forked from antonis.lempesis/dnet-hadoop
implementation for bulk tagging
This commit is contained in:
parent
e80f80ca93
commit
d9d2060561
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@ -5,11 +5,46 @@
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<parent>
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<artifactId>dhp-workflows</artifactId>
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<groupId>eu.dnetlib.dhp</groupId>
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<version>1.0.5-SNAPSHOT</version>
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<version>1.1.6-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>dhp-bulktag</artifactId>
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<dependencies>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-core_2.11</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.spark</groupId>
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<artifactId>spark-sql_2.11</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-common</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-schemas</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>dom4j</groupId>
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<artifactId>dom4j</artifactId>
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</dependency>
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<dependency>
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<groupId>com.jayway.jsonpath</groupId>
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<artifactId>json-path</artifactId>
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</dependency>
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<dependency>
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<groupId>org.reflections</groupId>
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<artifactId>reflections</artifactId>
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<version>0.9.11</version>
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<scope>compile</scope>
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</dependency>
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</dependencies>
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</project>
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@ -0,0 +1,64 @@
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package eu.dnetlib.dhp;
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import com.google.gson.Gson;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Created by miriam on 01/08/2018.
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*/
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public class Community {
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private static final Log log = LogFactory.getLog(Community.class);
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private String id;
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private List<String> subjects = new ArrayList<>();
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private List<Datasource> datasources = new ArrayList<>();
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private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
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public String toJson() {
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final Gson g = new Gson();
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return g.toJson(this);
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}
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public boolean isValid() {
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return !getSubjects().isEmpty() || !getDatasources().isEmpty() || !getZenodoCommunities().isEmpty();
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}
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public List<String> getSubjects() {
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return subjects;
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}
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public void setSubjects(List<String> subjects) {
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this.subjects = subjects;
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}
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public List<Datasource> getDatasources() {
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return datasources;
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}
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public void setDatasources(List<Datasource> datasources) {
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this.datasources = datasources;
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}
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public List<ZenodoCommunity> getZenodoCommunities() {
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return zenodoCommunities;
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}
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public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
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this.zenodoCommunities = zenodoCommunities;
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}
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}
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@ -0,0 +1,170 @@
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package eu.dnetlib.dhp;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
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import eu.dnetlib.dhp.selectioncriteria.Selection;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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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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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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/**
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* Created by miriam on 02/08/2018.
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*/
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public class CommunityConfiguration {
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private static final Log log = LogFactory.getLog(CommunityConfiguration.class);
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private Map<String,Community> communities;
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//map subject -> communityid
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private transient Map<String,List<Pair<String,SelectionConstraints>>> subjectMap = new HashMap<>();
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//map datasourceid -> communityid
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private transient Map<String,List<Pair<String,SelectionConstraints>>> datasourceMap = new HashMap<>();
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//map zenodocommunityid -> communityid
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private transient Map<String,List<Pair<String,SelectionConstraints>>> zenodocommunityMap = new HashMap<>();
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CommunityConfiguration(final Map<String, Community> communities) {
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this.communities = communities;
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init();
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}
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void init() {
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if (subjectMap == null) {
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subjectMap = Maps.newHashMap();
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}
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if (datasourceMap == null) {
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datasourceMap = Maps.newHashMap();
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}
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if (zenodocommunityMap == null) {
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zenodocommunityMap = Maps.newHashMap();
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}
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for(Community c : getCommunities().values()) {
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//get subjects
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final String id = c.getId();
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for(String sbj : c.getSubjects()){
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Pair<String,SelectionConstraints> p = new Pair<>(id,new SelectionConstraints());
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add(sbj.toLowerCase().trim() , p, subjectMap);
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}
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//get datasources
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for(Datasource d: c.getDatasources()){
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add(d.getOpenaireId(),new Pair<>(id,d.getSelectionConstraints()),datasourceMap);
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}
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//get zenodo communities
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for(ZenodoCommunity zc : c.getZenodoCommunities()){
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add(zc.getZenodoCommunityId(),new Pair<>(id,zc.getSelCriteria()),zenodocommunityMap);
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}
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}
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}
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private void add(String key, Pair<String,SelectionConstraints> value, Map<String,List<Pair<String,SelectionConstraints>>> map){
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List<Pair<String,SelectionConstraints>> values = map.get(key);
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if (values == null){
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values = new ArrayList<>();
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map.put(key,values);
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}
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values.add(value);
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}
