Migration to visyn_core (#55)

* Migration to visyn_core * Linting * Upgrade deps --------- Co-authored-by: Michael Puehringer <[email protected]>
Caleydo · Mar 1, 2023 · 45937d5 · 45937d5
1 parent 234dd2e
commit 45937d5
Show file tree

Hide file tree

Showing 16 changed files with 38 additions and 31 deletions.
diff --git a/coral/__init__.py b/coral/__init__.py
@@ -5,7 +5,7 @@
 ###############################################################################
 from os import path
 
-from tdp_core.plugin.model import AVisynPlugin, RegHelper
+from visyn_core.plugin.model import AVisynPlugin, RegHelper
 
 from .settings import CoralSettings
 

diff --git a/coral/migration/env.py b/coral/migration/env.py
@@ -1,3 +1,3 @@
-import tdp_core.dbmigration.env
+import visyn_core.dbmigration.env
 
-tdp_core.dbmigration.env.run_migrations_online()
+visyn_core.dbmigration.env.run_migrations_online()
diff --git a/coral/settings.py b/coral/settings.py
@@ -1,5 +1,5 @@
 from pydantic import BaseModel
-from tdp_core import manager
+from visyn_core import manager
 
 
 class CoralSettings(BaseModel):

diff --git a/coral/sql.py b/coral/sql.py
@@ -1,7 +1,7 @@
 import logging
 
 from flask import Flask, abort, jsonify, request
-from tdp_core.security import login_required
+from visyn_core.security import login_required
 
 from .settings import get_settings
 from .sql_query_mapper import QueryElements

diff --git a/coral/sql_query_mapper.py b/coral/sql_query_mapper.py
@@ -7,7 +7,7 @@
 from sqlalchemy import create_engine, exc, inspect, text
 from sqlalchemy.exc import NoInspectionAvailable
 from sqlalchemy.orm import sessionmaker
-from tdp_core import manager
+from visyn_core import manager
 
 from .settings import get_settings
 from .sql_tables import Cohort

diff --git a/coral/tests/conftest.py b/coral/tests/conftest.py
@@ -1,10 +1,10 @@
 import pytest
 from fastapi import FastAPI
 from fastapi.testclient import TestClient
-from tdp_core.security.manager import SecurityManager
-from tdp_core.security.model import User
-from tdp_core.server.visyn_server import create_visyn_server
-from tdp_core.tests.fixtures.postgres_db import postgres_db
+from visyn_core.security.manager import SecurityManager
+from visyn_core.security.model import User
+from visyn_core.server.visyn_server import create_visyn_server
+from visyn_core.tests.fixtures.postgres_db import postgres_db
 
 assert postgres_db  # silence unused import warning
 

diff --git a/src/Cohort.ts b/src/Cohort.ts
@@ -1,4 +1,5 @@
-import { IAllFilters, IDType, IDTypeLike, IDTypeManager, IRow, IServerColumn, UniqueIdManager } from 'tdp_core';
+import { IDType, IDTypeLike, IDTypeManager, IRow, IServerColumn } from 'visyn_core';
+import { IAllFilters, UniqueIdManager } from 'tdp_core';
 import { ElementProvType, ICohort, ICohortRep, IElement, IElementProvJSONCohort, IProvAttrAndValuesCohort } from './CohortInterfaces';
 import {
   createDBCohort,

diff --git a/src/CohortInterfaces.ts b/src/CohortInterfaces.ts
@@ -1,4 +1,4 @@
-import { IDType, IServerColumn } from 'tdp_core';
+import { IDType, IServerColumn } from 'visyn_core';
 import { Cohort } from './Cohort';
 import { IAttribute, IAttributeJSON } from './data/Attribute';
 import { IEqualsList, INumRange } from './rest';

diff --git a/src/Taskview/SearchBar.ts b/src/Taskview/SearchBar.ts
@@ -1,11 +1,12 @@
-import {select} from 'd3v7';
-import {IdTextPair, IServerColumn, RestBaseUtils} from 'tdp_core';
-import {dataTypes, depletion, IDataSubtypeConfig, IDataTypeConfig} from 'tdp_publicdb';
-import {colors} from '../colors';
-import {ScoreType} from '../data/Attribute';
-import {checkSpecialAttribute, ISpecialAttribute} from '../data/SpecialAttribute';
-import {deepCopy, getAnimatedLoadingText, log} from '../util';
-import {niceName} from '../utilLabels';
+import { select } from 'd3v7';
+import { IServerColumn } from 'visyn_core';
+import { IdTextPair, RestBaseUtils } from 'tdp_core';
+import { dataTypes, depletion, IDataSubtypeConfig, IDataTypeConfig } from 'tdp_publicdb';
+import { colors } from '../colors';
+import { ScoreType } from '../data/Attribute';
+import { checkSpecialAttribute, ISpecialAttribute } from '../data/SpecialAttribute';
+import { deepCopy, getAnimatedLoadingText, log } from '../util';
+import { niceName } from '../utilLabels';
 
 export class SearchBar {
   private _container: HTMLDivElement;

diff --git a/src/app.ts b/src/app.ts
@@ -1,12 +1,12 @@
 import { select, Selection } from 'd3v7';
 import SplitGrid from 'split-grid';
+import { IServerColumn } from 'visyn_core';
 import {
   AppContext,
   ATDPApplication,
   CLUEGraphManager,
   IDatabaseViewDesc,
   IObjectRef,
-  IServerColumn,
   ITDPOptions,
   NotificationHandler,
   ObjectRefUtils,

diff --git a/src/common/config.ts b/src/common/config.ts
@@ -3,7 +3,8 @@
  */
 
 import { Categories } from 'tdp_publicdb';
-import { IServerColumn, ColumnDescUtils, IAdditionalColumnDesc } from 'tdp_core';
+import { IServerColumn } from 'visyn_core';
+import { ColumnDescUtils, IAdditionalColumnDesc } from 'tdp_core';
 
