Ticket #132 (closed enhancement: fixed)

Opened 3 years ago

Last modified 3 years ago

Create a study generator page

Reported by: business@… Owned by: business@…
Priority: major Milestone: 0.5.1
Component: General Version:
Keywords: Cc:
Product: Operating system:
URL: Hardware:

Description

Insert a new menu item in GSCF under Studies: 'Generate new studies'. You can call the controller GenerateStudyController? or something like that. It should just be a simple form with the following options:

- Study name
- Study code
- Study start date
- Assay name
- Assay code (formerly called externalAssayID)
- Assay module
- Assay template

The latter can be confusing, unfortunately we don't have module - template mappings.
* assay module = concrete module, with URL, where assay data is stored
* assay template = template of the extra fields that are stored for this assay
In theory it is also possible to have templates that are used for multiple modules (e.g. a General Assay template, or a Metabolomics template which is used for 2 separate metabolomics modules which reside in different locations). We should think of a better data model or usage of the data model, because now, the user has to choose e.g. 'Metabolomics module [on nmcdsp.org]' as well as 'Metabolomics assay template' which can be confusing.

Change History

  Changed 3 years ago by m.s.vanvliet@…

  • status changed from new to accepted

I setup a Pilot controller
- index: explain pilot + start
- create: setup a study + metabolomics assay (by-pass the Wizard)
- show: show study + list metabolomics assay -> jump to...

@Kees: Currently I redirect the user the the assay/show page... but I guess you want the user to go to the assayModule? If so, how can the user then access the Import Sample/LabRef? Excel?

  Changed 3 years ago by m.s.vanvliet@…

  • status changed from accepted to assigned
  • owner changed from m.s.vanvliet@… to business@…

follow-up: ↓ 4   Changed 3 years ago by business@…

  • owner changed from business@… to m.s.vanvliet@…

In the pilot study view, add a line 'Samples' which shows a summary of the samples that are present in the study, together with a link to import new Samples (to /importer/simpleWizard).

Also, test this functionality. This depends on  https://trac.nbic.nl/gscf/ticket/128 being complete, in particular the change that parentEvent should become nullable. If that is not yet done by the time you need to save samples, go ahead and change it with notification to Jeroen in that ticket.

in reply to: ↑ 3   Changed 3 years ago by business@…

And also, the BootStrap? needs to be updated with an NMC sample template. The change to expect the metabolomics module at 8183 is already done in [948].

  Changed 3 years ago by m.s.vanvliet@…

  • owner changed from m.s.vanvliet@… to business@…

Kees can you test the pilot page(s)

../gscf/pilot/index

Tot test the sample import just create a 2 column Excel like this:
Sample DCL
sample0001 dcl-2010005ACA000001
sample0002 dcl-2010005ACA000002
sample0003 dcl-2010005ACA000003

Thanks...
Michael

follow-up: ↓ 7   Changed 3 years ago by business@…

  • owner changed from business@… to m.s.vanvliet@…

Thanks so far Michael!
The pilot page is not yet user-aware. it should only list studies you have access to. Also, it should not be possible to create a study when you are not logged in - who becomes thenghe owner?
Also, the sample import could be made slightlymore convenient if it already selects the study and data type as we discussed earlier. Just create an importer action stepPilot or something that only shows the upload box and template chooser and then goes straight into importer step 2.

in reply to: ↑ 6   Changed 3 years ago by m.s.vanvliet@…

  • owner changed from m.s.vanvliet@… to business@…

Replying to business@…:

Thanks so far Michael!
The pilot page is not yet user-aware. it should only list studies you have access to. Also, it should not be possible to create a study when you are not logged in - who becomes thenghe owner?
Also, the sample import could be made slightlymore convenient if it already selects the study and data type as we discussed earlier. Just create an importer action stepPilot or something that only shows the upload box and template chooser and then goes straight into importer step 2.

I added the user-aware part... only now it fails... but I think this due to a REST related bug. Injecting into step 2 of the importer is not possible... to make it REDIRECT to the Pilot page after import I have to go through the importer/index page. For the Pilot I think we should leave it like this... We just have to make this clear in the Pilot Test Documentation.

The other thing I added it a temp menu item called Pilot... which is only shown when people go through the pilot/index page to the GSCF... it leaves a session.pilot property which I use in the menu... Should be removed after the pilot(s).

I will wait for the REST services to be working again an then test it.

  Changed 3 years ago by business@…

  • status changed from assigned to closed
  • resolution set to fixed
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