forked from D-Net/dnet-hadoop
simple code to get file from URL
This commit is contained in:
parent
3aaad753fd
commit
22cb9e0da7
|
|
@ -0,0 +1,4 @@
|
||||||
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
|
public class Programme {
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,53 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.actionset.h2020programme;
|
||||||
|
|
||||||
|
import java.io.*;
|
||||||
|
import java.net.URL;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.apache.hadoop.conf.Configuration;
|
||||||
|
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||||
|
import org.apache.hadoop.fs.FileSystem;
|
||||||
|
import org.apache.hadoop.fs.Path;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
|
||||||
|
public class GetFile {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(GetFile.class);
|
||||||
|
|
||||||
|
public static void main(final String[] args) throws Exception {
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
IOUtils
|
||||||
|
.toString(
|
||||||
|
GetFile.class
|
||||||
|
.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/actionset/h2020programme/parameters.json")));
|
||||||
|
|
||||||
|
Configuration conf = new Configuration();
|
||||||
|
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
final String fileURL = parser.get("fileURL");
|
||||||
|
final String hdfsPath = parser.get("hdfsPath");
|
||||||
|
final String hdfsNameNode = parser.get("hdfsNameNode");
|
||||||
|
|
||||||
|
conf.set("fs.defaultFS", hdfsNameNode);
|
||||||
|
FileSystem fileSystem = FileSystem.get(conf);
|
||||||
|
Path hdfsWritePath = new Path(hdfsPath);
|
||||||
|
FSDataOutputStream fsDataOutputStream = null;
|
||||||
|
if (fileSystem.exists(hdfsWritePath)) {
|
||||||
|
fsDataOutputStream = fileSystem.append(hdfsWritePath);
|
||||||
|
} else {
|
||||||
|
fsDataOutputStream = fileSystem.create(hdfsWritePath);
|
||||||
|
}
|
||||||
|
|
||||||
|
InputStream is = new BufferedInputStream(new URL(fileURL).openStream());
|
||||||
|
|
||||||
|
org.apache.hadoop.io.IOUtils.copyBytes(is, fsDataOutputStream, 4096, true);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,112 @@
|
||||||
|
<workflow-app name="CollectionWorkflow" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sequenceFilePath</name>
|
||||||
|
<description>the path to store the sequence file of the native metadata collected</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>mdStorePath</name>
|
||||||
|
<description>the path of the native mdstore</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>apiDescription</name>
|
||||||
|
<description>A json encoding of the API Description class</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>dataSourceInfo</name>
|
||||||
|
<description>A json encoding of the Datasource Info</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>identifierPath</name>
|
||||||
|
<description>An xpath to retrieve the metadata idnentifier for the generation of DNet Identifier </description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>metadataEncoding</name>
|
||||||
|
<description> The type of the metadata XML/JSON</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>timestamp</name>
|
||||||
|
<description>The timestamp of the collection date</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>workflowId</name>
|
||||||
|
<description>The identifier of the workflow</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="DeleteMDStoresNative"/>
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
<action name="DeleteMDStoresNative">
|
||||||
|
<fs>
|
||||||
|
<mkdir path='${sequenceFilePath}'/>
|
||||||
|
<mkdir path='${mdStorePath}'/>
|
||||||
|
<delete path='${sequenceFilePath}'/>
|
||||||
|
<delete path='${mdStorePath}'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="CollectionWorker"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<action name="CollectionWorker">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.dhp.collection.worker.DnetCollectorWorker</main-class>
|
||||||
|
<java-opts>-p</java-opts><java-opts>${sequenceFilePath}</java-opts>
|
||||||
|
<java-opts>-a</java-opts><java-opts>${apiDescription}</java-opts>
|
||||||
|
<java-opts>-n</java-opts><java-opts>${nameNode}</java-opts>
|
||||||
|
<java-opts>-rh</java-opts><java-opts>${rmq_host}</java-opts>
|
||||||
|
<java-opts>-ru</java-opts><java-opts>${rmq_user}</java-opts>
|
||||||
|