 /**
  * maximal number of rows in which just the subset if fetched instead of all

diff --git a/src/common/forms.ts b/src/common/forms.ts
@@ -3,7 +3,8 @@
  */
 
 import { SpeciesUtils, FormSubtype } from 'tdp_publicdb';
-import { FormElementType, IFormElement, IFormSelectOption, ValueCache, RestStorageUtils, LineupUtils, RestBaseUtils, IServerColumn } from 'tdp_core';
+import { IServerColumn } from 'visyn_core';
+import { FormElementType, IFormElement, IFormSelectOption, ValueCache, RestStorageUtils, LineupUtils, RestBaseUtils } from 'tdp_core';
 import { gene, IDataSourceConfig, tissue, cellline, dataSources, dataTypes, dataSubtypes, depletion, drugScreen } from './config';
 import { GeneUtils } from './GeneUtils';
 

diff --git a/src/phovea.ts b/src/phovea.ts
@@ -3,7 +3,7 @@
  * Copyright (c) The Caleydo Team. All rights reserved.
  * Licensed under the new BSD license, available at http://caleydo.org/license
  **************************************************************************** */
-import { IRegistry } from 'tdp_core';
+import type { IRegistry } from 'visyn_core';
 
 export default function (registry: IRegistry) {
   // helper functions copied from tdp_core:
@@ -25,7 +25,7 @@ export default function (registry: IRegistry) {
   /**
    * Set the base data-set
    */
-  actionFunction('chtSetDataset', 'setDatasetImpl', () => import('./Provenance/General'), {
+  actionFunction('chtSetDataset', 'setDatasetImpl', () => import('./Provenance/General.js'), {
     // setDatasetImpl = function that acutally sets the dataset
     analytics: {
       category: 'data', // this one is a data operation (other options are visual, selections, layout, and analysis)
@@ -39,7 +39,7 @@ export default function (registry: IRegistry) {
   /**
    * Add Cohorts
    */
-  actionFunction('addCohorts', 'addOverviewCohortImpl', () => import('./Provenance/CohortEV').then(), {
+  actionFunction('addCohorts', 'addOverviewCohortImpl', () => import('./Provenance/CohortEV.js').then(), {
     //
     analytics: {
       category: 'data', // this one is a data operation (other options are visual, selections, layout, and analysis)
@@ -50,7 +50,7 @@ export default function (registry: IRegistry) {
   /**
    * Remove Cohorts
    */
-  actionFunction('removeCohorts', 'removeOverviewCohortImpl', () => import('./Provenance/CohortEV').then(), {
+  actionFunction('removeCohorts', 'removeOverviewCohortImpl', () => import('./Provenance/CohortEV.js').then(), {
     //
     analytics: {
       category: 'data', // this one is a data operation (other options are visual, selections, layout, and analysis)

diff --git a/src/phovea_registry.ts b/src/phovea_registry.ts
@@ -4,13 +4,14 @@
  * Licensed under the new BSD license, available at http://caleydo.org/license
  **************************************************************************** */
 
-import { PluginRegistry } from 'tdp_core';
+import { PluginRegistry } from 'visyn_core';
 import reg from './phovea';
 
 /**
  * build a registry by registering all phovea modules
  */
 // other modules
+import 'visyn_core/phovea_registry';
 import 'tdp_core/dist/phovea_registry';
 
 // self

diff --git a/src/rest.ts b/src/rest.ts
@@ -1,4 +1,5 @@
-import { Ajax, AppContext, IParams, IRow } from 'tdp_core';
+import { Ajax, AppContext, IRow } from 'visyn_core';
+import { IParams } from 'tdp_core';
 import { deepCopy, log } from './util';
 
 export interface ICohortDBParams extends IParams {

diff --git a/src/util.ts b/src/util.ts
@@ -1,4 +1,4 @@
-import {select, Selection} from 'd3v7';
+import { select, Selection } from 'd3v7';
 import * as logger from 'loglevel';
 import { NotificationHandler } from 'tdp_core';
 import { ICohort } from './CohortInterfaces';
@@ -32,7 +32,8 @@ export const deepCopy = <T>(target: T): T => {
     });
     return cp.map((n: any) => deepCopy<any>(n)) as any;
   }
-  if (typeof target === 'object' && target !== {}) {
+  // not empty object
+  if (typeof target === 'object' && Object.keys(target).length > 0) {
     const cp = { ...(target as { [key: string]: any }) } as { [key: string]: any };
     Object.keys(cp).forEach((k) => {
       cp[k] = deepCopy<any>(cp[k]);