D-Net

#1498 introducing major citations related refactoring including new generic direct citation matching moved to processing phase, introduced position field in all citations schemas and updated collapser taking position into account when merging citations details coming from 3 variuos sources: fuzzy citationmatching, direct citationmatching, references metadata

#1435 making PMC XML parser less strict in terms of expected input elements or attributes: article-type is set to 'unknown' value when attribute not defined in XML main element

#1431 fixing PMC XML records parser disallowing null reference type, reference value will be simply omitted

#1381 porting pmc citations ingestion from cascading framework to pig. Moving code from icm-iis-ingest-pmc to icm-iis-transformers including itegration tests, removing obsolete scala code along with unneded dependencies. Switching subworkflow in primary workflow.

#1329 setting affiliation string as raw text if parser produced empty Element object

#1329 adding affiliations field in ExtractedDocumentMetadata PMC schema. Metadata extraction code refactoring by extracting code responsible for building Affiliation avro records to AffiliationBuilder class and sharing it with pmc ingestion. Implementing affiliations ingestion functionality in PmcXmlHandler covered with unit tests. Adding affiliations field support in ingest pmc metadata transformer.

#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