Merge branch 'release-3.1.2'

MICommunity · Aug 15, 2016 · e00610c · e00610c
2 parents 90e8c8a + eb6e59e
commit e00610c
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Showing 28 changed files with 65 additions and 83 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>psidev.psi.mi</groupId>
     <artifactId>validator</artifactId>
-    <version>3.1.1</version>
+    <version>3.1.2</version>
     <packaging>pom</packaging>
 
     <name>PSI :: Schema Validator</name>
@@ -14,9 +14,8 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <spring.version>3.2.9.RELEASE</spring.version>
         <jami.version>3.0.1</jami.version>
-        <!--Maybe subtitute with psidev.psi.tool.version if we put them together-->
-        <ontology.manager.version>2.0.6</ontology.manager.version>
-    </properties>
+        <psidev.psi.tool.version>2.0.7</psidev.psi.tool.version>
+</properties>
 
     <scm>
         <connection>scm:git:https://github.com/MICommunity/psi-mi-validator.git</connection>

diff --git a/psimi-schema-validator-cli/pom.xml b/psimi-schema-validator-cli/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>psidev.psi.mi</groupId>
         <artifactId>validator</artifactId>
-        <version>3.1.1</version>
+        <version>3.1.2</version>
     </parent>
 
     <artifactId>psimi-schema-validator-cli</artifactId>
@@ -64,6 +64,7 @@
                     <plugin>
                         <groupId>org.codehaus.mojo</groupId>
                         <artifactId>exec-maven-plugin</artifactId>
+                        <version>1.5.0</version>
                         <executions>
                             <execution>
                                 <phase>install</phase>

diff --git a/psimi-schema-validator/pom.xml b/psimi-schema-validator/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>psidev.psi.mi</groupId>
         <artifactId>validator</artifactId>
-        <version>3.1.1</version>
+        <version>3.1.2</version>
     </parent>
 
     <artifactId>psimi-schema-validator</artifactId>
@@ -100,12 +100,7 @@
         <dependency>
             <groupId>psidev.psi.tools</groupId>
             <artifactId>validator</artifactId>
-            <version>2.0.5</version>
-        </dependency>
-        <dependency>
-            <groupId>psidev.psi.tools</groupId>
-            <artifactId>ontology-manager</artifactId>
-            <version>${ontology.manager.version}</version>
+            <version>${psidev.psi.tool.version}</version>
         </dependency>
 
         <!-- JAMI libs -->

diff --git a/...tension/rules/dependencies/ExperimentCrossReference2CrossReferenceTypeDependencyRule.java b/...tension/rules/dependencies/ExperimentCrossReference2CrossReferenceTypeDependencyRule.java
@@ -71,7 +71,7 @@ public ExperimentCrossReference2CrossReferenceTypeDependencyRule( OntologyManage
         setName( "Dependency Check : Experiment Cross reference database and cross reference qualifier" );
         setDescription( "Checks that each association database - qualifier respects IMEx curetion rules. For example, for each feature, all the interpro" +
                 " cross references should have a qualifier 'identity'.");
-        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/experimentCrossReference2CrossRefType.tsv for the possible dependencies cross reference database - qualifier" );
     }
 

diff --git a/.../extension/rules/dependencies/FeatureCrossReference2CrossReferenceTypeDependencyRule.java b/.../extension/rules/dependencies/FeatureCrossReference2CrossReferenceTypeDependencyRule.java
@@ -70,7 +70,7 @@ public FeatureCrossReference2CrossReferenceTypeDependencyRule( OntologyManager o
         setName( "Dependency Check : Feature Cross reference database and cross reference qualifier" );
         setDescription( "Checks that each association database - qualifier respects IMEx curetion rules. For example, for each feature, all the interpro" +
                 " cross references should have a qualifier 'identity'.");
-        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/featureCrossReference2CrossRefType.tsv for the possible dependencies cross reference database - qualifier" );
     }
 

diff --git a/...idator/extension/rules/dependencies/FeatureType2FeatureDetectionMethodDependencyRule.java b/...idator/extension/rules/dependencies/FeatureType2FeatureDetectionMethodDependencyRule.java
@@ -44,7 +44,7 @@ public FeatureType2FeatureDetectionMethodDependencyRule( OntologyManager ontolog
 
