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DrugbankParser: corrected file dependency
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+148
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‎parsers.iml

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,10 @@
33
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_7" inherit-compiler-output="false">
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<output url="file://$MODULE_DIR$/target/classes" />
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<output-test url="file://$MODULE_DIR$/target/test-classes" />
6-
<exclude-output />
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<content url="file://$MODULE_DIR$">
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<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
9-
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" isTestSource="false" />
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<sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
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<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
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<excludeFolder url="file://$MODULE_DIR$/target" />
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</content>
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<orderEntry type="inheritedJdk" />

‎src/main/java/drugbank/DrugbankParser.java

Lines changed: 31 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,14 @@
11
package drugbank;
22

3-
import com.fasterxml.jackson.databind.ObjectMapper;
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import drugbank.drugbank.DrugInteraction;
4+
import drugbank.xjc20131209.*;
55

6+
import javax.xml.bind.JAXBException;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* Created with IntelliJ IDEA.
@@ -17,11 +20,36 @@
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public class DrugbankParser {
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20-
public List<DrugInteraction> parse(Object drugbank, String species, Path outPath) {
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public List<DrugInteraction> parse(Drugs drugs, String species, Path outPath) throws JAXBException {
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List<DrugInteraction> drugInteractions = new ArrayList();
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24-
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System.out.println("Number of drugs: "+ drugs.getDrug().size());
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System.out.println("Number of partners: "+ drugs.getPartners().getPartner().size());
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List<PartnerType> partnertype = drugs.getPartners().getPartner();
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/**
33+
* Store all Partner Uniprot ID into a Map to speed up searching
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* Partner ID --> Uniprot ID
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*/
36+
Map<Integer, String> partnerTypesMap = new HashMap<Integer, String>(20000);
37+
for (PartnerType partner: drugs.getPartners().getPartner()){
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System.out.println(partner);
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// for (IdentifiersType.ExternalIdentifier xid: partner.getExternalIdentifiers().getExternalIdentifier()){
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// if (xid != null && xid.getResource().equalsIgnoreCase("UniProtKB")){
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// partnerTypesMap.put(partner.getId().intValue(), xid.getIdentifier());
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// }
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// }
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}
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// for (x partner:drugs.getPartners()){
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//
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// }
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// DrugbankXMLParser dxp = new DrugbankXMLParser();
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// drugbank = () dxp.loadXMLInfo("/home/mbleda/projects/2013_variability_drug_binding_proteins/1-data/drugbank/data_to_drugbank_parser/drugbank_20131209.xml");
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//
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return drugInteractions;

‎src/main/java/drugbank/DrugbankXMLParser.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@
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*/
2020
public class DrugbankXMLParser {
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22-
private final static String DRUGBANK_CONTEXT = "drugbank.xjc20131209";
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public final static String DRUGBANK_CONTEXT = "drugbank.xjc20131209";
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public static void saveXMLInfo(Object obj, String filename) throws FileNotFoundException, JAXBException {
2525
JAXBContext jaxbContext;

‎src/main/java/drugbank/xjc20131209/AffectedOrganisms.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
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// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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package xjc20131209;
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package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

‎src/main/java/drugbank/xjc20131209/AhfsCodes.java

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@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
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// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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package xjc20131209;
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package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

‎src/main/java/drugbank/xjc20131209/AtcCodes.java

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@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
5+
// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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9-
package xjc20131209;
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package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

‎src/main/java/drugbank/xjc20131209/BondActionsType.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
5+
// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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88

9-
package xjc20131209;
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package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

‎src/main/java/drugbank/xjc20131209/BondType.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
5+
// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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9-
package xjc20131209;
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package drugbank.xjc20131209;
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import java.math.BigInteger;
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import javax.xml.bind.annotation.XmlAccessType;

‎src/main/java/drugbank/xjc20131209/Brands.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
5+
// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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9-
package xjc20131209;
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package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

‎src/main/java/drugbank/xjc20131209/Carriers.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.4-2
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
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// Any modifications to this file will be lost upon recompilation of the source schema.
5-
// Generated on: 2013.12.09 at 12:57:02 PM CET
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// Generated on: 2013.12.10 at 11:00:55 AM CET
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//
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9-
package xjc20131209;
9+
package drugbank.xjc20131209;
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import java.util.ArrayList;
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import java.util.List;

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