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Stable git history fixup #332

Merged
merged 256 commits into from
Nov 13, 2023
Merged

Stable git history fixup #332

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8666255
update htsget submodule (#85)
daisieh Jul 15, 2021
f0b8505
add GitHub credentials (#86)
daisieh Jul 16, 2021
445d508
Switch back to Dockerhub registry (#87)
daisieh Jul 22, 2021
f62ca32
update to new stable commit for htsget (#89)
daisieh Aug 4, 2021
119b382
update datasets submodule to point to develop branch (#90)
daisieh Aug 17, 2021
71856ea
Switch for registries in Jenkins (#88)
daisieh Aug 17, 2021
c97b3f4
bump datasets version
shaikh-rashid Aug 18, 2021
c64e7a7
Reorganize submodules (#92)
daisieh Aug 19, 2021
5c7286d
Hotfix: update htsget app pointer (#93)
daisieh Aug 26, 2021
9ff08c4
Move submodules to candig forks (#94)
daisieh Aug 28, 2021
5b66f95
Hotfix/submodules redux (#95)
daisieh Aug 28, 2021
abae90f
Hotfix/submodules redux redux (#96)
daisieh Aug 28, 2021
a7f788c
quick fix: correct name of htsget repo
daisieh Sep 15, 2021
4874400
update htsget-server to stable
daisieh Oct 14, 2021
0755e93
update htsget-server to stable (#98)
daisieh Oct 14, 2021
7e59795
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Oct 14, 2021
791a3ce
update chord-metadata to use secrets file for password (#100)
daisieh Nov 11, 2021
e38dd73
Post Auth Merge Fixes (#91)
shaikh-rashid Nov 15, 2021
bf1e4d5
Forgot to tee to the logfile on a couple of lines (#103)
daisieh Nov 17, 2021
5ed239a
Update of submodules (#102)
shaikh-rashid Nov 18, 2021
1093d7b
Tyk add new API feature + New API for Katsu/Chord Metadata (#104)
amanjeev Dec 3, 2021
84ee5c8
Add CanDIG Data Portal to the stack (#107)
amanjeev Dec 9, 2021
e10ad27
CanDIG Data Portal - bugfixes (#108)
amanjeev Dec 10, 2021
4d9f7dd
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Dec 16, 2021
ac86bc7
Pushing htsget app jenkins script (#105)
jagdeepsason2021 Jan 7, 2022
4478d76
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Jan 24, 2022
9687b58
update submodule to catch up (#110)
daisieh Jan 25, 2022
a619e40
move submodule for katsu
daisieh Jan 27, 2022
a4c5298
move submodule for katsu (#111)
daisieh Jan 27, 2022
608c522
update submod for katsu (#113)
daisieh Feb 4, 2022
39d9bd4
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Feb 4, 2022
6c80ea4
bump version for CHORD_METADATA_VERSION to v1.4.1
daisieh Feb 4, 2022
060c6ff
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Feb 4, 2022
1574a37
CanDIG Data Portal and Katsu API + New Tyk Middlewares (#112)
amanjeev Feb 8, 2022
2290301
Add a note about updating hosts
daisieh Feb 8, 2022
a528578
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Feb 8, 2022
04ad4ea
Fix names of secrets files in compose/docker-compose (#115)
daisieh Feb 14, 2022
32700ce
Update htsget submodule (#116)
daisieh Feb 15, 2022
0a6af87
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Feb 15, 2022
6f3f9cb
DIG-772: GraphQL Integration with CanDIGv2 stack - Part 2 (#117)
AliRZ-02 Mar 8, 2022
e95628f
Integrating OPA into the stack (#119)
daisieh Mar 16, 2022
b30948d
corresponding move for https://github.com/CanDIG/candig-opa/pull/1701
daisieh Mar 23, 2022
cfafba3
Move Opa datasets permissions to separate file (#120)
daisieh Mar 23, 2022
2efdba9
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Mar 23, 2022
a1993c8
pass env vars in docker-compose
daisieh Mar 28, 2022
5b57310
pass CANDIG_AUTHORIZATION in to Dockerfile
daisieh Mar 28, 2022
41e0c4e
Update candig-server deployment to use Opa (#122)
