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<workflow-app xmlns="uri:oozie:workflow:0.4" name="mainworkflows_primary_main">
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<parameters>
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<property>
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<name>remove_sideproducts</name>
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<value>true</value>
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<description>flag indicating inference side products will be erased</description>
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</property>
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<property>
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<name>match_content_with_metadata</name>
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<value>true</value>
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<description>flag indicating contents should be filtered and their identifiers should be deduplicated against metadata entries retrieved from InformationSpace.
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This way only contents having metadata representation will be processed.
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To be disabled when processing new contents which metadata is not available in hbase or when original identifiers should be preserved (contents will not be filtered as well).</description>
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</property>
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<!-- processing modes -->
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<property>
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<name>active_metadataextraction_export</name>
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<value>false</value>
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<description>flag indicating metadata extraction export should be enabled</description>
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</property>
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<property>
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<name>active_referenceextraction_project</name>
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<value>false</value>
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<description>flag indicating project reference extraction should be enabled</description>
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</property>
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<property>
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<name>active_referenceextraction_dataset</name>
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<value>false</value>
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<description>flag indicating dataset reference extraction should be enabled</description>
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</property>
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<property>
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<!-- currently disabled by default -->
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<name>active_referenceextraction_researchinitiative</name>
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<value>false</value>
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<description>flag indicating researchinitiative reference extraction should be enabled</description>
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</property>
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<property>
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<!-- currently disabled by default -->
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<name>active_referenceextraction_pdb</name>
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<value>false</value>
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<description>flag indicating protein databank reference extraction should be enabled</description>
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</property>
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<property>
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<name>active_documentsclassification</name>
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<value>false</value>
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<description>flag indicating documents classification should be enabled</description>
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</property>
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<property>
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<name>active_documentssimilarity</name>
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<value>false</value>
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<description>flag indicating documents similarity should be enabled</description>
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</property>
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<property>
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<name>active_citationmatching</name>
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<value>false</value>
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<description>flag indicating citation matching should be enabled</description>
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</property>
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<property>
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<name>active_statistics</name>
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<value>false</value>
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<description>flag indicating statistics generation should be enabled</description>
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</property>
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<property>
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<name>active_websiteusage_analysis</name>
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<value>false</value>
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<description>flag indicating logs should be imported from HDFS log file into avro datastore
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and website usage analysis should be performed</description>
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</property>
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<property>
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<name>active_export_to_hbase</name>
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<value>true</value>
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<description>flag indicating hbase export should be performed</description>
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</property>
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<property>
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<name>active_export_to_json</name>
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<value>false</value>
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<description>flag indicating json export should be performed</description>
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</property>
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<!-- import concepts related -->
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<property>
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<name>import_islookup_service_location</name>
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<description>IS Lookup service location</description>
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</property>
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<property>
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<name>import_project_concepts_context_ids_csv</name>
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<value>fet-fp7,fet-h2020</value>
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<description>comma separated list of concepts context identifiers to be picked by ISLookup</description>
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</property>
