v2.1.0: Ingest and Query microservice, Debian, Model Changes#328

Merged

OrdiNeu merged 261 commits intostablefrom stable-candidate-2.1.0

Nov 13, 2023

+1,061-321

This pull request is big! We're only showing the most recent 250 commits

Commits on Aug 17, 2021

Switch for registries in Jenkins (#88 )
daisieh
authored

Commits on Aug 18, 2021

bump datasets version
shaikh-rashid
committed

Commits on Aug 19, 2021

Reorganize submodules (#92 )
daisieh
authored

Commits on Aug 26, 2021

Hotfix: update htsget app pointer (#93 )
daisieh
authored

Commits on Aug 28, 2021

Commits on Sep 15, 2021

quick fix: correct name of htsget repo
daisieh
authored

Commits on Oct 14, 2021

Commits on Nov 11, 2021

update chord-metadata to use secrets file for password (#100 )
daisieh
authored

Commits on Nov 15, 2021

Post Auth Merge Fixes (#91 )

authored

Commits on Nov 17, 2021

Forgot to tee to the logfile on a couple of lines (#103 )
daisieh
authored

Commits on Nov 18, 2021

Update of submodules (#102 )

shaikh-rashid
and
daisieh
authored

Commits on Dec 3, 2021

Tyk add new API feature + New API for Katsu/Chord Metadata (#104 )

authored

Commits on Dec 9, 2021

Add CanDIG Data Portal to the stack (#107 )
amanjeev
authored

Commits on Dec 10, 2021

CanDIG Data Portal - bugfixes (#108 )
amanjeev
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Commits on Dec 16, 2021

Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into develop
daisieh
committed

Commits on Jan 7, 2022

Pushing htsget app jenkins script (#105 )
jagdeepsason2021
authored

Commits on Jan 24, 2022

Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into develop
daisieh
committed

Commits on Jan 25, 2022

update submodule to catch up (#110 )
daisieh
authored

Commits on Jan 27, 2022

Commits on Feb 8, 2022

Commits on Feb 14, 2022

Fix names of secrets files in compose/docker-compose (#115 )
daisieh
authored

Commits on Feb 15, 2022

Commits on Mar 8, 2022

DIG-772: GraphQL Integration with CanDIGv2 stack - Part 2 (#117 )
AliRZ-02
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Commits on Mar 16, 2022

Integrating OPA into the stack (#119 )
daisieh
authored

Commits on Mar 28, 2022

Commits on Apr 4, 2022

Commits on Apr 7, 2022

template fixes
daisieh
committed

Commits on Apr 9, 2022

Commits on Apr 11, 2022

Commits on Apr 12, 2022

tiny setting tweaks (#130 )
daisieh
authored

Commits on Apr 21, 2022

Commits on Apr 22, 2022

More tweaks (#131 )
daisieh
authored

Commits on May 3, 2022

DIG-828: HTSget should be behind Tyk (#138 )
daisieh
authored

Commits on May 6, 2022

Assign site-admin credentials to user2 (#139 )
daisieh
authored

Commits on May 13, 2022

Commits on Jun 8, 2022

bump candig-data-portalversion ⬆
Shaikh Rashid
committed

Commits on Jun 11, 2022

Changes required in AuthX stack, bug fixes and tweaks 🐛🚀 (#143 )

authored

Commits on Jun 14, 2022

Commits on Jun 17, 2022

new release: (#146 )

shaikh-rashid
and
Shaikh Rashid
authored

Commits on Jun 21, 2022

Fix merge conflicts with branch stable
Shaikh Rashid
committed
pin python version and alpine version for katsu📌 (#149 )

shaikh-rashid
and
Shaikh Rashid
authored

Commits on Jun 22, 2022

Vault stores s3 secrets (#142 )
daisieh
authored

Commits on Jun 24, 2022

bump version and submodule for federation-service and data-portal 🆙
Shaikh Rashid
committed
Fix merge conflicts with stable
Shaikh Rashid
committed
federation-service needs to be started manually
Shaikh Rashid
committed
minor syntax fixes
Shaikh Rashid
committed

Commits on Jun 28, 2022

Small fixes (#151 )

authored

Commits on Jun 29, 2022

in case we're uploading things to our own minio
daisieh
committed

Commits on Jul 4, 2022

bump htsget_app to v0.1.6
Shaikh Rashid
committed
candig-data-portal v0.1.2 📜
Shaikh Rashid
committed

