Use consistent delimiter for seurat-related fields

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -333,7 +333,7 @@ else if (NumberUtils.isCreatable(val))
         else if ("sequenceanalysis-trimmingtextarea".equals(pd.getFieldXtype()))
         {
             val = val.replace("'", "\\\'");
-            String[] vals = val.split(",");
+            String[] vals = val.split(pd.getDelimiter());
             return "c('" + StringUtils.join(vals, "','") + "')";
         }
         else if (pd.isMultiValue())

singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java

@@ -23,6 +23,13 @@ public SeuratToolParameter(String name, String label, String description, String
         _isMultiValue = isMultiValue;
     }
 
+    public SeuratToolParameter delimiter(String delim)
+    {
+        _delimiter = delim;
+
+        return this;
+    }
+
     public static SeuratToolParameter create(String name, String label, String description, String fieldXtype, @Nullable JSONObject additionalExtConfig, @Nullable Object defaultValue)
     {
         return new SeuratToolParameter(name, label, description, fieldXtype, defaultValue, additionalExtConfig, null, true, false);

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

@@ -26,11 +26,11 @@ public Provider()
                     SeuratToolParameter.create("adtWhitelist", "ADT Whitelist", "If provided, these ADTs will be scaled and used for PCA. If empty, all ADTs will be used.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null),
+                    }}, null).delimiter(","),
                     SeuratToolParameter.create("adtBlacklist", "ADT Blacklist", "If provided, these ADTs will be excluded from scaling/PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null)
+                    }}, null).delimiter(",")
                     ), null, null);
         }
 

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

@@ -26,7 +26,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null)
+                    }}, null).delimiter(",")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 

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

@@ -26,7 +26,7 @@ public Provider()
                     SeuratToolParameter.create("subsetFields", "Additional Grouping Fields", "A comma-separated list of fields that will be used to subset data within each seurat object. For example, if 'BarcodePrefix' is provided and 500 target cells is selected, each incoming seurat object will be subset to no more than 500 cells per unique value of BarcodePrefix. If blank, each object will be treated as one unit of data.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null, "subsetFields", true, true),
+                    }}, null, "subsetFields", true, true).delimiter(","),
                     SeuratToolParameter.create("seed", "Random Seed", "This random seed, used for downsampling", "ldk-integerfield", new JSONObject(){{
 
                     }}, 1234)

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

@@ -26,7 +26,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null)
+                    }}, null).delimiter(",")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 

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

@@ -28,7 +28,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 200);
                         put("delimiter", ",");
-                    }}, null),
+                    }}, null).delimiter(","),
                     SeuratToolParameter.create("testsToUse", "Tests To Use", "The set of tests to perform.", "ldk-simplecombo", new JSONObject()
                     {{
                         put("multiSelect", true);

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

@@ -28,15 +28,15 @@ public Provider()
                     SeuratToolParameter.create("variableGenesWhitelist", "Genes to Add to VariableFeatures", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null),
+                    }}, null).delimiter(","),
                     SeuratToolParameter.create("variableGenesBlacklist", "Genes to Exclude From VariableFeatures", "These genes, entered comma-separated or one/line, will be excluded from the genes passed to RunPCA (which is otherwise determined by Seurat::VariableFeatures)", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null),
+                    }}, null).delimiter(","),
                     SeuratToolParameter.create("featuresToRegress", "Features to Regress", "These features, entered comma-separated or one/line, will be passed to Seurat::ScaleData vars.to.regress", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null),
+                    }}, null).delimiter(","),
                     SeuratToolParameter.create("scaleVariableFeaturesOnly", "ScaleData On Variable Features Only", "If checked, ScaleData will only be performed on VariableFeatures, which should dramatically reduce time and memory", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),

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

@@ -26,7 +26,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6")
+                    }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6").delimiter(",")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }