diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json deleted file mode 100644 index 63e0803372..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json +++ /dev/null @@ -1,21 +0,0 @@ -[ - { - "paramName": "s", - "paramLongName": "sourcePath", - "paramDescription": "the source mdstore path", - "paramRequired": true - }, - - { - "paramName": "t", - "paramLongName": "targetPath", - "paramDescription": "the target mdstore path", - "paramRequired": true - }, - { - "paramName": "m", - "paramLongName": "master", - "paramDescription": "the master name", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/config-default.xml deleted file mode 100644 index 508202e301..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/workflow.xml deleted file mode 100644 index 506d86a081..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_dump_reader/oozie_app/workflow.xml +++ /dev/null @@ -1,118 +0,0 @@ - - - - crossrefDumpPath - the working dir base path - - - inputPathCrossref - the working dir base path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - 2 - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords - --hdfsServerUri${nameNode} - --crossrefFileNameTarGz${crossrefDumpPath}/crossref.tar.gz - --workingPath${crossrefDumpPath} - --outputPath${workingDir}/files/ - - - - - - - - yarn-cluster - cluster - SparkGenerateCrossrefDataset - eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${crossrefDumpPath}/files - --targetPath${inputPathCrossref}/crossref_ds - - - - - - - - - yarn-cluster - cluster - SparkGenerateCrossrefDataset - eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${inputPathCrossref}/crossref_ds - --targetPath${inputPathCrossref}/crossref_ds_updates - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/config-default.xml deleted file mode 100644 index 508202e301..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/download.sh b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/download.sh deleted file mode 100644 index 1bb7aff1f0..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/download.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -curl -LSs -H "Crossref-Plus-API-Token: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJodHRwOi8vY3Jvc3NyZWYub3JnLyIsImF1ZCI6Im1kcGx1cyIsImp0aSI6Ijk3YTZkNGVkLTg5MjktNGQ2Yi05NWY1LTY2YmMyNDgzNTRjNCJ9.5DPM4gRibUBYBtrUSpRz3RGHYVB-8f61jQBW_q-r-hs" $1 | hdfs dfs -put - $2/$3 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/mock.sh b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/mock.sh deleted file mode 100644 index 30386d6134..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/mock.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -curl -LSs $1 | hdfs dfs -put - $2/$3 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/workflow.xml deleted file mode 100644 index 91de3bfb37..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/downloadandunpack/oozie_app/workflow.xml +++ /dev/null @@ -1,121 +0,0 @@ - - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - crossrefdumpfilename - the Crossref input path - - - crossrefDumpPath - the Crossref dump path - - - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - ${jobTracker} - ${nameNode} - - - mapred.job.queue.name - ${queueName} - - - download.sh - ${url} - ${crossrefDumpPath} - ${crossrefdumpfilename} - HADOOP_USER_NAME=${wf:user()} - download.sh - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords - --hdfsServerUri${nameNode} - --crossrefFileNameTarGz${crossrefdumpfilename} - --workingPath${crossrefDumpPath} - --outputPath${crossrefDumpPath}/files/ - - - - - - - - yarn-cluster - cluster - SparkUnpackCrossrefEntries - eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${crossrefDumpPath}/files - --targetPath${crossrefDumpPath}/crossref_unpack/ - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/download.sh b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/download.sh deleted file mode 100644 index 30386d6134..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/download.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -curl -LSs $1 | hdfs dfs -put - $2/$3 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index ecaeda7091..3700ce5d97 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -63,14 +63,10 @@ - ${wf:conf('resumeFrom') eq 'Skip'} - ${wf:conf('resumeFrom') eq 'ImportCrossRef'} - ${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'} - ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} ${wf:conf('resumeFrom') eq 'ConvertMagToDataset'} ${wf:conf('resumeFrom') eq 'PreProcessORCID'} - + @@ -79,67 +75,6 @@ - - - ${jobTracker} - ${nameNode} - - - mapred.job.queue.name - ${queueName} - - - download.sh - ${url} - ${crossrefDumpPath} - ${crossrefdumpfilename} - download.sh - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords - --hdfsServerUri${nameNode} - --crossrefFileNameTarGz${crossrefdumpfilename} - --workingPath${crossrefDumpPath} - --outputPath${crossrefDumpPath}/files/ - - - - - - - - yarn-cluster - cluster - SparkUnpackCrossrefEntries - eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${crossrefDumpPath}/files - --targetPath${crossrefDumpPath}/crossref_unpack/ - - - - - - yarn-cluster @@ -166,14 +101,7 @@ - - - - - - - - +