Merge branch 'main' of github.com:broadinstitute/taiga

Author: pgm

.github/workflows/build-docker.yaml

@@ -1,8 +1,6 @@
 name: Build Taiga image
 
-on: 
-    push:
-        branches: main
+on: push
 
 env:
   IMAGE_TAG: us.gcr.io/cds-docker-containers/taiga:ga-build-${{ github.run_number }}
@@ -18,6 +16,8 @@ jobs:
       - uses: actions/checkout@v2
       - name: write SHA to file
         run: "bash write_version.sh ${{ github.sha }}"
+      - name: bundle JS
+        run: "bash bundle_js.sh"
       - name: Login to GCR
         uses: docker/login-action@v2
         with:
@@ -31,6 +31,8 @@ jobs:
       - name: Push Docker image
         run: docker push ${{ env.IMAGE_TAG }}
       - name: Tag as latest
+        if: github.ref == 'refs/heads/main'
         run: docker tag ${{ env.IMAGE_TAG }} ${{ env.FINAL_IMAGE_TAG }}
       - name: Push Docker image
+        if: github.ref == 'refs/heads/main'
         run: docker push ${{ env.FINAL_IMAGE_TAG }}

README.md

@@ -14,7 +14,7 @@ Taiga 2 is built on the following stack:
 
 ### Database
 
-- PostGre (to store the app information)
+- PostgreSQL (to store the app information)
 - Psycopg2
 - SQLAlchemy
 - Amazon S3 (to store the files)

bundle_js.sh

@@ -0,0 +1,4 @@
+set -ex
+cd react_frontend
+yarn install
+./node_modules/.bin/webpack --mode=production

install_prereqs.sh

@@ -1,5 +1,4 @@
 set -ex
-pip install -r dev-requirements.txt
-python setup.py develop
 pre-commit install
+poetry install
 yarn install --cwd react_frontend

react_frontend/package.json

@@ -9,6 +9,7 @@
   "dependencies": {
     "aws-sdk": "^2.7.17",
     "bootstrap": "^3.3.7",
+    "classnames": "^2.5.1",
     "clipboard": "^1.6.0",
     "css-loader": "^5.2.4",
     "d3-array": "^1.2.1",

react_frontend/src/components/DatasetView.tsx

@@ -12,7 +12,7 @@ import * as Models from "../models/models";
 import { TaigaApi } from "../models/api";
 
 import * as Dialogs from "./Dialogs";
-import { CreateDatasetDialog, CreateVersionDialog } from "./modals/UploadForm";
+import {  CreateVersionDialog } from "./modals/UploadDialogs";
 
 import { toLocalDateString } from "../utilities/formats";
 import { LoadingOverlay } from "../utilities/loading";
@@ -461,7 +461,6 @@ export class DatasetView extends React.Component<
           // We stop the loading, and download the file because it is ready
           result.urls.forEach((url) => {
             window.location.href = url;
-            console.log("- " + url);
           });
         }
       })
@@ -1179,7 +1178,6 @@ export class DatasetView extends React.Component<
               initialValue={this.state.datasetVersion.description}
               save={(description: string) => {
                 this.setState({ showEditDescription: false });
-                console.log("Save description: " + description);
                 this.updateDescription(description);
               }}
             />

react_frontend/src/components/FolderView.tsx

@@ -11,7 +11,7 @@ import * as Dialogs from "./Dialogs";
 import { EntryUsersPermissions } from "./modals/EntryUsersPermissions";
 import { NotFound } from "./NotFound";
 import { SearchInput } from "./Search";
-import { CreateDatasetDialog } from "./modals/UploadForm";
+import { CreateDatasetDialog } from "./modals/UploadDialogs";
 import { toLocalDateString } from "../utilities/formats";
 import { relativePath } from "../utilities/route";
 import { LoadingOverlay } from "../utilities/loading";
@@ -103,9 +103,7 @@ export class FolderView extends React.Component<
     // respond to parameter change in scenario 3
     let oldId = prevProps.match.params.folderId;
     let newId = this.props.match.params.folderId;
-    console.log("componentDidUpdate");
     if (newId !== oldId) {
-      console.log("doFetch");
       this.doFetch().then(() => {
         this.logAccess();
       });
@@ -143,18 +141,15 @@ export class FolderView extends React.Component<
     } = {};
     let _folder: Folder.Folder = null;
 
-    console.log("get_folder fetch", this.props);
 
     return tapi
       .get_folder(this.props.match.params.folderId)
       .then((folder) => {
-        console.log("get_folder complete", folder);
         _folder = new Folder.Folder(folder);
         this.setState({ sharingEntries: [_folder] });
         return folder.entries;
       })
       .then((entries: Array<Folder.FolderEntries>) => {
-        console.log("get_folder entries", entries);
 
         // We want to ask the server a bulk of the datasets and the datasetVersions
         let datasetIds = entries
@@ -561,7 +556,6 @@ export class FolderView extends React.Component<
 
   render() {
     const { user } = this.props;
-    console.log("user", user);
 
     let entriesOutput: Array<any> = [];
     let navItems: MenuItem[] = [];

react_frontend/src/components/SearchView.tsx

@@ -99,8 +99,6 @@ export class SearchView extends React.Component<
 
     // Get the datasets from query + current_folder
     this.doFetchSearch().then((searchResult: Models.SearchResult) => {
-      console.log("Received the search results!");
-      console.log("=> " + searchResult);
 
       this.setState({
         folder: searchResult.current_folder,

react_frontend/src/components/UploadTracker.tsx

@@ -94,7 +94,6 @@ export class UploadTracker {
     params: CreateVersionParams | CreateDatasetParams,
     uploadProgressCallback: (status: Array<UploadStatus>) => void
   ): Promise<DatasetIdAndVersionId> {
-    console.log("uploading, params:", params);
 
     this.uploadProgressCallback = uploadProgressCallback;
 
@@ -108,7 +107,6 @@ export class UploadTracker {
         return this.submitCreateDataset(credentials, uploadFiles, sid, params);
       })
       .then((datasetId) => {
-        console.log("Created new dataset", datasetId);
         return datasetId;
       });
   }
@@ -270,7 +268,6 @@ export class UploadTracker {
 
     this.uploadStatus = uploadStatus;
 
-    // console.log("kicking off upload of " + uploadPromises.length + " files");
 
     return Promise.all(uploadPromises).then(
       (successes: Array<boolean>): Promise<DatasetIdAndVersionId> => {

react_frontend/src/components/modals/FigshareWYSIWYGEditor.tsx

@@ -6,12 +6,12 @@ let Inline = Quill.import("blots/inline");
 class BoldBlot extends Inline {}
 BoldBlot.blotName = "bold";
 BoldBlot.tagName = "b";
-Quill.register("formats/bold", BoldBlot);
+Quill.register("formats/bold", BoldBlot, true);
 
 class ItalicBlot extends Inline {}
 ItalicBlot.blotName = "italic";
 ItalicBlot.tagName = "i";
-Quill.register("formats/bold", ItalicBlot);
+Quill.register("formats/bold", ItalicBlot, true);
 
 const modules = {
   toolbar: [