Upstream recently added basic support for AIP tags. While useful, CPG requires better granularity of presentation before AIP tags can be usefully released to our collaborator projects.
This PR:
Builds on the AIP ingest machinery added upstream.
Adds the capability to ingest a full AIP report (as opposed to the cut-down seqr specific report currently supported)
Adds two new AIP tags "AIP-restrictive" and "AIP-permissive" that are populated by the new ingest.
Adds "AIP: first tagged" metadata to AIP tags based on the "first_seen" date in the AIP report
Adds two new sort options for saved variants:
AIP: Last tagged - sorts most recently AIP tagged variants to the top of the list
AIP: Evidence last updated - sorts variants by the most recent date a category was added to a given AIP tag
This is functioning on reanalysis dev, you should have access to play. Let me know if you want a report to test upload with.
I have attempted to isolate the changes required for this from the existing code as much as possible to keep upstream merges easy. However, there were a couple of small spots where I needed to update existing logic. If upstream reworks this specific feature we may need to rework this functionality (I am happy to accept this).
We have chosen to align some terminology with existing seqr terminology rather than the current AIP equivalents ("Last Tagged", "restrictive" vs "permissive" etc). I think this is the right call for the context as our aim it to make the results as intuitive as possible for existing seqr users.
Note: this will require a small existing change to the AIP json report. An array of one or more seqr projects must be present in the top-level metadata field of the report.
Out of scope: This will continue to need manual upload of the AIP reports via the UI. We will want to enable syncing via metamist but that will be a separate PR.
React is not my daily driver so very happy for feedback.
Upstream recently added basic support for AIP tags. While useful, CPG requires better granularity of presentation before AIP tags can be usefully released to our collaborator projects.
This PR:
This is functioning on reanalysis dev, you should have access to play. Let me know if you want a report to test upload with.
I have attempted to isolate the changes required for this from the existing code as much as possible to keep upstream merges easy. However, there were a couple of small spots where I needed to update existing logic. If upstream reworks this specific feature we may need to rework this functionality (I am happy to accept this).
We have chosen to align some terminology with existing seqr terminology rather than the current AIP equivalents ("Last Tagged", "restrictive" vs "permissive" etc). I think this is the right call for the context as our aim it to make the results as intuitive as possible for existing seqr users.
Note: this will require a small existing change to the AIP json report. An array of one or more seqr projects must be present in the top-level metadata field of the report.
Out of scope: This will continue to need manual upload of the AIP reports via the UI. We will want to enable syncing via metamist but that will be a separate PR.
React is not my daily driver so very happy for feedback.