Merge pull request #209 from CSCfi/develop

release 0.9.0

.github/dependabot.yml

@@ -0,0 +1,29 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "pip dependencies"
+    target-branch: "develop"
+    open-pull-requests-limit: 10
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "github actions"
+    target-branch: "develop"
+    open-pull-requests-limit: 10
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "docker dependencies"
+    target-branch: "develop"
+    open-pull-requests-limit: 10

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: [3.8]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/int.yml

@@ -8,7 +8,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: [3.8]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/production.yml

@@ -10,7 +10,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: [3.8]
 
     runs-on: ${{ matrix.os }}
 
@@ -31,6 +31,15 @@ jobs:
         with:
           driver-opts: network=host
 
+      - name: Set build target branch
+        run: |
+          if [[ ${{ github.event.pull_request.base.ref }} == master ]]; then
+            BRANCH=master
+          else
+            BRANCH=develop
+          fi
+          echo "BUILD_BRANCH=$BRANCH" >> $GITHUB_ENV
+
       - name: Build
         uses: docker/build-push-action@v2
         with:
@@ -40,6 +49,8 @@ jobs:
           tags: localhost:5000/metadata-submitter:latest
           cache-from: localhost:5000/metadata-submitter:latest
           cache-to: type=local,dest=/tmp/.buildx-cache
+          build-args: |
+            BRANCH=${{ env.BUILD_BRANCH }}
 
       - name: Run production container
         run: docker run --rm -p 5430:5430 --name ms -d -t localhost:5000/metadata-submitter:latest

.github/workflows/publish.yml

@@ -21,14 +21,18 @@ jobs:
           VERSION=edge
           if [[ $GITHUB_REF == refs/tags/* ]]; then
             VERSION=${GITHUB_REF#refs/tags/}
+            BRANCH=master
           elif [[ $GITHUB_REF == refs/heads/* ]]; then
             BRANCH=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
             if [[ $BRANCH == master ]]; then
               VERSION=latest
+              BRANCH=master
             elif [[ $BRANCH == develop ]]; then
               VERSION=stage
+              BRANCH=develop
             fi
           fi
+          echo "BUILD_BRANCH=$BRANCH" >> $GITHUB_ENV
           TAGS="${DOCKER_IMAGE}:${VERSION}"
           echo ::set-output name=version::${VERSION}
           echo ::set-output name=tags::${TAGS}
@@ -51,6 +55,8 @@ jobs:
           file: ./Dockerfile
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.prep.outputs.tags }}
+          build-args: |
+            BRANCH=${{ env.BUILD_BRANCH }}
           cache-from: type=registry,ref=cscfi/metadata-submitter:latest
           cache-to: type=local,dest=/tmp/.buildx-cache
           labels: |

.github/workflows/style.yml

@@ -8,7 +8,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: [3.8]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/unit.yml

@@ -8,7 +8,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
+        python-version: [3.8]
 
     runs-on: ${{ matrix.os }}
 
@@ -26,8 +26,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install tox tox-gh-actions
-    - name: Run unit tests for python 3.7
-      if: ${{ matrix.python-version == '3.7' }}
+    - name: Run unit tests for python 3.8
+      if: ${{ matrix.python-version == '3.8' }}
       env:
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-      run: tox -e py37
+      run: tox -e py38

Dockerfile

@@ -4,12 +4,17 @@ RUN apk add --update \
     && apk add --no-cache git\
     && rm -rf /var/cache/apk/*
 
-RUN git clone https://github.com/CSCfi/metadata-submitter-frontend.git
+ARG BRANCH=master
+
+RUN git clone -b ${BRANCH} https://github.com/CSCfi/metadata-submitter-frontend.git
 
 WORKDIR /metadata-submitter-frontend
-RUN npm install && npm run build --production
+RUN npm install -g [email protected] \
+    && npx --quiet pinst --disable \
+    && npm install --production \
+    && npm run build --production
 
-FROM python:3.7-alpine3.13 as BUILD-BACKEND
+FROM python:3.8-alpine3.13 as BUILD-BACKEND
 
