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malariagen / fits

File tracking system for group DK
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System for retrieving all samples from an Alfresco study #17

Open podpearson opened 6 years ago

podpearson commented 6 years ago

This is a placeholder for a potential future piece of work.

I get a few requests from @sclaugoncalves of the type "could you please send me a list of the samples sequenced under study 1128-PV-GSKMULTI-RAYNER". It would be great to have a system whereby Sonia can do this for herself.

This is not for the first release of FITS, and will probably need some discussion with Sonia before starting any actual work.

magnusmanske commented 6 years ago

Even more fundamentally, it would require a source from which I can retrieve the sample-to-study information. I have imported the associations for Alfresco studies from Solaris into FITS, and I have the study names from Multi-LIMS Warehouse, but the format are obviously incomplete, and the latter are not exactly reliable (more "kinda like Alfresco study names, mostly").

magnusmanske commented 6 years ago

Assuming FITS has Alfresco data imported, you can get detailed sample information like so:

SELECT * FROM vw_pivot_sample WHERE fits_sample_id IN (SELECT DISTINCT sample_id FROM sample2tag WHERE tag_id=3604 AND `value`='1128-PV-GSKMULTI-RAYNER')
magnusmanske commented 6 years ago

I can wrap this into a command-line script, or a website, though the latter should probably wait until we move FITS to a cloud DB.