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public List<Pair<String,SelectionConstraints>> getCommunityForSubject(String sbj){
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return subjectMap.get(sbj);
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}
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public List<Pair<String,SelectionConstraints>> getCommunityForDatasource(String dts){
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return datasourceMap.get(dts);
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}
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public List<String> getCommunityForDatasource(final String dts, final Map<String, List<String>> param) {
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List<Pair<String,SelectionConstraints>> lp = datasourceMap.get(dts);
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if (lp==null)
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return Lists.newArrayList();
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return lp.stream().map(p -> {
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if (p.getSnd() == null)
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return p.getFst();
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if (((SelectionConstraints) p.getSnd()).verifyCriteria(param))
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return p.getFst();
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else
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return null;
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}).filter(st->(st!=null)).collect(Collectors.toList());
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}
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public List<Pair<String,SelectionConstraints>> getCommunityForZenodoCommunity(String zc){
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return zenodocommunityMap.get(zc);
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}
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public List<String> getCommunityForSubjectValue(String value) {
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return getContextIds(subjectMap.get(value));
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}
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public List<String> getCommunityForDatasourceValue(String value) {
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return getContextIds(datasourceMap.get(value.toLowerCase()));
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}
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public List<String> getCommunityForZenodoCommunityValue(String value){
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return getContextIds(zenodocommunityMap.get(value.toLowerCase()));
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}
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private List<String> getContextIds(List<Pair<String, SelectionConstraints>> list) {
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if (list != null) {
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return list.stream().map(p -> p.getFst()).collect(Collectors.toList());
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}
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return Lists.newArrayList();
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}
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public Map<String, Community> getCommunities() {
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return communities;
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}
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public void setCommunities(Map<String, Community> communities) {
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this.communities = communities;
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}
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public String toJson() {
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GsonBuilder builder = new GsonBuilder();
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builder.registerTypeAdapter(Selection.class, new InterfaceAdapter());
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Gson gson = builder.create();
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return gson.toJson(this);
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}
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public int size() {
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return communities.keySet().size();
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}
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public Community getCommunityById(String id){
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return communities.get(id);
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}
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public List<Community> getCommunityList() {
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return Lists.newLinkedList(communities.values());
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}
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}
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@ -0,0 +1,146 @@
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package eu.dnetlib.dhp;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
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import eu.dnetlib.dhp.selectioncriteria.Selection;
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import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
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import eu.dnetlib.dhp.selectioncriteria.VerbResolverFactory;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import java.io.StringReader;
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import java.util.ArrayList;
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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 by miriam on 03/08/2018.
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*/
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public class CommunityConfigurationFactory {
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private static final Log log = LogFactory.getLog(CommunityConfigurationFactory.class);
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private static VerbResolver resolver = VerbResolverFactory.newInstance();
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public static CommunityConfiguration newInstance(final String xml) throws DocumentException {
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log.debug(String.format("parsing community configuration from:\n%s", xml));
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final Document doc = new SAXReader().read(new StringReader(xml));
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final Map<String,Community> communities = Maps.newHashMap();
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for(final Object o : doc.selectNodes("//community")) {
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final Node node = (Node) o;
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final Community community = parseCommunity(node);
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if (community.isValid()) {
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communities.put(community.getId(), community);
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}
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}
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log.info(String.format("loaded %s community configuration profiles", communities.size()));
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log.debug(String.format("loaded community configuration:\n%s", communities.toString()));
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return new CommunityConfiguration(communities);
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}
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public static CommunityConfiguration fromJson(final String json) {
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GsonBuilder builder = new GsonBuilder();
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builder.registerTypeAdapter(Selection.class, new InterfaceAdapter());
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Gson gson = builder.create();
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final CommunityConfiguration conf = gson.fromJson(json, CommunityConfiguration.class);
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log.info(String.format("loaded %s community configuration profiles", conf.size()));
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conf.init();
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log.info("created inverse maps");
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return conf;
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}
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private static Community parseCommunity(final Node node) {
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final Community c = new Community();
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c.setId(node.valueOf("./@id"));
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log.info(String.format("community id: %s", c.getId()));
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c.setSubjects(parseSubjects(node));
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c.setDatasources(parseDatasources(node));
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c.setZenodoCommunities(parseZenodoCommunities(node));
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return c;
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}
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private static List<String> parseSubjects(final Node node) {
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final List<String> subjects = Lists.newArrayList();
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final List <Node> list = node.selectNodes("./subjects/subject");
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for(Node n : list){
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log.debug("text of the node " + n.getText());
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subjects.add(StringUtils.trim(n.getText()));
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}