         OntologyAccess mi = ontologyManager.getOntologyAccess( "MI" );
         String fileName = validatorContext.getValidatorConfig().getFeatureType2FeatureDetectionMethod();
-        
+
         try {
             URL resource = FeatureType2FeatureDetectionMethodDependencyRule.class
                     .getResource( fileName );
@@ -61,7 +61,7 @@ public FeatureType2FeatureDetectionMethodDependencyRule( OntologyManager ontolog
         // describe the rule.
         setName( "Dependency Check : Participant's feature type and feature detection method" );
         setDescription( "Checks that each association participant's feature type - feature detection method is valid and respects IMEx curation rules.");
-        addTip( "Search the possible terms for feature type and feature detection method on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for feature type and feature detection method on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/featureType2FeatureDetectionMethod.tsv for the possible dependencies feature type - feature detection method" );
     }
 

diff --git a/...psi/mi/validator/extension/rules/dependencies/FeatureType2FeatureRangeDependencyRule.java b/...psi/mi/validator/extension/rules/dependencies/FeatureType2FeatureRangeDependencyRule.java
@@ -57,7 +57,7 @@ public FeatureType2FeatureRangeDependencyRule( OntologyManager ontologyManager )
         // describe the rule.
         setName( "Dependency Check : Participant's feature type and participant's feature range status" );
         setDescription( "Checks association participant's feature type - participant's feature range status is valid and respects IMEx curation rules.");
-        addTip( "Search the possible terms for feature type and feature range status on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for feature type and feature range status on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/featureType2FeatureRangeStatus.tsv for the possible dependencies feature type - feature range status" );
 
     }

diff --git a/...ension/rules/dependencies/InteractionCrossReference2CrossReferenceTypeDependencyRule.java b/...ension/rules/dependencies/InteractionCrossReference2CrossReferenceTypeDependencyRule.java
@@ -68,7 +68,7 @@ public InteractionCrossReference2CrossReferenceTypeDependencyRule( OntologyManag
         setName( "Dependency Check : Interaction Cross reference database and cross reference qualifier" );
         setDescription( "Checks that each association database - qualifier respects IMEx curetion rules. For example, for each feature, all the interpro" +
                 " cross references should have a qualifier 'identity'.");
-        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ols/ontologies/mi" );
 //        addTip( "Look at the file http://psimi.googlecode.com/svn/trunk/validator/psimi-schema-validator/src/main/resources/interactionCrossReference2Location2CrossRefType.tsv for the possible dependencies cross reference database - qualifier" );
     }
 

diff --git a/...extension/rules/dependencies/InteractionDetectionMethod2BiologicalRoleDependencyRule.java b/...extension/rules/dependencies/InteractionDetectionMethod2BiologicalRoleDependencyRule.java
@@ -41,7 +41,7 @@ public InteractionDetectionMethod2BiologicalRoleDependencyRule( OntologyManager
 
         OntologyAccess mi = ontologyManager.getOntologyAccess( "MI" );
         String fileName = validatorContext.getValidatorConfig().getInteractionDetectionMethod2BiologicalRole();
-        
+
         try {
 
             URL resource = InteractionDetectionMethod2BiologicalRoleDependencyRule.class
@@ -58,7 +58,7 @@ public InteractionDetectionMethod2BiologicalRoleDependencyRule( OntologyManager
         // describe the rule.
         setName( "Dependency Check : Interaction detection method and participant's biological role" );
         setDescription( "Checks that each association interaction detection method - participant's biological role is valid and respects IMEx curation rules");
-        addTip( "Search the possible terms for interaction detection method and biological role on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for interaction detection method and biological role on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/InteractionDetectionMethod2BiologicalRole.tsv for the possible dependencies interaction detection method - biological role" );
     }
 

diff --git a/...extension/rules/dependencies/InteractionDetectionMethod2ExperimentRoleDependencyRule.java b/...extension/rules/dependencies/InteractionDetectionMethod2ExperimentRoleDependencyRule.java
@@ -59,7 +59,7 @@ public InteractionDetectionMethod2ExperimentRoleDependencyRule( OntologyManager
         // describe the rule.
         setName( "Dependency Check : Interaction detection method and participant's experimental role" );
         setDescription( "Checks that each association interaction detection method - participant's experimental role is valid and respects IMEx curation rules" );
-        addTip( "Search the possible terms for interaction detection method and experimental role on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for interaction detection method and experimental role on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/InteractionDetectionMethod2ExperimentRole.tsv for the possible dependencies interaction detection method - experimental role" );
     }
 

