Controls Sequencing Requirements

src/main/java/com/velox/sloan/cmo/workflows/workflows/ControlFieldsPopulator.java

@@ -0,0 +1,148 @@
+package com.velox.sloan.cmo.workflows.workflows;
+
+import com.velox.api.datarecord.*;
+import com.velox.api.plugin.PluginResult;
+import com.velox.api.workflow.ActiveTask;
+import com.velox.sapioutils.server.plugin.DefaultGenericPlugin;
+import com.velox.sapioutils.shared.enums.PluginOrder;
+import org.apache.commons.lang3.exception.ExceptionUtils;
+
+import java.rmi.RemoteException;
+import java.rmi.ServerException;
+import java.util.*;
+
+/**
+ * Plugin to populate fields for control samples.
+ * 
+ * This plugin performs three main steps:
+ * 1. Reads species and recipe values from non-control samples
+ * 2. Populates control samples with the same species and recipe values
+ * 3. Links all control samples to a constant dummy request record
+ * 
+ * The plugin identifies controls using the "IsControl" boolean field in Sample records.
+ * Controls inherit the species and recipe from regular samples in the same workflow,
+ * ensuring consistency and enabling automated processing.
+ * 
+ * @author patelo2
+ */
+public class ControlFieldsPopulator extends DefaultGenericPlugin {
+
+  private static final String DUMMY_REQUEST_ID = "07000";
+
+    /**
+     * Constructor - sets plugin execution parameters
+     */
+    public ControlFieldsPopulator() {
+        setTaskEntry(true);
+        setOrder(PluginOrder.MIDDLE.getOrder());
+    }
+
+    /**
+     * Determines whether this plugin should run for the current task.
+     * 
+     * @return true if plugin should execute, false otherwise
+     * @throws RemoteException if there's an error accessing task information
+     */
+    @Override
+    public boolean shouldRun() throws RemoteException {
+        return activeTask.getStatus() != ActiveTask.COMPLETE &&
+               activeTask.getTask().getTaskOptions().containsKey("POPULATE CONTROL FIELDS") &&
+               !activeTask.getTask().getTaskOptions().containsKey("_CONTROL FIELDS POPULATED");
+    }
+
+    /**
+     * Main plugin execution method.
+     * 
+     * Executes the three-step control population process:
+     * 1. Find non-control samples and extract their species/recipe values
+     * 2. Populate all control samples with the extracted values
+     * 3. Link all controls to a constant dummy request record
+     * 
+     * @return PluginResult indicating success or failure
+     * @throws Exception if any error occurs during execution
+     */
+    public PluginResult run() throws Exception {
+        try {
+            List<DataRecord> samples = activeTask.getAttachedDataRecords("Sample", user);
+
+            // Step 1: Find species and recipe from non-control samples
+            String species = "";
+            String recipe = "";
+            for (DataRecord sample : samples) {
+                Object isControl = sample.getValue("IsControl", user);
+                // Only process non-control samples (ignore IsControl = false samples completely)
+                if (isControl == null || !(Boolean) isControl) {
+                    species = sample.getStringVal("Species", user);
+                    recipe = sample.getStringVal("Recipe", user);
+                    if (species != null && recipe != null) {
+                        logInfo("Found species: " + species + ", recipe: " + recipe + " from non-control sample");
+                        break;
+                    }
+                }
+            }
+            // Step 2: Populate control samples with species and recipe
+            for (DataRecord sample : samples) {
+                Object isControl = sample.getValue("IsControl", user);
+                if (isControl != null && (Boolean) isControl) {
+                    String sampleId = sample.getStringVal("SampleId", user);
+                    sample.setDataField("Species", species, user);
+                    sample.setDataField("Recipe", recipe, user);
+                    sample.setDataField("RequestId", DUMMY_REQUEST_ID, user);
+                    logInfo("Updated control sample " + sampleId + " with species: " + species + ", recipe: " + recipe);
+                }
+            }
+            // Step 3: Link all control samples to the constant dummy request record
+            DataRecord dummyRecord = getDummyRecord();
+            if (dummyRecord != null) {
+                for (DataRecord sample : samples) {
+                    Object isControl = sample.getValue("IsControl", user);
+                    if (isControl != null && (Boolean) isControl) {
+                        String sampleId = sample.getStringVal("SampleId", user);
+                        dummyRecord.addChild(sample, user);
+                        logInfo("Linked control sample " + sampleId + " to dummy request record");
+                    }
+                }
+            } else {
+                logError("Could not find or create dummy request record");
+                return new PluginResult(false);
+            }
+
+            // Mark task as completed
+            activeTask.getTask().getTaskOptions().put("_CONTROL FIELDS POPULATED", "");
+
+        } catch (ServerException e) {
+            String errMsg = String.format("ServerException while populating control fields:\n%s", ExceptionUtils.getStackTrace(e));
+            clientCallback.displayError(errMsg);
+            logError(errMsg);
+            return new PluginResult(false);
+        }
+
+        return new PluginResult(true);
+    }
+
+    /**
+     * Gets the constant dummy request record for linking controls.
+     * This method queries for the existing dummy request record using the predefined RequestId.
+     * The dummy request record should already exist in the system.
+     * 
+     * @return DataRecord representing the dummy request, or null if not found
+     */
+    private DataRecord getDummyRecord() {
+        try {
+            List<DataRecord> dummyRecords = dataRecordManager.queryDataRecords("Request", 
+                "RequestId = '" + DUMMY_REQUEST_ID + "'", user);
+
+            if (dummyRecords != null && !dummyRecords.isEmpty()) {
+                logInfo("Found existing dummy request record with ID: " + DUMMY_REQUEST_ID);
+                return dummyRecords.get(0);
+            } else {
+                logError("No dummy request record found with ID: " + DUMMY_REQUEST_ID + ". Please ensure the record exists in the system.");
+                return null;
+            }
+
+        } catch (Exception e) {
+            logError("Error querying for dummy request record: " + e.getMessage());
+        }
+        return null;
+    }
+}

