Merge master (#294) · helxplatform/dug@7f82e1f

Commit

Merge master (#294)

* 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…

Loading branch information

17 people authored Jul 18, 2023

1 parent 716db1b commit 7f82e1f

.github/workflows/build-push-dev-image.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -43,7 +43,6 @@ jobs: @@
         - name: Confirm git commit SHA output
           run: echo ${{ steps.vars.outputs.short_sha }}
         # Docker Buildx is important to caching in the Build And Push Container
         # step
         # https://github.com/marketplace/actions/build-and-push-docker-images
@@ Expand Down @@

.github/workflows/build-push-release.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -40,18 +40,18 @@ jobs:
  
        # https://github.com/marketplace/actions/git-semantic-version

        - name: Semver Check

          uses: paulhatch/semantic-version@v5.0.2

          uses: paulhatch/semantic-version@v5.0.3

          id: version

          with:

            # The prefix to use to identify tags

            tag_prefix: "v"

            # A string which, if present in a git commit, indicates that a change represents a

            # major (breaking) change, supports regular expressions wrapped with '/'

            major_pattern: "/breaking|major/"

            major_pattern: "/breaking:|major:/"

            # A string which indicates the flags used by the `major_pattern` regular expression. Supported flags: idgs

            major_regexp_flags: "ig"

            # Same as above except indicating a minor change, supports regular expressions wrapped with '/'

            minor_pattern: "/feat|feature|minor/"

            minor_pattern: "/feat:|feature:|minor:/"

            # A string which indicates the flags used by the `minor_pattern` regular expression. Supported flags: idgs

            minor_regexp_flags: "ig"

            # A string to determine the format of the version output

    @@ -113,10 +113,12 @@ jobs:
  
          run: |

            curl \

            -s --fail -X POST \

            -H "Accept: application/vnd.github+json" \

            -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \

            -H "X-GitHub-Api-Version: 2022-11-28" \

            https://api.github.com/repos/${{ github.repository }}/git/refs \

            -d '{"ref":"refs/tags/v${{ steps.version.outputs.version }}","sha":"${{ github.sha }}"}'

    #   https://cli.github.com/manual/gh_release_create

        - name: Create Release

          env:

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