Enhancement/dl/fix qc avg size

src/main/java/com/velox/sloan/cmo/workflows/qualitycontrol/sequencingqc/FixAvgLibSize.java

@@ -0,0 +1,141 @@
+package com.velox.sloan.cmo.workflows.qualitycontrol.sequencingqc;
+
+import com.velox.api.datarecord.DataRecord;
+import com.velox.api.datarecord.IoError;
+import com.velox.api.datarecord.NotFound;
+import com.velox.api.datarecord.InvalidValue;
+import com.velox.api.plugin.PluginResult;
+import com.velox.api.util.ServerException;
+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.StringUtils;
+import org.apache.commons.lang3.exception.ExceptionUtils;
+import com.velox.api.user.User;
+//import javax.xml.crypto.Data;
+import java.rmi.RemoteException;
+import java.util.List;
+import java.util.Arrays;
+import java.util.*;
+
+/**
+ * This plugin is designed to repopulate QCDatum with the Average Library Size value from
+ * Molar Concentration Assignment to update Lib QC Reports per the Calculate Molarity
+ * step of the Lib/Pool QC workflow
+ */
+public class FixAvgLibSize extends DefaultGenericPlugin {
+    User user;
+
+
+    public FixAvgLibSize() {
+        setTaskSubmit(true);
+        setOrder(PluginOrder.LAST.getOrder());
+        setIcon("com/velox/sloan/cmo/resources/import_32.gif");
+    }
+
+    @Override
+    public boolean shouldRun() throws RemoteException, ServerException, NotFound {
+        if (activeTask.getTaskName().equals("Calculate Molarity") && activeTask.getTask().getTaskOptions().containsKey("FixAvgLibSize")) {
+            return activeTask.getStatus() != ActiveTask.COMPLETE;
+        }
+        return false;
+    }
+
+    public PluginResult run() throws ServerException {
+        try {
+            List<DataRecord> samples = activeTask.getAttachedDataRecords("Sample", user);
+            if (samples.size() == 0) {
+                clientCallback.displayError(String.format("Sample attachments not found on task: %s", activeTask.getTask().getTaskName()));
+                return new PluginResult(false);
+            }
+            List<Object> sampleIds = getSampleIds(samples);
+            List<DataRecord> qcRecords = getQcRecordsForSamples(sampleIds, "QCDatum");
+            List<DataRecord> qcRecordsMCA = getQcRecordsForSamples(sampleIds, "MolarConcentrationAssignment");
+
+            if (qcRecords.size() < sampleIds.size()) {
+                clientCallback.displayWarning(String.format("Number of QC Records found: %d are LESS than number of samples attached %d." +
+                        "\nPlease make sure all the samples have at least one QC record.", qcRecords.size(), sampleIds.size()));
+            }
+
+            //for sample in qcrecords, for sample1 in qcrecordsMCA, if getAverageLibrarySizeValue(sample, qcrecords) =! getAverageLibrarySizeValue(sample1, qcrecordsMCA), sample.avgsize = sample1.avgsize
+            updateAvgSize(qcRecords, qcRecordsMCA);
+        } catch (RemoteException e) {
+            String errMsg = String.format("Remote Exception while assigning Lib Avg Size:\n%s", ExceptionUtils.getStackTrace(e));
+            logError(errMsg);
+            return new PluginResult(false);
+        }
+        return new PluginResult(true);
+    }
+
+    public List<DataRecord> getQcRecordsForSamples(List<Object> sampleIdList, String table) {
+        List<DataRecord> qcRecords = new ArrayList<>();
+        try {
+
+
+            qcRecords = dataRecordManager.queryDataRecords(table, "SampleId", sampleIdList, user);
+        } catch (NotFound notFound) {
+            logError(String.format("NotFound Exception while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(notFound)));
+        } catch (IoError ioError) {
+            logError(String.format("IoError Exception while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(ioError)));
+        } catch (ServerException e) {
+            logError(String.format("ServerException while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(e)));
+        } catch (RemoteException e) {
+            logError(String.format("RemoteException while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(e)));
+        }
+        return qcRecords;
+    }
+
+    public List<Object> getSampleIds(List<DataRecord> samples) {
+        List<Object> sampleIds = new ArrayList<>();
+        for (DataRecord sample : samples) {
+            String sampleId = null;
+            try {
+                sampleId = sample.getStringVal("SampleId", user);
+                logInfo("getSampleIds returns: " + sampleId);
+            } catch (RemoteException e) {
+                logError(String.format("Remote Exception while reading SampleId for sample with recordid %d:\n%s", sample.getRecordId(), ExceptionUtils.getStackTrace(e)));
+            } catch (NotFound e) {
+                logError(String.format("SampleId missing for sample with recordid %d:\n%s", sample.getRecordId(), ExceptionUtils.getStackTrace(e)));
+            }
+            if (!StringUtils.isBlank(sampleId)) {
+                sampleIds.add(sampleId);
+            }
+        }
+        return sampleIds;
+    }
+
+    public void updateAvgSize(List<DataRecord> QCDatum, List<DataRecord> MCA){
+        for (DataRecord rectoupdate : QCDatum) {
+            for (DataRecord rec : MCA) {
+            try {
+                String rectoupdateId = null;
+                String recId = null;
+                rectoupdateId = rectoupdate.getStringVal("SampleId", user).toLowerCase();//rectoupdate sample ID
+                recId = rec.getStringVal("SampleId", user).toLowerCase();//rec sample ID
+                Double rectoupdateavgsize = 0.0;
+                Double recavgsize = 0.0;
+                rectoupdateavgsize = rectoupdate.getDoubleVal("AvgSize", user);//rectoupdate avgsize
+                recavgsize = rec.getDoubleVal("AvgSize", user);//rec avgsize
+                if (rectoupdateId == recId && rectoupdateavgsize != recavgsize) {
+                    rectoupdate.setDataField("AvgSize", recavgsize, user);
+                }
+                }catch (NotFound notFound) {
+                    logError(String.format("NotFound Exception while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(notFound)));
+                } catch (IoError ioError) {
+                    logError(String.format("IoError Exception while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(ioError)));
+                } catch (ServerException e) {
+                    logError(String.format("ServerException while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(e)));
+                } catch (RemoteException e) {
+                    logError(String.format("RemoteException while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(e)));
+                } catch (InvalidValue e) {
+                    logError(String.format("RemoteException while getting QC records for attached Samples:\n%s", ExceptionUtils.getStackTrace(e)));
+                }
+            }
+        }
+    }
+}
+
+
+
+
+

