ZFIN-9213: (ZFIN#1152)

- Give helpful errors for issues with deleting features that have FeatureDnaMutationDetail.
rtaylorzfin · Sep 13, 2024 · 8303b21 · 8303b21
1 parent e9e0771
commit 8303b21
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Showing 5 changed files with 49 additions and 123 deletions.
diff --git a/source/org/zfin/feature/FeatureDnaMutationDetail.java b/source/org/zfin/feature/FeatureDnaMutationDetail.java
@@ -1,10 +1,14 @@
 package org.zfin.feature;
 
+import lombok.Getter;
+import lombok.Setter;
 import org.hibernate.annotations.GenericGenerator;
 import org.zfin.sequence.ReferenceDatabase;
 
 import javax.persistence.*;
 
+@Setter
+@Getter
 @Entity
 @Table(name = "feature_dna_mutation_detail")
 public class FeatureDnaMutationDetail implements Cloneable {
@@ -51,118 +55,6 @@ public class FeatureDnaMutationDetail implements Cloneable {
     private DnaMutationTerm dnaMutationTerm;
 
 
-    public Feature getFeature() {
-        return feature;
-    }
-
-    public void setFeature(Feature feature) {
-        this.feature = feature;
-    }
-
-    public ReferenceDatabase getReferenceDatabase() {
-        return referenceDatabase;
-    }
-
-    public void setReferenceDatabase(ReferenceDatabase referenceDatabase) {
-        this.referenceDatabase = referenceDatabase;
-    }
-
-    public DnaMutationTerm getDnaMutationTerm() {
-        return dnaMutationTerm;
-    }
-
-    public void setDnaMutationTerm(DnaMutationTerm dnaMutationTerm) {
-        this.dnaMutationTerm = dnaMutationTerm;
-    }
-
-    public Integer getDnaPositionEnd() {
-        return dnaPositionEnd;
-    }
-
-    public void setDnaPositionEnd(Integer dnaPositionEnd) {
-        this.dnaPositionEnd = dnaPositionEnd;
-    }
-
-    public Integer getDnaPositionStart() {
-        return dnaPositionStart;
-    }
-
-    public void setDnaPositionStart(Integer dnaPositionStart) {
-        this.dnaPositionStart = dnaPositionStart;
-    }
-
-    public String getDnaSequenceReferenceAccessionNumber() {
-        return dnaSequenceReferenceAccessionNumber;
-    }
-
-    public void setDnaSequenceReferenceAccessionNumber(String dnaSequenceReferenceAccessionNumber) {
-        this.dnaSequenceReferenceAccessionNumber = dnaSequenceReferenceAccessionNumber;
-    }
-
-    public Integer getNumberAddedBasePair() {
-        return numberAddedBasePair;
-    }
-
-    public void setNumberAddedBasePair(Integer numberAdditionalBasePair) {
-        this.numberAddedBasePair = numberAdditionalBasePair;
-    }
-
-    public Integer getExonNumber() {
-        return exonNumber;
-    }
-
-    public void setExonNumber(Integer exonNumber) {
-        this.exonNumber = exonNumber;
-    }
-
-    public Integer getIntronNumber() {
-        return intronNumber;
-    }
-
-    public void setIntronNumber(Integer intronNumber) {
-        this.intronNumber = intronNumber;
-    }
-
-    public Integer getNumberRemovedBasePair() {
-        return numberRemovedBasePair;
-    }
-
-    public void setNumberRemovedBasePair(Integer numberRemovedBasePair) {
-        this.numberRemovedBasePair = numberRemovedBasePair;
-    }
-
-    public String getInsertedSequence() {
-        return insertedSequence;
-    }
-
-    public void setInsertedSequence(String insertedSequence) {
-        this.insertedSequence = insertedSequence;
-    }
-
-    public String getDeletedSequence() {
-        return deletedSequence;
-    }
-
-    public void setDeletedSequence(String deletedSequence) {
-        this.deletedSequence = deletedSequence;
-    }
-
-    public String getZdbID() {
-        return zdbID;
-    }
-
-    public void setZdbID(String zdbID) {
-        this.zdbID = zdbID;
-    }
-
-    public GeneLocalizationTerm getGeneLocalizationTerm() {
-        return geneLocalizationTerm;
-    }
-
-    public void setGeneLocalizationTerm(GeneLocalizationTerm geneLocalizationTerm) {
-        this.geneLocalizationTerm = geneLocalizationTerm;
-    }
-
     public FeatureDnaMutationDetail clone() {
         try {
             FeatureDnaMutationDetail detail = (FeatureDnaMutationDetail) super.clone();

diff --git a/source/org/zfin/feature/repository/FeatureRepository.java b/source/org/zfin/feature/repository/FeatureRepository.java
@@ -131,7 +131,7 @@ public interface FeatureRepository {
 
     Feature getFeatureByAbbreviation(String featureAbbrev);
 
-    String getFeatureByAbbreviationInTrackingTable(String featureAbbrev);
+    FeatureTracking getFeatureByAbbreviationInTrackingTable(String featureAbbrev);
 
     String getFeatureByIDInTrackingTable(String featTrackingFeatZdbID);
 

diff --git a/source/org/zfin/feature/repository/HibernateFeatureRepository.java b/source/org/zfin/feature/repository/HibernateFeatureRepository.java
@@ -784,12 +784,12 @@ public Feature getFeatureByAbbreviation(String name) {
     }
 
