Merge pull request #2110 from broadinstitute/development

Release 1.77.1

.github/workflows/build-and-publish-docker-image.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Build requested Docker image
         run: |
           # determine if VERSION_TAG should be set
-          if [[ ${{ github.ref_name }} == 'master' ]]; then
+          if [[ ${{ github.ref_name }} == 'main' ]]; then
             bin/build_image.sh
           else
             bin/build_image.sh -v ${{ github.ref_name }}

.github/workflows/delete-branch-on-merge-to-development.yml

@@ -7,10 +7,10 @@ on:
       - closed
     branches:
       - 'development'
-    
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-  
+
 jobs:
   merge_job:
     # this job will only run if the PR has been merged
@@ -21,7 +21,7 @@ jobs:
     # from the github actions marketplace repo here: https://github.com/pabio/delete-merged-action
       uses: koj-co/delete-merged-action@master
       with:
-      # do not delete master, development branches
-        branches: "!master, !development, *"
+      # do not delete main, development branches
+        branches: "!main, !development, *"
       env:
-        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/delete-branch-on-merge-to-master.yml

@@ -1,16 +1,16 @@
 name: Selectively delete feature branch after merge to master
 
-# Only run the workflow when a PR that targets master is closed
+# Only run the workflow when a PR that targets main is closed
 on:
   pull_request:
     types:
       - closed
     branches:
-      - 'master'
+      - 'main'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-  
+
 jobs:
   merge_job:
     # this job will only run if the PR has been merged
@@ -21,7 +21,7 @@ jobs:
     # from the github actions marketplace repo here: https://github.com/pabio/delete-merged-action
       uses: koj-co/delete-merged-action@master
       with:
-      # do not delete master, development, or hotfix-release branches
-        branches: "!master, !development, !*hotfix*, *"
+      # do not delete main, development, or hotfix-release branches
+        branches: "!main, !development, !*hotfix*, *"
       env:
-        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/deploy-to-production.yml

@@ -63,4 +63,4 @@ jobs:
           if [[ "${{ github.event.inputs.rollback }}" = "Y" ]]; then
             ROLLBACK="-R"
           fi
-          bin/deploy-github.sh -b master -e production -g ${{ env.GOOGLE_CLOUD_PROJECT }} -h ${{ env.REMOTE_HOST }} -p ${{ env.CONFIG_FILENAME }} -s ${{ env.DEFAULT_SA_KEYFILE }} -r ${{ env.READONLY_SA_KEYFILE }} $ROLLBACK
+          bin/deploy-github.sh -b main -e production -g ${{ env.GOOGLE_CLOUD_PROJECT }} -h ${{ env.REMOTE_HOST }} -p ${{ env.CONFIG_FILENAME }} -s ${{ env.DEFAULT_SA_KEYFILE }} -r ${{ env.READONLY_SA_KEYFILE }} $ROLLBACK

.github/workflows/run-all-tests.yml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - development
-      - master
+      - main
   pull_request:
 env:
   DOCKER_IMAGE_NAME: "gcr.io/broad-singlecellportal-staging/single-cell-portal"

README.md

@@ -474,14 +474,14 @@ To deploy or access an instance of Single Cell Portal in production mode:
 * Once connected, switch to root via `sudo -i`.
 * Change directory to where the portal is running, for instance: `cd /home/docker-user/deployments/single_cell_portal`
 * Switch to the Docker user: `sudo -u docker-user -Hs`
-* Get latest source code from GitHub: `git pull origin master`
+* Get latest source code from GitHub: `git pull origin main`
 * Exit Docker user to return to root: `exit`
 * Ensure no uploads are occuring: `tail -n 1000 log/production.log`
 * Put the portal in maintenance mode: `bin/enable_maintenance.sh on`
 * Stop the portal: `docker stop single_cell`
 * Remove the container instance: `docker rm single_cell`
 * Launch a new instance of the portal with the updated container (please refer to the
-[bin/boot_docker](https://github.com/broadinstitute/single_cell_portal_core/blob/master/bin/boot_docker) script for more
+[bin/boot_docker](https://github.com/broadinstitute/single_cell_portal_core/blob/main/bin/boot_docker) script for more
 information regarding all possible arguments as they are not all listed here):
 
