Merge pull request #87 from MICommunity/develop

Develop > Master

jami-batch/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami</groupId>
         <artifactId>psi-jami</artifactId>
-        <version>3.4.1</version>
+        <version>3.5.0</version>
     </parent>
 
     <artifactId>jami-batch</artifactId>

jami-bridges/bridges-core/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.4.1</version>
+        <version>3.5.0</version>
     </parent>
 
     <artifactId>bridges-core</artifactId>

jami-bridges/bridges-core/src/main/java/psidev/psi/mi/jami/bridges/fetcher/InteractorFetcher.java

@@ -3,36 +3,45 @@
 import psidev.psi.mi.jami.bridges.exception.BridgeFailedException;
 import psidev.psi.mi.jami.model.Interactor;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * Fetches the complete records which match an interactor.
  *
  * @author Gabriel Aldam ([email protected])
  * @since 14/05/13
-
  */
 public interface InteractorFetcher<I extends Interactor> {
 
     /**
      * Takes a string identifier and returns the interactors which match.
      * Returns an empty collection of no entries are returned
      *
-     * @param identifier    The identifier to search for.
-     * @return              The proteins which match the search term. Empty if no matches.
+     * @param identifier The identifier to search for.
+     * @return The proteins which match the search term. Empty if no matches.
      * @throws psidev.psi.mi.jami.bridges.exception.BridgeFailedException A problem has been encountered when contacting the service
      */
-    public Collection<I> fetchByIdentifier(String identifier)
-            throws BridgeFailedException;
+    default Collection<I> fetchByIdentifier(String identifier)
+            throws BridgeFailedException {
+        return fetchByIdentifiers(List.of(identifier));
+    }
 
     /**
      * Takes a collection of string identifiers and returns the interactors which match.
      * Returns an empty collection of no entries are returned.
      *
-     * @param identifiers   The identifiers to search for.
-     * @return              The proteins which match the search term. Empty if no matches.
+     * @param identifiers The identifiers to search for.
+     * @return The proteins which match the search term. Empty if no matches.
      * @throws psidev.psi.mi.jami.bridges.exception.BridgeFailedException if any.
      */
-    public Collection<I> fetchByIdentifiers(Collection<String> identifiers)
-            throws BridgeFailedException;
+    default Collection<I> fetchByIdentifiers(Collection<String> identifiers)
+            throws BridgeFailedException {
+        List<I> list = new ArrayList<>();
+        for (String identifier : identifiers) {
+            list.addAll(fetchByIdentifier(identifier));
+        }
+        return list;
+    }
 }

jami-bridges/bridges-core/src/main/java/psidev/psi/mi/jami/bridges/fetcher/NucleicAcidFetcher.java

@@ -0,0 +1,49 @@
+package psidev.psi.mi.jami.bridges.fetcher;
+
+import psidev.psi.mi.jami.bridges.exception.BridgeFailedException;
+import psidev.psi.mi.jami.model.Gene;
+import psidev.psi.mi.jami.model.NucleicAcid;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * A fetcher for genes.
+ *
+ * @author Gabriel Aldam ([email protected])
+ * @since 08/08/13
+ */
+public interface NucleicAcidFetcher extends InteractorFetcher<NucleicAcid> {
+
+    /**
+     * <p>fetchByIdentifier.</p>
+     *
+     * @param identifier The identifier of the Nucleic Acid
+     * @param taxID      The organism the gene is from.
+     * @return The genes matching the search terms.
+     * @throws BridgeFailedException if any.
+     */
+    Collection<NucleicAcid> fetchByIdentifier(String identifier, int taxID)
+            throws BridgeFailedException;
+
+
+    /**
+     * <p>fetchByIdentifiers.</p>
+     *
+     * @param identifiers The identifiers of the Nucleic Acid
+     * @param taxID       The organism the gene is from.
+     * @return The genes matching the search terms.
+     * @throws BridgeFailedException if any.
+     */
+    default Collection<NucleicAcid> fetchByIdentifiers(Collection<String> identifiers, int taxID)
+            throws BridgeFailedException {
+        List<NucleicAcid> list = new ArrayList<>();
+        for (String identifier : identifiers) {
+            list.addAll(fetchByIdentifier(identifier, taxID));
+        }
+        return list;
+
+    }
+}

jami-bridges/bridges-core/src/main/java/psidev/psi/mi/jami/bridges/fetcher/mock/MockNucleicAcidFetcher.java

