D-Net

merging trunk changes with IIS-CDH-5.3.0 branch

merging trunk changes with IIS-CDH-5.3.0 branch

creating IIS-CDH-5.3.0 branch

#1017 fixing PMC and DOI identifiers retrieval from avro map: addressing by Utf8 objects not by String

#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.

#955 fixing reference raw text generation for pretty printed NLM documents

#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