src/main/java/com/velox/sloan/cmo/workflows/workflows/CreateSeqReqForControls.java

@@ -0,0 +1,72 @@
+package com.velox.sloan.cmo.workflows.workflows;
+
+import com.velox.api.datarecord.*;
+import com.velox.api.plugin.PluginResult;
+import com.velox.api.workflow.ActiveTask;
+import com.velox.sapio.commons.exemplar.plugin.PluginOrder;
+import com.velox.sapioutils.server.plugin.DefaultGenericPlugin;
+import org.apache.commons.lang3.exception.ExceptionUtils;
+
+import java.rmi.RemoteException;
+import java.rmi.ServerException;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+public class CreateSeqReqForControls extends DefaultGenericPlugin {
+    public CreateSeqReqForControls() {
+        setTaskEntry(true);
+        setOrder(PluginOrder.EARLY.getOrder());
+    }
+    @Override
+    public boolean shouldRun() throws RemoteException {
+        return activeTask.getStatus() != ActiveTask.COMPLETE && activeTask.getTask().getTaskOptions().containsKey("CREATE SEQ REQUIREMENTS FOR CONTROLS")
+                && !activeTask.getTask().getTaskOptions().containsKey("_CONTROLS SEQ REQUIREMENTS CREATED");
+    }
+
+    public PluginResult run() throws Exception {
+        try {
+            List<DataRecord> coverageReqRefs = this.dataRecordManager.queryDataRecords("ApplicationReadCoverageRef",
+                    "ReferenceOnly != 1 AND isControl = 1 ", this.user);
+            List<DataRecord> samples = activeTask.getAttachedDataRecords("Sample", user);
+            List<DataRecord> seqReuirements = new LinkedList<>();
+            for (DataRecord sample : samples) {
+                boolean isControl = sample.getBooleanVal("IsControl", user);
+                if (isControl) {
+                    Map<String, Object> values = new HashMap<>();
+                    String sampleId = sample.getStringVal("SampleId", user);
+                    String sampleName = sample.getStringVal("OtherSampleId", user);
+                    String recipe = sample.getStringVal("Recipe", user);
+                    String species = sample.getStringVal("Species", user);
+                    for (DataRecord ref : coverageReqRefs) {
+                        if (ref.getStringVal("PlatformApplication", user).equalsIgnoreCase(recipe)) {
+                            values.put("SequencingRunType", ref.getStringVal("SequencingRunType", user));
+                            if (species.equalsIgnoreCase("Human")) {
+                                values.put("RequestedReads", ref.getStringVal("MillionReadsHuman", user));
+                            }
+                            else if (species.equalsIgnoreCase("Mouse")) {
+                                values.put("RequestedReads", ref.getStringVal("MillionReadsMouse", user));
+                            }
+                        }
+                    }
+                    values.put("SampleId", sampleId);
+                    values.put("OtherSampleId", sampleName);
+                    DataRecord newSeqReqRecord = dataRecordManager.addDataRecord("SeqRequirement", user);
+                    newSeqReqRecord.setFields(values, user);
+                    sample.addChild(newSeqReqRecord, user);
+                    seqReuirements.add(newSeqReqRecord);
+                }
+            }
+            this.activeTask.addAttachedDataRecords(seqReuirements);
+
+            activeTask.getTask().getTaskOptions().put("_CONTROLS SEQ REQUIREMENTS CREATED", "");
+        } catch (ServerException e) {
+            String errMsg = String.format("ServerException while setting sequencing requirements for controls:\n%s", ExceptionUtils.getStackTrace(e));
+            clientCallback.displayError(errMsg);
+            logError(errMsg);
+            return new PluginResult(false);
+        }
+        return new PluginResult(true);
+        }
+}

