Comments (3)
@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?
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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.
from fits.
@magnusmanske yes, I am interested in the full Alfresco study name here (not just the 4-digit code). As with #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.
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Related Issues (20)
- Files with no sample_supplier_name in iRODS metadata
- Samples missing sample accessions
- Add source column to tag table HOT 2
- MalariaGEN sample ID tag? HOT 2
- Populate Alfresco study using sequencescape-alfresco study mapping file HOT 8
- Decision on whether to keep mlwh/iRODS and FITS in sync
- Decision on whether to apply solaris-vs-mlwh differences to mlwh
- Richard to create Pf manifest HOT 1
- Add historical context to manifest creation doc
- Fix missing taxon IDs
- Fix taxon IDs 62297 to 62323
- Fix other taxon IDs
- Decision on making FITS redeployable from scratch HOT 21
- Separating "notes" into a table, and use adapted code HOT 2
- Determine files for which we have information only from iRODS HOT 1
- Samples without files are not tracked HOT 3
- Data on library IDs and study are missing while present in mlwh
- MLWH/Subtrack-only import HOT 19
- missing legacy library IDs HOT 1
- Should we change ownership on Richard Durbin studies? HOT 3
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