Merge branch '79-fix-zodiac-crashing-with-corrupted-compounds' into '…

…stable' Resolve "Fix ZODIAC crashing with corrupted compounds" See merge request bright-giant/sirius/sirius-frontend!25
sirius-ms · Nov 9, 2023 · d2b862e · d2b862e
2 parents 5b659d0 + c1c04c4
commit d2b862e
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Showing 2 changed files with 22 additions and 4 deletions.
diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/DataSetJob.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/DataSetJob.java
@@ -66,7 +66,14 @@ protected Iterable<Instance> compute() throws Exception {
 
         if (!hasResults || recompute) {
             if (hasResults) {
-                inputInstances.forEach(this::invalidateResults);
+                inputInstances.forEach(ins->{
+                    //one corrupted instance should not make the whole dataset job fail
+                    try{
+                        invalidateResults(ins);
+                    } catch (Exception e){
+                        logWarn("Cannot invalidate results for "+ins.getID().getDirectoryName()+". Hence, this instance may be ignored in further computations. Error: "+e.getMessage());
+                    }
+                });
             }
             updateProgress(Math.round(.9 * inputInstances.size()), "Invalidate existing Results and Recompute!");
 

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/zodiac/ZodiacSubToolJob.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/zodiac/ZodiacSubToolJob.java
@@ -77,16 +77,27 @@ public ZodiacSubToolJob(ZodiacOptions cliOptions, @NotNull JobSubmitter jobSubmi
 
     @Override
     public boolean isAlreadyComputed(@NotNull Instance inst) {
-        return inst.loadCompoundContainer().hasResults() && inst.loadFormulaResults(FormulaScoring.class).stream().anyMatch(res -> res.getCandidate().getAnnotationOrThrow(FormulaScoring.class).hasAnnotation(ZodiacScore.class));
+        try {
+            return inst.loadCompoundContainer().hasResults() && inst.loadFormulaResults(FormulaScoring.class).stream().anyMatch(res -> res.getCandidate().getAnnotationOrThrow(FormulaScoring.class).hasAnnotation(ZodiacScore.class));
+        } catch (Exception e) {
+            //only debug output, since the same instance will fail again below in computeAndAnnotateResult
+            logDebug("Error while reading molecular formula scores for "+inst.getID().getDirectoryName()+". Error: "+e.getMessage());
+            return false;
+        }
     }
 
     @Override
     protected void computeAndAnnotateResult(@NotNull List<Instance> instances) throws Exception {
         logInfo("START ZODIAC JOB");
         final Map<Ms2Experiment, List<FormulaResult>> input = instances.stream()
                 .distinct().collect(Collectors.toMap(
-                        Instance::getExperiment,
-                        in -> in.loadFormulaResults(List.of(SiriusScore.class), FormulaScoring.class, FTree.class).stream().map(SScored::getCandidate).collect(Collectors.toList())
+                        Instance::getExperiment, in -> {
+                            try {
+                                return in.loadFormulaResults(List.of(SiriusScore.class), FormulaScoring.class, FTree.class).stream().map(SScored::getCandidate).collect(Collectors.toList());
+                            } catch (Exception e) {
+                                logWarn("Error while reading molecular formula scores for "+in.getID().getDirectoryName()+". Exclude it from ZODIAC computation. Error: "+e.getMessage());
+                                return Collections.emptyList(); //empty lists are filtered below.
+                            }}
                 ));
 
         //remove instances from input which don't have a single FTree