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log.info("size of the subject list " + subjects.size());
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return subjects;
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}
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private static List<Datasource> parseDatasources(final Node node) {
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final List <Node> list = node.selectNodes("./datasources/datasource");
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final List<Datasource> datasourceList = new ArrayList<>();
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for(Node n : list){
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Datasource d = new Datasource();
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d.setOpenaireId(n.selectSingleNode("./openaireId").getText());
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d.setSelCriteria(n.selectSingleNode("./selcriteria"), resolver);
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datasourceList.add(d);
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}
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log.info("size of the datasource list " + datasourceList.size());
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return datasourceList;
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}
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private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {
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final Node oacommunitynode = node.selectSingleNode("./oacommunity");
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String oacommunity = null;
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if (oacommunitynode != null){
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String tmp = oacommunitynode.getText();
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if(StringUtils.isNotBlank(tmp))
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oacommunity = tmp;
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}
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final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
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final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>();
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for(Node n : list){
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ZenodoCommunity zc = new ZenodoCommunity();
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zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
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zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
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zenodoCommunityList.add(zc);
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}
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if(oacommunity != null){
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ZenodoCommunity zc = new ZenodoCommunity();
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zc.setZenodoCommunityId(oacommunity);
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zenodoCommunityList.add(zc);
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}
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log.info("size of the zenodo community list " + zenodoCommunityList.size());
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return zenodoCommunityList;
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}
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}
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@ -0,0 +1,62 @@
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package eu.dnetlib.dhp;
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import eu.dnetlib.dhp.selectioncriteria.Selection;
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import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
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import java.io.Serializable;
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import java.lang.reflect.InvocationTargetException;
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public class Constraint implements Serializable {
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private String verb;
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private String field;
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private String value;
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private Selection selection;
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public Constraint() {
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}
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public String getVerb() {
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return verb;
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}
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public void setVerb(String verb) {
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this.verb = verb;
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}
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public String getField() {
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return field;
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}
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public void setField(String field) {
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this.field = field;
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}
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public String getValue() {
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return value;
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}
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public void setValue(String value) {
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this.value = value;
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}
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public void setSelection(Selection sel){
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selection = sel;
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}
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public void setSelection(VerbResolver resolver) throws InvocationTargetException, NoSuchMethodException, InstantiationException, IllegalAccessException {
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selection = resolver.getSelectionCriteria(verb,value);
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}
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public boolean verifyCriteria(String metadata){
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return selection.apply(metadata);
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}
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}
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@ -0,0 +1,79 @@
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package eu.dnetlib.dhp;
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import com.google.gson.Gson;
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import com.google.gson.reflect.TypeToken;
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import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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|
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import java.io.Serializable;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Type;
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import java.util.Collection;
|
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import java.util.List;
|
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import java.util.Map;
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|
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/**
|
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* Created by miriam on 02/08/2018.
|
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*/
|
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public class Constraints implements Serializable {
|
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private static final Log log = LogFactory.getLog(Constraints.class);
|
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//private ConstraintEncapsulator ce;
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private List<Constraint> constraint;
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|
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|
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public Constraints() {
|
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}
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public List<Constraint> getConstraint() {
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return constraint;
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}
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public void setConstraint(List<Constraint> constraint) {
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this.constraint = constraint;
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}
|
||||
|
||||
public void setSc(String json){
|
||||
Type collectionType = new TypeToken<Collection<Constraint>>(){}.getType();
|
||||
constraint = new Gson().fromJson(json, collectionType);
|
||||
|
||||
}
|
||||
|
||||
void setSelection(VerbResolver resolver) {
|
||||
for(Constraint st: constraint){
|
||||
|
||||
try {
|
||||
st.setSelection(resolver);
|
||||
} catch (NoSuchMethodException e) {
|
||||
log.error(e.getMessage());
|
||||
} catch (IllegalAccessException e) {
|
||||
log.error(e.getMessage());
|
||||
} catch (InvocationTargetException e) {
|
||||
log.error(e.getMessage());
|
||||
} catch (InstantiationException e) {
|
||||
log.error(e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
//Constraint in and
|
||||
public boolean verifyCriteria(final Map<String, List<String>> param) {
|
||||
|
||||
for(Constraint sc : constraint) {
|
||||
boolean verified = false;
|
||||
for(String value : param.get(sc.getField())){
|
||||
if (sc.verifyCriteria(value.trim())){
|
||||
verified = true;
|
||||
}
|
||||
}
|
||||
if(!verified)
|
||||
return verified;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
|
||||
import com.google.gson.Gson;
|
||||
|
||||
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.dom4j.Node;
|
||||
|
||||
/**
|
||||
* Created by miriam on 01/08/2018.
