forked from D-Net/dnet-hadoop
added shell actions to download all 11 activities files from ORCID
This commit is contained in:
parent
a1861b9eaa
commit
1edcd53581
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@ -23,6 +23,7 @@ import org.mortbay.log.Log;
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public class ActivitiesDecompressor {
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private static final int MAX_XML_WORKS_PARSED = -1;
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private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000;
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public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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@ -127,7 +128,7 @@ public class ActivitiesDecompressor {
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Log.warn(e);
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}
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if ((counter % 100000) == 0) {
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if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) {
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Log.info("Current xml works parsed: " + counter);
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}
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@ -1,9 +1,75 @@
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<workflow-app name="Generate Orcid Authors DOIs Data" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="Gen Orcid Authors DOIs" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPath_activities</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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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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@ -18,16 +84,47 @@
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<delete path='${workingPath_activities}/output'/>
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<mkdir path='${workingPath_activities}/output'/>
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</fs>
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<ok to="fork_generate_orcid_authors_dois"/>
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<ok to="fork_gen_orcid_authors_dois"/>
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<error to="Kill"/>
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</action>
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<fork name = "fork_generate_orcid_authors_dois">
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<path start = "Generate_Orcid_Authors_DOIs_0"/>
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<path start = "Generate_Orcid_Authors_DOIs_1"/>
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<fork name = "fork_gen_orcid_authors_dois">
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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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<action name="Generate_Orcid_Authors_DOIs_0">
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<decision name="check_exist_on_hdfs_activities_0">
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<switch>
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<case to="Gen_Orcid_Authors_DOIs_0">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))}
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</case>
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<default to="Download_0" />
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</switch>
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</decision>
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<action name="Download_0">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_0"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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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@ -41,7 +138,29 @@
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<error to="Kill"/>
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</action>
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<action name="Generate_Orcid_Authors_DOIs_1">
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<decision name="check_exist_on_hdfs_activities_1">
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<switch>
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<case to="Gen_Orcid_Authors_DOIs_1">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))}
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</case>
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<default to="Download_1" />
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</switch>
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</decision>
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<action name="Download_1">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_1"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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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@ -55,7 +174,332 @@
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<error to="Kill"/>
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</action>
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<join name = "join_node" to = "End"/>
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<decision name="check_exist_on_hdfs_activities_2">
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<switch>
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<case to="Gen_Orcid_Authors_DOIs_2">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))}
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</case>
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<default to="Download_2" />
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</switch>
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</decision>
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<action name="Download_2">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_2"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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.orcid.OrcidAuthorsDOIsDataGen</main-class>
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<arg>-d</arg><arg>${workingPath_activities}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
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<arg>-o</arg><arg>output/authors_dois_2.seq</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="Gen_Orcid_Authors_DOIs_3">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))}
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</case>
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<default to="Download_3" />
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</switch>
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</decision>
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<action name="Download_3">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_3"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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.orcid.OrcidAuthorsDOIsDataGen</main-class>
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<arg>-d</arg><arg>${workingPath_activities}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
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<arg>-o</arg><arg>output/authors_dois_3.seq</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="Gen_Orcid_Authors_DOIs_4">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))}
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</case>
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<default to="Download_4" />
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</switch>
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</decision>
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<action name="Download_4">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_4"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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.orcid.OrcidAuthorsDOIsDataGen</main-class>
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<arg>-d</arg><arg>${workingPath_activities}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
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<arg>-o</arg><arg>output/authors_dois_4.seq</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="Gen_Orcid_Authors_DOIs_5">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))}
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</case>
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<default to="Download_5" />
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</switch>
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</decision>
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<action name="Download_5">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_5"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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.orcid.OrcidAuthorsDOIsDataGen</main-class>
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<arg>-d</arg><arg>${workingPath_activities}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
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<arg>-o</arg><arg>output/authors_dois_5.seq</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="Gen_Orcid_Authors_DOIs_6">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))}
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</case>
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<default to="Download_6" />
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</switch>
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</decision>
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<action name="Download_6">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${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="Gen_Orcid_Authors_DOIs_6"/>
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<error to="Kill"/>
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</action>
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<action name="Gen_Orcid_Authors_DOIs_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.orcid.OrcidAuthorsDOIsDataGen</main-class>
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<arg>-d</arg><arg>${workingPath_activities}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
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<arg>-o</arg><arg>output/authors_dois_6.seq</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="Gen_Orcid_Authors_DOIs_7">
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${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))}
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</case>
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<default to="Download_7" />
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</switch>
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</decision>
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<action name="Download_7">
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<shell xmlns="uri:oozie:shell-action:0.1">
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<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>bash</exec>
|
||||
<argument>-c</argument>
|
||||
<argument>${shell_cmd_7}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="Gen_Orcid_Authors_DOIs_7"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Orcid_Authors_DOIs_7">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
|
||||
<arg>-d</arg><arg>${workingPath_activities}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
|
||||
<arg>-o</arg><arg>output/authors_dois_7.seq</arg>
|
||||
</java>
|
||||
<ok to="join_node"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<decision name="check_exist_on_hdfs_activities_8">
|
||||
<switch>
|
||||
<case to="Gen_Orcid_Authors_DOIs_8">
|
||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))}
|
||||
</case>
|
||||
<default to="Download_8" />
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="Download_8">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>bash</exec>
|
||||
<argument>-c</argument>
|
||||
<argument>${shell_cmd_8}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="Gen_Orcid_Authors_DOIs_8"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Orcid_Authors_DOIs_8">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
|
||||
<arg>-d</arg><arg>${workingPath_activities}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
|
||||
<arg>-o</arg><arg>output/authors_dois_8.seq</arg>
|
||||
</java>
|
||||
<ok to="join_node"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<decision name="check_exist_on_hdfs_activities_9">
|
||||
<switch>
|
||||
<case to="Gen_Orcid_Authors_DOIs_9">
|
||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))}
|
||||
</case>
|
||||
<default to="Download_9" />
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="Download_9">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>bash</exec>
|
||||
<argument>-c</argument>
|
||||
<argument>${shell_cmd_9}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="Gen_Orcid_Authors_DOIs_9"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Orcid_Authors_DOIs_9">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
|
||||
<arg>-d</arg><arg>${workingPath_activities}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
|
||||
<arg>-o</arg><arg>output/authors_dois_9.seq</arg>
|
||||
</java>
|
||||
<ok to="join_node"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<decision name="check_exist_on_hdfs_activities_X">
|
||||
<switch>
|
||||
<case to="Gen_Orcid_Authors_DOIs_X">
|
||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))}
|
||||
</case>
|
||||
<default to="Download_X" />
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="Download_X">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>bash</exec>
|
||||
<argument>-c</argument>
|
||||
<argument>${shell_cmd_X}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="Gen_Orcid_Authors_DOIs_X"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Orcid_Authors_DOIs_X">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
|
||||
<arg>-d</arg><arg>${workingPath_activities}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
|
||||
<arg>-o</arg><arg>output/authors_dois_X.seq</arg>
|
||||
</java>
|
||||
<ok to="join_node"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name = "join_node" to = "End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue