Merge branch 'release-2.4.x'

Author: imedina

.github/workflows/develop.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - develop
-      - release-2.2.x
+      - release-*
 
 jobs:
   build:
@@ -27,23 +27,17 @@ jobs:
         with:
           fetch-depth: '10'
       - name: Set up JDK 8
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
           java-version: '8'
           cache: 'maven'
-      - name: Cache Maven packages
-        uses: actions/cache@v2
-        with:
-          path: ~/.m2/repository
-          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-          restore-keys: ${{ runner.os }}-maven
       - name: Install Samtools
         run: sudo apt-get install samtools
       - name: Run tests with Maven
         run: mvn -T 2 clean install
 
-  deploy:
+  deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     secrets:

.github/workflows/release.yml

@@ -29,23 +29,17 @@ jobs:
         with:
           fetch-depth: '10'
       - name: Set up JDK 8
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
           java-version: '8'
           cache: 'maven'
-      - name: Cache Maven packages
-        uses: actions/cache@v2
-        with:
-          path: ~/.m2/repository
-          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-          restore-keys: ${{ runner.os }}-maven
       - name: Install Samtools
         run: sudo apt-get install samtools
       - name: Run tests with Maven
         run: mvn -T 2 clean install
 
-  deploy:
+  deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     secrets:
@@ -56,4 +50,4 @@ jobs:
 
   release:
     uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
-    needs: deploy
+    needs: deploy-maven

.github/workflows/task.yml

@@ -26,17 +26,11 @@ jobs:
         with:
           fetch-depth: '10'
       - name: Set up JDK 8
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
           java-version: '8'
           cache: 'maven'
-      - name: Cache Maven packages
-        uses: actions/cache@v2
-        with:
-          path: ~/.m2/repository
-          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-          restore-keys: ${{ runner.os }}-maven
       - name: Install Samtools
         run: sudo apt-get install samtools
       - name: Run tests with Maven

biodata-external/pom.xml

@@ -6,12 +6,11 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.3.0</version>
+        <version>2.4.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
     <artifactId>biodata-external</artifactId>
-    <version>${biodata.version}</version>
     <packaging>jar</packaging>
 
     <dependencies>

biodata-formats/pom.xml

@@ -22,12 +22,11 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.3.0</version>
+        <version>2.4.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
     <artifactId>biodata-formats</artifactId>
-    <version>${biodata.version}</version>
     <packaging>jar</packaging>
 
     <dependencies>

biodata-formats/src/main/java/org/opencb/biodata/formats/pubmed/PubMedParser.java

@@ -0,0 +1,46 @@
+package org.opencb.biodata.formats.pubmed;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
+import java.io.*;
+import java.util.zip.GZIPInputStream;
+
+public class PubMedParser {
+
+
+    public final static String PUBMED_CONTEXT = "org.opencb.biodata.formats.pubmed.v233jaxb";
+
+    public static void saveXMLInfo(Object obj, String filename) throws FileNotFoundException, JAXBException {
+        JAXBContext jaxbContext;
+        jaxbContext = JAXBContext.newInstance(PUBMED_CONTEXT);
+        Marshaller marshaller = jaxbContext.createMarshaller();
+        marshaller.marshal(obj, new FileOutputStream(filename));
+    }
+
+    /**
+     * Checks if XML info path exists and loads it
+     *
+     * @throws javax.xml.bind.JAXBException
+     * @throws java.io.IOException
+     */
+    public static Object loadXMLInfo(String filename) throws JAXBException, IOException {
+        System.setProperty("javax.xml.accessExternalDTD", "all");
+
+        Object obj = null;
+        JAXBContext jaxbContext = JAXBContext.newInstance(PUBMED_CONTEXT);
+        Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+
+        if (filename.endsWith("gz")) {
+            FileInputStream fis = new FileInputStream(filename);
+            GZIPInputStream gis = new GZIPInputStream(fis);
+            obj = unmarshaller.unmarshal(gis);
+        } else {
+            obj = unmarshaller.unmarshal(new File(filename));
+        }
+
+
+        return obj;
+    }
+}

biodata-formats/src/main/java/org/opencb/biodata/formats/pubmed/v233jaxb/Abstract.java

@@ -0,0 +1,102 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.3.0.1 
+// See <a href="https://javaee.github.io/jaxb-v2/">https://javaee.github.io/jaxb-v2/</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2022.05.23 at 12:52:46 PM UTC 
+//
+
+
+package org.opencb.biodata.formats.pubmed.v233jaxb;
+
+import javax.xml.bind.annotation.*;
+import java.util.ArrayList;
+import java.util.List;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType&gt;
+ *   &lt;complexContent&gt;
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ *       &lt;sequence&gt;
+ *         &lt;element ref="{}AbstractText" maxOccurs="unbounded"/&gt;
+ *         &lt;element ref="{}CopyrightInformation" minOccurs="0"/&gt;
+ *       &lt;/sequence&gt;
+ *     &lt;/restriction&gt;
+ *   &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "abstractText",
+    "copyrightInformation"
+})
+@XmlRootElement(name = "Abstract")
+public class Abstract {
+
+    @XmlElement(name = "AbstractText", required = true)
+    protected List<AbstractText> abstractText;
+    @XmlElement(name = "CopyrightInformation")
+    protected String copyrightInformation;
+
+    /**
+     * Gets the value of the abstractText property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the abstractText property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAbstractText().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AbstractText }
+     * 
+     * 
+     */
+    public List<AbstractText> getAbstractText() {
+        if (abstractText == null) {
+            abstractText = new ArrayList<AbstractText>();
+        }
+        return this.abstractText;
+    }
+
+    /**
+     * Gets the value of the copyrightInformation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCopyrightInformation() {
+        return copyrightInformation;
+    }
+
+    /**
+     * Sets the value of the copyrightInformation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCopyrightInformation(String value) {
+        this.copyrightInformation = value;
+    }
+
+}