114 update job configurations to study configurations

[powersaudrey25]

Overview

!!!! Waiting to merge until bug is fixed in main

This pull request merges our work on refactoring the job_monitoring_application to refer to 'study_configuration' instead of 'job_configuration'. It includes a renaming of all references to a 'job_configuration' to a 'study_configuration' in the frontend, backend, trackerapi, and internal_servers.

The following migrations were created:

• creation of the study_configuration table
• addition of the study_configuration_id column to the study table
• addition of the study_configuration_id column to the step_configuration table
• deletion of job_configs table
• deletion of job_config column from study table
• deletion of job_config column from step table
• move data from job_config table to study_config table

These refactorings make our app more coherent and are more in line with real world medical imaging applications.

Implementation

Migrations to the database Refactoring in frontend, backend, trackerapi, and internal_servers

Testing

All tests related to job_config were changed to reference study_config. All tests in backend, trackerapi, and frontend pass. All Cypress tests pass.

Problems Faced

I had accidentally changed a step configuration reference to a study config reference which broke a lot of tests. After fixing that though no other significant problems since I followed the procedure outlined in PR 113

Notes

No visible frontend changes.

[github-actions[bot]]

Jest Coverage

Summary

Lines	Statements	Branches	Functions
	75.65% (432/571)	57.14% (68/119)	68.2% (118/173)

Junit Summary

Tests	Skipped	Failures	Errors	Time
35	0 :zzz:	0 :x:	0 :fire:	3.666s :stopwatch:

Coverage Report (75%)

File	% Stmts	% Branch	% Funcs	% Lines	Uncovered Line #s
All files	75.65	57.14	68.2	75.14
fixtures	100	100	100	100
kidneyStudyFixture.tsx	100	100	100	100
src/components	90.09	44.44	82.75	91.17
ErrorMessageBox.tsx	83.33	100	0	100
EventTimeline.tsx	71.42	0	0	75	79–83
Metadata.tsx	85.71	0	80	84.61	74–75
Navbar.tsx	90.47	50	100	90	150, 163
StackedChart.tsx	100	66.66	100	100	72–85
withAuthenticated.tsx	100	100	100	100
src/contexts	90	100	58.33	89.28
authContext.tsx	90	100	58.33	89.28	72, 90, 104
src/data	28.08	28.57	36.11	16.88
index.ts	28.08	28.57	36.11	16.88	14–24, 35–45, 53–63, 73–83, 95–104, 116–126, 136–145, 155–160, 172–189, 199–207, 217–222, 235–274
src/hooks	100	100	100	100
useAuthContext.ts	100	100	100	100
src/pages	86.84	77.41	83.33	87.5
analytics.tsx	96.15	100	88.88	96	90
dashboard.tsx	100	100	100	100
index.tsx	100	100	100	100
login.tsx	83.87	88.88	85.71	83.33	52–57, 109
profile.tsx	78.57	66.66	75	83.33	63–66
signup.tsx	80.48	57.14	72.72	80	65–67, 82–83, 163–170, 194
src/pages/apikeys	73.21	54.54	64.28	71.69
index.tsx	73.21	54.54	64.28	71.69	74–77, 89, 94–99, 104–108, 195
src/pages/studies	75.23	47.22	67.74	78.12
[id].tsx	68.57	37.5	57.89	71.42	84, 93–107, 111–113, 124–125, 129, 133, 142, 218
index.tsx	88.57	66.66	83.33	90.9	69, 78, 95

[sonarcloud[bot]]

Quality Gate passed

Issues
2 New issues
1 Accepted issue

Measures
0 Security Hotspots
No data about Coverage
8.6% Duplication on New Code

See analysis details on SonarCloud

[powersaudrey25]

@mbrzus Michal I know you were running into some problems with the agent/logger, was that related to this PR or is this fine to merge? @zmorris248 were you able to run the agent/logger and create a job with this PR?

[mbrzus]

@mbrzus Michal I know you were running into some problems with the agent/logger, was that related to this PR or is this fine to merge? @zmorris248 were you able to run the agent/logger and create a job with this PR?

Yes, I was getting issues on this branch, I described them on teams (conversation on March 8th).

[zmorris248]

@powersaudrey25 When I ran it with you on the last day before break, I did see some information on the Orthancs already, related to @mbrzus's first issue on teams. This didn't affect me running the system though or the agent. I could see things getting updated on the front end. I would get an error on step 4, as I think everyone else is. I believe it would keep re-running the study because step 4 was never marked as completed, so our system finishes the process and still finds a study in queue and restarts the process.

[powersaudrey25]

@mbrzus @zmorris248 thanks! just wanted to get the problems documented on this branch/pr