label_id) { - move_label(text_label_id, - utils.c_times_scalar(saved_displacement, -1)) - }) - map.draw_these_nodes(saved_node_ids) - map.draw_these_reactions(saved_reaction_ids) - map.draw_these_text_labels(saved_text_label_ids) - }, function () { - // redo - saved_node_ids.forEach(function (node_id) { - var node = map.nodes[node_id] - build.move_node_and_dependents(node, node_id, map.reactions, - map.beziers, - saved_displacement) - }) - saved_text_label_ids.forEach(function (text_label_id) { - move_label(text_label_id, saved_displacement) - }) - map.draw_these_nodes(saved_node_ids) - map.draw_these_reactions(saved_reaction_ids) - map.draw_these_text_labels(saved_text_label_ids) - }) + this.bezierDrag = this.emptyBehavior + this.bezierMouseover = null + this.bezierMouseout = null } + } - // stop combining metabolites - map.sel.selectAll('.metabolite-circle') - .on('mouseover.combine', null) - .on('mouseout.combine', null) - - // clear the timeout - clearTimeout(the_timeout) - - // clear the shared variables - total_displacement = null - node_ids_to_drag = null - text_label_ids_to_drag = null - reaction_ids = null - the_timeout = null - }) - - return behavior - - // definitions - function combine_nodes_and_draw (fixed_node_id, dragged_node_id) { - var dragged_node = map.nodes[dragged_node_id] - var fixed_node = map.nodes[fixed_node_id] - var updated_segment_objs = [] - dragged_node.connected_segments.forEach(function (segment_obj) { + turnOffDrag (sel) { + sel.on('mousedown.drag', null) + sel.on('touchstart.drag', null) + } + + combineNodesAndDraw (fixedNodeId, draggedNodeId) { + const map = this.map + const draggedNode = map.nodes[draggedNodeId] + const fixedNode = map.nodes[fixedNodeId] + const updatedSegmentObjs = [] + draggedNode.connectedSegments.forEach(segmentObj => { // change the segments to reflect - var segment + let segment = null try { - segment = map.reactions[segment_obj.reaction_id].segments[segment_obj.segment_id] + segment = map.reactions[segmentObj.reactionId].segments[segmentObj.segmentId] if (segment === undefined) throw new Error('undefined segment') } catch (e) { - console.warn('Could not find connected segment ' + segment_obj.segment_id) + console.warn('Could not find connected segment ' + segmentObj.segmentId) return } - if (segment.from_node_id==dragged_node_id) segment.from_node_id = fixed_node_id - else if (segment.to_node_id==dragged_node_id) segment.to_node_id = fixed_node_id + if (segment.fromNodeId==draggedNodeId) segment.fromNodeId = fixedNodeId + else if (segment.toNodeId==draggedNodeId) segment.toNodeId = fixedNodeId else { console.error('Segment does not connect to dragged node') return } - // moved segment_obj to fixed_node - fixed_node.connected_segments.push(segment_obj) - updated_segment_objs.push(utils.clone(segment_obj)) + // moved segmentObj to fixedNode + fixedNode.connectedSegments.push(segmentObj) + updatedSegmentObjs.push(utils.clone(segmentObj)) return }) // delete the old node - map.delete_node_data([dragged_node_id]) + map.delete_node_data([draggedNodeId]) // turn off the class map.sel.selectAll('.node-to-combine').classed('node-to-combine', false) // draw - map.draw_everything() + map.drawEverything() // return for undo - return updated_segment_objs - } -} + return updatedSegmentObjs + } + + /** + * Drag the selected nodes and text labels. + * @param {} map - + * @param {} undo_stack - + */ + getSelectableDrag (map, undoStack) { + // define some variables + const behavior = d3Drag() + let theTimeout = null + let totalDisplacement = null + // for nodes + let nodeIdsToDrag = null + let reactionIds = null + // for text labels + let textLabelIdsToDrag = null + const moveLabel = (textLabelId, displacement) => { + const textLabel = map.text_labels[textLabelId] + textLabel.x = textLabel.x + displacement.x + textLabel.y = textLabel.y + displacement.y + } + const setDragging = onOff => { + this.dragging = onOff + } -function _get_bezier_drag (map) { - var move_bezier = function (reaction_id, segment_id, bez, bezier_id, - displacement) { - var segment = map.reactions[reaction_id].segments[segment_id] - segment[bez] = utils.c_plus_c(segment[bez], displacement) - map.beziers[bezier_id].x = segment[bez].x - map.beziers[bezier_id].y = segment[bez].y - } - var start_fn = function (d) { - d.dragging = true - } - var drag_fn = function (d, displacement, total_displacement) { - // draw - move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, - displacement) - map.draw_these_reactions([d.reaction_id], false) - map.draw_these_beziers([d.bezier_id]) - } - var end_fn = function (d) { - d.dragging = false - } - var undo_fn = function (d, displacement) { - move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, - utils.c_times_scalar(displacement, -1)) - map.draw_these_reactions([d.reaction_id], false) - map.draw_these_beziers([d.bezier_id]) - } - var redo_fn = function (d, displacement) { - move_bezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, - displacement) - map.draw_these_reactions([d.reaction_id], false) - map.draw_these_beziers([d.bezier_id]) - } - return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn, redo_fn, - this.map.sel) -} + behavior.on('start', function (d) { + setDragging(true) + + // silence other listeners (e.g. nodes BELOW this one) + d3Selection.event.sourceEvent.stopPropagation() + // remember the total displacement for later + totalDisplacement = { x: 0, y: 0 } + + // If a text label is selected, the rest is not necessary + if (d3Select(this).attr('class').indexOf('label') === -1) { + // Note that drag start is called even for a click event + const data = this.parentNode.__data__ + const biggId = data.biggId + const nodeGroup = this.parentNode + // Move element to back (for the next step to work). Wait 200ms + // before making the move, becuase otherwise the element will be + // deleted before the click event gets called, and selection + // will stop working. + theTimeout = setTimeout(() => { + nodeGroup.parentNode.insertBefore(nodeGroup, nodeGroup.parentNode.firstChild) + }, 200) + // prepare to combine metabolites + map.sel.selectAll('.metabolite-circle') + .on('mouseover.combine', function (d) { + if (d.bigg_id === biggId && d.node_id !== data.nodeId) { + d3Select(this).style('stroke-width', String(12) + 'px') + .classed('node-to-combine', true) + } + }) + .on('mouseout.combine', d => { + if (d.bigg_id === biggId) { + map.sel.selectAll('.node-to-combine') + .style('stroke-width', String(2) + 'px') + .classed('node-to-combine', false) + } + }) + } + }) -function _get_reaction_label_drag (map) { - var move_label = function (reaction_id, displacement) { - var reaction = map.reactions[reaction_id] - reaction.label_x = reaction.label_x + displacement.x - reaction.label_y = reaction.label_y + displacement.y - } - var start_fn = function (d) { - // hide tooltips when drag starts - map.callback_manager.run('hide_tooltip') - } - var drag_fn = function (d, displacement, total_displacement) { - // draw - move_label(d.reaction_id, displacement) - map.draw_these_reactions([ d.reaction_id ]) - } - var end_fn = function (d) { - } - var undo_fn = function (d, displacement) { - move_label(d.reaction_id, utils.c_times_scalar(displacement, -1)) - map.draw_these_reactions([ d.reaction_id ]) - } - var redo_fn = function (d, displacement) { - move_label(d.reaction_id, displacement) - map.draw_these_reactions([ d.reaction_id ]) - } - return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn, redo_fn, - this.map.sel) -} + behavior.on('drag', function (d) { + // if this node is not already selected, then select this one and + // deselect all other nodes. Otherwise, leave the selection alone. + if (!d3Select(this.parentNode).classed('selected')) { + map.select_selectable(this, d) + } -function _get_node_label_drag (map) { - var move_label = function (node_id, displacement) { - var node = map.nodes[node_id] - node.label_x = node.label_x + displacement.x - node.label_y = node.label_y + displacement.y - } - var start_fn = function (d) { - // hide tooltips when drag starts - map.callback_manager.run('hide_tooltip') - } - var drag_fn = function (d, displacement, total_displacement) { - // draw - move_label(d.node_id, displacement) - map.draw_these_nodes([ d.node_id ]) - } - var end_fn = function (d) { + // get the grabbed id + const grabbed = {} + if (d3Select(this).attr('class').indexOf('label') === -1) { + // if it is a node + grabbed['type'] = 'node' + grabbed['id'] = this.parentNode.__data__.node_id + } else { + // if it is a text label + grabbed['type'] = 'label' + grabbed['id'] = this.__data__.text_label_id + } + + const selectedNodeIds = map.get_selected_node_ids() + const selectedTextLabelIds = map.get_selected_text_label_ids() + nodeIdsToDrag = [] + textLabelIdsToDrag = [] + // choose the nodes and text labels to drag + if (grabbed['type'] === 'node' && + selectedNodeIds.indexOf(grabbed['id']) === -1) { + nodeIdsToDrag.push(grabbed['id']) + } else if (grabbed['type'] === 'label' && + selectedTextLabelIds.indexOf(grabbed['id']) === -1) { + textLabelIdsToDrag.push(grabbed['id']) + } else { + nodeIdsToDrag = selectedNodeIds + textLabelIdsToDrag = selectedTextLabelIds + } + reactionIds = [] + const displacement = { + x: d3Selection.event.dx, + y: d3Selection.event.dy + } + totalDisplacement = utils.c_plus_c(totalDisplacement, displacement) + nodeIdsToDrag.forEach(nodeId => { + // update data + const node = map.nodes[nodeId] + const updated = build.move_node_and_dependents(node, nodeId, + map.reactions, + map.beziers, + displacement) + reactionIds = utils.uniqueConcat([ reactionIds, updated.reaction_ids ]) + // remember the displacements + // if (!(nodeId in totalDisplacement)) totalDisplacement[nodeId] = { x: 0, y: 0 } + // totalDisplacement[nodeId] = utils.c_plus_c(totalDisplacement[nodeId], displacement) + }) + textLabelIdsToDrag.forEach(textLabelId => { + moveLabel(textLabelId, displacement) + // remember the displacements + // if (!(nodeId in totalDisplacement)) totalDisplacement[nodeId] = { x: 0, y: 0 } + // totalDisplacement[nodeId] = utils.c_plus_c(totalDisplacement[nodeId], displacement) + }) + // draw + map.draw_these_nodes(nodeIdsToDrag) + map.draw_these_reactions(reactionIds) + map.draw_these_text_labels(textLabelIdsToDrag) + }) + + behavior.on('end', () => { + setDragging(false) + + if (nodeIdsToDrag === null) { + // Drag end can be called when drag has not been called. In this, case, do + // nothing. + totalDisplacement = null + nodeIdsToDrag = null + textLabelIdsToDrag = null + reactionIds = null + theTimeout = null + return + } + + // look for mets to combine + const nodeToCombineArray = [] + map.sel.selectAll('.node-to-combine').each(d => { + nodeToCombineArray.push(d.node_id) + }) + + if (nodeToCombineArray.length === 1) { + // If a node is ready for it, combine nodes + const fixedNodeId = nodeToCombineArray[0] + const draggedNodeId = this.parentNode.__data__.node_id + const savedDraggedNode = utils.clone(map.nodes[draggedNodeId]) + const segmentObjsMovedToCombine = this.combineNodesAndDraw(fixedNodeId, + draggedNodeId) + undoStack.push(() => { + // undo + // put the old node back + map.nodes[draggedNodeId] = savedDraggedNode + const fixedNode = map.nodes[fixedNodeId] + const updatedReactions = [] + segmentObjsMovedToCombine.forEach(segmentObj => { + const segment = map.reactions[segmentObj.reactionId].segments[segmentObj.segmentId] + if (segment.fromNodeId === fixedNodeId) { + segment.fromNodeId = draggedNodeId + } else if (segment.toNodeId === fixedNodeId) { + segment.toNodeId = draggedNodeId + } else { + console.error('Segment does not connect to fixed node') + } + // removed this segmentObj from the fixed node + fixedNode.connectedSegments = fixedNode.connectedSegments.filter(x => { + return !(x.reactionId === segmentObj.reactionId && x.segmentId === segmentObj.segmentId) + }) + if (updatedReactions.indexOf(segmentObj.reactionId) === -1) { + updatedReactions.push(segmentObj.reactionId) + } + }) + map.draw_these_nodes([draggedNodeId]) + map.draw_these_reactions(updatedReactions) + }, () => { + // redo + this.combineNodesAndDraw(fixedNodeId, draggedNodeId) + }) + } else { + // otherwise, drag node + + // add to undo/redo stack + // remember the displacement, dragged nodes, and reactions + const savedDisplacement = utils.clone(totalDisplacement) + // BUG TODO this variable disappears! + // Happens sometimes when you drag a node, then delete it, then undo twice + const savedNodeIds = utils.clone(nodeIdsToDrag) + const savedTextLabelIds = utils.clone(textLabelIdsToDrag) + const savedReactionIds = utils.clone(reactionIds) + undoStack.push(() => { + // undo + savedNodeIds.forEach(nodeId => { + const node = map.nodes[nodeId] + build.move_node_and_dependents(node, nodeId, map.reactions, + map.beziers, + utils.c_times_scalar(savedDisplacement, -1)) + }) + savedTextLabelIds.forEach(textLabelId => { + moveLabel(textLabelId, + utils.c_times_scalar(savedDisplacement, -1)) + }) + map.draw_these_nodes(savedNodeIds) + map.draw_these_reactions(savedReactionIds) + map.draw_these_text_labels(savedTextLabelIds) + }, () => { + // redo + savedNodeIds.forEach(nodeId => { + const node = map.nodes[nodeId] + build.move_node_and_dependents(node, nodeId, map.reactions, + map.beziers, + savedDisplacement) + }) + savedTextLabelIds.forEach(textLabelId => { + moveLabel(textLabelId, savedDisplacement) + }) + map.draw_these_nodes(savedNodeIds) + map.draw_these_reactions(savedReactionIds) + map.draw_these_text_labels(savedTextLabelIds) + }) + } + + // stop combining metabolites + map.sel.selectAll('.metabolite-circle') + .on('mouseover.combine', null) + .on('mouseout.combine', null) + + // clear the timeout + clearTimeout(theTimeout) + + // clear the shared variables + totalDisplacement = null + nodeIdsToDrag = null + textLabelIdsToDrag = null + reactionIds = null + theTimeout = null + }) + + return behavior } - var undo_fn = function (d, displacement) { - move_label(d.node_id, utils.c_times_scalar(displacement, -1)) - map.draw_these_nodes ([ d.node_id ]) + + getBezierDrag (map) { + const moveBezier = (reactionId, segmentId, bez, bezierId, displacement) => { + const segment = map.reactions[reactionId].segments[segmentId] + segment[bez] = utils.c_plus_c(segment[bez], displacement) + map.beziers[bezierId].x = segment[bez].x + map.beziers[bezierId].y = segment[bez].y + } + const startFn = d => { + d.dragging = true + } + const dragFn = (d, displacement, totalDisplacement) => { + // draw + moveBezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, + displacement) + map.draw_these_reactions([d.reaction_id], false) + map.draw_these_beziers([d.bezier_id]) + } + const