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‎.DS_Store

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‎.gitignore

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.idea/
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target/
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application.properties

‎Aztec-Digest.iml

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‎README.md

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****Aztec-Digest

‎pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.aztec.digest</groupId>
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<artifactId>digest</artifactId>
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<version>1.0-SNAPSHOT</version>
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<name>Aztec Digest</name>
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<description>Aztec Digest v1</description>
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<parent>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-parent</artifactId>
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<version>1.5.7.RELEASE</version>
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<relativePath/> <!-- lookup parent from repository -->
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</parent>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
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<java.version>1.8</java.version>
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</properties>
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<dependencies>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-thymeleaf</artifactId>
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-web</artifactId>
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</dependency>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-test</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.json</groupId>
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<artifactId>json</artifactId>
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</dependency>
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.8.2</version>
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</dependency>
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<dependency>
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<groupId>org.jdom2</groupId>
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<artifactId>jdom2</artifactId>
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</dependency>
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.8.2</version>
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</dependency>
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<dependency>
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<groupId>javax.mail</groupId>
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<artifactId>mail</artifactId>
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<version>1.5.0-b01</version>
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</dependency>
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<dependency>
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<groupId>org.apache.solr</groupId>
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<artifactId>solr-solrj</artifactId>
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<version>6.6.1</version>
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</dependency>
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<dependency>
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<groupId>com.github.BD2K-Aztec</groupId>
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<artifactId>Aztec-Cermine</artifactId>
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<version>v1.0.5</version>
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</dependency>
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<dependency>
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<groupId>org.deeplearning4j</groupId>
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<artifactId>deeplearning4j-core</artifactId>
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<version>0.9.1</version>
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</dependency>
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<dependency>
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<groupId>org.deeplearning4j</groupId>
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<artifactId>deeplearning4j-nlp</artifactId>
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<version>0.9.1</version>
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</dependency>
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<dependency>
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<groupId>org.nd4j</groupId>
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<artifactId>nd4j-native</artifactId>
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<version>0.9.1</version>
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</dependency>
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</dependencies>
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<repositories>
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<repository>
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<id>jitpack.io</id>
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<url>https://jitpack.io</url>
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</repository>
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</repositories>
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</project>

‎src/.DS_Store

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‎src/main/.DS_Store

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‎src/main/java/attributes/Attributes.java

