griffithlab/civic-server issues and pull requests

#100 - /users endpoint needs search, filters, and paging options to support a community page

Issue - State: closed - Opened by jmcmichael about 9 years ago - 2 comments

#99 - add "rep transcript 2" field for positional information

Issue - State: closed - Opened by acoffman about 9 years ago - 1 comment

#98 - Unable to submit new evidence

Issue - State: closed - Opened by pondycrane about 9 years ago - 2 comments

#97 - need a 'reject' endpoint for suggested evidence items

Issue - State: closed - Opened by jmcmichael about 9 years ago - 2 comments
Labels: enhancement

#96 - Currently can not view the BRAF entry?

Issue - State: closed - Opened by malachig about 9 years ago - 2 comments
Labels: bug

#95 - Variant type parameter

Issue - State: closed - Opened by bainscou about 9 years ago - 3 comments
Labels: question

#94 - Data releases don't seem to be autogenerating

Issue - State: closed - Opened by acoffman about 9 years ago - 1 comment

#93 - gene objects should return transcription strand attribute (-ve / +ve)

Issue - State: closed - Opened by jmcmichael about 9 years ago - 2 comments

#92 - Order items in 'SUGGESTER' drop down menu of admin interface

Issue - State: closed - Opened by malachig about 9 years ago - 1 comment

#91 - Add new database field for Ensembl version (e.g., v75)

Issue - State: closed - Opened by kkrysiak about 9 years ago - 1 comment

#90 - 500 error on add evidence

Issue - State: closed - Opened by obigriffith about 9 years ago - 3 comments

#89 - Some genes list no Gene Aliases but it seems like they do have synonyms

Issue - State: closed - Opened by malachig about 9 years ago - 2 comments

#88 - Unable to merge or otherwise fix a duplicate variant for a gene

Issue - State: closed - Opened by malachig about 9 years ago - 9 comments

#87 - Variant Group Edit POST returns 500 error

Issue - State: closed - Opened by jmcmichael about 9 years ago - 1 comment

#86 - Some variant pages do not load or are invalid?

Issue - State: closed - Opened by malachig over 9 years ago - 4 comments

#85 - Add evidence losing many details

Issue - State: closed - Opened by obigriffith over 9 years ago - 4 comments

#84 - Variant PDGFRA V536E exists without evidence statement

Issue - State: closed - Opened by obigriffith over 9 years ago - 2 comments

#83 - variant coordinates should by numeric integer type and chromosome should be enumerated

Issue - State: closed - Opened by obigriffith over 9 years ago - 1 comment

#82 - Genes endpoint in API does not contain all the genes

Issue - State: closed - Opened by Shane-Neeley over 9 years ago - 6 comments

#81 - different results from variants/typeahead_results and datatables/variants endpoints

Issue - State: closed - Opened by jmcmichael over 9 years ago - 1 comment

#80 - Unable to change correct disease

Issue - State: closed - Opened by obigriffith over 9 years ago - 1 comment

#79 - migrate error

Issue - State: closed - Opened by malachig over 9 years ago - 3 comments

#78 - Add evidence statement currently does not populate variant/gene and can't be accepted

Issue - State: closed - Opened by obigriffith over 9 years ago - 2 comments

#77 - Some evidence statements still appear under user "Admin"

Issue - State: closed - Opened by obigriffith over 9 years ago - 7 comments
Labels: high priority

#76 - Variants with no evidence statements (or at least none that display) in public instance

Issue - State: closed - Opened by malachig over 9 years ago - 3 comments

#75 - Duplicate entries in public instance

Issue - State: closed - Opened by malachig over 9 years ago - 2 comments

#74 - Login to admin console from public site resolves to "http://127.0.0.1:3000/admin"

Issue - State: closed - Opened by malachig over 9 years ago - 2 comments

#73 - Variant group contributor values blank

Issue - State: closed - Opened by obigriffith over 9 years ago - 1 comment

#72 - Data releases not intuitive

Issue - State: closed - Opened by obigriffith over 9 years ago - 3 comments

#71 - Unable to start ./bin/delayed_job

Issue - State: closed - Opened by malachig over 9 years ago - 12 comments
Labels: question

#70 - Submitting new evidence items fails on local instance with subscription related error

Issue - State: closed - Opened by malachig over 9 years ago - 1 comment
Labels: bug

#69 - Support in-text linking for citing evidence items from a variant summary

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment
Labels: wontfix

#68 - Pending evidence can be viewed by everyone

Issue - State: closed - Opened by jmcmichael over 9 years ago - 7 comments

#67 - Allow adding and editing of sources for Gene Summary

Issue - State: closed - Opened by rbilski over 9 years ago - 1 comment

#66 - Enumerated field: "reference_build" for variants

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment

#65 - Disable drug validation

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment

#64 - Enumerated Type For Drug Relations

Issue - State: closed - Opened by acoffman over 9 years ago

#63 - Page not found in API documentation

Issue - State: closed - Opened by Shane-Neeley over 9 years ago - 5 comments
Labels: high priority

#62 - evidence item's clinical significance field returns N/a instead of N/A

Issue - State: closed - Opened by jmcmichael over 9 years ago - 3 comments

#61 - Deleting an evidence item breaks the admin interface

Issue - State: closed - Opened by malachig over 9 years ago - 1 comment

#60 - When adding new evidence items, the drug that I entered doesn't appear in the resulting entry

Issue - State: closed - Opened by malachig over 9 years ago - 1 comment

#59 - Missing evidence field in admin interface

Issue - State: closed - Opened by obigriffith over 9 years ago - 5 comments

#58 - expected behavior when user submits suggested revision identical to existing suggested revision?

