phenopolis/phenopolis_genomics_browser issues and pull requests

#243 - pull publications automatically

Issue - State: open - Opened by pontikos over 4 years ago - 2 comments
Labels: Frontend

#243 - pull publications automatically

Issue - State: open - Opened by pontikos over 4 years ago - 2 comments
Labels: Frontend

#242 - create new patient

Issue - State: closed - Opened by pontikos over 4 years ago - 3 comments
Labels: Frontend

#242 - create new patient

Issue - State: closed - Opened by pontikos over 4 years ago - 3 comments
Labels: Frontend

#241 - Reorder columns by dragging

Issue - State: closed - Opened by pontikos over 4 years ago
Labels: Frontend

#241 - Reorder columns by dragging

Issue - State: closed - Opened by pontikos over 4 years ago
Labels: Frontend

#240 - Related HPO OMIMs in meta table

Issue - State: open - Opened by IsmailM over 5 years ago - 3 comments
Labels: Frontend

#240 - Related HPO OMIMs in meta table

Issue - State: open - Opened by IsmailM over 5 years ago - 3 comments
Labels: Frontend

#98 - Make limit for autocomplete results configurable

Issue - State: closed - Opened by priesgo over 4 years ago

#98 - Make limit for autocomplete results configurable

Issue - State: closed - Opened by priesgo over 4 years ago

#97 - Code tidy

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 2 comments

#97 - Code tidy

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 2 comments

#96 - With pytest

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 3 comments

#96 - With pytest

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 3 comments

#95 - refactor queries to avoid code injection issue

Pull Request - State: closed - Opened by priesgo over 4 years ago - 2 comments

#95 - refactor queries to avoid code injection issue

Pull Request - State: closed - Opened by priesgo over 4 years ago - 2 comments

#94 - Indels in the variants table are not normalised

Issue - State: open - Opened by priesgo over 4 years ago - 2 comments
Labels: Python API

#94 - Indels in the variants table are not normalised

Issue - State: open - Opened by priesgo over 4 years ago - 2 comments
Labels: Python API

#93 - Improve variant table search with a new index

Issue - State: closed - Opened by alanwilter over 4 years ago - 5 comments
Labels: Python API

#93 - Improve variant table search with a new index

Issue - State: closed - Opened by alanwilter over 4 years ago - 5 comments
Labels: Python API

#92 - Refactor sql queries

Issue - State: closed - Opened by alanwilter over 4 years ago - 2 comments
Labels: Python API

#92 - Refactor sql queries

Issue - State: closed - Opened by alanwilter over 4 years ago - 2 comments
Labels: Python API

#91 - Create tests

Issue - State: closed - Opened by alanwilter over 4 years ago - 1 comment

#91 - Create tests

Issue - State: closed - Opened by alanwilter over 4 years ago - 1 comment

#90 - adding variant search + some refactoring around conversion of results…

Pull Request - State: closed - Opened by priesgo over 4 years ago - 1 comment

#90 - adding variant search + some refactoring around conversion of results…

Pull Request - State: closed - Opened by priesgo over 4 years ago - 1 comment

#89 - endpoint to create new user

Issue - State: closed - Opened by pontikos over 4 years ago - 6 comments

#89 - endpoint to create new user

Issue - State: closed - Opened by pontikos over 4 years ago - 6 comments

#88 - Alternatives for obtaining ClinVar data

Issue - State: open - Opened by alanwilter over 4 years ago - 4 comments
Labels: Python API

#88 - Alternatives for obtaining ClinVar data

Issue - State: open - Opened by alanwilter over 4 years ago - 4 comments
Labels: Python API

#87 - update consanguinity on patient page failes

Issue - State: closed - Opened by pontikos over 4 years ago - 1 comment
Labels: duplicate

#87 - update consanguinity on patient page failes

Issue - State: closed - Opened by pontikos over 4 years ago - 1 comment
Labels: duplicate

#86 - update patient currently fails

Issue - State: closed - Opened by pontikos over 4 years ago

#86 - update patient currently fails

Issue - State: closed - Opened by pontikos over 4 years ago

#85 - To use sqlalchemy instead of raw sql commands

Issue - State: closed - Opened by alanwilter over 4 years ago - 7 comments
Labels: Python API

#85 - To use sqlalchemy instead of raw sql commands

Issue - State: closed - Opened by alanwilter over 4 years ago - 7 comments
Labels: Python API

#84 - saving selected columns doesn't work

Issue - State: closed - Opened by pontikos over 4 years ago

#84 - saving selected columns doesn't work

Issue - State: closed - Opened by pontikos over 4 years ago

#83 - create s3/wasabi bucket for each individual in db

Issue - State: closed - Opened by pontikos over 4 years ago - 12 comments
Labels: Python API

#83 - create s3/wasabi bucket for each individual in db

Issue - State: closed - Opened by pontikos over 4 years ago - 12 comments
Labels: Python API

#82 - 51 integrate logging

Pull Request - State: closed - Opened by priesgo over 4 years ago

#82 - 51 integrate logging

Pull Request - State: closed - Opened by priesgo over 4 years ago

#81 - Working on Docker

Issue - State: closed - Opened by pontikos over 4 years ago - 6 comments

#81 - Working on Docker

Issue - State: closed - Opened by pontikos over 4 years ago - 6 comments

#80 - integrate flask logging + fix some issues in error handling

Pull Request - State: closed - Opened by priesgo over 4 years ago

#80 - integrate flask logging + fix some issues in error handling

Pull Request - State: closed - Opened by priesgo over 4 years ago

#79 - strip [Source:HGNC Symbol;Acc:.*] from gene name

Issue - State: closed - Opened by pontikos over 4 years ago - 3 comments

#79 - strip [Source:HGNC Symbol;Acc:.*] from gene name

Issue - State: closed - Opened by pontikos over 4 years ago - 3 comments

#78 - contract between backend and frontend for JSON objects

Issue - State: open - Opened by pontikos over 4 years ago - 20 comments
Labels: enhancement, question, Python API

