Release/2.9.5 #266

YaphetKG · 2022-10-04T15:11:36Z

Adds SPRINT parser

* support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org>

* Include ES scores in variable results * Round ES score to 6

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org>

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org>

* Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org>

Co-authored-by: Nathan Braswell <nbraswell@rti.org>

Jenkins test merge

* Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns>

Jenkins test merge to develop

Use pipeline-utils

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org>

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * version bump Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com>

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * sprint parser * adding parser to plugin manager * sprint form names parse from file name * moving sprint to sprint parser * remove old import * empty desc Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com>

waTeim · 2022-10-04T15:17:56Z

Well it looks reasonable kind of stuff, though the particular changes I don't have great insight.

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * Release/2.9.5 (#266) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Master to develop sync (#262) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. …

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * Release/2.9.5 (#266) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Master to develop sync (#262) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree vari…

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * Release/2.9.5 (#266) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Master to develop sync (#262) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * P…

* Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * update version * remove cruft from merge Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Hoid <tylerlcheek@gmail.com> * Release/2.9.5 (#266) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Bump version. * Revert version to dug format. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Add github creds env var. * Fix version typo. * Initial commit * Reduce ephemeral storage limits and requests * More parsers (#248) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * consolidate dbgap format parser in single file , adds crdc and kfdrc parsers * adding tests * bump version * parser when versions of studies are > 9 * test for version * fix long text issues, and encoding errors * nltk initialization * change nltk approach for sliding window Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Master to develop sync (#262) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Release/2.9.1 (#205) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Release/2.9.1 Renames SPARC datasets as SPARC instead of dbgap Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> * Update _version.py (#206) * Release/2.9.2 (#209) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> * Release 2.9.3 (#244) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. * Programatically remove quotes from version tag. * dug dump concepts api created and tested (#229) Co-authored-by: Nathan Braswell <nbraswell@rti.org> * Update _version.py (#234) * Version changes + separate build and publish. * Semantic versioning prep. * Add develop and master versioning and tagging. * Ncpi index fix (#232) * Renamed anvil to ncpi * Update ncpi datasets catalog * Modified script to download NCPI datasets into platform subfolders * Updated NCPI integration dataset * Removed unused variable * Removed ncpi top level folder to spread results among subfolders * Change output dir to data instead of ncpi subdir * Moved NCPI subdirs into main data folder for ingest as per Yaphet's request Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: Nathaniel Braswell <braswent6@gmail.com> Co-authored-by: Nathan Braswell <nbraswell@rti.org> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop <awaldrop@RTI-108292.rti.ns> * Release/2.9.4 (#260) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Dev version bump (#202) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Attribute mapping from node to dug element (#203) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Changed DbGaP to SPARC in the scicrunch parser (#204) * Anvil (#207) * Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing * Anvil parser (#208) * Release/2.8.0 (#198) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Release/v2.9.0 (#201) * Bumping version * support for extracting dug elements from graph (#197) * support for extracting dug elements from graph * adding flag for enabling dug element extraction from graph * adding new config for node_to dug element parsing * adding more parameters to crawler to able configuration to element extraction logic * add tests * add tests for crawler Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Display es scores (#199) * Include ES scores in variable results * Round ES score to 6 * Update _version.py (#200) * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * anvil parser * bump number of files test * Update dbgap_parser.py * Update anvil_dbgap_parser.py change to AnVIL * Update test_parsers.py update test Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Ginnie Hench <vhench@rti.org> * Initial Kaniko build. * Move version file definition. * Quote env vars. * Update env vars. * Update env vars. * Update env vars. * env var changes. * env var changes. * env var changes. * env var changes. * Update DOCKER_IMAGE var. * Update DOCKER_IMAGE var in kaniko cmd. * Update kaniko destination line. * Update kaniko destination line. * Moree variable madness. …

Carl Schreep and others added 30 commits December 2, 2021 15:02

Bumping version

40ac323

Display es scores (#199)

a66ca59

* Include ES scores in variable results * Round ES score to 6

Update _version.py (#200)

e648bba

Changed DbGaP to SPARC in the scicrunch parser (#204)

b43ee87

Anvil (#207)

447d325

* Added updated anvil dataset catalog * Added script for downloading all anvil data dicts * Added current anvil data dictionaries to data folder to be used for indexing

Initial Kaniko build.

7d3f541

Move version file definition.

38f8bc8

Quote env vars.

4aabf6f

Update env vars.

403b9b7

Update env vars.

fe82b95

Update env vars.

2968acd

env var changes.

e63ac74

env var changes.

39b79d6

env var changes.

e821a44

env var changes.

cd23318

Update DOCKER_IMAGE var.

c034754

Update DOCKER_IMAGE var in kaniko cmd.

eb43dc8

Update kaniko destination line.

337f3b2

Update kaniko destination line.

4d0a723

Moree variable madness.

b7674fe

Programatically remove quotes from version tag.

2674ef0

dug dump concepts api created and tested (#229)

06c09b7

Co-authored-by: Nathan Braswell <nbraswell@rti.org>

Update _version.py (#234)

4e06ca6

Version changes + separate build and publish.

af3fe8b

Semantic versioning prep.

70ed22f

Add develop and master versioning and tagging.

3d2bbd7

cnbennett3 and others added 15 commits June 29, 2022 11:02

Merge pull request #242 from helxplatform/jenkins-test

c68a991

Jenkins test merge

Bump version.

4784983

Revert version to dug format.

c3642bd

Add github creds env var.

0401a14

Fix version typo.

f5eb706

Merge pull request #245 from helxplatform/jenkins-test

57612d7

Jenkins test merge to develop

Initial commit

5e2d5a6

Reduce ephemeral storage limits and requests

0294ed2

Merge pull request #247 from helxplatform/use-pipeline-utils

87b374d

Use pipeline-utils

Update _version.py

d045e23

Merge branch 'master' into Release/2.9.5

ab6e973

YaphetKG requested review from waTeim and HowardLander October 4, 2022 15:11

waTeim approved these changes Oct 4, 2022

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HowardLander approved these changes Oct 4, 2022

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YaphetKG merged commit 63f2b01 into master Oct 4, 2022

YaphetKG deleted the Release/2.9.5 branch October 4, 2022 16:41

YaphetKG mentioned this pull request Jul 19, 2023

Master back to dev (#297) #298

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Release/2.9.5 #266

Release/2.9.5 #266

YaphetKG commented Oct 4, 2022

waTeim commented Oct 4, 2022

Release/2.9.5 #266

Release/2.9.5 #266

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YaphetKG commented Oct 4, 2022

waTeim commented Oct 4, 2022