src/test/java/com/velox/sloan/cmo/workflows/qualitycontrol/sequencingqc/FixAvgLibSizeTest.java

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+package com.velox.sloan.cmo.workflows.qualitycontrol.sequencingqc;
+
+import com.velox.api.datarecord.DataRecord;
+import com.velox.api.datamgmtserver.DataMgmtServer;
+import com.velox.api.user.User;
+import com.velox.sapioutils.client.standalone.VeloxConnection;
+import com.velox.api.datarecord.*;
+import com.velox.api.datarecord.IoError;
+import com.velox.api.datarecord.NotFound;
+import com.velox.api.datarecord.InvalidValue;
+import com.velox.api.util.ServerException;
+import java.rmi.RemoteException;
+import com.velox.api.user.User;
+import java.util.*;
+
+import org.junit.Ignore;
+import org.junit.Before;
+import org.junit.After;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+//@Ignore
+public class FixAvgLibSizeTest {
+    FixAvgLibSize fixAvgLibSize = new FixAvgLibSize();
+    User user;
+    DataRecordManager dataRecordManager;
+    DataMgmtServer dataMgmtServer;
+    VeloxConnection connection = null;
+
+    @Before
+    public void setUp() {
+        try {
+            //FixAvgLibSize fixAvgLibSize = new FixAvgLibSize();
+            connection = new VeloxConnection("/Users/desmondlambe/igo-lims-plugins/Connection.txt");
+            System.out.println("Connection start");
+            connection.open();
+            user = connection.getUser();
+            dataRecordManager = connection.getDataRecordManager();
+            System.out.println("Connected successfully.");
+            dataMgmtServer = connection.getDataMgmtServer();
+        } catch (Throwable e) {
+            e.printStackTrace();
+        }
+    }
+
+    @After
+    public void tearUp() {
+        try {
+            connection.close();
+        } catch (Throwable t) {
+        }
+    }
+
+    @Test
+    public void testUpdateAvgSize() {
+        try {
+            // Create sample DataRecords for testing
+            List<DataRecord> QCDatum;
+            List<DataRecord> MCA;
+            List<Object> testSamples = new ArrayList<>();
+            testSamples.add("05500_IG_1");
+            testSamples.add("05500_IG_2");
+            //testSamples.add("sample3");
+
+            // Get data records
+            QCDatum = fixAvgLibSize.getQcRecordsForSamples(testSamples, "QCDatum");
+            MCA = fixAvgLibSize.getQcRecordsForSamples(testSamples, "MolarConcentrationAssignment");
+
+//            QCDatum = dataRecordManager.queryDataRecords("QCDatum", "SampleId", testSamples, user);
+//            MCA = dataRecordManager.queryDataRecords("MolarConcentrationAssignment", "SampleId", testSamples, user);
+
+            // Modify MCA
+            for (DataRecord sampleMCA : MCA) {
+                sampleMCA.setDataField("AvgSize", "500", user);
+
+                //call updateAvgSize
+                fixAvgLibSize.updateAvgSize(QCDatum, MCA);
+
+                // Verify that the AvgSize field is updated as expected
+                for (DataRecord sampleQCDatum : QCDatum) {
+                    double QCDatumavgsize = sampleQCDatum.getDoubleVal("AvgSize", user);
+                    assertEquals(500, QCDatumavgsize, 0.001);
+                }
+            }
+        } catch (NotFound | RemoteException | ServerException | IoError | InvalidValue e) {
+            e.printStackTrace();
+        }
+    }
+}
+
+