Release 2.10.2 #306
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Release 2.10.2 #306
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concept_types dict added to results with types and number of results. types parameter added to API query dict, restricting search results to set of types.
* adds reconnect to timed out ftp session * adds reconnect to timed out ftp session * remove PASV command
… ES from json str to dict
…d_search Feature/concept type backend search
* 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. …
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