daisieh Mar 30, 2022
427dd45
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Mar 30, 2022
c6c00ef
HTSGET uses Opa to authorize user access to datasets (#121)
daisieh Mar 30, 2022
b6aa87f
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Mar 30, 2022
29f29ed
fixes for keycloak container port, candig-server build disable (#123)
shaikh-rashid Apr 4, 2022
2138aee
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Apr 4, 2022
f7d1a37
changes to match opa tweaks (#124)
daisieh Apr 5, 2022
b172de5
remove quotes from policies.json.tpl (#125)
daisieh Apr 5, 2022
65cc22f
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Apr 5, 2022
c06b254
clean up the way we start opa
daisieh Apr 5, 2022
5cab0c5
clean up opa startup call (#126)
daisieh Apr 5, 2022
ca0915a
template fixes
daisieh Apr 7, 2022
a980ec0
candig-data-portal docker fixes
daisieh Apr 8, 2022
71247a5
another docker fix
daisieh Apr 8, 2022
7f4b5d7
opa_runner uses internal ip addresses
daisieh Apr 8, 2022
761e44e
straighten out uses of internal and external urls
daisieh Apr 8, 2022
b624ecc
portal port
daisieh Apr 8, 2022
0e4a839
Update opa
daisieh Apr 8, 2022
8d1835e
pass in IDP to env in opa-runner
daisieh Apr 9, 2022
2939716
move script exec
daisieh Apr 9, 2022
6b55036
short internal container name for vault
daisieh Apr 11, 2022
881d5a4
Consolidate to just API_SLUG instead of separate API_NAME
daisieh Apr 11, 2022
f10a3c2
move to a variable set in .env
daisieh Apr 11, 2022
591c1e9
Update htsget_app
daisieh Apr 11, 2022
142c5d7
Update opa
daisieh Apr 11, 2022
26127c8
Update candig-data-portal
daisieh Apr 11, 2022
1d195d1
Building with Vagrant on VirtualBox no longer works (#127)
sdumitriu Apr 11, 2022
89ab09e
update opa
daisieh Apr 11, 2022
ab148d4
add quotes back
daisieh Apr 11, 2022
a48a020
Miscellaneous changes to server deployment settings (#128)
daisieh Apr 11, 2022
d3dddfa
Update htsget_app
daisieh Apr 11, 2022
c5e1672
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Apr 11, 2022
497231f
Update htsget_app
daisieh Apr 11, 2022
4000472
tiny setting tweaks (#130)
daisieh Apr 12, 2022
5972270
Build the auth containers as well on VirtualBox (#136)
sdumitriu Apr 21, 2022
7b4fd36
Updated list of module names in the example (#133)
sdumitriu Apr 21, 2022
524f077
More tweaks (#131)
daisieh Apr 22, 2022
9a360f3
DIG-828: HTSget should be behind Tyk (#138)
daisieh May 3, 2022
f702256
Assign site-admin credentials to user2 (#139)
daisieh May 6, 2022
f7b3e71
need to pass opa_site_admin_key to opa's Dockerfile
daisieh May 13, 2022
34944a5
DIG-663 & DIG-763 - Adding Vault Helper Tool to Candigv2 & Documentat…
Zamm178 May 13, 2022
c080c51
remove directory for VHT
daisieh May 13, 2022
c1af316
bump candig-data-portalversion ⬆
Jun 8, 2022
85f99b9
Changes required in AuthX stack, bug fixes and tweaks 🐛🚀 (#143)
shaikh-rashid Jun 11, 2022
dd44bd5
Update minio container (#140)
daisieh Jun 14, 2022
af148a3
Opa behind Tyk (#141)
daisieh Jun 14, 2022
8c12931
new release: (#146)
shaikh-rashid Jun 17, 2022
f143fad
Fix merge conflicts with branch stable
Jun 21, 2022
c3521be
pin python version and alpine version for katsu📌 (#149)
shaikh-rashid Jun 21, 2022
bd8248b
Vault stores s3 secrets (#142)
daisieh Jun 22, 2022
047bc51
bump version and submodule for federation-service and data-portal 🆙
Jun 24, 2022
2723299
Fix merge conflicts with stable
Jun 24, 2022
96b759e
federation-service needs to be started manually
Jun 24, 2022
23889f1
minor syntax fixes
Jun 24, 2022
f069d3b
Small fixes (#151)
daisieh Jun 28, 2022
4929c1c
