fixed wrong test

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java

@@ -0,0 +1,108 @@
+package eu.dnetlib.dhp.provision.update;
+
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+import eu.dnetlib.dhp.provision.scholix.ScholixCollectedFrom;
+import eu.dnetlib.dhp.provision.scholix.ScholixEntityId;
+import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier;
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import eu.dnetlib.dhp.utils.DHPUtils;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class CrossRefParserJSON {
+
+    private static List<ScholixCollectedFrom> collectedFrom =generateCrossrefCollectedFrom("complete");
+
+    public static ScholixResource parseRecord(final String record) {
+        if (record == null) return null;
+        JsonElement jElement = new JsonParser().parse(record);
+        JsonElement source = null;
+        if (jElement.getAsJsonObject().has("_source")) {
+            source = jElement.getAsJsonObject().get("_source");
+            if (source == null || !source.isJsonObject())
+                return null;
+        }
+        else if(jElement.getAsJsonObject().has("DOI")){
+            source = jElement;
+        } else {
+            return null;
+        }
+
+        final JsonObject message = source.getAsJsonObject();
+        ScholixResource currentObject = new ScholixResource();
+
+        if (message.get("DOI") != null) {
+            final String doi = message.get("DOI").getAsString();
+            currentObject.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi")));
+        }
+
+        if ((!message.get("created").isJsonNull()) && (message.getAsJsonObject("created").get("date-time") != null)) {
+            currentObject.setPublicationDate(message.getAsJsonObject("created").get("date-time").getAsString());
+        }
+
+        if (message.get("title")!= null && !message.get("title").isJsonNull() && message.get("title").isJsonArray() ) {
+
+            JsonArray array = message.get("title").getAsJsonArray();
+            currentObject.setTitle(array.get(0).getAsString());
+        }
+        if (message.get("author") != null && !message.get("author").isJsonNull()) {
+            JsonArray author = message.getAsJsonArray("author");
+            List<ScholixEntityId> authorList = new ArrayList<>();
+            for (JsonElement anAuthor : author) {
+                JsonObject currentAuth = anAuthor.getAsJsonObject();
+
+                String family = "";
+                String given = "";
+                if (currentAuth != null && currentAuth.get("family") != null && !currentAuth.get("family").isJsonNull()) {
+                    family = currentAuth.get("family").getAsString();
+                }
+                if (currentAuth != null && currentAuth.get("given") != null && !currentAuth.get("given").isJsonNull()) {
+                    given = currentAuth.get("given").getAsString();
+                }
+                authorList.add(new ScholixEntityId(String.format("%s %s", family, given), null));
+            }
+            currentObject.setCreator(authorList);
+        }
+        if (message.get("publisher") != null && !message.get("publisher").isJsonNull()) {
+            currentObject.setPublisher(Collections.singletonList(new ScholixEntityId(message.get("publisher").getAsString(), null)));
+        }
+        currentObject.setCollectedFrom(collectedFrom);
+        currentObject.setObjectType("publication");
+        currentObject.setDnetIdentifier(generateId(message.get("DOI").getAsString(), "doi", "publication"));
+
+        return currentObject;
+    }
+
+    private static List<ScholixCollectedFrom> generateCrossrefCollectedFrom(final String completionStatus) {
+        final ScholixEntityId scholixEntityId = new ScholixEntityId("Crossref",
+                Collections.singletonList(new ScholixIdentifier("dli_________::crossref", "dnet_identifier")));
+        return Collections.singletonList(
+                new ScholixCollectedFrom(
+                        scholixEntityId,"resolved", completionStatus));
+    }
+
+    private static String generateId(final String pid, final String pidType, final String entityType) {
+        String type;
+        switch (entityType){
+            case "publication":
+                type = "50|";
+                break;
+            case "dataset":
+                type = "60|";
+                break;
+            case "unknown":
+                type = "70|";
+                break;
+            default:
+                throw new IllegalArgumentException("unexpected value "+entityType);
+        }
+        return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim()));
+    }
+
+
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java