 RUN apk add --update \
     && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev libffi-dev \
@@ -27,15 +32,15 @@ RUN pip install --upgrade pip && \
     pip install -r /root/submitter/requirements.txt && \
     pip install /root/submitter
 
-FROM python:3.7-alpine3.13
+FROM python:3.8-alpine3.13
 
 RUN apk add --no-cache --update bash
 
 LABEL maintainer="CSC Developers"
 LABEL org.label-schema.schema-version="1.0"
 LABEL org.label-schema.vcs-url="https://github.com/CSCfi/metadata-submitter"
 
-COPY --from=BUILD-BACKEND /usr/local/lib/python3.7/ /usr/local/lib/python3.7/
+COPY --from=BUILD-BACKEND /usr/local/lib/python3.8/ /usr/local/lib/python3.8/
 
 COPY --from=BUILD-BACKEND /usr/local/bin/gunicorn /usr/local/bin/
 

Dockerfile-dev

@@ -1,4 +1,4 @@
-FROM python:3.7-slim
+FROM python:3.8-slim
 
 RUN apt-get install ca-certificates
 

README.md

@@ -12,7 +12,7 @@ Service also validates submitted metadata objects against EGA XSD metadata model
 ## Install and run
 
 Requirements:
-- Python 3.7+
+- Python 3.8+
 - MongoDB
 - Docker + docker-compose
 
@@ -22,9 +22,11 @@ For more detailed setup, do following:
 - Install project by running: `pip install .` in project root
 - Setup mongodb and env variables via desired way, details:
   - Server expects to find mongodb instance running, specified with following environment variables:
-    - `MONGO_INITDB_ROOT_USERNAME`, username for admin user to mondogdb instance
-    - `MONGO_INITDB_ROOT_PASSWORD`, password for admin user to mondogdb instance
+    - `MONGO_USERNAME`, username for connecting to mondogdb instance
+    - `MONGO_PASSWORD`, password for connecting to mondogdb instance
     - `MONGO_HOST`, host and port for mongodb instance (e.g. `localhost:27017`)
+    - `MONGO_DATABASE`, If a specific database is to be used, set the name here. 
+    - `MONGO_AUTHDB`, if `MONGO_DATABASE` is set and the user doesn't exists in the database, set this to the database where the user exists (e.g. `admin`)
   - Out of the box, metadata submitter is configured with default values from MongoDB Docker image
   - Suitable mongodb instance can be launched with Docker by running `docker-compose up database`
 - After installing and setting up database, server can be launched with `metadata_submitter`

docker-compose.yml

@@ -25,6 +25,8 @@ services:
       - "AUTH_REFERER=http://mockauth:8000"
       - "JWK_URL=http://mockauth:8000/keyset"
       - "LOG_LEVEL=DEBUG"
+      - "MONGO_DATABASE=default"
+      - "MONGO_AUTHDB=admin"
   database:
     image: "mongo"
     container_name: "metadata_submitter_database_dev"

docs/code.rst

@@ -24,6 +24,7 @@ Metadata Backend API
 
     metadata_backend.api.auth
     metadata_backend.api.handlers
+    metadata_backend.api.health
     metadata_backend.api.middlewares
     metadata_backend.api.operators
 

docs/conf.py

@@ -11,7 +11,7 @@
 author = "CSC Developers"
 
 # The full version, including alpha/beta/rc tags
-release = "0.8.1"
+release = "0.9.0"
 
 
 # -- General configuration ---------------------------------------------------

docs/frontend.rst

@@ -41,11 +41,10 @@ To run the frontend from command line use:
 
 After installing and running, frontend can be found from ``http://localhost:3000``.
 
-.. hint:: Some functionality in frontend required a working backend.
+.. hint:: Some functionality in frontend requires a working backend.
           Follow the instructions in :ref:`deploy` for setting it up.
 