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<!-- import metadata related -->
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<property>
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<name>import_hbase_input_table</name>
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<description>HBase input table holding InformationSpace, available on local cluster</description>
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</property>
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<property>
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<name>import_hbase_approved_datasources_csv</name>
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<value>$UNDEFINED$</value>
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<description>CSV list of datasource ids to be approved during import. Applied on result and person entities.</description>
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</property>
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<!-- import datacite related -->
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<property>
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<name>import_mdstore_service_location</name>
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<value>$UNDEFINED$</value>
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<description>MDStore service (not WSDL) location URL</description>
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</property>
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<property>
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<name>import_dataset_mdstore_ids_csv</name>
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<value>$UNDEFINED$</value>
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<description>MDStore identifier</description>
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</property>
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<!-- import content related -->
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<property>
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<name>import_content_object_store_location</name>
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<value>$UNDEFINED$</value>
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<description>object store service location required for content retrieval</description>
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</property>
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<property>
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<name>import_content_objectstores_csv</name>
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<value>$UNDEFINED$</value>
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<description>CSV list of object stores identifiers to be processed</description>
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</property>
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<property>
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<name>import_content_mimetypes_pdf</name>
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<value>pdf,application/pdf</value>
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<description>pdf mime types</description>
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</property>
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<property>
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<name>import_content_mimetypes_text</name>
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<value>text,text/plain</value>
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<description>text mime types</description>
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</property>
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<property>
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<name>import_content_mimetypes_html</name>
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<value>text/html</value>
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<description>html mime types</description>
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</property>
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<property>
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<name>import_content_mimetypes_xml_pmc</name>
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<value>xml</value>
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<description>xml pmc types</description>
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</property>
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<property>
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<name>import_content_mimetypes_wos</name>
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<value>file::WoS</value>
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<description>WoS types</description>
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</property>
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<!-- import timeouts related -->
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<property>
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<name>import_resultset_client_read_timeout</name>
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<value>60000</value>
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<description>resultset client read timeout</description>
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</property>
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<property>
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<name>import_content_connection_timeout</name>
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<value>60000</value>
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<description>import content connection timeout</description>
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</property>
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<property>
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<name>import_content_read_timeout</name>
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<value>60000</value>
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<description>import content read timeout</description>
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</property>
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<!-- import logs related -->
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<property>
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<name>portal_logs_location</name>
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<value>/cache/portal-piwik-logs</value>
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<description>portal log files HDFS location</description>
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</property>
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<!-- metadata extraction related -->
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<property>
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<name>metadataextraction_excluded_checksums</name>
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<value>$UNDEFINED$</value>
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<description>list of content checksums excluded from metadataextraction processing</description>
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</property>
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<property>
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<name>metadataextraction_max_file_size_mb</name>
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<value>500</value>
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<description>maximum allowed file size in Megabytes</description>
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</property>
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<property>
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<name>metadataextraction_default_cache_location</name>
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<value>/cache/metadataextraction</value>
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<description>metadata extraction HDFS cache location</description>