endFn = d => { + d.dragging = false + } + const undoFn = (d, displacement) => { + moveBezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, + utils.c_times_scalar(displacement, -1)) + map.draw_these_reactions([d.reaction_id], false) + map.draw_these_beziers([d.bezier_id]) + } + const redoFn = (d, displacement) => { + moveBezier(d.reaction_id, d.segment_id, d.bezier, d.bezier_id, + displacement) + map.draw_these_reactions([d.reaction_id], false) + map.draw_these_beziers([d.bezier_id]) + } + return this.getGenericDrag(startFn, dragFn, endFn, undoFn, redoFn, + this.map.sel) } - var redo_fn = function (d, displacement) { - move_label(d.node_id, displacement) - map.draw_these_nodes([ d.node_id ]) + + getReactionLabelDrag (map) { + const moveLabel = (reactionId, displacement) => { + const reaction = map.reactions[reactionId] + reaction.label_x = reaction.label_x + displacement.x + reaction.label_y = reaction.label_y + displacement.y + } + const startFn = d => { + // hide tooltips when drag starts + map.callback_manager.run('hide_tooltip') + } + const dragFn = (d, displacement, totalDisplacement) => { + // draw + moveLabel(d.reaction_id, displacement) + map.draw_these_reactions([ d.reaction_id ]) + } + const endFn = () => {} + const undoFn = (d, displacement) => { + moveLabel(d.reaction_id, utils.c_times_scalar(displacement, -1)) + map.draw_these_reactions([ d.reaction_id ]) + } + const redoFn = (d, displacement) => { + moveLabel(d.reaction_id, displacement) + map.draw_these_reactions([ d.reaction_id ]) + } + return this.getGenericDrag(startFn, dragFn, endFn, undoFn, redoFn, + this.map.sel) } - return this._get_generic_drag(start_fn, drag_fn, end_fn, undo_fn, redo_fn, - this.map.sel) -} -/** - * Make a generic drag behavior, with undo/redo. - * - * start_fn: function (d) Called at drag start. - * - * drag_fn: function (d, displacement, total_displacement) Called during drag. - * - * end_fn - * - * undo_fn - * - * redo_fn - * - * relative_to_selection: a d3 selection that the locations are calculated - * against. - * - */ -function _get_generic_drag (start_fn, drag_fn, end_fn, undo_fn, redo_fn, - relative_to_selection) { - // define some variables - var behavior = d3_drag() - var total_displacement - var undo_stack = this.undo_stack - var rel = relative_to_selection.node() - - behavior.on('start', function (d) { - this.dragging = true - - // silence other listeners - d3_selection.event.sourceEvent.stopPropagation() - total_displacement = { x: 0, y: 0 } - start_fn(d) - }.bind(this)) - - behavior.on('drag', function (d) { - // update data - var displacement = { - x: d3_selection.event.dx, - y: d3_selection.event.dy, + getNodeLabelDrag (map) { + const moveLabel = (nodeId, displacement) => { + const node = map.nodes[nodeId] + node.label_x = node.label_x + displacement.x + node.label_y = node.label_y + displacement.y } - var location = { - x: d3_mouse(rel)[0], - y: d3_mouse(rel)[1], + const startFn = d => { + // hide tooltips when drag starts + map.callback_manager.run('hide_tooltip') } + const dragFn = (d, displacement, totalDisplacement) => { + // draw + moveLabel(d.node_id, displacement) + map.draw_these_nodes([ d.node_id ]) + } + const endFn = () => {} + const undoFn = (d, displacement) => { + moveLabel(d.node_id, utils.c_times_scalar(displacement, -1)) + map.draw_these_nodes([ d.node_id ]) + } + const redoFn = (d, displacement) => { + moveLabel(d.node_id, displacement) + map.draw_these_nodes([ d.node_id ]) + } + return this.getGenericDrag(startFn, dragFn, endFn, undoFn, redoFn, + this.map.sel) + } + + /** + * Make a generic drag behavior, with undo/redo. + * + * startFn: function (d) Called at drag start. + * + * dragFn: function (d, displacement, totalDisplacement) Called during drag. + * + * endFn + * + * undoFn + * + * redoFn + * + * relativeToSelection: a d3 selection that the locations are calculated + * against. + * + */ + getGenericDrag (startFn, dragFn, endFn, undoFn, redoFn, + relativeToSelection) { + // define some variables + const behavior = d3Drag() + const undoStack = this.undoStack + const rel = relativeToSelection.node() + let totalDisplacement + + behavior.on('start', d => { + this.dragging = true + + // silence other listeners + d3Selection.event.sourceEvent.stopPropagation() + totalDisplacement = { x: 0, y: 0 } + startFn(d) + }) - // remember the displacement - total_displacement = utils.c_plus_c(total_displacement, displacement) - drag_fn(d, displacement, total_displacement, location) - }.bind(this)) + behavior.on('drag', d => { + // update data + const displacement = { + x: d3Selection.event.dx, + y: d3Selection.event.dy + } + const location = { + x: d3Mouse(rel)[0], + y: d3Mouse(rel)[1] + } - behavior.on('end', function (d) { - this.dragging = false + // remember the displacement + totalDisplacement = utils.c_plus_c(totalDisplacement, displacement) + dragFn(d, displacement, totalDisplacement, location) + }) - // add to undo/redo stack - // remember the displacement, dragged nodes, and reactions - var saved_d = utils.clone(d) - var saved_displacement = utils.clone(total_displacement) // BUG TODO this variable disappears! - var saved_location = { - x: d3_mouse(rel)[0], - y: d3_mouse(rel)[1], - } + behavior.on('end', d => { + this.dragging = false - undo_stack.push(function () { - // undo - undo_fn(saved_d, saved_displacement, saved_location) - }, function () { - // redo - redo_fn(saved_d, saved_displacement, saved_location) + // add to undo/redo stack + // remember the displacement, dragged nodes, and reactions + const savedD = utils.clone(d) + const savedDisplacement = utils.clone(totalDisplacement) // BUG TODO this variable disappears! + const savedLocation = { + x: d3Mouse(rel)[0], + y: d3Mouse(rel)[1], + } + + undoStack.push(function () { + // undo + undoFn(savedD, savedDisplacement, savedLocation) + }, function () { + // redo + redoFn(savedD, savedDisplacement, savedLocation) + }) + endFn(d) }) - end_fn(d) - }.bind(this)) - return behavior -} + return behavior + } + + /** Make a generic drag behavior, with undo/redo. Supplies angles in place of + * displacements. + * + * startFn: function (d) Called at drag start. + * + * dragFn: function (d, displacement, totalDisplacement) Called during drag. + * + * endFn: + * + * undoFn: + * + * redoFn: + * + * getCenter: + * + * relativeToSelection: a d3 selection that the locations are calculated + * against. + * + */ + getGenericAngularDrag (startFn, dragFn, endFn, undoFn, redoFn, + getCenter, relativeToSelection) { + // define some variables + const behavior = d3Drag() + const undoStack = this.undoStack + const rel = relativeToSelection.node() + let totalAngle + + behavior.on('start', d => { + this.dragging = true -/** Make a generic drag behavior, with undo/redo. Supplies angles in place of - * displacements. - * - * start_fn: function (d) Called at drag start. - * - * drag_fn: function (d, displacement, total_displacement) Called during drag. - * - * end_fn: - * - * undo_fn: - * - * redo_fn: - * - * get_center: - * - * relative_to_selection: a d3 selection that the locations are calculated - * against. - * - */ -function _get_generic_angular_drag (start_fn, drag_fn, end_fn, undo_fn, redo_fn, - get_center, relative_to_selection) { - - // define some variables - var behavior = d3_drag() - var total_angle - var undo_stack = this.undo_stack - var rel = relative_to_selection.node() - - behavior.on('start', function (d) { - this.dragging = true - - // silence other listeners - d3_selection.event.sourceEvent.stopPropagation() - total_angle = 0 - start_fn(d) - }.bind(this)) - - behavior.on('drag', function (d) { - // update data - var displacement = { - x: d3_selection.event.dx, - y: d3_selection.event.dy, - } - var location = { - x: d3_mouse(rel)[0], - y: d3_mouse(rel)[1], - } - var center = get_center() - var angle = utils.angle_for_event(displacement, location, center) - // remember the displacement - total_angle = total_angle + angle - drag_fn(d, angle, total_angle, center) - }.bind(this)) - - behavior.on('end', function (d) { - this.dragging = false + // silence other listeners + d3Selection.event.sourceEvent.stopPropagation() + totalAngle = 0 + startFn(d) + }) - // add to undo/redo stack - // remember the displacement, dragged nodes, and reactions - var saved_d = utils.clone(d) - var saved_angle = total_angle - var saved_center = utils.clone(get_center()) - - undo_stack.push(function () { - // undo - undo_fn(saved_d, saved_angle, saved_center) - }, function () { - // redo - redo_fn(saved_d, saved_angle, saved_center) + behavior.on('drag', d => { + // update data + const displacement = { + x: d3Selection.event.dx, + y: d3Selection.event.dy + } + const location = { + x: d3Mouse(rel)[0], + y: d3Mouse(rel)[1] + } + const center = getCenter() + const angle = utils.angle_for_event(displacement, location, center) + // remember the displacement + totalAngle = totalAngle + angle + dragFn(d, angle, totalAngle, center) }) - end_fn(d) - }.bind(this)) - return behavior + behavior.on('end', d => { + this.dragging = false + + // add to undo/redo stack + // remember the displacement, dragged nodes, and reactions + const savedD = utils.clone(d) + const savedAngle = totalAngle + const savedCenter = utils.clone(getCenter()) + + undoStack.push( + () => undoFn(savedD, savedAngle, savedCenter), + () => redoFn(savedD, savedAngle, savedCenter) + ) + + endFn(d) + }) + + return behavior + } } diff --git a/src/Brush.js b/src/Brush.js index 09e82394..6bd8456a 100644 --- a/src/Brush.js +++ b/src/Brush.js @@ -53,11 +53,11 @@ function brush_is_enabled () { * Turn the brush on or off * @param {Boolean} on_off */ -function toggle (on_off) { - if (on_off === undefined) { - on_off = !this.enabled +function toggle (onOff) { + if (onOff === undefined) { + onOff = !this.enabled } - if (on_off) { + if (onOff) { this.setup_selection_brush() } else { this.brush_sel.selectAll('*').remove() @@ -93,8 +93,8 @@ function setup_selection_brush () { .on('start', function () { turn_off_crosshair(selection) // unhide secondary metabolites if they are hidden - if (map.settings.get_option('hide_secondary_metabolites')) { - map.settings.set_conditional('hide_secondary_metabolites', false) + if (map.settings.get('hide_secondary_metabolites')) { + map.settings.set('hide_secondary_metabolites', false) map.draw_everything() map.set_status('Showing secondary metabolites. You can hide them ' + 'again in Settings.', 2000) diff --git a/src/BuildInput.js b/src/BuildInput.js index d52289b5..575506d7 100644 --- a/src/BuildInput.js +++ b/src/BuildInput.js @@ -1,409 +1,374 @@ -/** BuildInput - - Arguments - --------- - - selection: A d3 selection for the BuildInput. - - map: A Map instance. - - zoom_container: A ZoomContainer instance. - - settings: A Settings instance. - -*/ - -var utils = require('./utils') -var PlacedDiv = require('./PlacedDiv') -var completely = require('./completely') -var DirectionArrow = require('./DirectionArrow') -var CobraModel = require('./CobraModel') -var _ = require('underscore') -var d3_select = require('d3-selection').select -var d3_mouse = require('d3-selection').mouse - -var BuildInput = utils.make_class() -BuildInput.prototype = { - init: init, - setup_map_callbacks: setup_map_callbacks, - setup_zoom_callbacks: setup_zoom_callbacks, - is_visible: is_visible, - toggle: toggle, - show_dropdown: show_dropdown, - hide_dropdown: hide_dropdown, - place_at_selected: place_at_selected, - place: place, - reload_at_selected: reload_at_selected, - reload: reload, - toggle_start_reaction_listener: toggle_start_reaction_listener, - hide_target: hide_target, - show_target: show_target -} -module.exports = BuildInput - -function init (selection, map, zoom_container, settings) { - // set up container - var new_sel = selection.append('div').attr('id', 'rxn-input') - this.placed_div = PlacedDiv(new_sel, map, { x: 240, y: 0 }) - this.placed_div.hide() - - // set up complete.ly - var c = completely(new_sel.node(), { backgroundColor: '#eee' }) - - d3_select(c.input) - this.completely = c - // close button - new_sel.append('button').attr('class', 'button input-close-button') - .text("×") - .on('mousedown', function () { this.hide_dropdown() }.bind(this)) - - // map - this.map = map - // set up the reaction direction arrow - var default_angle = 90 // degrees - this.direction_arrow = new DirectionArrow(map.sel) - this.direction_arrow.set_rotation(default_angle) - this.setup_map_callbacks(map) - - // zoom container - this.zoom_container = zoom_container - this.setup_zoom_callbacks(zoom_container) - - // settings - this.settings = settings - - // toggle off - this.toggle(false) - this.target_coords = null -} - -function setup_map_callbacks (map) { - // input - map.callback_manager.set('select_metabolite_with_id.input', function (selected_node, coords) { - if (this.is_active) { - this.reload(selected_node, coords, false) - this.show_dropdown(coords) - } - this.hide_target() - }.bind(this)) - map.callback_manager.set('select_selectable.input', function (count, selected_node, coords) { - this.hide_target() - if (count == 1 && this.is_active && coords) { - this.reload(selected_node, coords, false) - this.show_dropdown(coords) - } else { - this.toggle(false) - } - }.bind(this)) - map.callback_manager.set('deselect_nodes', function() { - this.direction_arrow.hide() - this.hide_dropdown() - }.bind(this)) - - // svg export - map.callback_manager.set('before_svg_export', function() { - this.direction_arrow.hide() - this.hide_target() - }.bind(this)) -} - -function setup_zoom_callbacks(zoom_container) { - zoom_container.callback_manager.set('zoom.input', function() { - if (this.is_active) { - this.place_at_selected() - } - }.bind(this)) -} +import utils from './utils' +import PlacedDiv from './PlacedDiv' +import completely from './completely' +import DirectionArrow from './DirectionArrow' +import CobraModel from './CobraModel' +import _ from 'underscore' +import { mouse as d3Mouse } from 'd3-selection' -function is_visible() { - return this.placed_div.is_visible() -} - -function toggle(on_off) { - if (on_off===undefined) this.is_active = !this.is_active - else this.is_active = on_off - if (this.is_active) { - this.toggle_start_reaction_listener(true) - if (_.isNull(this.target_coords)) - this.reload_at_selected() - else - this.placed_div.place(this.target_coords) - this.show_dropdown() - this.map.set_status('Click on the canvas or an existing metabolite') - this.direction_arrow.show() - } else { - this.toggle_start_reaction_listener(false) - this.hide_dropdown() - this.map.set_status(null) - this.direction_arrow.hide() +/** + * BuildInput + * @param selection - A d3 