Issue - State: closed - Opened by jmcmichael over 9 years ago
Labels: question

#57 - Incorporate coordinates

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment

#56 - Add more information to tables in Admin interface

Issue - State: closed - Opened by malachig over 9 years ago - 1 comment

#55 - add an applied_by attribute to suggested_changes objects?

Issue - State: closed - Opened by jmcmichael over 9 years ago - 2 comments
Labels: enhancement, question

#54 - ohsu data import

Pull Request - State: closed - Opened by bwalsh over 9 years ago - 9 comments

#53 - add to /api/ccc apito support batch

Pull Request - State: closed - Opened by bwalsh over 9 years ago - 2 comments

#52 - should admin Apply entity edit generate a revision event and diff record?

Issue - State: closed - Opened by jmcmichael over 9 years ago
Labels: question

#51 - OHSU data from CGD

Pull Request - State: closed - Opened by bwalsh over 9 years ago - 5 comments

#50 - genes/:geneId/variant_groups returns multiple instances of the same variant

Issue - State: closed - Opened by jmcmichael over 9 years ago - 2 comments

#49 - Preserve ability to query by entrez_id

Pull Request - State: closed - Opened by bwalsh over 9 years ago - 2 comments

#48 - This PR turns variant groups into "first class" civic entities.

Pull Request - State: closed - Opened by acoffman over 9 years ago - 2 comments

#47 - Additional stats endpoint(s)

Issue - State: closed - Opened by acoffman over 9 years ago - 2 comments

#46 - Create a browse sources/publication view that also acts as a curation queue

Issue - State: closed - Opened by malachig over 9 years ago - 1 comment
Labels: enhancement

#45 - Add feature to merge accounts in admin

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment

#44 - User Profile Completion Flow

Issue - State: closed - Opened by acoffman over 9 years ago - 2 comments

#43 - implement REST API versioning?

Issue - State: closed - Opened by jmcmichael over 9 years ago - 3 comments
Labels: question

#42 - Error on Edit Variant Admin page

Issue - State: closed - Opened by nspies13 over 9 years ago - 3 comments

#41 - endpoints returning multiple variants should include a field the client can use for sorting by amino acid or germline coord

Issue - State: closed - Opened by jmcmichael over 9 years ago - 2 comments
Labels: enhancement, v2

#40 - Establish formal backups of the CIViC database

Issue - State: open - Opened by malachig over 9 years ago - 1 comment
Labels: enhancement, high priority

#39 - variants endpoint needs gene aliases returned

Issue - State: closed - Opened by jmcmichael over 9 years ago - 10 comments

#38 - Pull in mutation recurrence data

Issue - State: closed - Opened by nspies13 over 9 years ago - 1 comment
Labels: reviewer feedback

#37 - check out prerender_service and prerender_rails for generating static crawler-friendly pages

Issue - State: closed - Opened by jmcmichael over 9 years ago - 2 comments

#36 - Admin Dashboard should provide meaningful at-a-glance information

Issue - State: closed - Opened by acoffman over 9 years ago - 2 comments

#35 - ALK F1174L has a leading comma in disease column

Issue - State: closed - Opened by obigriffith over 9 years ago - 1 comment

#34 - Include "created by" information in responses and admin pages

Issue - State: closed - Opened by acoffman over 9 years ago - 2 comments

#33 - Background task for resolving DOIDs should be resilient to multiple formats.

Issue - State: closed - Opened by acoffman over 9 years ago - 1 comment

#32 - Allow for each field in the evidence statements to be editable.

Issue - State: closed - Opened by nspies13 over 9 years ago - 1 comment

#31 - importer should insert something in the last_modified field on imported records

Issue - State: closed - Opened by jmcmichael over 9 years ago - 1 comment

#30 - The importer didn't throw an error on missing DOIDs

Issue - State: closed - Opened by kkrysiak almost 10 years ago - 5 comments

#29 - typeahead results should include all fields searched

Issue - State: closed - Opened by jmcmichael almost 10 years ago - 1 comment

#28 - Add HGVS

Issue - State: closed - Opened by nspies13 almost 10 years ago - 3 comments

#27 - Do the Screencast

Issue - State: open - Opened by nspies13 almost 10 years ago - 2 comments
Labels: documentation

#26 - Finish the Gene Summaries Nicholas!

Issue - State: closed - Opened by nspies13 almost 10 years ago

#25 - API Docs

Issue - State: closed - Opened by acoffman almost 10 years ago - 1 comment

#24 - Data Dump Ordering

Issue - State: closed - Opened by acoffman almost 10 years ago - 2 comments

#23 - Error page on SuggestedChange apply

Issue - State: closed - Opened by acoffman almost 10 years ago - 1 comment

#22 - missing details in API output

Issue - State: closed - Opened by obigriffith almost 10 years ago - 1 comment

#21 - Add HGVS to data model

Issue - State: closed - Opened by nspies13 almost 10 years ago - 1 comment

#20 - Evidence Items with two drugs are being separated into two evidence statements.

Issue - State: closed - Opened by nspies13 almost 10 years ago - 8 comments

#19 - Import somatic/germline status from spreadsheets

Issue - State: closed - Opened by obigriffith almost 10 years ago - 5 comments

#18 - Document somewhere (README.md?) how the test suite works and how to run the tests

Issue - State: closed - Opened by malachig almost 10 years ago - 1 comment

#17 - Set up Google Analytics for CIViC so that we can gather usage statistics

Issue - State: closed - Opened by malachig almost 10 years ago - 7 comments

#16 - civic import fails on error

Issue - State: closed - Opened by obigriffith almost 10 years ago - 3 comments