@@ -0,0 +1,73 @@
+package psidev.psi.mi.jami.bridges.fetcher.mock;
+
+import psidev.psi.mi.jami.bridges.exception.BridgeFailedException;
+import psidev.psi.mi.jami.bridges.fetcher.NucleicAcidFetcher;
+import psidev.psi.mi.jami.model.NucleicAcid;
+
+import java.util.ArrayList;
+import java.util.Collection;
+
+/**
+ * A mock fetcher for testing.
+ * It extends all the methods of the true fetcher, but does not access an external service.
+ * Instead, it holds a map which can be loaded with objects and keys. which are then returned.
+ * It attempts to replicate the responses of the fetcher in most scenarios.
+ *
+ * @author Marine Dumousseau ([email protected])
+ * @version $Id$
+ * @since <pre>23/05/13</pre>
+ */
+public class MockNucleicAcidFetcher
+        extends AbstractMockFetcher<Collection<NucleicAcid>>
+        implements NucleicAcidFetcher {
+
+    /**
+     * {@inheritDoc}
+     */
+    protected Collection<NucleicAcid> getEntry(String identifier) throws BridgeFailedException {
+        if (identifier == null) throw new IllegalArgumentException(
+                "Attempted to query mock NucleicAcid fetcher for null identifier.");
+
+        if (!localMap.containsKey(identifier)) {
+            return new ArrayList<>();
+        } else {
+            return super.getEntry(identifier);
+        }
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    public Collection<NucleicAcid> fetchByIdentifier(String identifier) throws BridgeFailedException {
+        return getEntry(identifier);
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    public Collection<NucleicAcid> fetchByIdentifiers(Collection<String> identifiers) throws BridgeFailedException {
+        Collection<NucleicAcid> resultsList = new ArrayList<>();
+        for (String identifier : identifiers) {
+            resultsList.addAll(getEntry(identifier));
+        }
+        return resultsList;
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public Collection<NucleicAcid> fetchByIdentifier(String identifier, int taxID) throws BridgeFailedException {
+        return getEntry(identifier);
+    }
+
+    @Override
+    public Collection<NucleicAcid> fetchByIdentifiers(Collection<String> identifiers, int taxID) throws BridgeFailedException {
+        Collection<NucleicAcid> resultsList = new ArrayList<>();
+        for (String identifier : identifiers) {
+            resultsList.addAll(getEntry(identifier));
+        }
+        return resultsList;
+    }
+
+}

jami-bridges/jami-chebi/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.mi.jami.bridges</groupId>
         <artifactId>jami-bridges</artifactId>
-        <version>3.4.1</version>
+        <version>3.5.0</version>
     </parent>
 
     <artifactId>jami-chebi</artifactId>

jami-bridges/jami-ensembl/pom.xml

@@ -0,0 +1,67 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>psidev.psi.mi.jami.bridges</groupId>
+        <artifactId>jami-bridges</artifactId>
+        <version>3.5.0</version>
+    </parent>
+
+    <artifactId>jami-ensembl</artifactId>
+    <packaging>jar</packaging>
+
+    <name>PSI :: JAMI - Bridges - Ensembl</name>
+    <description>JAMI - Ensembl bridge</description>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <lombok.version>1.18.28</lombok.version>
+    </properties>
+
+    <dependencies>
+        <!-- bridges core -->
+        <dependency>
+            <groupId>psidev.psi.mi.jami.bridges</groupId>
+            <artifactId>bridges-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>psidev.psi.mi.jami.bridges</groupId>
+            <artifactId>jami-ols</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>${lombok.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.11.0</version>
+                <configuration>
+                    <annotationProcessorPaths>
+                        <path>
+                            <groupId>org.projectlombok</groupId>
+                            <artifactId>lombok</artifactId>
+                            <version>${lombok.version}</version>
+                        </path>
+                    </annotationProcessorPaths>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>