D-Net

reverting 37153 rev change by removing oozie-sharelib-distcp dependency from pom.xml file and relying on oozie.use.system.libpath=true set among job.properties

updating job.properties

merging trunk changes with IIS-CDH-5.3.0 branch

#1197 introducing job.properties changes aligning paths to rumcajs cluster HDFS structure

creating IIS-CDH-5.3.0 branch

#1195 removing obsolete ports docreation and datasetid from hbase mapred import, removing references to those ports in workflow.xml files, updating transformer by removing filtering by datasetid due to decisions made in #1072

#1176 defining remove_sideproducts property in workflows headers

#1176 introducing side products removal in common import by maintaining remove_sideproducts flag set to true by default.
Notice: do not provide any output directory location pointing to workingDir subdirectory!

removing duplicate collapser import and aligning worklfow definition

#1172 introducing support for active_export parameter in both preprocessing and primary workflows

updating job.properties

#1153 utilizing ${user.name} placeholder in ${workingDir} generation process, copying version.properties from oozie_app to mark execution environment with application version

#1147 introducing HTML import and HTML plaintext ingestion in main workflows: primary and preprocessing

updating job.properties

#1133 dropping useless workfing_dir creation for java nodes

#118 fixing typos

updating job.properties

#118 introducing website usage analysis as integral part of primary workflow

updating job.properties

#118 propagating configuration in main workflow.xml

#118 updating job.properties

comments added

#118 introducing mainworkflows_websiteusage_document_main workflow binding all subworkflows required to process logs and generate document similarities

#1083 enabling webcrawl ingester module extracting FX field from plaintext before executing project reference extraction

updating default job properties

#1070 updating import_project_concepts_context_ids_csv default value to "fet-fp7,fet-h2020"

#1070 introducing support for multiple context identifiers, replacing import_project_concepts_context_id IIS input parameter with import_project_concepts_context_ids_csv

updating job.properties

#1072 transition fix: replacing forking_skip_imported_data with export

#1072 dropping IIS feature filtering out already existing project and dataset references from IIS export

updating job.properties

updating job.properties

#919 renaming DocumentToResearchInitiative to DocumentToConceptId and DocumentToResearchInitiatives to DocumentToConceptIds

#1022 introducing PMC extracted document metadata collapser removing duplicates before sending output to PMC citation ingestion module

#919 enabling concepts matching for FET projects in mainworkflows: import, export, primary and preprocessing

#1017 accepting ExtractedDocumentMetadata instead of DocumentText at PMC citation ingestion input. Aliging integration test and importer workflow.

#1022 introducing extracted document metadata collapser at importing phase.
Propagating extracted document mentadata (including PMC ingested metadata) to processing part of workflow what can be exploited by citation matching module.
Introducing citations collapser in last stage of processing phase collapsing ingested citations with matched citations.

#1017 introducing new PMC metadata ingestion currently extracing references, journal and pages fields.
Replacing DOM/XPath based citations ingestion with much faster SAX version. Changing pmidtooaid transformer utilizing ExtractedDocumentMetadata instead of parsing XML file. Enabling PMC metadata ingestion in common/import.

#963 propagating dataset -> mdstore from import to exporting phase: importer produces DocumentToMDStore datasetore utilized by exporter module. Updating transformer definition to handle DocumentToMDStore instead of Identifier schema

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties: adding metadataextraction_excluded_checksums=4f5cc34f137de4dc89766a9366ca66de,6495a568200b1cee40baa00072b1800a

updating job.properties

introducing support for active_existence_filter, set to true by default. Setting this parameter to false allows processing contents not having its counterpart among metadata records retrieved from HBase. This solution was required to e.g. process ubiquity contents which were not present in HBase dump metadata.

updating job.properties

renaming metadataextraction_excluded_ids to more appropriate metadataextraction_excluded_checksums

#913 introducing support for max file size parameter, currently checked against Content-Lenght header

updating job.properties

#757 hooking up ingest_pmc_idmapping_pmidtooaid subworkflow with mainworkflows/common/import. From now on citations are matched by pmid as well.

updating job.properties

#883 providing blacklisted_objectstores_csv input parameter set to $UNDEFINED$ value by default

updating job.properties

input port name fix: input_citation->input_citations

introducing merge_body_with_updates flag support in common/import, setting to true in statistics workflow

introducing regex support in result approver to support iis::* kind of provenance, updating workflow definitions with proper regex values

#840 moving IdentifierMapping from importer to common package

#840 renaming DeduplicationMapping to more generic IdentifierMapping

#757 aligning common importer with current API of PMC citations ingestion

#637 renaming document_extractedMetadata algorithm to more descriptive document_affiliations, propagating changes to action set identifier properties names

reenabling PMC ingestion when citationmatching flag is set

updating job properties

setting export_action_set_id_entity_dataset to $UNDEFINED$ by default, this should not be required because dataset reference extraction module might be deactivated. Check will be performed at dataset entity exporter module and when value is not set - exception will be raised.

#757 temporarily disabling PMC ingestion until fixing openaire identifiers building process

#568, #577 enabling proper citations export by introducing PMC citation ingestion and citation matching outcome merging and grouping for exporting purposes. Introducing union instead of collapser which should be introduced in near future.

removing output_citation_pmc port duplicate

removing common import input parameters which are not required in this context

introducing trust_level_threshold support in statistics workflow

introducing trust_level_threshold support in common import workflow

providing default value for action_set_id_entity_dataset set to $UNDEFINED$. This change is required when exporting in statistics export mode where no entities are exported and such parameter should not be required.

introducing dedicated statistics mainworkflow encapsulating importing, processing and exporting phases. This workflow was introduced explicitly for statistics purposes because we want to operate over InformationSpace imported data in contrary to primary workflow where some of the statistics input was inferred and it wasn't clear whether it will become part of InformationSpace.

allowing overriding inference_provenance_blacklist default 'iis' value which will be required in mainworkflows/statistcs where inferenced document to project relations should be taken into account

setting default $undefined$ value for 'input_aux_dataset_existing_id'

setting default undefined values for 'mdstore_service_location' and 'dataset_mdstore_ids_csv'

#9059 reverting #717 change: shortening app_path for primary workflow due to the fix applied by Paweł on WF_JOBS MODIFY mysql table: canging varchar(255) to mediumtext.

updating job.properties

fixing placeholder name

#717 shortening app_path for primary workflow

updating job.properties

fixing output port names: removing default values for citation_pmc and dataset, setting proper output_citation_pmc in both preprocessing and primary workflows

updating job.properties

#717 shortening app_path for preprocessing workflow and subworkflows

#712 introducing plaintext caching

shortening node names

updating workingDir for generating empty outputs: removing import_dataset part

skipping PMC citations ingestion when citationmatching algorithm is not enabled

shortening transformer_export_documentto* action names to be less than 50 characters

#354 hooking up primary/main workflow with documenttodataset and documenttoproject transformers skipping export of already existing relations in HBase

updating default job.properties

#486 introducing last piece missing: text collapser in front of referenceextraction_researchinitiatives joining text contents coming from already existing document_text input port and newly introduced document_text_wos input port providing WoS contents

#486 bugfix: reordering existence filter with id relacer: we need to update identifiers first, then update existence filter

intregrating pmc citations ingestion with primary workflow, adjust port names, deduplicating dependencies

updating default job.properties

renaming input ports from input_citation to input_citations to be aligned with exporter subworkflow