selection for the BuildInput. + * @param map - A Map instance. + * @param zoom_container - A ZoomContainer instance. + * @param settings - A Settings instance. + */ +export default class BuildInput { + constructor (selection, map, zoomContainer, settings) { + // set up container + const newSel = selection.append('div').attr('id', 'rxn-input') + this.placed_div = PlacedDiv(newSel, map, { x: 240, y: 0 }) + this.placed_div.hide() + + // set up complete.ly + this.completely = completely(newSel.node(), { backgroundColor: '#eee' }) + + // close button + newSel.append('button').attr('class', 'button input-close-button') + .text('×') + .on('mousedown', () => this.hideDropdown()) + + // map + this.map = map + // set up the reaction direction arrow + const defaultAngle = 90 // degrees + this.direction_arrow = new DirectionArrow(map.sel) + this.direction_arrow.set_rotation(defaultAngle) + this.setUpMapCallbacks(map) + + // zoom container + this.zoom_container = zoomContainer + this.setUpZoomCallbacks(zoomContainer) + + // settings + this.settings = settings + + // toggle off + this.toggle(false) + this.target_coords = null } -} - -function show_dropdown (coords) { - // escape key - this.clear_escape = this.map.key_manager - .add_escape_listener(function() { - this.hide_dropdown() - }.bind(this), true) - // dropdown - this.completely.input.blur() - this.completely.repaint() - this.completely.setText('') - this.completely.input.focus() -} -function hide_dropdown () { - // escape key - if (this.clear_escape) this.clear_escape() - this.clear_escape = null - // dropdown - this.placed_div.hide() - this.completely.input.blur() - this.completely.hideDropDown() -} - -function place_at_selected() { - /** Place autocomplete box at the first selected node. */ - // get the selected node - this.map.deselect_text_labels() - var selected_node = this.map.select_single_node() - if (selected_node==null) return - var coords = { x: selected_node.x, y: selected_node.y } - this.place(coords) -} + setUpMapCallbacks (map) { + // input + map.callback_manager.set('select_metabolite_with_id.input', (selectedNode, coords) => { + if (this.is_active) { + const hasModel = this.reload(selectedNode, coords, false) + if (hasModel) this.showDropdown(coords) + } + this.hideTarget() + }) + map.callback_manager.set('select_selectable.input', (count, selectedNode, coords) => { + this.hideTarget() + if (count === 1 && this.is_active && coords) { + const hasModel = this.reload(selectedNode, coords, false) + if (hasModel) this.showDropdown(coords) + } else { + this.toggle(false) + } + }) + map.callback_manager.set('deselect_nodes', () => { + this.direction_arrow.hide() + this.hideDropdown() + }) + + // svg export + map.callback_manager.set('before_svg_export', () => { + this.direction_arrow.hide() + this.hideTarget() + }) + } -function place(coords) { - this.placed_div.place(coords) - this.direction_arrow.set_location(coords) - this.direction_arrow.show() -} + setUpZoomCallbacks (zoomContainer) { + // TODO this is broken. + // Should place either for selected or for location on zoom or pan. + // zoomContainer.callback_manager.set('zoom_change.input', () => { + // if (this.is_active) { + // this.place_at_selected() + // } + // }) + } -function reload_at_selected() { - /** Reload data for autocomplete box and redraw box at the first selected - node. */ - // get the selected node - this.map.deselect_text_labels() - var selected_node = this.map.select_single_node() - if (selected_node==null) return false - var coords = { x: selected_node.x, y: selected_node.y } - // reload the reaction input - this.reload(selected_node, coords, false) - return true -} + is_visible () { // eslint-disable-line camelcase + return this.placed_div.is_visible() + } -/** - * Reload data for autocomplete box and redraw box at the new coordinates. - */ -function reload (selected_node, coords, starting_from_scratch) { - // Try finding the selected node - if (!starting_from_scratch && !selected_node) { - console.error('No selected node, and not starting from scratch') - return + toggle (onOff) { + if (onOff === undefined) this.is_active = !this.is_active + else this.is_active = onOff + if (this.is_active) { + this.toggleStartReactionListener(true) + let hasModelAndSelection = true + if (_.isNull(this.target_coords)) { + hasModelAndSelection = this.reloadAtSelected() + } else { + this.placed_div.place(this.target_coords) + } + if (hasModelAndSelection) { + this.showDropdown() + this.map.set_status('Click on the canvas or an existing metabolite') + } + this.direction_arrow.show() + } else { + this.toggleStartReactionListener(false) + this.hideDropdown() + this.map.set_status(null) + this.direction_arrow.hide() + } } - this.place(coords) + showDropdown (coords) { + // escape key + this.clear_escape = this.map.key_manager + .add_escape_listener(() => this.hideDropdown(), true) + // dropdown + this.completely.input.blur() + this.completely.repaint() + this.completely.setText('') + this.completely.input.focus() + } - if (this.map.cobra_model===null) { - this.completely.setText('Cannot add: No model.') - return + hideDropdown () { + // escape key + if (this.clear_escape) this.clear_escape() + this.clear_escape = null + // dropdown + this.placed_div.hide() + this.completely.input.blur() + this.completely.hideDropDown() } - // settings - var show_names = this.settings.get_option('identifiers_on_map') === 'name' - var allow_duplicates = this.settings.get_option('allow_building_duplicate_reactions') - - // Find selected - var options = [], - cobra_reactions = this.map.cobra_model.reactions, - cobra_metabolites = this.map.cobra_model.metabolites, - reactions = this.map.reactions, - has_data_on_reactions = this.map.has_data_on_reactions, - reaction_data = this.map.reaction_data, - reaction_data_styles = this.map.reaction_data_styles, - selected_m_name = (selected_node ? (show_names ? selected_node.name : selected_node.bigg_id) : ''), - bold_mets_in_str = function(str, mets) { - return str.replace(new RegExp('(^| )(' + mets.join('|') + ')($| )', 'g'), - '$1$2$3') + place (coords) { + this.placed_div.place(coords) + this.direction_arrow.set_location(coords) + this.direction_arrow.show() } - // for reactions - var reaction_suggestions = {} - for (var bigg_id in cobra_reactions) { - var reaction = cobra_reactions[bigg_id] - var reaction_name = reaction.name - var show_r_name = (show_names ? reaction_name : bigg_id) + /** + * Reload data for autocomplete box and redraw box at the first selected node. + * @return {Boolean} Returns true if a model is present and a node is selected. + */ + reloadAtSelected () { + // get the selected node + this.map.deselect_text_labels() + var selectedNode = this.map.select_single_node() + if (selectedNode === null) return false + var coords = { x: selectedNode.x, y: selectedNode.y } + // reload the reaction input + return this.reload(selectedNode, coords, false) + } - // ignore drawn reactions - if ((!allow_duplicates) && already_drawn(bigg_id, reactions)) { - continue + alreadyDrawn (biggId, reactions) { + for (let drawnId in reactions) { + if (reactions[drawnId].bigg_id === biggId) { + return true + } } + return false + } - // check segments for match to selected metabolite - for (var met_bigg_id in reaction.metabolites) { + /** + * Reload data for autocomplete box and redraw box at the new coordinates. + * @param {} selectedNode - + * @param {} coords - + * @param {Boolean} startingFromScratch - + * @return {Boolean} Returns true if a model is present. + */ + reload (selectedNode, coords, startingFromScratch) { + // Try finding the selected node + if (!startingFromScratch && !selectedNode) { + console.error('No selected node, and not starting from scratch') + return + } - // if starting with a selected metabolite, check for that id - if (starting_from_scratch || met_bigg_id == selected_node.bigg_id) { + this.place(coords) - // don't add suggestions twice - if (bigg_id in reaction_suggestions) continue + if (this.map.cobra_model === null) { + this.completely.setText('Cannot add: No model.') + // this.completely.repaint() + return false + } - var met_name = cobra_metabolites[met_bigg_id].name + // settings + const showNames = this.settings.get('identifiers_on_map') === 'name' + const allowDuplicates = this.settings.get('allow_building_duplicate_reactions') + + // Find selected + const options = [] + const cobraReactions = this.map.cobra_model.reactions + const cobraMetabolites = this.map.cobra_model.metabolites + const reactions = this.map.reactions + const hasDataOnReactions = this.map.hasDataOnReactions + const selectedMetName = (selectedNode ? (showNames ? selectedNode.name : selectedNode.bigg_id) : '') + const boldMetsInStr = (str, mets) => + str.replace(new RegExp('(^| )(' + mets.join('|') + ')($| )', 'g'), '$1$2$3') + + // for reactions + const reactionSuggestions = {} + for (let biggId in cobraReactions) { + const reaction = cobraReactions[biggId] + const reactionName = reaction.name + const showReactionName = (showNames ? reactionName : biggId) + + // ignore drawn reactions + if ((!allowDuplicates) && this.alreadyDrawn(biggId, reactions)) { + continue + } - if (has_data_on_reactions) { - options.push({ reaction_data: reaction.data, - html: ('' + show_r_name + '' + - ': ' + - reaction.data_string), - matches: [show_r_name], - id: bigg_id }) - reaction_suggestions[bigg_id] = true - } else { - // get the metabolite names or IDs - var mets = {} - var show_met_names = [] - var met_id - if (show_names) { - for (met_id in reaction.metabolites) { - var name = cobra_metabolites[met_id].name - mets[name] = reaction.metabolites[met_id] - show_met_names.push(name) - } + // check segments for match to selected metabolite + for (let metBiggId in reaction.metabolites) { + // if starting with a selected metabolite, check for that id + if (startingFromScratch || metBiggId === selectedNode.biggId) { + // don't add suggestions twice + if (biggId in reactionSuggestions) continue + + if (hasDataOnReactions) { + options.push({ + reaction_data: reaction.data, + html: '' + showReactionName + '' + ': ' + reaction.data_string, + matches: [showReactionName], + id: biggId + }) + reactionSuggestions[biggId] = true } else { - mets = utils.clone(reaction.metabolites) - for (met_id in reaction.metabolites) { - show_met_names.push(met_id) + // get the metabolite names or IDs + let mets = {} + const showMetNames = [] + let metId + if (showNames) { + for (metId in reaction.metabolites) { + var name = cobraMetabolites[metId].name + mets[name] = reaction.metabolites[metId] + showMetNames.push(name) + } + } else { + mets = utils.clone(reaction.metabolites) + for (metId in reaction.metabolites) { + showMetNames.push(metId) + } } + const showGeneNames = _.flatten( + reaction.genes.map(g => [ g.name, g.biggId ]) + ) + // get the reaction string + const reactionString = CobraModel.build_reaction_string(mets, + reaction.reversibility, + reaction.lower_bound, + reaction.upper_bound) + // make the matches list and filter out any missing entries (e.g. + // missing gene names from model + const matches = [ showReactionName ].concat(showMetNames).concat(showGeneNames).filter(x => x) + options.push({ + html: ('' + showReactionName + '' + '\t' + + boldMetsInStr(reactionString, [selectedMetName])), + matches, + id: biggId + }) + reactionSuggestions[biggId] = true } - var show_gene_names = _.flatten(reaction.genes.map(function(g_obj) { - return [ g_obj.name, g_obj.bigg_id ] - })) - // get the reaction string - var reaction_string = CobraModel.build_reaction_string(mets, - reaction.reversibility, - reaction.lower_bound, - reaction.upper_bound) - options.push({ - html: ('' + show_r_name + '' + '\t' + - bold_mets_in_str(reaction_string, [selected_m_name])), - matches: [ show_r_name ].concat(show_met_names).concat(show_gene_names), - id: bigg_id - }) - reaction_suggestions[bigg_id] = true } } } - } - // Generate the array of reactions to suggest and sort it - var sort_fn - if (has_data_on_reactions) { - sort_fn = function(x, y) { - return Math.abs(y.reaction_data) - Math.abs(x.reaction_data) - } - } else { - sort_fn = function(x, y) { - return (x.html.toLowerCase() < y.html.toLowerCase() ? -1 : 1) - } - } - options = options.sort(sort_fn) - // set up the box with data - var complete = this.completely - complete.options = options - - // TODO test this behavior - // if (strings_to_display.length==1) complete.setText(strings_to_display[0]) - // else complete.setText("") - complete.setText('') - - var direction_arrow = this.direction_arrow, - check_and_build = function(id) { - if (id !== null) { - // make sure the selected node exists, in case changes were made in the meantime - if (starting_from_scratch) { - this.map.new_reaction_from_scratch(id, - coords, - direction_arrow.get_rotation()) - } else { - if (!(selected_node.node_id in this.map.nodes)) { - console.error('Selected node no longer exists') - this.hide_dropdown() - return + // Generate the array of reactions to suggest and sort it + const sortFn = hasDataOnReactions + ? (x, y) => Math.abs(y.reactionData) - Math.abs(x.reactionData) + : (x, y) => x.html.toLowerCase() < y.html.toLowerCase() ? -1 : 1 + + // set up the box with data + this.completely.options = options.sort(sortFn) + + // TODO test this behavior + // if (strings_to_display.length==1) this.completely.setText(strings_to_display[0]) + // else this.completely.setText("") + this.completely.setText('') + + const checkAndBuild = id => { + if (id !== null) { + // make sure the selected node exists, in case changes were made in the meantime + if (startingFromScratch) { + this.map.new_reaction_from_scratch(id, + coords, + this.direction_arrow.get_rotation()) + } else { + if (!