|
||||
*/
|
||||
public class Datasource {
|
||||
private static final Log log = LogFactory.getLog(Datasource.class);
|
||||
|
||||
private String openaireId;
|
||||
|
||||
private SelectionConstraints selectionConstraints;
|
||||
|
||||
|
||||
public SelectionConstraints getSelCriteria() {
|
||||
return selectionConstraints;
|
||||
}
|
||||
|
||||
public SelectionConstraints getSelectionConstraints() {
|
||||
return selectionConstraints;
|
||||
}
|
||||
|
||||
public void setSelectionConstraints(SelectionConstraints selectionConstraints) {
|
||||
this.selectionConstraints = selectionConstraints;
|
||||
}
|
||||
|
||||
public void setSelCriteria(SelectionConstraints selCriteria) {
|
||||
this.selectionConstraints = selCriteria;
|
||||
}
|
||||
|
||||
public String getOpenaireId() {
|
||||
return openaireId;
|
||||
}
|
||||
|
||||
public void setOpenaireId(String openaireId) {
|
||||
this.openaireId = openaireId;
|
||||
}
|
||||
|
||||
private void setSelCriteria(String json, VerbResolver resolver){
|
||||
log.info("Selection constraints for datasource = " + json);
|
||||
selectionConstraints = new Gson().fromJson(json, SelectionConstraints.class);
|
||||
|
||||
selectionConstraints.setSelection(resolver);
|
||||
}
|
||||
|
||||
public void setSelCriteria(Node n, VerbResolver resolver){
|
||||
try{
|
||||
setSelCriteria(n.getText(),resolver);
|
||||
}catch(Exception e) {
|
||||
log.info("not set selection criteria... ");
|
||||
selectionConstraints =null;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
|
||||
/**
|
||||
* Created by miriam on 03/08/2018.
|
||||
*/
|
||||
public class Pair<A,B> {
|
||||
private A fst;
|
||||
private B snd;
|
||||
|
||||
public A getFst() {
|
||||
return fst;
|
||||
}
|
||||
|
||||
public Pair setFst(A fst) {
|
||||
this.fst = fst;
|
||||
return this;
|
||||
}
|
||||
|
||||
public B getSnd() {
|
||||
return snd;
|
||||
}
|
||||
|
||||
public Pair setSnd(B snd) {
|
||||
this.snd = snd;
|
||||
return this;
|
||||
}
|
||||
|
||||
public Pair(A a, B b){
|
||||
fst = a;
|
||||
snd = b;
|
||||
}
|
||||
|
||||
public String toJson(){
|
||||
return new Gson().toJson(this);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import java.util.HashMap;
|
||||
|
||||
public class ProtoMap extends HashMap<String,String> {
|
||||
|
||||
public ProtoMap(){
|
||||
super();
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import com.google.common.base.Joiner;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import org.dom4j.DocumentException;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
|
||||
public class QueryInformationSystem {
|
||||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " +
|
||||
" let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() " +
|
||||
" let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept " +
|
||||
" let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept " +
|
||||
" let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept " +
|
||||
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
||||
" return " +
|
||||
" <community> " +
|
||||
" { $x//CONFIGURATION/context/@id} " +
|
||||
" <subjects> " +
|
||||
" {for $y in tokenize($subj,',') " +
|
||||
" return " +
|
||||
" <subject>{$y}</subject>} " +
|
||||
" </subjects> " +
|
||||
" <datasources> " +
|
||||
" {for $d in $datasources " +
|
||||
" where $d/param[./@name='enabled']/text()='true' " +
|
||||
" return " +
|
||||
" <datasource> " +
|
||||
" <openaireId> " +
|
||||
" {$d//param[./@name='openaireId']/text()} " +
|
||||
" </openaireId> " +
|
||||
" <selcriteria> " +
|
||||
" {$d/param[./@name='selcriteria']/text()} " +
|
||||
" </selcriteria> " +
|
||||
" </datasource> } " +
|
||||
" </datasources> " +
|
||||
" <zenodocommunities> " +
|
||||
" {for $zc in $communities " +
|
||||
" return " +
|
||||
" <zenodocommunity> " +
|
||||
" <zenodoid> " +
|
||||
" {$zc/param[./@name='zenodoid']/text()} " +
|
||||
" </zenodoid> " +
|
||||
" <selcriteria> " +
|
||||
" {$zc/param[./@name='selcriteria']/text()} " +
|
||||
" </selcriteria> " +
|
||||
" </zenodocommunity>} " +
|
||||
" </zenodocommunities> " +
|
||||
" </community>";
|
||||
|
||||
public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl) throws ISLookUpException, DocumentException {
|
||||
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||
final List<String> res = isLookUp.quickSearchProfile(XQUERY);
|
||||
|
||||
final String xmlConf = "<communities>" + Joiner.on(" ").join(res) + "</communities>";
|
||||
|
||||
|
||||
return CommunityConfigurationFactory.newInstance(xmlConf);
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,175 @@
|
|||
package eu.dnetlib.dhp;
|
||||
import com.google.gson.Gson;
|
||||
import com.jayway.jsonpath.DocumentContext;
|
||||
import com.jayway.jsonpath.JsonPath;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import static eu.dnetlib.dhp.TagginConstants.*;
|
||||
|
||||
|
||||
/**
|
||||
* Created by miriam on 02/08/2018.
