Merge pull request #18 from EBI-IntAct/develop

Develop > Master
EBI-IntAct · Sep 27, 2024 · 7732c6b · 7732c6b
2 parents 218145d + 18f7fb6
commit 7732c6b
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Showing 12 changed files with 74 additions and 20 deletions.
diff --git a/feature-shortlabel-generator/pom.xml b/feature-shortlabel-generator/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>uk.ac.ebi.intact.tools</groupId>
         <artifactId>tools-master</artifactId>
-        <version>1.2.5</version>
+        <version>2.0.1</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>

diff --git a/...rc/main/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/ShortlabelGenerator.java b/...rc/main/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/ShortlabelGenerator.java
@@ -11,6 +11,7 @@
 import uk.ac.ebi.intact.jami.model.extension.ExperimentalRange;
 import uk.ac.ebi.intact.jami.model.extension.IntactFeatureEvidence;
 import uk.ac.ebi.intact.jami.model.extension.IntactInteractor;
+import uk.ac.ebi.intact.jami.utils.IntactUtils;
 import uk.ac.ebi.intact.tools.feature.shortlabel.generator.events.*;
 import uk.ac.ebi.intact.tools.feature.shortlabel.generator.listener.ShortlabelGeneratorListener;
 import uk.ac.ebi.intact.tools.feature.shortlabel.generator.manager.ShortlabelGeneratorManager;
@@ -368,6 +369,9 @@ public void generateNewShortLabel(IntactFeatureEvidence featureEvidence) {
         if (noMutationUpdate || orgShortlabel.equals(featureEvidence.getShortName())) {
             UnmodifiedMutationShortlabelEvent event = new UnmodifiedMutationShortlabelEvent(featureAc, interactorAc, featureEvidence, noMutationUpdate);
             manager.fireOnUnmodifiedMutationShortlabelEvent(event);
+        } else if (featureEvidence.getShortName().length() > IntactUtils.MAX_SHORT_LABEL_LEN) {
+            OtherErrorEvent event = new OtherErrorEvent(featureAc, OtherErrorEvent.ErrorType.SHORT_LABEL_TOO_LONG, featureEvidence.getShortName());
+            manager.fireOnOtherErrorEvent(event);
         } else {
             ModifiedMutationShortlabelEvent event = new ModifiedMutationShortlabelEvent(featureAc, interactorAc, featureEvidence, orgShortlabel, false);
             manager.fireOnModifiedMutationShortlabelEvent(event);

diff --git a/...main/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/events/OtherErrorEvent.java b/...main/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/events/OtherErrorEvent.java
@@ -0,0 +1,39 @@
+package uk.ac.ebi.intact.tools.feature.shortlabel.generator.events;
+
+public class OtherErrorEvent {
+    private final String featureAc;
+    private final ErrorType errorType;
+    private final String errorDetails;
+
+    public OtherErrorEvent(String featureAc, ErrorType errorType, String errorDetails) {
+        this.featureAc = (featureAc == null) ? "undefined" : featureAc;
+        this.errorType = errorType;
+        this.errorDetails = errorDetails;
+    }
+
+    public String getFeatureAc() {
+        return featureAc;
+    }
+
+    public ErrorType getErrorType() {
+        return errorType;
+    }
+
+    public String getErrorDetails() {
+        return errorDetails;
+    }
+
+    public enum ErrorType {
+        SHORT_LABEL_TOO_LONG("New short label is too long");
+
+        private final String message;
+
+        ErrorType(String message) {
+            this.message = message;
+        }
+
+        public String getMessage() {
+            return message;
+        }
+    }
+}
diff --git a/...c/ebi/intact/tools/feature/shortlabel/generator/listener/ShortlabelGeneratorListener.java b/...c/ebi/intact/tools/feature/shortlabel/generator/listener/ShortlabelGeneratorListener.java
@@ -23,4 +23,6 @@ public interface ShortlabelGeneratorListener extends EventListener {
     void onResultingSequenceChanged(ResultingSequenceChangedEvent event);
 
     void onObjectTypeError(TypeErrorEvent event);
+
+    void onOtherErrorEvent(OtherErrorEvent event);
 }
diff --git a/.../ac/ebi/intact/tools/feature/shortlabel/generator/manager/ShortlabelGeneratorManager.java b/.../ac/ebi/intact/tools/feature/shortlabel/generator/manager/ShortlabelGeneratorManager.java
@@ -62,6 +62,11 @@ public void fireOnObjectTypeErrorEvent(TypeErrorEvent event) {
         }
     }
 