@@ -0,0 +1,88 @@
+package eu.dnetlib.dhp.provision.update;
+
+import com.google.gson.JsonElement;
+import com.google.gson.JsonParser;
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import org.apache.commons.codec.binary.Base64;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+
+import java.io.ByteArrayOutputStream;
+import java.util.zip.Inflater;
+
+public class CrossrefClient {
+
+    private String host;
+    private String index ="crossref";
+    private String indexType = "item";
+
+
+    public CrossrefClient(String host) {
+        this.host = host;
+    }
+
+    public String getHost() {
+        return host;
+    }
+
+    public void setHost(String host) {
+        this.host = host;
+    }
+
+    public String getIndex() {
+        return index;
+    }
+
+    public void setIndex(String index) {
+        this.index = index;
+    }
+
+    public String getIndexType() {
+        return indexType;
+    }
+
+    public void setIndexType(String indexType) {
+        this.indexType = indexType;
+    }
+
+    private static String decompressBlob(final String blob) {
+        try {
+            byte[] byteArray = Base64.decodeBase64(blob.getBytes());
+            final Inflater decompresser = new Inflater();
+            decompresser.setInput(byteArray);
+            final ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length);
+            byte[] buffer = new byte[8192];
+            while (!decompresser.finished()) {
+                int size = decompresser.inflate(buffer);
+                bos.write(buffer, 0, size);
+            }
+            byte[] unzippeddata = bos.toByteArray();
+            decompresser.end();
+            return new String(unzippeddata);
+        } catch (Throwable e) {
+            throw new RuntimeException("Wrong record:" + blob,e);
+        }
+    }
+
+
+
+    public ScholixResource getResourceByDOI(final String doi) {
+        try (CloseableHttpClient client = HttpClients.createDefault()) {
+            HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F")));
+            CloseableHttpResponse response = client.execute(httpGet);
+            String json = IOUtils.toString(response.getEntity().getContent());
+            if (json.contains("blob")) {
+                JsonParser p = new JsonParser();
+                final JsonElement root = p.parse(json);
+                json =decompressBlob(root.getAsJsonObject().get("_source").getAsJsonObject().get("blob").getAsString());
+            }
+            return CrossRefParserJSON.parseRecord(json);
+        } catch (Throwable e) {
+            return null;
+        }
+
+    }
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.provision;
+package eu.dnetlib.dhp.provision.update;
 
 import com.jayway.jsonpath.JsonPath;
 import eu.dnetlib.dhp.provision.scholix.*;
@@ -15,16 +15,14 @@ import java.util.stream.Collectors;
 
 public class Datacite2Scholix {
 
-
+    private String rootPath = "$.attributes";
     final RelationMapper relationMapper;
 
     public Datacite2Scholix(RelationMapper relationMapper) {
         this.relationMapper = relationMapper;
     }
 
-
     public List<Scholix> generateScholixFromJson(final String dJson) {
-
         List<Map<String, String>> relIds = getRelatedIendtifiers(dJson);
         relIds = relIds!= null ? relIds.stream().filter(m->
                 m.containsKey("relatedIdentifierType") && m.containsKey("relationType" ) && m.containsKey( "relatedIdentifier")
@@ -32,22 +30,24 @@ public class Datacite2Scholix {
         if(relIds== null || relIds.size() ==0 )
             return null;
 
-
+        final String updated = JsonPath.read(dJson, rootPath + ".updated");
-
-        final String updated = JsonPath.read(dJson,"$.attributes.updated" );
         ScholixResource resource = generateDataciteScholixResource(dJson);
 
         return relIds.stream().flatMap(s-> {
             final List<Scholix> result = generateScholix(resource, s.get("relatedIdentifier"), s.get("relatedIdentifierType"), s.get("relationType"), updated);
             return result.stream();
         }).collect(Collectors.toList());
-
     }
 