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</property>
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<property>
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<name>metadataextraction_processing_mode</name>
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<value>StreamingMetadataExtractorMapper</value>
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<description>metadata extraction processing mode</description>
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</property>
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<property>
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<name>metadataextraction_input_classname</name>
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<value>eu.dnetlib.iis.importer.auxiliary.schemas.DocumentContentUrl</value>
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<description>metadata extraction input classname</description>
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</property>
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<!-- export related -->
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<property>
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<name>export_action_hbase_table_name</name>
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<description>action manager hbase table name</description>
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</property>
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<property>
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<name>export_action_hbase_table_initialize</name>
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<description>flag indicating input table should be initialized</description>
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</property>
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<!-- action set id properties -->
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<property>
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<name>export_action_set_id</name>
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<value>$UNDEFINED$</value>
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<description>action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_dataset_similarities_websiteusage</name>
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<value>$UNDEFINED$</value>
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<description>dataset_similarities_websiteusage action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_person_similarities_websiteusage</name>
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<value>$UNDEFINED$</value>
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<description>person_similarities_websiteusage action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_person_statistics</name>
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<value>$UNDEFINED$</value>
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<description>person_statistics action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_project_statistics</name>
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<value>$UNDEFINED$</value>
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<description>project_statistics action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_document_similarities_standard</name>
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<value>$UNDEFINED$</value>
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<description>document_similarities_standard action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_document_similarities_websiteusage</name>
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<value>$UNDEFINED$</value>
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<description>document_similarities_websiteusage action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_document_statistics</name>
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<value>$UNDEFINED$</value>
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<description>document_statistics action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_document_classes</name>
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<value>$UNDEFINED$</value>
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<description>document_classes action-set identifier of exported data</description>
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</property>
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<property>
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<name>export_action_set_id_document_referencedProjects</name>
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<value>$UNDEFINED$</value>
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253
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<description>document_referencedProjects action-set identifier of exported data</description>
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</property>
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<property>
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256
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<name>export_action_set_id_document_referencedDatasets</name>
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257
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<value>$UNDEFINED$</value>
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258
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<description>document_referencedDatasets action-set identifier of exported data</description>
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259
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</property>
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<property>
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261
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<name>export_action_set_id_document_referencedDocuments</name>
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<value>$UNDEFINED$</value>
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263
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<description>document_referencedDocuments action-set identifier of exported data</description>
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</property>
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265
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<property>
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266
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<name>export_action_set_id_document_research_initiative</name>
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<value>$UNDEFINED$</value>
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<description>document research initiative action-set identifier of exported data</description>
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269
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</property>
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270
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<property>
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271
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<name>export_action_set_id_document_pdb</name>
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272
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<value>$UNDEFINED$</value>
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273
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<description>document to protein databank action-set identifier of exported data</description>
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274
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</property>
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275
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<!-- -->
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276
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<property>
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277
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<name>export_action_set_id_entity_dataset</name>
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278
