Merging 2.x-dev version 2.1.3 with ticket FGPTO-1429 (obsolete bug) a…

…nd bug fix in query when datasources required
dsi-icl · Jun 14, 2017 · 866b4ef · 866b4ef
2 parents f65fcaa + 83ab0ca
commit 866b4ef
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Showing 24 changed files with 72 additions and 66 deletions.
diff --git a/ols-client b/ols-client
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>uk.ac.ebi.fgpt</groupId>
     <artifactId>zooma2</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
     <packaging>pom</packaging>
 
     <name>ZOOMA 2</name>

diff --git a/zooma-api/pom.xml b/zooma-api/pom.xml
@@ -4,17 +4,17 @@
     <parent>
         <artifactId>zooma2</artifactId>
         <groupId>uk.ac.ebi.fgpt</groupId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-api</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: API</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-bootstrap/pom.xml b/zooma-bootstrap/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <artifactId>zooma2</artifactId>
         <groupId>uk.ac.ebi.fgpt</groupId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-bootstrap</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Bootstrap configuration</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>

diff --git a/zooma-builder-app/pom.xml b/zooma-builder-app/pom.xml
@@ -6,18 +6,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-builder-app</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Command line build tools</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
 
@@ -77,14 +77,14 @@
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-lodestar</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
 
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-ols-service</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
         <!-- ZOOMA basic loaders for namespace functionality -->

diff --git a/zooma-client/pom.xml b/zooma-client/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-client</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: REST API search client</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-core/pom.xml b/zooma-core/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-core</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Core search engine classes</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>
@@ -45,7 +45,7 @@
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-ols-service</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
     </dependencies>
 

diff --git a/zooma-impl/pom.xml b/zooma-impl/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <artifactId>zooma2</artifactId>
         <groupId>uk.ac.ebi.fgpt</groupId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-impl</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Standard model implementation</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-jdbc/pom.xml b/zooma-jdbc/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-jdbc</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: JDBC Bindings</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <build>

diff --git a/zooma-js/pom.xml b/zooma-js/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <artifactId>zooma2</artifactId>
         <groupId>uk.ac.ebi.fgpt</groupId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-js</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Javascript webjar</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>

diff --git a/zooma-loading/pom.xml b/zooma-loading/pom.xml
@@ -4,19 +4,19 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-loading</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
     <packaging>pom</packaging>
 
     <name>ZOOMA 2: Parent project for all loaders</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-loading/zooma-csv-loader/pom.xml b/zooma-loading/zooma-csv-loader/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma-loading</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-csv-loader</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Custom Annotation Loader (CSV files)</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-loading/zooma-owl-loader/pom.xml b/zooma-loading/zooma-owl-loader/pom.xml
@@ -4,18 +4,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma-loading</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-owl-loader</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: OWL-format Ontology Loader</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/zooma-lodestar/pom.xml b/zooma-lodestar/pom.xml
@@ -3,12 +3,12 @@
     <parent>
         <artifactId>zooma2</artifactId>
         <groupId>uk.ac.ebi.fgpt</groupId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
     <artifactId>zooma-lodestar</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: SPARQL DAO Lodestar implementations</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
@@ -22,13 +22,13 @@
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-impl</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-owlapi</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
 

diff --git a/zooma-lucene-services/pom.xml b/zooma-lucene-services/pom.xml
@@ -4,19 +4,19 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-lucene-services</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: Lucene-driven service implementations</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>

diff --git a/...ices/src/main/java/uk/ac/ebi/fgpt/zooma/service/LuceneAnnotationSummarySearchService.java b/...ices/src/main/java/uk/ac/ebi/fgpt/zooma/service/LuceneAnnotationSummarySearchService.java
@@ -275,7 +275,7 @@ protected Collection<AnnotationSummary> doSearch(AnnotationSummaryMapper mapper,
         Query q;
         if (sources.length > 0) {
             // unify processed queries into a single query
-            Query uq = formulateCombinedQuery(true, false, pqs.toArray(new Query[pqs.size()]));
+            Query uq = formulateCombinedQuery(false, false, pqs.toArray(new Query[pqs.size()]));
 
             // next generate a series of source queries
             List<Query> sqs = new ArrayList<>();

diff --git a/zooma-ols-service/pom.xml b/zooma-ols-service/pom.xml
@@ -6,27 +6,27 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-ols-service</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: OLS Search Service</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <dependencies>
 
         <dependency>
             <groupId>uk.ac.ebi.fgpt</groupId>
             <artifactId>zooma-impl</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
         <dependency>

diff --git a/zooma-ols-service/src/main/java/uk/ac/ebi/fgpt/zooma/service/OLSSearchService.java b/zooma-ols-service/src/main/java/uk/ac/ebi/fgpt/zooma/service/OLSSearchService.java
@@ -148,7 +148,13 @@ public URI replaceSemanticTag(URI semanticTag){
     }
 
     private URI tryToReplaceSemanticTag(URI semanticTag){
-        Term replaceBy = olsClient.getReplacedBy(semanticTag.toString());
+        Term replaceBy = null;
+        try {
+            replaceBy = olsClient.getReplacedBy(semanticTag.toString());
+        } catch (RestClientException e){
+            getLog().debug(semanticTag + " something went wrong when we tried to find a replacement in OLS!");
+            replaceBy = null;
+        }
         if(replaceBy != null && replaceBy.getIri() != null && replaceBy.getIri().getIdentifier() != null) {
             return URI.create(replaceBy.getIri().getIdentifier());
         }

diff --git a/zooma-owlapi/pom.xml b/zooma-owlapi/pom.xml
@@ -6,18 +6,18 @@
     <parent>
         <groupId>uk.ac.ebi.fgpt</groupId>
         <artifactId>zooma2</artifactId>
-        <version>2.1.2</version>
+        <version>2.1.3</version>
     </parent>
 
     <artifactId>zooma-owlapi</artifactId>
-    <version>2.1.2</version>
+    <version>2.1.3</version>
 
     <name>ZOOMA 2: OWL-API Binding</name>
     <url>http://www.ebi.ac.uk/fgpt/zooma</url>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <zooma.version>2.1.2</zooma.version>
+        <zooma.version>2.1.3</zooma.version>
     </properties>
 
     <build>
+98 −11		src/main/java/uk/ac/ebi/pride/utilities/ols/web/service/client/OLSClient.java
+18 −7		src/test/java/uk/ac/ebi/pride/utilities/ols/web/service/client/OLSClientTest.java