TASK-5278 - Add haploid calls treatment parameter to family-qc and relatedness

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcAnalysis.java

@@ -17,10 +17,11 @@
 package org.opencb.opencga.analysis.family.qc;
 
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.clinical.qc.RelatednessReport;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.analysis.AnalysisUtils;
 import org.opencb.opencga.analysis.individual.qc.IndividualQcUtils;
-import org.opencb.opencga.analysis.tools.OpenCgaTool;
+import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
 import org.opencb.opencga.analysis.variant.relatedness.RelatednessAnalysis;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.utils.CatalogFqn;
@@ -32,7 +33,10 @@
 import org.opencb.opencga.core.models.family.FamilyQualityControl;
 import org.opencb.opencga.core.models.family.FamilyUpdateParams;
 import org.opencb.opencga.core.models.study.Study;
+import org.opencb.opencga.core.models.variant.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.MutationalSignatureAnalysisParams;
 import org.opencb.opencga.core.tools.annotations.Tool;
+import org.opencb.opencga.core.tools.annotations.ToolParams;
 import org.opencb.opencga.core.tools.variant.FamilyQcAnalysisExecutor;
 
 import java.nio.file.Path;
@@ -43,62 +47,78 @@
 import static org.opencb.opencga.core.models.study.StudyPermissions.Permissions.WRITE_FAMILIES;
 
 @Tool(id = FamilyQcAnalysis.ID, resource = Enums.Resource.FAMILY, description = FamilyQcAnalysis.DESCRIPTION)
-public class FamilyQcAnalysis extends OpenCgaTool {
+public class FamilyQcAnalysis extends OpenCgaToolScopeStudy {
 
     public static final String ID = "family-qc";
     public static final String DESCRIPTION = "Run quality control (QC) for a given family. It computes the relatedness scores among the"
-    + " family members";
+            + " family members";
 
     public  static final String RELATEDNESS_STEP = "relatedness";
 
-    private String studyId;
-    private String familyId;
-    private String relatednessMethod;
+    @ToolParams
+    private FamilyQcAnalysisParams familyQcParams = new FamilyQcAnalysisParams();
+
     private String relatednessMaf;
+    private String haploidCallMode;
     private Map<String, Map<String, Float>> relatednessThresholds;
 
     private Family family;
 
     @Override
     protected void check() throws Exception {
         super.check();
-        setUpStorageEngineExecutor(studyId);
+        setUpStorageEngineExecutor(study);
 
-        if (StringUtils.isEmpty(studyId)) {
+        if (StringUtils.isEmpty(study)) {
             throw new ToolException("Missing study ID.");
         }
 
         // Check permissions
         try {
             JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
-            CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+            CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(study, jwtPayload);
             String organizationId = studyFqn.getOrganizationId();
             String userId = jwtPayload.getUserId(organizationId);
 
-            Study study = catalogManager.getStudyManager().get(studyId, QueryOptions.empty(), token).first();
-            catalogManager.getAuthorizationManager().checkStudyPermission(organizationId, study.getUid(), userId, WRITE_FAMILIES);
+            Study auxStudy = catalogManager.getStudyManager().get(study, QueryOptions.empty(), token).first();
+            catalogManager.getAuthorizationManager().checkStudyPermission(organizationId, auxStudy.getUid(), userId, WRITE_FAMILIES);
         } catch (CatalogException e) {
             throw new ToolException(e);
         }
 
         // Sanity check
-        if (StringUtils.isEmpty(familyId)) {
+        if (StringUtils.isEmpty(familyQcParams.getFamily())) {
             throw new ToolException("Missing family ID.");
         }
 
-        family = IndividualQcUtils.getFamilyById(studyId, familyId, catalogManager, token);
+        family = IndividualQcUtils.getFamilyById(study, familyQcParams.getFamily(), catalogManager, token);
         if (family == null) {
-            throw new ToolException("Family '" + familyId + "' not found.");
+            throw new ToolException("Family '" + familyQcParams.getFamily() + "' not found.");
         }
 
-        // As relatedness is the only QC to compute, it is mandatory
-        if (StringUtils.isEmpty(relatednessMethod)) {
-            relatednessMethod = "PLINK/IBD";
-        }
+        // Check MAF
+        relatednessMaf = familyQcParams.getRelatednessMaf();
         if (StringUtils.isEmpty(relatednessMaf)) {
             relatednessMaf = RelatednessAnalysis.MAF_DEFAULT_VALUE;
         }
 
+        // Check haploid call mode
+        haploidCallMode = familyQcParams.getHaploidCallMode();
+        if (StringUtils.isEmpty(haploidCallMode)) {
+            haploidCallMode = RelatednessReport.HAPLOID_CALL_MODE_DEFAUT_VALUE;
+        } else {
+            switch (haploidCallMode) {
+                case RelatednessReport.HAPLOID_CALL_MODE_HAPLOID_VALUE:
+                case RelatednessReport.HAPLOID_CALL_MODE_MISSING_VALUE:
+                case RelatednessReport.HAPLOID_CALL_MODE_REF_VALUE:
+                    break;
+                default:
+                    throw new ToolException("Invalid haploid call value '" + haploidCallMode + "', accepted values are: "
+                            + RelatednessReport.HAPLOID_CALL_MODE_HAPLOID_VALUE + ", " + RelatednessReport.HAPLOID_CALL_MODE_MISSING_VALUE
+                            + " and " + RelatednessReport.HAPLOID_CALL_MODE_REF_VALUE);
+            }
+        }
+
         Path thresholdsPath = getOpencgaHome().resolve("analysis").resolve(FamilyQcAnalysis.ID).resolve("relatedness_thresholds.csv");
         relatednessThresholds = AnalysisUtils.parseRelatednessThresholds(thresholdsPath);
     }
@@ -120,10 +140,10 @@ protected void run() throws ToolException {
         FamilyQcAnalysisExecutor executor = getToolExecutor(FamilyQcAnalysisExecutor.class);
 
         // Set up executor
-        executor.setStudyId(studyId)
+        executor.setStudyId(study)
                 .setFamily(family)
-                .setRelatednessMethod(relatednessMethod)
                 .setRelatednessMaf(relatednessMaf)
+                .setHaploidCallMode(haploidCallMode)
                 .setRelatednessThresholds(relatednessThresholds)
                 .setRelatednesResourcePath(getOpencgaHome().resolve("analysis/resources").resolve(RelatednessAnalysis.ID))
                 .setQualityControl(qualityControl);
@@ -135,47 +155,29 @@ protected void run() throws ToolException {
         try {
             qualityControl = executor.getQualityControl();
             if (qualityControl != null) {
-                catalogManager.getFamilyManager().update(getStudyId(), familyId, new FamilyUpdateParams().setQualityControl(qualityControl),
+                catalogManager.getFamilyManager().update(study, familyQcParams.getFamily(), new FamilyUpdateParams().setQualityControl(qualityControl),
                         QueryOptions.empty(), token);
             }
         } catch (CatalogException e) {
             throw new ToolException(e);
         }
     }
 
-    public String getStudyId() {
-        return studyId;
-    }
-
-    public FamilyQcAnalysis setStudyId(String studyId) {
-        this.studyId = studyId;
-        return this;
-    }
-
-    public String getFamilyId() {
-        return familyId;
-    }
-
-    public FamilyQcAnalysis setFamilyId(String familyId) {
-        this.familyId = familyId;
-        return this;
-    }
-
-    public String getRelatednessMethod() {
-        return relatednessMethod;
+    public String getRelatednessMaf() {
+        return relatednessMaf;
     }
 
-    public FamilyQcAnalysis setRelatednessMethod(String relatednessMethod) {
-        this.relatednessMethod = relatednessMethod;
+    public FamilyQcAnalysis setRelatednessMaf(String relatednessMaf) {
+        this.relatednessMaf = relatednessMaf;
         return this;
     }
 
-    public String getRelatednessMaf() {
-        return relatednessMaf;
+    public String getHaploidCallMode() {
+        return haploidCallMode;
     }
 
-    public FamilyQcAnalysis setRelatednessMaf(String relatednessMaf) {
-        this.relatednessMaf = relatednessMaf;
+    public FamilyQcAnalysis setHaploidCallMode(String haploidCallMode) {
+        this.haploidCallMode = haploidCallMode;
         return this;
     }
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java

@@ -66,10 +66,10 @@ private void runRelatedness() throws ToolException {
 
         if (CollectionUtils.isNotEmpty(qualityControl.getRelatedness())) {
             for (RelatednessReport relatedness : qualityControl.getRelatedness()) {
-                if (relatednessMethod.equals(relatedness.getMethod()) && relatednessMaf.equals(relatedness.getMaf())) {
+                if (IBDComputation.PLINK_IBD_METHOD.equals(relatedness.getMethod()) && relatednessMaf.equals(relatedness.getMaf())) {
                     // Nothing to update
-                    addWarning("Skipping relatedness analysis: it was already computed for method '" + relatednessMethod + "' and MAF '"
-                            + relatednessMaf + "'");
+                    addWarning("Skipping relatedness analysis: it was already computed for method '" + IBDComputation.PLINK_IBD_METHOD
+                            + "' and MAF '" + relatednessMaf + "'");
                     qualityControl = null;
                     return;
                 }
@@ -113,7 +113,7 @@ private void runRelatedness() throws ToolException {
 
         // Run IBD/IBS computation using PLINK in docker
         RelatednessReport report = IBDComputation.compute(getStudyId(), getFamily(), sampleIds, getRelatednessMaf(),
-                getRelatednessThresholds(), getRelatednesResourcePath(), getOutDir(), getVariantStorageManager(), getToken());
+                getHaploidCallMode(), getRelatednessThresholds(), getRelatednesResourcePath(), getOutDir(), getVariantStorageManager(), getToken());
 
         // Sanity check
         if (report == null) {