The analysis front/back needs some redoing to also support pgt, now it is very centered around the dda pipeline

glormph / kantele

Lab proteomics raw and search data management

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The analysis front/back needs some redoing to also support pgt, now it is very centered around the dda pipeline #47

Closed glormph closed 3 months ago

glormph commented 1 year ago

The analysis front/back needs some redoing to also support pgt, now it is very centered around the dda pipeline. Look at #28 before redoing since otherwise you'll spend time looking at it later.

glormph commented 1 year ago

This includes some ground work, making things a bit more overseeable:

[x] write some tests
[x] remove v1 UI pipeline API
[x] put wfs in page render
[x] UI components to solve this
[x] look at your mzmldefs for unifying possibility, --input, also https://github.com/lehtiolab/ddamsproteomics/issues/24
[x] analysis blocks shouldnt allow saving, check that they do (e.g. get dataset errors)
[x] make sure you can run with files which are not mzMLs

glormph commented 1 year ago

To remove the v1 pipeline API we'll have to:

have pipeline validate no-mixed isobaric, instruments
predefined files in static-resources repo
update pipeline isobaric spec

So that item will likely be done later.

glormph commented 11 months ago

Remember to deploy in two steps:

[x] PR1 #49 migrations that add fields (value to PsetComponent)
[x] PR2 #53 Some more code to start using PsetComponents in analyses
[x] deploy master, fill in mzmldef values in admin
[ ] PR3 - rest of code and other migrations
[ ] deploy

glormph commented 11 months ago

The migrations in that PR have been deployed but the value field is not in the code on prod yet, so we can't edit it :( Deploy more code as soon as ready with the PsetComponents.

glormph commented 7 months ago

Psetcomponents PR is live, proceed with non-mzml stuff and ui-api versioning deletion

glormph commented 7 months ago

The analysis should be blocked by:

having not defined set names for all datasets

glormph commented 5 months ago

Almost there, also need to rework setname/samplename to be able to include stuff from the input def per file or dataset (pep prefix etc). Specifically, all the things we don't have already explicit support for (plate, fraction, etc) - we can have dynamic parameter fields.

They would all have to be text for now, until we'd include "picking inputdef from an enum" but that would limit the amount of pipelines we can run. This was done in #82