From c7cce2aefdbe66a039bb3eba1e7fccf696a991fc Mon Sep 17 00:00:00 2001 From: jmedinaebi Date: Tue, 20 Aug 2024 08:58:53 +0100 Subject: [PATCH] Update protein update fatal errors --- .../dbupdate/prot/ProteinUpdateProcessor.java | 2 +- .../prot/errors/FatalErrorDuringUpdate.java | 2 +- .../dbupdate/prot/event/UpdateErrorEvent.java | 39 ++++++++++++------- .../prot/listener/ReportWriterListener.java | 5 ++- .../protein/errors/FatalUpdateError.java | 2 +- 5 files changed, 32 insertions(+), 18 deletions(-) diff --git a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java index be9b4954..2e4428e2 100644 --- a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java +++ b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/ProteinUpdateProcessor.java @@ -308,7 +308,7 @@ public void updateByACs(List 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/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/errors/FatalErrorDuringUpdate.java b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/errors/FatalErrorDuringUpdate.java index 8b7649f9..8bb5c651 100644 --- a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/errors/FatalErrorDuringUpdate.java +++ b/intact-proteins-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/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/event/UpdateErrorEvent.java b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/event/UpdateErrorEvent.java index 76da7d0f..c06d5a79 100644 --- a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/event/UpdateErrorEvent.java +++ b/intact-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; + } } \ No newline at end of file diff --git a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java index 75f8ee87..56db6efa 100644 --- a/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java +++ b/intact-proteins-update/src/main/java/uk/ac/ebi/intact/dbupdate/prot/listener/ReportWriterListener.java @@ -323,6 +323,8 @@ 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", @@ -330,7 +332,8 @@ public void onProcessErrorFound(UpdateErrorEvent evt) throws ProcessorException{ "Uniprot ac", "error type", "error description"); - writer.writeColumnValues(proteinAc, + writer.writeColumnValues( + proteinAc, proteinShortlablel, uniprotAc, errorType, diff --git a/intact-update-model/src/main/java/uk/ac/ebi/intact/update/model/protein/errors/FatalUpdateError.java b/intact-update-model/src/main/java/uk/ac/ebi/intact/update/model/protein/errors/FatalUpdateError.java index 18f78b59..8f7c4cd6 100644 --- a/intact-update-model/src/main/java/uk/ac/ebi/intact/update/model/protein/errors/FatalUpdateError.java +++ b/intact-update-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); }