Revision 29471
Added by Eri Katsari over 10 years ago
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/examples/javamapreduce/stats/oozie_app/workflow.xml | ||
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<workflow-app name="test-core_examples_javamapreduce_stats" xmlns="uri:oozie:workflow:0.4"> |
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<!-- map reduce job that exports hbase data and prepares them for import to the relation database used for statistics generation --> |
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<global> |
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration> |
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<property> |
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<name>mapred.job.queue.name</name> |
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<value>${queueName}</value>
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</property> |
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<property> |
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<name>oozie.sqoop.log.level</name> |
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<value>DEBUG</value> |
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</property> |
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</configuration> |
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</global> |
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<start to='get-scanner' /> |
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<action name='get-scanner'> |
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<java> |
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<main-class>eu.dnetlib.iis.core.workflows.stats.HbaseScannerGenerator |
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</main-class> |
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<!-- column families: --> |
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<arg> |
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-f datasource |
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<!-- , --> |
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<!-- datasourceOrganization_provision_provides , --> |
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<!-- organization, --> |
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<!-- project, projectOrganization_participation_hasParticipant --> |
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<!-- result,resultProject_outcome_produces, --> |
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| 32 |
<!-- personResult_authorship_hasAuthor,resultResult_publicationDataset_isRelatedTo --> |
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</arg> |
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<capture-output /> |
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</java> |
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<ok to="mr_export" /> |
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<error to="fail" /> |
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</action> |
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<action name="mr_export"> |
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<map-reduce> |
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<prepare> |
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<delete path="${nameNode}${Stats_output_Path}" />
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</prepare> |
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<configuration> |
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<property> |
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<name>hbase.mapreduce.scan</name> |
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<value>${wf:actionData('get-scanner')['scan']}</value>
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</property> |
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<property> |
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<name>hbase.rootdir</name> |
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<value>hdfs://nmis-hadoop-cluster/hbase</value> |
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</property> |
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<property> |
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<name>hbase.security.authentication</name> |
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<value>simple</value> |
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</property> |
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<!-- ZOOKEEPER --> |
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<property> |
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<name>hbase.zookeeper.quorum</name> |
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<value> |
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quorum1.t.hadoop.research-infrastructures.eu,quorum2.t.hadoop.research-infrastructures.eu,quorum3.t.hadoop.research-infrastructures.eu,quorum4.t.hadoop.research-infrastructures.eu,jobtracker.t.hadoop.research-infrastructures.eu |
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</value> |
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</property> |
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<property> |
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<name>zookeeper.znode.rootserver</name> |
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<value>root-region-server</value> |
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</property> |
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<property> |
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<name>hbase.zookeeper.property.clientPort</name> |
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<value>2182</value> |
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</property> |
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<!-- MR IO --> |
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<property> |
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<name>mapreduce.inputformat.class</name> |
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<value>org.apache.hadoop.hbase.mapreduce.TableInputFormat</value> |
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</property> |
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<property> |
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<name>mapred.mapoutput.key.class</name> |
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapred.mapoutput.value.class</name> |
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<value>org.apache.hadoop.hbase.io.ImmutableBytesWritable</value> |
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</property> |
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<property> |
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<name>mapred.output.key.class</name> |
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapred.output.value.class</name> |
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<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat |
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</value> |
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</property> |
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<!-- ## This is required for new MapReduce API usage --> |
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<property> |
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<name>mapred.mapper.new-api</name> |
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<value>true</value> |
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</property> |
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<property> |
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<name>mapred.reducer.new-api</name> |
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<value>true</value> |
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</property> |
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<!-- # Job-specific options --> |
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<property> |
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<name>dfs.blocksize</name> |
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<value>32M</value> |
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</property> |
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<property> |
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<name>mapred.output.compress</name> |
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<value>false</value> |
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</property> |
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<property> |
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<name>mapred.reduce.tasks.speculative.execution</name> |
