📝 Adds rabbit ss1d example script for public-api [skip actions] #3138

pcrespov · 2022-06-24T12:59:00Z

What do these changes do?

Adds a sample script that runs the Rabbit Soltis-Saucerman model with full b-AR signalling (or "Rabbit SS 1D cardiac") from dataset 4 via the public api.

Related issue/s

M4.5.7 “High-level” simulation experiment editor to present an interface on the SPARC Portal for users to configure simulation/analyses to execute on oSPARC
- Iteration with SIM Core re input/output : this script was requested in this task
port annotation osparc-issues#625: support Alan

How to test

Install packages

$ pip install osparc python-dotenv

Set up url, user and password to access the api endpoint in .env file (see .env-devel)
Run script

$ cd tests/pubic-api/examples
$ python rabbit_cardiac_ss1d.py
Entrypoint https://api.osparc-master.speag.com
Job created {'created_at': datetime.datetime(2022, 6, 24, 13, 45, 28, 114000, tzinfo=tzutc()),
 'id': '03e35f94-16e0-4861-8b3a-9e87d5f32a74',
 'inputs_checksum': 'b81d82fd92426910fc86febc362b5843ded1e9c447b508e40f6fbcf59d9f5232',
 'name': 'solvers/simcore%2Fservices%2Fcomp%2Frabbit-ss-1d-cardiac-model/releases/1.0.0/jobs/03e35f94-16e0-4861-8b3a-9e87d5f32a74',
 'outputs_url': 'http://api.osparc-master.speag.com/v0/solvers/simcore/services/comp/rabbit-ss-1d-cardiac-model/releases/1.0.0/jobs/03e35f94-16e0-4861-8b3a-9e87d5f32a74/outputs',
 'runner_name': 'solvers/simcore%2Fservices%2Fcomp%2Frabbit-ss-1d-cardiac-model/releases/1.0.0',
 'runner_url': 'http://api.osparc-master.speag.com/v0/solvers/simcore/services/comp/rabbit-ss-1d-cardiac-model/releases/1.0.0',
 'url': 'http://api.osparc-master.speag.com/v0/solvers/simcore/services/comp/rabbit-ss-1d-cardiac-model/releases/1.0.0/jobs/03e35f94-16e0-4861-8b3a-9e87d5f32a74'}
>>> Progress: 0%  [elapsed:0.04s]...