+    public String getRootPath() {
+        return rootPath;
+    }
+
+    public void setRootPath(String rootPath) {
+        this.rootPath = rootPath;
+    }
 
     private List<Scholix> generateScholix(ScholixResource source, final String pid, final String pidtype, final String relType, final String updated) {
-
-
         if ("doi".equalsIgnoreCase(pidtype)) {
             ScholixResource target = new ScholixResource();
             target.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, pidtype)));
@@ -92,20 +92,17 @@ public class Datacite2Scholix {
             result.add(s2);
             return result;
         }
-
-
-
     }
 
     public ScholixResource generateDataciteScholixResource(String dJson) {
         ScholixResource resource = new ScholixResource();
-        String DOI_PATH = "$.attributes.doi";
+        String DOI_PATH = rootPath + ".doi";
         final String doi = JsonPath.read(dJson, DOI_PATH);
         resource.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi")));
         resource.setObjectType(getType(dJson));
         resource.setDnetIdentifier(generateId(doi, "doi", resource.getObjectType()));
         resource.setCollectedFrom(generateDataciteCollectedFrom("complete"));
-        final String publisher = JsonPath.read(dJson, "$.attributes.publisher");
+        final String publisher = JsonPath.read(dJson, rootPath + ".publisher");
         if (StringUtils.isNotBlank(publisher))
             resource.setPublisher(Collections.singletonList(new ScholixEntityId(publisher, null)));
         final String date = getDate(dJson);
@@ -119,7 +116,7 @@ public class Datacite2Scholix {
     }
 
     private List<ScholixEntityId> getCreators(final String json) {
-        final List<String> creatorName = JsonPath.read(json, "$.attributes.creators[*].name");
+        final List<String> creatorName = JsonPath.read(json, rootPath + ".creators[*].name");
         if (creatorName!= null && creatorName.size() >0) {
             return  creatorName.stream().map(s-> new ScholixEntityId(s, null)).collect(Collectors.toList());
         }
@@ -127,12 +124,12 @@ public class Datacite2Scholix {
     }
 
     private String getTitle(final String json){
-        final List<String> titles = JsonPath.read(json, "$.attributes.titles[*].title");
+        final List<String> titles = JsonPath.read(json, rootPath + ".titles[*].title");
         return titles!= null && titles.size()>0?titles.get(0): null;
     }
 
     private String getDate(final String json) {
-        final  List<Map<String,String>> dates = JsonPath.read(json,"$.attributes.dates");
+        final  List<Map<String,String>> dates = JsonPath.read(json, rootPath + ".dates");
         if(dates!= null && dates.size()>0){
 
             List<Map<String, String>> issued = dates.stream().filter(s -> "issued".equalsIgnoreCase(s.get("dateType"))).collect(Collectors.toList());
@@ -152,7 +149,7 @@ public class Datacite2Scholix {
 
     private String getType(final String json) {
         try {
-            final String bibtext = JsonPath.read(json, "$.attributes.types.bibtex");
+            final String bibtext = JsonPath.read(json, rootPath + ".types.bibtex");
             if ("article".equalsIgnoreCase(bibtext)) {
                 return "publication";
             }
@@ -162,14 +159,10 @@ public class Datacite2Scholix {
         }
     }
 
-
-
-
     private List<Map<String, String>> getRelatedIendtifiers(final String json) {
-        String REL_IDENTIFIER_PATH = "$.attributes.relatedIdentifiers[*]";
+        String REL_IDENTIFIER_PATH = rootPath + ".relatedIdentifiers[*]";
         List<Map<String, String>> res = JsonPath.read(json, REL_IDENTIFIER_PATH);
         return res;
-
     }
 
     protected String generateId(final String pid, final String pidType, final String entityType) {
@@ -186,18 +179,7 @@ public class Datacite2Scholix {
                 break;
             default:
                 throw new IllegalArgumentException("unexpected value "+entityType);
-
         }
-
         return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim()));
     }
-
-
-
-
-
-
-
-
-
 }