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<value>false</value> |
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</property> |
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<property> |
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<name>mapred.reduce.tasks.speculative.execution</name> |
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<value>false</value> |
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</property> |
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<property> |
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<name>mapreduce.map.speculative</name> |
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<value>false</value> |
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</property> |
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<!-- I/O FORMAT --> |
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<!-- IMPORTANT: sets default delimeter used by text output writer. Required to fix issue with traling tab added between id and value in multiple outputs --> |
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<property> |
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<name>mapred.textoutputformat.separator</name> |
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<value>${Stats_delim_Character}</value>
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</property> |
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<!-- ## Names of all output ports --> |
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<property> |
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<name>mapreduce.multipleoutputs</name> |
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<value>${out1} ${out2} ${out3} ${out4} ${out5} ${out6} ${out7} ${out8} ${out9} ${out10} ${out11} ${out12} ${out13} ${out14} ${out15} ${out16} ${out17} ${out18} ${out19} ${out20}
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</value> |
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</property> |
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<!-- datasource --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out1}.key</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out1}.value</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out1}.format</name>
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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<!-- datasourceLanguage --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out2}.key</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out2}.value</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out2}.format</name>
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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<!-- datasourceOrganization --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out3}.key</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out3}.value</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out3}.format</name>
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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|
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<!-- datasourceTopic --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out4}.key</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out4}.value</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out4}.format</name>
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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|
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<!-- resultDatasource --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out5}.key</name>
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out5}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out5}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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<!-- organization --> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out6}.key</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out6}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out6}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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| 242 |
|
|
| 243 |
<!-- projectOrganization --> |
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| 244 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out7}.key</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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| 248 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out7}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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| 251 |
</property> |
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| 252 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out7}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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| 256 |
</property> |
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| 257 |
<!-- resultProject --> |
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| 258 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out8}.key</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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| 261 |
</property> |
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| 262 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out8}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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| 265 |
</property> |
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| 266 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out8}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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| 271 |
|
|
| 272 |
<!-- project --> |
|
| 273 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out9}.key</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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| 277 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out9}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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| 280 |
</property> |
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| 281 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out9}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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| 286 |
|
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| 287 |
<!-- resultConcept --> |
|
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out10}.key</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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| 292 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out10}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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</property> |
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<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out10}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
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</property> |
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| 301 |
|
|
| 302 |
<!-- resultClaim --> |
|
| 303 |
<property> |
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| 304 |
<name>mapreduce.multipleoutputs.namedOutput.${out11}.key</name>
|
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| 305 |
<value>org.apache.hadoop.io.Text</value> |
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| 306 |
</property> |
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| 307 |
<property> |
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<name>mapreduce.multipleoutputs.namedOutput.${out11}.value</name>
|
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<value>org.apache.hadoop.io.Text</value> |
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| 310 |
</property> |
|
| 311 |
<property> |
|
| 312 |
<name>mapreduce.multipleoutputs.namedOutput.${out11}.format</name>
|
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<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
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</value> |
|
| 315 |
</property> |
|
| 316 |
|
|
| 317 |
<!-- resultClassification --> |
|
| 318 |
<property> |
|
| 319 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.key</name>
|
|
| 320 |
<value>org.apache.hadoop.io.Text</value> |
|
| 321 |
</property> |
|
| 322 |
<property> |
|
| 323 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.value</name>
|
|
| 324 |
<value>org.apache.hadoop.io.Text</value> |
|
| 325 |
</property> |
|
| 326 |
<property> |
|
| 327 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.format</name>
|
|
| 328 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 329 |