|
||||
*/
|
||||
public class ResultTagger {
|
||||
|
||||
|
||||
private String trust = "0.8";
|
||||
|
||||
|
||||
private boolean clearContext(Result result){
|
||||
int tmp = result.getContext().size();
|
||||
List<Context> clist = result.getContext().stream()
|
||||
.filter(c -> (!c.getId().contains(ZENODO_COMMUNITY_INDICATOR))).collect(Collectors.toList());
|
||||
result.setContext(clist);
|
||||
return (tmp != clist.size());
|
||||
}
|
||||
|
||||
private Map<String,List<String>> getParamMap(final Result result, Map<String,String> params) {
|
||||
Map<String,List<String>> param = new HashMap<>();
|
||||
String json = new Gson().toJson(result,Result.class);
|
||||
DocumentContext jsonContext = JsonPath.parse(json);
|
||||
if (params == null){
|
||||
params = new HashMap<>();
|
||||
}
|
||||
for(String key : params.keySet()) {
|
||||
try {
|
||||
param.put(key, jsonContext.read(params.get(key)));
|
||||
} catch (com.jayway.jsonpath.PathNotFoundException e) {
|
||||
param.put(key, new ArrayList<>());
|
||||
// throw e;
|
||||
}
|
||||
}
|
||||
return param;
|
||||
|
||||
}
|
||||
|
||||
|
||||
public Result enrichContextCriteria(final Result result, final CommunityConfiguration conf, final Map<String,String> criteria) {
|
||||
final Map<String, List<String>> param = getParamMap(result, criteria);
|
||||
|
||||
//Verify if the entity is deletedbyinference. In case verify if to clean the context list from all the zenodo communities
|
||||
if(result.getDataInfo().getDeletedbyinference()){
|
||||
return result;
|
||||
}
|
||||
|
||||
//communities contains all the communities to be added as context for the result
|
||||
final Set<String> communities = new HashSet<>();
|
||||
|
||||
|
||||
//tagging for Subject
|
||||
final Set<String> subjects = new HashSet<>();
|
||||
result.getSubject().stream()
|
||||
.map(subject -> subject.getValue())
|
||||
.filter(StringUtils::isNotBlank)
|
||||
.map(String::toLowerCase)
|
||||
.map(String::trim)
|
||||
.collect(Collectors.toCollection(HashSet::new))
|
||||
.forEach(s -> subjects.addAll(conf.getCommunityForSubjectValue(s)));
|
||||
|
||||
communities.addAll(subjects);
|
||||
|
||||
|
||||
//Tagging for datasource
|
||||
final Set<String> datasources = new HashSet<>();
|
||||
final Set<String> tmp = new HashSet<>();
|
||||
|
||||
for(Instance i : result.getInstance()){
|
||||
tmp.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(),"|"));
|
||||
tmp.add(StringUtils.substringAfter(i.getHostedby().getKey(),"|"));
|
||||
}
|
||||
|
||||
result.getInstance()
|
||||
.stream()
|
||||
.map(i -> new Pair<>(i.getCollectedfrom().getKey(), i.getHostedby().getKey()))
|
||||
.flatMap(p -> Stream.of(p.getFst(), p.getSnd()))
|
||||
.map(s -> StringUtils.substringAfter(s, "|"))
|
||||
.collect(Collectors.toCollection(HashSet::new))
|
||||
.forEach(dsId -> datasources.addAll(conf.getCommunityForDatasource(dsId,param)));
|
||||
|
||||
communities.addAll(datasources);
|
||||
|
||||
/*Tagging for Zenodo Communities*/
|
||||
final Set<String> czenodo = new HashSet<>();
|
||||
//final ResultProtos.Result.Metadata.Builder mBuilder = builder.getEntityBuilder().getResultBuilder().getMetadataBuilder();
|
||||
result.getContext()
|
||||
.stream()
|
||||
.filter(c -> c.getId().contains(ZENODO_COMMUNITY_INDICATOR))
|
||||
.collect(Collectors.toList())
|
||||
.forEach(c->czenodo.addAll(conf.getCommunityForZenodoCommunityValue(c.getId().substring(c.getId().lastIndexOf("/")+1).trim())));
|
||||
|
||||
communities.addAll(czenodo);
|
||||
|
||||
clearContext(result);
|
||||
|
||||
/*Verify if there is something to bulktag*/
|
||||
if(communities.isEmpty()){
|
||||
return result;
|
||||
|
||||
}
|
||||
|
||||
result.getContext()
|
||||
.stream()
|
||||
.map(c -> {
|
||||
if(communities.contains(c.getId())){
|
||||
List<DataInfo> dataInfoList = c.getDataInfo();
|
||||
if (subjects.contains(c.getId()))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT));
|
||||
if (datasources.contains(c.getId()))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE));
|
||||
if (czenodo.contains(c.getId()))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO));
|
||||
}
|
||||
