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updated stuff for zenodo upload

This commit is contained in:
Sandro La Bruzzo 2020-11-23 14:41:38 +01:00
parent eeebd5a920
commit 264723ffd8
4 changed files with 107 additions and 95 deletions
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37
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala
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@ -42,22 +42,33 @@ class QueryTest {
} }
def myQuery(spark:SparkSession, sc:SparkContext): Unit = {
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
def extractId(input:String):String = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val mapper = new ObjectMapper() lazy val json: json4s.JValue = parse(input)
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) (json \ "id").extractOrElse[String](null)
val ds:Dataset[Publication] = spark.read.load("/tmp/p").as[Publication]
ds.filter(p =>p.getBestaccessright!= null && p.getBestaccessright.getClassname.nonEmpty).count()
} }
def myQuery(spark:SparkSession, sc:SparkContext): Unit = {
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
val mapper = new ObjectMapper()
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val ds:Dataset[Publication] = spark.read.load("/tmp/p").as[Publication]
val sc = spark.sparkContext
ds.filter(p =>p.getBestaccessright!= null && p.getBestaccessright.getClassname.nonEmpty).count()
val typologies =List("dataset","datasource","organization","otherresearchproduct","project","publication","software")
val basePath ="/tt"
typologies.map(tp => sc.textFile(s"$basePath/dataset").map(s =>extractId(tp) ).distinct.count()).sum()
}
} }

127
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java
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@ -12,6 +12,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.MakeTarArchive;
public class MakeTar implements Serializable { public class MakeTar implements Serializable {
@ -41,71 +42,71 @@ public class MakeTar implements Serializable {
FileSystem fileSystem = FileSystem.get(conf); FileSystem fileSystem = FileSystem.get(conf);
makeTArArchive(fileSystem, inputPath, outputPath); MakeTarArchive.tarMaxSize(fileSystem, inputPath, outputPath, "scholix_dump", 25);
} }
public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException { // public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
//
RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); // RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
//
while (dir_iterator.hasNext()) { // while (dir_iterator.hasNext()) {
LocatedFileStatus fileStatus = dir_iterator.next(); // LocatedFileStatus fileStatus = dir_iterator.next();
//
Path p = fileStatus.getPath(); // Path p = fileStatus.getPath();
String p_string = p.toString(); // String p_string = p.toString();
String entity = p_string.substring(p_string.lastIndexOf("/") + 1); // String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
//
write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity); // write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
} // }
//
} // }
//
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name) // private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
throws IOException { // throws IOException {
//
Path hdfsWritePath = new Path(outputPath); // Path hdfsWritePath = new Path(outputPath);
FSDataOutputStream fsDataOutputStream = null; // FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) { // if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, true); // fileSystem.delete(hdfsWritePath, true);
//
} // }
fsDataOutputStream = fileSystem.create(hdfsWritePath); // fsDataOutputStream = fileSystem.create(hdfsWritePath);
//
TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream()); // TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
//
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem // RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles( // .listFiles(
new Path(inputPath), true); // new Path(inputPath), true);
//
while (fileStatusListIterator.hasNext()) { // while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next(); // LocatedFileStatus fileStatus = fileStatusListIterator.next();
//
Path p = fileStatus.getPath(); // Path p = fileStatus.getPath();
String p_string = p.toString(); // String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) { // if (!p_string.endsWith("_SUCCESS")) {
String name = p_string.substring(p_string.lastIndexOf("/") + 1); // String name = p_string.substring(p_string.lastIndexOf("/") + 1);
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz"); // TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
entry.setSize(fileStatus.getLen()); // entry.setSize(fileStatus.getLen());
ar.putArchiveEntry(entry); // ar.putArchiveEntry(entry);
//
InputStream is = fileSystem.open(fileStatus.getPath()); // InputStream is = fileSystem.open(fileStatus.getPath());
//
BufferedInputStream bis = new BufferedInputStream(is); // BufferedInputStream bis = new BufferedInputStream(is);
//
int count; // int count;
byte data[] = new byte[1024]; // byte data[] = new byte[1024];
while ((count = bis.read(data, 0, data.length)) != -1) { // while ((count = bis.read(data, 0, data.length)) != -1) {
ar.write(data, 0, count); // ar.write(data, 0, count);
} // }
bis.close(); // bis.close();
ar.closeArchiveEntry(); // ar.closeArchiveEntry();
//
} // }
//
} // }
//
ar.close(); // ar.close();
} // }
} }

2
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java
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@ -73,7 +73,7 @@ public class SendToZenodoHDFS implements Serializable {
} }
zenodoApiClient.sendMretadata(metadata); zenodoApiClient.sendMretadata(metadata);
zenodoApiClient.publish(); // zenodoApiClient.publish();
} }

36
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml
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@ -8,10 +8,10 @@
<name>targetPath</name> <name>targetPath</name>
<description>the target path</description> <description>the target path</description>
</property> </property>
<property> <!-- <property>-->
<name>metadata</name> <!-- <name>metadata</name>-->
<description>the metadata</description> <!-- <description>the metadata</description>-->
</property> <!-- </property>-->
</parameters> </parameters>
<start to="send_zenodo"/> <start to="send_zenodo"/>
@ -34,20 +34,20 @@
</action> </action>
<action name="send_zenodo"> <!-- <action name="send_zenodo">-->
<java> <!-- <java>-->
<main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class> <!-- <main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class>-->
<arg>--hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg> <!-- <arg>&#45;&#45;hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg>-->
<arg>--nameNode</arg><arg>${nameNode}</arg> <!-- <arg>&#45;&#45;nameNode</arg><arg>${nameNode}</arg>-->
<arg>--accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg> <!-- <arg>&#45;&#45;accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg>-->
<arg>--connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg> <!-- <arg>&#45;&#45;connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg>-->
<arg>--metadata</arg><arg>${metadata}</arg> <!-- <arg>&#45;&#45;metadata</arg><arg>${metadata}</arg>-->
<arg>--conceptRecordId</arg><arg>1200252</arg> <!-- <arg>&#45;&#45;conceptRecordId</arg><arg>1200252</arg>-->
<arg>--newDeposition</arg><arg>false</arg> <!-- <arg>&#45;&#45;newDeposition</arg><arg>false</arg>-->
</java> <!-- </java>-->
<ok to="End"/> <!-- <ok to="End"/>-->
<error to="Kill"/> <!-- <error to="Kill"/>-->
</action> <!-- </action>-->
<end name="End"/> <end name="End"/>
</workflow-app> </workflow-app>