+    public void fireOnOtherErrorEvent(OtherErrorEvent event) {
+        for (ShortlabelGeneratorListener eventListener : getListeners(ShortlabelGeneratorListener.class)){
+            eventListener.onOtherErrorEvent(event);
+        }
+    }
 
     public void addListener(ShortlabelGeneratorListener listener) {
         listenerList.add(ShortlabelGeneratorListener.class, listener);

diff --git a/feature-shortlabel-generator/src/main/resources/META-INF/shortlabel-generator-config.xml b/feature-shortlabel-generator/src/main/resources/META-INF/shortlabel-generator-config.xml
@@ -64,13 +64,13 @@
                 <prop key="hibernate.generate_statistics">true</prop>
                 <prop key="hibernate.format_sql">false</prop>
                 <prop key="hibernate.hbm2ddl.auto">none</prop>
-                <prop key="hibernate.connection.release_mode">after_transaction</prop>
                 <prop key="hibernate.enable_lazy_load_no_trans">true</prop>
+                <prop key="hibernate.default_schema">intact</prop>
             </props>
         </property>
         <property name="jpaVendorAdapter">
             <bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
-                <property name="databasePlatform" value="org.hibernate.dialect.Oracle12cDialect"/>
+                <property name="databasePlatform" value="org.hibernate.dialect.PostgreSQL82Dialect"/>
                 <property name="showSql" value="false"/>
                 <property name="generateDdl" value="false"/>
             </bean>

diff --git a/...c/test/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/impl/FeatureListener.java b/...c/test/java/uk/ac/ebi/intact/tools/feature/shortlabel/generator/impl/FeatureListener.java
@@ -32,6 +32,11 @@ public void onUnmodifiedMutationShortlabel(UnmodifiedMutationShortlabelEvent eve
         System.out.println(event.getFeatureAc()  + "\t original shortlabel is correct: " + "\t" + event.getFeatureEvidence().getShortName());
     }
 
+    @Override
+    public void onOtherErrorEvent(OtherErrorEvent event) {
+        System.out.println(event.getFeatureAc()  + "\t " + event.getErrorType().getMessage() + ":\t" + event.getErrorDetails());
+    }
+
     @Override
     public void onRetrieveObjectError(ObjRetrieveErrorEvent event) {
         System.out.println(event.getMessage());

diff --git a/pom.xml b/pom.xml
@@ -3,26 +3,26 @@
     <parent>
         <groupId>uk.ac.ebi.intact.maven</groupId>
         <artifactId>intact-hibernate-master</artifactId>
-        <version>47</version>
+        <version>48</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>uk.ac.ebi.intact.tools</groupId>
     <artifactId>tools-master</artifactId>
     <packaging>pom</packaging>
-    <version>1.2.5</version>
+    <version>2.0.1</version>
 
     <name>IntAct Tools</name>
     <description>Tools Master POM</description>
 
     <properties>
         <currentVersion>${project.version}</currentVersion>
         <spring.version>4.3.30.RELEASE</spring.version>
-        <psi.jami.version>3.5.0</psi.jami.version>
-        <intact.jami.version>2.2.6</intact.jami.version>
-        <intact.bridges.version>2.2.2</intact.bridges.version>
-        <intact.core.version>2.8.1</intact.core.version>
+        <psi.jami.version>3.6.0</psi.jami.version>
+        <intact.jami.version>3.1.0</intact.jami.version>
+        <intact.bridges.version>2.2.3</intact.bridges.version>
+        <intact.core.version>3.1.0</intact.core.version>
         <maven.pmd.skip>true</maven.pmd.skip>
     </properties>
 
