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252 workflow automation berkley rc1 #272

Merged
merged 154 commits into from
Oct 15, 2024
Merged

252 workflow automation berkley rc1 #272

merged 154 commits into from
Oct 15, 2024

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mbthornton-lbl
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This PR merges the Berkley RC1 branch into main

aclum and others added 30 commits August 19, 2024 15:56
@aclum
Update workflows.yaml for berkeley
3237aee
@aclum
Berkeley compatible workflows-mt.yaml
8230b40
@aclum
Berkeley compatibility for workflows.yaml
ad2f143
@aclum
Berkeley update import.yaml
afb2c48
@aclum
Berkeley pdate import_test.yaml
9fa3737
@aclum
Update test_activities.py
a4b9cfd
@aclum
Berkeley Update activity_mapper.py to match config changes
5767100
@aclum
bump nmdc-schema verison to berkeley
2f47fbf
@aclum
Merge branch 'update-berkeley-configs' of https://github.com/microbio…
a58a9a5 
…medata/nmdc_automation into update-berkeley-configs
@aclum
updating poetry.lock file
99db9ee
@aclum
update how nmdc package is imported
5fc6d51
@aclum
update nmdc import
05f7e8e
@aclum
remove extra space
1194436
@aclum
update some tests to berkeley
e209d15
@aclum
updates to test data for berkeley
88268df
@aclum
udpates to test_import.py
cad7731
@aclum
remove part_of on workflow executions
af1e2e8
@aclum
pinning to rc16 until release files issue is resolved
08f9185
@aclum
get most tests working for berkeley
58e9583
@aclum
adding back data object reference to metagenome_annotation_activity_s…
308d0c2 
…et.json
@aclum
updating workflow endpoint from activites to workflow_executions
39a75fa
@mbthornton-lbl
Merge pull request #243 from microbiomedata/221-update-workflow-autom…
e4bd43d 
…ation-to-use-berkley-style-api-endpoints

update workflow endpoint from activities to workflow_executions
@mbthornton-lbl
Merge in main after 195 -> main
f0fb546
@mbthornton-lbl
Merge branch '219-refactor-workflow_automation-to-use-berkley-metadat…
f774152 
…a-models' into update-berkeley-configs
@mbthornton-lbl
Merge pull request #237 from microbiomedata/update-berkeley-configs
12fca7e 
Update berkeley configs
@mbthornton-lbl
Update test fixtures and fix failing rest_activities
24b01f4
@mbthornton-lbl
Merge in update berkley configs and fix failing tests
d00cb3d
@mbthornton-lbl
remove commented-out assertions
a79eaf8
@mbthornton-lbl
clean up redundant test fixtures
eca5dd7
@mbthornton-lbl
Refactor Watcher class
95fa281
mbthornton-lbl and others added 25 commits October 9, 2024 11:30
@mbthornton-lbl
Handle eukaryot_evaluation data in MAGs records
44866d0
@mbthornton-lbl
Merge branch '251-missing-keys-in-workflow-records' into 265-inplemen…
ff52225 
…t-cromwell-runner
@mbthornton-lbl
implement get_job_status method with tests
c1c80b8
@mbthornton-lbl
implement get_job_metadata
da6acec
@aclum
Update workflows.yaml
fba57ff 
bump mag version
@aclum
bump MAG version in import.yaml
239b40c
@mbthornton-lbl
Clean up test fixtures
a981c0e
@mbthornton-lbl
reorganize test fixtures
6a2fe30
@mbthornton-lbl
Merge branch '252-workflow-automation-berkley-rc1' into 251-missing-k…
9230913 
…eys-in-workflow-records
@mbthornton-lbl
Merge branch '252-workflow-automation-berkley-rc1' into 265-inplement…
4350e66 
…-cromwell-runner
@mbthornton-lbl
add job_id setter and clean up unused fixture
c2fcd90
@mbthornton-lbl
Merge pull request #262 from microbiomedata/251-missing-keys-in-workf…
1ac043e 
…low-records

251 missing keys in workflow records
@mbthornton-lbl
add test for fetch_release_file
2dddc24
@mbthornton-lbl
Merge branch '252-workflow-automation-berkley-rc1' into 265-inplement…
e5e910b 
…-cromwell-runner
@mbthornton-lbl
add fetch_release)file and unit test
eb68d1f
@mbthornton-lbl
add additional unit tests for fetch_release_file
a0daf87
@mbthornton-lbl
Merge pull request #269 from microbiomedata/268-berkeley-bump-to-nmdc…
4768863 
…-schema-version-1101

Update nmdc-schema to version 11.0.1
@mbthornton-lbl
add generate_inputs and workflow_labels helper functions with test
da8bec7
@mbthornton-lbl
add generate_submission_files function with test
c7dd32d
@mbthornton-lbl
add unit test
0aa85ae
@mbthornton-lbl
patch watcher test with cromwell URL response
0a6e1d8
@mbthornton-lbl
Update tests and test fixtures
7ece6cc
@mbthornton-lbl
Add test for watcher
62f067d
@mbthornton-lbl
reformatted and added doc strings
ae9b270
@mbthornton-lbl
Merge pull request #271 from microbiomedata/265-inplement-cromwell-ru…
74a6c92 
…nner

265 inplement cromwell runner
@mbthornton-lbl mbthornton-lbl linked an issue Oct 15, 2024 that may be closed by this pull request
Workflow Automation Deploy Berkley RC1 #252
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@mbthornton-lbl mbthornton-lbl requested a review from aclum October 15, 2024 15:44
aclum
aclum approved these changes Oct 15, 2024
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These changes have all been reviewed previously with merging to the staging branch 252-workflow-automation-berkley-rc1

@aclum aclum merged commit 495142f into main Oct 15, 2024
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@aclum aclum deleted the 252-workflow-automation-berkley-rc1 branch October 15, 2024 15:59
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Workflow Automation Deploy Berkley RC1
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@mbthornton-lbl @aclum