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<value>$UNDEFINED$</value>
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279
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<description>action-set identifier of exported data containing dataset entities</description>
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280
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</property>
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281
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<property>
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282
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<name>export_action_hbase_remote_zookeeper_quorum</name>
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283
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<value>$UNDEFINED$</value>
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284
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<description>external hbase zookeeper quorum, set to empty value by default which means data will be exported to local hbase instance</description>
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285
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</property>
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286
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<property>
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287
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<name>export_action_hbase_remote_zookeeper_clientport</name>
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288
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<value>$UNDEFINED$</value>
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289
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<description>external hbase zookeeper client port, required only whe zookeeper quorum property is set</description>
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290
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</property>
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291
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<!-- trust level threshold section -->
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292
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<property>
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293
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<name>export_trust_level_threshold</name>
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294
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<value>$UNDEFINED$</value>
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295
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<description>default trust level threshold of exported data</description>
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296
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</property>
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297
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<property>
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298
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<name>export_trust_level_threshold_document_classes</name>
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299
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<value>$UNDEFINED$</value>
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300
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<description>document_classes trust level threshold</description>
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301
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</property>
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302
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<property>
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303
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<name>export_trust_level_threshold_document_referencedProjects</name>
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304
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<value>$UNDEFINED$</value>
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305
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<description>document_referencedProjects trust level threshold</description>
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306
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</property>
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307
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<property>
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308
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<name>export_trust_level_threshold_document_referencedDatasets</name>
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309
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<value>$UNDEFINED$</value>
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310
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<description>document_referencedDatasets trust level threshold</description>
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311
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</property>
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312
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<property>
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313
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<name>export_trust_level_threshold_document_pdb</name>
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314
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<value>$UNDEFINED$</value>
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315
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<description>document to protein databank trust level threshold</description>
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316
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</property>
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317
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<!-- -->
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318
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<property>
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319
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<name>export_documentssimilarity_threshold</name>
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320
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<value>$UNDEFINED$</value>
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321
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<description>documents similarity threshold value below which similarity export is omitted</description>
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322
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</property>
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323
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<property>
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324
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<name>export_referenceextraction_pdb_url_root</name>
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325
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<value>http://www.rcsb.org/pdb/explore/explore.do?structureId=</value>
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326
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<description>protein databank URL root part to be concatenated with pdb identifier when forming final URL</description>
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327
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</property>
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328
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<!-- working directory related -->
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329
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<property>
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330
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<name>execution_environment</name>
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331
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<value>primary</value>
