forked from D-Net/dnet-hadoop
This commit is contained in:
parent
edeb862476
commit
e8f914f8b3
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@ -80,7 +80,7 @@
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</configuration>
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</configuration>
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</global>
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</global>
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<start to="reset_outputpath"/>
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<start to="send_zenodo"/>
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<kill name="Kill">
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -366,146 +366,19 @@
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<error to="Kill"/>
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<error to="Kill"/>
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</action>
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</action>
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<!-- <join name="join_extend" to="fork_splitForCommunities"/>-->
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<action name="send_zenodo">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodo</main-class>
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<!-- <fork name="fork_splitForCommunities">-->
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<!-- <path start="split_publication"/>-->
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<!-- <path start="split_dataset"/>-->
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<arg>--accessToken</arg><arg>${accessToken}</arg>
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<!-- <path start="split_orp"/>-->
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<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
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<!-- <path start="split_software"/>-->
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<arg>--metadata</arg><arg>${metadata}</arg>
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<!-- </fork>-->
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</java>
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<!-- <action name="split_publication">-->
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<ok to="End"/>
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<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
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<error to="Kill"/>
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<!-- <master>yarn</master>-->
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</action>
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<!-- <mode>cluster</mode>-->
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<!-- <name>Split dumped result for community</name>-->
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<!-- <class>eu.dnetlib.dhp.oa.graph.dump.SparkSplitForCommunity</class>-->
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<!-- <jar>dhp-graph-mapper-${projectVersion}.jar</jar>-->
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<!-- <spark-opts>-->
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<!-- --executor-memory=${sparkExecutorMemory}-->
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<!-- --executor-cores=${sparkExecutorCores}-->
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<!-- --driver-memory=${sparkDriverMemory}-->
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<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
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<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
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<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
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<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
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<!-- --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
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<!-- </spark-opts>-->
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/ext/publication</arg>-->
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<!-- <arg>--outputPath</arg><arg>${outputPath}</arg>-->
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<!-- <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.dump.oaf.Publication</arg>-->
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<!-- <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>-->
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<!-- </spark>-->
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<!-- <ok to="join_split"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<!-- <action name="split_dataset">-->
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<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
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<!-- <master>yarn</master>-->
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<!-- <mode>cluster</mode>-->
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<!-- <name>Split dumped result for community</name>-->
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<!-- <class>eu.dnetlib.dhp.oa.graph.dump.SparkSplitForCommunity</class>-->
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<!-- <jar>dhp-graph-mapper-${projectVersion}.jar</jar>-->
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<!-- <spark-opts>-->
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<!-- --executor-memory=${sparkExecutorMemory}-->
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<!-- --executor-cores=${sparkExecutorCores}-->
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<!-- --driver-memory=${sparkDriverMemory}-->
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<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
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<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
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<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
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<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
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<!-- --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
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<!-- </spark-opts>-->
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/ext/dataset</arg>-->
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<!-- <arg>--outputPath</arg><arg>${outputPath}</arg>-->
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<!-- <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.dump.oaf.Dataset</arg>-->
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<!-- <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>-->
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<!-- </spark>-->
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<!-- <ok to="join_split"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<!-- <action name="split_orp">-->
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<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
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<!-- <master>yarn</master>-->
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<!-- <mode>cluster</mode>-->
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<!-- <name>Split dumped result for community</name>-->