 

app/javascript/components/upload/ClusteringFileForm.jsx

@@ -47,7 +47,7 @@ export default function ClusteringFileForm({
         trigger={['hover', 'focus']}
         rootClose placement="top"
         overlay={obsmKeyNameHelpContent()}>
-        <span> .obsm key name <FontAwesomeIcon icon={faQuestionCircle}/></span>
+        <span> .obsm key name * <FontAwesomeIcon icon={faQuestionCircle}/></span>
       </OverlayTrigger>
     </span>
 

app/javascript/components/upload/ClusteringStep.jsx

@@ -70,7 +70,7 @@ function getDetailsContent(isAnnDataExperience, clusterFiles, addNewFile) {
           <div className="form-terra">
             <div className="row">
               <div className="col-md-12">
-                <p>A <a href="https://github.com/broadinstitute/single_cell_portal/blob/master/demo_data/cluster_example.txt" target="_blank" rel="noreferrer">cluster file</a> (.txt or .txt.gz) contains any cluster ordinations and optional cluster-specific metadata.</p>
+                <p>A <a href="https://github.com/broadinstitute/single_cell_portal/blob/main/demo_data/cluster_example.txt" target="_blank" rel="noreferrer">cluster file</a> (.txt or .txt.gz) contains any cluster ordinations and optional cluster-specific metadata.</p>
               </div>
             </div>
             <div className="row">

app/javascript/components/upload/CoordinateLabelStep.jsx

@@ -51,7 +51,7 @@ function CoordinateLabelForm({
       <div className="col-md-12">
         <div className="form-terra">
           <p>
-            A <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/master/demo_data/coordinate_labels_example.txt" target="_blank" rel="noopener noreferrer">Coordinate Label File</a>
+            A <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/main/demo_data/coordinate_labels_example.txt" target="_blank" rel="noopener noreferrer">Coordinate Label File</a>
             &nbsp;specifies labels to display at specified coordinates of a cluster.
           </p>
           <pre>

app/javascript/components/upload/GeneListStep.jsx

@@ -53,7 +53,7 @@ function GeneListForm({
           <p>
             The file must be tab- or comma-delimited plain text (.txt) with the value &quot;GENE NAMES&quot; in the first column, and cluster names in each successive column.
             <br/>
-            <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/master/demo_data/marker_gene_list_example.txt" target="_blank" rel="noreferrer noopener">
+            <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/main/demo_data/marker_gene_list_example.txt" target="_blank" rel="noreferrer noopener">
               Example file
             </a>
             <br/>

app/javascript/components/upload/RawCountsStep.jsx

@@ -98,12 +98,12 @@ export function getExpressionFileInfoMessage(isAnnDataExperience, expressionType
 const expressionFileStructureHelp = <>
   <div className="row">
     <div className="col-sm-6 padded">
-      <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/master/demo_data/expression_example.txt" target="_blank" rel="noreferrer noopener">Dense matrix</a>
+      <a href="https://raw.githubusercontent.com/broadinstitute/single_cell_portal/main/demo_data/expression_example.txt" target="_blank" rel="noreferrer noopener">Dense matrix</a>
       <pre>GENE&#09;CELL_1&#9;CELL_2&#09;CELL_3&#09;...<br/>It2ma&#09;0&#09;0&#09;0&#09;...<br/>Sergef&#09;0&#09;7.092&#09;0&#09;...<br/>Chil5&#09;0&#09;0&#09;0&#09;...<br/>Fgfr3&#09;0&#9;0&#09;0.978&#09;<br/>...</pre>
       A “Dense matrix” is a file (.txt, .tsv, or .csv)** that has a header row containing the value “GENE” in the first column, and single cell names in each successive column.
     </div>
     <div className="col-sm-6 padded" >
-      <a href="https://github.com/broadinstitute/single_cell_portal_core/blob/master/test/test_data/GRCh38/matrix.mtx" target="_blank" rel="noreferrer noopener">Sparse matrix (.mtx)</a>
+      <a href="https://github.com/broadinstitute/single_cell_portal_core/blob/main/test/test_data/GRCh38/matrix.mtx" target="_blank" rel="noreferrer noopener">Sparse matrix (.mtx)</a>
       <pre>%%MatrixMarket matrix coordinate real general<br/>%<br/>17123 31231 124124<br/>1 1241 1.0<br/>1 1552 2.0<br/>...</pre>
       A “Sparse matrix,” as seen in <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices" target="_blank" rel="noreferrer noopener">10x Genomics</a>
       , is a Matrix Market file (.mtx, .mm, or .txt)** that contains a sparse matrix in coordinate form.<br/>

app/javascript/components/upload/SpatialStep.jsx

@@ -54,7 +54,7 @@ export function SpatialUploadForm({
           <div className="row">
             <div className="col-md-12">
               <p>
-                A <a href="https://github.com/broadinstitute/single_cell_portal/blob/master/demo_data/spatial_example.txt" target="_blank" rel="noreferrer">spatial file</a>
+                A <a href="https://github.com/broadinstitute/single_cell_portal/blob/main/demo_data/spatial_example.txt" target="_blank" rel="noreferrer">spatial file</a>
                 &nbsp;(.txt or .txt.gz) contains <a href="https://en.wikipedia.org/wiki/Spatial_transcriptomics" target="_blank" rel="noreferrer">spatial transcriptomics</a> cell coordinates and optional metadata.
               </p>
             </div>

