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46 changes: 46 additions & 0 deletions
46
biodata-formats/src/main/java/org/opencb/biodata/formats/pubmed/PubMedParser.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| package org.opencb.biodata.formats.pubmed; | ||
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| 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; | ||
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| public class PubMedParser { | ||
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| public final static String PUBMED_CONTEXT = "org.opencb.biodata.formats.pubmed.v233jaxb"; | ||
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| 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)); | ||
| } | ||
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| /** | ||
| * 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"); | ||
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| Object obj = null; | ||
| JAXBContext jaxbContext = JAXBContext.newInstance(PUBMED_CONTEXT); | ||
| Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); | ||
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| 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)); | ||
| } | ||
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| return obj; | ||
| } | ||
| } |
102 changes: 102 additions & 0 deletions
102
biodata-formats/src/main/java/org/opencb/biodata/formats/pubmed/v233jaxb/Abstract.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| // | ||
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| package org.opencb.biodata.formats.pubmed.v233jaxb; | ||
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| import javax.xml.bind.annotation.*; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| /** | ||
| * <p>Java class for anonymous complex type. | ||
| * | ||
| * <p>The following schema fragment specifies the expected content contained within this class. | ||
| * | ||
| * <pre> | ||
| * <complexType> | ||
| * <complexContent> | ||
| * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | ||
| * <sequence> | ||
| * <element ref="{}AbstractText" maxOccurs="unbounded"/> | ||
| * <element ref="{}CopyrightInformation" minOccurs="0"/> | ||
| * </sequence> | ||
| * </restriction> | ||
| * </complexContent> | ||
| * </complexType> | ||
| * </pre> | ||
| * | ||
| * | ||
| */ | ||
| @XmlAccessorType(XmlAccessType.FIELD) | ||
| @XmlType(name = "", propOrder = { | ||
| "abstractText", | ||
| "copyrightInformation" | ||
| }) | ||
| @XmlRootElement(name = "Abstract") | ||
| public class Abstract { | ||
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| @XmlElement(name = "AbstractText", required = true) | ||
| protected List<AbstractText> abstractText; | ||
| @XmlElement(name = "CopyrightInformation") | ||
| protected String copyrightInformation; | ||
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| /** | ||
| * 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; | ||
| } | ||
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| /** | ||
| * Gets the value of the copyrightInformation property. | ||
| * | ||
| * @return | ||
| * possible object is | ||
| * {@link String } | ||
| * | ||
| */ | ||
| public String getCopyrightInformation() { | ||
| return copyrightInformation; | ||
| } | ||
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| /** | ||
| * Sets the value of the copyrightInformation property. | ||
| * | ||
| * @param value | ||
| * allowed object is | ||
| * {@link String } | ||
| * | ||
| */ | ||
| public void setCopyrightInformation(String value) { | ||
| this.copyrightInformation = value; | ||
| } | ||
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| } |
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