#78 - contract between backend and frontend for JSON objects

Issue - State: open - Opened by pontikos over 4 years ago - 20 comments
Labels: enhancement, question, Python API

#76 - Allow variants to be searched on the frontend

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#76 - Allow variants to be searched on the frontend

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#75 - Add "Type" for each table Column

Issue - State: open - Opened by YuanTian1991 over 4 years ago - 3 comments
Labels: Python API

#75 - Add "Type" for each table Column

Issue - State: open - Opened by YuanTian1991 over 4 years ago - 3 comments
Labels: Python API

#74 - Clean init file

Pull Request - State: closed - Opened by IsmailM over 4 years ago

#74 - Clean init file

Pull Request - State: closed - Opened by IsmailM over 4 years ago

#73 - Docker updates

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 2 comments

#73 - Docker updates

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 2 comments

#72 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago - 1 comment

#72 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago - 1 comment

#71 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago

#71 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago

#70 - Docker entrypoint

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 3 comments

#70 - Docker entrypoint

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 3 comments

#69 - Docker entrypoint

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 1 comment

#69 - Docker entrypoint

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 1 comment

#68 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago

#68 - Dev live

Pull Request - State: closed - Opened by pontikos over 4 years ago

#67 - fix case sensitiveness on autocomplete endpoint

Pull Request - State: closed - Opened by priesgo over 4 years ago

#67 - fix case sensitiveness on autocomplete endpoint

Pull Request - State: closed - Opened by priesgo over 4 years ago

#66 - Gene search: search is case sensitive and only supports upper case

Issue - State: closed - Opened by priesgo over 4 years ago

#66 - Gene search: search is case sensitive and only supports upper case

Issue - State: closed - Opened by priesgo over 4 years ago

#65 - 12 load genes from biomart

Pull Request - State: closed - Opened by priesgo over 4 years ago - 8 comments

#65 - 12 load genes from biomart

Pull Request - State: closed - Opened by priesgo over 4 years ago - 8 comments

#64 - KeyError: '09G06954_S4_L001_R1_001.fastq.gz'

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment
Labels: Python API

#64 - KeyError: '09G06954_S4_L001_R1_001.fastq.gz'

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment
Labels: Python API

#63 - AttributeError: 'NoneType' object has no attribute 'split'

Issue - State: closed - Opened by IsmailM over 4 years ago - 2 comments
Labels: Python API

#63 - AttributeError: 'NoneType' object has no attribute 'split'

Issue - State: closed - Opened by IsmailM over 4 years ago - 2 comments
Labels: Python API

#62 - Remove all unnecessary tables from the database

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment
Labels: Python API

#62 - Remove all unnecessary tables from the database

Issue - State: closed - Opened by IsmailM over 4 years ago - 1 comment
Labels: Python API

#61 - Consanguinity editing doesn't work

Issue - State: closed - Opened by pontikos over 4 years ago - 2 comments
Labels: bug

#61 - Consanguinity editing doesn't work

Issue - State: closed - Opened by pontikos over 4 years ago - 2 comments
Labels: bug

#60 - Env variables

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#60 - Env variables

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#59 - Add demo Postgres db

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#59 - Add demo Postgres db

Pull Request - State: closed - Opened by IsmailM over 4 years ago - 1 comment

#58 - Docker with db

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 18 comments

#58 - Docker with db

Pull Request - State: closed - Opened by alanwilter over 4 years ago - 18 comments

#57 - Docker dev mode

Pull Request - State: closed - Opened by alanwilter over 4 years ago

#57 - Docker dev mode

Pull Request - State: closed - Opened by alanwilter over 4 years ago

#56 - Link variants to genes tables using the gene id (ensembl) instead of the gene name

Issue - State: closed - Opened by priesgo over 4 years ago - 13 comments

#56 - Link variants to genes tables using the gene id (ensembl) instead of the gene name

Issue - State: closed - Opened by priesgo over 4 years ago - 13 comments

#55 - corrects handling of gene synonyms and upper/lower case

Pull Request - State: closed - Opened by priesgo over 4 years ago

#55 - corrects handling of gene synonyms and upper/lower case

Pull Request - State: closed - Opened by priesgo over 4 years ago

#54 - 500 when trying to acess all patients page

Issue - State: closed - Opened by pontikos over 4 years ago - 2 comments
Labels: Python API

#54 - 500 when trying to acess all patients page

Issue - State: closed - Opened by pontikos over 4 years ago - 2 comments
Labels: Python API

#53 - variant search doesn't seem to provide suggestions or search

Issue - State: closed - Opened by pontikos over 4 years ago - 5 comments
Labels: enhancement

#53 - variant search doesn't seem to provide suggestions or search

Issue - State: closed - Opened by pontikos over 4 years ago - 5 comments
Labels: enhancement

#52 - The genes table first row is the header of the file defining genes

Issue - State: closed - Opened by priesgo over 4 years ago - 1 comment

#52 - The genes table first row is the header of the file defining genes

Issue - State: closed - Opened by priesgo over 4 years ago - 1 comment

GitHub / phenopolis/phenopolis_genomics_browser issues and pull requests