</value> |
|
| 330 |
</property> |
|
| 331 |
|
|
| 332 |
<!-- resultLanguage --> |
|
| 333 |
<property> |
|
| 334 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.key</name>
|
|
| 335 |
<value>org.apache.hadoop.io.Text</value> |
|
| 336 |
</property> |
|
| 337 |
<property> |
|
| 338 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.value</name>
|
|
| 339 |
<value>org.apache.hadoop.io.Text</value> |
|
| 340 |
</property> |
|
| 341 |
<property> |
|
| 342 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.format</name>
|
|
| 343 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 344 |
</value> |
|
| 345 |
</property> |
|
| 346 |
|
|
| 347 |
<!-- resultProject --> |
|
| 348 |
<property> |
|
| 349 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.key</name>
|
|
| 350 |
<value>org.apache.hadoop.io.Text</value> |
|
| 351 |
</property> |
|
| 352 |
<property> |
|
| 353 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.value</name>
|
|
| 354 |
<value>org.apache.hadoop.io.Text</value> |
|
| 355 |
</property> |
|
| 356 |
<property> |
|
| 357 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.format</name>
|
|
| 358 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 359 |
</value> |
|
| 360 |
</property> |
|
| 361 |
<!-- resultResult --> |
|
| 362 |
<property> |
|
| 363 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.key</name>
|
|
| 364 |
<value>org.apache.hadoop.io.Text</value> |
|
| 365 |
</property> |
|
| 366 |
<property> |
|
| 367 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.value</name>
|
|
| 368 |
<value>org.apache.hadoop.io.Text</value> |
|
| 369 |
</property> |
|
| 370 |
<property> |
|
| 371 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.format</name>
|
|
| 372 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 373 |
</value> |
|
| 374 |
</property> |
|
| 375 |
<!-- resultTopic --> |
|
| 376 |
<property> |
|
| 377 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.key</name>
|
|
| 378 |
<value>org.apache.hadoop.io.Text</value> |
|
| 379 |
</property> |
|
| 380 |
<property> |
|
| 381 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.value</name>
|
|
| 382 |
<value>org.apache.hadoop.io.Text</value> |
|
| 383 |
</property> |
|
| 384 |
<property> |
|
| 385 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.format</name>
|
|
| 386 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 387 |
</value> |
|
| 388 |
</property> |
|
| 389 |
|
|
| 390 |
<!-- resultDatasource --> |
|
| 391 |
<property> |
|
| 392 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.key</name>
|
|
| 393 |
<value>org.apache.hadoop.io.Text</value> |
|
| 394 |
</property> |
|
| 395 |
<property> |
|
| 396 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.value</name>
|
|
| 397 |
<value>org.apache.hadoop.io.Text</value> |
|
| 398 |
</property> |
|
| 399 |
<property> |
|
| 400 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.format</name>
|
|
| 401 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 402 |
</value> |
|
| 403 |
</property> |
|
| 404 |
|
|
| 405 |
|
|
| 406 |
|
|
| 407 |
<!-- result --> |
|
| 408 |
<property> |
|
| 409 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.key</name>
|
|
| 410 |
<value>org.apache.hadoop.io.Text</value> |
|
| 411 |
</property> |
|
| 412 |
<property> |
|
| 413 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.value</name>
|
|
| 414 |
<value>org.apache.hadoop.io.Text</value> |
|
| 415 |
</property> |
|
| 416 |
<property> |
|
| 417 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.format</name>
|
|
| 418 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 419 |
</value> |
|
| 420 |
</property> |
|
| 421 |
|
|
| 422 |
<!-- claim --> |
|
| 423 |
<property> |
|
| 424 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.key</name>
|
|
| 425 |
<value>org.apache.hadoop.io.Text</value> |
|
| 426 |
</property> |
|
| 427 |
<property> |
|
| 428 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.value</name>
|
|
| 429 |
<value>org.apache.hadoop.io.Text</value> |
|
| 430 |
</property> |
|
| 431 |
<property> |
|
| 432 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.format</name>
|
|
| 433 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 434 |
</value> |
|
| 435 |
</property> |
|
| 436 |
<!-- cncept --> |
|
| 437 |
<property> |
|
| 438 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.key</name>
|
|
| 439 |
<value>org.apache.hadoop.io.Text</value> |
|
| 440 |
</property> |
|
| 441 |
<property> |
|
| 442 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.value</name>
|
|
| 443 |
<value>org.apache.hadoop.io.Text</value> |
|
| 444 |
</property> |
|
| 445 |
<property> |
|
| 446 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.format</name>
|
|
| 447 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 448 |
</value> |
|
| 449 |
</property> |
|
| 450 |
|
|
| 451 |
|
|
| 452 |
<!-- ## Classes of mapper and reducer --> |
|
| 453 |
|
|
| 454 |
<property> |
|
| 455 |
<name>mapreduce.map.class</name> |
|
| 456 |
<value>eu.dnetlib.data.mapreduce.hbase.statsExport.StatsMapper |
|
| 457 |
</value> |
|
| 458 |
</property> |
|
| 459 |
<property> |
|
| 460 |
<name>mapreduce.reduce.class</name> |
|
| 461 |
<value>eu.dnetlib.data.mapreduce.hbase.statsExport.StatsReducer |
|
| 462 |
</value> |
|
| 463 |
</property> |
|
| 464 |
<property> |
|
| 465 |
<name>io.serializations</name> |
|
| 466 |
<value>org.apache.hadoop.io.serializer.WritableSerialization |
|
| 467 |
</value> |
|
| 468 |
</property> |
|
| 469 |
<!-- ## Custom config --> |
|
| 470 |
|
|
| 471 |
<!--delim character used to seperate fields in hdfs dump files <property> --> |
|
| 472 |
<property> |
|
| 473 |
<name>stats.delim</name> |
|
| 474 |
<value>${Stats_delim_Character}</value>
|
|
| 475 |
</property> |
|
| 476 |
<!--default string for Null String Values --> |
|
| 477 |
<property> |
|
| 478 |
<name>stats.nullString</name> |
|
| 479 |
<value>${Stats_null_String_Field}</value>
|
|
| 480 |
</property> |
|
| 481 |
<!--default string for Null Numeric Values --> |
|
| 482 |
<property> |
|
| 483 |
<name>stats.nullNum</name> |
|
| 484 |
<value>${Stats_null_Numeric_Field}</value>
|
|
| 485 |
</property> |
|
| 486 |
<property> |
|
| 487 |
<name>stats.enclChar</name> |
|
| 488 |
<value>${Stats_enclosing_Character}</value>
|
|
| 489 |
</property> |
|
| 490 |
|
|
| 491 |
|
|
| 492 |
<!--source hbase table --> |
|
| 493 |
<property> |
|
| 494 |
<name>hbase.mapreduce.inputtable</name> |
|
| 495 |
<value>${Stats_Hbase_Source_Table}</value>
|
|
| 496 |
</property> |
|
| 497 |
<property> |
|
| 498 |
<!-- mapping of protos entities to tables in the relDB --> |
|
| 499 |
<name>stats.dbTablesMap</name> |
|
| 500 |
<value>${Stats_db_table_map}</value>
|
|
| 501 |
</property> |
|
| 502 |
|
|
| 503 |
<!-- This directory does not correspond to a data store. In fact, this directory only contains multiple data stores. It has to be set to the name of the workflow node. --> |
|
| 504 |
<property> |
|
| 505 |
<name>mapred.output.dir</name> |
|
| 506 |
<value>${Stats_output_Path}</value>
|
|
| 507 |
</property> |
|
| 508 |
<property> |
|
| 509 |
<name>stats.indexConf</name> |
|
| 510 |
<value>${Stats_indexConf}</value>
|
|
| 511 |
</property> |
|
| 512 |
<!-- ## Workflow node parameters --> |
|
| 513 |
<property> |
|
| 514 |
<name>mapred.reduce.tasks</name> |
|
| 515 |
<value>${numReducers}</value>
|
|
| 516 |
</property> |
|
| 517 |
</configuration> |
|
| 518 |
</map-reduce> |
|
| 519 |
<ok to="exportContext" /> |
|
| 520 |
<error to="fail" /> |
|
| 521 |
</action> |
|
| 522 |
|
|
| 523 |
|
|
| 524 |
<action name="exportContext"> |
|
| 525 |
<java> |
|
| 526 |
|
|
| 527 |
<prepare> |
|
| 528 |
</prepare> |
|
| 529 |
<configuration> |
|
| 530 |
<property> |
|
| 531 |
<name>mapred.job.queue.name</name> |
|
| 532 |
<value>${queueName}</value>
|
|
| 533 |
</property> |
|
| 534 |
</configuration> |
|
| 535 |
|
|
| 536 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 537 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 538 |
<arg>eu.dnetlib.iis.core.workflows.stats.ExportContextWrapper</arg> |
|
| 539 |
<arg>-PStats_output_Path=${Stats_output_Path}</arg>
|
|
| 540 |
<arg>-PStats_ContextResourceXML=${ContextResourceXML}</arg>
|
|
| 541 |
|
|
| 542 |
</java> |
|
| 543 |
<ok to="prepareDatabase" /> |
|
| 544 |
<error to="fail" /> |
|
| 545 |
</action> |
|
| 546 |
|
|
| 547 |
<action name="prepareDatabase"> |
|
| 548 |
<java> |
|
| 549 |
|
|
| 550 |
<prepare> |
|
| 551 |
</prepare> |
|
| 552 |
<configuration> |
|
| 553 |
<property> |
|
| 554 |
<name>mapred.job.queue.name</name> |
|
| 555 |
<value>${queueName}</value>
|
|
| 556 |
</property> |
|
| 557 |