diff --git a/...xtension/rules/dependencies/InteractionDetectionMethod2InteractionTypeDependencyRule.java b/...xtension/rules/dependencies/InteractionDetectionMethod2InteractionTypeDependencyRule.java
@@ -62,7 +62,7 @@ public InteractionDetectionMethod2InteractionTypeDependencyRule( OntologyManager
         // describe the rule.
         setName( "Dependency Check : Interaction detection method and interaction type" );
         setDescription( "Checks that each association interaction detection method - interaction type is valid and respects IMEx curation rules." );
-        addTip( "Search the possible terms for interaction detection method and interaction type on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for interaction detection method and interaction type on http://www.ebi.ac.uk/ols/ontologies/mi" );
 //        addTip( "Look at the file http://psimi.googlecode.com/svn/trunk/validator/psimi-schema-validator/src/main/resources/InteractionDetectionMethod2InteractionTypes.tsv for the possible dependencies interaction detection method - interaction type" );
     }
 

diff --git a/...ependencies/InteractionDetectionMethod2ParticipantIdentificationMethodDependencyRule.java b/...ependencies/InteractionDetectionMethod2ParticipantIdentificationMethodDependencyRule.java
@@ -39,7 +39,7 @@ public InteractionDetectionMethod2ParticipantIdentificationMethodDependencyRule(
 
         OntologyAccess mi = ontologyManager.getOntologyAccess( "MI" );
         String fileName = validatorContext.getValidatorConfig().getInteractionDetectionMethod2ParticipantIdentificationMethod();
-        
+
             try {
 
                 URL resource = InteractionDetectionMethod2ParticipantIdentificationMethodDependencyRule.class
@@ -56,7 +56,7 @@ public InteractionDetectionMethod2ParticipantIdentificationMethodDependencyRule(
             // describe the rule.
         setName( "Dependency Check : Interaction detection method and participant identification method" );
         setDescription( "Checks that each association interaction detection method - participant identification methods is valid and respects IMEx curation rules." );
-        addTip( "Search the possible terms for interaction detection method and participant identification method on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for interaction detection method and participant identification method on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/InteractionDetectionMethod2ParticipantIdentificationMethod.tsv for the possible dependencies interaction detection method - participant identification method" );
     }
 

diff --git a/...tension/rules/dependencies/InteractorCrossReference2CrossReferenceTypeDependencyRule.java b/...tension/rules/dependencies/InteractorCrossReference2CrossReferenceTypeDependencyRule.java
@@ -71,7 +71,7 @@ public InteractorCrossReference2CrossReferenceTypeDependencyRule( OntologyManage
         setName( "Dependency Check : interactor Cross reference database and cross reference qualifier" );
         setDescription( "Checks that each association database - qualifier respects IMEx curetion rules. For example, for each feature, all the interpro" +
                 " cross references should have a qualifier 'identity'.");
-        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI" );
+        addTip( "Search the possible terms for database cross reference and reference type on http://www.ebi.ac.uk/ols/ontologies/mi" );
         addTip( "Look at the file https://github.com/MICommunity/PSI-MI-Validator/blob/master/psimi-schema-validator/src/main/resources/interactorCrossReference2CrossRefType.tsv for the possible dependencies cross reference database - qualifier" );
     }
 

diff --git a/...tor/src/main/java/psidev/psi/mi/validator/extension/rules/imex/BindingDomainSizeRule.java b/...tor/src/main/java/psidev/psi/mi/validator/extension/rules/imex/BindingDomainSizeRule.java
@@ -30,7 +30,7 @@ public BindingDomainSizeRule(OntologyManager ontologyManager) {
         setName("Binding domain Check");
         setDescription("Checks that each binding domain contains more than three amino acids. ");
         addTip("when the feature type is any children of binding site (MI:0117), the range should contain at least three amino acids, otherwise it is considered as a mutant.");
-        addTip( "Mutant accessions in the PSI-MI ontology can be found at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0118&termName=mutation");
+        addTip( "Mutant accessions in the PSI-MI ontology can be found at http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0118");
     }
 
     private long getMaxRangeLength(psidev.psi.mi.jami.model.Range range, boolean isStartDefined, boolean isEndDefined){

diff --git a/...validator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/FeatureTypeRule.java b/...validator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/FeatureTypeRule.java
@@ -36,7 +36,7 @@ public FeatureTypeRule(OntologyManager ontologyManager) {
         setName("Participant's feature Type Check");
         setDescription("Checks that each participant's feature has a feature type with " +
                 "a valid PSI MI/PSI-MOD cross reference.");
-        addTip( "See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0116&termName=feature%20type for the existing feature types" );
+        addTip( "See http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0116 for the existing feature types" );
     }
 