(selectedNode.node_id in this.map.nodes)) { + console.error('Selected node no longer exists') + this.hideDropdown() + return + } + this.map.new_reaction_for_metabolite(id, + selectedNode.node_id, + this.direction_arrow.get_rotation()) } - this.map.new_reaction_for_metabolite(id, - selected_node.node_id, - direction_arrow.get_rotation()) } } - }.bind(this) - complete.onEnter = function(id) { - this.setText('') - this.onChange('') - check_and_build(id) - } - - //definitions - function already_drawn (bigg_id, reactions) { - for (var drawn_id in reactions) { - if (reactions[drawn_id].bigg_id === bigg_id) - return true + this.completely.onEnter = function (id) { + this.setText('') + this.onChange('') + checkAndBuild(id) } - return false - } -} -/** - * Toggle listening for a click to place a new reaction on the canvas. - */ -function toggle_start_reaction_listener (on_off) { - if (on_off === undefined) { - this.start_reaction_listener = !this.start_reaction_listener - } else if (this.start_reaction_listener === on_off) { - return - } else { - this.start_reaction_listener = on_off + return true } - if (this.start_reaction_listener) { - this.map.sel.on('click.start_reaction', function(node) { - // TODO fix this hack - if (this.direction_arrow.dragging) return - // reload the reaction input - var coords = { x: d3_mouse(node)[0], - y: d3_mouse(node)[1] } - // unselect metabolites - this.map.deselect_nodes() - this.map.deselect_text_labels() - // reload the reaction input - this.reload(null, coords, true) - // generate the target symbol - this.show_target(this.map, coords) - // show the dropdown - this.show_dropdown(coords) - }.bind(this, this.map.sel.node())) - this.map.sel.classed('start-reaction-cursor', true) - } else { - this.map.sel.on('click.start_reaction', null) - this.map.sel.classed('start-reaction-cursor', false) - this.hide_target() + /** + * Toggle listening for a click to place a new reaction on the canvas. + */ + toggleStartReactionListener (onOff) { + if (onOff === undefined) { + this.start_reaction_listener = !this.start_reaction_listener + } else if (this.start_reaction_listener === onOff) { + return + } else { + this.start_reaction_listener = onOff + } + + if (this.start_reaction_listener) { + const node = this.map.sel.node() + this.map.sel.on('click.start_reaction', () => { + // TODO fix this hack + if (this.direction_arrow.dragging) return + // reload the reaction input + var coords = { + x: d3Mouse(node)[0], + y: d3Mouse(node)[1] + } + // unselect metabolites + this.map.deselect_nodes() + this.map.deselect_text_labels() + // reload the reaction input + const hasModel = this.reload(null, coords, true) + if (hasModel) { + // show the dropdown + this.showDropdown(coords) + } + // generate the target symbol + this.showTarget(this.map, coords) + }) + this.map.sel.classed('start-reaction-cursor', true) + } else { + this.map.sel.on('click.start_reaction', null) + this.map.sel.classed('start-reaction-cursor', false) + this.hideTarget() + } } -} -function hide_target () { - if (this.target_coords) { - this.map.sel.selectAll('.start-reaction-target').remove() + hideTarget () { + if (this.target_coords) { + this.map.sel.selectAll('.start-reaction-target').remove() + } + this.target_coords = null } - this.target_coords = null -} -function show_target (map, coords) { - var s = map.sel.selectAll('.start-reaction-target').data([12, 5]) - s.enter() - .append('circle') + showTarget (map, coords) { + var s = map.sel.selectAll('.start-reaction-target').data([12, 5]) + s.enter() + .append('circle') .classed('start-reaction-target', true) .attr('r', function (d) { return d }) .style('stroke-width', 4) .merge(s) - .style('visibility', 'visible') - .attr('transform', 'translate(' + coords.x + ',' + coords.y + ')') - this.target_coords = coords + .style('visibility', 'visible') + .attr('transform', 'translate(' + coords.x + ',' + coords.y + ')') + this.target_coords = coords + } } diff --git a/src/Builder.css b/src/Builder.css index 242deeb1..7be819c0 100644 --- a/src/Builder.css +++ b/src/Builder.css @@ -45,12 +45,22 @@ resizes. */ } /* The zoom container classes. */ -.escher-zoom-container, .escher-3d-transform-container, svg.escher-svg { +.escher-container .escher-zoom-container, +.escher-container .escher-3d-transform-container, +.escher-container svg.escher-svg { width: 100% !important; height: 100% !important; overflow: hidden; } +/* SVG text should not be selectable */ +.escher-container svg text { + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; +} + /* Status */ .escher-container #status { position:absolute; @@ -60,51 +70,8 @@ resizes. */ background-color: white; font-size: 16px } -/* Menus */ -.escher-container #menu { - display: block; - margin: 5px auto 0 auto; - border: 1px solid #ddd; - background-color: rgba(255, 255, 255, 0.95); - border-radius: 0px; -} -.escher-container .help-button { - float: right; - padding: 0 5px; - font-size: 12px; - background-color: rgb(245, 245, 245); -} -.escher-container .dropdown-menu { - border: 1px solid #ddd; - background-color: rgba(255, 255, 255, 0.95); - border-radius: 0px; - margin: 0; - text-align: left; -} -.escher-container .dropdown-menu>li>a { - font-size: 15px; -} -.escher-container .dropdown-menu>.escher-disabled>a { - color: #E0E0E0; - pointer-events: none; -} -.escher-container .dropdown { - background-color: rgba(255, 255, 255, 0.95); -} -@media (max-width: 550px) { - .escher-container .dropdown-button { - padding: 5px 9px; - } -} -@media (min-width: 550px) { - .escher-container .dropdown-button { - font-size: 18px; - } - .escher-container .help-button { - font-size: 16px; - } -} -/* Search */ + +/* Search & Menu */ .escher-container .search-menu-container { position: absolute; width: 100%; @@ -126,240 +93,30 @@ resizes. */ width: 410px; } } -.escher-container .search-container { - display: block; - background: rgba(255, 255, 255, 0.95); - padding: 3px; - border: 1px solid #DDD; - margin: 2px 0 0 0; -} -.escher-container .search-bar { - display: inline-block; - border: 1px solid #DDD; - margin-right: 4px; - width: 114px; - height: 29px; - border-radius: 3px; -} -.escher-container .search-counter { - display: inline-block; - padding: 0 8px; -} -/* Settings */ -.escher-container .settings-box-background { - display: block; - position: absolute; - top: 0; - left: 0; - width: 100%; - height: 100%; - z-index: 9; - background: rgba(0, 0, 0, 0.4); - padding: 5% 0 5% 0; - text-align: center; -} -.escher-container .settings-box-container { - display: inline-block; - position: relative; - width: 90%; - max-width: 520px; - height: 100%; - z-index: 10; -} -.escher-container .settings-button { - position: absolute; - top: 5px; - right: 20px; - z-index: 10; -} -.escher-container .settings-button-close { - right: 60px; -} -.escher-container .settings-box { - display: inline-block; - max-height: 100%; - width: 100%; - /* max-width: 520px; */ - overflow-y: scroll; - overflow-x: hidden; - background: rgba(255, 255, 255, 0.95); - padding: 8px; - margin: 0; - border: 1px solid #DDD; - text-align: left; -} -.escher-container .settings-section-heading-large { - font-size: 17px; - font-weight: bold; - margin-top: 15px; -} -.escher-container .settings-section-heading { - font-weight: bold; - margin-top: 15px; -} -.escher-container .settings-table { - width: 100%; -} -.escher-container .settings-table td { - padding: 3px 5px; -} -.escher-container td.options-label { - width: 88px; -} -.escher-container td.options-label-wide { - width: 192px; -} -.escher-container .settings-number { - text-align: center; - color: #AAA; - font-style: italic; -} -.escher-container .input-cell { - width: 23%; - /* padding: 3px 5px; */ - font-size: 13px; -} -.escher-container .scale-bar-input { - width: 100%; - text-align: left; -} -.escher-container .no-data-input { - width: 23%; - margin: 0 4px 0 4px; -} -.escher-container label.option-group { - margin: 0 10px 0 0; -} -.escher-container label.option-group span { - margin: 0 0 0 4px; -} -.escher-container label.full-line { - width: 100%; -} -.escher-container label { - font-weight: inherit; -} -.escher-container .settings-tip { - font-style: italic; -} -/* Live scale */ -.escher-container .scale-editor { - position: relative; - width: 100%; - height: 190px; - font-size: 12px; -} -.escher-container .scale-editor .centered { - position: absolute; - width: 440px; - left: 35px; - top: 0px; -} -.escher-container .scale-editor .data-not-loaded { - position: absolute; - z-index: 5; - left: 60px; - top: 25px; - text-align: center; - width: 400px; - font-size: 15px; - color: #B19EC0; -} -.escher-container .scale-editor .add { - position: absolute; - top: 0px; - right: 0px; - width: 20px; - cursor: pointer; -} -.escher-container .scale-editor .trash-container { - position: absolute; - top: 0px; - left: 0px; - width: 420px; - height: 20px; -} -.escher-container .scale-editor .trash { - position: absolute; - top: 0px; - left: 0px; - cursor: pointer; -} -.escher-container .scale-editor .scale-svg { - position: absolute; - width: 440px; - height: 80px; - top: 20px; - left: 0px; -} -.escher-container .scale-editor .input-container { - position: absolute; - top: 56px; - left: 0px; - width: 420px; -} -.escher-container .scale-editor .input-container input { - position: absolute; - left: 0px; - top: 0px; -} -.escher-container .scale-editor input[disabled] { - background-color: #F1ECFA; -} -.escher-container .scale-editor .row-label { - position: absolute; - left: 0px; -} -.escher-container .scale-editor .input-set { - position: absolute; - top: 0px; - box-shadow: 0px 2px 14px rgb(197, 197, 197); -} -.escher-container .scale-editor .input-set.selected-set { - z-index: 5; -} -.escher-container .scale-editor .domain-type-picker { - position: absolute; - top: 0px; - right: 0px; - height: 14px; - background-color: rgb(232, 232, 232); -} -.escher-container .scale-editor .picker rect { - color: black; - opacity: 0.4; -} -.escher-container .scale-editor .no-data { - position: absolute; - left: 0px; - width: 100%; -} -.escher-container .scale-editor .no-data-heading { - font-weight: bold; -} -.escher-container .scale-editor .no-data .input-group { - position: absolute; - top: 0px; - left: 0px; -} -.escher-container .scale-editor .no-data .input-group span, -.escher-container .scale-editor .no-data .input-group input { - position: absolute; - top: 17px; -} /* Reaction input */ .escher-container #rxn-input { z-index: 10; + width: 200px; +} +.escher-container .input-close-button { + position: absolute; + right: 0px; + width: 18px; + bottom: 0px; + padding: 0px; + border-width: 0px; + margin: 0px; + background: none; + font-size: 20px; + font-weight: normal; + top: -8px; } .escher-container .input-close-button:hover { color: #ff3333; font-weight: bold; } -.escher-container .light { - color: #8b8b8b; - font-weight: normal; -} + /* text edit input */ .escher-container #text-edit-input input { width: 500px; diff --git a/src/Builder.jsx b/src/Builder.jsx index 62427022..ec77b6dc 100644 --- a/src/Builder.jsx +++ b/src/Builder.jsx @@ -3,12 +3,6 @@ */ /** @jsx h */ -import preact, { h } from 'preact' -import ReactWrapper from './ReactWrapper' -import BuilderSettingsMenu from './BuilderSettingsMenu' -import ButtonPanel from './ButtonPanel' -import BuilderMenuBar from './BuilderMenuBar' -import SearchBar from './SearchBar' import * as utils from './utils' import BuildInput from './BuildInput' import ZoomContainer from './ZoomContainer' @@ -20,6 +14,11 @@ import Settings from './Settings' import TextEditInput from './TextEditInput' import QuickJump from './QuickJump' import dataStyles from './data_styles' +import renderWrapper from './renderWrapper' +import SettingsMenu from './SettingsMenu' +import MenuBar from './MenuBar' +import SearchBar from './SearchBar' +import ButtonPanel from './ButtonPanel' import TooltipContainer from './TooltipContainer' import DefaultTooltip from './DefaultTooltip' import _ from 'underscore' @@ -34,10 +33,11 @@ import './Builder.css' // Import CSS as a string to embed. This also works from lib because css/src get // uploaded to NPM. -import builder_embed from '!!raw-loader!./Builder-embed.css' +// eslint-disable-next-line import/no-webpack-loader-syntax +import builderEmbed from '!!raw-loader!./Builder-embed.css' class Builder { - constructor (map_data, model_data, embedded_css, selection, options) { + constructor (mapData, modelData, embeddedCss, selection, options) { // Defaults if (!selection) { selection = d3Select('body').append('div') @@ -54,21 +54,20 @@ class Builder { if (!options) { options = {} } - if (!embedded_css) { - embedded_css = builder_embed + if (!embeddedCss) { + embeddedCss = builderEmbed } - this.map_data = map_data - this.model_data = model_data - this.embedded_css = embedded_css + this.map_data = mapData + this.model_data = modelData + this.embeddedCss = embeddedCss this.selection = selection this.menu_div = null this.button_div = null - this.settings_div = null - this.settingsMenuRef = null this.search_bar_div = null this.searchBarRef = null this.semanticOptions = null + this.mode = 'zoom' // apply this object as data for the selection this.selection.datum(this) @@ -78,11 +77,11 @@ class Builder { this.has_custom_reaction_styles = Boolean(options.reaction_styles) // set defaults - this.options = utils.set_options(options, { + const optionsWithDefaults = utils.set_options(options, { // view options menu: 'all', scroll_behavior: 'pan', - use_3d_transform: !utils.check_browser('safari'), + use_3d_transform: false, enable_editing: true, enable_keys: true, enable_search: true, @@ -136,7 +135,8 @@ class Builder { ], // Extensions tooltip_component: DefaultTooltip, - enable_tooltips: ['label', 'object'], + enable_tooltips: ['label'], + enable_keys_with_tooltip: true, reaction_scale_preset: null, metabolite_scale_preset: null, // Callbacks @@ -156,21 +156,6 @@ class Builder { 'because UI elements are html-based.') } - // Warn if scales are too short - ;['reaction_scale', 'metabolite_scale'].map(scaleType => { - if (this.options[scaleType] && this.options[scaleType].length < 2) { - console.warn(`Bad value for option "${scaleType}". Scales must have at least 2 points.`) - } - }) - - // Initialize the settings - var set_option = function (option, new_value) { - this.options[option] = new_value - }.bind(this) - var get_option = function (option) { - return this.options[option] - }.bind(this) - // The options that are erased when the settings menu is canceled var conditional = [ 'identifiers_on_map', @@ -195,92 +180,89 @@ class Builder { 'metabolite_no_data_color', 'metabolite_no_data_size' ] - this.settings = new Settings(set_option, get_option, conditional) + // this.options and this.settings used to have different functions, but now + // they are aliases + this.settings = new Settings(optionsWithDefaults, conditional) + + // Warn if scales are too short + ;['reaction_scale', 'metabolite_scale'].map(scaleType => { + if (this.settings.get(scaleType) && this.settings.get(scaleType).length < 2) { + console.warn(`Bad value for option "${scaleType}". Scales must have at least 2 points.`) + } + }) // Set up this callback manager this.callback_manager = CallbackManager() - if (this.options.first_load_callback !== null) { - this.callback_manager.set('first_load', this.options.first_load_callback) + const firstLoadCallback = this.settings.get('first_load_callback') + if (firstLoadCallback !