Merge pull request #27 from EBI-IntAct/uniplex-import

Update dependencies
EBI-IntAct · Aug 20, 2024 · a7190c1 · a7190c1
2 parents c45ecd3 + c7cce2a
commit a7190c1
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Showing 13 changed files with 57 additions and 21 deletions.
diff --git a/intact-cv-update/pom.xml b/intact-cv-update/pom.xml
@@ -10,6 +10,12 @@
     <artifactId>intact-cv-update</artifactId>
     <name>IntAct Database Update :: CV Update</name>
 
+    <properties>
+        <retry.maxAttempts>5</retry.maxAttempts>
+        <retry.multiplier>2</retry.multiplier>
+        <retry.maxDelay>5000</retry.maxDelay>
+    </properties>
+
     <dependencies>
         <dependency>
             <groupId>uk.ac.ebi.intact.core</groupId>
@@ -45,5 +51,10 @@
             <artifactId>spring-beans</artifactId>
             <version>${spring.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.retry</groupId>
+            <artifactId>spring-retry</artifactId>
+            <version>${spring.retry.version}</version>
+        </dependency>
     </dependencies>
 </project>
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
@@ -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
@@ -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
@@ -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/...cv-update/src/test/java/uk/ac/ebi/intact/dbupdate/cv/remapper/ObsoleteCvRemapperTest.java b/...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
@@ -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
@@ -1 +1 @@
-update.report=reports
+update.report=reports
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);
         }
 

diff --git a/pom.xml b/pom.xml
@@ -19,13 +19,14 @@
     <url>http://www.ebi.ac.uk/~intact/devsite/dbupdate</url>
 
     <properties>
-        <core.version>3.0.2-SNAPSHOT</core.version>
+        <core.version>3.1.0-SNAPSHOT</core.version>
         <bridges.version>2.2.3-SNAPSHOT</bridges.version>
         <intact.tools.version>2.0.1-SNAPSHOT</intact.tools.version>
         <uniprot.japi.version>1.1.2</uniprot.japi.version>
         <spring.version>4.3.30.RELEASE</spring.version>
         <chebi.ws.version>2.4</chebi.ws.version>
-        <jami.version>3.5.2-SNAPSHOT</jami.version>
+        <jami.version>3.6.0-SNAPSHOT</jami.version>
+        <spring.retry.version>1.3.4</spring.retry.version>
     </properties>
 
     <scm>