</configuration> |
|
| 558 |
|
|
| 559 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 560 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 561 |
<arg>eu.dnetlib.iis.core.workflows.stats.DBInitWrapper</arg> |
|
| 562 |
|
|
| 563 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 564 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 565 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 566 |
<arg>-PStats_db_Driver=${Stats_db_Driver}</arg>
|
|
| 567 |
|
|
| 568 |
</java> |
|
| 569 |
<ok to="sqoopImport" /> |
|
| 570 |
<error to="fail" /> |
|
| 571 |
</action> |
|
| 572 |
|
|
| 573 |
<action name="sqoopImport"> |
|
| 574 |
<java> |
|
| 575 |
<prepare> |
|
| 576 |
</prepare> |
|
| 577 |
<configuration> |
|
| 578 |
<property> |
|
| 579 |
<name>mapred.job.queue.name</name> |
|
| 580 |
<value>${queueName}</value>
|
|
| 581 |
</property> |
|
| 582 |
|
|
| 583 |
<property> |
|
| 584 |
<name>oozie.sqoop.log.level</name> |
|
| 585 |
<value>DEBUG</value> |
|
| 586 |
</property> |
|
| 587 |
|
|
| 588 |
</configuration> |
|
| 589 |
|
|
| 590 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 591 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 592 |
<arg>eu.dnetlib.iis.core.workflows.stats.SqoopWrapper</arg> |
|
| 593 |
|
|
| 594 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 595 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 596 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 597 |
|
|
| 598 |
<arg>-PStats_output_Path=${Stats_output_Path}</arg>
|
|
| 599 |
<arg>-PStats_sqoop_RecsPerStatement=${Stats_sqoop_RecsPerStatement}
|
|
| 600 |
</arg> |
|
| 601 |
<arg>-PStats_sqoop_ReducersCount=${Stats_sqoop_ReducersCount}</arg>
|
|
| 602 |
<arg>-PStats_sqoop_StatementPerTrans=${Stats_sqoop_StatementPerTrans}
|
|
| 603 |
</arg> |
|
| 604 |
<arg>-PStats_delim_Character=${Stats_delim_Character}</arg>
|
|
| 605 |
<arg>-PStats_db_table_map=${Stats_db_table_map}</arg>
|
|
| 606 |
<arg>-PStats_enclosing_Character=${Stats_enclosing_Character} </arg>
|
|
| 607 |
|
|
| 608 |
</java> |
|
| 609 |
<ok to="finalizeDatabase" /> |
|
| 610 |
<error to="fail" /> |
|
| 611 |
</action> |
|
| 612 |
|
|
| 613 |
<action name="finalizeDatabase"> |
|
| 614 |
<java> |
|
| 615 |
|
|
| 616 |
<prepare> |
|
| 617 |
</prepare> |
|
| 618 |
<configuration> |
|
| 619 |
<property> |
|
| 620 |
<name>mapred.job.queue.name</name> |
|
| 621 |
<value>${queueName}</value>
|
|
| 622 |
</property> |
|
| 623 |
</configuration> |
|
| 624 |
|
|
| 625 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 626 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 627 |
<arg>eu.dnetlib.iis.core.workflows.stats.DBFinalizeWrapper</arg> |
|
| 628 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 629 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 630 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 631 |
<arg>-PStats_db_Driver=${Stats_db_Driver}</arg>
|
|
| 632 |
|
|
| 633 |
|
|
| 634 |
</java> |
|
| 635 |
<ok to="end" /> |
|
| 636 |
<error to="fail" /> |
|
| 637 |
</action> |
|
| 638 |
<kill name="fail"> |
|
| 639 |
<message> |
|
| 640 |
Unfortunately, the process failed -- error message: |
|
| 641 |
[${wf:errorMessage(wf:lastErrorNode())}]
|
|
| 642 |
</message> |
|
| 643 |
</kill> |
|
| 644 |
<end name="end" /> |
|
| 645 |
</workflow-app> |
|
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/examples/javamapreduce/stats/job.properties | ||
|---|---|---|
| 1 |
oozieServiceLoc=http://oozie.t.hadoop.research-infrastructures.eu:11000/oozie |
|
| 2 |
nameNode=hdfs://nmis-hadoop-cluster |
|
| 3 |
jobTracker=nmis-hadoop-jt |
|
| 4 |
queueName=default |
|
| 5 |
user.name=eri.katsari |
|
| 6 |
numReducers=1 |
|
| 7 |
Stats_db_Url = jdbc:postgresql://duffy.di.uoa.gr:5432/test_stats |
|
| 8 |
Stats_db_User = sqoop |
|
| 9 |
Stats_db_Pass = sqoop |
|
| 10 |
Stats_db_Driver = org.postgresql.Driver |
|
| 11 |
Stats_sqoop_RecsPerStatement = 1000 |
|
| 12 |
Stats_sqoop_StatementPerTrans = 1000 |
|
| 13 |
Stats_sqoop_ReducersCount=4 |
|
| 14 |
Stats_Hbase_Source_Table=db_openaireplus_node6_t |
|
| 15 |
Stats_output_Path=/tmp/test_stats/ |
|
| 16 |
Stats_null_String_Field=NULL |
|
| 17 |
Stats_null_Numeric_Field=-1 |
|
| 18 |
Stats_delim_Character=! |
|
| 19 |
Stats_enclosing_Character=# |
|
| 20 |
Stats_db_table_map=datasourceLanguage=datasource_languages,datasource=datasource,project=project,result=result,organization=organization,datasourceOrganization=datasource_organizations,datasourceTopic=datasource_topics,projectOrganization=project_organizations,resultClaim=result_claims,resultClassification=result_classifications,resultConcept=result_concepts,resultLanguage=result_languages,resultOrganization=result_organizations,resultResult=result_results,resultProject=project_results,resultResult=result_results,resultTopic=result_topics,category=category,claim=claim,concept=concept,datasourceLanguage=datasource_languages,resultLanguage=result_languages,resultDatasource=result_datasources |
|
| 21 |
out1=datasource |
|
| 22 |
out2=project |
|
| 23 |
out3=organization |
|
| 24 |
out4=datasourceOrganization |
|
| 25 |
out5=datasourceTopic |
|
| 26 |
out6=datasourceLanguage |
|
| 27 |
out7=projectOrganization |
|
| 28 |
out8=resultClaim |
|
| 29 |
out9=resultClassification |
|
| 30 |
out10=resultConcept |
|
| 31 |
out11=resultLanguage |
|
| 32 |
out12=resultOrganization |
|
| 33 |
out13=resultResult |
|
| 34 |
out14=resultProject |
|
| 35 |
out15=resultTopic |
|
| 36 |
out16=resultDatasource |
|
| 37 |
out17=result |
|
| 38 |
out18=claim |
|
| 39 |
out19=concept |
|
| 40 |
out20=category |
|
| 41 |
Stats_indexConf=index.conf { result { dups = true, links = [{ relType = personResult_authorship_hasAuthor, targetEntity = person, expandAs = rel, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_dedup_isMergedIn, targetEntity = result, expandAs = child, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_dedup_merges, targetEntity = result, expandAs = child, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_publicationDataset_isRelatedTo, targetEntity = result, expandAs = rel, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] },{ relType = resultResult_similarity_isAmongTopNSimilarDocuments, targetEntity = result, expandAs = rel, symmetric = false, fields = [title,dateofacceptance,publisher,resulttype,similarity,type] },{ relType = resultResult_similarity_hasAmongTopNSimilarDocuments, targetEntity = result, expandAs = rel, symmetric = false, fields = [title,dateofacceptance,publisher,resulttype,similarity,type] }]}, person { dups = false, links = [ { relType = personResult_authorship_isAuthorOf, targetEntity = result, expandAs = rel, symmetric = true, fields = [fullname,ranking] }, { relType = projectPerson_contactPerson_isContact, targetEntity = project, expandAs = rel, symmetric = true, fields = [fullname,email,fax,phone] } ]}, datasource { dups = false, links = [ { relType = datasourceOrganization_provision_provides, targetEntity = organization, expandAs = rel, symmetric = true, fields = [officialname,websiteurl,datasourcetype,aggregatortype] } ]},organization { dups = false, links = [{ relType = projectOrganization_participation_isParticipant, targetEntity = project, expandAs = rel, symmetric = true, fields = [legalname,legalshortname,websiteurl,country] }, { relType = datasourceOrganization_provision_isProvidedBy, targetEntity = datasource, expandAs = rel, symmetric = true, fields = [legalname,legalshortname,websiteurl,country] } ]}, project { dups = false, links = [ { relType = projectOrganization_participation_hasParticipant, targetEntity = organization, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] }, { relType = resultProject_outcome_produces, targetEntity = result, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] }, { relType = projectPerson_contactPerson_hasContact, targetEntity = person, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] } ]}}
|
|
| 42 |
ContextResourceXML=<?xml version="1.0" encoding="UTF-8"?><?xml-stylesheet type="text/xsl" href="context.xsl"?><RESOURCE_PROFILE><HEADER><RESOURCE_IDENTIFIER value="1284f828-6c12-4905-a9c9-43f143b36e08_Q29udGV4dERTUmVzb3VyY2VzL0NvbnRleHREU1Jlc291cmNlVHlwZQ=="/><RESOURCE_TYPE value="ContextDSResourceType"/><RESOURCE_KIND value="ContextDSResources"/><RESOURCE_URI value=""/><DATE_OF_CREATION value=""/></HEADER><BODY><CONFIGURATION><context id="egi" type="community" label="EGI"><category claim="true" label="Scientific Disciplines" id="egi::classification"><concept label="Natural Sciences" claim="true" id="egi::classification::natsc"><param name="originalID">1</param><concept label="Mathematics" claim="true" id="egi::classification::natsc::math"><param name="originalID">1.1</param><concept label="Applied Mathematics" id="egi::classification::natsc::math::applied" claim="true"><param name="originalID">1.1.1</param></concept></concept></concept></category></context></CONFIGURATION><STATUS/><SECURITY_PARAMETERS/></BODY></RESOURCE_PROFILE> |
