#4347 - CAS doctor fails to generate a proper report on projects not …

…containing INITIAL_CASes - Disable implicit CAS doctor check when creating the INITIAL_CAS since either CAS Doctor on the panel is run immediately after or the usual option CAS Doctor check is run on document open
inception-project · Dec 5, 2023 · 6de7202 · 6de7202
1 parent 7e899cc
commit 6de7202
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Showing 4 changed files with 46 additions and 10 deletions.
diff --git a/...n-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java b/...n-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java
@@ -867,7 +867,7 @@ public CAS createOrReadInitialCas(SourceDocument aDocument, CasUpgradeMode aUpgr
                     // adding this feature, the existing projects do not yet have initial CASes, so
                     // we create them here lazily
                     try {
-                        return importExportService.importCasFromFile(
+                        return importExportService.importCasFromFileNoChecks(
                                 getSourceDocumentFile(aDocument), aDocument,
                                 aFullProjectTypeSystem);
                     }

diff --git a/...c/main/java/de/tudarmstadt/ukp/clarin/webanno/api/export/DocumentImportExportService.java b/...c/main/java/de/tudarmstadt/ukp/clarin/webanno/api/export/DocumentImportExportService.java
@@ -158,6 +158,13 @@ CAS importCasFromFile(File aFile, SourceDocument aDocument, String aFormat,
             TypeSystemDescription aFullProjectTypeSystem)
         throws UIMAException, IOException;
 
+    CAS importCasFromFileNoChecks(File aFile, SourceDocument aDocument)
+        throws UIMAException, IOException;
+
+    CAS importCasFromFileNoChecks(File aFile, SourceDocument aDocument,
+            TypeSystemDescription aFullProjectTypeSystem)
+        throws UIMAException, IOException;
+
     /**
      * Exports the given CAS to a file on disk.
      * 

diff --git a/...rt/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java b/...rt/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java
@@ -303,6 +303,37 @@ public CAS importCasFromFile(File aFile, SourceDocument aDocument,
     public CAS importCasFromFile(File aFile, SourceDocument aDocument, String aFormat,
             TypeSystemDescription aFullProjectTypeSystem)
         throws UIMAException, IOException
+    {
+        var cas = importCasFromFileNoChecks(aFile, aDocument, aFormat, aFullProjectTypeSystem);
+
+        // Convert the source document to CAS
+        var format = getReadableFormatById(aFormat).orElseThrow(
+                () -> new IOException("No reader available for format [" + aFormat + "]"));
+
+        runCasDoctorOnImport(aDocument, format, cas);
+
+        return cas;
+    }
+
+    @Override
+    public CAS importCasFromFileNoChecks(File aFile, SourceDocument aDocument)
+        throws UIMAException, IOException
+    {
+        return importCasFromFileNoChecks(aFile, aDocument, aDocument.getFormat(), null);
+    }
+
+    @Override
+    public CAS importCasFromFileNoChecks(File aFile, SourceDocument aDocument,
+            TypeSystemDescription aFullProjectTypeSystem)
+        throws UIMAException, IOException
+    {
+        return importCasFromFileNoChecks(aFile, aDocument, aDocument.getFormat(),
+                aFullProjectTypeSystem);
+    }
+
+    private CAS importCasFromFileNoChecks(File aFile, SourceDocument aDocument, String aFormat,
+            TypeSystemDescription aFullProjectTypeSystem)
+        throws UIMAException, IOException
     {
         TypeSystemDescription tsd = aFullProjectTypeSystem;
 
@@ -311,11 +342,11 @@ public CAS importCasFromFile(File aFile, SourceDocument aDocument, String aForma
         }
 
         // Convert the source document to CAS
-        FormatSupport format = getReadableFormatById(aFormat).orElseThrow(
+        var format = getReadableFormatById(aFormat).orElseThrow(
                 () -> new IOException("No reader available for format [" + aFormat + "]"));
 
         // Prepare a CAS with the project type system
-        CAS cas = WebAnnoCasUtil.createCas(tsd);
+        var cas = WebAnnoCasUtil.createCas(tsd);
         format.read(aDocument.getProject(), WebAnnoCasUtil.getRealCas(cas), aFile);
 
         // Create sentence / token annotations if they are missing - sentences first because
@@ -327,8 +358,6 @@ public CAS importCasFromFile(File aFile, SourceDocument aDocument, String aForma
                 cas.getAnnotationIndex(getType(cas, Token.class)).size(),
                 cas.getAnnotationIndex(getType(cas, Sentence.class)).size(), aFile, aFile.length());
 
-        runCasDoctorOnImport(aDocument, format, cas);
-
         return cas;
     }
 

diff --git a/...in/java/de/tudarmstadt/ukp/clarin/webanno/ui/project/casdoctor/ProjectCasDoctorPanel.java b/...in/java/de/tudarmstadt/ukp/clarin/webanno/ui/project/casdoctor/ProjectCasDoctorPanel.java
@@ -159,7 +159,7 @@ private void actionRepair(AjaxRequestTarget aTarget, Form<?> aForm)
 
                 try {
                     casStorageService.forceActionOnCas(sd, INITIAL_CAS_PSEUDO_USER,
-                            (doc, user) -> createOrReadInitialCasWithoutSaving(doc, messageSet),
+                            (doc, user) -> createOrReadInitialCasWithoutSavingOrChecks(doc, messageSet),
                             (cas) -> casDoctor.repair(project, cas, messageSet.messages), //
                             true);
                 }
@@ -257,7 +257,7 @@ private void actionCheck(AjaxRequestTarget aTarget, Form<?> aForm)
                 try {
                     objectCount++;
                     casStorageService.forceActionOnCas(sd, INITIAL_CAS_PSEUDO_USER,
-                            (doc, user) -> createOrReadInitialCasWithoutSaving(doc, messageSet),
+                            (doc, user) -> createOrReadInitialCasWithoutSavingOrChecks(doc, messageSet),
                             (cas) -> casDoctor.analyze(project, cas, messageSet.messages), //
                             false);
                 }
@@ -341,7 +341,7 @@ private void actionCheck(AjaxRequestTarget aTarget, Form<?> aForm)
         aTarget.add(this);
     }
 
-    private CAS createOrReadInitialCasWithoutSaving(SourceDocument aDocument,
+    private CAS createOrReadInitialCasWithoutSavingOrChecks(SourceDocument aDocument,
             LogMessageSet aMessageSet)
         throws IOException, UIMAException
     {
@@ -350,8 +350,8 @@ private CAS createOrReadInitialCasWithoutSaving(SourceDocument aDocument,
                     UNMANAGED_NON_INITIALIZING_ACCESS);
         }
 
-        CAS cas = importExportService
-                .importCasFromFile(documentService.getSourceDocumentFile(aDocument), aDocument);
+        var cas = importExportService.importCasFromFileNoChecks(
+                documentService.getSourceDocumentFile(aDocument), aDocument);
         aMessageSet.messages.add(
                 LogMessage.info(getClass(), "Created initial CAS for [%s]", aDocument.getName()));
         return cas;