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332
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<description>execution environment used for workingDir creation</description>
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333
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</property>
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334
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<property>
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335
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<name>workingDir</name>
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336
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<value>/user/${user.name}/iis/working_dirs/${execution_environment}</value>
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337
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<description>working directory</description>
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338
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</property>
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339
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</parameters>
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340
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341
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<global>
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342
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<job-tracker>${jobTracker}</job-tracker>
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343
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<name-node>${nameNode}</name-node>
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344
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<configuration>
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345
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<property>
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346
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<name>mapred.job.queue.name</name>
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347
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<value>${queueName}</value>
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348
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</property>
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349
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</configuration>
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350
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</global>
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351
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352
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<start to="init-workingDir"/>
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353
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354
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<action name="init-workingDir">
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355
|
<fs>
|
|
356
|
<delete path="${nameNode}${workingDir}" />
|
|
357
|
<mkdir path="${nameNode}${workingDir}" />
|
|
358
|
</fs>
|
|
359
|
<ok to="copy-version"/>
|
|
360
|
<error to="fail"/>
|
|
361
|
</action>
|
|
362
|
|
|
363
|
<action name="copy-version">
|
|
364
|
<distcp xmlns="uri:oozie:distcp-action:0.1">
|
|
365
|
<job-tracker>${jobTracker}</job-tracker>
|
|
366
|
<name-node>${nameNode}</name-node>
|
|
367
|
<arg>${wf:appPath()}/version.properties</arg>
|
|
368
|
<arg>${nameNode}${workingDir}</arg>
|
|
369
|
</distcp>
|
|
370
|
<ok to="import"/>
|
|
371
|
<error to="fail"/>
|
|
372
|
</action>
|
|
373
|
|
|
374
|
<action name="import">
|
|
375
|
<sub-workflow>
|
|
376
|
<app-path>${wf:appPath()}/mainworkflows_common_import</app-path>
|
|
377
|
<propagate-configuration/>
|
|
378
|
<configuration>
|
|
379
|
<property>
|
|
380
|
<name>workingDir</name>
|
|
381
|
<value>${workingDir}/mainworkflows_common_import/working_dir</value>
|
|
382
|
</property>
|
|
383
|
<!-- importing modes -->
|
|
384
|
<property>
|
|
385
|
<name>match_content_with_metadata</name>
|
|
386
|
<value>${match_content_with_metadata}</value>
|
|
387
|
</property>
|
|
388
|
<property>
|
|
389
|
<name>active_import_metadata</name>
|
|
390
|
<value>true</value>
|
|
391
|
</property>
|
|
392
|
<property>
|
|
393
|
<name>active_import_dataset</name>
|
|
394
|
<value>${active_referenceextraction_dataset}</value>
|
|
395
|
</property>
|
|
396
|
<property>
|
|
397
|
<name>active_import_concept</name>
|
|
398
|
<value>${active_referenceextraction_project}</value>
|
|
399
|
</property>
|
|
400
|
<property>
|
|
401
|
<name>active_ingest_pmc</name>
|
|
402
|
<!-- enabling when either citation matching is enabled or metadata export which may include pmc affiliations -->
|
|
403
|
<value>${active_citationmatching eq "true" or active_metadataextraction_export eq "true"}</value>
|
|
404
|
</property>
|
|
405
|
<!-- import metadata related -->
|
|
406
|
<property>
|
|
407
|
<name>hbase_input_table</name>
|
|
408
|
<value>${import_hbase_input_table}</value>
|
|
409
|
</property>
|
|
410
|
<property>
|
|
411
|
<name>hbase_approved_datasources_csv</name>
|
|
412
|
<value>${import_hbase_approved_datasources_csv}</value>
|
|
413
|
</property>
|
|
414
|
<!-- import datacite related -->
|
|
415
|
<property>
|
|
416
|
<name>mdstore_service_location</name>
|
|
417
|
<value>${import_mdstore_service_location}</value>
|
|
418
|
</property>
|
|
419
|
<property>
|
|
420
|
<name>dataset_mdstore_ids_csv</name>
|
|
421
|
<value>${import_dataset_mdstore_ids_csv}</value>
|
|
422
|
</property>
|
|
423
|
<!-- project concept related -->
|
|
424
|
<property>
|
|
425
|
<name>islookup_service_location</name>
|
|
426
|
<value>${import_islookup_service_location}</value>
|
|
427
|
</property>
|
|
428
|
<property>
|
|
429
|
<name>project_concepts_context_ids_csv</name>
|
|
430
|
<value>${import_project_concepts_context_ids_csv}</value>
|
|
431
|
</property>
|
|
432
|
<!-- import content related -->
|
|
433
|
<property>
|
|
434
|
<name>objectstore_service_location</name>
|
|
435
|
<value>${import_content_object_store_location}</value>
|
|
436
|
</property>
|
|
437
|
<property>
|
|
438
|
<name>approved_objectstores_csv</name>
|
|
439
|
<value>${import_content_objectstores_csv}</value>
|
|
440
|
</property>
|
|
441
|
<property>
|
|
442
|
<name>mimetypes_pdf</name>
|
|
443
|
<value>${import_content_mimetypes_pdf}</value>
|
|
444
|
</property>
|
|
445
|
<property>
|
|
446
|
<name>mimetypes_text</name>
|
|
447
|
<value>${import_content_mimetypes_text}</value>
|
|
448
|
</property>
|
|
449
|
<property>
|
|
450
|
<name>mimetypes_html</name>
|
|
451
|
<value>${import_content_mimetypes_html}</value>
|
|
452
|
</property>
|
|
453
|
<property>
|
|
454
|
<name>mimetypes_xml_pmc</name>
|
|
455
|
<value>${import_content_mimetypes_xml_pmc}</value>
|
|
456
|
</property>
|
|
457
|
<property>
|
|
458
|
<name>mimetypes_wos</name>
|
|
459
|
<value>${import_content_mimetypes_wos}</value>
|
|
460
|
</property>
|
|
461
|
<!-- import timeouts related -->
|
|
462
|
<property>
|
|
463
|
<name>resultset_client_read_timeout</name>
|
|
464
|
<value>${import_resultset_client_read_timeout}</value>
|
|
465
|
</property>
|
|
466
|
<property>
|
|
467
|
<name>content_connection_timeout</name>
|
|
468
|
<value>${import_content_connection_timeout}</value>
|
|
469
|
</property>
|
|
470
|
<property>
|
|
471
|
<name>content_read_timeout</name>
|
|
472
|
<value>${import_content_read_timeout}</value>
|
|
473
|
</property>
|
|
474
|
<!-- metadata extraction related are autmatically propagated-->
|
|
475
|
<!-- metadatainput and metadataextraction output subdirectory names -->
|
|
476
|
<property>
|
|
477
|
<name>metadataimport_output_name_document_meta</name>
|
|
478
|
<value>docmeta</value>
|
|
479
|
</property>
|
|
480
|
<property>
|
|
481
|
<name>metadataimport_output_name_document_project</name>
|
|
482
|
<value>docproject</value>
|
|
483
|
</property>
|
|
484
|
<property>
|
|
485
|
<name>metadataimport_output_name_project</name>
|
|
486
|
<value>project</value>
|
|
487
|
</property>
|
|