app/javascript/lib/metrics-api.js

@@ -384,12 +384,15 @@ function getAnalyticsPageName() {
 /**
  * gets the tab name for analytics
  */
-function getTabProperty() {
-  if (window.location.href?.match(/\?tab=/)) {
-    return window.location.href.split('?tab=')[1]
-  } else {
-    return window.location.hash?.replace(/#/, '')
+export function getTabProperty() {
+  let tabParam = window.location.hash?.replace(/#/, '')
+  if (window.location.search) {
+    const searchParams = new URLSearchParams(window.location.search)
+    if (searchParams.has('tab')) {
+      tabParam = searchParams.get('tab')
+    }
   }
+  return tabParam
 }
 
 /**

app/javascript/lib/plot.js

@@ -25,6 +25,7 @@ const SPECIAL_LEGEND_ENTRIES = [UNSPECIFIED_ANNOTATION_NAME, FILTERED_TRACE_NAME
  * central memory CD4-positive, alpha-beta T cell
  */
 export function safenLabels(labels) {
+  if (!labels) {return labels} // Prevents erroring gene exp scatter on legend filter
   if (Array.isArray(labels)) {
     return labels.map(label => label.replaceAll(',', '-'))
   } else {

bin/deploy-github.sh

@@ -14,7 +14,7 @@ function main {
   # defaults
   SSH_USER="jenkins"
   DESTINATION_BASE_DIR='/home/jenkins/deployments/single_cell_portal_core'
-  GIT_BRANCH="master"
+  GIT_BRANCH="main"
   PASSENGER_APP_ENV="production"
   BOOT_COMMAND="bin/remote_deploy.sh"
   SCP_REPO="https://github.com/broadinstitute/single_cell_portal_core.git"
@@ -170,7 +170,7 @@ USAGE:
 
 [OPTIONS]
 -e VALUE    set the environment to boot the portal in (defaults to production)
--b VALUE    set the branch to pull from git (defaults to master)
+-b VALUE    set the branch to pull from git (defaults to main)
 -d VALUE    set the target directory to deploy from (defaults to $DESTINATION_BASE_DIR)
 -S VALUE    set the path to SSH_KEYFILE (private key for SSH auth, no default, not needing except for manual testing)
 -h VALUE    set the DESTINATION_HOST (remote GCP VM to SSH into, no default)

test/js/explore/plot-utils.test.js

@@ -1,4 +1,4 @@
-import PlotUtils from 'lib/plot'
+import PlotUtils, { safenLabels } from 'lib/plot'
 
 describe('Plot grouping function cache', () => {
   it('makes traces based on the annotation groups', async () => {
@@ -165,4 +165,10 @@ describe('Plot grouping function cache', () => {
       ...data
     })
   })
+
+  it('does not error when raw labels are undefined', async () => {
+    // This prevents erroring gene expression scatter plots up applying a legend filter
+    const safeLabels = safenLabels(undefined)
+    expect(safeLabels).toBeUndefined()
+  })
 })

test/js/metrics-api.test.js

@@ -5,7 +5,7 @@ const fetch = require('node-fetch')
 import { screen, render, fireEvent } from '@testing-library/react'
 import React from 'react';
 
-import {logClick, logClickLink, logMenuChange, setMetricsApiMockFlag} from 'lib/metrics-api'
+import { logClick, logClickLink, logMenuChange, setMetricsApiMockFlag, getTabProperty } from 'lib/metrics-api'
 import {logToSentry} from 'lib/sentry-logging'
 import * as SCPContextProvider from '~/providers/SCPContextProvider'
 import * as Sentry from '@sentry/react'
@@ -157,4 +157,27 @@ describe('Library for client-side usage analytics', () => {
     expect(numDroppedWhenInfo).toEqual(1)
   })
 
+  it('sets tab parameter correctly', () => {
+    delete global.window.location
+    global.window = Object.create(window)
+    global.window.location = {
+      pathname: '/single_cell/study/SCP1234'
+    }
+    let enabledTab = getTabProperty()
+    expect(enabledTab).toBeUndefined()
+
+    global.window.location = {
+      hash: '#study-visualize',
+      pathname: '/single_cell/study/SCP1234'
+    }
+    enabledTab = getTabProperty()
+    expect(enabledTab).toEqual('study-visualize')
+
+    global.window.location = {
+      search: '?cluster=foo&genes=bar&tab=distribution',
+      pathname: '/single_cell/study/SCP1234'
+    }
+    enabledTab = getTabProperty()
+    expect(enabledTab).toEqual('distribution')
+  })
 })