Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adding QC checks for example SSSOM files #268

Merged
merged 3 commits into from
Mar 16, 2023
Merged

Adding QC checks for example SSSOM files #268

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e6053e2
Add qc for example mappings
matentzn Mar 14, 2023
2457ca6
Update project.Makefile
matentzn Mar 14, 2023
71e1c75
Update project.Makefile
matentzn Mar 14, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 31 additions & 0 deletions .github/workflows/qc.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
# Basic ODK workflow

name: CI

# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the master branch
push:
branches: [ master ]
pull_request:
branches: [ master ]

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
sssom_validation:
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.4
steps:
- name: Install latest SSSOM
env:
DEFAULT_BRANCH: master
run: pip install --upgrade pip && pip install -U sssom
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

should this not install SSSOM locally from the repository that's been pulled, so it can be used to test changes to the code as well? Otherwise, this PR is great.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This requires more work, because the sssom toolkit is in a different location, and maintained differently then the stuff maintained here. We know what to do: #115

But we have not gotten around to this yet.

- uses: actions/checkout@v2
- name: Run Mapping QC checks
env:
DEFAULT_BRANCH: master
run: make validate_mappings

13 changes: 7 additions & 6 deletions examples/embedded/foodie-inc-2022-05-01.sssom.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,10 @@
# curie_map:
# FOODON: http://purl.obolibrary.org/obo/FOODON_
# KF_FOOD: https://kewl-foodie.inc/food/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# orcid: https://orcid.org/
# wikidata: https://www.wikidata.org/wiki/
# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
# license: https://creativecommons.org/licenses/by/4.0/
# mapping_date: '2022-05-02'
Expand All @@ -10,15 +17,9 @@
# subject_source: KF_FOOD:DB
# comment: We could map to FOODON:00004187 instead which more specifically refers to
# 'raw' Pink apples. Decided against to be consistent with other mapping choices.
# curie_map:
# FOODON: http://purl.obolibrary.org/obo/FOODON_
# KF_FOOD: https://kewl-foodie.inc/food/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0

Loading