488
|
<property>
|
|
489
|
<name>metadataimport_output_name_person</name>
|
|
490
|
<value>person</value>
|
|
491
|
</property>
|
|
492
|
<property>
|
|
493
|
<name>metadataimport_output_name_dedup_mapping</name>
|
|
494
|
<value>dedupmapping</value>
|
|
495
|
</property>
|
|
496
|
<!-- output parameters -->
|
|
497
|
<property>
|
|
498
|
<name>output_extracted_document_metadata</name>
|
|
499
|
<value>${workingDir}/mainworkflows_common_import/extracted_document_metadata</value>
|
|
500
|
</property>
|
|
501
|
<property>
|
|
502
|
<name>output_metadataimport_root</name>
|
|
503
|
<value>${workingDir}/mainworkflows_common_import/metadataimport</value>
|
|
504
|
</property>
|
|
505
|
<property>
|
|
506
|
<name>output_dataset</name>
|
|
507
|
<value>${workingDir}/mainworkflows_common_import/dataset</value>
|
|
508
|
</property>
|
|
509
|
<property>
|
|
510
|
<name>output_dataset_to_mdstore</name>
|
|
511
|
<value>${workingDir}/mainworkflows_common_import/dataset_to_mdstore</value>
|
|
512
|
</property>
|
|
513
|
<property>
|
|
514
|
<name>output_citation_pmc</name>
|
|
515
|
<value>${workingDir}/mainworkflows_common_import/citation_pmc</value>
|
|
516
|
</property>
|
|
517
|
<property>
|
|
518
|
<name>output_document_text</name>
|
|
519
|
<value>${workingDir}/mainworkflows_common_import/document-text</value>
|
|
520
|
</property>
|
|
521
|
<property>
|
|
522
|
<name>output_project_concept</name>
|
|
523
|
<value>${workingDir}/mainworkflows_common_import/project-concept</value>
|
|
524
|
</property>
|
|
525
|
<property>
|
|
526
|
<name>output_wos</name>
|
|
527
|
<value>${workingDir}/mainworkflows_common_import/wos</value>
|
|
528
|
</property>
|
|
529
|
<property>
|
|
530
|
<name>output_faults</name>
|
|
531
|
<value>${workingDir}/mainworkflows_common_import/faults</value>
|
|
532
|
</property>
|
|
533
|
</configuration>
|
|
534
|
</sub-workflow>
|
|
535
|
<ok to="decision-import_logs"/>
|
|
536
|
<error to="fail" />
|
|
537
|
</action>
|
|
538
|
|
|
539
|
<decision name="decision-import_logs">
|
|
540
|
<switch>
|
|
541
|
<case to="import_logs">${active_websiteusage_analysis eq "true"}</case>
|
|
542
|
<default to="mainworkflows_primary_processing"/>
|
|
543
|
</switch>
|
|
544
|
</decision>
|
|
545
|
|
|
546
|
<action name="import_logs">
|
|
547
|
<sub-workflow>
|
|
548
|
<app-path>${wf:appPath()}/import_logs</app-path>
|
|
549
|
<propagate-configuration/>
|
|
550
|
<configuration>
|
|
551
|
<property>
|
|
552
|
<name>workingDir</name>
|
|
553
|
<value>${workingDir}/websiteusage_analysis/import_logs/working_dir</value>
|
|
554
|
</property>
|
|
555
|
<property>
|
|
556
|
<name>input</name>
|
|
557
|
<value>${portal_logs_location}</value>
|
|
558
|
</property>
|
|
559
|
<property>
|
|
560
|
<name>output</name>
|
|
561
|
<value>${workingDir}/websiteusage_analysis/import_logs/output</value>
|
|
562
|
</property>
|
|
563
|
</configuration>
|
|
564
|
</sub-workflow>
|
|
565
|
<ok to="mainworkflows_primary_processing" />
|
|
566
|
<error to="fail" />
|
|
567
|
</action>
|
|
568
|
|
|
569
|
<action name="mainworkflows_primary_processing">
|
|
570
|
<sub-workflow>
|
|
571
|
<app-path>${wf:appPath()}/mainworkflows_primary_processing</app-path>
|
|
572
|
<propagate-configuration/>
|
|
573
|
<configuration>
|
|
574
|
<property>
|
|
575
|
<name>input_document_metadata</name>
|
|
576
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/docmeta</value>
|
|
577
|
</property>
|
|
578
|
<property>
|
|
579
|
<name>input_document_to_project</name>
|
|
580
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/docproject</value>
|
|
581
|
</property>
|
|
582
|
<property>
|
|
583
|
<name>input_document_text</name>
|
|
584
|
<value>${workingDir}/mainworkflows_common_import/document-text</value>
|
|
585
|
</property>
|
|
586
|
<property>
|
|
587
|
<name>input_document_text_wos</name>
|
|
588
|
<value>${workingDir}/mainworkflows_common_import/wos</value>
|
|
589
|
</property>
|
|
590
|
<property>
|
|
591
|
<name>input_project</name>
|
|
592
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/project</value>
|
|
593
|
</property>
|
|
594
|
<property>
|
|
595
|
<name>input_person</name>
|
|
596
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/person</value>
|
|
597
|
</property>
|
|
598
|
<property>
|
|
599
|
<name>input_dataset</name>
|
|
600
|
<value>${workingDir}/mainworkflows_common_import/dataset</value>
|
|
601
|
</property>
|
|
602
|
<property>
|
|
603
|
<name>input_extracted_document_metadata</name>
|
|
604
|
<value>${workingDir}/mainworkflows_common_import/extracted_document_metadata</value>
|
|
605
|
</property>
|
|
606
|
<property>
|
|
607
|
<name>input_citation_pmc</name>
|
|
608
|
<value>${workingDir}/mainworkflows_common_import/citation_pmc</value>
|
|
609
|
</property>
|
|
610
|
<property>
|
|
611
|
<name>input_project_concept</name>
|
|
612
|
<value>${workingDir}/mainworkflows_common_import/project-concept</value>
|
|
613
|
</property>
|
|
614
|
<property>
|
|
615
|
<name>output_document_to_project</name>
|
|
616
|
<value>${workingDir}/exported/document_to_project</value>
|
|
617
|
</property>
|
|
618
|
<property>
|
|
619
|
<name>output_document_to_project_concepts</name>
|
|
620
|
<value>${workingDir}/exported/document_to_project_concepts</value>
|
|
621
|
</property>
|
|
622
|
<property>
|
|
623
|
<name>output_document_to_dataset</name>
|
|
624
|
<value>${workingDir}/exported/document_to_dataset</value>
|
|
625
|
</property>
|
|
626
|
<property>
|
|
627
|
<name>output_document_to_research_initiatives</name>
|
|
628
|
<value>${workingDir}/exported/document_to_research_initiatives</value>
|
|
629
|
</property>
|
|
630
|
<property>
|
|
631
|
<name>output_document_to_pdb</name>
|
|
632
|
<value>${workingDir}/exported/document_to_pdb</value>
|
|
633
|
</property>
|
|
634
|
<property>
|
|
635
|
<name>output_document_to_document_classes</name>
|
|
636
|
<value>${workingDir}/exported/document_to_document_classes</value>
|
|
637
|
</property>
|
|
638
|
<property>
|
|
639
|
<name>output_citation</name>
|
|
640
|
<value>${workingDir}/exported/citation</value>
|
|
641
|
</property>
|
|
642
|
<property>
|
|
643
|
<name>output_document_similarity</name>
|
|
644
|
<value>${workingDir}/exported/document_similarity</value>
|
|
645
|
</property>
|
|
646
|
<property>
|
|
647
|
<name>output_document_statistics</name>
|
|
648
|
<value>${workingDir}/exported/document_statistics</value>
|
|
649
|
</property>
|
|
650
|
<property>
|
|
651
|
<name>output_author_statistics</name>
|
|
652
|
<value>${workingDir}/exported/author_statistics</value>
|
|
653
|
</property>
|
|
654
|
<property>
|
|
655
|
<name>output_project_statistics</name>
|
|
656
|
<value>${workingDir}/exported/project_statistics</value>
|
|
657
|
</property>
|
|
658
|
</configuration>
|
|
659
|
</sub-workflow>
|
|
660
|
<ok to="decision-websiteusage_analysis"/>
|
|
661
|
<error to="fail" />
|
|
662
|
</action>
|
|
663
|
|
|
664
|
<!-- website usage analysis block -->
|
|
665
|
<decision name="decision-websiteusage_analysis">
|
|
666
|
<switch>
|
|
667
|
<case to="websiteusage-idextractor">${active_websiteusage_analysis eq "true"}</case>
|
|
668
|
<default to="skip-websiteusage"/>
|
|
669
|
</switch>
|
|
670
|
</decision>
|
|
671
|
|
|
672
|
<action name="websiteusage-idextractor">
|
|
673
|
<sub-workflow>
|
|
674
|
<app-path>${wf:appPath()}/transformers_idextractor</app-path>
|
|
675
|
<propagate-configuration/>
|
|
676
|
<configuration>
|
|
677
|
<property>
|
|
678
|
<name>workingDir</name>
|
|
679
|
<value>${workingDir}/websiteusage_analysis/transformers_idextractor/working_dir</value>
|
|
680
|
</property>
|
|
681
|
<property>
|
|
682
|
<name>input_document_metadata</name>
|
|
683
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/docmeta</value>
|
|
684
|
</property>
|
|
685
|
<property>
|
|
686
|
<name>output_identifier</name>
|
|
687
|
<value>${workingDir}/websiteusage_analysis/transformers_idextractor/output</value>
|
|
688
|
</property>
|
|
689
|
</configuration>
|
|
690
|
</sub-workflow>
|
|
691
|
<ok to="mainworkflows_websiteusage_document"/>