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java

@@ -0,0 +1,75 @@
+package eu.dnetlib.dhp.provision.update;
+
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+
+import java.io.IOException;
+
+public class DataciteClient {
+
+
+    private String host;
+    private String index ="datacite";
+    private String indexType = "dump";
+    private Datacite2Scholix d2s;
+
+    public DataciteClient(String host) {
+        this.host = host;
+
+        d2s = new Datacite2Scholix(null);
+        d2s.setRootPath("$._source.attributes");
+    }
+
+    public Iterable<String> getDatasetsFromTs(final Long timestamp) {
+        return ()-> {
+            try {
+                return new DataciteClientIterator(host, index, timestamp);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        };
+
+
+    }
+
+    public String getHost() {
+        return host;
+    }
+
+    public void setHost(String host) {
+        this.host = host;
+    }
+
+    public String getIndex() {
+        return index;
+    }
+
+    public void setIndex(String index) {
+        this.index = index;
+    }
+
+    public String getIndexType() {
+        return indexType;
+    }
+
+    public void setIndexType(String indexType) {
+        this.indexType = indexType;
+    }
+
+    public ScholixResource getDatasetByDOI(final String doi) {
+        try (CloseableHttpClient client = HttpClients.createDefault()) {
+            HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F")));
+            CloseableHttpResponse response = client.execute(httpGet);
+            final String json =IOUtils.toString(response.getEntity().getContent());
+            return d2s.generateDataciteScholixResource(json);
+        } catch (Throwable e) {
+            return null;
+        }
+    }
+
+
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.provision;
+package eu.dnetlib.dhp.provision.update;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.jayway.jsonpath.JsonPath;
 import net.minidev.json.JSONArray;
@@ -14,7 +14,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.stream.Collectors;
 
-public class DataciteClient implements Iterator<String> {
+public class DataciteClientIterator implements Iterator<String> {
 
     final static String blobPath = "$.hits.hits[*]._source";
     final static String scrollIdPath = "$._scroll_id";
@@ -27,7 +27,7 @@ public class DataciteClient implements Iterator<String> {
     final String esIndex;
     final ObjectMapper mapper = new ObjectMapper();
 
-    public DataciteClient(final String esHost, final String esIndex, final long timestamp) throws IOException {
+    public DataciteClientIterator(final String esHost, final String esIndex, final long timestamp) throws IOException {
 
         this.esHost = esHost;
         this.esIndex = esIndex;

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java

@@ -1,8 +1,10 @@
-package eu.dnetlib.dhp.provision;
+package eu.dnetlib.dhp.provision.update;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.provision.scholix.Scholix;
+import eu.dnetlib.scholexplorer.relation.RelationMapper;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
@@ -11,17 +13,19 @@ import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
 
 import java.net.URI;
+import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 
 public class RetrieveUpdateFromDatacite {
 
     public static void main(String[] args) throws Exception{
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(RetrieveUpdateFromDatacite.class.getResourceAsStream("/eu/dnetlib/dhp/provision/retrieve_update_parameters.json")));
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(RetrieveUpdateFromDatacite.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json")));
         parser.parseArgument(args);
         final String hdfsuri = parser.get("namenode");
         Path hdfswritepath = new Path(parser.get("targetPath"));
-        final String timestamp = parser.get("timestamp");
+        final long timestamp = Long.parseLong(parser.get("timestamp"));
-
+        final String host = parser.get("indexHost");
+        final String index = parser.get("indexName");
 
         // ====== Init HDFS File System Object
         Configuration conf = new Configuration();
@@ -32,13 +36,28 @@ public class RetrieveUpdateFromDatacite {
         conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
 
         FileSystem.get(URI.create(hdfsuri), conf);
-
+        final Datacite2Scholix d2s = new Datacite2Scholix(RelationMapper.load());
-        final AtomicInteger counter = new AtomicInteger(0);
+        final ObjectMapper mapper = new ObjectMapper();
         try (SequenceFile.Writer writer = SequenceFile.createWriter(conf,
                 SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class),
                 SequenceFile.Writer.valueClass(Text.class))) {
-
+            final Text value = new Text();
+            final IntWritable key = new IntWritable();
+            int i = 0;
+            for(String dataset: new DataciteClient(host).getDatasetsFromTs(timestamp)) {
+                i++;
+                List<Scholix> scholix = d2s.generateScholixFromJson(dataset);
+                if (scholix!= null)
+                    for(Scholix s: scholix) {
+                        key.set(i);
+                        value.set(mapper.writeValueAsString(s));
+                        writer.append(key, value);
+                        if (i % 10000 == 0) {
+                            System.out.println("wrote "+i);
+                        }
                     }
             }
 