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<!-- <class>eu.dnetlib.dhp.oa.graph.dump.SparkSplitForCommunity</class>-->
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<!-- <jar>dhp-graph-mapper-${projectVersion}.jar</jar>-->
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<!-- <spark-opts>-->
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<!-- --executor-memory=${sparkExecutorMemory}-->
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<!-- --executor-cores=${sparkExecutorCores}-->
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<!-- --driver-memory=${sparkDriverMemory}-->
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<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
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<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
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<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
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<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
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<!-- --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
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<!-- </spark-opts>-->
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/ext/orp</arg>-->
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<!-- <arg>--outputPath</arg><arg>${outputPath}</arg>-->
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<!-- <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.dump.oaf.OtherResearchProduct</arg>-->
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<!-- <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>-->
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<!-- </spark>-->
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<!-- <ok to="join_split"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<!-- <action name="split_software">-->
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<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
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<!-- <master>yarn</master>-->
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<!-- <mode>cluster</mode>-->
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<!-- <name>Split dumped result for community</name>-->
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<!-- <class>eu.dnetlib.dhp.oa.graph.dump.SparkSplitForCommunity</class>-->
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<!-- <jar>dhp-graph-mapper-${projectVersion}.jar</jar>-->
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<!-- <spark-opts>-->
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<!-- --executor-memory=${sparkExecutorMemory}-->
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<!-- --executor-cores=${sparkExecutorCores}-->
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<!-- --driver-memory=${sparkDriverMemory}-->
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<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
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<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
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<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
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<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
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<!-- --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
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<!-- </spark-opts>-->
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/ext/software</arg>-->
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<!-- <arg>--outputPath</arg><arg>${outputPath}</arg>-->
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<!-- <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.dump.oaf.Software</arg>-->
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<!-- <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>-->
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<!-- </spark>-->
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<!-- <ok to="join_split"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<!-- <join name="join_split" to="loadInZenodo"/>-->
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<!-- <join name="join_split" to="End"/>-->
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<!-- <action name="loadInZenodo">-->
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<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
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<!-- <master>yarn</master>-->
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<!-- <mode>cluster</mode>-->
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<!-- <name>Import table software</name>-->
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<!-- <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>-->
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<!-- <jar>dhp-graph-mapper-${projectVersion}.jar</jar>-->
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<!-- <spark-opts>-->
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<!-- --executor-memory=${sparkExecutorMemory}-->
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<!-- --executor-cores=${sparkExecutorCores}-->
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<!-- --driver-memory=${sparkDriverMemory}-->
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<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
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<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
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<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
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<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
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<!-- --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
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<!-- </spark-opts>-->
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<!-- <arg>--inputPath</arg><arg>${workingDir}/ext/publication</arg>-->
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<!-- <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>-->
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<!-- <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.dump.oaf.Publication</arg>-->
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<!-- -->
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<!-- </spark>-->
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<!-- <ok to="End"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<end name="End"/>
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<end name="End"/>
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@ -0,0 +1,39 @@
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[
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{
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"paramName":"is",
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"paramLongName":"isLookUpUrl",
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"paramDescription": "URL of the isLookUp Service",
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"paramRequired": true
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},
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{