== null) { + this.callback_manager.set('first_load', () => { + firstLoadCallback(this) + }) } // Set up the zoom container this.zoom_container = new ZoomContainer(this.selection, - this.options.scroll_behavior, - this.options.use_3d_transform, - this.options.fill_screen) + this.settings.get('scroll_behavior'), + this.settings.get('use_3d_transform'), + this.settings.get('fill_screen')) // Zoom container status changes - this.zoom_container.callback_manager.set('svg_start', function () { - if (this.map) this.map.set_status('Drawing ...') - }.bind(this)) - this.zoom_container.callback_manager.set('svg_finish', function () { - if (this.map) this.map.set_status('') - }.bind(this)) - this.zoom_container.callback_manager.set('zoomChange', function () { - if (this.options.semantic_zoom) { + // this.zoom_container.callback_manager.set('svg_start', () => { + // if (this.map) this.map.set_status('Drawing ...') + // }) + // this.zoom_container.callback_manager.set('svg_finish', () => { + // if (this.map) this.map.set_status('') + // }) + this.zoom_container.callback_manager.set('zoom_change', () => { + if (this.settings.get('semantic_zoom')) { const scale = this.zoom_container.window_scale - const optionObject = this.options.semantic_zoom - .sort((a, b) => a.zoomLevel - b.zoomLevel) - .find(a => a.zoomLevel > scale) + const optionObject = this.settings.get('semantic_zoom') + .sort((a, b) => a.zoomLevel - b.zoomLevel) + .find(a => a.zoomLevel > scale) if (optionObject) { - Object.entries(optionObject.options).map(([option, value]) => { - if (this.options[option] !== value) { - this.settings.set_conditional(option, value) - this._update_data(false, true) + let didChange = false + _.mapObject(optionObject.options, (value, key) => { + if (this.settings.get(key) !== value) { + this.settings.set(key, value) + didChange = true } }) + if (didChange) this._updateData(false, true) } } - }.bind(this)) - - // Set up the tooltip container - this.tooltip_container = new TooltipContainer(this.selection, - this.options.tooltip_component, - this.zoom_container) + }) + this.settings.streams.use_3d_transform.onValue(val => { + this.zoom_container.set_use_3d_transform(val) + }) // Status in both modes - this._create_status(this.selection) + this._createStatus(this.selection) // Load the model, map, and update data in both this.load_model(this.model_data, false) // Append the bars and menu divs to the document var s = this.selection - .append('div').attr('class', 'search-menu-container') - .append('div').attr('class', 'search-menu-container-inline') + .append('div').attr('class', 'search-menu-container') + .append('div').attr('class', 'search-menu-container-inline') this.menu_div = s.append('div') this.search_bar_div = s.append('div') this.button_div = this.selection.append('div') - this.settings_div = this.selection.append('div') // Need to defer map loading to let webpack CSS load properly _.defer(() => { this.load_map(this.map_data, false) - const message_fn = this._reaction_check_add_abs() - if (message_fn !== null) { - this._update_data(true, true) - } - - _.mapObject(this.settings.streams, (stream, key) => { - stream.onValue(value => { - this.pass_settings_menu_props({ - ...this.options, - map: this.map, - settings: this.settings - }) - if (key === 'reaction_styles' || key === 'metabolite_styles') { - this._update_data(false, true) - } - }) - }) + const messageFn = this._reactionCheckAddAbs() + this._updateData(true, true) // Setting callbacks. TODO enable atomic updates. Right now, every time the // menu closes, everything is drawn. - this.settings.status_bus.onValue(x => { + this.settings.statusBus.onValue(x => { if (x === 'accept') { - this._update_data(true, true, [ 'reaction', 'metabolite' ], false) + this._updateData(true, true, [ 'reaction', 'metabolite' ], false) if (this.zoom_container !== null) { - const new_behavior = this.settings.get_option('scroll_behavior') - this.zoom_container.set_scroll_behavior(new_behavior) + // TODO make this automatic + const newBehavior = this.settings.get('scroll_behavior') + this.zoom_container.set_scroll_behavior(newBehavior) } if (this.map !== null) { this.map.draw_all_nodes(false) @@ -293,108 +275,103 @@ class Builder { // Set up quick jump this._setup_quick_jump(this.selection) - if (message_fn !== null) setTimeout(message_fn, 500) + if (messageFn !== null) setTimeout(messageFn, 500) // Finally run callback _.defer(() => this.callback_manager.run('first_load', this)) }) } + // builder.options is deprecated + get options () { + throw new Error('builder.options is deprecated. Use builder.settings.get() ' + + 'and builder.settings.set() instead.') + } + set options (_) { + throw new Error('builder.options is deprecated. Use builder.settings.get() ' + + 'and builder.settings.set() instead.') + } + /** * For documentation of this function, see docs/javascript_api.rst. */ - load_model (model_data, should_update_data) { - if (_.isUndefined(should_update_data)) { - should_update_data = true - } - + load_model (modelData, shouldUpdateData = true) { // eslint-disable-line camelcase // Check the cobra model - if (_.isNull(model_data)) { + if (_.isNull(modelData)) { this.cobra_model = null } else { - this.cobra_model = CobraModel.from_cobra_json(model_data) + this.cobra_model = CobraModel.from_cobra_json(modelData) } if (this.map) { this.map.cobra_model = this.cobra_model - if (should_update_data) { - this._update_data(true, false) + if (shouldUpdateData) { + this._updateData(true, false) } - if (this.settings.get_option('highlight_missing')) { + if (this.settings.get('highlight_missing')) { this.map.draw_all_reactions(false, false) } } - this.callback_manager.run('load_model', null, model_data, should_update_data) + this.callback_manager.run('load_model', null, modelData, shouldUpdateData) } /** * For documentation of this function, see docs/javascript_api.rst */ - load_map (map_data, should_update_data) { - if (_.isUndefined(should_update_data)) { - should_update_data = true - } - + load_map (mapData, shouldUpdateData = true) { // eslint-disable-line camelcase // Store map options that might be changed by semantic_zoom function const tempSemanticOptions = {} - if (this.options.semantic_zoom) { - for (let level of this.options.semantic_zoom) { + if (this.settings.get('semantic_zoom')) { + for (let level of this.settings.get('semantic_zoom')) { Object.keys(level.options).map(option => { if (tempSemanticOptions[option] === undefined) { - tempSemanticOptions[option] = this.options[option] + tempSemanticOptions[option] = this.settings.get(option) } }) } this.semanticOptions = Object.assign({}, tempSemanticOptions) } - // Begin with some definitions - var selectable_mousedown_enabled = true - var shift_key_on = false - // remove the old builder utils.remove_child_nodes(this.zoom_container.zoomed_sel) - var zoomed_sel = this.zoom_container.zoomed_sel - var svg = this.zoom_container.svg + const zoomedSel = this.zoom_container.zoomed_sel + const svg = this.zoom_container.svg // remove the old map side effects if (this.map) { this.map.key_manager.toggle(false) } - if (map_data !== null) { + if (mapData !== null) { // import map - this.map = Map.from_data(map_data, + this.map = Map.from_data(mapData, svg, - this.embedded_css, - zoomed_sel, + this.embeddedCss, + zoomedSel, this.zoom_container, this.settings, this.cobra_model, - this.options.enable_search) + this.settings.get('enable_search')) } else { // new map this.map = new Map(svg, - this.embedded_css, - zoomed_sel, + this.embeddedCss, + zoomedSel, this.zoom_container, this.settings, this.cobra_model, - this.options.canvas_size_and_loc, - this.options.enable_search) + this.settings.get('canvas_size_and_loc'), + this.settings.get('enable_search')) } // Connect status bar this._setup_status(this.map) - // Connect status bar - this._setup_status(this.map) - // Set the data for the map - if (should_update_data) { - this._update_data(false, true) + if (shouldUpdateData) { + this._updateData(false, true) } // Set up the reaction input with complete.ly @@ -405,98 +382,96 @@ class Builder { this.text_edit_input = new TextEditInput(this.selection, this.map, this.zoom_container) - // Connect the tooltip - this.tooltip_container.setup_map_callbacks(this.map) - // Set up the Brush - this.brush = new Brush(zoomed_sel, false, this.map, '.canvas-group') - this.map.canvas.callback_manager.set('resize', function () { - this.brush.toggle(true) - }.bind(this)) + this.brush = new Brush(zoomedSel, false, this.map, '.canvas-group') + // reset brush when canvas resizes in brush mode + this.map.canvas.callback_manager.set('resize', () => { + if (this.mode === 'brush') this.brush.toggle(true) + }) // Set up the modes - this._setup_modes(this.map, this.brush, this.zoom_container) - - // Set up settings menu - preact.render( - { this.settingsMenuRef = instance }} - closeMenu={() => this.pass_settings_menu_props({display: false})} - />, - this.settings_div.node(), - this.settings_div.node().children.length > 0 - ? this.settings_div.node().firstChild - : undefined - ) + this._setUpModes(this.map, this.brush, this.zoom_container) + + // Set up menus + this.setUpSettingsMenu() + // share a parent container for menu bar and search bar + const sel = this.selection + .append('div').attr('class', 'search-menu-container') + .append('div').attr('class', 'search-menu-container-inline') + this.setUpMenuBar(sel) + this.setUpSearchBar(sel) + this.setUpButtonPanel() - if (this.options.enable_search) { - this.renderSearchBar(true) - } - - // Set up key manager - var keys = this._get_keys( - this.map, + // Set up the tooltip container + this.tooltip_container = new TooltipContainer( + this.selection, + this.settings.get('tooltip_component'), this.zoom_container, - this.search_bar, - this.settings_bar, - this.options.enable_editing, - this.options.full_screen_button + this.map ) + + // Set up key manager + const keys = this.getKeys() this.map.key_manager.assigned_keys = keys // Tell the key manager about the reaction input and search bar this.map.key_manager.input_list = [ this.build_input, this.searchBarRef, () => this.settingsMenuRef, - this.text_edit_input, - this.tooltip_container + this.text_edit_input ] + if (!this.settings.get('enable_keys_with_tooltip')) { + this.map.key_manager.input_list.push(this.tooltip_container) + } + // Make sure the key manager remembers all those changes this.map.key_manager.update() // Turn it on/off - this.map.key_manager.toggle(this.options.enable_keys) + this.map.key_manager.toggle(this.settings.get('enable_keys')) // Disable clears - if (this.options.disabled_buttons === null) { - this.options.disabled_buttons = []; + const newDisabledButtons = this.settings.get('disabled_buttons') || [] + if (!this.settings.get('reaction_data')) { + newDisabledButtons.push('Clear reaction data') + } + if (!this.settings.get('gene_data')) { + newDisabledButtons.push('Clear gene data') } - if (!this.options.reaction_data && this.options.disabled_buttons) { - this.options.disabled_buttons.push('Clear reaction data') + if (!this.settings.get('metabolite_data')) { + newDisabledButtons.push('Clear metabolite data') } - if (!this.options.gene_data && this.options.disabled_buttons) { - this.options.disabled_buttons.push('Clear gene data') + if (!this.settings.get('enable_search')) { + newDisabledButtons.push('Find') } - if (!this.options.metabolite_data && this.options.disabled_buttons) { - this.options.disabled_buttons.push('Clear metabolite data') + if (!this.settings.get('enable_editing')) { + newDisabledButtons.push('Show control points') } + this.settings.set('disabled_buttons', newDisabledButtons) - // Setup selection box - if (this.options.zoom_to_element) { - const type = this.options.zoom_to_element.type - const element_id = this.options.zoom_to_element.id + // Set up selection box + if (this.settings.get('zoom_to_element')) { + const type = this.settings.get('zoom_to_element').type + const elementId = this.settings.get('zoom_to_element').id if (_.isUndefined(type) || [ 'reaction', 'node' ].indexOf(type) === -1) { throw new Error('zoom_to_element type must be "reaction" or "node"') } - if (_.isUndefined(element_id)) { + if (_.isUndefined(elementId)) { throw new Error('zoom_to_element must include id') } if (type === 'reaction') { - this.map.zoom_to_reaction(element_id) + this.map.zoom_to_reaction(elementId) } else if (type === 'node') { - this.map.zoom_to_node(element_id) + this.map.zoom_to_node(elementId) } - } else if (map_data !== null) { + } else if (mapData !== null) { this.map.zoom_extent_canvas() } else { - if (this.options.starting_reaction !== null && this.cobra_model !== null) { + if (this.settings.get('starting_reaction') !== null && this.cobra_model !