+        }
+    }
 }

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java

@@ -0,0 +1,81 @@
+package eu.dnetlib.dhp.provision.update;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.provision.scholix.Scholix;
+import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier;
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import eu.dnetlib.dhp.utils.DHPUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.*;
+import scala.Tuple2;
+
+import java.util.Collections;
+
+public class SparkResolveScholixTarget {
+
+    public static void main(String[] args) throws  Exception {
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResolveScholixTarget.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json")));
+        parser.parseArgument(args);
+
+        final SparkConf conf = new SparkConf();
+
+        final String master = parser.get("master");
+        final String sourcePath = parser.get("sourcePath");
+        final String workingDirPath= parser.get("workingDirPath");
+        final String indexHost= parser.get("indexHost");
+
+
+        try (SparkSession spark = getSession(conf, master)){
+
+            final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+
+            spark.createDataset(sc.sequenceFile(sourcePath, IntWritable.class,Text.class)
+                    .map(Tuple2::_2)
+                    .map(s-> new ObjectMapper().readValue(s.toString(), Scholix.class)).rdd(), Encoders.bean(Scholix.class))
+                    .write().save(workingDirPath+"/stepA");
+
+
+
+            Dataset<Scholix> s1 = spark.read().load(workingDirPath+"/stepA").as(Encoders.bean(Scholix.class));
+
+            s1.where(s1.col("target.dnetIdentifier").isNull()).select(s1.col("target.identifier")).distinct()
+                    .map((MapFunction<Row, ScholixResource>) f-> {
+                        final String pid = ((Row) f.getList(0).get(0)).getString(0);
+                        ScholixResource publication  = new CrossrefClient(indexHost).getResourceByDOI(pid);
+                        if (publication != null) {
+                            return  publication;
+                        }
+                        ScholixResource dataset = new DataciteClient(indexHost).getDatasetByDOI(pid);
+                        if (dataset!= null) {
+                            return dataset;
+                        }
+                        ScholixResource r = new ScholixResource();
+                        r.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, "doi")));
+                        r.setObjectType("unknown");
+                        r.setDnetIdentifier("70|"+DHPUtils.md5(String.format("%s::doi", pid.toLowerCase().trim())));
+
+                        return r;
+                    }, Encoders.bean(ScholixResource.class)).write().mode(SaveMode.Overwrite).save(workingDirPath+"/stepB");
+
+
+
+        }
+    }
+
+    private static SparkSession getSession(SparkConf conf, String master) {
+        return SparkSession
+                .builder()
+                .config(conf)
+                .appName(SparkResolveScholixTarget.class.getSimpleName())
+                .master(master)
+                .getOrCreate();
+    }
+
+}

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "m",
+    "paramLongName": "master",
+    "paramDescription": "the name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "s",
+    "paramLongName": "sourcePath",
+    "paramDescription": "the source path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "w",
+    "paramLongName": "workingDirPath",
+    "paramDescription": "the working Dir Path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "h",
+    "paramLongName": "indexHost",
+    "paramDescription": "the working Dir Path",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json

@@ -0,0 +1,33 @@
+[
+  {
+    "paramName": "n",
+    "paramLongName": "namenode",
+    "paramDescription": "the name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "t",
+    "paramLongName": "targetPath",
+    "paramDescription": "the working path where generated files",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ts",
+    "paramLongName": "timestamp",
+    "paramDescription": "the timestamp for incremental harvesting",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ih",
+    "paramLongName": "indexHost",
+    "paramDescription": "the ip name of the index",
+    "paramRequired": true
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "indexName",
+    "paramDescription": "the name of the index",
+    "paramRequired": true
+  }
+
+]