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"paramName":"hdfsp",
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"paramLongName":"hdfsPath",
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"paramDescription": "the path of the folder tofind files to send to Zenodo",
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"paramRequired": true
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},
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{
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"paramName": "hdfsnn",
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"paramLongName": "hdfsNameNode",
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"paramDescription": "the name node",
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"paramRequired": true
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},
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{
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"paramName": "at",
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"paramLongName": "accessToken",
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"paramDescription": "the access token for the deposition",
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"paramRequired": false
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},
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{
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"paramName":"cu",
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"paramLongName":"connectionUrl",
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"paramDescription": "the url to connect to deposit",
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"paramRequired": false
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},
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{
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"paramName":"m",
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"paramLongName":"metadata",
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"paramDescription": "metadata associated to the deposition",
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"paramRequired": false
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}
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]
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@ -1,54 +1,180 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.IOException;
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import java.io.*;
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import java.nio.charset.StandardCharsets;
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import java.nio.file.Files;
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import java.util.Arrays;
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import java.util.Arrays;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.*;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import com.google.gson.Gson;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.Creator;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.Creator;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.Metadata;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.Metadata;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.ZenodoModel;
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import eu.dnetlib.dhp.oa.graph.dump.zenodo.ZenodoModel;
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import org.apache.commons.io.IOUtils;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.Test;
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public class ZenodoUploadTest {
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public class ZenodoUploadTest {
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private static String workingDir;
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// private static FileSystem fileSystem;
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//
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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||||||
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.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName())
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.toString();
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}
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//
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// Configuration conf = new Configuration();
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// conf.set("fs.defaultFS", "localhost");
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//
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// fileSystem = FileSystem.get(conf);
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//
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// FSDataOutputStream fsDataOutputStream = fileSystem.create(new org.apache.hadoop.fs.Path(workingDir + "/ni"));
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//
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// BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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//
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//
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// writer.write(ZenodoUploadTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni").toString());
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// }
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@Test
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public void HDFSConnection() throws IOException {
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CommunityMap communityMap = new CommunityMap();
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communityMap.put("ni", "Neuroinformatics");
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communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage");
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LocalFileSystem fs = FileSystem.getLocal(new Configuration());
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
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.getPath()),
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new Path(workingDir + "/zenodo/ni/ni"));
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
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.getPath()),
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new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
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System.out.println("pr");
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// Configuration conf = new Configuration();
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// conf.set("fs.defaultFS", "localhost");
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//
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// APIClient s = new APIClient(
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// "https://sandbox.zenodo.org/api/deposit/depositions");
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//
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// s.connect();
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// s.upload(workingDir +"/ni", "Neuroinformatics", fs);
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APIClient client = new APIClient("https://sandbox.zenodo.org/api/deposit/depositions",
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||||||
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"5ImUj0VC1ICg4ifK5dc3AGzJhcfAB4osxrFlsr8WxHXxjaYgCE0hY8HZcDoe");
