Remove logging of config; contains redis and S3 keys - #52
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waTeim
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Feb 8, 2022
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Sure looks right. What's up with jenkins?
waTeim
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February 8, 2022 23:11
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Hey the problem with build failing has been address by Yaphet's merge. Can you merge in those, or re-branch from develop (easiest). |
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YaphetKG
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Feb 14, 2022
* Bumping version * Feature/cde crawls (#51) * adding cde kgx files * extracted elements path * adding methods for extracting dug elements from graph * adding indexing step to dag * adding dug config for expansion queries * adapting to latest dug code * adapting to latest dug code * moving cde kgxs as new entry in metadata, adding dug release , fix long running python dep resolution * adding enabled flag for concept -> dug element crawls * adding legacy resolver for make file aswell * parse bool as string in yaml , since all env vars are going to be strings * Update config.yaml * Update requirements.txt updating dug lib to the current release * resolving long taking pip installs, with Jeffs help Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Remove logging of config; contains redis and S3 keys (#52) * when two graph sets are downloaded, bug that deletes the first download (#53) Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Mac Chaffee <me@macchaffee.com>
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YaphetKG
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Jan 5, 2023
* Bumping version * Feature/cde crawls (#51) * adding cde kgx files * extracted elements path * adding methods for extracting dug elements from graph * adding indexing step to dag * adding dug config for expansion queries * adapting to latest dug code * adapting to latest dug code * moving cde kgxs as new entry in metadata, adding dug release , fix long running python dep resolution * adding enabled flag for concept -> dug element crawls * adding legacy resolver for make file aswell * parse bool as string in yaml , since all env vars are going to be strings * Update config.yaml * Update requirements.txt updating dug lib to the current release * resolving long taking pip installs, with Jeffs help Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Remove logging of config; contains redis and S3 keys (#52) * when two graph sets are downloaded, bug that deletes the first download (#53) Co-authored-by: Yaphetkg <yaphetkg@renci.org> * added the version and the new tag * Changed git to https to satisfy the git gods * changed the requirements.txt to match the latest branch * Cde harmonization 2 (#57) * adding new dug config * add new method parameters * query logging * restoring expand_to_dug_element method call * bump dug version and roger version Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update requirements.txt bumping dug version * Update _version.py * Anvil pipeline (#60) * adds anvil related data dirs * reorganize file fetching, putting duplicate code in a single function. * adds anvil in default dataset list * add metadata for anvil dataset * add anvil to cli * add anvil to airflow dag * add option to clear out redis http cache by default it will not be cleared * logs * typo fix * update dug dependency Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Initial commit * Remove unnecessary Install stage * Change user to root during part of Dockerfile * Increase ephemeral storage limit * Maybe fix pip command? * Increase ephemeral storage limits * Reduce ephemeral storage limits a bit to test * Cleanup * Separate build and publish, initial feature branch tagging, prep for SemVer tagging. * Update script for extracting version from version file. * Add versioning and tagging for develop and master + bump version. * Initial commit * Add third tag back to master branch tag push * Increase ephemeral storage limits and requests * Move test stage to before stuff * Ncpi datasets (#64) * adding dug parsers for kids first and cancer commons * dir for new dag tasks * adding steps for kfdrc and crdc * bump dug version * adding indexes * changing create index for v2.8.4 * Sprint task (#65) * adding dug parsers for kids first and cancer commons * dir for new dag tasks * adding steps for kfdrc and crdc * bump dug version * adding indexes * changing create index for v2.8.4 * adding sprint parsers * fixing merge issue * adding dug new code * correct sprint path * bump dug version * bump dug version Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Bacpac parsing (#66) * bacpac parser * point to bacpac dug * fix typo * Changed kaniko build to kaniko buildAndPush * Removed items from Jenkinsfile to allow successful build of image * Removed crane image from k8s manifest * point to dug develop * bump version * adding bacpac dag tasks * bump dug version Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Joshua Seals <jseals@renci.org> * bump version for release Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Mac Chaffee <me@macchaffee.com> Co-authored-by: Howard Lander <howard@renci.org> Co-authored-by: Jeff Waller <truthset@gmail.com> Co-authored-by: Hoid <tylerlcheek@gmail.com> Co-authored-by: Charles Bennett <cnbennett3@gmail.com> Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com> Co-authored-by: Joshua Seals <jseals@renci.org>
YaphetKG
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Jan 26, 2023
* Release/0.8.rc0 (#54) * Bumping version * Feature/cde crawls (#51) * adding cde kgx files * extracted elements path * adding methods for extracting dug elements from graph * adding indexing step to dag * adding dug config for expansion queries * adapting to latest dug code * adapting to latest dug code * moving cde kgxs as new entry in metadata, adding dug release , fix long running python dep resolution * adding enabled flag for concept -> dug element crawls * adding legacy resolver for make file aswell * parse bool as string in yaml , since all env vars are going to be strings * Update config.yaml * Update requirements.txt updating dug lib to the current release * resolving long taking pip installs, with Jeffs help Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Remove logging of config; contains redis and S3 keys (#52) * when two graph sets are downloaded, bug that deletes the first download (#53) Co-authored-by: Yaphetkg <yaphetkg@renci.org> * Update _version.py * Update _version.py Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Mac Chaffee <me@macchaffee.com> * bump version for release * fix topmed kgx structure * adjusting a bit * adjusting a bit * docker file updates * docker file updates * Update _version.py * Update requirements.txt Co-authored-by: Carl Schreep <schreepc@renci.org> Co-authored-by: Yaphetkg <yaphetkg@renci.org> Co-authored-by: Mac Chaffee <me@macchaffee.com>
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