D-Net

#1339 fixing input_dedup_map in pmc citation ingestion when match_content_with_metadata=false. Should not be set dynamically but statically, it will be enabled only when metadata_import is enabled

#1339 replacing active_existence_filter flag with match_content_with_metadata and changing identifiers matching logic: when flag is disabled neither contents identifiers will be filtered nor deduplicated against metadata identifiers. Up unit now, when active_existence_filter flag was disabled contents were deduplicated which is not desired when running IIS in standalone mode on contents having their representatives in HBase

#1329 enabling pmc ingestion when active_metadataextraction_export flag is enabled

introducing missing pdb reference extraction missing parameters

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

#1315 providing missing confidenceLevel

#1315 providing missing confidenceLevel

#1315 updating expected jsons in integration test after DocumentToConceptIds schema refactoring

#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

#118 explicitly defining input_document_websiteusage_similarity parameter. This is not a bug fix because exporter works properly without explicitly defining input port due to propagate-configuration mode but we should have all input port definitions aligned to avoid confusions.

bugfixing existing fault removal which was missing

bugfixing existing fault removal which was missing

upgrading xmlns version to 0.4 in order to support global element

setting false to remove_sideproducts, otherwise whole workingDir will be erased

#1257 dropping schema generation related hacks in all map-reduce modules, switching to literal schema parameters

updating job.properties, disabling all algorithms by default

#1248 fixing transition node name postprocessing-joining to merge-joining

#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.

updating job.properties

Removing usage of working_dir from Java workflow node.

reenabling document to project reference import validation

updating expected documents list

temporarily skipping docproject validation

#1195 removing obsolete ports docreation and datasetid from hbase mapred import, removing references to those ports in workflow.xml files, updating transformer by removing filtering by datasetid due to decisions made in #1072

fixing json escape character by putting \\ in place of \

extending mapreduce metadata importer test with validating import of different kind of relations and dataset identifier

extending mapreduce metadata importer test with validating import of different kind of relations and dataset identifier

removing obsolete citations

updating confidence level value to 1.0 for record coming from PMC

removing obsolete pdf directory

adding missing "confidenceLevel" field

maintaining pmc citation and testing citations merging process

reintroducing multiple citations after introducing sorting in transformer

limiting citations count to 1 until results order produced by citation matching module is repetitive

including: FET project reference extraction, EGI case, dataset reference extraction outcome validation

enabling citation matching algorithm

updating expected citations

removing comment

primary processing integration test major refactoring: dropping cermine execution and providing plaintext and extracted metadata as json records

#1176 defining remove_sideproducts property in workflows headers

#1176 introducing side products removal in common import by maintaining remove_sideproducts flag set to true by default.
Notice: do not provide any output directory location pointing to workingDir subdirectory!

removing duplicate collapser import and aligning worklfow definition

#1172 introducing support for active_export parameter in both preprocessing and primary workflows

updating job.properties

#1153 utilizing ${user.name} placeholder in ${workingDir} generation process, copying version.properties from oozie_app to mark execution environment with application version

#1147 introducing HTML import and HTML plaintext ingestion in main workflows: primary and preprocessing

updating job.properties

overriding memory parameter due to test cluster memory limitations, setting it to Xmx256m

overriding memory parameter due to test cluster memory limitations, setting it to Xmx128m

overriding memory parameter due to test cluster memory limitations, setting it to Xmx512m

updating expected classes in integration test after recent #720 change and fixing confidence level distribution

overriding memory parameter due to test cluster memory limitations

#1133 dropping useless workfing_dir creation for java nodes

#118 fixing typos

updating job.properties

#118 introducing website usage analysis as integral part of primary workflow

updating job.properties

#118 propagating configuration in main workflow.xml

#118 updating job.properties

comments added

#118 introducing mainworkflows_websiteusage_document_main workflow binding all subworkflows required to process logs and generate document similarities

#1083 enabling webcrawl ingester module extracting FX field from plaintext before executing project reference extraction

updating default job properties

#1070 updating import_project_concepts_context_ids_csv default value to "fet-fp7,fet-h2020"

#1070 introducing support for multiple context identifiers, replacing import_project_concepts_context_id IIS input parameter with import_project_concepts_context_ids_csv

updating job.properties

#1072 transition fix: replacing forking_skip_imported_data with export

#1072 dropping IIS feature filtering out already existing project and dataset references from IIS export

updating job.properties

updating job.properties

#919 renaming DocumentToResearchInitiative to DocumentToConceptId and DocumentToResearchInitiatives to DocumentToConceptIds

#1022 introducing PMC extracted document metadata collapser removing duplicates before sending output to PMC citation ingestion module

#919 adding missing i/o ports related to FET projects reference extraction

#919 enabling concepts matching for FET projects in mainworkflows: import, export, primary and preprocessing

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

#1022 introducing extracted document metadata collapser at importing phase.
Propagating extracted document mentadata (including PMC ingested metadata) to processing part of workflow what can be exploited by citation matching module.
Introducing citations collapser in last stage of processing phase collapsing ingested citations with matched citations.

#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.

#963 propagating dataset -> mdstore from import to exporting phase: importer produces DocumentToMDStore datasetore utilized by exporter module. Updating transformer definition to handle DocumentToMDStore instead of Identifier schema

introducing separate citations json containing expected results, not enabled in workflow yet

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties

updating job.properties: adding metadataextraction_excluded_checksums=4f5cc34f137de4dc89766a9366ca66de,6495a568200b1cee40baa00072b1800a

updating job.properties

introducing support for active_existence_filter, set to true by default. Setting this parameter to false allows processing contents not having its counterpart among metadata records retrieved from HBase. This solution was required to e.g. process ubiquity contents which were not present in HBase dump metadata.

fixing citations schema type

updating job.properties

renaming metadataextraction_excluded_ids to more appropriate metadataextraction_excluded_checksums

#913 introducing support for max file size parameter, currently checked against Content-Lenght header

updating job.properties

enabling document classification and reserach initiatives reference extraction algorithms