|
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/examples/javamapreduce/stats/NewFile.xml | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/javamapreduce/stats/job.properties | ||
|---|---|---|
| 1 |
oozieServiceLoc=http://oozie.t.hadoop.research-infrastructures.eu:11000/oozie |
|
| 2 |
nameNode=hdfs://nmis-hadoop-cluster |
|
| 3 |
jobTracker=nmis-hadoop-jt |
|
| 4 |
queueName=default |
|
| 5 |
user.name=eri.katsari |
|
| 6 |
numReducers=1 |
|
| 7 |
Stats_db_Url = jdbc:postgresql://duffy.di.uoa.gr:5432/test_stats |
|
| 8 |
Stats_db_User = sqoop |
|
| 9 |
Stats_db_Pass = sqoop |
|
| 10 |
Stats_db_Driver = org.postgresql.Driver |
|
| 11 |
Stats_sqoop_RecsPerStatement = 1000 |
|
| 12 |
Stats_sqoop_StatementPerTrans = 1000 |
|
| 13 |
Stats_sqoop_ReducersCount=4 |
|
| 14 |
Stats_Hbase_Source_Table=db_openaireplus_node6_t |
|
| 15 |
Stats_output_Path=/tmp/test_stats/ |
|
| 16 |
Stats_null_String_Field=NULL |
|
| 17 |
Stats_null_Numeric_Field=-1 |
|
| 18 |
Stats_delim_Character=! |
|
| 19 |
Stats_enclosing_Character=# |
|
| 20 |
Stats_db_table_map=datasourceLanguage=datasource_languages,datasource=datasource,project=project,result=result,organization=organization,datasourceOrganization=datasource_organizations,datasourceTopic=datasource_topics,projectOrganization=project_organizations,resultClaim=result_claims,resultClassification=result_classifications,resultConcept=result_concepts,resultLanguage=result_languages,resultOrganization=result_organizations,resultResult=result_results,resultProject=project_results,resultResult=result_results,resultTopic=result_topics,category=category,claim=claim,concept=concept,datasourceLanguage=datasource_languages,resultLanguage=result_languages,resultDatasource=result_datasources |
|
| 21 |
out1=datasource |
|
| 22 |
out2=project |
|
| 23 |
out3=organization |
|
| 24 |
out4=datasourceOrganization |
|
| 25 |
out5=datasourceTopic |
|
| 26 |
out6=datasourceLanguage |
|
| 27 |
out7=projectOrganization |
|
| 28 |
out8=resultClaim |
|
| 29 |
out9=resultClassification |
|
| 30 |
out10=resultConcept |
|
| 31 |
out11=resultLanguage |
|
| 32 |
out12=resultOrganization |
|
| 33 |
out13=resultResult |
|
| 34 |
out14=resultProject |
|
| 35 |
out15=resultTopic |
|
| 36 |
out16=resultDatasource |
|
| 37 |
out17=result |
|
| 38 |
out18=claim |
|
| 39 |
out19=concept |
|
| 40 |
out20=category |
|
| 41 |
Stats_indexConf=index.conf { result { dups = true, links = [{ relType = personResult_authorship_hasAuthor, targetEntity = person, expandAs = rel, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_dedup_isMergedIn, targetEntity = result, expandAs = child, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_dedup_merges, targetEntity = result, expandAs = child, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] }, { relType = resultResult_publicationDataset_isRelatedTo, targetEntity = result, expandAs = rel, symmetric = true, fields = [title,dateofacceptance,publisher,resulttype] },{ relType = resultResult_similarity_isAmongTopNSimilarDocuments, targetEntity = result, expandAs = rel, symmetric = false, fields = [title,dateofacceptance,publisher,resulttype,similarity,type] },{ relType = resultResult_similarity_hasAmongTopNSimilarDocuments, targetEntity = result, expandAs = rel, symmetric = false, fields = [title,dateofacceptance,publisher,resulttype,similarity,type] }]}, person { dups = false, links = [ { relType = personResult_authorship_isAuthorOf, targetEntity = result, expandAs = rel, symmetric = true, fields = [fullname,ranking] }, { relType = projectPerson_contactPerson_isContact, targetEntity = project, expandAs = rel, symmetric = true, fields = [fullname,email,fax,phone] } ]}, datasource { dups = false, links = [ { relType = datasourceOrganization_provision_provides, targetEntity = organization, expandAs = rel, symmetric = true, fields = [officialname,websiteurl,datasourcetype,aggregatortype] } ]},organization { dups = false, links = [{ relType = projectOrganization_participation_isParticipant, targetEntity = project, expandAs = rel, symmetric = true, fields = [legalname,legalshortname,websiteurl,country] }, { relType = datasourceOrganization_provision_isProvidedBy, targetEntity = datasource, expandAs = rel, symmetric = true, fields = [legalname,legalshortname,websiteurl,country] } ]}, project { dups = false, links = [ { relType = projectOrganization_participation_hasParticipant, targetEntity = organization, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] }, { relType = resultProject_outcome_produces, targetEntity = result, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] }, { relType = projectPerson_contactPerson_hasContact, targetEntity = person, expandAs = rel, symmetric = true, fields = [code,acronym,title,websiteurl,contracttype,fundingtree] } ]}}
|
|
| 42 |
ContextResourceXML=<?xml version="1.0" encoding="UTF-8"?><?xml-stylesheet type="text/xsl" href="context.xsl"?><RESOURCE_PROFILES><RESOURCE_PROFILE><HEADER><RESOURCE_IDENTIFIER value="1284f828-6c12-4905-a9c9-43f143b36e08_Q29udGV4dERTUmVzb3VyY2VzL0NvbnRleHREU1Jlc291cmNlVHlwZQ=="/><RESOURCE_TYPE value="ContextDSResourceType"/><RESOURCE_KIND value="ContextDSResources"/><RESOURCE_URI value=""/><DATE_OF_CREATION value=""/></HEADER><BODY><CONFIGURATION><context id="egi" type="community" label="EGI"><category claim="true" label="Scientific Disciplines" id="egi::classification"><concept label="Natural Sciences" claim="true" id="egi::classification::natsc"><param name="originalID">1</param><concept label="Mathematics" claim="true" id="egi::classification::natsc::math"><param name="originalID">1.1</param><concept label="Applied Mathematics" id="egi::classification::natsc::math::applied" claim="true"><param name="originalID">1.1.1</param></concept></concept></concept></category></context></CONFIGURATION><STATUS/><SECURITY_PARAMETERS/></BODY></RESOURCE_PROFILE></RESOURCE_PROFILES> |
|
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/javamapreduce/stats/oozie_app/workflow.xml | ||
|---|---|---|
| 1 |
<workflow-app name="test-core_examples_javamapreduce_stats" xmlns="uri:oozie:workflow:0.4"> |
|
| 2 |
<!-- map reduce job that exports hbase data and prepares them for import to the relation database used for statistics generation --> |
|
| 3 |
|
|
| 4 |
<global> |
|
| 5 |
<job-tracker>${jobTracker}</job-tracker>
|
|
| 6 |
<name-node>${nameNode}</name-node>
|
|
| 7 |
<configuration> |
|
| 8 |
<property> |
|
| 9 |
<name>mapred.job.queue.name</name> |
|
| 10 |
<value>${queueName}</value>
|
|
| 11 |
</property> |
|
| 12 |
<property> |
|
| 13 |
<name>oozie.sqoop.log.level</name> |
|
| 14 |
<value>DEBUG</value> |
|
| 15 |
</property> |
|
| 16 |
</configuration> |
|
| 17 |
</global> |
|
| 18 |
<start to='get-scanner' /> |
|
| 19 |
<action name='get-scanner'> |
|
| 20 |
<java> |
|
| 21 |
<main-class>eu.dnetlib.iis.core.workflows.stats.HbaseScannerGenerator |
|
| 22 |
</main-class> |
|
| 23 |
<!-- column families: --> |
|
| 24 |
|
|
| 25 |
<arg> |
|
| 26 |
-f datasource |
|
| 27 |
<!-- , --> |
|
| 28 |
<!-- datasourceOrganization_provision_provides , --> |
|
| 29 |
<!-- organization, --> |
|
| 30 |
<!-- project, projectOrganization_participation_hasParticipant --> |
|
| 31 |
<!-- result,resultProject_outcome_produces, --> |
|
| 32 |
<!-- personResult_authorship_hasAuthor,resultResult_publicationDataset_isRelatedTo --> |
|
| 33 |
</arg> |
|
| 34 |
|
|
| 35 |
<capture-output /> |
|
| 36 |
</java> |
|
| 37 |
<ok to="mr_export" /> |
|
| 38 |
<error to="fail" /> |
|
| 39 |
</action> |
|
| 40 |
<action name="mr_export"> |
|
| 41 |
<map-reduce> |
|
| 42 |
|
|
| 43 |
<prepare> |
|
| 44 |
<delete path="${nameNode}${Stats_output_Path}" />
|
|
| 45 |
|
|
| 46 |
</prepare> |
|
| 47 |
<configuration> |
|
| 48 |
<property> |
|
| 49 |
<name>hbase.mapreduce.scan</name> |
|
| 50 |
<value>${wf:actionData('get-scanner')['scan']}</value>
|
|
| 51 |
</property> |
|
| 52 |
<property> |
|
| 53 |
<name>hbase.rootdir</name> |
|
| 54 |
<value>hdfs://nmis-hadoop-cluster/hbase</value> |
|
| 55 |
</property> |
|
| 56 |
|
|
| 57 |
<property> |
|
| 58 |
<name>hbase.security.authentication</name> |
|
| 59 |
<value>simple</value> |
|
| 60 |
</property> |
|
| 61 |
<!-- ZOOKEEPER --> |
|
| 62 |
|
|
| 63 |
<property> |
|
| 64 |
<name>hbase.zookeeper.quorum</name> |
|
| 65 |
<value> |
|
| 66 |