< ... >

>>> Progress: 100%  [elapsed:354.94s]...
---------------------------------------
>>> What is the status? {'job_id': '03e35f94-16e0-4861-8b3a-9e87d5f32a74',
 'progress': 100,
 'started_at': None,
 'state': 'SUCCESS',
 'stopped_at': datetime.datetime(2022, 6, 24, 13, 51, 23, 448854),
 'submitted_at': datetime.datetime(2022, 6, 24, 13, 51, 23, 448812)}
>>> output_1 = {'checksum': 'c5111b91456d4fc5d3215a21e727b2a2',
 'content_type': 'text/plain',
 'filename': 'ECGs.txt',
 'id': '23041654-8b4f-3953-8dc6-aba6c007df06'}
>>> output_2 = {'checksum': '1f636e762a19039a09ee7dbd7dd0798a',
 'content_type': 'text/plain',
 'filename': 'ap_1D.txt',
 'id': 'cbb393a8-b478-3181-96a4-e65ecd471fb7'}
>>> output_3 = {'checksum': 'fab98ef1f96e749eccc5ada76c920d32',
 'content_type': 'text/plain',
 'filename': 'cai_1D.txt',
 'id': '1ee715e1-31f4-3c97-a0b0-931bb3eb2bcf'}
>>> output_4 = {'checksum': '6f4d3414fbe8183be14c702a9311c9d4',
 'content_type': 'application/octet-stream',
 'filename': 'model_INPUT.from1D',
 'id': 'eb231a48-ce91-3702-a259-5e1185621dd0'}
---------------------------------------
---------------------------------------
>>>  23041654-8b4f-3953-8dc6-aba6c007df06
Downloaded to /tmp/tmp3hr4i7b3
Content-Type:  text/plain
Result:     26.000        0.216117
    27.000        0.009865
    28.000        0.020980
    29.000        0.016861
    30.000       
Status:  os.stat_result(st_mode=33204, st_ino=4068214, st_dev=2081, st_nlink=1, st_uid=1000, st_gid=1000, st_size=550, st_atime=1656078683, st_mtime=1656078683, st_ctime=1656078683)
---------------------------------------
>>>  cbb393a8-b478-3181-96a4-e65ecd471fb7
Downloaded to /tmp/tmpgu1c4bwj
Content-Type:  text/plain
Result: 2.600000e+01    24.073404       24.077454       24.083536       24.090840       24.099230       24.108661       24.119051       24.130284       24.1422
Status:  os.stat_result(st_mode=33204, st_ino=4068216, st_dev=2081, st_nlink=1, st_uid=1000, st_gid=1000, st_size=41575, st_atime=1656078683, st_mtime=1656078683, st_ctime=1656078683)
---------------------------------------
>>>  1ee715e1-31f4-3c97-a0b0-931bb3eb2bcf
Downloaded to /tmp/tmpfq4a3mt0
Content-Type:  text/plain
Result: 2.600000e+01    0.000143        0.000143        0.000142        0.000142        0.000141        0.000139        0.000138        0.000137        0.000136        0.0001
Status:  os.stat_result(st_mode=33204, st_ino=4068217, st_dev=2081, st_nlink=1, st_uid=1000, st_gid=1000, st_size=37475, st_atime=1656078684, st_mtime=1656078684, st_ctime=1656078684)
---------------------------------------
>>>  eb231a48-ce91-3702-a259-5e1185621dd0
Downloaded to /tmp/tmpwh6iumxs
Content-Type:  application/octet-stream
Status:  os.stat_result(st_mode=33204, st_ino=4068218, st_dev=2081, st_nlink=1, st_uid=1000, st_gid=1000, st_size=349800, st_atime=1656078684, st_mtime=1656078684, st_ctime=1656078684)
---------------------------------------
[{'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': '49b7db0b-b081-3fcc-ae5f-e25c9ec66178'}, {'checksum': 'fab98ef1f96e749eccc5ada76c920d32',
 'content_type': 'text/plain',
 'filename': 'cai_1D.txt',
 'id': 'faf6d62b-9510-3d7f-950b-5f9d3feb006f'}, {'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': '46d7f6f2-16fd-3fd7-851e-d562ec941211'}, {'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': 'eeaaac91-92d7-35ad-bee2-36d4a068a815'}, {'checksum': '6f4d3414fbe8183be14c702a9311c9d4',
 'content_type': 'application/octet-stream',
 'filename': 'model_INPUT.from1D',
 'id': '8d2a2c3a-3b48-372e-ae3b-7f0f27852b6f'}, {'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': '34c70352-122b-3005-9be8-e6690db4ee36'}, {'checksum': 'c5111b91456d4fc5d3215a21e727b2a2',
 'content_type': 'text/plain',
 'filename': 'ECGs.txt',
 'id': '64bd4bac-1d21-3562-97c4-bd4d166ba9d6'}, {'checksum': '1f636e762a19039a09ee7dbd7dd0798a',
 'content_type': 'text/plain',
 'filename': 'ap_1D.txt',
 'id': 'ed8e778e-b2c4-3b67-9488-b3f6a0105ff0'}, {'checksum': 'c5111b91456d4fc5d3215a21e727b2a2',
 'content_type': 'text/plain',
 'filename': 'ECGs.txt',
 'id': '23041654-8b4f-3953-8dc6-aba6c007df06'}, {'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': '5c41862b-bd6a-3454-9987-9b1e3c9f01c0'}, {'checksum': '6f4d3414fbe8183be14c702a9311c9d4',
 'content_type': 'application/octet-stream',
 'filename': 'model_INPUT.from1D',
 'id': 'eb231a48-ce91-3702-a259-5e1185621dd0'}, {'checksum': '1f636e762a19039a09ee7dbd7dd0798a',
 'content_type': 'text/plain',
 'filename': 'ap_1D.txt',
 'id': 'cbb393a8-b478-3181-96a4-e65ecd471fb7'}, {'checksum': '97c1e306c099367e949f916136f5f28d',
 'content_type': 'text/plain',
 'filename': 'initial_WTstates.txt',
 'id': '7d2be5d1-7545-326d-963b-380ab2d20c65'}, {'checksum': 'fab98ef1f96e749eccc5ada76c920d32',
 'content_type': 'text/plain',
 'filename': 'cai_1D.txt',
 'id': '1ee715e1-31f4-3c97-a0b0-931bb3eb2bcf'}, {'checksum': 'c5111b91456d4fc5d3215a21e727b2a2',
 'content_type': 'text/plain',
 'filename': 'ECGs.txt',
 'id': 'cb091ad0-bd24-3e6f-b232-c878d098e2bc'}, {'checksum': '1f636e762a19039a09ee7dbd7dd0798a',
 'content_type': 'text/plain',
 'filename': 'ap_1D.txt',
 'id': 'b4c3dcf6-54b0-34e8-a642-b10959021ad8'}, {'checksum': 'fab98ef1f96e749eccc5ada76c920d32',
 'content_type': 'text/plain',
 'filename': 'cai_1D.txt',
 'id': '437193b4-1c58-36ad-bbfa-bae64dee9c0e'}, {'checksum': '6f4d3414fbe8183be14c702a9311c9d4',
 'content_type': 'application/octet-stream',
 'filename': 'model_INPUT.from1D',
 'id': '0583c966-7a93-3820-8362-43ac934e9474'}]

Checklist

adds time and fixes loop fixes non-text results

codecov · 2022-06-27T07:42:12Z

Codecov Report

Merging #3138 (6c3288c) into master (326d0e9) will increase coverage by 0.0%.
The diff coverage is n/a.