Commits on Jul 18, 2022

in case we're uploading things to our own minio (#152 )
daisieh
authored

Commits on Jul 26, 2022

Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into develop
daisieh
committed

Commits on Aug 4, 2022

OPA secrets as docker secrets (#153 )
daisieh
authored

Commits on Aug 19, 2022

Commits on Sep 7, 2022

quick patch for federation_service 🩹
Shaikh Rashid
committed

Commits on Sep 8, 2022

bump candig-data-portalto v0.1.3
Shaikh Rashid
committed

Commits on Sep 13, 2022

Update submodules (#158 )
daisieh
authored

Commits on Sep 23, 2022

fix: add compatibility (#160 )
SonQBChau
authored

Commits on Sep 30, 2022

pass container name into chord_metadata (#162 )
daisieh
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Commits on Oct 13, 2022

Feature/federation behind tyk api (#163 )

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Commits on Oct 20, 2022

Sonchau/install docker m1 (#170 )

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Commits on Oct 24, 2022

Commits on Oct 26, 2022

Refresh token rotation (#173 )
daisieh
authored

Commits on Nov 15, 2022

Update submods (#169 )
daisieh
authored

Commits on Nov 22, 2022

Tyk federation fixes (#175 )

authored

Commits on Nov 25, 2022

Commits on Nov 28, 2022

set emails for fake users (#178 )
daisieh
authored

Commits on Nov 29, 2022

Commits on Nov 30, 2022

Commits on Dec 2, 2022

Add documentation for Docker and submodules (#182 )

CourtneyGosselin
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kcranston
authored

Commits on Dec 6, 2022

Commits on Dec 7, 2022

cleanup of docs (#186 )

shaikh-rashid
and
Shaikh Rashid
authored

Commits on Dec 9, 2022

Update docs (#187 )

shaikh-rashid
and
Shaikh Rashid
authored

Commits on Dec 14, 2022

Module cleanup (#184 )

authored

Commits on Dec 19, 2022

Commits on Dec 21, 2022

add instructions to mohccn-data and integration testing (#191 )
daisieh
authored

Commits on Jan 9, 2023

cleanup of conda related scripts that are no longer needed (#189 )

authored

Commits on Jan 11, 2023

Sonchau/docs mac m1 (#194 )

SonQBChau
and
kcranston
authored

Commits on Jan 12, 2023

Keycloak m1 patch (#192 )

shaikh-rashid
and
Shaikh Rashid
authored

Commits on Jan 26, 2023

Add no-cache build instructions (#196 )
OrdiNeu
authored

Commits on Mar 7, 2023

DIG-1071: Revert "cleanup of conda related scripts that are no longer needed" (#197 )

OrdiNeu
and
kcranston
authored

Commits on Mar 8, 2023

Update katsu docker-compose.yml (#199 )
SonQBChau
authored

Commits on Mar 9, 2023

Conda path fixes (#200 )
kcranston
authored

Commits on Mar 24, 2023

Sonchau/edit chord metadata compose (#204 )
SonQBChau
authored

Commits on Mar 28, 2023

Bake the make init_hosts_file step so it is no longer needed + Add a make build-all command (#203 )

OrdiNeu
and
daisieh
authored

Commits on Mar 29, 2023

Fix a bug where make compose-% was missing the IP address (#206 )
OrdiNeu
authored

Commits on Mar 31, 2023

Update chord_metadata_service (#209 )
SonQBChau
authored

Commits on Apr 3, 2023

DIG-999: Automate integration tests (#207 )
daisieh
authored

Commits on Apr 6, 2023

Commits on Apr 17, 2023

DIG-1133: changing CANDIG_DOMAIN from docker.localhost to candig.docker.internal (#214 )
daisieh
authored

Commits on Apr 18, 2023

small HTSGet updates (#215 )
daisieh
authored

Commits on Apr 24, 2023

Diff the .env file, fix typo (#220 )
daisieh
authored

Commits on Apr 25, 2023

Remove diff flag not available on all versions (#221 )
daisieh
authored

Commits on Apr 27, 2023

Replace all instances of Chord/Chord-metadata with Katsu (#195 )

OrdiNeu
and
daisieh
authored

Commits on Apr 28, 2023

Commits on May 4, 2023

Bump versions and submodules (#226 )
daisieh
authored

Commits on May 5, 2023

katsu update (#225 )
SonQBChau
authored

Commits on May 17, 2023

copy things first to /app, then copy to /vault in entrypoint (#233 )
daisieh
authored