== null) { // Draw default reaction if no map is provided - var size = this.zoom_container.get_size() - var start_coords = { x: size.width / 2, y: size.height / 4 } - this.map.new_reaction_from_scratch(this.options.starting_reaction, - start_coords, 90) + const size = this.zoom_container.get_size() + const startCoords = { x: size.width / 2, y: size.height / 4 } + this.map.new_reaction_from_scratch(this.settings.get('starting_reaction'), + startCoords, 90) this.map.zoom_extent_nodes() } else { this.map.zoom_extent_canvas() @@ -504,14 +479,14 @@ class Builder { } // Start in zoom mode for builder, view mode for viewer - if (this.options.enable_editing) { + if (this.settings.get('enable_editing')) { this.zoom_mode() } else { this.view_mode() } // confirm before leaving the page - if (this.options.enable_editing) { + if (this.settings.get('enable_editing')) { this._setup_confirm_before_exit() } @@ -519,114 +494,230 @@ class Builder { this.map.draw_everything() } - renderMenu (mode) { - const menuDivNode = this.menu_div.node() - if (this.options.menu === 'all') { - preact.render( - { - // Revert options changed by semanticZoom to their original values if option is active - if (this.semanticOptions) { - Object.entries(this.semanticOptions).map(([key, value]) => { - this.settings.set_conditional(key, value) - }) - this._update_data() - } - this.map.save() - }} - loadMap={(file) => this.load_map(file)} - saveSvg={() => this.map.save_svg()} - savePng={() => this.map.save_png()} - clearMap={() => this.map.clear_map()} - loadModel={file => this.load_model(file, true)} - updateRules={() => this.map.convert_map()} - loadReactionData={file => { - this.set_reaction_data(file) - this._set_mode(mode) - }} - loadGeneData={file => { - this.set_gene_data(file) - this._set_mode(mode) - }} - loadMetaboliteData={file => { - this.set_metabolite_data(file) - this._set_mode(mode) - }} - setMode={(newMode) => this._set_mode(newMode)} - deleteSelected={() => this.map.delete_selected()} - undo={() => this.map.undo_stack.undo()} - redo={() => this.map.undo_stack.redo()} - togglePrimary={() => this.map.toggle_selected_node_primary()} - cyclePrimary={() => this.map.cycle_primary_node()} - selectAll={() => this.map.select_all()} - selectNone={() => this.map.select_none()} - invertSelection={() => this.map.invert_selection()} - zoomIn={() => this.zoom_container.zoom_in()} - zoomOut={() => this.zoom_container.zoom_out()} - zoomExtentNodes={() => this.map.zoom_extent_nodes()} - zoomExtentCanvas={() => this.map.zoom_extent_canvas()} - search={() => this.renderSearchBar()} - toggleBeziers={() => this.map.toggle_beziers()} - renderSettingsMenu={() => this.pass_settings_menu_props({ - ...this.options, - map: this.map, - settings: this.settings, - display: true - })} - />, - menuDivNode, - menuDivNode.children.length > 0 // If there is already a div, re-render it. Otherwise make a new one - ? menuDivNode.firstChild - : undefined - ) - } + /** + * Function to pass props for the settings menu. Run without an argument to + * rerender the component + * @param {Object} props - Props that the settings menu will use + */ + passPropsSettingsMenu (props = {}) { + this.callback_manager.run('passPropsSettingsMenu', null, props) + } + + /** + * Initialize the settings menu + */ + setUpSettingsMenu () { + this.settingsMenuRef = null + renderWrapper( + SettingsMenu, + instance => { this.settingsMenuRef = instance }, + passProps => this.callback_manager.set('passPropsSettingsMenu', passProps), + this.selection.append('div').node() + ) + this.passPropsSettingsMenu({ + display: false, + settings: this.settings, + map: this.map + }) + + // redraw menu when settings change + _.mapObject(this.settings.streams, (stream, key) => { + stream.onValue(value => { + this.passPropsSettingsMenu() + }) + }) + + // recalculate data when switching to/from absolute value + this.settings.streams.reaction_styles + .map(x => _.contains(x, 'abs')) + .skipDuplicates() + .onValue(() => this._updateData(false, true)) + this.settings.streams.metabolite_styles + .map(x => _.contains(x, 'abs')) + .skipDuplicates() + .onValue(() => this._updateData(false, true)) + } + + /** + * Function to pass props for the menu bar + * @param {Object} props - Props that the menu bar will use + */ + passPropsMenuBar (props = {}) { + this.callback_manager.run('passPropsMenuBar', null, props) + } + + /** + * Initialize the menu bar + * @param {D3 Selection} sel - The d3 selection to render in. + */ + setUpMenuBar (sel) { + this.menuBarRef = null + renderWrapper( + MenuBar, + instance => { this.menuBarRef = instance }, + passProps => this.callback_manager.set('passPropsMenuBar', passProps), + sel.append('div').node() + ) + this.passPropsMenuBar({ + display: this.settings.get('menu') === 'all', + settings: this.settings, + sel: this.selection, + mode: this.mode, + map: this.map, + saveMap: () => { + // Revert options changed by semanticZoom to their original values if option is active + if (this.semanticOptions) { + Object.entries(this.semanticOptions).map(([key, value]) => { + this.settings.set(key, value) + }) + this._updateData() + } + this.map.save() + }, + loadMap: (file) => this.load_map(file), + saveSvg: () => this.map.save_svg(), + savePng: () => this.map.save_png(), + clearMap: () => { + this.map.clear_map() + this.callback_manager.run('clear_map') + }, + loadModel: file => this.load_model(file, true), + clearModel: () => { + this.load_model(null) + this.callback_manager.run('clear_model') + }, + updateRules: () => this.map.convert_map(), + setReactionData: d => this.set_reaction_data(d), + setGeneData: d => this.set_gene_data(d), + setMetaboliteData: d => this.set_metabolite_data(d), + setMode: mode => this._setMode(mode), + deleteSelected: () => this.map.delete_selected(), + undo: () => this.map.undo_stack.undo(), + redo: () => this.map.undo_stack.redo(), + togglePrimary: () => this.map.toggle_selected_node_primary(), + cyclePrimary: () => this.map.cycle_primary_node(), + selectAll: () => this.map.select_all(), + selectNone: () => this.map.select_none(), + invertSelection: () => this.map.invert_selection(), + zoomIn: () => this.zoom_container.zoom_in(), + zoomOut: () => this.zoom_container.zoom_out(), + zoomExtentNodes: () => this.map.zoom_extent_nodes(), + zoomExtentCanvas: () => this.map.zoom_extent_canvas(), + search: () => this.passPropsSearchBar({ display: true }), + toggleBeziers: () => this.map.toggle_beziers(), + renderSettingsMenu: () => this.passPropsSettingsMenu({ display: true }) + }) + + // redraw when beziers change + this.map.callback_manager.set('toggle_beziers', () => { + this.passPropsMenuBar() + }) + + // redraw when disabledButtons change + this.settings.streams.disabled_buttons.onValue(value => { + this.passPropsMenuBar() + }) + + // redraw when mode changes + this.callback_manager.set('set_mode', mode => { + this.passPropsMenuBar({ mode }) + }) + } + + /** + * Function to pass props for the search bar + * @param {Object} props - Props that the search bar will use + */ + passPropsSearchBar (props = {}) { + this.callback_manager.run('passPropsSearchBar', null, props) } - renderSearchBar (hide, searchItem) { - if (!this.options.enable_search) { return } - const searchBarNode = this.search_bar_div.node() - preact.render( - { this.searchBarRef = instance }} - />, - searchBarNode, - searchBarNode.children.length > 0 // If there is already a div, re-render it. Otherwise make a new one - ? searchBarNode.firstChild - : undefined + /** + * Initialize the search bar + * @param {D3 Selection} sel - The d3 selection to render in. + */ + setUpSearchBar (sel) { + this.searchBarRef = null + renderWrapper( + SearchBar, + instance => { this.searchBarRef = instance }, + passProps => this.callback_manager.set('passPropsSearchBar', passProps), + sel.append('div').node() ) + this.passPropsSearchBar({ + display: false, + searchIndex: this.map.search_index, + map: this.map + }) } - renderButtonPanel (mode) { - const buttonPanelDivNode = this.button_div.node() - preact.render( - this._set_mode(newMode)} - zoomContainer={this.zoom_container} - map={this.map} - mode={mode} - buildInput={this.build_input} - />, - buttonPanelDivNode, - buttonPanelDivNode.children.length > 0 // If there is already a div, re-render it. Otherwise make a new one - ? buttonPanelDivNode.firstChild - : undefined + /** + * Function to pass props for the button panel + * @param {Object} props - Props that the tooltip will use + */ + passPropsButtonPanel (props = {}) { + this.callback_manager.run('passPropsButtonPanel', null, props) + } + + /** + * Initialize the button panel + */ + setUpButtonPanel () { + renderWrapper( + ButtonPanel, + null, + passProps => this.callback_manager.set('passPropsButtonPanel', passProps), + this.selection.append('div').node() ) + this.passPropsButtonPanel({ + display: _.contains(['all', 'zoom'], this.settings.get('menu')), + mode: this.mode, + settings: this.settings, + setMode: mode => this._setMode(mode), + zoomContainer: this.zoom_container, + map: this.map, + buildInput: this.build_input + }) + // redraw when mode changes + this.callback_manager.set('set_mode', mode => { + this.passPropsButtonPanel({ mode }) + }) } - _set_mode (mode) { - this.renderMenu(mode) - this.renderButtonPanel(mode) + /** + * Set up callbacks for the rotation mode + */ + _setUpModes (map, brush, zoomContainer) { + // set up zoom+pan and brush modes + var wasEnabled = {} + map.callback_manager.set('start_rotation', function () { + wasEnabled.brush = brush.enabled + brush.toggle(false) + wasEnabled.zoom = zoomContainer.zoom_on + zoomContainer.toggle_pan_drag(false) + wasEnabled.selectableMousedown = map.behavior.selectableMousedown !== null + map.behavior.toggleSelectableClick(false) + wasEnabled.labelMouseover = map.behavior.labelMouseover !== null + wasEnabled.labelTouch = map.behavior.labelTouch !== null + map.behavior.toggleLabelMouseover(false) + map.behavior.toggleLabelTouch(false) + }) + map.callback_manager.set('end_rotation', function () { + brush.toggle(wasEnabled.brush) + zoomContainer.toggle_pan_drag(wasEnabled.zoom) + map.behavior.toggleSelectableClick(wasEnabled.selectableMousedown) + map.behavior.toggleLabelMouseover(wasEnabled.labelMouseover) + map.behavior.toggleLabelTouch(wasEnabled.labelTouch) + wasEnabled = {} + }) + } + + /** + * Set the mode + */ + _setMode (mode) { + this.mode = mode + // input this.build_input.toggle(mode === 'build') this.build_input.direction_arrow.toggle(mode === 'build') @@ -635,22 +726,24 @@ class Builder { // zoom this.zoom_container.toggle_pan_drag(mode === 'zoom' || mode === 'view') // resize canvas - this.map.canvas.toggle_resize(mode === 'zoom' || mode === 'brush') + this.map.canvas.toggle_resize(mode !== 'view') + // Behavior. Be careful of the order becuase rotation and - // toggle_selectable_drag both use Behavior.selectable_drag. + // toggle_selectable_drag both use Behavior.selectableDrag. if (mode === 'rotate') { - this.map.behavior.toggle_selectable_drag(false) // before toggle_rotation_mode - this.map.behavior.toggle_rotation_mode(true) + this.map.behavior.toggleSelectableDrag(false) // before toggle_rotation_mode + this.map.behavior.toggleRotationMode(true) // XX } else { - this.map.behavior.toggle_rotation_mode(mode === 'rotate') // before toggle_selectable_drag - this.map.behavior.toggle_selectable_drag(mode === 'brush') + this.map.behavior.toggleRotationMode(mode === 'rotate') // before toggleSelectableDrag + this.map.behavior.toggleSelectableDrag(mode === 'brush') // XX } - this.map.behavior.toggle_selectable_click(mode === 'build' || mode === 'brush') - this.map.behavior.toggle_label_drag(mode === 'brush') - this.map.behavior.toggle_label_mouseover(true) - this.map.behavior.toggle_label_touch(true) - this.map.behavior.toggle_text_label_edit(mode === 'text') - this.map.behavior.toggle_bezier_drag(mode === 'brush') + this.map.behavior.toggleSelectableClick(mode === 'build' || mode === 'brush') // XX + this.map.behavior.toggleLabelDrag(mode === 'brush') // XX + // this.map.behavior.toggleLabelMouseover(true) + // this.map.behavior.toggleLabelTouch(true) + this.map.behavior.toggleTextLabelEdit(mode === 'text') // XX + this.map.behavior.toggleBezierDrag(mode === 'brush') // XX + // edit selections if (mode === 'view' || mode === 'text') { this.map.select_none() @@ -658,134 +751,144 @@ class Builder { if (mode === 'rotate') { this.map.deselect_text_labels() } + this.map.draw_everything() + // what's not allowing me to delete this? XX above + + // callback + this.callback_manager.run('set_mode', null, mode) } - view_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + view_mode () { // eslint-disable-line camelcase this.callback_manager.run('view_mode') - this._set_mode('view') + this._setMode('view') } - build_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + build_mode () { // eslint-disable-line camelcase this.callback_manager.run('build_mode') - this._set_mode('build') + this._setMode('build') } - brush_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + brush_mode () { // eslint-disable-line camelcase this.callback_manager.run('brush_mode') - this._set_mode('brush') + this._setMode('brush') } - zoom_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + zoom_mode () { // eslint-disable-line camelcase this.callback_manager.run('zoom_mode') - this._set_mode('zoom') + this._setMode('zoom') } - rotate_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + rotate_mode () { // eslint-disable-line camelcase this.callback_manager.run('rotate_mode') - this._set_mode('rotate') + this._setMode('rotate') } - text_mode () { - /** For documentation of this function, see docs/javascript_api.rst. */ + /** For documentation of this function, see docs/javascript_api.rst. */ + text_mode () { // eslint-disable-line camelcase this.callback_manager.run('text_mode') - this._set_mode('text') + this._setMode('text') } - _reaction_check_add_abs () { - const curr_style = this.options.reaction_styles - const did_abs = false - if (this.options.reaction_data !== null && - !this.has_custom_reaction_styles && - !_.contains(curr_style, 'abs')) { - this.settings.set_conditional('reaction_styles', curr_style.concat('abs')) - return function () { + _reactionCheckAddAbs () { + const currStyle = this.settings.get('reaction_styles') + if ( + this.settings.get('reaction_data') !== null && + !this.has_custom_reaction_styles && + !_.contains(currStyle, 'abs') + ) { + this.settings.set('reaction_styles', currStyle.concat('abs')) + return () => { this.map.set_status('Visualizing absolute value of reaction data. ' + 'Change this option in Settings.', 5000) - }.bind(this) + } } return null } /** - * Function to get props for the tooltip component - * @param {Object} props - Props that the tooltip will use - */ - pass_tooltip_component_props (props) { - this.tooltip_container.callback_manager.run('setState', null, props) - } - - /** - * Function to get props for the settings menu - * @param {Object} props - Props that the settings menu will use + * For documentation of this function, see docs/javascript_api.rst. */ - pass_settings_menu_props (props) { - // if (this.settings_menu.visible) { // <- pseudocode - // pass the props - // } - this.callback_manager.run('setState', null, props) + set_reaction_data (data) { // eslint-disable-line camelcase + this.settings.set('reaction_data', data) + + var messageFn = this._reactionCheckAddAbs() + + this._updateData(true, true, 'reaction') + + if (messageFn) messageFn() + else this.map.set_status('') + + const disabledButtons = this.settings.get('disabled_buttons') || [] + const buttonName = 'Clear reaction data' + const index = disabledButtons.indexOf(buttonName) + if (data !== null && index !== -1) { + this.settings.set('disabled_buttons', [ + ...disabledButtons.slice(0, index), + ...disabledButtons.slice(index + 1) + ]) + } else if (data === null && index === -1) { + this.settings.set('disabled_buttons', [...disabledButtons, buttonName]) + } } /** * For documentation of this function, see docs/javascript_api.rst. */ - set_reaction_data (data) { - this.options.reaction_data = data - var message_fn = this._reaction_check_add_abs() - if (message_fn !