in case we're uploading things to our own minio
daisieh Jun 29, 2022
d3aa19b
bump htsget_app to v0.1.6
Jul 4, 2022
6c47869
candig-data-portal v0.1.2 📜
Jul 4, 2022
d4c7055
in case we're uploading things to our own minio (#152)
daisieh Jul 18, 2022
56bf73e
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Jul 26, 2022
5db6968
OPA secrets as docker secrets (#153)
daisieh Aug 4, 2022
d639186
Add switches to Makefile to download M1 binaries (#154)
daisieh Aug 19, 2022
f9aaf6d
Update python and pip version to Apple Silicon (#155)
SonQBChau Aug 19, 2022
26ef949
quick patch for federation_service 🩹
Sep 7, 2022
5277b12
bump candig-data-portalto v0.1.3
Sep 8, 2022
bc67cea
Update submodules (#158)
daisieh Sep 13, 2022
a526eb1
fix: add compatibility (#160)
SonQBChau Sep 23, 2022
eee3579
pass container name into chord_metadata (#162)
daisieh Sep 30, 2022
5f18432
Feature/federation behind tyk api (#163)
shaikh-rashid Oct 13, 2022
844a274
Sonchau/install docker m1 (#161)
SonQBChau Oct 19, 2022
a65710f
pass in env var for HTSGET_URL (#166)
daisieh Oct 19, 2022
1c004bf
Update keycloak_setup.sh (#165)
daisieh Oct 19, 2022
c7c37a7
Updates for docker build of candig-data-portal (#167)
daisieh Oct 19, 2022
610bf92
Sonchau/install docker m1 (#170)
SonQBChau Oct 20, 2022
d58179a
Remove chord-drs/drs-server from stack (#168)
daisieh Oct 24, 2022
64cd1b7
Tiny fixes (#171)
daisieh Oct 24, 2022
8356100
Refresh token rotation (#173)
daisieh Oct 26, 2022
6833ed2
Update submods (#169)
daisieh Nov 15, 2022
b5281d5
Tyk federation fixes (#175)
shaikh-rashid Nov 22, 2022
ecba832
DIG-895: integrating candig-authx module (#177)
daisieh Nov 25, 2022
abc0b8b
fix reversion
daisieh Nov 25, 2022
5c446c5
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Nov 25, 2022
3ed66e3
set emails for fake users (#178)
daisieh Nov 28, 2022
857c619
Update opa
daisieh Nov 29, 2022
1946ded
post-deployment party instruction cleanup (#179)
SonQBChau Nov 29, 2022
0ef9bd7
DIG-931: Vault aws policy needs update permissions (#180)
daisieh Nov 30, 2022
d8f8969
Remove candig server and update module list (#181)
kcranston Nov 30, 2022
4c784e3
Add documentation for Docker and submodules (#182)
CourtneyGosselin Dec 2, 2022
e56a876
Update install-docker.md
kcranston Dec 6, 2022
643b3d7
Documentation for WSL federation configuration (#183)
CourtneyGosselin Dec 6, 2022
abd9dc4
cleanup of docs (#186)
shaikh-rashid Dec 7, 2022
f130723
Update docs (#187)
shaikh-rashid Dec 9, 2022
6d6fc94
Module cleanup (#184)
shaikh-rashid Dec 14, 2022
3df0a8d
Move settings.py here (#190)
daisieh Dec 19, 2022
76d9ee2
DIG-996: Automate /etc/hosts step during init-authx (#188)
OrdiNeu Dec 19, 2022
2774e73
add instructions to mohccn-data and integration testing (#191)
daisieh Dec 21, 2022
dc209a5
cleanup of conda related scripts that are no longer needed (#189)
shaikh-rashid Jan 9, 2023
a460d6d
Sonchau/docs mac m1 (#194)
SonQBChau Jan 11, 2023
cb5a7dc
Keycloak m1 patch (#192)
shaikh-rashid Jan 12, 2023
62ff73a
Add no-cache build instructions (#196)
OrdiNeu Jan 26, 2023
00aae0e
DIG-1071: Revert "cleanup of conda related scripts that are no longer…
OrdiNeu Mar 7, 2023
f01889c
Update katsu docker-compose.yml (#199)
SonQBChau Mar 8, 2023
44cb73a
Conda path fixes (#200)
kcranston Mar 9, 2023
b7305a1
Sonchau/edit chord metadata compose (#204)
SonQBChau Mar 24, 2023
0324184
Bake the `make init_hosts_file` step so it is no longer needed + Add …
OrdiNeu Mar 28, 2023
0e0663a
Fix a bug where make compose-% was missing the IP address (#206)
OrdiNeu Mar 29, 2023
948aa95
Update chord_metadata_service (#209)