return c;
|
||||
})
|
||||
.collect(Collectors.toList());
|
||||
|
||||
|
||||
communities.removeAll(result.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet()));
|
||||
|
||||
if(communities.isEmpty())
|
||||
return result;
|
||||
|
||||
List<Context> toaddcontext = communities
|
||||
.stream()
|
||||
.map(c -> {
|
||||
Context context = new Context();
|
||||
context.setId(c);
|
||||
List<DataInfo> dataInfoList = Arrays.asList();
|
||||
if (subjects.contains(c))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT));
|
||||
if (datasources.contains(c))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE));
|
||||
if (czenodo.contains(c))
|
||||
dataInfoList.add(getDataInfo(BULKTAG_DATA_INFO_TYPE, CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO));
|
||||
context.setDataInfo(dataInfoList);
|
||||
return context;
|
||||
})
|
||||
.collect(Collectors.toList());
|
||||
|
||||
result.getContext().addAll(toaddcontext);
|
||||
return result;
|
||||
}
|
||||
|
||||
public static DataInfo getDataInfo(String inference_provenance, String inference_class_id, String inference_class_name){
|
||||
DataInfo di = new DataInfo();
|
||||
di.setInferred(true);
|
||||
di.setInferenceprovenance(inference_provenance);
|
||||
di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name));
|
||||
return di;
|
||||
}
|
||||
|
||||
public static Qualifier getQualifier(String inference_class_id, String inference_class_name) {
|
||||
Qualifier pa = new Qualifier();
|
||||
pa.setClassid(inference_class_id);
|
||||
pa.setClassname(inference_class_name);
|
||||
pa.setSchemeid(DNET_SCHEMA_ID);
|
||||
pa.setSchemename(DNET_SCHEMA_NAME);
|
||||
return pa;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
import com.google.gson.reflect.TypeToken;
|
||||
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
|
||||
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.lang.reflect.Type;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
public class SelectionConstraints implements Serializable {
|
||||
private List<Constraints> criteria;
|
||||
|
||||
public SelectionConstraints() {
|
||||
}
|
||||
|
||||
|
||||
public List<Constraints> getCriteria() {
|
||||
return criteria;
|
||||
}
|
||||
|
||||
public void setCriteria(List<Constraints> criteria) {
|
||||
this.criteria = criteria;
|
||||
}
|
||||
|
||||
public void setSc(String json){
|
||||
Type collectionType = new TypeToken<Collection<Constraints>>(){}.getType();
|
||||
criteria = new Gson().fromJson(json, collectionType);
|
||||
}
|
||||
|
||||
//Constraints in or
|
||||
public boolean verifyCriteria(final Map<String, List<String>> param){
|
||||
for(Constraints selc : criteria) {
|
||||
if(selc.verifyCriteria(param)){
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
public void setSelection(VerbResolver resolver) {
|
||||
|
||||
for(Constraints cs : criteria){
|
||||
cs.setSelection(resolver);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.gson.Gson;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
|
||||
|
||||
public class SparkBulkTagJob {
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkBulkTagJob.class.getResourceAsStream("/eu/dnetlib/dhp/input_bulktag_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkBulkTagJob.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/bulktagging";
|
||||
|
||||
final ResultTagger resultTagger = new ResultTagger();
|
||||
ProtoMap protoMappingParams = new Gson().fromJson(parser.get("mappingProto"),ProtoMap.class);;
|
||||
|
||||
File directory = new File(outputPath);
|
||||
|
||||
if (!directory.exists()) {
|
||||
directory.mkdirs();
|
||||
}
|
||||
|
||||
CommunityConfiguration cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookupUrl"));
|
||||
|
||||
|
||||
sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
|
||||
.map(p -> resultTagger.enrichContextCriteria(p, cc, protoMappingParams))
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath+"/publication");
|
||||
sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
|
||||
.map(p -> resultTagger.enrichContextCriteria(p, cc, protoMappingParams))
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath+"/dataset");