== null) { - this._update_data(true, true, 'reaction') - message_fn() - } else { - this.map.set_status('') + set_gene_data (data, clearGeneReactionRules) { // eslint-disable-line camelcase + if (clearGeneReactionRules) { + // default undefined + this.settings.set('show_gene_reaction_rules', false) } + this.settings.set('gene_data', data) + this._updateData(true, true, 'reaction') + this.map.set_status('') - let index = this.options.disabled_buttons.indexOf('Clear reaction data') + const disabledButtonsArray = this.settings.get('disabled_buttons') || [] + const index = disabledButtonsArray.indexOf('Clear gene data') if (index > -1) { - this.options.disabled_buttons.splice(index, 1) + disabledButtonsArray.splice(index, 1) + this.settings.set('disabled_buttons', disabledButtonsArray) } else if (index === -1 && data === null) { - this.options.disabled_buttons.push('Clear reaction data') + this.settings.set('disabled_buttons', [...disabledButtonsArray, 'Clear gene data']) } } /** * For documentation of this function, see docs/javascript_api.rst. */ - set_gene_data (data, clear_gene_reaction_rules) { - if (clear_gene_reaction_rules) { - // default undefined - this.settings.set_conditional('show_gene_reaction_rules', false) - } - this.options.gene_data = data - this._update_data(true, true, 'reaction') + set_metabolite_data (data) { // eslint-disable-line camelcase + this.settings.set('metabolite_data', data) + this._updateData(true, true, 'metabolite') this.map.set_status('') - let index = this.options.disabled_buttons.indexOf('Clear gene data') + const disabledButtonsArray = this.settings.get('disabled_buttons') || [] + const index = disabledButtonsArray.indexOf('Clear metabolite data') if (index > -1) { - this.options.disabled_buttons.splice(index, 1) + disabledButtonsArray.splice(index, 1) + this.settings.set('disabled_buttons', disabledButtonsArray) } else if (index === -1 && data === null) { - this.options.disabled_buttons.push('Clear gene data') + this.settings.set('disabled_buttons', [...disabledButtonsArray, 'Clear metabolite data']) } } - set_metabolite_data (data) { - /** For documentation of this function, see docs/javascript_api.rst. - - */ - this.options.metabolite_data = data - this._update_data(true, true, 'metabolite') - this.map.set_status('') - - let index = this.options.disabled_buttons.indexOf('Clear metabolite data') - if (index > -1) { - this.options.disabled_buttons.splice(index, 1) - } else if (index === -1 && data === null) { - this.options.disabled_buttons.push('Clear metabolite data') + _makeGeneDataObject (geneData, cobraModel, map) { + const allReactions = {} + if (cobraModel !== null) { + utils.extend(allReactions, cobraModel.reactions) } + // extend, overwrite + if (map !== null) { + utils.extend(allReactions, map.reactions, true) + } + + // this object has reaction keys and values containing associated genes + return dataStyles.import_and_check(geneData, 'gene_data', allReactions) } /** @@ -797,55 +900,52 @@ class Builder { * should_draw: (Optional, Default: true) Whether to redraw the update sections * of the map. */ - _update_data (update_model, update_map, kind, should_draw) { - // defaults - if (kind === undefined) { - kind = [ 'reaction', 'metabolite' ] - } - if (should_draw === undefined) { - should_draw = true - } - - var update_metabolite_data = (kind.indexOf('metabolite') !== -1) - var update_reaction_data = (kind.indexOf('reaction') !== -1) - var met_data_object - var reaction_data_object - var gene_data_object + _updateData ( + updateModel = false, + updateMap = false, + kind = ['reaction', 'metabolite'], + shouldDraw = true + ) { + const updateReactionData = _.contains(kind, 'reaction') + const updateMetaboliteData = _.contains(kind, 'metabolite') + let metaboliteDataObject + let reactionDataObject + let geneDataObject // ------------------- // First map, and draw // ------------------- // metabolite data - if (update_metabolite_data && update_map && this.map !== null) { - met_data_object = dataStyles.import_and_check(this.options.metabolite_data, - 'metabolite_data') - this.map.apply_metabolite_data_to_map(met_data_object) - if (should_draw) { + if (updateMetaboliteData && updateMap && this.map !== null) { + metaboliteDataObject = dataStyles.import_and_check(this.settings.get('metabolite_data'), + 'metabolite_data') + this.map.apply_metabolite_data_to_map(metaboliteDataObject) + if (shouldDraw) { this.map.draw_all_nodes(false) } } // reaction data - if (update_reaction_data) { - if (this.options.reaction_data !== null && update_map && this.map !== null) { - reaction_data_object = dataStyles.import_and_check(this.options.reaction_data, - 'reaction_data') - this.map.apply_reaction_data_to_map(reaction_data_object) - if (should_draw) { + if (updateReactionData) { + if (this.settings.get('reaction_data') !== null && updateMap && this.map !== null) { + reactionDataObject = dataStyles.import_and_check(this.settings.get('reaction_data'), + 'reaction_data') + this.map.apply_reaction_data_to_map(reactionDataObject) + if (shouldDraw) { this.map.draw_all_reactions(false, false) } - } else if (this.options.gene_data !== null && update_map && this.map !== null) { - gene_data_object = make_gene_data_object(this.options.gene_data, - this.cobra_model, this.map) - this.map.apply_gene_data_to_map(gene_data_object) - if (should_draw) { + } else if (this.settings.get('gene_data') !== null && updateMap && this.map !== null) { + geneDataObject = this._makeGeneDataObject(this.settings.get('gene_data'), + this.cobra_model, this.map) + this.map.apply_gene_data_to_map(geneDataObject) + if (shouldDraw) { this.map.draw_all_reactions(false, false) } - } else if (update_map && this.map !== null) { + } else if (updateMap && this.map !== null) { // clear the data this.map.apply_reaction_data_to_map(null) - if (should_draw) { + if (shouldDraw) { this.map.draw_all_reactions(false, false) } } @@ -862,71 +962,55 @@ class Builder { } var delay = 5 - this.update_model_timer = setTimeout(function () { - + this.update_model_timer = setTimeout(() => { // metabolite_data - if (update_metabolite_data && update_model && this.cobra_model !== null) { + if (updateMetaboliteData && updateModel && this.cobra_model !== null) { // if we haven't already made this - if (!met_data_object) { - met_data_object = dataStyles.import_and_check(this.options.metabolite_data, - 'metabolite_data') + if (!metaboliteDataObject) { + metaboliteDataObject = dataStyles.import_and_check(this.settings.get('metabolite_data'), + 'metabolite_data') } - this.cobra_model.apply_metabolite_data(met_data_object, - this.options.metabolite_styles, - this.options.metabolite_compare_style) + this.cobra_model.apply_metabolite_data(metaboliteDataObject, + this.settings.get('metabolite_styles'), + this.settings.get('metabolite_compare_style')) } // reaction data - if (update_reaction_data) { - if (this.options.reaction_data !== null && update_model && this.cobra_model !== null) { + if (updateReactionData) { + if (this.settings.get('reaction_data') !== null && updateModel && this.cobra_model !== null) { // if we haven't already made this - if (!reaction_data_object) { - reaction_data_object = dataStyles.import_and_check(this.options.reaction_data, - 'reaction_data') + if (!reactionDataObject) { + reactionDataObject = dataStyles.import_and_check(this.settings.get('reaction_data'), + 'reaction_data') } - this.cobra_model.apply_reaction_data(reaction_data_object, - this.options.reaction_styles, - this.options.reaction_compare_style) - } else if (this.options.gene_data !== null && update_model && this.cobra_model !== null) { - if (!gene_data_object) { - gene_data_object = make_gene_data_object(this.options.gene_data, - this.cobra_model, this.map) + this.cobra_model.apply_reaction_data(reactionDataObject, + this.settings.get('reaction_styles'), + this.settings.get('reaction_compare_style')) + } else if (this.settings.get('gene_data') !== null && updateModel && this.cobra_model !== null) { + if (!geneDataObject) { + geneDataObject = this._makeGeneDataObject(this.settings.get('gene_data'), + this.cobra_model, this.map) } - this.cobra_model.apply_gene_data(gene_data_object, - this.options.reaction_styles, - this.options.identifiers_on_map, - this.options.reaction_compare_style, - this.options.and_method_in_gene_reaction_rule) - } else if (update_model && this.cobra_model !== null) { + this.cobra_model.apply_gene_data(geneDataObject, + this.settings.get('reaction_styles'), + this.settings.get('identifiers_on_map'), + this.settings.get('reaction_compare_style'), + this.settings.get('and_method_in_gene_reaction_rule')) + } else if (updateModel && this.cobra_model !== null) { // clear the data this.cobra_model.apply_reaction_data(null, - this.options.reaction_styles, - this.options.reaction_compare_style) + this.settings.get('reaction_styles'), + this.settings.get('reaction_compare_style')) } } // callback - this.callback_manager.run('update_data', null, update_model, update_map, - kind, should_draw) - }.bind(this), delay) - - // definitions - function make_gene_data_object (gene_data, cobra_model, map) { - var all_reactions = {} - if (cobra_model !== null) { - utils.extend(all_reactions, cobra_model.reactions) - } - // extend, overwrite - if (map !== null) { - utils.extend(all_reactions, map.reactions, true) - } - - // this object has reaction keys and values containing associated genes - return dataStyles.import_and_check(gene_data, 'gene_data', all_reactions) - } + this.callback_manager.run('update_data', null, updateModel, updateMap, + kind, shouldDraw) + }, delay) } - _create_status (selection) { + _createStatus (selection) { this.status_bar = selection.append('div').attr('id', 'status') } @@ -937,7 +1021,7 @@ class Builder { _setup_quick_jump (selection) { // function to load a map var load_fn = function (new_map_name, quick_jump_path, callback) { - if (this.options.enable_editing && !this.options.never_ask_before_quit) { + if (this.settings.get('enable_editing') && !this.settings.get('never_ask_before_quit')) { if (!(confirm(('You will lose any unsaved changes.\n\n' + 'Are you sure you want to switch maps?')))) { if (callback) callback(false) @@ -966,37 +1050,13 @@ class Builder { this.quick_jump = QuickJump(selection, load_fn) } - _setup_modes (map, brush, zoom_container) { - // set up zoom+pan and brush modes - var was_enabled = {} - map.callback_manager.set('start_rotation', function () { - was_enabled.brush = brush.enabled - brush.toggle(false) - was_enabled.zoom = zoom_container.zoom_on - zoom_container.toggle_pan_drag(false) - was_enabled.selectable_mousedown = map.behavior.selectable_mousedown !== null - map.behavior.toggle_selectable_click(false) - was_enabled.label_mouseover = map.behavior.label_mouseover !== null - was_enabled.label_touch = map.behavior.label_touch !== null - map.behavior.toggle_label_mouseover(false) - map.behavior.toggle_label_touch(false) - }) - map.callback_manager.set('end_rotation', function () { - brush.toggle(was_enabled.brush) - zoom_container.toggle_pan_drag(was_enabled.zoom) - map.behavior.toggle_selectable_click(was_enabled.selectable_mousedown) - map.behavior.toggle_label_mouseover(was_enabled.label_mouseover) - map.behavior.toggle_label_touch(was_enabled.label_touch) - was_enabled = {} - }) - } - /** * Define keyboard shortcuts */ - _get_keys (map, zoom_container, search_bar, settings_bar, - enable_editing, full_screen_button) { - var keys = { + getKeys () { + const map = this.map + const zoomContainer = this.zoom_container + let keys = { save: { key: 'ctrl+s', target: map, @@ -1048,24 +1108,24 @@ class Builder { }, zoom_in_ctrl: { key: 'ctrl+=', - target: zoom_container, - fn: zoom_container.zoom_in + target: zoomContainer, + fn: zoomContainer.zoom_in }, zoom_in: { key: '=', - target: zoom_container, - fn: zoom_container.zoom_in, + target: zoomContainer, + fn: zoomContainer.zoom_in, ignore_with_input: true }, zoom_out_ctrl: { key: 'ctrl+-', - target: zoom_container, - fn: zoom_container.zoom_out + target: zoomContainer, + fn: zoomContainer.zoom_out }, zoom_out: { key: '-', - target: zoom_container, - fn: zoom_container.zoom_out, + target: zoomContainer, + fn: zoomContainer.zoom_out, ignore_with_input: true }, extent_nodes_ctrl: { @@ -1090,15 +1150,6 @@ class Builder { fn: map.zoom_extent_canvas, ignore_with_input: true }, - search_ctrl: { - key: 'ctrl+f', - fn: () => this.renderSearchBar() - }, - search: { - key: 'f', - fn: () => this.renderSearchBar(), - ignore_with_input: true - }, view_mode: { target: this, fn: this.view_mode, @@ -1106,27 +1157,15 @@ class Builder { }, show_settings_ctrl: { key: 'ctrl+,', - target: settings_bar, - fn: () => this.pass_settings_menu_props({ - ...this.options, - map: this.map, - settings: this.settings, - display: true - }) + fn: () => this.passPropsSettingsMenu({ display: true }) }, show_settings: { key: ',', - target: this, - fn: () => this.pass_settings_menu_props({ - ...this.options, - map: this.map, - settings: this.settings, - display: true - }), + fn: () => this.passPropsSettingsMenu({ display: true }), ignore_with_input: true } } - if (full_screen_button) { + if (this.settings.get('full_screen_button')) { utils.extend(keys, { full_screen_ctrl: { key: 'ctrl+2', @@ -1141,7 +1180,7 @@ class Builder { } }) } - if (enable_editing) { + if (this.settings.get('enable_editing')) { utils.extend(keys, { build_mode: { key: 'n', @@ -1246,12 +1285,14 @@ class Builder { select_all: { key: 'ctrl+a', target: map, - fn: map.select_all + fn: map.select_all, + ignore_with_input: true }, select_none: { key: 'ctrl+shift+a', target: map, - fn: map.select_none + fn: map.select_none, + ignore_with_input: true }, invert_selection: { target: map, @@ -1259,6 +1300,19 @@ class Builder { } }) } + if (this.settings.get('enable_search')) { + utils.extend(keys, { + search_ctrl: { + key: 'ctrl+f', + fn: () => this.passPropsSearchBar({ display: true }) + }, + search: { + key: 'f', + fn: () => this.passPropsSearchBar({ display: true }), + ignore_with_input: true + } + }) + } return keys } @@ -1269,7 +1323,7 @@ class Builder { window.onbeforeunload = function (e) { // If we haven't been passed the event get the window.event e = e || window.event - return (this.options.never_ask_before_quit + return (this.settings.get('never_ask_before_quit') ? null : 'You will lose any unsaved changes.' ) diff --git a/src/BuilderMenuBar.jsx b/src/BuilderMenuBar.jsx deleted file mode 100644 index 9bea754b..00000000 --- a/src/BuilderMenuBar.jsx +++ /dev/null @@ -1,243 +0,0 @@ -/** @jsx h */ -import { h, Component } from 'preact' -import Dropdown from './Dropdown' -import MenuButton from './MenuButton' - -/** - * BuilderMenuBar. Wrapper class that implements generic Dropdown and MenuButton - * objects to create the Builder menu bar. Currently re-renders every time an - * edit mode is chosen. This can be changed once Builder is ported to Preact. - */ -class BuilderMenuBar extends Component { - - componentDidMount () { - this.props.sel.selectAll('#canvas').on( - 'touchend', () => this.setState({visible: false}) - ) - this.props.sel.selectAll('#canvas').on( - 'click', () => this.setState({visible: false}) - ) - } - - render () { - return ( -