|
|
692
|
<error to="fail"/>
|
|
693
|
</action>
|
|
694
|
|
|
695
|
<action name="mainworkflows_websiteusage_document">
|
|
696
|
<sub-workflow>
|
|
697
|
<app-path>${wf:appPath()}/mainworkflows_websiteusage_document</app-path>
|
|
698
|
<propagate-configuration/>
|
|
699
|
<configuration>
|
|
700
|
<property>
|
|
701
|
<name>workingDir</name>
|
|
702
|
<value>${workingDir}/websiteusage_analysis/working_dir</value>
|
|
703
|
</property>
|
|
704
|
<property>
|
|
705
|
<name>input_logs</name>
|
|
706
|
<value>${workingDir}/websiteusage_analysis/import_logs/output</value>
|
|
707
|
</property>
|
|
708
|
<property>
|
|
709
|
<name>input_id_mapping</name>
|
|
710
|
<value>${workingDir}/mainworkflows_common_import/metadataimport/dedupmapping</value>
|
|
711
|
</property>
|
|
712
|
<property>
|
|
713
|
<name>input_document_id</name>
|
|
714
|
<value>${workingDir}/websiteusage_analysis/transformers_idextractor/output</value>
|
|
715
|
</property>
|
|
716
|
<property>
|
|
717
|
<name>output</name>
|
|
718
|
<value>${workingDir}/websiteusage_analysis/output</value>
|
|
719
|
</property>
|
|
720
|
</configuration>
|
|
721
|
</sub-workflow>
|
|
722
|
<ok to="decision-transform-metadataextraction-for-export"/>
|
|
723
|
<error to="fail"/>
|
|
724
|
</action>
|
|
725
|
|
|
726
|
<action name="skip-websiteusage">
|
|
727
|
<java>
|
|
728
|
<prepare>
|
|
729
|
<!-- notice: directory have to aligned with skipped action output -->
|
|
730
|
<delete path="${nameNode}${workingDir}/websiteusage_analysis" />
|
|
731
|
<mkdir path="${nameNode}${workingDir}/websiteusage_analysis" />
|
|
732
|
</prepare>
|
|
733
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
|
734
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
|
735
|
<arg>-C{websiteusage_analysis_document,
|
|
736
|
eu.dnetlib.iis.websiteusage.schemas.DocumentsWithWebsiteUsageSimilarities,
|
|
737
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
|
738
|
<arg>-Owebsiteusage_analysis_document=${workingDir}/websiteusage_analysis/output</arg>
|
|
739
|
</java>
|
|
740
|
<ok to="decision-transform-metadataextraction-for-export"/>
|
|
741
|
<error to="fail"/>
|
|
742
|
</action>
|
|
743
|
<!-- end of website usage analysis block -->
|
|
744
|
|
|
745
|
<decision name="decision-transform-metadataextraction-for-export">
|
|
746
|
<switch>
|
|
747
|
<case to="transformers_export_documentmetadata">${active_metadataextraction_export eq "true"}</case>
|
|
748
|
<default to="skip-transformers_export_documentmetadata"/>
|
|
749
|
</switch>
|
|
750
|
</decision>
|
|
751
|
|
|
752
|
<action name="transformers_export_documentmetadata">
|
|
753
|
<sub-workflow>
|
|
754
|
<app-path>${wf:appPath()}/transformers_export_documentmetadata</app-path>
|
|
755
|
<propagate-configuration/>
|
|
756
|
<configuration>
|
|
757
|
<property>
|
|
758
|
<name>workingDir</name>
|
|
759
|
<value>${workingDir}/transformers_export_documentmetadata/working_dir</value>
|
|
760
|
</property>
|
|
761
|
<property>
|
|
762
|
<name>input_extracted_metadata</name>
|
|
763
|
<value>${workingDir}/mainworkflows_common_import/extracted_document_metadata</value>
|
|
764
|
</property>
|
|
765
|
<property>
|
|
766
|
<name>output_metadata</name>
|
|
767
|
<value>${workingDir}/transformers_export_documentmetadata/output_metadata</value>
|
|
768
|
</property>
|
|
769
|
</configuration>
|
|
770
|
</sub-workflow>
|
|
771
|
<ok to="decision-export-to-hbase"/>
|
|
772
|
<error to="fail"/>
|
|
773
|
</action>
|
|
774
|
|
|
775
|
<action name="skip-transformers_export_documentmetadata">
|
|
776
|
<java>
|
|
777
|
<prepare>
|
|
778
|
<!-- notice: directory have to aligned with skipped action output -->
|
|
779
|
<delete path="${nameNode}${workingDir}/transformers_export_documentmetadata" />
|
|
780
|
<mkdir path="${nameNode}${workingDir}/transformers_export_documentmetadata" />
|
|
781
|
</prepare>
|
|
782
|
<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
|
|
783
|
<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg>
|
|
784
|
<arg>-C{document_metadata,
|
|
785
|
eu.dnetlib.iis.export.schemas.DocumentMetadata,
|
|
786
|
eu/dnetlib/iis/mainworkflows/data/empty.json}</arg>
|
|
787
|
<!-- notice: directory have to aligned with skipped action output -->
|
|
788
|
<arg>-Odocument_metadata=${workingDir}/transformers_export_documentmetadata/output_metadata</arg>
|
|
789
|
</java>
|
|
790
|
<ok to="decision-export-to-hbase"/>
|
|
791
|
<error to="fail"/>
|
|
792
|
</action>
|
|
793
|
|
|
794
|
<decision name="decision-export-to-hbase">
|
|
795
|
<switch>
|
|
796
|
<case to="export-to-hbase">${active_export_to_hbase eq "true"}</case>
|
|
797
|
<default to="decision-export-to-json"/>
|
|
798
|
</switch>
|
|
799
|
</decision>
|
|
800
|
|
|
801
|
<action name="export-to-hbase">
|
|
802
|
<sub-workflow>
|
|
803
|
<app-path>${wf:appPath()}/mainworkflows_common_export</app-path>
|
|
804
|
<propagate-configuration/>
|
|
805
|
<configuration>
|
|
806
|
<property>
|
|
807
|
<name>workingDir</name>
|
|
808
|
<value>${workingDir}/mainworkflows_common_export/working_dir</value>
|
|
809
|
</property>
|
|
810
|
<!-- input ports -->
|
|
811
|
<property>
|
|
812
|
<name>input_document_metadata</name>
|
|
813
|
<value>${workingDir}/transformers_export_documentmetadata/output_metadata</value>
|
|
814
|
</property>
|
|
815
|
<property>
|
|
816
|
<name>input_document_to_project</name>
|
|
817
|
<value>${workingDir}/exported/document_to_project</value>
|
|
818
|
</property>
|
|
819
|
<property>
|
|
820
|
<name>input_document_to_project_concepts</name>
|
|
821
|
<value>${workingDir}/exported/document_to_project_concepts</value>
|
|
822
|
</property>
|
|
823
|
<property>
|
|
824
|
<name>input_document_to_dataset</name>
|
|
825
|
<value>${workingDir}/exported/document_to_dataset</value>
|
|
826
|
</property>
|
|
827
|
<property>
|
|
828
|
<name>input_document_to_mdstore</name>
|
|
829
|
<value>${workingDir}/mainworkflows_common_import/dataset_to_mdstore</value>
|
|
830
|
</property>
|
|
831
|
<property>
|
|
832
|
<name>input_document_to_research_initiatives</name>
|
|
833
|
<value>${workingDir}/exported/document_to_research_initiatives</value>
|
|
834
|
</property>
|
|
835
|
<property>
|
|
836
|
<name>input_document_to_pdb</name>
|
|
837
|
<value>${workingDir}/exported/document_to_pdb</value>
|
|
838
|
</property>
|
|
839
|
<property>
|
|
840
|
<name>input_document_to_document_classes</name>
|
|
841
|
<value>${workingDir}/exported/document_to_document_classes</value>
|
|
842
|
</property>
|
|
843
|
<property>
|
|
844
|
<name>input_citations</name>
|
|
845
|
<value>${workingDir}/exported/citation</value>
|
|
846
|
</property>
|
|
847
|
<property>
|
|
848
|
<name>input_document_similarity</name>
|
|
849
|
<value>${workingDir}/exported/document_similarity</value>
|
|
850
|
</property>
|
|
851
|
<property>
|
|
852
|
<name>input_document_statistics</name>
|
|
853
|
<value>${workingDir}/exported/document_statistics</value>
|
|
854
|
</property>
|
|
855
|
<property>
|
|
856
|
<name>input_document_websiteusage_similarity</name>
|
|
857
|
<value>${workingDir}/websiteusage_analysis/output</value>
|
|
858
|
</property>
|
|
859
|
<property>
|
|
860
|
<name>input_author_statistics</name>
|
|
861
|
<value>${workingDir}/exported/author_statistics</value>
|
|
862
|
</property>
|
|
863
|
<property>
|
|
864
|
<name>input_project_statistics</name>
|
|
865
|
<value>${workingDir}/exported/project_statistics</value>
|
|
866
|
</property>
|
|
867
|
<!-- entities exporting modes -->
|
|
868
|
<property>
|
|
869
|
<name>active_export_referenceddataset_datasets</name>
|
|
870
|
<value>${active_referenceextraction_dataset}</value>
|
|
871
|
</property>
|
|
872
|
<property>
|
|
873
|
<name>active_export_referencedproject_entities</name>
|
|
874
|
<value>false</value>
|
|
875
|
</property>
|
|
876
|
<property>
|
|
877
|
<name>mdstore_service_location</name>
|
|
878
|
<value>${import_mdstore_service_location}</value>
|
|
879
|
</property>
|
|
880
|
<!-- export related -->
|
|
881
|
<property>
|
|
882
|
<name>action_hbase_table_name</name>
|
|
883
|