Commits on May 19, 2023

Commits on May 29, 2023

Commits on May 30, 2023

Commits on May 31, 2023

Clean federation during make clean-authx (#240 )
OrdiNeu
authored

Commits on Jun 2, 2023

Commits on Jun 16, 2023

Fix the "Websocket error: Could not connect to ws:// <x>" error (#243 )
OrdiNeu
authored

Commits on Jun 27, 2023

Add issue template for deployment errors
kcranston
authored

Commits on Jul 11, 2023

small fixes for Vault setup (#247 )
daisieh
authored

Commits on Jul 12, 2023

GitHub Actions for CanDIGv2 (#248 )

justin-ys
and
daisieh
authored

Commits on Jul 19, 2023

Conda hotfix (#249 )
justin-ys
authored

Commits on Jul 21, 2023

Commits on Jul 22, 2023

Commits on Jul 24, 2023

Update katsu_service
daisieh
committed

Commits on Jul 27, 2023

Add candigv2-ingest container (#242 )
justin-ys
authored

Commits on Jul 31, 2023

change opa image to latest-static to support arm64
kcranston
committed
Add candigv2-ingest container (#242 )

justin-ys
authored and
daisieh
committed

Commits on Aug 1, 2023

change opa image to latest-static to support arm64 (#269 )
kcranston
authored

Commits on Aug 3, 2023

Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into develop
daisieh
committed

Commits on Aug 15, 2023

Commits on Aug 17, 2023

updating submodules (#277 )

candigbot
and
github-actions
authored
[Auto-generated] Submodule Updates for CanDIG/katsu (5868372733) (#273 )

authored
updating submodules (#276 )

candigbot
and
github-actions
authored

Commits on Aug 21, 2023

Add ingest to the TYk configuration (#278 )
OrdiNeu
authored

Commits on Aug 23, 2023

Sonchau/update katsu tests (#279 )
SonQBChau
authored

Commits on Sep 6, 2023

[Auto-generated] Submodule Updates for CanDIG/katsu (6045785341) (#281 )

authored

Commits on Sep 13, 2023

updating submodules (#282 )

candigbot
and
github-actions
authored
updating submodules (#284 )
candigbot
authored

Commits on Sep 14, 2023

updating submodules (#285 )

candigbot
and
github-actions
authored

Commits on Sep 15, 2023

updating submodules (#287 )

candigbot
and
github-actions
authored
updating submodules (#286 )

candigbot
and
github-actions
authored

Commits on Sep 19, 2023

Commits on Sep 20, 2023

remove alpine variable from htsget compose (#290 )
kcranston
authored

Commits on Sep 27, 2023

Commits on Oct 6, 2023

fix incorrect query service link (#297 )
mshadbolt
authored

Commits on Oct 11, 2023

updating submodules (#294 )

candigbot
and
github-actions
authored

Commits on Oct 12, 2023

Add requirements for HTSGet to access Postgres (#296 )
OrdiNeu
authored

Commits on Oct 13, 2023

DIG-1240: API middleware service to handle queries across federated instances (#291 )
OrdiNeu
authored

Commits on Oct 14, 2023

Commits on Oct 26, 2023

Commits on Oct 27, 2023

Commits on Oct 30, 2023

DIG-1301: delete cascades, rename htsget dataset to cohort (#312 )
daisieh
authored

Commits on Nov 1, 2023

updating submodules (#314 )

candigbot
and
github-actions
authored
not using alpine anymore (#315 )
daisieh
authored
updating submodules (#316 )

candigbot
and
github-actions
authored

Commits on Nov 2, 2023

updating submodules (#317 )
candigbot
authored
updating submodules (#318 )

candigbot
and
github-actions
authored

Commits on Nov 3, 2023

DIG-1342: update ingest to cleaned-up version (#302 )
daisieh
authored

Commits on Nov 6, 2023

DIG-1171: merge Makefile.authx into Makefile (#319 )

authored

Commits on Nov 8, 2023

updating submodules (#321 )

candigbot
and
github-actions
authored
updating submodules (#320 )

authored

Commits on Nov 9, 2023

updating submodules (#322 )

candigbot
and
github-actions
authored

Commits on Nov 10, 2023

updating submodules (#323 )
candigbot
authored
updating submodules (#324 )

candigbot
and
github-actions
authored

Commits on Nov 11, 2023

fix: etc/venv/requirements-dev.txt to reduce vulnerabilities (#326 )

daisieh
and
snyk-bot
authored