D-Net

bugfix: renaming obsolete decision-export to decision-export-to-hbase

#1308 reverting uri:oozie:distcp-action:0.2 change: version is not properly recognized by oozie 3.3.2-cdh4.3.1

#1260 enabling document to protein databank reference extraction in primary workflow, supporting 3 new parameters: active_referenceextraction_pdb, export_action_set_id_document_pdb, export_referenceextraction_pdb_url_root

#1301 introducing explicit export mode flags: active_export_to_hbase and active_export_to_json. This way both exports can be enabled or both of them can be disabled.

#1308 switching distcp namespace to uri:oozie:distcp-action:0.2

disabling export by setting active_export flag to false. Results will be converted to JSON records

#1301 introducing common/export_to_json and utilizing this subworkflow in both primary and preprocessing workflows executing it when active_export=false which means hbase export is disabled

updating job.properties, disabling all algorithms by default

#1248 introducing fault subdirectory support in all workflows wrapping metadataextraction subworkflow up to the processing and primary root workflows. This should prevent fault directory from being removed when ${remove_sideproducts} flag is enabled, it will be propagated along with metadata and plaintext.

Removing usage of working_dir from Java workflow node.