<value>${export_action_hbase_table_name}</value>
|
|
884
|
</property>
|
|
885
|
<property>
|
|
886
|
<name>action_hbase_table_initialize</name>
|
|
887
|
<value>${export_action_hbase_table_initialize}</value>
|
|
888
|
</property>
|
|
889
|
<!-- action set id properties -->
|
|
890
|
<property>
|
|
891
|
<name>action_set_id</name>
|
|
892
|
<value>${export_action_set_id}</value>
|
|
893
|
</property>
|
|
894
|
<property>
|
|
895
|
<name>action_set_id_dataset_similarities_websiteusage</name>
|
|
896
|
<value>${export_action_set_id_dataset_similarities_websiteusage}</value>
|
|
897
|
</property>
|
|
898
|
<property>
|
|
899
|
<name>action_set_id_person_similarities_websiteusage</name>
|
|
900
|
<value>${export_action_set_id_person_similarities_websiteusage}</value>
|
|
901
|
</property>
|
|
902
|
<property>
|
|
903
|
<name>action_set_id_person_statistics</name>
|
|
904
|
<value>${export_action_set_id_person_statistics}</value>
|
|
905
|
</property>
|
|
906
|
<property>
|
|
907
|
<name>action_set_id_project_statistics</name>
|
|
908
|
<value>${export_action_set_id_project_statistics}</value>
|
|
909
|
</property>
|
|
910
|
<property>
|
|
911
|
<name>action_set_id_document_similarities_standard</name>
|
|
912
|
<value>${export_action_set_id_document_similarities_standard}</value>
|
|
913
|
</property>
|
|
914
|
<property>
|
|
915
|
<name>action_set_id_document_similarities_websiteusage</name>
|
|
916
|
<value>${export_action_set_id_document_similarities_websiteusage}</value>
|
|
917
|
</property>
|
|
918
|
<property>
|
|
919
|
<name>action_set_id_document_statistics</name>
|
|
920
|
<value>${export_action_set_id_document_statistics}</value>
|
|
921
|
</property>
|
|
922
|
<property>
|
|
923
|
<name>action_set_id_document_classes</name>
|
|
924
|
<value>${export_action_set_id_document_classes}</value>
|
|
925
|
</property>
|
|
926
|
<property>
|
|
927
|
<name>action_set_id_document_referencedProjects</name>
|
|
928
|
<value>${export_action_set_id_document_referencedProjects}</value>
|
|
929
|
</property>
|
|
930
|
<property>
|
|
931
|
<name>action_set_id_document_referencedDatasets</name>
|
|
932
|
<value>${export_action_set_id_document_referencedDatasets}</value>
|
|
933
|
</property>
|
|
934
|
<property>
|
|
935
|
<name>action_set_id_document_referencedDocuments</name>
|
|
936
|
<value>${export_action_set_id_document_referencedDocuments}</value>
|
|
937
|
</property>
|
|
938
|
<property>
|
|
939
|
<name>action_set_id_document_research_initiative</name>
|
|
940
|
<value>${export_action_set_id_document_research_initiative}</value>
|
|
941
|
</property>
|
|
942
|
<property>
|
|
943
|
<name>action_set_id_document_pdb</name>
|
|
944
|
<value>${export_action_set_id_document_pdb}</value>
|
|
945
|
</property>
|
|
946
|
<property>
|
|
947
|
<name>action_set_id_entity_dataset</name>
|
|
948
|
<value>${export_action_set_id_entity_dataset}</value>
|
|
949
|
</property>
|
|
950
|
|
|
951
|
<property>
|
|
952
|
<name>trust_level_threshold</name>
|
|
953
|
<value>${export_trust_level_threshold}</value>
|
|
954
|
</property>
|
|
955
|
<property>
|
|
956
|
<name>trust_level_threshold_document_referencedProjects</name>
|
|
957
|
<value>${export_trust_level_threshold_document_referencedProjects}</value>
|
|
958
|
</property>
|
|
959
|
<property>
|
|
960
|
<name>trust_level_threshold_document_referencedDatasets</name>
|
|
961
|
<value>${export_trust_level_threshold_document_referencedDatasets}</value>
|
|
962
|
</property>
|
|
963
|
<property>
|
|
964
|
<name>trust_level_threshold_document_classes</name>
|
|
965
|
<value>${export_trust_level_threshold_document_classes}</value>
|
|
966
|
</property>
|
|
967
|
<property>
|
|
968
|
<name>trust_level_threshold_document_pdb</name>
|
|
969
|
<value>${export_trust_level_threshold_document_pdb}</value>
|
|
970
|
</property>
|
|
971
|
<property>
|
|
972
|
<name>action_hbase_remote_zookeeper_quorum</name>
|
|
973
|
<value>${export_action_hbase_remote_zookeeper_quorum}</value>
|
|
974
|
</property>
|
|
975
|
<property>
|
|
976
|
<name>action_hbase_remote_zookeeper_clientport</name>
|
|
977
|
<value>${export_action_hbase_remote_zookeeper_clientport}</value>
|
|
978
|
</property>
|
|
979
|
<property>
|
|
980
|
<name>documentssimilarity_threshold</name>
|
|
981
|
<value>${export_documentssimilarity_threshold}</value>
|
|
982
|
</property>
|
|
983
|
<property>
|
|
984
|
<name>referenceextraction_pdb_url_root</name>
|
|
985
|
<value>${export_referenceextraction_pdb_url_root}</value>
|
|
986
|
</property>
|
|
987
|
</configuration>
|
|
988
|
</sub-workflow>
|
|
989
|
<ok to="decision-export-to-json"/>
|
|
990
|
<error to="fail" />
|
|
991
|
</action>
|
|
992
|
|
|
993
|
<decision name="decision-export-to-json">
|
|
994
|
<switch>
|
|
995
|
<case to="export-to-json">${active_export_to_json eq "true"}</case>
|
|
996
|
<default to="end"/>
|
|
997
|
</switch>
|
|
998
|
</decision>
|
|
999
|
|
|
1000
|
<action name="export-to-json">
|
|
1001
|
<sub-workflow>
|
|
1002
|
<app-path>${wf:appPath()}/mainworkflows_common_export_to_json</app-path>
|
|
1003
|
<propagate-configuration/>
|
|
1004
|
<configuration>
|
|
1005
|
<!-- input ports -->
|
|
1006
|
<property>
|
|
1007
|
<name>input_document_metadata</name>
|
|
1008
|
<value>${workingDir}/transformers_export_documentmetadata/output_metadata</value>
|
|
1009
|
</property>
|
|
1010
|
<property>
|
|
1011
|
<name>input_document_to_project</name>
|
|
1012
|
<value>${workingDir}/exported/document_to_project</value>
|
|
1013
|
</property>
|
|
1014
|
<property>
|
|
1015
|
<name>input_document_to_project_concepts</name>
|
|
1016
|
<value>${workingDir}/exported/document_to_project_concepts</value>
|
|
1017
|
</property>
|
|
1018
|
<property>
|
|
1019
|
<name>input_document_to_dataset</name>
|
|
1020
|
<value>${workingDir}/exported/document_to_dataset</value>
|
|
1021
|
</property>
|
|
1022
|
<property>
|
|
1023
|
<name>input_document_to_mdstore</name>
|
|
1024
|
<value>${workingDir}/mainworkflows_common_import/dataset_to_mdstore</value>
|
|
1025
|
</property>
|
|
1026
|
<property>
|
|
1027
|
<name>input_document_to_research_initiatives</name>
|
|
1028
|
<value>${workingDir}/exported/document_to_research_initiatives</value>
|
|
1029
|
</property>
|
|
1030
|
<property>
|
|
1031
|
<name>input_document_to_pdb</name>
|
|
1032
|
<value>${workingDir}/exported/document_to_pdb</value>
|
|
1033
|
</property>
|
|
1034
|
<property>
|
|
1035
|
<name>input_document_to_document_classes</name>
|
|
1036
|
<value>${workingDir}/exported/document_to_document_classes</value>
|
|
1037
|
</property>
|
|
1038
|
<property>
|
|
1039
|
<name>input_citations</name>
|
|
1040
|
<value>${workingDir}/exported/citation</value>
|
|
1041
|
</property>
|
|
1042
|
<property>
|
|
1043
|
<name>input_document_similarity</name>
|
|
1044
|
<value>${workingDir}/exported/document_similarity</value>
|
|
1045
|
</property>
|
|
1046
|
<property>
|
|
1047
|
<name>input_document_statistics</name>
|
|
1048
|
<value>${workingDir}/exported/document_statistics</value>
|
|
1049
|
</property>
|
|
1050
|
<property>
|
|
1051
|
<name>input_document_websiteusage_similarity</name>
|
|
1052
|
<value>${workingDir}/websiteusage_analysis/output</value>
|
|
1053
|
</property>
|
|
1054
|
<property>
|
|
1055
|
<name>input_author_statistics</name>
|
|
1056
|
<value>${workingDir}/exported/author_statistics</value>
|
|
1057
|
</property>
|
|
1058
|
<property>
|
|
1059
|
<name>input_project_statistics</name>
|
|
1060
|
<value>${workingDir}/exported/project_statistics</value>
|
|
1061
|
</property>
|
|
1062
|
<property>
|
|
1063
|
<name>output_root</name>
|
|
1064
|
<value>${workingDir}/exported_as_json</value>
|
|
1065
|
</property>
|
|
1066
|
</configuration>
|
|
1067
|
</sub-workflow>
|
|
1068
|
<ok to="end"/>
|
|
1069
|
<error to="fail" />
|
|
1070
|
</action>
|
|
1071
|
|
|
1072
|
<kill name="fail">
|
|
1073
|
<message>Unfortunately, the process failed -- error message:
|
|
1074
|
[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
|
1075
|
</kill>
|
|
1076
|
<end name="end" />
|
|
1077
|
</workflow-app>
|