From 23155d9c62fb777319d87ba400deed65a187c71a Mon Sep 17 00:00:00 2001 From: jmedinaebi Date: Thu, 15 Aug 2024 13:41:53 +0100 Subject: [PATCH 1/3] Update dependencies --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 71c492df..05922199 100644 --- a/pom.xml +++ b/pom.xml @@ -19,13 +19,13 @@ http://www.ebi.ac.uk/~intact/devsite/dbupdate - 3.0.2-SNAPSHOT + 3.1.0-SNAPSHOT 2.2.3-SNAPSHOT 2.0.1-SNAPSHOT 1.1.2 4.3.30.RELEASE 2.4 - 3.5.2-SNAPSHOT + 3.6.0-SNAPSHOT From f3c4b2c4aa185b6796102bf85417d5e80cd9f6dc Mon Sep 17 00:00:00 2001 From: jmedinaebi Date: Tue, 20 Aug 2024 08:58:39 +0100 Subject: [PATCH 2/3] Fix failing unit tests --- intact-cv-update/pom.xml | 11 +++++++++++ .../ebi/intact/dbupdate/cv/CvUpdateManagerTest.java | 2 ++ .../intact/dbupdate/cv/GlobalCvUpdateRunnerTest.java | 2 ++ .../intact/dbupdate/cv/importer/CvImporterTest.java | 2 ++ .../dbupdate/cv/remapper/ObsoleteCvRemapperTest.java | 2 ++ .../ebi/intact/dbupdate/cv/updater/CvUpdaterTest.java | 2 ++ .../src/test/resources/META-INF/cv-update.properties | 2 +- pom.xml | 1 + 8 files changed, 23 insertions(+), 1 deletion(-) diff --git a/intact-cv-update/pom.xml b/intact-cv-update/pom.xml index d5ce094d..b74e8f65 100644 --- a/intact-cv-update/pom.xml +++ b/intact-cv-update/pom.xml @@ -10,6 +10,12 @@ intact-cv-update IntAct Database Update :: CV Update + + 5 + 2 + 5000 + + uk.ac.ebi.intact.core @@ -45,5 +51,10 @@ spring-beans ${spring.version} + + org.springframework.retry + spring-retry + ${spring.retry.version} + diff --git a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/CvUpdateManagerTest.java b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/CvUpdateManagerTest.java index e6f594dc..f677eea0 100644 --- a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/CvUpdateManagerTest.java +++ b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/CvUpdateManagerTest.java @@ -6,6 +6,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -27,6 +28,7 @@ @ContextConfiguration(locations = {"classpath*:/META-INF/intact.spring.xml", "classpath*:/META-INF/standalone/*-standalone.spring.xml", "classpath*:/META-INF/beanscv*.spring.xml"}) +@TestPropertySource(locations="classpath:/META-INF/cv-update.properties") public class CvUpdateManagerTest extends IntactBasicTestCase{ @Autowired diff --git a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/GlobalCvUpdateRunnerTest.java b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/GlobalCvUpdateRunnerTest.java index 44403d88..aca923a8 100644 --- a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/GlobalCvUpdateRunnerTest.java +++ b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/GlobalCvUpdateRunnerTest.java @@ -6,6 +6,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -28,6 +29,7 @@ "classpath*:/META-INF/standalone/*-standalone.spring.xml", "classpath*:/META-INF/beanscv*.spring.xml" }) +@TestPropertySource(locations="classpath:/META-INF/cv-update.properties") public class GlobalCvUpdateRunnerTest extends IntactBasicTestCase { @Autowired diff --git a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/importer/CvImporterTest.java b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/importer/CvImporterTest.java index 47018a82..cf941ab3 100644 --- a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/importer/CvImporterTest.java +++ b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/importer/CvImporterTest.java @@ -7,6 +7,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -35,6 +36,7 @@ @ContextConfiguration(locations = {"classpath*:/META-INF/intact.spring.xml", "classpath*:/META-INF/standalone/*-standalone.spring.xml", "classpath*:/META-INF/beanscv*.spring.xml"}) +@TestPropertySource(locations="classpath:/META-INF/cv-update.properties") public class CvImporterTest extends IntactBasicTestCase{ private CvUpdateManager cvManager; diff --git a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/remapper/ObsoleteCvRemapperTest.java b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/remapper/ObsoleteCvRemapperTest.java index 2759d449..4aa6ac85 100644 --- a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/remapper/ObsoleteCvRemapperTest.java +++ b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/remapper/ObsoleteCvRemapperTest.java @@ -7,6 +7,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -35,6 +36,7 @@ @ContextConfiguration(locations = {"classpath*:/META-INF/intact.spring.xml", "classpath*:/META-INF/standalone/*-standalone.spring.xml", "classpath*:/META-INF/beanscv*.spring.xml"}) +@TestPropertySource(locations="classpath:/META-INF/cv-update.properties") public class ObsoleteCvRemapperTest extends IntactBasicTestCase { private CvUpdateManager cvManager; diff --git a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/updater/CvUpdaterTest.java b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/updater/CvUpdaterTest.java index 4f010669..de8c2946 100644 --- a/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/updater/CvUpdaterTest.java +++ b/intact-cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/updater/CvUpdaterTest.java @@ -7,6 +7,7 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.TestPropertySource; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; @@ -32,6 +33,7 @@ @ContextConfiguration(locations = {"classpath*:/META-INF/intact.spring.xml", "classpath*:/META-INF/standalone/*-standalone.spring.xml", "classpath*:/META-INF/beanscv*.spring.xml"}) +@TestPropertySource(locations="classpath:/META-INF/cv-update.properties") public class CvUpdaterTest extends IntactBasicTestCase{ private CvUpdateManager cvManager; diff --git a/intact-cv-update/src/test/resources/META-INF/cv-update.properties b/intact-cv-update/src/test/resources/META-INF/cv-update.properties index 4b2b2ad5..8bd12a92 100644 --- a/intact-cv-update/src/test/resources/META-INF/cv-update.properties +++ b/intact-cv-update/src/test/resources/META-INF/cv-update.properties @@ -1 +1 @@ -update.report=reports \ No newline at end of file +update.report=reports diff --git a/pom.xml b/pom.xml index 05922199..b674185e 100644 --- a/pom.xml +++ b/pom.xml @@ -26,6 +26,7 @@ 4.3.30.RELEASE 2.4 3.6.0-SNAPSHOT + 1.3.4 From c7cce2aefdbe66a039bb3eba1e7fccf696a991fc Mon Sep 17 00:00:00 2001 From: jmedinaebi Date: Tue, 20 Aug 2024 08:58:53 +0100 Subject: [PATCH 3/3] 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); }