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml

@@ -16,21 +16,21 @@
             <name>sparkExecutorMemory</name>
             <description>memory for individual executor</description>
         </property>
-        <property>
+<!--        <property>-->
-            <name>index</name>
+<!--            <name>index</name>-->
-            <description>index name</description>
+<!--            <description>index name</description>-->
-        </property>
+<!--        </property>-->
-        <property>
+<!--        <property>-->
-            <name>idScholix</name>
+<!--            <name>idScholix</name>-->
-            <description>the identifier name of the scholix </description>
+<!--            <description>the identifier name of the scholix </description>-->
-        </property>
+<!--        </property>-->
-        <property>
+<!--        <property>-->
-            <name>idSummary</name>
+<!--            <name>idSummary</name>-->
-            <description>the identifier name of the summary</description>
+<!--            <description>the identifier name of the summary</description>-->
-        </property>
+<!--        </property>-->
     </parameters>
 
-    <start to="indexSummary"/>
+    <start to="DeleteTargetPath"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -98,45 +98,45 @@
         <error to="Kill"/>
     </action>
 
-    <action name="indexSummary">
+<!--    <action name="indexSummary">-->
-        <spark xmlns="uri:oozie:spark-action:0.2">
+<!--        <spark xmlns="uri:oozie:spark-action:0.2">-->
-            <job-tracker>${jobTracker}</job-tracker>
+<!--            <job-tracker>${jobTracker}</job-tracker>-->
-            <name-node>${nameNode}</name-node>
+<!--            <name-node>${nameNode}</name-node>-->
-            <master>yarn-cluster</master>
+<!--            <master>yarn-cluster</master>-->
-            <mode>cluster</mode>
+<!--            <mode>cluster</mode>-->
-            <name>index Summary</name>
+<!--            <name>index Summary</name>-->
-            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
+<!--            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>-->
-            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
+<!--            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>-->
-            <spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>
+<!--            <spark-opts>&#45;&#45;executor-memory ${sparkExecutorMemory} &#45;&#45;driver-memory=${sparkDriverMemory} ${sparkExtraOPT} &#45;&#45;conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>-->
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
+<!--            <arg>-mt</arg> <arg>yarn-cluster</arg>-->
-            <arg>--sourcePath</arg><arg>${workingDirPath}/summary</arg>
+<!--            <arg>&#45;&#45;sourcePath</arg><arg>${workingDirPath}/summary</arg>-->
-            <arg>--index</arg><arg>${index}_object</arg>
+<!--            <arg>&#45;&#45;index</arg><arg>${index}_object</arg>-->
-            <arg>--idPath</arg><arg>id</arg>
+<!--            <arg>&#45;&#45;idPath</arg><arg>id</arg>-->
-            <arg>--type</arg><arg>summary</arg>
+<!--            <arg>&#45;&#45;type</arg><arg>summary</arg>-->
-        </spark>
+<!--        </spark>-->
-        <ok to="indexScholix"/>
+<!--        <ok to="indexScholix"/>-->
-        <error to="Kill"/>
+<!--        <error to="Kill"/>-->
-    </action>
+<!--    </action>-->
 
-    <action name="indexScholix">
+<!--    <action name="indexScholix">-->
-        <spark xmlns="uri:oozie:spark-action:0.2">
+<!--        <spark xmlns="uri:oozie:spark-action:0.2">-->
-            <job-tracker>${jobTracker}</job-tracker>
+<!--            <job-tracker>${jobTracker}</job-tracker>-->
-            <name-node>${nameNode}</name-node>
+<!--            <name-node>${nameNode}</name-node>-->
-            <master>yarn-cluster</master>
+<!--            <master>yarn-cluster</master>-->
-            <mode>cluster</mode>
+<!--            <mode>cluster</mode>-->
-            <name>index scholix</name>
+<!--            <name>index scholix</name>-->
-            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
+<!--            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>-->
-            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
+<!--            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>-->
-            <spark-opts>--executor-memory ${sparkExecutorMemory}  --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
+<!--            <spark-opts>&#45;&#45;executor-memory ${sparkExecutorMemory}  &#45;&#45;driver-memory=${sparkDriverMemory} ${sparkExtraOPT} &#45;&#45;conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>-->
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
+<!--            <arg>-mt</arg> <arg>yarn-cluster</arg>-->
-            <arg>--sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>
+<!--            <arg>&#45;&#45;sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>-->
-            <arg>--index</arg><arg>${index}_scholix</arg>
+<!--            <arg>&#45;&#45;index</arg><arg>${index}_scholix</arg>-->
-            <arg>--idPath</arg><arg>identifier</arg>
+<!--            <arg>&#45;&#45;idPath</arg><arg>identifier</arg>-->
-            <arg>--type</arg><arg>scholix</arg>
+<!--            <arg>&#45;&#45;type</arg><arg>scholix</arg>-->
-        </spark>
+<!--        </spark>-->
-        <ok to="End"/>
+<!--        <ok to="End"/>-->
-        <error to="Kill"/>
+<!--        <error to="Kill"/>-->
-    </action>
+<!--    </action>-->
 