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client.connect();
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||||||
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// the second boolean parameter here sets the recursion to true
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
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.listFiles(
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new Path(workingDir + "/zenodo"), true);
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||||||
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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// do stuff with the file like ...
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// BufferedInputStream bis = new BufferedInputStream(fs.open( fileStatus.getPath()));
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String p_string = fileStatus.getPath().toString();
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int index = p_string.lastIndexOf("/");
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String community = p_string.substring(0, index);
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community = community.substring(community.lastIndexOf("/") + 1);
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String community_name = communityMap.get(community).replace(" ", "_");
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fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name));
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System.out.println(community);
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// System.out.println(client.upload(bis, community));
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File f = new File("/tmp/" + community_name);
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client.upload(f, community_name);
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if (f.exists()) {
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f.delete();
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}
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}
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||||||
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ZenodoModel zenodo = new ZenodoModel();
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Metadata data = new Metadata();
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data.setTitle("Dump of OpenAIRE Communities related graph");
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data.setUpload_type("dataset");
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data.setDescription("this is a fake uploade done for testing purposes");
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Creator c = new Creator();
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c.setName("Miriam Baglioni");
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c.setAffiliation("CNR _ISTI");
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data.setCreators(Arrays.asList(c));
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zenodo.setMetadata(data);
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System.out.println(client.sendMretadata(new Gson().toJson(zenodo)));
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|
|
||||||
|
System.out.println(client.publish());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void serializeMetadata() {
|
||||||
|
ZenodoModel zenodo = new ZenodoModel();
|
||||||
|
Metadata data = new Metadata();
|
||||||
|
|
||||||
|
data.setTitle("Dump of OpenAIRE Communities related graph");
|
||||||
|
data.setUpload_type("dataset");
|
||||||
|
data.setDescription("this is a fake uploade done for testing purposes");
|
||||||
|
Creator c = new Creator();
|
||||||
|
c.setName("Miriam Baglioni");
|
||||||
|
c.setAffiliation("CNR _ISTI");
|
||||||
|
data.setCreators(Arrays.asList(c));
|
||||||
|
zenodo.setMetadata(data);
|
||||||
|
|
||||||
|
System.out.println(new Gson().toJson(zenodo));
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
public void testConnection() throws IOException {
|
public void testConnection() throws IOException {
|
||||||
|
|
||||||
|
// InputStream is = getClass().getClassLoader().getResourceAsStream("eu/dnetlib/dhp/oa/graph/dump/zenodo/ni");
|
||||||
APIClient s = new APIClient(
|
APIClient s = new APIClient(
|
||||||
// "https://sandbox.zenodo.org/api/deposit/depositions?access_token=5ImUj0VC1ICg4ifK5dc3AGzJhcfAB4osxrFlsr8WxHXxjaYgCE0hY8HZcDoe");
|
"https://sandbox.zenodo.org/api/deposit/depositions",
|
||||||
"https://sandbox.zenodo.org/api/deposit/depositions");
|
"5ImUj0VC1ICg4ifK5dc3AGzJhcfAB4osxrFlsr8WxHXxjaYgCE0hY8HZcDoe");
|
||||||
|
|
||||||
Assertions.assertEquals(201, s.connect());
|
Assertions.assertEquals(201, s.connect());
|
||||||
|
|
||||||
s.upload(getClass()
|
s
|
||||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
|
.upload(
|
||||||
.getPath(), "Neuroinformatics");
|
new File(getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
|
||||||
|
.getPath()),
|
||||||
|
"Neuroinformatics");
|
||||||
|
|
||||||
s.upload(getClass()
|
// s.upload(getClass()
|
||||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
|
// .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
|
||||||
.getPath(), "DigitalHumanitiesandCulturalHeritage");
|
// .getPath(), "DigitalHumanitiesandCulturalHeritage");
|
||||||
|
//
|
||||||
|
// s.upload(getClass()
|
||||||
|
// .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi")
|
||||||
|
// .getPath(), "EGI");
|
||||||
|
//
|
||||||
|
// s.upload(getClass()
|
||||||
|
// .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy")
|
||||||
|
// .getPath(), "ScienceandInnovationPolicyStudies");
|
||||||
|
|
||||||
s.upload(getClass()
|
|
||||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi")
|
|
||||||
.getPath(), "EGI");
|
|
||||||
|
|
||||||
s.upload(getClass()
|
|
||||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy")
|
|
||||||
.getPath(), "ScienceandInnovationPolicyStudies");
|
|
||||||
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// String data = "{\"metadata\": {\"title\": \"My first upload\", " +
|
|
||||||
// "\"upload_type\": \"poster\", " +
|
|
||||||
// "\"description\": \"This is my first upload\", " +
|
|
||||||
// "\"creators\": [{\"name\": \"Doe, John\", " +
|
|
||||||
// "\"affiliation': 'Zenodo'}]
|
|
||||||
//... }
|
|
||||||
//... }
|
|
||||||
//
|
|
||||||
//
|
|
||||||
ZenodoModel zenodo = new ZenodoModel();
|
ZenodoModel zenodo = new ZenodoModel();
|
||||||
Metadata data = new Metadata();
|
Metadata data = new Metadata();
|
||||||
|
|
||||||
|
|
@ -67,24 +193,4 @@ public class ZenodoUploadTest {
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void testPublish() throws IOException {
|
|
||||||
APIClient s = new APIClient("https://sandbox.zenodo.org/api/deposit/depositions");
|
|
||||||
s.publish();
|
|
||||||
}
|
|
||||||
@Test
|
|
||||||
public void testUpload() throws IOException {
|
|
||||||
|
|
||||||
APIClient s = new APIClient(
|
|
||||||
"https://sandbox.zenodo.org/api/deposit/depositions?access_token=5ImUj0VC1ICg4ifK5dc3AGzJhcfAB4osxrFlsr8WxHXxjaYgCE0hY8HZcDoe");
|
|
||||||
final String sourcePath = getClass()
|
|
||||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
|
|
||||||
.getPath();
|
|
||||||
|
|
||||||
s.upload(sourcePath, "Neuroinformatics");
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue