Merge pull request #271 from BimberLab/24.3_fb_merge

Merge discvr-23.11 to discvr-24.3

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java

@@ -6,20 +6,16 @@
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
 import org.labkey.api.data.RenderContext;
-import org.labkey.api.data.Sort;
-import org.labkey.api.data.UrlColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.util.PageFlowUtil;
-import org.labkey.api.util.StringExpression;
-import org.labkey.api.util.StringExpressionFactory;
-import org.labkey.api.util.URLHelper;
+import org.labkey.api.view.HttpView;
 import org.labkey.api.view.template.ClientDependency;
 
 import java.io.IOException;
 import java.io.Writer;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.LinkedHashSet;
+import java.util.Map;
 import java.util.Set;
 
 /**
@@ -39,11 +35,21 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
     {
         DataColumn ret = new DataColumn(colInfo)
         {
+            private boolean _handlerRegistered = false;
+
             @Override
             public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
             {
                 Object val = ctx.get(FieldKey.fromString(getBoundColumn().getFieldKey().getParent(), "rowId"));
-                out.write(PageFlowUtil.link("Download Sequence").onClick("SequenceAnalysis.window.DownloadSequencesWindow.downloadSingle(" + val + ")").toString());
+                out.write(PageFlowUtil.link("Download Sequence").attributes(Map.of(
+                    "data-rowid", val.toString()
+                )).addClass("sdc-row").toString());
+
+                if (!_handlerRegistered)
+                {
+                    HttpView.currentPageConfig().addHandlerForQuerySelector("a.sdc-row", "click", "SequenceAnalysis.window.DownloadSequencesWindow.downloadSingle(this.attributes.getNamedItem('data-rowid').value); return false;");
+                    _handlerRegistered = true;
+                }
             }
 
             @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java

@@ -28,6 +28,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
+import org.labkey.api.view.HttpView;
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 
@@ -232,6 +233,8 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
         {
             return new DataColumn(colInfo)
             {
+                private boolean _handlerRegistered = false;
+
                 @Override
                 public @NotNull Set<ClientDependency> getClientDependencies()
                 {
@@ -275,8 +278,13 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
                             }
                         }
 
-                        String onclick = "onclick=\"SequenceAnalysis.window.ManageFileSetsWindow.buttonHandlerForOutputFiles(" + PageFlowUtil.jsString(rowId.toString()) + ", " + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + ");\"";
-                        out.write("<a class=\"fa fa-pencil lk-dr-action-icon\" data-tt=\"tooltip\" data-original-title=\"add/edit\" " + onclick + "></a>");
+                        out.write("<a class=\"fa fa-pencil lk-dr-action-icon sfs-row\" data-tt=\"tooltip\" data-rowid=\"" + rowId +"\" data-original-title=\"add/edit\"></a>");
+
+                        if (!_handlerRegistered)
+                        {
+                            HttpView.currentPageConfig().addHandlerForQuerySelector("a.sfs-row", "click", "SequenceAnalysis.window.ManageFileSetsWindow.buttonHandlerForOutputFiles(this.attributes.getNamedItem('data-rowid').value, " + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + "); return false;");
+                            _handlerRegistered = true;
+                        }
                     }
                 }
             };

singlecell/resources/chunks/Functions.R

@@ -173,17 +173,21 @@ readSeuratRDS <- function(filePath) {
     return(seuratObj)
 }
 
-print('Updating future.globals.maxSize')
-options(future.globals.maxSize = Inf)
-
-options('Seurat.memsafe' = TRUE, future.globals.onReference = "warning")
+options(future.globals.maxSize = Inf, future.globals.onReference = "warning")
+options('Seurat.memsafe' = TRUE)
 
 if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
-    print(paste0('Setting future::plan workers to: ', Sys.getenv('SEURAT_MAX_THREADS')))
+    logger::log_info(paste0('Setting future::plan workers to: ', Sys.getenv('SEURAT_MAX_THREADS')))
     mt <- as.integer(Sys.getenv('SEURAT_MAX_THREADS'))
     if (is.na(mt)) {
         stop(paste0('SEURAT_MAX_THREAD is not an integer: ', mt <- Sys.getenv('SEURAT_MAX_THREADS')))
     }
 
-    future::plan(strategy='multisession', workers=mt)
+    fs <- ifelse(exists('futureStrategy'), yes = get('futureStrategy'), no = 'multicore')
+    if (mt == 1) {
+        fs <- 'sequential'
+    }
+    logger::log_info(paste0('Setting future::strategy to: ', fs))
+
+    future::plan(strategy = fs, workers = mt)
 }