quorum1.t.hadoop.research-infrastructures.eu,quorum2.t.hadoop.research-infrastructures.eu,quorum3.t.hadoop.research-infrastructures.eu,quorum4.t.hadoop.research-infrastructures.eu,jobtracker.t.hadoop.research-infrastructures.eu |
|
| 67 |
</value> |
|
| 68 |
</property> |
|
| 69 |
<property> |
|
| 70 |
<name>zookeeper.znode.rootserver</name> |
|
| 71 |
<value>root-region-server</value> |
|
| 72 |
</property> |
|
| 73 |
|
|
| 74 |
<property> |
|
| 75 |
<name>hbase.zookeeper.property.clientPort</name> |
|
| 76 |
<value>2182</value> |
|
| 77 |
</property> |
|
| 78 |
|
|
| 79 |
|
|
| 80 |
<!-- MR IO --> |
|
| 81 |
|
|
| 82 |
|
|
| 83 |
<property> |
|
| 84 |
<name>mapreduce.inputformat.class</name> |
|
| 85 |
<value>org.apache.hadoop.hbase.mapreduce.TableInputFormat</value> |
|
| 86 |
</property> |
|
| 87 |
|
|
| 88 |
<property> |
|
| 89 |
<name>mapred.mapoutput.key.class</name> |
|
| 90 |
<value>org.apache.hadoop.io.Text</value> |
|
| 91 |
</property> |
|
| 92 |
<property> |
|
| 93 |
<name>mapred.mapoutput.value.class</name> |
|
| 94 |
<value>org.apache.hadoop.hbase.io.ImmutableBytesWritable</value> |
|
| 95 |
</property> |
|
| 96 |
<property> |
|
| 97 |
<name>mapred.output.key.class</name> |
|
| 98 |
<value>org.apache.hadoop.io.Text</value> |
|
| 99 |
</property> |
|
| 100 |
<property> |
|
| 101 |
<name>mapred.output.value.class</name> |
|
| 102 |
<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat |
|
| 103 |
</value> |
|
| 104 |
</property> |
|
| 105 |
|
|
| 106 |
<!-- ## This is required for new MapReduce API usage --> |
|
| 107 |
<property> |
|
| 108 |
<name>mapred.mapper.new-api</name> |
|
| 109 |
<value>true</value> |
|
| 110 |
</property> |
|
| 111 |
<property> |
|
| 112 |
<name>mapred.reducer.new-api</name> |
|
| 113 |
<value>true</value> |
|
| 114 |
</property> |
|
| 115 |
|
|
| 116 |
<!-- # Job-specific options --> |
|
| 117 |
<property> |
|
| 118 |
<name>dfs.blocksize</name> |
|
| 119 |
<value>32M</value> |
|
| 120 |
</property> |
|
| 121 |
<property> |
|
| 122 |
<name>mapred.output.compress</name> |
|
| 123 |
<value>false</value> |
|
| 124 |
</property> |
|
| 125 |
<property> |
|
| 126 |
<name>mapred.reduce.tasks.speculative.execution</name> |
|
| 127 |
<value>false</value> |
|
| 128 |
</property> |
|
| 129 |
<property> |
|
| 130 |
<name>mapred.reduce.tasks.speculative.execution</name> |
|
| 131 |
<value>false</value> |
|
| 132 |
</property> |
|
| 133 |
<property> |
|
| 134 |
<name>mapreduce.map.speculative</name> |
|
| 135 |
<value>false</value> |
|
| 136 |
</property> |
|
| 137 |
|
|
| 138 |
<!-- I/O FORMAT --> |
|
| 139 |
<!-- IMPORTANT: sets default delimeter used by text output writer. Required to fix issue with traling tab added between id and value in multiple outputs --> |
|
| 140 |
<property> |
|
| 141 |
<name>mapred.textoutputformat.separator</name> |
|
| 142 |
<value>${Stats_delim_Character}</value>
|
|
| 143 |
</property> |
|
| 144 |
<!-- ## Names of all output ports --> |
|
| 145 |
|
|
| 146 |
<property> |
|
| 147 |
<name>mapreduce.multipleoutputs</name> |
|
| 148 |
|
|
| 149 |
<value>${out1} ${out2} ${out3} ${out4} ${out5} ${out6} ${out7} ${out8} ${out9} ${out10} ${out11} ${out12} ${out13} ${out14} ${out15} ${out16} ${out17} ${out18} ${out19} ${out20}
|
|
| 150 |
</value> |
|
| 151 |
|
|
| 152 |
</property> |
|
| 153 |
<!-- datasource --> |
|
| 154 |
<property> |
|
| 155 |
<name>mapreduce.multipleoutputs.namedOutput.${out1}.key</name>
|
|
| 156 |
<value>org.apache.hadoop.io.Text</value> |
|
| 157 |
</property> |
|
| 158 |
<property> |
|
| 159 |
<name>mapreduce.multipleoutputs.namedOutput.${out1}.value</name>
|
|
| 160 |
<value>org.apache.hadoop.io.Text</value> |
|
| 161 |
</property> |
|
| 162 |
<property> |
|
| 163 |
<name>mapreduce.multipleoutputs.namedOutput.${out1}.format</name>
|
|
| 164 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 165 |
</value> |
|
| 166 |
</property> |
|
| 167 |
<!-- datasourceLanguage --> |
|
| 168 |
<property> |
|
| 169 |
<name>mapreduce.multipleoutputs.namedOutput.${out2}.key</name>
|
|
| 170 |
<value>org.apache.hadoop.io.Text</value> |
|
| 171 |
</property> |
|
| 172 |
<property> |
|
| 173 |
<name>mapreduce.multipleoutputs.namedOutput.${out2}.value</name>
|
|
| 174 |
<value>org.apache.hadoop.io.Text</value> |
|
| 175 |
</property> |
|
| 176 |
<property> |
|
| 177 |
<name>mapreduce.multipleoutputs.namedOutput.${out2}.format</name>
|
|
| 178 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 179 |
</value> |
|
| 180 |
</property> |
|
| 181 |
|
|
| 182 |
|
|
| 183 |
|
|
| 184 |
<!-- datasourceOrganization --> |
|
| 185 |
<property> |
|
| 186 |
<name>mapreduce.multipleoutputs.namedOutput.${out3}.key</name>
|
|
| 187 |
<value>org.apache.hadoop.io.Text</value> |
|
| 188 |
</property> |
|
| 189 |
<property> |
|
| 190 |
<name>mapreduce.multipleoutputs.namedOutput.${out3}.value</name>
|
|
| 191 |
<value>org.apache.hadoop.io.Text</value> |
|
| 192 |
</property> |
|
| 193 |
<property> |
|
| 194 |
<name>mapreduce.multipleoutputs.namedOutput.${out3}.format</name>
|
|
| 195 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 196 |
</value> |
|
| 197 |
</property> |
|
| 198 |
|
|
| 199 |
<!-- datasourceTopic --> |
|
| 200 |
<property> |
|
| 201 |
<name>mapreduce.multipleoutputs.namedOutput.${out4}.key</name>
|
|
| 202 |
<value>org.apache.hadoop.io.Text</value> |
|
| 203 |
</property> |
|
| 204 |
<property> |
|
| 205 |
<name>mapreduce.multipleoutputs.namedOutput.${out4}.value</name>
|
|
| 206 |
<value>org.apache.hadoop.io.Text</value> |
|
| 207 |
</property> |
|
| 208 |
<property> |
|
| 209 |
<name>mapreduce.multipleoutputs.namedOutput.${out4}.format</name>
|
|
| 210 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 211 |
</value> |
|
| 212 |
</property> |
|
| 213 |
|
|
| 214 |
<!-- resultDatasource --> |
|
| 215 |
<property> |
|
| 216 |
<name>mapreduce.multipleoutputs.namedOutput.${out5}.key</name>
|
|
| 217 |
<value>org.apache.hadoop.io.Text</value> |
|
| 218 |
</property> |
|
| 219 |
<property> |
|
| 220 |
<name>mapreduce.multipleoutputs.namedOutput.${out5}.value</name>
|
|
| 221 |
<value>org.apache.hadoop.io.Text</value> |
|
| 222 |
</property> |
|
| 223 |
<property> |
|
| 224 |
<name>mapreduce.multipleoutputs.namedOutput.${out5}.format</name>
|
|
| 225 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 226 |
</value> |
|
| 227 |
</property> |
|
| 228 |
<!-- organization --> |
|
| 229 |
<property> |
|
| 230 |
<name>mapreduce.multipleoutputs.namedOutput.${out6}.key</name>
|
|
| 231 |
<value>org.apache.hadoop.io.Text</value> |
|
| 232 |
</property> |
|
| 233 |
<property> |
|
| 234 |
<name>mapreduce.multipleoutputs.namedOutput.${out6}.value</name>
|
|
| 235 |
<value>org.apache.hadoop.io.Text</value> |
|
| 236 |
</property> |
|
| 237 |
<property> |
|
| 238 |
<name>mapreduce.multipleoutputs.namedOutput.${out6}.format</name>
|
|
| 239 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 240 |
</value> |
|
| 241 |
</property> |
|
| 242 |
|
|
| 243 |
<!-- projectOrganization --> |
|
| 244 |
<property> |
|
| 245 |
<name>mapreduce.multipleoutputs.namedOutput.${out7}.key</name>
|
|
| 246 |
<value>org.apache.hadoop.io.Text</value> |
|
| 247 |
</property> |
|
| 248 |
<property> |
|
| 249 |
<name>mapreduce.multipleoutputs.namedOutput.${out7}.value</name>
|
|
| 250 |
<value>org.apache.hadoop.io.Text</value> |
|
| 251 |
</property> |
|
| 252 |
<property> |
|
| 253 |
<name>mapreduce.multipleoutputs.namedOutput.${out7}.format</name>
|
|
| 254 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 255 |
</value> |
|
| 256 |
</property> |
|
| 257 |
<!-- resultProject --> |
|
| 258 |
<property> |
|
| 259 |
<name>mapreduce.multipleoutputs.namedOutput.${out8}.key</name>
|
|
| 260 |
<value>org.apache.hadoop.io.Text</value> |
|
| 261 |
</property> |
|
| 262 |
<property> |
|
| 263 |
<name>mapreduce.multipleoutputs.namedOutput.${out8}.value</name>
|
|
| 264 |
<value>org.apache.hadoop.io.Text</value> |
|
| 265 |
</property> |
|
| 266 |
<property> |
|
| 267 |
<name>mapreduce.multipleoutputs.namedOutput.${out8}.format</name>
|
|
| 268 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 269 |
</value> |
|
| 270 |
</property> |
|
| 271 |
|
|
| 272 |
<!-- project --> |
|
| 273 |
<property> |
|
| 274 |
<name>mapreduce.multipleoutputs.namedOutput.${out9}.key</name>
|
|
| 275 |
<value>org.apache.hadoop.io.Text</value> |
|
| 276 |
</property> |
|
| 277 |
<property> |
|
| 278 |
<name>mapreduce.multipleoutputs.namedOutput.${out9}.value</name>
|
|
| 279 |
<value>org.apache.hadoop.io.Text</value> |
|
| 280 |
</property> |
|
| 281 |
<property> |
|
| 282 |
<name>mapreduce.multipleoutputs.namedOutput.${out9}.format</name>
|
|
| 283 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 284 |
</value> |