|
||||
sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
|
||||
.map(p -> resultTagger.enrichContextCriteria(p, cc, protoMappingParams))
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath+"/software");
|
||||
sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
|
||||
.map(p -> resultTagger.enrichContextCriteria(p, cc, protoMappingParams))
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath+"/otherresearchproduct");
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
|
||||
public class TagginConstants {
|
||||
|
||||
|
||||
public final static String BULKTAG_DATA_INFO_TYPE = "bulktagging";
|
||||
|
||||
public final static String DNET_SCHEMA_NAME = "dnet:provenanceActions";
|
||||
public final static String DNET_SCHEMA_ID = "dnet:provenanceActions";
|
||||
|
||||
public final static String CLASS_ID_SUBJECT = "bulktagging:community:subject";
|
||||
public final static String CLASS_ID_DATASOURCE = "bulktagging:community:datasource";
|
||||
public final static String CLASS_ID_CZENODO = "bulktagging:community:zenodocommunity";
|
||||
|
||||
public final static String SCHEMA_ID = "dnet:provenanceActions";
|
||||
public final static String COUNTER_GROUP = "Bulk Tagging";
|
||||
|
||||
public final static String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
|
||||
|
||||
public final static String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";
|
||||
public final static String CLASS_NAME_BULKTAG_DATASOURCE = "Bulktagging for Community - Datasource";
|
||||
public final static String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo";
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
package eu.dnetlib.dhp;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
import org.dom4j.Node;
|
||||
|
||||
|
||||
/**
|
||||
* Created by miriam on 01/08/2018.
|
||||
*/
|
||||
public class ZenodoCommunity {
|
||||
|
||||
private String zenodoCommunityId;
|
||||
|
||||
private SelectionConstraints selCriteria;
|
||||
|
||||
public String getZenodoCommunityId() {
|
||||
return zenodoCommunityId;
|
||||
}
|
||||
|
||||
public void setZenodoCommunityId(String zenodoCommunityId) {
|
||||
this.zenodoCommunityId = zenodoCommunityId;
|
||||
}
|
||||
|
||||
public SelectionConstraints getSelCriteria() {
|
||||
return selCriteria;
|
||||
}
|
||||
|
||||
public void setSelCriteria(SelectionConstraints selCriteria) {
|
||||
this.selCriteria = selCriteria;
|
||||
}
|
||||
|
||||
private void setSelCriteria(String json){
|
||||
//Type collectionType = new TypeToken<Collection<Constraints>>(){}.getType();
|
||||
selCriteria = new Gson().fromJson(json, SelectionConstraints.class);
|
||||
|
||||
}
|
||||
|
||||
public void setSelCriteria(Node n){
|
||||
if (n==null){
|
||||
selCriteria = null;
|
||||
}else{
|
||||
setSelCriteria(n.getText());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
@VerbClass("contains")
|
||||
public class ContainsVerb implements Selection {
|
||||
|
||||
private String param;
|
||||
|
||||
public ContainsVerb() {
|
||||
}
|
||||
|
||||
public ContainsVerb(final String param) {
|
||||
this.param = param;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean apply(String value) {
|
||||
return value.contains(param);
|
||||
}
|
||||
|
||||
public String getParam() {
|
||||
return param;
|
||||
}
|
||||
|
||||
public void setParam(String param) {
|
||||
this.param = param;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
|
||||
@VerbClass("equals")
|
||||
public class EqualVerb implements Selection {
|
||||
|
||||
private String param;
|
||||
|
||||
public EqualVerb() {
|
||||
}
|
||||
|
||||
public EqualVerb(final String param) {
|
||||
this.param = param;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public boolean apply(String value) {
|
||||
return value.equalsIgnoreCase(param);
|
||||
}
|
||||
|
||||
public String getParam() {
|
||||
return param;
|
||||
}
|
||||
|
||||
public void setParam(String param) {
|
||||
this.param = param;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
import com.google.gson.*;
|
||||
|
||||
import java.lang.reflect.Type;
|
||||
|
||||
public class InterfaceAdapter implements JsonSerializer, JsonDeserializer {
|
||||
|
||||
private static final String CLASSNAME = "CLASSNAME";
|
||||
private static final String DATA = "DATA";
|
||||
|
||||
public Object deserialize(JsonElement jsonElement, Type type,
|
||||
JsonDeserializationContext jsonDeserializationContext) throws JsonParseException {
|
||||
|
||||
JsonObject jsonObject = jsonElement.getAsJsonObject();
|
||||
JsonPrimitive prim = (JsonPrimitive) jsonObject.get(CLASSNAME);
|
||||
String className = prim.getAsString();
|
||||
Class klass = getObjectClass(className);
|
||||
return jsonDeserializationContext.deserialize(jsonObject.get(DATA), klass);
|
||||
}
|
||||
public JsonElement serialize(Object jsonElement, Type type, JsonSerializationContext jsonSerializationContext) {
|
||||
JsonObject jsonObject = new JsonObject();
|
||||
jsonObject.addProperty(CLASSNAME, jsonElement.getClass().getName());
|
||||
jsonObject.add(DATA, jsonSerializationContext.serialize(jsonElement));
|
||||
return jsonObject;
|
||||
}
|
||||
/****** Helper method to get the className of the object to be deserialized *****/
|
||||
public Class getObjectClass(String className) {
|
||||
try {
|
||||
return Class.forName(className);
|
||||
} catch (ClassNotFoundException e) {
|
||||
//e.printStackTrace();
|
||||
throw new JsonParseException(e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
@VerbClass("not_contains")
|
||||
public class NotContainsVerb implements Selection {
|
||||
|
||||
private String param;
|
||||
|
||||
public NotContainsVerb() {
|
||||
}
|
||||
|
||||
public NotContainsVerb(final String param) {
|
||||
this.param = param;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean apply(String value) {
|
||||
return !value.contains(param);
|
||||
}
|
||||
|
||||
public String getParam() {
|
||||
return param;
|
||||
}
|
||||
|
||||
public void setParam(String param) {
|
||||
this.param = param;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
|
||||
@VerbClass("not_equals")
|
||||
public class NotEqualVerb implements Selection {
|
||||
|
||||
private String param;
|
||||
|
||||
|
||||
public NotEqualVerb(final String param) {
|
||||
this.param = param;
|
||||
}
|
||||
|
||||
public NotEqualVerb() {
|
||||
}
|
||||
|
||||
public String getParam() {
|
||||
return param;
|
||||
}
|
||||
|
||||
public void setParam(String param) {
|
||||
this.param = param;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean apply(String value) {
|
||||
return !value.equalsIgnoreCase(param);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
public interface Selection {
|
||||
|
||||
boolean apply(String value);
|
||||
}
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
import java.lang.annotation.ElementType;
|
||||
import java.lang.annotation.Retention;
|
||||
import java.lang.annotation.RetentionPolicy;
|
||||
import java.lang.annotation.Target;
|
||||
|
||||
@Retention(RetentionPolicy.RUNTIME)
|
||||
@Target(ElementType.TYPE)
|
||||
public @interface VerbClass {
|
||||
|
||||
public String value();
|
||||
}
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
|
||||
import org.reflections.Reflections;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.lang.reflect.InvocationTargetException;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
public class VerbResolver implements Serializable {
|
||||
private final Map<String, Class<Selection>> map;
|
||||
|
||||
public VerbResolver(){
|
||||
this.map = new Reflections("eu.dnetlib").getTypesAnnotatedWith(VerbClass.class).stream()
|
||||
.collect(Collectors.toMap(v -> v.getAnnotation(VerbClass.class).value(), v->(Class<Selection>)v));
|
||||
}
|
||||
|
||||
|
||||
public Selection getSelectionCriteria(String name, String param) throws NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
|
||||
|
||||
return map.get(name).getDeclaredConstructor((String.class)).newInstance(param);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
package eu.dnetlib.dhp.selectioncriteria;
|
||||
|
||||
public class VerbResolverFactory {
|
||||
|
||||
public static VerbResolver newInstance(){
|
||||
|
||||
return new VerbResolver();
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue