D-Net

#1498 removing obsolete ingest pmc citation resources

#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

#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.

expecting null affiliations instead of empty array

adding missing affiliations field in input data, removing duplicates from outut

adding missing affiliations field in integration test expected output

#1315 propagating confidenceLevel to DocumentToConceptIds. Updating PIG transformer script by introducing concept identifiers deduplication UDF function picking record with the highest confidence level, introducing unit and integration tests. Propagating changes in document to concepts exporter module.

removing obsolete test resources

Removing usage of working_dir from Java workflow node.

#1169 fixing duplicate context issue, introducing integration test proving implemented solution works properly