     @Override
@@ -67,7 +67,7 @@ public Collection<ValidatorMessage> check(Feature feature) throws ValidatorExcep
                     if (messages.isEmpty()){
                         messages = new ArrayList<ValidatorMessage>();
                     }
-                    messages.add( new ValidatorMessage( "The feature type is not a valid MI term. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0116&termName=feature%20type",
+                    messages.add( new ValidatorMessage( "The feature type is not a valid MI term. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0116",
                             MessageLevel.ERROR,
                             context,
                             this ) );
@@ -89,7 +89,7 @@ public Collection<ValidatorMessage> check(Feature feature) throws ValidatorExcep
                         if (messages.isEmpty()){
                             messages = new ArrayList<ValidatorMessage>();
                         }
-                        messages.add( new ValidatorMessage( "The feature type is not a valid MI term. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0116&termName=feature%20type",
+                        messages.add( new ValidatorMessage( "The feature type is not a valid MI term. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0116",
                                 MessageLevel.ERROR,
                                 context,
                                 this ) );

diff --git a/...dator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/InteractionTypeRule.java b/...dator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/InteractionTypeRule.java
@@ -34,7 +34,7 @@ public InteractionTypeRule(OntologyManager ontologyManager) {
         setName("Interaction Type Check");
         setDescription("Checks that each interaction has at least one interaction type and all the interactions types should have " +
                 "a valid PSI MI cross reference.");
-        addTip( "See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0190&termName=interaction%20type for the existing interaction types" );
+        addTip( "See http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0190 for the existing interaction types" );
     }
 
     @Override

diff --git a/...idator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/InteractorTypeRule.java b/...idator/src/main/java/psidev/psi/mi/validator/extension/rules/imex/InteractorTypeRule.java
@@ -32,7 +32,7 @@ public InteractorTypeRule(OntologyManager ontologyMaganer) {
         setDescription( "Interactor's type cannot be set to 'nucleic acid' or 'small molecule' as it is currently outside " +
                 "of the remit of IMEx." );
 
-        addTip( "The possible interactor types can be found at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0313&termName=interactor%20type" );
+        addTip( "The possible interactor types can be found at http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0313" );
     }
 
     @Override

diff --git a/...va/psidev/psi/mi/validator/extension/rules/mimix/ParticipantIdentificationMethodRule.java b/...va/psidev/psi/mi/validator/extension/rules/mimix/ParticipantIdentificationMethodRule.java
@@ -30,7 +30,7 @@ public ParticipantIdentificationMethodRule(OntologyManager ontologyMaganer) {
         setDescription( "Checks that each participant has at least one Participant Identification Method (MI:0002)." );
         addTip( "Each participant should have a Participant Identification method" );
         addTip( "Each participant identification method should have a PSI MI cross reference with a reference type set to identical object (MI:0356)" );
-        addTip( "Any child of MI:0002 is a Participant Identification method. You can look at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI." );
+        addTip( "Any child of MI:0002 is a Participant Identification method. You can look at http://www.ebi.ac.uk/ols/ontologies/mi." );
         addTip( "The PSI-MI identifier for identical object is: MI:0356" );
     }
 

diff --git a/...alidator/src/main/java/psidev/psi/mi/validator/extension/rules/psimi/AliasSyntaxRule.java b/...alidator/src/main/java/psidev/psi/mi/validator/extension/rules/psimi/AliasSyntaxRule.java
@@ -64,7 +64,7 @@ public Collection<ValidatorMessage> check(Alias alias) throws ValidatorException
                     if (messages.isEmpty()){
                        messages = new ArrayList<ValidatorMessage>();
                     }
-                    messages.add( new ValidatorMessage( "The alias type MI identifier "+alias.getType().getMIIdentifier()+"  does not exist in the PSI-MI ontology. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0300&termName=alias%20type",
+                    messages.add( new ValidatorMessage( "The alias type MI identifier "+alias.getType().getMIIdentifier()+"  does not exist in the PSI-MI ontology. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0300",
                             MessageLevel.ERROR,
                             context,
                             this ) );
@@ -86,7 +86,7 @@ public Collection<ValidatorMessage> check(Alias alias) throws ValidatorException
                         if (messages.isEmpty()){
                             messages = new ArrayList<ValidatorMessage>();
                         }
-                        messages.add( new ValidatorMessage( "The MI identifier "+alias.getType().getMIIdentifier()+" is not a valid MI identifier for alias types. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0300&termName=alias%20type",
+                        messages.add( new ValidatorMessage( "The MI identifier "+alias.getType().getMIIdentifier()+" is not a valid MI identifier for alias types. The valid MI terms for alias types are available here: http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:0300",
                                 MessageLevel.ERROR,
                                 context,
                                 this ) );