src/main/java/com/velox/sloan/cmo/workflows/workflows/SmartSeq/CreateSequencingRequirments.java

@@ -35,7 +35,6 @@ public PluginResult run() throws Exception {
                 Map<String, Object> values = new HashMap<>();
                 String sampleId = sample.getStringVal("SampleId", user);
                 String sampleName = sample.getStringVal("OtherSampleId", user);
-                String otherSampleId = sample.getStringVal("OtherSampleId", user);
                 String tumorOrNormal = sample.getStringVal("TumorOrNormal", user);
                 values.put("SampleId", sampleId);
                 values.put("SequencingRunType","PE100");
@@ -54,7 +53,7 @@ public PluginResult run() throws Exception {
 
             activeTask.getTask().getTaskOptions().put("_SEQ REQUIREMENTS CREATED", "");
         } catch (ServerException e) {
-            String errMsg = String.format("ServerException while splitting SmartSeq samples:\n%s", ExceptionUtils.getStackTrace(e));
+            String errMsg = String.format("ServerException while setting sequencing requirements for SMARTSeq samples:\n%s", ExceptionUtils.getStackTrace(e));
             clientCallback.displayError(errMsg);
             logError(errMsg);
             return new PluginResult(false);

src/main/java/com/velox/sloan/cmo/workflows/workflows/SmartSeq/SmartSeqSampleSplitter.java

@@ -153,20 +153,12 @@ public PluginResult run() throws RemoteException, com.velox.api.util.ServerExcep
                     }
                 }
                 this.activeTask.removeTaskAttachment(sample.getRecordId());
-                logInfo("Removed the attached sample!!");
                 this.activeTask.addAttachedDataRecords(toGetAttached);
-                logInfo("Attached new splitted samples");
                 sample.setDataField("ExemplarSampleStatus", "Completed - Smart-Seq cDNA Preparation", user);
                 logInfo("Original sample status updated to: Completed - Smart-Seq cDNA Preparation");
                 activeWorkflow.getNext(activeTask).addAttachedDataRecords(toGetAttached);
-                logInfo("Add new attachments to the next step!");
-                //this.activeTask.removeTaskAttachment(sample.getRecordId());
-
             }
-
-
             activeTask.getTask().getTaskOptions().put("_SMARTSEQ SAMPLE SPLITTED", "");
-            logInfo("Task option updated!");
 
         } catch (NotFound | InvalidValue e) {
             String errMsg = String.format("Not Found or Invalid Value exception while splitting SmartSeq samples:\n%s", ExceptionUtils.getStackTrace(e));
@@ -187,7 +179,6 @@ public PluginResult run() throws RemoteException, com.velox.api.util.ServerExcep
         } catch (AlreadyExists e) {
             throw new RuntimeException(e);
         }
-        logInfo("Right before returning true for plugin result!");
         return new PluginResult(true);
     }
 }