@@ -100,10 +100,6 @@
     </dependencies>
 
     <repositories>
-        <repository>
-            <id>nexus-ebi-repo-old</id>
-            <url>https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
-        </repository>
         <repository>
             <id>nexus-ebi-release-repo</id>
             <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>

diff --git a/protein-mapping/pom.xml b/protein-mapping/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <groupId>uk.ac.ebi.intact.tools</groupId>
         <artifactId>tools-master</artifactId>
-        <version>1.2.5</version>
+        <version>2.0.1</version>
     </parent>
 
 

diff --git a/protein-mapping/run_protein_sequence_blast.sh b/protein-mapping/run_protein_sequence_blast.sh
@@ -9,4 +9,4 @@ echo "input file $1"
 echo "ouput file $2"
 echo "taxid $3"
 
-mvn -U clean install -Pprotein-sequence-identification -Dinput.file=$1 -Douput.file=$2 -Dtaxid=$3 -Dmaven.repo.local=repository -Dmaven.test.skip -Ddb=oracle
+mvn -U clean install -Pprotein-sequence-identification -Dinput.file=$1 -Douput.file=$2 -Dtaxid=$3 -Dmaven.repo.local=repository -Dmaven.test.skip -Ddb=postgres
diff --git a/...n-mapping/src/main/java/uk/ac/ebi/intact/protein/mapping/update/ProteinUpdateManager.java b/...n-mapping/src/main/java/uk/ac/ebi/intact/protein/mapping/update/ProteinUpdateManager.java
@@ -78,10 +78,11 @@ protected Query getProteinsWithoutUniprotXrefs(DataContext dataContext){
                 "left join p.xrefs as xrefs " +
                 "left join p.annotations as annotations " +
                 "where p.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
-                "and p not in ( "+
+                "and not exists ( "+
                 "select p2 "+
                 "from InteractorImpl p2 join p2.xrefs as xrefs "+
-                "where p2.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
+                "where p2.ac = p.ac " +
+                "and p2.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
                 "and xrefs.cvDatabase.ac = 'EBI-31' " +
                 "and xrefs.cvXrefQualifier.shortLabel <> 'uniprot-removed-ac' )");
 
@@ -96,10 +97,11 @@ protected Query getProteinsWithUniprotXrefsWithoutIdentity(DataContext dataConte
                 "left join p.xrefs as xrefs " +
                 "left join p.annotations as annotations " +
                 "where p.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
-                "and p not in ( "+
+                "and not exists ( "+
                 "select p2 "+
                 "from InteractorImpl p2 join p2.xrefs as xrefs "+
-                "where p2.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
+                "where p2.ac = p.ac " +
+                "and p2.objClass = 'uk.ac.ebi.intact.model.ProteinImpl' "+
                 "and xrefs.cvDatabase.ac = 'EBI-31' " +
                 "and xrefs.cvXrefQualifier.shortLabel = 'identity') " +
                 "and p in ( " +

diff --git a/protein-mapping/src/test/resources/META-INF/jpa.test.spring.xml b/protein-mapping/src/test/resources/META-INF/jpa.test.spring.xml
@@ -16,6 +16,7 @@
                 <prop key="hibernate.generate_statistics">true</prop>
                 <prop key="hibernate.format_sql">false</prop>
                 <prop key="hibernate.hbm2ddl.auto">create-drop</prop>
+                <prop key="hibernate.default_schema">intact</prop>
             </props>
         </property>
 
@@ -30,7 +31,7 @@
 
     <bean id="intactCoreDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
         <property name="driverClassName" value="org.h2.Driver"/>
-        <property name="url" value="jdbc:h2:mem:intactcore;DB_CLOSE_DELAY=-1;LOCK_MODE=0"/>
+        <property name="url" value="jdbc:h2:mem:intactcore;DB_CLOSE_DELAY=-1;LOCK_MODE=0;INIT=CREATE SCHEMA IF NOT EXISTS INTACT"/>
         <property name="username" value="sa"/>
         <property name="password" value=""/>
     </bean>