Merge client into server #142

tcompa · 2022-08-26T06:29:44Z

No description provided.

…/mwe_fractal into tasks

…and all other field), closes #117

…hunks

…argument passing within fractal_cmd.py

…tform/fractal into tasks-ROIs

Merge tasks-ROIs into tasks

…/mwe_fractal into tasks

…g tasks directy (from tests)

jacopo-exact

There are a few things to review. Some are minor, at least one can lead to serious bugs (using mutable deafult in function args).

Please address and proceed to merge.
cheers

.gitignore

fractal/server/app/runner/__init__.py

fractal/server/app/runner/runner_utils.py

fractal/client/client.py

fractal/server/app/api/v1/task.py

fractal/server/app/models/security.py

…models/project.py

…point

tcompa · 2022-08-29T11:31:30Z

Thanks for all comments. I'll wait for some feedback on the last open point (see above) and then fix and merge.

…alprovider Allow LocalProvider execution (despite SLURM username being set)

jluethi and others added 30 commits July 20, 2022 14:42

Add a check & message if wrong input image type is specified

c2dd24f

Update options for 2x2 test case to improve labeling performance

0c8668c

Merge branch 'tasks' of https://github.com/fractal-analytics-platform…

8593193

…/mwe_fractal into tasks

Fix cellprob threshold argument in 2x2 example

e4652ee

Update metadata parsing for #112

7a39e2a

More robust parsing of Yokogawa metadata from filename (both channel …

abc36d5

…and all other field), closes #117

Update example file

c9ea292

Fix test_unit_illumination_correction to work with ROIs rather than c…

2391151

…hunks

Update test data, to make it compatible with tasks-ROIs branch

2ac2977

Add a num_threads argument to illumination correction + simplify its …

978734e

…argument passing within fractal_cmd.py

git pushMerge branch 'tasks-ROIs' of github.com:fractal-analytics-pla…

b50ca90

…tform/fractal into tasks-ROIs

Add more Cellpose logging info

2462631

Add a check & message if wrong input image type is specified

aef841a

Use typing.Iterable

3121bda

Add test_unit_ROI_indices.py (closes #116)

90164e6

Fix conflict in example file

4bc5e35

Merge pull request #129 from fractal-analytics-platform/tasks-ROIs

0ac4ae6

Merge tasks-ROIs into tasks

Fix one example file

ebf33e4

Clean up example folder

5e58760

Clean up legacy tests folder (waiting for #130)

a928f0c

Improve CLI of illumination_correction

d80e832

Fix per-ROI illumination correction, by explicitly looping over Z planes

31fe853

Put back num_threads in illumination_correction (ref #131)

31444cb

Update example with mlf/mrf files (ref #130)

19c48b5

Update tests/test_workflow_on_fake_data.py (ref #130)

e57bf1b

Use relative paths in tests

1f36039

In illumination correction, try some auto rechunking (ref #131)

2ee3e22

Add support for parsing yokogawa metadata for 2D acquisitions

50ffc46

Add basic tests for metadata parsing from yokogawa

f3e1119

Merge branch 'tasks' of https://github.com/fractal-analytics-platform…

e63a796

…/mwe_fractal into tasks

Remove needs_gpu and __PROVIDER_ARGS__ from default_args, when runnin…

aab9ef1

…g tasks directy (from tests)

tcompa mentioned this pull request Aug 26, 2022

Review parsl config location (possibly move away from default_args) #143

Closed

tcompa added 2 commits August 26, 2022 10:10

In client, only use {project,dataset,task} names, and not IDs

61cf75d

Update examples after 61cf75d

ba8f8cf

jacopo-exact suggested changes Aug 29, 2022

View reviewed changes

tcompa added 7 commits August 29, 2022 09:27

Fix gitignore

4fa690b

Remove {} arg from parsl_config

a466cea

Remove devtools.debug from server/app/runner/__init__.py

b5abdd7

Clarify mapping from project.read_only to ✅/❌ icon

857ec34

Removing devtools.debug from server/app/api/v1/task.py

0d148f8

Add docstring re: #140

b4d9661

Fix docstring for new_uuid

6b7b3e0

tcompa marked this pull request as ready for review August 29, 2022 09:16

tcompa added 5 commits August 29, 2022 12:11

Move unique constraint on projects from common/models/ to server/app/…

5b00bca

…models/project.py

Include meaningful error message in client/_auth.py

d71cba9

Remove comment from client and add TODO comment in endpoint

65ff0d9

typo

500f7c6

Verify the per-user unicity of project.slug in the create_project end…

4b5aeaa

…point

tcompa added 4 commits August 29, 2022 14:21

Change pytest.mark.skip into pytest.mark.xfail for a relevant case

88bc72a

Remove unique=True flag from slug

9dc4a6a

Rewrite endpoint check for unique (user,project_name) pair

27bcccc

Add test_project_creation_name_constraint

d2d941b

tcompa requested a review from jacopo-exact August 29, 2022 12:37

tcompa merged commit 26bec2f into server Aug 29, 2022

tcompa deleted the client branch August 29, 2022 12:44

tcompa restored the client branch August 29, 2022 12:44

tcompa mentioned this pull request Aug 29, 2022

Blocking step in submit_workflow #140

Closed

tcompa deleted the client branch September 1, 2022 14:52

jacopo-exact pushed a commit that referenced this pull request Nov 16, 2022

Merge pull request #142 from fractal-analytics-platform/140_allow_loc…

1196bb1

…alprovider Allow LocalProvider execution (despite SLURM username being set)

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Merge client into server #142

Merge client into server #142

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tcompa commented Aug 26, 2022

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tcompa commented Aug 29, 2022

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Merge client into server #142

Merge client into server #142

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tcompa commented Aug 26, 2022

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tcompa commented Aug 29, 2022

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