<java-opts>-rp</java-opts><java-opts>${rmq_pwd}</java-opts>
|
||||||
|
<java-opts>-rr</java-opts><java-opts>${rmq_report}</java-opts>
|
||||||
|
<java-opts>-ro</java-opts><java-opts>${rmq_ongoing}</java-opts>
|
||||||
|
<java-opts>-u</java-opts><java-opts>sandro.labruzzo</java-opts>
|
||||||
|
<java-opts>-w</java-opts><java-opts>${workflowId}</java-opts>
|
||||||
|
</java>
|
||||||
|
<ok to="GenerateNativeStoreSparkJob"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<action name="GenerateNativeStoreSparkJob">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>GenerateNativeStoreSparkJob</name>
|
||||||
|
<class>eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob</class>
|
||||||
|
<jar>dhp-aggregations-1.0.0-SNAPSHOT.jar</jar>
|
||||||
|
<spark-opts>--num-executors 50 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2"</spark-opts>
|
||||||
|
<arg>--encoding</arg> <arg>${metadataEncoding}</arg>
|
||||||
|
<arg>--dateOfCollection</arg> <arg>${timestamp}</arg>
|
||||||
|
<arg>--provenance</arg> <arg> ${dataSourceInfo}</arg>
|
||||||
|
<arg>--xpath</arg><arg>${identifierPath}</arg>
|
||||||
|
<arg>--input</arg><arg>${sequenceFilePath}</arg>
|
||||||
|
<arg>--output</arg><arg>${mdStorePath}</arg>
|
||||||
|
<arg>-rh</arg><arg>${rmq_host}</arg>
|
||||||
|
<arg>-ru</arg><arg>${rmq_user}</arg>
|
||||||
|
<arg>-rp</arg><arg>${rmq_pwd}</arg>
|
||||||
|
<arg>-rr</arg><arg>${rmq_report}</arg>
|
||||||
|
<arg>-ro</arg><arg>${rmq_ongoing}</arg>
|
||||||
|
<arg>-w</arg><arg>${workflowId}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="DropInvalidStore"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="DropInvalidStore">
|
||||||
|
<fs>
|
||||||
|
<delete path='${mdStorePath}/../'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="Kill"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,86 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "issm",
|
||||||
|
"paramLongName": "isSparkSessionManaged",
|
||||||
|
"paramDescription": "when true will stop SparkSession after job execution",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "e",
|
||||||
|
"paramLongName": "encoding",
|
||||||
|
"paramDescription": "the encoding of the input record should be JSON or XML",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "d",
|
||||||
|
"paramLongName": "dateOfCollection",
|
||||||
|
"paramDescription": "the date when the record has been stored",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "p",
|
||||||
|
"paramLongName": "provenance",
|
||||||
|
"paramDescription": "the infos about the provenance of the collected records",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "x",
|
||||||
|
"paramLongName": "xpath",
|
||||||
|
"paramDescription": "the xpath to identify the record identifier",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "i",
|
||||||
|
"paramLongName": "input",
|
||||||
|
"paramDescription": "the path of the sequencial file to read",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "o",
|
||||||
|
"paramLongName": "output",
|
||||||
|
"paramDescription": "the path of the result DataFrame on HDFS",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "ru",
|
||||||
|
"paramLongName": "rabbitUser",
|
||||||
|
"paramDescription": "the user to connect with RabbitMq for messaging",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "rp",
|
||||||
|
"paramLongName": "rabbitPassword",
|
||||||
|
"paramDescription": "the password to connect with RabbitMq for messaging",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "rh",
|
||||||
|
"paramLongName": "rabbitHost",
|
||||||
|
"paramDescription": "the host of the RabbitMq server",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "ro",
|
||||||
|
"paramLongName": "rabbitOngoingQueue",
|
||||||
|
"paramDescription": "the name of the ongoing queue",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "rr",
|
||||||
|
"paramLongName": "rabbitReportQueue",
|
||||||
|
"paramDescription": "the name of the report queue",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "w",
|
||||||
|
"paramLongName": "workflowId",
|
||||||
|
"paramDescription": "the identifier of the dnet Workflow",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "t",
|
||||||
|
"paramLongName": "isTest",
|
||||||
|
"paramDescription": "the name of the report queue",
|
||||||
|
"paramRequired": false
|
||||||
|
}
|
||||||
|
]
|
||||||
Loading…
Reference in New Issue