514 lines
20 KiB
XML
514 lines
20 KiB
XML
<workflow-app name="Import Orcid Activities" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>shell_cmd_0</name>
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<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
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</property>
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<property>
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<name>shell_cmd_1</name>
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<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
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</property>
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<property>
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<name>shell_cmd_2</name>
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<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
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</property>
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<property>
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<name>shell_cmd_3</name>
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<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
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</property>
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<property>
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<name>shell_cmd_4</name>
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<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
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</property>
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<property>
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<name>shell_cmd_5</name>
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<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
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</property>
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<property>
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<name>shell_cmd_6</name>
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<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
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</property>
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<property>
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<name>shell_cmd_7</name>
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<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
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</property>
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<property>
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<name>shell_cmd_8</name>
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<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
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</property>
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<property>
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<name>shell_cmd_9</name>
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<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
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</property>
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<property>
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<name>shell_cmd_X</name>
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<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz
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</value>
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<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${workingPath}/no_doi_works/*'/>
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</fs>
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<ok to="fork_gen_orcid_author_work"/>
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<error to="Kill"/>
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</action>
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<fork name = "fork_gen_orcid_author_work">
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<path start = "check_exist_on_hdfs_activities_0"/>
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<path start = "check_exist_on_hdfs_activities_1"/>
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<path start = "check_exist_on_hdfs_activities_2"/>
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<path start = "check_exist_on_hdfs_activities_3"/>
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<path start = "check_exist_on_hdfs_activities_4"/>
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<path start = "check_exist_on_hdfs_activities_5"/>
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<path start = "check_exist_on_hdfs_activities_6"/>
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<path start = "check_exist_on_hdfs_activities_7"/>
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<path start = "check_exist_on_hdfs_activities_8"/>
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<path start = "check_exist_on_hdfs_activities_9"/>
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<path start = "check_exist_on_hdfs_activities_X"/>
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</fork>
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<decision name="check_exist_on_hdfs_activities_0">
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<switch>
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<case to="GenOrcidAuthorWork_0">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_0.tar.gz'))}
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</case>
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<default to="Download_0" />
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</switch>
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</decision>
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<action name="Download_0">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_0}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_0"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_0">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_0.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_1">
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<switch>
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<case to="GenOrcidAuthorWork_1">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_1.tar.gz'))}
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</case>
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<default to="Download_1" />
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</switch>
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</decision>
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<action name="Download_1">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_1}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_1"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_1">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_1.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_2">
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<switch>
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<case to="GenOrcidAuthorWork_2">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_2.tar.gz'))}
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</case>
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<default to="Download_2" />
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</switch>
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</decision>
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<action name="Download_2">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_2}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_2"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_2">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_2.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_3">
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<switch>
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<case to="GenOrcidAuthorWork_3">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_3.tar.gz'))}
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</case>
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<default to="Download_3" />
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</switch>
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</decision>
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<action name="Download_3">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_3}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_3"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_3">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_3.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_4">
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<switch>
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<case to="GenOrcidAuthorWork_4">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_4.tar.gz'))}
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</case>
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<default to="Download_4" />
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</switch>
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</decision>
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<action name="Download_4">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_4}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_4"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_4">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_4.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_5">
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<switch>
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<case to="GenOrcidAuthorWork_5">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_5.tar.gz'))}
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</case>
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<default to="Download_5" />
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</switch>
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</decision>
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<action name="Download_5">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_5}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_5"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_5">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_5.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_6">
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<switch>
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<case to="GenOrcidAuthorWork_6">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_6.tar.gz'))}
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</case>
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<default to="Download_6" />
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</switch>
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</decision>
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<action name="Download_6">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_6}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_6"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_6">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
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<arg>-ow</arg><arg>no_doi_works/works_6.seq</arg>
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<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
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</java>
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<ok to="join_node"/>
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<error to="Kill"/>
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</action>
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<decision name="check_exist_on_hdfs_activities_7">
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<switch>
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<case to="GenOrcidAuthorWork_7">
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${fs:exists(concat(workingPath,'/ORCID_2019_activites_7.tar.gz'))}
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</case>
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<default to="Download_7" />
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</switch>
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</decision>
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<action name="Download_7">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<exec>bash</exec>
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<argument>-c</argument>
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<argument>${shell_cmd_7}</argument>
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<capture-output/>
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</shell>
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<ok to="GenOrcidAuthorWork_7"/>
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<error to="Kill"/>
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</action>
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<action name="GenOrcidAuthorWork_7">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
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<arg>-w</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
|
|
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
|
|
<arg>-ow</arg><arg>no_doi_works/works_7.seq</arg>
|
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
</java>
|
|
<ok to="join_node"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<decision name="check_exist_on_hdfs_activities_8">
|
|
<switch>
|
|
<case to="GenOrcidAuthorWork_8">
|
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_8.tar.gz'))}
|
|
</case>
|
|
<default to="Download_8" />
|
|
</switch>
|
|
</decision>
|
|
|
|
<action name="Download_8">
|
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<exec>bash</exec>
|
|
<argument>-c</argument>
|
|
<argument>${shell_cmd_8}</argument>
|
|
<capture-output/>
|
|
</shell>
|
|
<ok to="GenOrcidAuthorWork_8"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<action name="GenOrcidAuthorWork_8">
|
|
<java>
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
|
<arg>-n</arg><arg>${nameNode}</arg>
|
|
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
|
|
<arg>-ow</arg><arg>no_doi_works/works_8.seq</arg>
|
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
</java>
|
|
<ok to="join_node"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<decision name="check_exist_on_hdfs_activities_9">
|
|
<switch>
|
|
<case to="GenOrcidAuthorWork_9">
|
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_9.tar.gz'))}
|
|
</case>
|
|
<default to="Download_9" />
|
|
</switch>
|
|
</decision>
|
|
|
|
<action name="Download_9">
|
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<exec>bash</exec>
|
|
<argument>-c</argument>
|
|
<argument>${shell_cmd_9}</argument>
|
|
<capture-output/>
|
|
</shell>
|
|
<ok to="GenOrcidAuthorWork_9"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<action name="GenOrcidAuthorWork_9">
|
|
<java>
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
|
<arg>-n</arg><arg>${nameNode}</arg>
|
|
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
|
|
<arg>-ow</arg><arg>no_doi_works/works_9.seq</arg>
|
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
</java>
|
|
<ok to="join_node"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<decision name="check_exist_on_hdfs_activities_X">
|
|
<switch>
|
|
<case to="GenOrcidAuthorWork_X">
|
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_X.tar.gz'))}
|
|
</case>
|
|
<default to="Download_X" />
|
|
</switch>
|
|
</decision>
|
|
|
|
<action name="Download_X">
|
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<exec>bash</exec>
|
|
<argument>-c</argument>
|
|
<argument>${shell_cmd_X}</argument>
|
|
<capture-output/>
|
|
</shell>
|
|
<ok to="GenOrcidAuthorWork_X"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<action name="GenOrcidAuthorWork_X">
|
|
<java>
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
<name-node>${nameNode}</name-node>
|
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
|
<arg>-n</arg><arg>${nameNode}</arg>
|
|
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
|
|
<arg>-ow</arg><arg>no_doi_works/works_X.seq</arg>
|
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
</java>
|
|
<ok to="join_node"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<join name = "join_node" to = "End"/>
|
|
|
|
<end name="End"/>
|
|
</workflow-app> |