D-Net

merging trunk changes with IIS-CDH-5.3.0 branch

merging trunk changes with IIS-CDH-5.3.0 branch

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

updating job.properties

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

#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.

#840 moving IdentifierMapping from importer to common package

#840 renaming DeduplicationMapping to more generic IdentifierMapping

#757 adding reducing phase for filtering out pmids by article type, mapping phase groups PmidMapping objects by pmid and at reducer phase duplicates will be filtered out

#757 fixing pmid and doi matching, fixing sourceDocumentId and destinationDocumentId generation

#757 fixing pmid and doi matching, fixing sourceDocumentId and destinationDocumentId generation

updating default job properties

renaming workflow to ingest_pmc_plaintext

updating job.properties

dir names in parameters should not contain nameNode