Merge pull request #323 from BimberLab/25.3_fb_merge

Merge discvr-24.11 to discvr-25.3

Author: bbimber

jbrowse/src/client/JBrowse/Browser/app.tsx

@@ -2,7 +2,6 @@ import View from './Browser';
 import { createRoot } from 'react-dom/client';
 import React from 'react';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
     createRoot(document.getElementById('app')).render(<View />)
 });

jbrowse/src/client/JBrowse/Browser/dev.tsx

@@ -2,7 +2,6 @@ import View from './Browser';
 import { createRoot } from 'react-dom/client';
 import React from 'react';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
     createRoot(document.getElementById('app')).render(<View />)
 }, true);

…t/JBrowse/VariantSearch/VariantTable.tsx …/JBrowse/VariantSearch/VariantSearch.tsxjbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx renamed to jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx renamed to jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx

@@ -11,12 +11,11 @@ import ExtendedVariantPlugin from '../Browser/plugins/ExtendedVariantPlugin/inde
 import VariantTableWidget from './components/VariantTableWidget';
 import { fetchSession } from '../utils';
 import { ErrorBoundary } from './components/ErrorBoundary';
-import LoadingIndicator from './components/LoadingIndicator';
 import deepmerge from '@mui/utils/deepmerge';
 
 const nativePlugins = [ExtendedVariantPlugin, LogSession]
 
-function VariantTable() {
+function VariantSearch() {
     const queryParam = new URLSearchParams(window.location.search);
     const sessionId = queryParam.get('session') || queryParam.get('database') || queryParam.get('sessionId')
     const locString = queryParam.get('location') || queryParam.get('loc')
@@ -97,4 +96,4 @@ function VariantTable() {
     )
 }
 
-export default observer(VariantTable)
+export default observer(VariantSearch)

jbrowse/src/client/JBrowse/VariantSearch/app.tsx

@@ -1,9 +1,8 @@
 import React from 'react';
 
-import VariantTable from './VariantTable';
+import VariantSearch from './VariantSearch';
 import { createRoot } from 'react-dom/client';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
-    createRoot(document.getElementById('app')).render(<VariantTable />)
+    createRoot(document.getElementById('app')).render(<VariantSearch />)
 });

jbrowse/src/client/JBrowse/VariantSearch/dev.tsx

@@ -1,9 +1,8 @@
 import React from 'react';
 
-import VariantTable from './VariantTable';
+import VariantSearch from './VariantSearch';
 import { createRoot } from 'react-dom/client';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
-    createRoot(document.getElementById('app')).render(<VariantTable />)
+    createRoot(document.getElementById('app')).render(<VariantSearch />)
 }, true);

jbrowse/src/client/JBrowse/VariantTable/app.tsx

@@ -3,7 +3,6 @@ import React from 'react';
 import VariantTable from './VariantTable';
 import { createRoot } from 'react-dom/client';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
     createRoot(document.getElementById('app')).render(<VariantTable />)
 });

jbrowse/src/client/JBrowse/VariantTable/dev.tsx

@@ -3,7 +3,6 @@ import React from 'react';
 import VariantTable from './VariantTable';
 import { createRoot } from 'react-dom/client';
 
-// Need to wait for container element to be available in labkey wrapper before render
 window.addEventListener('DOMContentLoaded', (event) => {
     createRoot(document.getElementById('app')).render(<VariantTable />)
 }, true);

singlecell/resources/chunks/RunEscape.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayName = outputAssayName, doPlot = TRUE, performDimRedux = performDimRedux)
+    seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayBaseName = outputAssayBaseName, doPlot = TRUE, performDimRedux = performDimRedux)
 
     saveData(seuratObj, datasetId)
 

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java

@@ -21,9 +21,9 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunEscape", "Escape/ssGSEA", "escape", "Runs escape to perform ssGSEA using Hallmark gene sets.", Arrays.asList(
-                    SeuratToolParameter.create("outputAssayName", "Output Assay Name", "The name of the assay to store results", "textfield", new JSONObject(){{
+                    SeuratToolParameter.create("outputAssayBaseName", "Output Assay Basename", "The name of the assay to store results", "textfield", new JSONObject(){{
                         put("allowBank", false);
-                    }}, "escape.ssGSEA"),
+                    }}, "escape."),
                     SeuratToolParameter.create("performDimRedux", "Perform DimRedux", "If true, the standard seurat PCA/FindClusters/UMAP process will be run on the escape data. This may be most useful when using a customGeneSet or a smaller set of features/pathways", "checkbox", new JSONObject(){{
 
                     }}, false, null, true)