SonQBChau Mar 31, 2023
1a3ce95
DIG-999: Automate integration tests (#207)
daisieh Apr 3, 2023
9fb48b7
DIG-1018, DIG-1019, DIG-1020, DIG-1021: fix make clean targets (#208)
daisieh Apr 4, 2023
41cc919
Add a label onto the container spawned by postgresql (#210)
OrdiNeu Apr 4, 2023
0c9bf81
Catching up (#211)
daisieh Apr 4, 2023
f445382
Update opa (#212)
daisieh Apr 4, 2023
6ce67f0
Test htsget inside its container (#213)
daisieh Apr 6, 2023
b422424
Update htsget_app
daisieh Apr 6, 2023
4255098
DIG-1133: changing CANDIG_DOMAIN from docker.localhost to candig.dock…
daisieh Apr 17, 2023
0bb907b
small HTSGet updates (#215)
daisieh Apr 18, 2023
c55f724
add LGPL-3.0 license (#219)
kcranston Apr 21, 2023
f39da8b
DIG-1028: standardize preflight/setup files in compose targets (#216)
daisieh Apr 21, 2023
b82d060
Fix an issue with pre-build-check which caused it to fail on certain …
OrdiNeu Apr 21, 2023
9fe6118
Diff the .env file, fix typo (#220)
daisieh Apr 24, 2023
69498c2
Remove diff flag not available on all versions (#221)
daisieh Apr 25, 2023
7508131
Replace all instances of Chord/Chord-metadata with Katsu (#195)
OrdiNeu Apr 27, 2023
2870d89
Rename htsget-server/htsget-app to htsget (#222)
daisieh Apr 28, 2023
e5e5983
Update opa version (#223)
daisieh Apr 28, 2023
6f235c5
Bump htsget version (#224)
daisieh Apr 28, 2023
5d52eb5
Bump versions and submodules (#226)
daisieh May 4, 2023
4376ba8
katsu update (#225)
SonQBChau May 5, 2023
bff75bd
Add pre-build-checks to prevent the problems found during BCGSC test …
OrdiNeu May 9, 2023
5dded70
Add check in case $CANDIG_DOMAIN isn't set
daisieh May 9, 2023
1e56b37
Add pre-build-checks to prevent the problems found during BCGSC test …
OrdiNeu May 9, 2023
ad45229
Merge branch 'daisieh/prebuildcheck-updates' of https://github.com/Ca…
daisieh May 9, 2023
dbe944d
copy things first to /app, then copy to /vault in entrypoint (#233)
daisieh May 17, 2023
c994b45
Remove explicit use of PWD from Makefiles (#230)
justin-ys May 19, 2023
9cc095f
DIG-1131: Federation refactoring (#231)
daisieh May 19, 2023
9c998f7
DIG-1172: Build validation (#235)
justin-ys May 29, 2023
510a07b
DIG-1143: test SampleDrsObjects (#234)
daisieh May 29, 2023
a1b7d1d
Bump htsget
daisieh May 29, 2023
ac674e0
Update issue templates
daisieh May 30, 2023
6db0e22
Sonchau/katsu update (#232)
SonQBChau May 30, 2023
3eae741
Clean federation during `make clean-authx` (#240)
OrdiNeu May 31, 2023
8acbd30
Post build fixes (#239)
justin-ys Jun 2, 2023
67caf0d
Update ingest-and-test.md (#241)
SonQBChau Jun 2, 2023
1dd3d5f
Fix the "Websocket error: Could not connect to ws:// <x>" error (#243)
OrdiNeu Jun 16, 2023
010f7ac
Add issue template for deployment errors
kcranston Jun 27, 2023
f667bbf
small fixes for Vault setup (#247)
daisieh Jul 11, 2023
4b98a0f
GitHub Actions for CanDIGv2 (#248)
justin-ys Jul 12, 2023
b8376d7
Conda hotfix (#249)
justin-ys Jul 19, 2023
59801fa
Sonchau/add katsu secret (#250)
SonQBChau Jul 21, 2023
8ae462e
Create stable_pr_template.md
daisieh Jul 21, 2023
3351eef
Update katsu, fix integration tests (#253)
SonQBChau Jul 22, 2023
15db896
Update the candig-data-portal ref (#251)
OrdiNeu Jul 22, 2023
d707e04
Updating all submodules to latest stable release (#254)
daisieh Jul 22, 2023
0402ea8
Update katsu_service
daisieh Jul 24, 2023
9f577d3
Add candigv2-ingest container (#242)
justin-ys Jul 27, 2023
d79d47d
change opa image to latest-static to support arm64
kcranston Jul 31, 2023
27d71ed
Add candigv2-ingest container (#242)
justin-ys Jul 27, 2023
38ca198