|
| 285 |
</property> |
|
| 286 |
|
|
| 287 |
<!-- resultConcept --> |
|
| 288 |
<property> |
|
| 289 |
<name>mapreduce.multipleoutputs.namedOutput.${out10}.key</name>
|
|
| 290 |
<value>org.apache.hadoop.io.Text</value> |
|
| 291 |
</property> |
|
| 292 |
<property> |
|
| 293 |
<name>mapreduce.multipleoutputs.namedOutput.${out10}.value</name>
|
|
| 294 |
<value>org.apache.hadoop.io.Text</value> |
|
| 295 |
</property> |
|
| 296 |
<property> |
|
| 297 |
<name>mapreduce.multipleoutputs.namedOutput.${out10}.format</name>
|
|
| 298 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 299 |
</value> |
|
| 300 |
</property> |
|
| 301 |
|
|
| 302 |
<!-- resultClaim --> |
|
| 303 |
<property> |
|
| 304 |
<name>mapreduce.multipleoutputs.namedOutput.${out11}.key</name>
|
|
| 305 |
<value>org.apache.hadoop.io.Text</value> |
|
| 306 |
</property> |
|
| 307 |
<property> |
|
| 308 |
<name>mapreduce.multipleoutputs.namedOutput.${out11}.value</name>
|
|
| 309 |
<value>org.apache.hadoop.io.Text</value> |
|
| 310 |
</property> |
|
| 311 |
<property> |
|
| 312 |
<name>mapreduce.multipleoutputs.namedOutput.${out11}.format</name>
|
|
| 313 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 314 |
</value> |
|
| 315 |
</property> |
|
| 316 |
|
|
| 317 |
<!-- resultClassification --> |
|
| 318 |
<property> |
|
| 319 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.key</name>
|
|
| 320 |
<value>org.apache.hadoop.io.Text</value> |
|
| 321 |
</property> |
|
| 322 |
<property> |
|
| 323 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.value</name>
|
|
| 324 |
<value>org.apache.hadoop.io.Text</value> |
|
| 325 |
</property> |
|
| 326 |
<property> |
|
| 327 |
<name>mapreduce.multipleoutputs.namedOutput.${out12}.format</name>
|
|
| 328 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 329 |
</value> |
|
| 330 |
</property> |
|
| 331 |
|
|
| 332 |
<!-- resultLanguage --> |
|
| 333 |
<property> |
|
| 334 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.key</name>
|
|
| 335 |
<value>org.apache.hadoop.io.Text</value> |
|
| 336 |
</property> |
|
| 337 |
<property> |
|
| 338 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.value</name>
|
|
| 339 |
<value>org.apache.hadoop.io.Text</value> |
|
| 340 |
</property> |
|
| 341 |
<property> |
|
| 342 |
<name>mapreduce.multipleoutputs.namedOutput.${out13}.format</name>
|
|
| 343 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 344 |
</value> |
|
| 345 |
</property> |
|
| 346 |
|
|
| 347 |
<!-- resultProject --> |
|
| 348 |
<property> |
|
| 349 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.key</name>
|
|
| 350 |
<value>org.apache.hadoop.io.Text</value> |
|
| 351 |
</property> |
|
| 352 |
<property> |
|
| 353 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.value</name>
|
|
| 354 |
<value>org.apache.hadoop.io.Text</value> |
|
| 355 |
</property> |
|
| 356 |
<property> |
|
| 357 |
<name>mapreduce.multipleoutputs.namedOutput.${out14}.format</name>
|
|
| 358 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 359 |
</value> |
|
| 360 |
</property> |
|
| 361 |
<!-- resultResult --> |
|
| 362 |
<property> |
|
| 363 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.key</name>
|
|
| 364 |
<value>org.apache.hadoop.io.Text</value> |
|
| 365 |
</property> |
|
| 366 |
<property> |
|
| 367 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.value</name>
|
|
| 368 |
<value>org.apache.hadoop.io.Text</value> |
|
| 369 |
</property> |
|
| 370 |
<property> |
|
| 371 |
<name>mapreduce.multipleoutputs.namedOutput.${out15}.format</name>
|
|
| 372 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 373 |
</value> |
|
| 374 |
</property> |
|
| 375 |
<!-- resultTopic --> |
|
| 376 |
<property> |
|
| 377 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.key</name>
|
|
| 378 |
<value>org.apache.hadoop.io.Text</value> |
|
| 379 |
</property> |
|
| 380 |
<property> |
|
| 381 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.value</name>
|
|
| 382 |
<value>org.apache.hadoop.io.Text</value> |
|
| 383 |
</property> |
|
| 384 |
<property> |
|
| 385 |
<name>mapreduce.multipleoutputs.namedOutput.${out16}.format</name>
|
|
| 386 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 387 |
</value> |
|
| 388 |
</property> |
|
| 389 |
|
|
| 390 |
<!-- resultDatasource --> |
|
| 391 |
<property> |
|
| 392 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.key</name>
|
|
| 393 |
<value>org.apache.hadoop.io.Text</value> |
|
| 394 |
</property> |
|
| 395 |
<property> |
|
| 396 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.value</name>
|
|
| 397 |
<value>org.apache.hadoop.io.Text</value> |
|
| 398 |
</property> |
|
| 399 |
<property> |
|
| 400 |
<name>mapreduce.multipleoutputs.namedOutput.${out17}.format</name>
|
|
| 401 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 402 |
</value> |
|
| 403 |
</property> |
|
| 404 |
|
|
| 405 |
|
|
| 406 |
|
|
| 407 |
<!-- result --> |
|
| 408 |
<property> |
|
| 409 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.key</name>
|
|
| 410 |
<value>org.apache.hadoop.io.Text</value> |
|
| 411 |
</property> |
|
| 412 |
<property> |
|
| 413 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.value</name>
|
|
| 414 |
<value>org.apache.hadoop.io.Text</value> |
|
| 415 |
</property> |
|
| 416 |
<property> |
|
| 417 |
<name>mapreduce.multipleoutputs.namedOutput.${out18}.format</name>
|
|
| 418 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 419 |
</value> |
|
| 420 |
</property> |
|
| 421 |
|
|
| 422 |
<!-- claim --> |
|
| 423 |
<property> |
|
| 424 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.key</name>
|
|
| 425 |
<value>org.apache.hadoop.io.Text</value> |
|
| 426 |
</property> |
|
| 427 |
<property> |
|
| 428 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.value</name>
|
|
| 429 |
<value>org.apache.hadoop.io.Text</value> |
|
| 430 |
</property> |
|
| 431 |
<property> |
|
| 432 |
<name>mapreduce.multipleoutputs.namedOutput.${out19}.format</name>
|
|
| 433 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 434 |
</value> |
|
| 435 |
</property> |
|
| 436 |
<!-- cncept --> |
|
| 437 |
<property> |
|
| 438 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.key</name>
|
|
| 439 |
<value>org.apache.hadoop.io.Text</value> |
|
| 440 |
</property> |
|
| 441 |
<property> |
|
| 442 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.value</name>
|
|
| 443 |
<value>org.apache.hadoop.io.Text</value> |
|
| 444 |
</property> |
|
| 445 |
<property> |
|
| 446 |
<name>mapreduce.multipleoutputs.namedOutput.${out20}.format</name>
|
|
| 447 |
<value>org.apache.hadoop.mapreduce.lib.output.TextOutputFormat |
|
| 448 |
</value> |
|
| 449 |
</property> |
|
| 450 |
|
|
| 451 |
|
|
| 452 |
<!-- ## Classes of mapper and reducer --> |
|
| 453 |
|
|
| 454 |
<property> |
|
| 455 |
<name>mapreduce.map.class</name> |
|
| 456 |
<value>eu.dnetlib.data.mapreduce.hbase.statsExport.StatsMapper |
|
| 457 |
</value> |
|
| 458 |
</property> |
|
| 459 |
<property> |
|
| 460 |
<name>mapreduce.reduce.class</name> |
|
| 461 |
<value>eu.dnetlib.data.mapreduce.hbase.statsExport.StatsReducer |
|
| 462 |
</value> |
|
| 463 |
</property> |
|
| 464 |
<property> |
|
| 465 |
<name>io.serializations</name> |
|
| 466 |
<value>org.apache.hadoop.io.serializer.WritableSerialization |
|
| 467 |
</value> |
|
| 468 |
</property> |
|
| 469 |
<!-- ## Custom config --> |
|
| 470 |
|
|
| 471 |
<!--delim character used to seperate fields in hdfs dump files <property> --> |
|
| 472 |
<property> |
|
| 473 |
<name>stats.delim</name> |
|
| 474 |
<value>${Stats_delim_Character}</value>
|
|
| 475 |
</property> |
|
| 476 |
<!--default string for Null String Values --> |
|
| 477 |
<property> |
|
| 478 |
<name>stats.nullString</name> |
|
| 479 |
<value>${Stats_null_String_Field}</value>
|
|
| 480 |
</property> |
|
| 481 |
<!--default string for Null Numeric Values --> |
|
| 482 |
<property> |
|
| 483 |
<name>stats.nullNum</name> |
|
| 484 |
<value>${Stats_null_Numeric_Field}</value>
|
|
| 485 |
</property> |
|
| 486 |
<property> |
|
| 487 |
<name>stats.enclChar</name> |
|
| 488 |
<value>${Stats_enclosing_Character}</value>
|
|
| 489 |
</property> |
|
| 490 |
|
|
| 491 |
|
|
| 492 |
<!--source hbase table --> |
|
| 493 |
<property> |
|
| 494 |
<name>hbase.mapreduce.inputtable</name> |
|
| 495 |
<value>${Stats_Hbase_Source_Table}</value>
|
|
| 496 |
</property> |
|
| 497 |
<property> |
|
| 498 |
<!-- mapping of protos entities to tables in the relDB --> |
|
| 499 |
<name>stats.dbTablesMap</name> |
|
| 500 |
<value>${Stats_db_table_map}</value>
|
|
| 501 |
</property> |
|
| 502 |
|
|
| 503 |