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java

@@ -2,6 +2,8 @@ package eu.dnetlib.dhp.provision;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.provision.scholix.Scholix;
+import eu.dnetlib.dhp.provision.scholix.ScholixResource;
+import eu.dnetlib.dhp.provision.update.*;
 import eu.dnetlib.scholexplorer.relation.RelationMapper;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -9,10 +11,9 @@ import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
-import java.io.BufferedWriter;
-import java.io.FileWriter;
 import java.io.IOException;
 import java.util.List;
 
@@ -27,58 +28,45 @@ public class DataciteClientTest {
 
         Datacite2Scholix ds = new Datacite2Scholix(mapper);
         final List<Scholix> s = ds.generateScholixFromJson(json);
-
-
         System.out.println(new ObjectMapper().writeValueAsString(s));
-
     }
 
 
-    @Test
+
     public void testClient() throws Exception {
-        DataciteClient client = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it","datacite",1585454082);
+        RetrieveUpdateFromDatacite.main(new String[]{
-        int i = 0;
+                "-n", "file:///data/new_s2.txt",
-        final RelationMapper mapper = RelationMapper.load();
+                "-t", "/data/new_s2.txt",
-
+                "-ts", "1585760736",
-        Datacite2Scholix ds = new Datacite2Scholix(mapper);
+                "-ih", "ip-90-147-167-25.ct1.garrservices.it",
-        BufferedWriter writer = new BufferedWriter(new FileWriter("/Users/sandro/new_s.txt"));
+                "-in", "datacite",
-
+        });
-        final ObjectMapper m  = new ObjectMapper();
 
 
+        SparkResolveScholixTarget.main(new String[]{
+                "-s", "file:///data/new_s.txt",
+                "-m", "local[*]",
+                "-w", "/data/scholix/provision",
+                "-h", "ip-90-147-167-25.ct1.garrservices.it",
 
-
+        });
-
-        while (client.hasNext()){
-            i ++;
-
-
-            final String next = client.next();
-            try {
-                final List<Scholix> res = ds.generateScholixFromJson(next);
-                if (res!= null)
-                res
-                        .forEach(
-                                s -> {
-                                    try {
-
-                                        writer.write(m.writeValueAsString(s));
-                                        writer.write("\n");
-                                    } catch (Throwable e) {
-                                        throw new RuntimeException(e);
-                                    }
     }
 
 
-                        );
+    public void testResolveDataset() throws Exception {
-            }catch (Throwable t) {
+        DataciteClient dc  = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it");
-                System.out.println(next);
+        ScholixResource datasetByDOI = dc.getDatasetByDOI("10.17182/hepdata.15392.v1/t5");
-                throw new RuntimeException(t);
+        Assertions.assertNotNull(datasetByDOI);
-            }
+        System.out.println(new ObjectMapper().writeValueAsString(datasetByDOI));
-            if(i %1000 == 0) {
+
-                System.out.println("added "+i);
+
-            }
+        CrossrefClient cr = new CrossrefClient("ip-90-147-167-25.ct1.garrservices.it");
-        }
+        ScholixResource crossrefByDOI =  cr.getResourceByDOI("10.26850/1678-4618eqj.v35.1.2010.p41-46");
+        Assertions.assertNotNull(crossrefByDOI);
+        System.out.println(new ObjectMapper().writeValueAsString(crossrefByDOI));
+
+
+
     }
 
     private String getResponse(final String url,final String json ) {