     @Override
-    public String getFeatureByAbbreviationInTrackingTable(String featTrackingFeatAbbrev) {
+    public FeatureTracking getFeatureByAbbreviationInTrackingTable(String featTrackingFeatAbbrev) {
         Session session = HibernateUtil.currentSession();
-        String hqlFtrTrack = " select ft.featTrackingFeatAbbrev from  FeatureTracking ft where ft.feature.zdbID =:featTrackingFeatAbbrev ";
-        Query queryTracker = session.createQuery(hqlFtrTrack);
+        String hqlFtrTrack = "from FeatureTracking where featTrackingFeatAbbrev = :featTrackingFeatAbbrev";
+        Query<FeatureTracking> queryTracker = session.createQuery(hqlFtrTrack, FeatureTracking.class);
         queryTracker.setParameter("featTrackingFeatAbbrev", featTrackingFeatAbbrev);
-        return (String) queryTracker.uniqueResult();
+        return queryTracker.uniqueResult();
     }
 
     public String getFeatureByIDInTrackingTable(String featTrackingFeatZdbID) {

diff --git a/source/org/zfin/gwt/curation/server/FeatureRPCServiceImpl.java b/source/org/zfin/gwt/curation/server/FeatureRPCServiceImpl.java
@@ -47,6 +47,8 @@
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import static org.zfin.framework.HibernateUtil.currentSession;
@@ -96,14 +98,36 @@ private void checkDupes(FeatureDTO featureDTO) throws DuplicateEntryException {
         }
     }
 
-    private void checkDupesinTrackingTable(FeatureDTO featureDTO) throws DuplicateEntryException {
-        String featureInTrackingTable = featureRepository.getFeatureByAbbreviationInTrackingTable(featureDTO.getAbbreviation());
-
+    private void checkDupesinTrackingTable(String featureAbbreviation) throws DuplicateEntryException {
+        FeatureTracking featureInTrackingTable = featureRepository.getFeatureByAbbreviationInTrackingTable(featureAbbreviation);
 
         if (featureInTrackingTable != null) {
-            throw new DuplicateEntryException("Feature exists in the tracking table for this abbreviation: " + featureDTO.getAbbreviation());
+            String labPrefix = getLabPrefixFromFeatureAbbreviation(featureAbbreviation);
+
+            String nextLine = null;
+            if (labPrefix != null) {
+                nextLine = getFeatureRepository().getNextLineNumberForLabPrefix(labPrefix);
+            }
+
+            String helpfulTip = "";
+            if (nextLine != null && labPrefix != null) {
+                helpfulTip = " Next line number for this lab prefix is: " + nextLine + ".";
+            }
+
+            throw new DuplicateEntryException(
+                    "Feature exists in the tracking table for this abbreviation: " + featureAbbreviation + ". " + helpfulTip);
         }
+    }
+
+    private String getLabPrefixFromFeatureAbbreviation(String line) {
+        String pattern = "(.*?)(\\d+)";
+        Pattern r = Pattern.compile(pattern);
+        Matcher m = r.matcher(line);
 
+        if (m.find()) {
+            return m.group(1);
+        }
+        return null;
     }
 
     private void updateFeatureLocation(FeatureLocation fl, FeatureDTO dto) {
@@ -579,7 +603,7 @@ public FeatureDTO createFeature(FeatureDTO featureDTO) throws DuplicateEntryExce
 
         DTOConversionService.escapeFeatureDTO(featureDTO);
         checkDupes(featureDTO);
-        checkDupesinTrackingTable(featureDTO);
+        checkDupesinTrackingTable(featureDTO.getAbbreviation());
         validateUnspecified(featureDTO);
 
         FeatureDTO newFeatureDTO;
@@ -607,7 +631,7 @@ public FeatureDTO createFeature(FeatureDTO featureDTO) throws DuplicateEntryExce
                 feature.getAliases().add(featureAlias);
             }
 
-
+            checkDupesinTrackingTable(feature.getAbbreviation());
             getFeatureRepository().saveFeature(feature, publication);
             if (CollectionUtils.isNotEmpty(featureDTO.getPublicNoteList())) {
 

diff --git a/source/org/zfin/infrastructure/delete/DeleteFeatureRule.java b/source/org/zfin/infrastructure/delete/DeleteFeatureRule.java
@@ -41,6 +41,16 @@ public List<DeleteValidationReport> validate() {
             addToValidationReport(feature.getAbbreviation() + " has the following accession numbers associated: ", feature.getDbLinks());
         }
 
+        // Can't delete the feature if it has mutation details
+        if (CollectionUtils.isNotEmpty(feature.getFeatureDnaMutationDetailSet())) {
+            addToValidationReport("Need to remove Mutation Detail data.");
+        }
+
+        // Can't delete the feature if it has protein mutation details
+        if (CollectionUtils.isNotEmpty(feature.getFeatureProteinMutationDetailSet())) {
+            addToValidationReport("Need to remove Protein Mutation Detail data.");
+        }
+
         // Can't delete the feature if it has more than 1 publications
         if (CollectionUtils.isNotEmpty(featurePublications) && featurePublications.size() > 1) {
             addToValidationReport(feature.getAbbreviation() + " associated with more than one publication: ", featurePublications);