change opa image to latest-static to support arm64 (#269)
kcranston Aug 1, 2023
7420e85
Merge branch 'develop' of https://github.com/CanDIG/CanDIGv2 into dev…
daisieh Aug 3, 2023
84aedaf
DIG-1282: Fix docker-compose dependency issues & GitHub Actions (#272)
justin-ys Aug 15, 2023
23236be
DIG-1273: Add more endpoints to the Tyk test, and add a timeout (#270)
OrdiNeu Aug 15, 2023
63bdddf
updating submodules (#277)
candigbot Aug 17, 2023
c020cc8
[Auto-generated] Submodule Updates for CanDIG/katsu (5868372733) (#273)
candigbot Aug 17, 2023
34f1e14
updating submodules (#276)
candigbot Aug 17, 2023
e5c82ff
Add ingest to the TYk configuration (#278)
OrdiNeu Aug 21, 2023
5082f8e
Sonchau/update katsu tests (#279)
SonQBChau Aug 23, 2023
7bb1a6f
[Auto-generated] Submodule Updates for CanDIG/katsu (6045785341) (#281)
candigbot Sep 6, 2023
d2bb67a
updating submodules (#282)
candigbot Sep 13, 2023
fdc5379
updating submodules (#284)
candigbot Sep 13, 2023
d74b4b3
updating submodules (#285)
candigbot Sep 14, 2023
7f9bad6
updating submodules (#287)
candigbot Sep 15, 2023
fa8d0eb
updating submodules (#286)
candigbot Sep 15, 2023
ac29f4a
Update services and components list in README (#288)
mshadbolt Sep 19, 2023
d71cf81
[Auto-generated] Submodule Updates for CanDIG/katsu (6237712014) (#289)
candigbot Sep 19, 2023
ab1e860
remove alpine variable from htsget compose (#290)
kcranston Sep 20, 2023
1c7be6e
Update candigv2-ingest (#293)
daisieh Sep 27, 2023
9fe27c5
updating submodules (#295)
candigbot Sep 27, 2023
d115b62
DIG-1318: Opa starts up with only its own keycloak IDP (#292)
daisieh Sep 27, 2023
8337c1b
fix incorrect query service link (#297)
mshadbolt Oct 6, 2023
38d0003
updating submodules (#294)
candigbot Oct 11, 2023
086dd67
Add requirements for HTSGet to access Postgres (#296)
OrdiNeu Oct 12, 2023
1176422
DIG-1240: API middleware service to handle queries across federated i…
OrdiNeu Oct 13, 2023
a3ce376
updating submodules (#301)
candigbot Oct 14, 2023
23c420c
updating submodules (#299)
candigbot Oct 14, 2023
881334f
DIG-1321: Update Postgres to 16 (#304)
OrdiNeu Oct 26, 2023
24faf5c
[Auto-generated] Submodule Updates for CanDIG/htsget_app (6618652479)…
candigbot Oct 26, 2023
5172113
[Auto-generated] Submodule Updates for CanDIG/katsu (6649772121) (#306)
candigbot Oct 27, 2023
94c84b6
updating submodules (#305)
candigbot Oct 27, 2023
dc07779
[Auto-generated] Submodule Updates for CanDIG/katsu (6660167013) (#309)
candigbot Oct 27, 2023
e417b6e
Yavyx/update installation guide (#310)
yavyx Oct 27, 2023
a67527d
DIG-1301: delete cascades, rename htsget dataset to cohort (#312)
daisieh Oct 30, 2023
1345452
updating submodules (#314)
candigbot Nov 1, 2023
d33ef02
not using alpine anymore (#315)
daisieh Nov 1, 2023
5c076b9
updating submodules (#316)
candigbot Nov 1, 2023
4b49ec2
updating submodules (#317)
candigbot Nov 2, 2023
283553e
updating submodules (#318)
candigbot Nov 2, 2023
330117f
DIG-1342: update ingest to cleaned-up version (#302)
daisieh Nov 3, 2023
c76c420
DIG-1171: merge Makefile.authx into Makefile (#319)
daisieh Nov 6, 2023
3125d91
updating submodules (#321)
candigbot Nov 8, 2023
e1a5827
updating submodules (#320)
candigbot Nov 8, 2023
e8e16a6
updating submodules (#322)
candigbot Nov 9, 2023
349c0e9
updating submodules (#323)
candigbot Nov 10, 2023
eb02ccc
updating submodules (#324)
candigbot Nov 10, 2023
cfa87c1
fix: etc/venv/requirements-dev.txt to reduce vulnerabilities (#326)
daisieh Nov 11, 2023
e30f753
Merge branch 'develop' into stable
OrdiNeu Nov 13, 2023
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