From 083d6e729726b49959449c0a07f53402de3c9cd6 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 1 Apr 2025 13:49:36 -0700
Subject: [PATCH 1/2] Update escape argument name

---
 singlecell/resources/chunks/RunEscape.R                       | 2 +-
 .../org/labkey/singlecell/pipeline/singlecell/RunEscape.java  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/singlecell/resources/chunks/RunEscape.R b/singlecell/resources/chunks/RunEscape.R
index 582d0589f..af9c44251 100644
--- a/singlecell/resources/chunks/RunEscape.R
+++ b/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)
 
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java
index 84e299ca7..639f4f094 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunEscape.java
+++ b/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)

From e8caa8863d1c67b22654292bf134a16ce8aa61e7 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 3 Apr 2025 09:39:06 -0700
Subject: [PATCH 2/2] Update app/dev.tsx

---
 jbrowse/src/client/JBrowse/Browser/app.tsx                   | 1 -
 jbrowse/src/client/JBrowse/Browser/dev.tsx                   | 1 -
 .../VariantSearch/{VariantTable.tsx => VariantSearch.tsx}    | 5 ++---
 jbrowse/src/client/JBrowse/VariantSearch/app.tsx             | 5 ++---
 jbrowse/src/client/JBrowse/VariantSearch/dev.tsx             | 5 ++---
 jbrowse/src/client/JBrowse/VariantTable/app.tsx              | 1 -
 jbrowse/src/client/JBrowse/VariantTable/dev.tsx              | 1 -
 7 files changed, 6 insertions(+), 13 deletions(-)
 rename jbrowse/src/client/JBrowse/VariantSearch/{VariantTable.tsx => VariantSearch.tsx} (96%)

diff --git a/jbrowse/src/client/JBrowse/Browser/app.tsx b/jbrowse/src/client/JBrowse/Browser/app.tsx
index 2cfcb689a..8b000d9d1 100644
--- a/jbrowse/src/client/JBrowse/Browser/app.tsx
+++ b/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 />)
 });
diff --git a/jbrowse/src/client/JBrowse/Browser/dev.tsx b/jbrowse/src/client/JBrowse/Browser/dev.tsx
index 18acf9e82..0b64adbe2 100644
--- a/jbrowse/src/client/JBrowse/Browser/dev.tsx
+++ b/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);
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx b/jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx
similarity index 96%
rename from jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx
rename to jbrowse/src/client/JBrowse/VariantSearch/VariantSearch.tsx
index 75dd70709..a0332e66f 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/VariantTable.tsx
+++ b/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)
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/app.tsx b/jbrowse/src/client/JBrowse/VariantSearch/app.tsx
index e477e2194..9565db3a1 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/app.tsx
+++ b/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 />)
 });
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx b/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx
index 6d9ee77b1..162a0308a 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx
+++ b/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);
diff --git a/jbrowse/src/client/JBrowse/VariantTable/app.tsx b/jbrowse/src/client/JBrowse/VariantTable/app.tsx
index e477e2194..7ffd104e6 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/app.tsx
+++ b/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 />)
 });
diff --git a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx b/jbrowse/src/client/JBrowse/VariantTable/dev.tsx
index 6d9ee77b1..3e874750c 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx
+++ b/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);