 
-
 Internal structure
 ------------------
 
@@ -61,11 +60,117 @@ Form components
 Form components are crucial part of the application:
 
 - All submissions and folder creation are made with `react-hook-form <https://react-hook-form.com/>`_. 
-  Latter uses form as a reference so submission can be triggered outside the form.
-- Form for json schema based forms are created with custom json schema parser, which builds 
-  ``react-hook-form`` based forms from given json schema. Json schema-based forms are validated against json schema with ``Ajv``. 
+  Latter uses form as a reference so submission can be triggered outside the form. JSON schema based forms are created with custom JSON schema parser, which builds 
+  ``react-hook-form`` based forms from given schema. The forms are validated against the JSON schema with ``Ajv``. 
   React-hook-form is used for performance reasons: it uses uncontrolled components so adding a lot of fields to array doesn't slow rendering of the application.
 
+Constants
+---------
+
+Folder ``src/constants`` holds all the constants used in the application. The constants are uniquely defined and separated into different files according to its related context. For example, the file ``constants/wizardObject.js`` contains unique constants regarding to ``wizardObject`` such as: ``ObjectTypes, ObjectStatus, etc.``
+
+The purposes of using these `constants` are:
+
+- to avoid hard coding the values of variables repeatedly
+- to keep the consistency when defining the values of variables
+- to reuse those predefined values across the application
+
+Example of defining and using a constant:
+
+- First, define the constant object ``ObjectSubmissionTypes`` in ``constants/wizardObject.js``
+
+.. code-block:: javascript
+
+    export const ObjectSubmissionTypes = {
+    form: "Form",
+    xml: "XML",
+    existing: "Existing",
+    }
+
+
+- Then, use this constant in `WizardComponents/WizardObjectIndex`:
+
+.. code-block:: javascript
+
+    import { ObjectSubmissionTypes } from "constants/wizardObject"
+
+    switch (currentSubmissionType) {
+        case ObjectSubmissionTypes.form: {
+        target = "form"
+        break
+        }
+        case ObjectSubmissionTypes.xml: {
+        target = "XML upload"
+        break
+        }
+        case ObjectSubmissionTypes.existing: {
+        target = "drafts"
+        break
+        }
+    }
+
+
+Commonly used data types
+------------------------
+
+All commonly used data types of variables are defined in the file ``index.js`` in folder ``src/types``. The purposes are:
+
+- to avoid hard coding the same data types frequently in different files
+- to keep track and consistency of the data types across different files
+
+For example:
+
+- declare and export these data types in ``src/types/index.js``
+
+.. code-block:: javascript
+
+    export type ObjectInsideFolder = {
+    accessionId: string,
+    schema: string,
+    }
+
+    export type ObjectTags = {
+    submissionType: string,
+    fileName?: string,
+    }
+
+    export type ObjectInsideFolderWithTags = ObjectInsideFolder & { tags: ObjectTags }
+
+
+- import and reuse the data types in different files:
+- Reuse type ``ObjectInsideFolder`` in ``features/wizardSubmissionFolderSlice.js``:
+
+.. code-block:: javascript
+
+    import type { ObjectInsideFolder } from "types"
+
+    export const addObjectToFolder = (
+    folderID: string,
+    objectDetails: ObjectInsideFolder
+    ) => {}
+
+    export const addObjectToDrafts = (
+    folderID: string,
+    objectDetails: ObjectInsideFolder
+    ) => {}
+
+
+- Reuse type ``ObjectInsideFolderWithTags`` consequently in both ``WizardComponents/WizardSavedObjectsList.js`` and ``WizardSteps/WizardShowSummaryStep.js``:
+
+.. code-block:: javascript
+
+    import type { ObjectInsideFolderWithTags } from "types"
+
+    type WizardSavedObjectsListProps = { submissions: Array<ObjectInsideFolderWithTags> }
+
+
+.. code-block:: javascript
+
+    import type { ObjectInsideFolderWithTags } from "types"
+
+    type GroupedBySchema = {| [Schema]: Array<ObjectInsideFolderWithTags> |}
+
+
 Redux store
 -----------