Closed anneodonnell closed 2 years ago
hanars
commented
2 years ago @Caustint this is now available in seqr. In the "Update Individual Metadata" you can upload a file which has an "Assigned Analyst" column that contains the email addresses of the analysts you want to assign
Caustint
commented
2 years ago This is fantastic, thank you! Did you intend to add the Assigned Analyst column to the downloadable template files? I manually added it and it worked fine, but just wanted to check.
On Fri, Feb 4, 2022 at 1:58 PM hanars @.***> wrote:
@Caustint https://github.com/Caustint this is now available in seqr. In the "Update Individual Metadata" you can upload a file which has an "Assigned Analyst" column that contains the email addresses of the analysts you want to assign
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/seqr/issues/2230#issuecomment-1030263963, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQEFBFN3NI3QLYBLHXUBD4DUZQOVBANCNFSM5GWTCGOQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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hanars
commented
2 years ago My intention was not to add it because I think the vast majority of the time people are updating metadata they won't want to assign the analyst, so I left it out of the download
Caustint
commented
2 years ago Got it. It might be nice to indicate somewhere on the bulk edit pages that this is an available optional column (I couldn't see it there, forgive me if I missed it)?
Some troubleshooting: I was able to get this to work nicely in the Proband-only Pathways project but the table doesn't upload when I try to go through the same process for RGP. Can you advise if there is any specific formatting I need to adhere to in projects with family structures (like RGP)? I.e. should I choose one individual in each family to add info within the Assigned Analyst column? Does it matter which individual?
For what it's worth, for the table that wouldn't upload I had the Assigned Analyst column filled in for every family member: [image: image.png]
Related question: Can I upload a file containing just the families/individuals I want to update? Would that leave all the other families as they are? I am a little nervous about somehow messing up the entire project!
Christina Austin-Tse, PhD, FACMG Analysis Team Lead, Center for Mendelian Genomics, Broad Institute of MIT and Harvard Clinical Molecular Geneticist, Center for Genomic Medicine, Massachusetts General Hospital Instructor in Pathology, Harvard Medical School Pronouns: She/her
On Tue, Feb 8, 2022 at 12:40 PM hanars @.***> wrote:
My intention was not to add it because I think the vast majority of the time people are updating metadata they won't want to assign the analyst, so I left it out of the download
— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/seqr/issues/2230#issuecomment-1032884871, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQEFBFILN266QJEELO5UHF3U2FIRRANCNFSM5GWTCGOQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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hanars
commented
2 years ago Got it. It might be nice to indicate somewhere on the bulk edit pages that this is an available optional column (I couldn't see it there, forgive me if I missed it)?
Its not shown, feel free to submit a new gtihub issue if you would like me to add it
Some troubleshooting: I was able to get this to work nicely in the Proband-only Pathways project but the table doesn't upload when I try to go through the same process for RGP. Can you advise if there is any specific formatting I need to adhere to in projects with family structures (like RGP)? I.e. should I choose one individual in each family to add info within the Assigned Analyst column? Does it matter which individual? For what it's worth, for the table that wouldn't upload I had the Assigned Analyst column filled in for every family member: [image: image.png]
I think it shouldn't matter whether you choose one individual in each family, or whether you set all of them to the same analyst, but one is sufficient and it shouldn't matter which one. Just make sure both the family ID and individual ID are correctly set. Also, note that when you reply to emails in github it won't attach anything, you need to go to the github website for that
Related question: Can I upload a file containing just the families/individuals I want to update? Would that leave all the other families as they are? I am a little nervous about somehow messing up the entire project!
Yes I would in fact strongly recommend you ONLY include families you want to change, as families that are left out will remain unchanged and families that you include but don't want to change you might accidentally mess up
Is your feature request related to a problem? Please describe. Be able to assign cases in a bulk upload
Describe the solution you'd like Add assign analyst as an option for bulk upload. It would often be uploaded at a separate time from the other metadata but should have the option to also upload with the other metadata.