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Master back to dev (#297) #298

Merged
merged 1 commit into from
Jul 19, 2023
Merged

Master back to dev (#297) #298

merged 1 commit into from
Jul 19, 2023

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YaphetKG
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  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • Release/2.9.1 (Release/2.9.1 #205)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

Renames SPARC datasets as SPARC instead of dbgap

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • Release 2.9.3 (Release 2.9.3 #244)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • 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 (dug dump concepts api created and tested #229)

  • Update _version.py (Update _version.py #234)

  • Version changes + separate build and publish.

  • Semantic versioning prep.

  • Add develop and master versioning and tagging.

  • Ncpi index fix (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

  • Release/2.9.4 (Release/2.9.4 #260)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • 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 (dug dump concepts api created and tested #229)

  • Update _version.py (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 (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

  • Add github creds env var.

  • Fix version typo.

  • Initial commit

  • Reduce ephemeral storage limits and requests

  • More parsers (More parsers #248)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • update version

  • remove cruft from merge

  • Release/2.9.5 (Release/2.9.5 #266)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • 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 (dug dump concepts api created and tested #229)

  • Update _version.py (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 (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

  • Add github creds env var.

  • Fix version typo.

  • Initial commit

  • Reduce ephemeral storage limits and requests

  • More parsers (More parsers #248)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • Master to develop sync (Master to develop sync #262)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • Release/2.9.1 (Release/2.9.1 #205)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

Renames SPARC datasets as SPARC instead of dbgap

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • Release 2.9.3 (Release 2.9.3 #244)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • 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 (dug dump concepts api created and tested #229)

  • Update _version.py (Update _version.py #234)

  • Version changes + separate build and publish.

  • Semantic versioning prep.

  • Add develop and master versioning and tagging.

  • Ncpi index fix (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

  • Release/2.9.4 (Release/2.9.4 #260)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Dev version bump (Dev version bump #202)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • adding more config options for node extraction

  • some refactoring

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

  • Anvil (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 (Anvil parser #208)

  • Release/2.8.0 (Release/2.8.0 #198)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Update _version.py

  • Update _version.py

updating version for final push to master

  • Update factory.py

Adding more comments

  • Release/v2.9.0 (Release/v2.9.0 #201)

  • Bumping version

  • support for extracting dug elements from graph (support for extracting dug elements from graph #197)

  • support for extracting dug elements from graph

  • adding flag for enabling dug element extraction from graph

  • adding new config for node_to dug element parsing

  • adding more parameters to crawler to able configuration to element extraction logic

  • add tests

  • add tests for crawler

  • Display es scores (Display es scores #199)

  • Include ES scores in variable results

  • Round ES score to 6

  • Update _version.py (Bumping version #200)

  • Update _version.py

  • 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

  • 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.
    …

@YaphetKG @gingin77
@HowardLander @alexwaldrop @cnbennett3 @braswent @Hoid @gaurav @dependabot @joshua-seals @vladimir2217
Master back to dev (#297)
d4e3698 
* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* update version

* remove cruft from merge

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Hoid <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>
Co-authored-by: Howard Lander <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>
Co-authored-by: Charles Bennett <[email protected]>
Co-authored-by: Nathaniel Braswell <[email protected]>
Co-authored-by: Nathan Braswell <[email protected]>
Co-authored-by: cnbennett3 <[email protected]>
Co-authored-by: Alex Waldrop <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* adding more config options for node extraction

* some refactoring

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>

* Update _version.py

* Update _version.py

updating version for final push to master

* Update factory.py

Adding more comments

Co-authored-by: Carl Schreep <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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 <[email protected]>
Co-authored-by: Yaphetkg <[email protected]>
Co-authored-by: Ginnie Hench <[email protected]>

* 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.
…
@YaphetKG YaphetKG merged commit 43a7bc3 into master Jul 19, 2023
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