Use case: Create a build manifest given a set of sequencescape IDs, oxford code/ROMA IDs or Alfresco study codes

[magnusmanske]

In the following, a build manifest is considered to be a file with one line per file, and to contain at the minimum:

• iRODs path
• Sample ID (Oxford code or ROMA ID)
• Alfresco study code
• NCBI taxon ID
• Manual QC status
• Date manual QC complete
• ENA run accession
• ENA sample accession

Create a build manifest given a set of sequencescape IDs

Possible with current version:

SELECT vw_sample_tag.value,full_path FROM vw_sample_tag,vw_sample_file WHERE tag_id=3585 AND vw_sample_tag.sample_id=vw_sample_file.sample_id AND `value` IN (list_of_sequenscape_IDs);

See (how to build a manifest)[https://github.com/wtsi-team112/fits/blob/master/documentation/How_to_build_a_manifest.md].

Create a build manifest given a set of Oxford codes and/or ROMA IDs

Possible with current version, similar to above.

Create a build manifest given a set of Alfresco study codes

The current version does not track Alfresco study codes. These can be imported, though a sample tracking system might be a more appropriate place for this information. Alfresco study names (number&text) are present in FITS for many samples, imported from Solaris and study names from sequenscape, in various stages of completion/correctness.

[podpearson]

@magnusmanske you say "The current version does not track Alfresco study codes", but issue #25 says it is possible to build a manifest with Alfresco study code with the current version. These can't both be correct. Does the current version contain Alfresco study codes or not?

[magnusmanske]

Trying to be specific here:

• FITS current does track 44,582 samples (by FITS definition) with an Alfresco study name, such as "1087-AN-HAPMAP-DONNELLY".
• FITS current does NOT track dedicated Alfresco study IDs, such as "1087". These can be extracted from the Alfresco study name on-the-fly. There is no mechanism at the moment to automatically add new associations of samples to Alfresco study names; sequenscape study names are imported from MLWH automatically, but I hesitate to implement a "guessing game" to set them as Alfresco studies based on some pattern, especially since some sequenscape study names supposed to be Alfresco study names are mangled/wrong.

[podpearson]

@magnusmanske yes, I am interested in the full Alfresco study name here (not just the 4-digit code). As with https://github.com/malariagen/fits/issues/28 I guess what I'm still unclear about what are the data sources for "Alfresco study", and whether this can be complete without first addressing #44. I think I can live with this not being in MVP v1, in which case we should perhaps close this issue and create a new one, but let's get feedback from production team before we close this issue. Also, if not in MVP v1, I think this should be high priority of v2.