From de738e0a24aafc3306e318f7675d075a5a2e4b73 Mon Sep 17 00:00:00 2001 From: YaphetKG <45075777+YaphetKG@users.noreply.github.com> Date: Thu, 25 Aug 2022 09:46:15 -0400 Subject: [PATCH] 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Howard Lander * 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 * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Howard Lander 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 * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * 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 Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Howard Lander Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett Co-authored-by: Nathaniel Braswell Co-authored-by: Nathan Braswell Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop * 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 * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * adding more config options for node extraction * some refactoring Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 * 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 * 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 * Update _version.py * Update _version.py updating version for final push to master * Update factory.py Adding more comments Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg * 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 * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * 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 Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench * update version * remove cruft from merge Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Howard Lander Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett Co-authored-by: Nathaniel Braswell Co-authored-by: Nathan Braswell Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop Co-authored-by: Hoid * version bump Co-authored-by: Carl Schreep Co-authored-by: Yaphetkg Co-authored-by: Ginnie Hench Co-authored-by: Howard Lander Co-authored-by: Alex Waldrop <39315592+alexwaldrop@users.noreply.github.com> Co-authored-by: Charles Bennett Co-authored-by: Nathaniel Braswell Co-authored-by: Nathan Braswell Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Alex Waldrop Co-authored-by: Hoid --- src/dug/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dug/_version.py b/src/dug/_version.py index 7eec20a5..0a9188ff 100644 --- a/src/dug/_version.py +++ b/src/dug/_version.py @@ -1 +1 @@ -__version__ = "2.9.4dev" +__version__ = "2.9.5dev"