ClinVar data fetching and parsing #39

joj0s · 2020-06-16T08:18:39Z

This PR adds a script to download and parse data from ClinVar, as well as a dummy 'datasources' page, containing a button to trigger this proccess. Closes #14

…ion to clinvar.py

tskir

I like everything about this implementation. Left some comments, most are minor ones.

traitcuration/traits/datasources/clinvar.py

traitcuration/traits/templates/traits/datasources.html

tskir · 2020-06-18T01:45:25Z

@joj0s Also some more comments:

There appear to be minor merge conflicts after merging two previous PRs
You might want to include changes from Small follow-up actions from code reviews #40 which are follow-ups from PR Prototype #35, although you could also do that in a separate PR if you'd like

tskir

All very good, I left some suggestions, mostly style & simplifying some commands. If you agree with them, please feel free to address them & then merge this PR without further reviews from me.

traitcuration/traits/datasources/clinvar.py

Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com>

joj0s added 3 commits June 15, 2020 12:57

Add ClinVar data fetching and storing

d5f2b5b

Add updating source record numbers for existing traits and documentat…

0d0fd8d

…ion to clinvar.py

Add 'datasources' page for triggering clinvar fetching

a1fc9c2

joj0s added the Scope: Backend Backend logic & data processing scripts label Jun 16, 2020

joj0s requested a review from tskir June 16, 2020 08:18

tskir temporarily deployed to trait-curation-pr-39 June 16, 2020 08:18 Inactive

joj0s changed the title ~~Clinvar~~ ClinVar data fetching and parsing Jun 16, 2020

tskir changed the base branch from master to browse_page June 18, 2020 00:37

tskir changed the base branch from browse_page to master June 18, 2020 00:37

tskir mentioned this pull request Jun 18, 2020

Design a page to display status & trigger external imports #32

Closed

tskir requested changes Jun 18, 2020

View reviewed changes

joj0s added 7 commits June 18, 2020 11:39

Remove extracting and add documentation in clinvar.py

640ad9c

Fix source record calculation in clivar.py

2af8862

Rename method from extract_clinvar_data to download_clinvar_data

aac0e55

Move error checking from clinvar.py to views.py for ClinVar fetching

7bc2aad

Remove messages from datasources.html

6bc00bb

Make number of records to parse from clinvar a constant

02763a4

Add minor documentation corrections in clivar.py

b3c4ffa

joj0s temporarily deployed to trait-curation-pr-39 June 18, 2020 09:54 Inactive

Merge branch 'master' into clinvar

1564e62

joj0s temporarily deployed to trait-curation-pr-39 June 18, 2020 09:59 Inactive

joj0s requested a review from tskir June 18, 2020 09:59

Remove blank line whitespace in views.py

c3bef93

joj0s temporarily deployed to trait-curation-pr-39 June 19, 2020 09:28 Inactive

tskir mentioned this pull request Jun 19, 2020

Rolling minutes for weekly calls #9

Open

tskir approved these changes Jun 24, 2020

View reviewed changes

Apply clean-up suggestions from review

bd38d2a

Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com>

joj0s temporarily deployed to trait-curation-pr-39 June 26, 2020 07:49 Inactive

joj0s merged commit 6f87810 into master Jun 26, 2020

joj0s deleted the clinvar branch June 26, 2020 07:54

This pull request was closed.

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ClinVar data fetching and parsing #39

ClinVar data fetching and parsing #39

joj0s commented Jun 16, 2020

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tskir commented Jun 18, 2020

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ClinVar data fetching and parsing #39

ClinVar data fetching and parsing #39

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