@@          Coverage Diff           @@
##           master   #3138   +/-   ##
======================================
  Coverage    81.1%   81.1%           
======================================
  Files         710     710           
  Lines       30621   30621           
  Branches     3948    3948           
======================================
+ Hits        24843   24850    +7     
+ Misses       4937    4930    -7     
  Partials      841     841

Flag	Coverage Δ
integrationtests	`66.2% <ø> (-0.1%)`	⬇️
unittests	`77.5% <ø> (+<0.1%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...ector_v2/modules/comp_scheduler/background_task.py	`83.3% <0.0%> (-8.4%)`	⬇️
...imcore_service_webserver/garbage_collector_core.py	`67.4% <0.0%> (ø)`
.../director/src/simcore_service_director/producer.py	`62.1% <0.0%> (+0.2%)`	⬆️
...imcore_service_webserver/garbage_collector_task.py	`100.0% <0.0%> (+2.3%)`	⬆️
...ore_service_director_v2/utils/dask_client_utils.py	`82.6% <0.0%> (+4.3%)`	⬆️
...rvice_datcore_adapter/utils/requests_decorators.py	`78.9% <0.0%> (+10.5%)`	⬆️

tests/public-api/examples/data_rabbit_cardiac/ss1d_meta.json

KZzizzle

very nice, thanks for the example!

sonarqubecloud · 2022-06-28T07:01:36Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.4% Duplication

elisabettai

Looks great!

Only thing that might not be very clear for a user is this part on the instructions on how to test:

"Set up url, user and password to access the api endpoint in .env file (see .env-devel)". I guess you meant what is nicely explained in the API doc.

pcrespov · 2022-06-28T07:24:57Z

Looks great!

Only thing that might not be very clear for a user is this part on the instructions on how to test:

"Set up url, user and password to access the api endpoint in .env file (see .env-devel)". I guess you meant what is nicely explained in the API doc.

yes

pcrespov added 4 commits June 24, 2022 14:55

adds comment

b1ebf07

adds rabbit_ss1d example

9a0f68b

inputs

ebf6e6c

[skip actions]

d74d8b5

adds time and fixes loop fixes non-text results

pcrespov self-assigned this Jun 24, 2022

pcrespov added this to the Diolkos milestone Jun 24, 2022

pcrespov added a:api framework api, data schemas, a:doc documentation, reporting, admin tasks labels Jun 24, 2022

pcrespov marked this pull request as ready for review June 24, 2022 14:00

pcrespov requested review from elisabettai, esraneufeld, KZzizzle and mguidon June 24, 2022 14:01

Merge branch 'master' into m4_5_7/map-core-example-dataset-4

0f85027

KZzizzle reviewed Jun 27, 2022

View reviewed changes

tests/public-api/examples/data_rabbit_cardiac/ss1d_meta.json Show resolved Hide resolved

KZzizzle approved these changes Jun 27, 2022

View reviewed changes

Merge branch 'master' into m4_5_7/map-core-example-dataset-4

6c3288c

pcrespov changed the title ~~Adds rabbit ss1d example script for public-api~~ Adds rabbit ss1d example script for public-api [skip actions] Jun 28, 2022

elisabettai approved these changes Jun 28, 2022

View reviewed changes

pcrespov changed the title ~~Adds rabbit ss1d example script for public-api [skip actions]~~ 📝 Adds rabbit ss1d example script for public-api [skip actions] Jun 28, 2022

mguidon approved these changes Jun 28, 2022

View reviewed changes

pcrespov merged commit b3d7fa3 into ITISFoundation:master Jun 28, 2022

pcrespov deleted the m4_5_7/map-core-example-dataset-4 branch June 28, 2022 10:06

pcrespov mentioned this pull request Jul 4, 2022

port annotation ITISFoundation/osparc-issues#625

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

📝 Adds rabbit ss1d example script for public-api [skip actions] #3138

📝 Adds rabbit ss1d example script for public-api [skip actions] #3138

pcrespov commented Jun 24, 2022 •

edited

Loading

codecov bot commented Jun 27, 2022 •

edited

Loading

KZzizzle left a comment

sonarqubecloud bot commented Jun 28, 2022

elisabettai left a comment •

edited

Loading

pcrespov commented Jun 28, 2022

📝 Adds rabbit ss1d example script for public-api [skip actions] #3138

📝 Adds rabbit ss1d example script for public-api [skip actions] #3138

Conversation

pcrespov commented Jun 24, 2022 • edited Loading

What do these changes do?

Related issue/s

How to test

Checklist

codecov bot commented Jun 27, 2022 • edited Loading

Codecov Report

KZzizzle left a comment

Choose a reason for hiding this comment

sonarqubecloud bot commented Jun 28, 2022

elisabettai left a comment • edited Loading

Choose a reason for hiding this comment

pcrespov commented Jun 28, 2022

pcrespov commented Jun 24, 2022 •

edited

Loading

codecov bot commented Jun 27, 2022 •

edited

Loading

elisabettai left a comment •

edited

Loading