Add links to mzXML file lists to detail view pages

lparsons commented 7 months ago

FEATURE REQUEST

Inspiration

It is difficult to find the mzXML files used in study, from an animal, for a sample, for a peak, etc.

Description

Add links to a list of mzXML files to detail pages for:

[ ] Study
[ ] Animal
[ ] Sample
[ ] PeakGroup
[ ] PeakData

Alternatives

None

Dependencies

This issue cannot be started until the completion of the following issue(s)/ pull request(s):

issue_number_1
pull_request_1

Comment

None

ISSUE OWNER SECTION

Assumptions

List of assumptions that the code will not explicitly address/check
E.g. We will assume input is correct (explaining why there is no validation)

Limitations

A list of things this work will specifically not do
E.g. This feature will only handle the most frequent use case X

Affected Components

change: File path or DB table ...
add: Environment variable or server setting
delete: External executable or cron job

Requirements

[ ] 1. List of numbered conditions to be met for the feature
[ ] 2. E.g. Every column/row must display a value, i.e. cannot be empty
[ ] 3. Numbers for reference & checkboxes for progress tracking

DESIGN

Interface Change description

None provided

Code Change Description

None provided

Tests

[ ] 1. A description of at least one test for each requirement above.
[ ] 2. E.g. Test for req 2 that there's an exception when display value is ''
[ ] 3. Numbers for reference & checkboxes for progress tracking

hepcat72 commented 1 week ago

@lparsons @fkang-pu @jcmatese

This would be a good parallel issue to tackle that is needed before the lab training/presentation in November...

fkang-pu commented 1 week ago

I don't have time to work on TraceBase right now, but took a few minutes to understand this issue. I could be wrong, but it seems to me the link MSRunSample Detail should lead to a page including mzXML file info. I took a look at the following records, but didn't see MZ file name or details:


example 1:

https://tracebase-dev.princeton.edu/DataRepo/animals/136/
linked to MSRun detail:
https://tracebase-dev.princeton.edu/DataRepo/msrunsamples/1538/
No MZ file link

example 2:

https://tracebase-dev.princeton.edu/DataRepo/animals/393/
None for MSRun detail

hepcat72 commented 1 week ago

10/2/2024 Meeting discussion points:

Advanced search to find mzXMLs possibly containing unanalyzed data
Break up this issue
- Maybe take a screenshot and draw on it
Define precisely how/what to present
Possibly use Xi's automated peak picking compared to curated data to identify unanalyzed data and have it browsable in an "unanalyzed data explorer"
- We would want to know whether data was automatically generated or not
Nov meeting could focus on the upload process and hold mzXML to after
Demo data should be an issue in the Nov meeting milestone
Update the zoom link

hepcat72 commented 1 week ago

This issue should be broken up into sub-issues with specific requirements/design, based on:

https://github.com/Princeton-LSI-ResearchComputing/tracebase/discussions/1155#discussioncomment-10825269

Princeton-LSI-ResearchComputing / tracebase