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Merge pull request #77 from sensein/bids-like-updates
Update the BIDS-like saving to align with template directory
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name: Update BIDS-like data template dir CHANGES.md | ||
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on: | ||
push: | ||
paths: | ||
- 'src/b2aiprep/data' | ||
workflow_dispatch: # This allows manual triggering of the workflow | ||
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jobs: | ||
update-changelog: | ||
runs-on: ubuntu-latest | ||
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steps: | ||
# Step 1: Check out the repository | ||
- uses: actions/checkout@v3 | ||
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# Step 2: Set up Node.js environment (required for auto-changelog) | ||
- name: Set up Node.js | ||
uses: actions/setup-node@v3 | ||
with: | ||
node-version: '16' | ||
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# Step 3: Install auto-changelog or any other changelog tool | ||
- name: Install auto-changelog | ||
run: npm install -g auto-changelog | ||
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# Step 4: Generate the changelog | ||
- name: Generate changelog | ||
run: auto-changelog -p | ||
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# Step 5: Commit and push the updated CHANGES.md file | ||
- name: Commit and push changes | ||
run: | | ||
git config user.name "GitHub Actions" | ||
git config user.email "[email protected]" | ||
git add src/b2aiprep/data/b2ai-data-bids-like-template/CHANGES.md | ||
git commit -m "Update b2ai-data-bids-like-template/CHANGES.md" | ||
git push origin HEAD:main |
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@@ -146,5 +146,5 @@ cython_debug/ | |
# guide data | ||
guide/data/ | ||
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.DS_Store | ||
*.DS_Store | ||
cache-wf/ |
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105 changes: 105 additions & 0 deletions
105
...-e9dd-486e-b0d4-0001ee7f861d/sub-01401050-e9dd-486e-b0d4-0001ee7f861d_airwaystenosis.json
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{ | ||
"resourceType": "QuestionnaireResponse", | ||
"id": "01401050-e9dd-486e-b0d4-0001ee7f861d-airwaystenosis", | ||
"questionnaire": "https://kind-lab.github.io/vbai-fhir/Questionnaire-drespairwaystenosisschema", | ||
"status": "completed", | ||
"item": [ | ||
{ | ||
"linkId": "record_id", | ||
"answer": [ | ||
{ | ||
"valueString": "01401050-e9dd-486e-b0d4-0001ee7f861d" | ||
} | ||
] | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_pft" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_gsd" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_gsd_yes___bronchoscopy" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_gsd_yes___ct" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_bvfi_gs" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_etiology" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_etiology_auto_immune" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_mcg" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_bc" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_agw" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_ac" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_ac_grade_4" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_ods" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_ds_eps" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment___no_treatment" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment___surgery" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment___in_office_treatment" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___endoscopic_intervention", | ||
"answer": [ | ||
{ | ||
"valueBoolean": false | ||
} | ||
] | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___endoscopic_excision" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___laryngotracheal_reconstruction" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___laryngotracheoplasty" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___tracheostomy" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_surgery___other" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_in_office___steroid_injections_sole" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_in_office___steroid_injections_adjunct" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_in_office___dilation" | ||
}, | ||
{ | ||
"linkId": "diagnosis_as_treatment_in_office___laser" | ||
} | ||
] | ||
} |
128 changes: 128 additions & 0 deletions
128
...ub-01401050-e9dd-486e-b0d4-0001ee7f861d/sub-01401050-e9dd-486e-b0d4-0001ee7f861d_als.json
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{ | ||
"resourceType": "QuestionnaireResponse", | ||
"id": "01401050-e9dd-486e-b0d4-0001ee7f861d-als", | ||
"questionnaire": "https://kind-lab.github.io/vbai-fhir/Questionnaire-dneuroamyotrophiclateralsclerosisalsschema", | ||
"status": "completed", | ||
"item": [ | ||
{ | ||
"linkId": "record_id", | ||
"answer": [ | ||
{ | ||
"valueString": "01401050-e9dd-486e-b0d4-0001ee7f861d" | ||
} | ||
] | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_gsd_category_1" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_gsd_category_2" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_gsd_category_3" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_gsd_calculation" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_disease_subtype" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_disease_subtype_familial" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_etiology___genetic_factors" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_etiology___environmental_factors" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_etiology_genetic_factors___c9orf72" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_etiology_genetic_factors___sod1" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_etiology_genetic_factors___other" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_cp___upper_motor_neuron" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_cp___lower_motor_neuron" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_cp___bulbar_symptoms" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_cp___respiratory_involvement" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_dp" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_na_alsfrs_r_score" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_na_fvc_percentage" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes___medications" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes___supportive_care" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___riluzole" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___edaravone" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___sodium" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___tofersen" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___symptomatic_treatment" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_medications___other" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___physical_therapy", | ||
"answer": [ | ||
{ | ||
"valueBoolean": false | ||
} | ||
] | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___occupational_therapy" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___speech_therapy" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___respiratory_support" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___nutrition_support", | ||
"answer": [ | ||
{ | ||
"valueBoolean": false | ||
} | ||
] | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___psychotherapy" | ||
}, | ||
{ | ||
"linkId": "diagnosis_als_treatment_and_management_yes_supportive_care___other" | ||
} | ||
] | ||
} |
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