<!-- This directory does not correspond to a data store. In fact, this directory only contains multiple data stores. It has to be set to the name of the workflow node. --> |
|
| 504 |
<property> |
|
| 505 |
<name>mapred.output.dir</name> |
|
| 506 |
<value>${Stats_output_Path}</value>
|
|
| 507 |
</property> |
|
| 508 |
<property> |
|
| 509 |
<name>stats.indexConf</name> |
|
| 510 |
<value>${Stats_indexConf}</value>
|
|
| 511 |
</property> |
|
| 512 |
<!-- ## Workflow node parameters --> |
|
| 513 |
<property> |
|
| 514 |
<name>mapred.reduce.tasks</name> |
|
| 515 |
<value>${numReducers}</value>
|
|
| 516 |
</property> |
|
| 517 |
</configuration> |
|
| 518 |
</map-reduce> |
|
| 519 |
<ok to="exportContext" /> |
|
| 520 |
<error to="fail" /> |
|
| 521 |
</action> |
|
| 522 |
|
|
| 523 |
|
|
| 524 |
<action name="exportContext"> |
|
| 525 |
<java> |
|
| 526 |
|
|
| 527 |
<prepare> |
|
| 528 |
</prepare> |
|
| 529 |
<configuration> |
|
| 530 |
<property> |
|
| 531 |
<name>mapred.job.queue.name</name> |
|
| 532 |
<value>${queueName}</value>
|
|
| 533 |
</property> |
|
| 534 |
</configuration> |
|
| 535 |
|
|
| 536 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 537 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 538 |
<arg>eu.dnetlib.iis.core.workflows.stats.ExportContextWrapper</arg> |
|
| 539 |
<arg>-PStats_output_Path=${Stats_output_Path}</arg>
|
|
| 540 |
<arg>-PStats_ContextResourceXML=${ContextResourceXML}</arg>
|
|
| 541 |
|
|
| 542 |
</java> |
|
| 543 |
<ok to="prepareDatabase" /> |
|
| 544 |
<error to="fail" /> |
|
| 545 |
</action> |
|
| 546 |
|
|
| 547 |
<action name="prepareDatabase"> |
|
| 548 |
<java> |
|
| 549 |
|
|
| 550 |
<prepare> |
|
| 551 |
</prepare> |
|
| 552 |
<configuration> |
|
| 553 |
<property> |
|
| 554 |
<name>mapred.job.queue.name</name> |
|
| 555 |
<value>${queueName}</value>
|
|
| 556 |
</property> |
|
| 557 |
</configuration> |
|
| 558 |
|
|
| 559 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 560 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 561 |
<arg>eu.dnetlib.iis.core.workflows.stats.DBInitWrapper</arg> |
|
| 562 |
|
|
| 563 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 564 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 565 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 566 |
<arg>-PStats_db_Driver=${Stats_db_Driver}</arg>
|
|
| 567 |
|
|
| 568 |
</java> |
|
| 569 |
<ok to="sqoopImport" /> |
|
| 570 |
<error to="fail" /> |
|
| 571 |
</action> |
|
| 572 |
|
|
| 573 |
<action name="sqoopImport"> |
|
| 574 |
<java> |
|
| 575 |
<prepare> |
|
| 576 |
</prepare> |
|
| 577 |
<configuration> |
|
| 578 |
<property> |
|
| 579 |
<name>mapred.job.queue.name</name> |
|
| 580 |
<value>${queueName}</value>
|
|
| 581 |
</property> |
|
| 582 |
|
|
| 583 |
<property> |
|
| 584 |
<name>oozie.sqoop.log.level</name> |
|
| 585 |
<value>DEBUG</value> |
|
| 586 |
</property> |
|
| 587 |
|
|
| 588 |
</configuration> |
|
| 589 |
|
|
| 590 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 591 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 592 |
<arg>eu.dnetlib.iis.core.workflows.stats.SqoopWrapper</arg> |
|
| 593 |
|
|
| 594 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 595 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 596 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 597 |
|
|
| 598 |
<arg>-PStats_output_Path=${Stats_output_Path}</arg>
|
|
| 599 |
<arg>-PStats_sqoop_RecsPerStatement=${Stats_sqoop_RecsPerStatement}
|
|
| 600 |
</arg> |
|
| 601 |
<arg>-PStats_sqoop_ReducersCount=${Stats_sqoop_ReducersCount}</arg>
|
|
| 602 |
<arg>-PStats_sqoop_StatementPerTrans=${Stats_sqoop_StatementPerTrans}
|
|
| 603 |
</arg> |
|
| 604 |
<arg>-PStats_delim_Character=${Stats_delim_Character}</arg>
|
|
| 605 |
<arg>-PStats_db_table_map=${Stats_db_table_map}</arg>
|
|
| 606 |
<arg>-PStats_enclosing_Character=${Stats_enclosing_Character} </arg>
|
|
| 607 |
|
|
| 608 |
</java> |
|
| 609 |
<ok to="finalizeDatabase" /> |
|
| 610 |
<error to="fail" /> |
|
| 611 |
</action> |
|
| 612 |
|
|
| 613 |
<action name="finalizeDatabase"> |
|
| 614 |
<java> |
|
| 615 |
|
|
| 616 |
<prepare> |
|
| 617 |
</prepare> |
|
| 618 |
<configuration> |
|
| 619 |
<property> |
|
| 620 |
<name>mapred.job.queue.name</name> |
|
| 621 |
<value>${queueName}</value>
|
|
| 622 |
</property> |
|
| 623 |
</configuration> |
|
| 624 |
|
|
| 625 |
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
|
| 626 |
<arg>-SworkingDir=${workingDir}</arg>
|
|
| 627 |
<arg>eu.dnetlib.iis.core.workflows.stats.DBFinalizeWrapper</arg> |
|
| 628 |
<arg>-PStats_db_Url=${Stats_db_Url}</arg>
|
|
| 629 |
<arg>-PStats_db_User=${Stats_db_User}</arg>
|
|
| 630 |
<arg>-PStats_db_Pass=${Stats_db_Pass}</arg>
|
|
| 631 |
<arg>-PStats_db_Driver=${Stats_db_Driver}</arg>
|
|
| 632 |
|
|
| 633 |
|
|
| 634 |
</java> |
|
| 635 |
<ok to="end" /> |
|
| 636 |
<error to="fail" /> |
|
| 637 |
</action> |
|
| 638 |
<kill name="fail"> |
|
| 639 |
<message> |
|
| 640 |
Unfortunately, the process failed -- error message: |
|
| 641 |
[${wf:errorMessage(wf:lastErrorNode())}]
|
|
| 642 |
</message> |
|
| 643 |
</kill> |
|
| 644 |
<end name="end" /> |
|
| 645 |
</workflow-app> |
|
| modules/dnet-openaire-stats-workflow/src/main/resources/eu/dnetlib/iis/core/examples/simpleTest/oozie_app/workflow.xml | ||
|---|---|---|
| 1 |
<workflow-app name="test-core_examples_javamapreduce_stats" xmlns="uri:oozie:workflow:0.4"> |
|
| 2 |
<!-- map reduce job that exports hbase data and prepares them for import to the relation database used for statistics generation --> |
|
| 3 |
|
|
| 1 |
<workflow-app name="test " xmlns="uri:oozie:workflow:0.4"> |
|
| 2 |
|
|
| 4 | 3 |
<global> |
| 5 | 4 |
<job-tracker>${jobTracker}</job-tracker>
|
| 6 | 5 |
<name-node>${nameNode}</name-node>
|
| ... | ... | |
| 28 | 27 |
|
| 29 | 28 |
</java> |
| 30 | 29 |
</action> |
| 31 |
|
|
| 32 |
|
|
| 33 |
|
|
| 34 |
<action name='get-scanner'> |
|
| 35 |
<java> |
|
| 36 |
<main-class>eu.dnetlib.iis.core.workflows.stats.HbaseScannerGenerator |
|
| 37 |
</main-class> |
|
| 38 |
<!-- column families: --> |
|
| 39 |
|
|
| 40 |
<arg> |
|
| 41 |
-f datasource |
|
| 42 |
<!-- , datasourceOrganization_provision_provides ,organization, --> |
|
| 43 |
<!-- projectOrganization_participation_isParticipant, --> |
|
| 44 |
<!-- project --> |
|
| 45 |
<!-- ,projectOrganization_participation_hasParticipant --> |
|
| 46 |
<!-- , --> |
|
| 47 |
<!-- result --> |
|
| 48 |
<!-- , resultProject_outcome_produces, --> |
|
| 49 |
<!-- personResult_authorship_hasAuthor,resultResult_publicationDataset_isRelatedTo --> |
|
| 50 |
</arg> |
|
| 51 |
|
|
| 52 |
<capture-output /> |
|
| 53 |
</java> |
|
| 54 |
<ok to="mr_export" /> |
|
| 55 |
<error to="fail" /> |
|
| 56 |
</action> |
|
| 57 |
<action name="mr_export"> |
|
| 58 |
<map-reduce> |
|
| 59 |
|
|
| 60 |
<prepare> |
|
| 61 |
<delete path="${nameNode}${Stats_output_Path}" />
|
|
| 62 |
|
|
| 63 |
</prepare> |
|
| 64 |
<configuration> |
|
| 65 |
<property> |
|
| 66 |
<name>hbase.mapreduce.scan</name> |
|
| 67 |
<value>${wf:actionData('get-scanner')['scan']}</value>
|
|
| 68 |
</property> |
|
| 69 |
<property> |
|
| 70 |
<name>hbase.rootdir</name> |
|
| 71 |
<value>hdfs://nmis-hadoop-cluster/hbase</value> |
|
| 72 |
</property> |
|
| 73 |
|
|
| 74 |
<property> |
|
| 75 |
<name>hbase.security.authentication</name> |
|
| 76 |
<value>simple</value> |
|
| 77 |
</property> |
|
| 78 |
<!-- ZOOKEEPER --> |
|
| 79 |
|
|
| 80 |
<property> |
|
| 81 |
<name>hbase.zookeeper.quorum</name> |
|
| 82 |
<value> |
|
| 83 |
quorum1.t.hadoop.research-infrastructures.eu,quorum2.t.hadoop.research-infrastructures.eu,quorum3.t.hadoop.research-infrastructures.eu,quorum4.t.hadoop.research-infrastructures.eu,jobtracker.t.hadoop.research-infrastructures.eu |
|
| 84 |
</value> |
|
| 85 |
</property> |
|
| 86 |
<property> |
|
| 87 |
<name>zookeeper.znode.rootserver</name> |
|
| 88 |
<value>root-region-server</value> |
|
| 89 |
</property> |
|
| 90 |
|
|
| 91 |
<property> |
|
| 92 |
<name>hbase.zookeeper.property.clientPort</name> |
|
| 93 |
<value>2182</value> |
|
| 94 |
</property> |
|
| 95 |
|
|
| 96 |
|
|
| 97 |
<!-- MR IO --> |
|
| 98 |
|
|
| 99 |
|
|
| 100 |
<property> |
|
| 101 |
<name>mapreduce.inputformat.class</name> |
|
| 102 |
<value>org.apache.hadoop.hbase.mapreduce.TableInputFormat</value> |
|
| 103 |
</property> |
|
| 104 |
|
|
| 105 |
<property> |
|
| 106 |
<name>mapred.mapoutput.key.class</name> |
|
| 107 |
<value>org.apache.hadoop.io.Text</value> |
|
| 108 |
</property> |
|
| 109 |
<property> |
|
| 110 |
<name>mapred.mapoutput.value.class</name> |
|
| 111 |
<value>org.apache.hadoop.hbase.io.ImmutableBytesWritable</value> |
|
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