    - - this.props.saveMap()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.loadMap(file)} - type='load' - disabledButtons={this.props.disabled_buttons} - /> - this.props.saveSvg()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.savePng()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.clearMap()} - disabledButtons={this.props.disabled_buttons} - /> - - - this.props.loadModel(file)} - type='load' - disabledButtons={this.props.disabled_buttons} - /> - this.props.updateRules()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.loadModel(null)} - disabledButtons={this.props.disabled_buttons} - /> - - - this.props.loadReactionData(file)} - type='load' - disabledButtons={this.props.disabled_buttons} - /> - this.props.loadReactionData(null)} - disabledButtons={this.props.disabled_buttons} - /> -
  • - this.props.loadGeneData(file)} - type='load' - disabledButtons={this.props.disabled_buttons} - /> - this.props.loadGeneData(null)} - disabledButtons={this.props.disabled_buttons} - /> -
  • - this.props.loadMetaboliteData(file)} - type='load' - disabledButtons={this.props.disabled_buttons} - /> - this.props.loadMetaboliteData(null)} - disabledButtons={this.props.disabled_buttons} - /> - - - this.props.setMode('zoom')} - disabledButtons={this.props.disabled_buttons} - /> - this.props.setMode('brush')} - disabledButtons={this.props.disabled_buttons} - /> - this.props.setMode('build')} - disabledButtons={this.props.disabled_buttons} - /> - this.props.setMode('rotate')} - disabledButtons={this.props.disabled_buttons} - /> - this.props.setMode('text')} - disabledButtons={this.props.disabled_buttons} - /> -
  • - this.props.deleteSelected()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.undo()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.redo()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.togglePrimary()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.cyclePrimary()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.selectAll()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.selectNone()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.invertSelection()} - disabledButtons={this.props.disabled_buttons} - /> - - - this.props.zoomIn()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.zoomOut()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.zoomExtentNodes()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.zoomExtentCanvas()} - disabledButtons={this.props.disabled_buttons} - /> - this.props.search()} - disabledButtons={this.props.disabled_buttons} - /> - { - this.props.toggleBeziers() - this.props.setMode(this.props.mode) - } - } - disabledButtons={this.props.disabled_buttons} - /> -
  • - this.props.renderSettingsMenu()} - disabledButtons={this.props.disabled_buttons} - type='settings' - /> - - ? -
- ) - } -} - -export default BuilderMenuBar diff --git a/src/ButtonPanel.css b/src/ButtonPanel.css index 01c540b1..772ce159 100644 --- a/src/ButtonPanel.css +++ b/src/ButtonPanel.css @@ -1,18 +1,13 @@ -.escher-container .buttonPanel * { - box-sizing: border-box; -} - -.escher-container .buttonPanel { +.escher-container .button-panel { position: absolute; left: 4px; top: 20%; margin-top: -32px; padding-left: 0; - -ms-touch-action: none; touch-action: none; } -.escher-container .buttonPanel>li { +.escher-container .button-panel>li { margin-top: 5px; } @@ -37,7 +32,7 @@ border-bottom-right-radius: 4px; } -.escher-container .buttonPanel>.grouping:last-child { +.escher-container .button-panel>.grouping:last-child { margin-top: 4px; } @@ -68,15 +63,15 @@ height: 40px; } -.escher-container .buttonPanel .button:active, .escher-container .buttonGroup label:active, .escher-container .buttonPanel .buttonGroup:active { +.escher-container .button-panel .button:active, .escher-container .buttonGroup label:active, .escher-container .button-panel .buttonGroup:active { background-image: linear-gradient(#3F4141, #474949 6%, #4F5151); } -.escher-container .buttonPanel .fa { +.escher-container .button-panel .fa { font-size: 24px; } /* Icons */ -.escher-container .buttonPanel [class^='icon-'] { +.escher-container .button-panel [class^='icon-'] { font-size: 23px; } diff --git a/src/ButtonPanel.jsx b/src/ButtonPanel.jsx index 47179dde..5cd08498 100644 --- a/src/ButtonPanel.jsx +++ b/src/ButtonPanel.jsx @@ -9,13 +9,17 @@ import './ButtonPanel.css' */ class ButtonPanel extends Component { render () { + const menuSetting = this.props.settings.get('menu') + const enableKeys = this.props.settings.get('enable_keys') + const enableEditing = this.props.settings.get('enable_editing') + return ( -
    +
    • @@ -24,46 +28,36 @@ class ButtonPanel extends Component {
      • -
    • +
      • -
    • +
    • - -
      - {this.state.counter} -
      +
      + this.handleInput(event.target.value)} + ref={input => { this.inputRef = input }} + /> + + +
      + {this.state.counter}
      -
      ) diff --git a/src/Settings.js b/src/Settings.js index d932f440..8199f6b5 100644 --- a/src/Settings.js +++ b/src/Settings.js @@ -1,58 +1,9 @@ -/** Settings. A class to manage settings for a Map. - - Arguments - --------- - - setOption: A function, fn(key), that returns the option value for the - key. - - getOption: A function, fn(key, value), that sets the option for the key - and value. - - conditionalOptions: The options to that are conditionally accepted when - changed. Changes can be abandoned by calling abandon_changes(), or accepted - by calling accept_changes(). - - */ - -import utils from './utils' import bacon from 'baconjs' - -var Settings = utils.make_class() -// instance methods -Settings.prototype = { - init, - set_conditional, - hold_changes, - abandon_changes, - accept_changes, - createConditionalSetting, - convertToConditionalStream -} -module.exports = Settings - -function init (setOption, getOption, conditionalOptions) { - this.set_option = setOption - this.get_option = getOption - - // Manage accepting/abandoning changes - this.status_bus = new bacon.Bus() - - // Create the options - this.busses = {} - this.streams = {} - for (var i = 0, l = conditionalOptions.length; i < l; i++) { - var name = conditionalOptions[i] - var out = createConditionalSetting(name, getOption(name), setOption, - this.status_bus) - this.busses[name] = out.bus - this.streams[name] = out.stream - } -} +import _ from 'underscore' /** - * Hold on to event when hold_property is true, and only keep them if - * accept_property is true (when hold_property becomes false). + * Hold on to event when holdProperty is true, and only keep them if + * acceptProperty is true (when holdProperty becomes false). */ function convertToConditionalStream (valueStream, statusStream) { // Combine values with status to revert to last value when a reject is passed. @@ -104,61 +55,128 @@ function convertToConditionalStream (valueStream, statusStream) { } } }) - // Skip the initial null value + // Skip the initial null value .skip(1) - // Get the current value + // Get the current value .map(({ currentValue }) => currentValue) - // Skip duplicate values + // Skip duplicate values .skipDuplicates() - // property -> event stream + // property -> event stream .toEventStream() return held } -function createConditionalSetting (name, initialValue, setOption, statusBus) { - // Set up the bus - var bus = new bacon.Bus() +/** + * Settings. A class to manage settings for a Map. + * + * Arguments + * --------- + * + * setOption: A function, fn(key), that returns the option value for the key. + * + * getOption: A function, fn(key, value), that sets the option for the key and + * value. + * + * conditionalOptions: The options to that are conditionally accepted when + * changed. Changes can be abandoned by calling abandonChanges(), or accepted + * by calling acceptChanges(). + * @param optionsWithDefaults - The current option values + * @param conditionalOptions - The options to that are conditionally accepted + * when changed. Changes can be abandoned by calling + * abandon_changes(), or accepted by calling + * accept_changes(). + */ +export default class Settings { + constructor (optionsWithDefaults, conditionalOptions) { + this._options = optionsWithDefaults + + // Manage accepting/abandoning changes + this.statusBus = new bacon.Bus() + + // Create the options + ;[ this.busses, this.streams ] = _.chain(optionsWithDefaults) + .mapObject((value, key) => { + const isConditional = _.contains(conditionalOptions, key) + const { bus, stream } = this.createSetting(key, value, isConditional) + return [ bus, stream ] + }) // { k: [ b, s ], ... } + .pairs() // [ [ k, [ b, s ] ], ... ] + .map(([ name, [ bus, stream ] ]) => [[ name, bus ], [ name, stream ]]) + // [ [ [ k, b ], [ k, s ] ], ... ] + .unzip() // [ [ [ k, b ], ... ], [ [ k, s ], ... ] ] + .map(x => _.object(x)) // [ { k: b, ... }, { k: s, ... } ] + .value() + } - // Make the event stream and conditionally accept changes - var stream = convertToConditionalStream(bus, statusBus) + /** + * Set up a new bus and stream for a conditional setting (i.e. one that can be + * canceledin the settings menu. + */ + createSetting (name, initialValue, isConditional) { + // Set up the bus + const bus = new bacon.Bus() - // Get the latest - stream.onValue(v => setOption(name, v)) + // Make the event stream and conditionally accept changes + const stream = isConditional + ? convertToConditionalStream(bus, this.statusBus) + : bus.toEventStream() - // Push the initial value - bus.push(initialValue) + // Get the latest + stream.onValue(v => { this._options[name] = v }) - return { bus, stream } -} + // Push the initial value + bus.push(initialValue) -/** Set the value of a conditional setting, one that will only be - accepted if this.accept_changes() is called. + return { bus, stream } + } - Arguments - --------- + /** + * Deprecated. Use `set` instead. + */ + set_conditional (name, value) { // eslint-disable-line camelcase + console.warn('set_conditional is deprecated. Use Settings.set() instead') + return this.set(name, value) + } - name: The option name + /** + * Set the option. This should always be used instead of setting options + * directly. To set options that respect the Settings menu Accept/Abandon, use + * setConditional(). + * @param {String} name - The option name + * @param {} value - The new value + */ + set (name, value) { + if (!(name in this.busses)) { + throw new Error(`Invalid setting name ${name}`) + } + this.busses[name].push(value) + } - value: The new value + /** + * Deprecated. Use `get` intead. + */ + get_option (name) { // eslint-disable-line camelcase + console.warn('get_option is deprecated. Use Settings.get() instead') + return this.get(name) + } - */ -function set_conditional (name, value) { - if (!(name in this.busses)) { - console.error(`Invalid setting name ${name}`) - } else { - this.busses[name].push(value) + /** + * Get an option + */ + get (name) { + return this._options[name] } -} -function hold_changes () { - this.status_bus.push('hold') -} + holdChanges () { + this.statusBus.push('hold') + } -function abandon_changes () { - this.status_bus.push('abandon') -} + abandonChanges () { + this.statusBus.push('abandon') + } -function accept_changes() { - this.status_bus.push('accept') + acceptChanges () { + this.statusBus.push('accept') + } } diff --git a/src/BuilderSettingsMenu.css b/src/SettingsMenu.css similarity index 100% rename from src/BuilderSettingsMenu.css rename to src/SettingsMenu.css diff --git a/src/BuilderSettingsMenu.jsx b/src/SettingsMenu.jsx similarity index 62% rename from src/BuilderSettingsMenu.jsx rename to src/SettingsMenu.jsx index 5740f392..3d480bac 100644 --- a/src/BuilderSettingsMenu.jsx +++ b/src/SettingsMenu.jsx @@ -3,9 +3,8 @@ import { h, Component } from 'preact' import ScaleSelector from './ScaleSelector' import ScaleSlider from './ScaleSlider' import ScaleSelection from './ScaleSelection' -import update from 'immutability-helper' import _ from 'underscore' -import './BuilderSettingsMenu.css' +import './SettingsMenu.css' import scalePresets from './colorPresets' /** @@ -13,29 +12,9 @@ import scalePresets from './colorPresets' * settings. Implements Settings.js but otherwise only uses * Preact. */ -class BuilderSettingsMenu extends Component { - constructor (props) { - super(props) - this.state = { - display: props.display - } - if (props.display) { - this.componentWillAppear() - } - } - - componentWillReceiveProps (nextProps) { - this.setState({display: nextProps.display}) - if (nextProps.display && !this.props.display) { - this.componentWillAppear() - } - if (!nextProps.display && this.props.display) { - this.componentWillDisappear() - } - } - - componentWillAppear () { - this.props.settings.hold_changes() +class SettingsMenu extends Component { + componentWillMount () { + this.props.settings.holdChanges() this.setState({ clearEscape: this.props.map.key_manager.add_escape_listener( () => this.abandonChanges(), @@ -49,49 +28,46 @@ class BuilderSettingsMenu extends Component { }) } - componentWillDisappear () { - this.props.closeMenu() // Function to pass display = false to the settings menu + componentWillUnmount () { this.state.clearEscape() this.state.clearEnter() } abandonChanges () { - this.props.settings.abandon_changes() - this.componentWillDisappear() + this.props.settings.abandonChanges() + this.props.setDisplay(false) } saveChanges () { - this.props.settings.accept_changes() - this.componentWillDisappear() + this.props.settings.acceptChanges() + this.props.setDisplay(false) } /** - * Function to handle changes to the reaction or metabolite styling. + * Function to toggle one option in the reaction or metabolite styling. * @param {String} value - the style option to be added or removed * @param {String} type - reaction_style or metabolite_style */ handleStyle (value, type) { - if (this.props[type].indexOf(value) === -1) { - this.props.settings.set_conditional(type, - update(this.props[type], {$push: [value]}) - ) - } else if (this.props[type].indexOf(value) > -1) { - this.props.settings.set_conditional(type, - update(this.props[type], {$splice: [[this.props[type].indexOf(value), 1]]}) - ) + const currentSetting = this.props.settings.get(type) + const index = currentSetting.indexOf(value) + if (index === -1) { + this.props.settings.set(type, [...currentSetting, value]) + } else { + this.props.settings.set(type, [ + ...currentSetting.slice(0, index), + ...currentSetting.slice(index + 1) + ]) } } - is_visible () { - return this.state.display - } - render () { + const settings = this.props.settings + const enableTooltips = settings.get('enable_tooltips') || [] + const dataStatistics = this.props.map.get_data_statistics() + return ( -
      +