Update protein update fatal errors

EBI-IntAct · Aug 20, 2024 · c7cce2a · c7cce2a
1 parent f3c4b2c
commit c7cce2a
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Showing 5 changed files with 32 additions and 18 deletions.
diff --git a/...-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java b/...-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java
@@ -308,7 +308,7 @@ public void updateByACs(List<String> protACsToUpdate) throws ProcessorException
                     for (String ac : chunkIntactProteins) {
                         log.fatal("FATAL: We failed to update the protein " + ac, e);
                         ProteinUpdateError fatalError = errorFactory.createFatalUpdateError(ac, null, e);
-                        fireOnProcessErrorFound(new UpdateErrorEvent(this, dataContext, fatalError, null, ac));
+                        fireOnProcessErrorFound(new UpdateErrorEvent(this, dataContext, fatalError, null, null, ac));
                     }
                     dataContext.rollbackTransaction(transactionStatus);
                 }

diff --git a/...ns-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/errors/FatalErrorDuringUpdate.java b/...ns-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/errors/FatalErrorDuringUpdate.java
@@ -54,7 +54,7 @@ public String getErrorMessage(){
         }
 
         if (uniprotAc != null){
-            error.append("attached to the uniprot entry ");
+            error.append(" attached to the uniprot entry ");
             error.append(uniprotAc);
         }
 

diff --git a/...-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/event/UpdateErrorEvent.java b/...-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/event/UpdateErrorEvent.java
@@ -24,29 +24,32 @@ public class UpdateErrorEvent extends EventObject implements ProteinProcessorEve
     private DataContext dataContext;
     private Protein protein;
     private String uniprotAc;
+    private String proteinAc;
 
-    public UpdateErrorEvent(Object source, DataContext dataContext, ProteinUpdateError error, Protein protein) {
+    public UpdateErrorEvent(Object source,
+                            DataContext dataContext,
+                            ProteinUpdateError error,
+                            Protein protein,
+                            String uniprotAc,
+                            String proteinAc) {
         super(source);
         this.error = error;
         this.dataContext = dataContext;
         this.protein = protein;
-        this.uniprotAc = null;
-    }
-
-    public UpdateErrorEvent(Object source, DataContext dataContext, ProteinUpdateError error, String uniprotAc) {
-        super(source);
-        this.error = error;
-        this.dataContext = dataContext;
-        this.protein = null;
         this.uniprotAc = uniprotAc;
+        this.proteinAc = proteinAc;
     }
 
     public UpdateErrorEvent(Object source, DataContext dataContext, ProteinUpdateError error, Protein protein, String uniprotAc) {
-        super(source);
-        this.error = error;
-        this.dataContext = dataContext;
-        this.protein = protein;
-        this.uniprotAc = uniprotAc;
+        this(source, dataContext, error, protein, uniprotAc, null);
+    }
+
+    public UpdateErrorEvent(Object source, DataContext dataContext, ProteinUpdateError error, Protein protein) {
+        this(source, dataContext, error, protein, null, null);
+    }
+
+    public UpdateErrorEvent(Object source, DataContext dataContext, ProteinUpdateError error, String uniprotAc) {
+        this(source, dataContext, error, null, uniprotAc, null);
     }
 
     public ProteinUpdateError getError() {
@@ -73,4 +76,12 @@ public String getUniprotAc() {
     public void setUniprotAc(String uniprotAc) {
         this.uniprotAc = uniprotAc;
     }
+
+    public String getProteinAc() {
+        return proteinAc;
+    }
+
+    public void setProteinAc(String proteinAc) {
+        this.proteinAc = proteinAc;
+    }
 }
diff --git a/...ns-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java b/...ns-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java
@@ -323,14 +323,17 @@ public void onProcessErrorFound(UpdateErrorEvent evt) throws ProcessorException{
             if (evt.getProtein() != null){
                 proteinAc = evt.getProtein().getAc();
                 proteinShortlablel = evt.getProtein().getShortLabel();
+            } else if (evt.getProteinAc() != null) {
+                proteinAc = evt.getProteinAc();
             }
 
             writer.writeHeaderIfNecessary("Protein ac",
                     "Protein shortlabel",
                     "Uniprot ac",
                     "error type",
                     "error description");
-            writer.writeColumnValues(proteinAc,
+            writer.writeColumnValues(
+                    proteinAc,
                     proteinShortlablel,
                     uniprotAc,
                     errorType,

diff --git a/...te-model/src/main/java/uk/ac/ebi/intact/update/model/protein/errors/FatalUpdateError.java b/...te-model/src/main/java/uk/ac/ebi/intact/update/model/protein/errors/FatalUpdateError.java
@@ -94,7 +94,7 @@ public String toString(){
         }
 
         if (uniprotAc != null){
-            error.append("attached to the uniprot entry ");
+            error.append(" attached to the uniprot entry ");
             error.append(uniprotAc);
         }