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package attributes;
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import attributes.abstrakt.Abstract;
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import attributes.affiliations.Affiliations;
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import attributes.authors.Authors;
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import attributes.contact.ContactInfo;
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import attributes.date.PublicationDate;
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import attributes.doi.DOI;
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import attributes.language.Language;
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import attributes.title.Title;
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import attributes.url.Url;
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import org.json.JSONObject;
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import org.json.XML;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.List;
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public class Attributes implements Runnable {
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private final String title;
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private final String name;
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private final String abstrakt;
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private final String summary="";
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private final List<String> authors;
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private final List<String> affiliations;
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private final List<String> contact;
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private final String doi;
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private final String date;
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private final String status;
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private final List<String> URLs;
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private final List<String> tags=new ArrayList<>();
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private List<String> funding;
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private String language;
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private CodeStats cs;
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private final JSONObject xmlJSONObj;
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private final String m_nlm;
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// private List<FundingInfo> funding_list;
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private JSONObject final_object;
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// ------------------------------------------------------------- //
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public Attributes(String nlm, String filename, boolean fromPMC) throws Exception {
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m_nlm = nlm;
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xmlJSONObj = XML.toJSONObject(nlm);
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funding = null;
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language = null;
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cs = null;
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run();
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Calendar title_start = Calendar.getInstance();
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Title t = new Title(xmlJSONObj);
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title = t.getTitle();
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Calendar title_end = Calendar.getInstance();
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Calendar author_start = Calendar.getInstance();
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Authors au = new Authors(xmlJSONObj,fromPMC);
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authors = au.getAuthors();
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for (int i = 0; i < authors.size(); i++) {
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authors.set(i, authors.get(i).trim());
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}
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Calendar author_end = Calendar.getInstance();
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Calendar aff_start = Calendar.getInstance();
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Affiliations aff = new Affiliations(xmlJSONObj,fromPMC);
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affiliations = aff.getAffiliations();
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for (int i = 0; i < affiliations.size(); i++) {
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affiliations.set(i, affiliations.get(i).trim());
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}
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Calendar aff_end = Calendar.getInstance();
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Calendar contact_start = Calendar.getInstance();
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ContactInfo con = new ContactInfo(nlm, fromPMC);
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contact = con.getContact();
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for (int i = 0; i < contact.size(); i++) {
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contact.set(i, contact.get(i).trim());
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}
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Calendar contact_end = Calendar.getInstance();
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Calendar doi_start = Calendar.getInstance();
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DOI d2 = new DOI(xmlJSONObj, fromPMC);
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doi = d2.getDoi();
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Calendar doi_end = Calendar.getInstance();
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Calendar date_start = Calendar.getInstance();
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PublicationDate d = new PublicationDate(xmlJSONObj, fromPMC);
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date = d.getDate();
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Calendar date_end = Calendar.getInstance();
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Calendar url_start = Calendar.getInstance();
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Url url_link = new Url(xmlJSONObj, filename);
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URLs = url_link.getUrl();
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for (int i = 0; i < URLs.size(); i++) {
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URLs.set(i, URLs.get(i).trim());
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}
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if(URLs.isEmpty()){
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status = "URL links are no longer valid";
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}else{
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status = "Success";
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}
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Calendar url_end = Calendar.getInstance();
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Calendar abstract_start = Calendar.getInstance();
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Abstract a = new Abstract(nlm,fromPMC);
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abstrakt = a.getAbstract().trim();
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Calendar abstract_end = Calendar.getInstance();
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Calendar name_start = Calendar.getInstance();
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ToolName tool_name = new ToolName(title, URLs);
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if(tool_name.getName()==null){
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name = "";
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}else{
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name = tool_name.getName();
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}
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Calendar name_end = Calendar.getInstance();
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Calendar lang_start = Calendar.getInstance();
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String code_url = "";
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for(String url: URLs){
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if(url.contains("github")){
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code_url = url;
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cs = new CodeStats(code_url, name);
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if(cs.hasStats()){
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break;
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}
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}
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if(url.contains("sourceforge") || url.contains("bitbucket")){
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code_url = url;
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}
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}
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if(cs==null){
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cs = new CodeStats(code_url, name);
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}
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final_object = new JSONObject();
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final_object.put("publicationTitle", title);
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final_object.put("publicationAbstract", abstrakt);
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final_object.put("title", title);
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final_object.put("authors", authors.toArray());
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final_object.put("institutions", affiliations.toArray());
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final_object.put("contactInfo", contact.toArray());
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final_object.put("publicationDOI", doi);
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final_object.put("publicationDate", date);
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final_object.put("URLs", URLs.toArray());
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final_object.put("status", status);
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final_object.put("toolName", name);
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final_object.put("fulltext", this.m_nlm.replaceAll("<.*?>", " "));
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if(cs.hasStats()) {
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final_object.put("programmingLanguage", cs.getLanguage());
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final_object.put("forks", cs.getForks());
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final_object.put("shortDescription", cs.getDescription());
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final_object.put("license", cs.getLicense());
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final_object.put("sourceCodeLink", cs.getRepo_link());
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final_object.put("dateCreated", cs.getDate_created());
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final_object.put("dateUpdated", cs.getDate_updated());
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final_object.put("downloads", cs.getDownloads());
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final_object.put("codeSize", cs.getSize());
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final_object.put("sourceCodeLink", cs.getRepo_link());
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final_object.put("numIssues", cs.getIssues());
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final_object.put("subscribers", cs.getSubscribers());
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if(!cs.getHomepage().isEmpty()) {
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final_object.put("homepage", cs.getHomepage());
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}
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if(cs.getRepo_name()!=null && !cs.getRepo_name().isEmpty()){
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final_object.put("toolName", cs.getRepo_name());
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}
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Calendar lang_end = Calendar.getInstance();
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}
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}
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// ------------------------------------------------------------ //
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public void run() {
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try {
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Calendar funding_start = Calendar.getInstance();
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// Funding f = new Funding(m_nlm, 0);
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// funding_list = f.getFunding();
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Calendar funding_end = Calendar.getInstance();
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// System.out.println("Time funding: ");
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// System.out.println(funding_end.getTimeInMillis() - funding_start.getTimeInMillis());
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} catch (Exception e) {
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e.printStackTrace();
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}
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}
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public void setID(int id){
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final_object.put("id", id);
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}
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public String getTitle(){
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return title;
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}
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public String getName() {
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return name;
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}
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public String getSummary() {
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return summary;
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}
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public List<String> getAuthor(){
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return authors;
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}
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public List<String> getAffiliation(){
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return affiliations;
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}
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public String getAbstrakt(){
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return abstrakt;
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}
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public List<String> getContact(){
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return contact;
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}
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public String getDOI(){
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return doi;
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}
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public String getDate() {
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return date;
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}
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public String getStatus() {
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return status;
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}
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public List<String> getURL(){
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return URLs;
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}
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// private List<FundingInfo> getFundingList() {
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// return funding_list;
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// }
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public List<String> getFundingStr() {
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// List<String> fa = new ArrayList<>();
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// for (FundingInfo fi : getFundingList()) {
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// fa.add(fi.toString());
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// }
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// funding = fa;
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return this.funding;
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}
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public String getLanguage(){
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return language;
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}
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public List<String> getTags(){
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return tags;
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}
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public JSONObject getFinalJSONObject(){
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return final_object;
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}
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public CodeStats getCodeStats() {
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return cs;
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}
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}

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