From 43cba16344dc4090b07823db71e9c92f515d1d89 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Tue, 18 Feb 2025 11:05:56 +0000
Subject: [PATCH] added ACMC_GITHUB_PAT and ACMC_GITLAB_PAT as environmnet
variables and reconstructed the url, no now need to username and password, or
to include tokens in the API
---
.../clinical-codes-org/About the source.docx | Bin
.../Where this code list comes from .docx | Bin
.../Alcohol intake/res47-alcohol-intake.csv | 0
.../Where this code list comes from .docx | Bin
.../res47-physical-activity.csv | 0
.../Where this code list comes from .docx | Bin
.../Smoking status/res56-smoking-status.csv | 0
.../Where this code list comes from .docx | Bin
.../res52-cardiovascular-events-icd10.csv | 0
.../Where this code list comes from .docx | Bin
..._PH62_ver_124_concepts_20230719T112819.csv | 0
.../Where this code list comes from .docx | Bin
.../res201-did-not-attend-appointment.csv | 0
.../Where this code list comes from .docx | Bin
...PH223_ver_446_concepts_20230719T114228.csv | 0
.../Where this code list comes from .docx | Bin
...res176-palliative-and-end-of-life-care.csv | 0
.../Where this code list comes from .docx | Bin
...1091_ver_2385_concepts_20230719T122902.csv | 0
.../Where this code list comes from .docx | Bin
.../res38-personality-disorder.csv | 0
.../Where this code list comes from .docx | Bin
.../Self harm/res41-self-harm.csv | 0
.../Where this code list comes from .docx | Bin
.../Abdominal pain/res176-abdominal-pain.csv | 0
.../Where this code list comes from .docx | Bin
.../Symptom code lists/Falls/res178-fall.csv | 0
.../Falls/res202-falls-outcome.csv | 0
.../Where this code list comes from .docx | Bin
.../Fatigue/res175-fatigue.csv | 0
.../Where this code list comes from .docx | Bin
.../Headache/res175-headache.csv | 0
.../Where this code list comes from .docx | Bin
.../Incontinence/res11-incontinence.csv | 0
.../Where this code list comes from .docx | Bin
.../Musculoskeletal pain/res175-msk-pain.csv | 0
.../Where this code list comes from .docx | Bin
.../res55-neuropathic_pain.csv | 0
.../Where this code list comes from .docx | Bin
.../Sleep problems/res175-sleep-problems.csv | 0
.../Where this code list comes from .docx | Bin
.../Stress/res175-stress.csv | 0
.../Where this code list comes from .docx | Bin
..._PH87_ver_174_concepts_20230719T113229.csv | 0
.../Where this code list comes from .docx | Bin
...PH331_ver_662_concepts_20230719T121545.csv | 0
{example => examples}/config.json | 0
{example => examples}/config2.json | 0
phen.py | 62 ++++++++++--------
trud.py | 5 +-
50 files changed, 38 insertions(+), 29 deletions(-)
rename {example => examples}/codes/clinical-codes-org/About the source.docx (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Self harm/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Self harm/res41-self-harm.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Tuberculosis/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv (100%)
rename {example => examples}/codes/clinical-codes-org/Urinary tract stones/Where this code list comes from .docx (100%)
rename {example => examples}/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv (100%)
rename {example => examples}/config.json (100%)
rename {example => examples}/config2.json (100%)
diff --git a/example/codes/clinical-codes-org/About the source.docx b/examples/codes/clinical-codes-org/About the source.docx
similarity index 100%
rename from example/codes/clinical-codes-org/About the source.docx
rename to examples/codes/clinical-codes-org/About the source.docx
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv b/examples/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
rename to examples/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv b/examples/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
rename to examples/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv b/examples/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
rename to examples/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
diff --git a/example/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv b/examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
rename to examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
diff --git a/example/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv b/examples/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv
rename to examples/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv
diff --git a/example/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv b/examples/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
rename to examples/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
diff --git a/example/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv b/examples/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv
rename to examples/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv
diff --git a/example/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv b/examples/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv
rename to examples/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv
diff --git a/example/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv b/examples/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv
rename to examples/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv
diff --git a/example/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv b/examples/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv
rename to examples/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv
diff --git a/example/codes/clinical-codes-org/Self harm/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Self harm/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Self harm/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Self harm/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Self harm/res41-self-harm.csv b/examples/codes/clinical-codes-org/Self harm/res41-self-harm.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Self harm/res41-self-harm.csv
rename to examples/codes/clinical-codes-org/Self harm/res41-self-harm.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv b/examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv b/examples/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv b/examples/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv b/examples/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv b/examples/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv b/examples/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv b/examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv b/examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv b/examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv b/examples/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
rename to examples/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
diff --git a/example/codes/clinical-codes-org/Tuberculosis/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Tuberculosis/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Tuberculosis/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Tuberculosis/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv b/examples/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv
rename to examples/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv
diff --git a/example/codes/clinical-codes-org/Urinary tract stones/Where this code list comes from .docx b/examples/codes/clinical-codes-org/Urinary tract stones/Where this code list comes from .docx
similarity index 100%
rename from example/codes/clinical-codes-org/Urinary tract stones/Where this code list comes from .docx
rename to examples/codes/clinical-codes-org/Urinary tract stones/Where this code list comes from .docx
diff --git a/example/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv b/examples/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
similarity index 100%
rename from example/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
rename to examples/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
diff --git a/example/config.json b/examples/config.json
similarity index 100%
rename from example/config.json
rename to examples/config.json
diff --git a/example/config2.json b/examples/config2.json
similarity index 100%
rename from example/config2.json
rename to examples/config2.json
diff --git a/phen.py b/phen.py
index 7af3ebc..ebfcc33 100644
--- a/phen.py
+++ b/phen.py
@@ -10,23 +10,13 @@ import git
import re
import requests
from pathlib import Path
+from urllib.parse import urlparse, urlunparse
+# acmc dependencies
import trud
-from base import log_invalid_code
-from base import bcolors
-from base import raise_
-from parse import Read2_code
-from parse import Read3_code
-from parse import Icd10_code
-from parse import Snomed_code
-from parse import Opcs4_code
-from parse import Atc_code
-from parse import Med_code
-from parse import code_types
-from parse import vocab_types
-from omop import OMOP_DB_PATH
-from omop import publish_concept_sets
-from omop import setup
+from base import log_invalid_code, bcolors, raise_
+from parse import Read2_code, Read3_code, Icd10_code, Snomed_code, Opcs4_code, Atc_code, code_types, vocab_types
+from omop import OMOP_DB_PATH, publish_concept_sets, setup
pd.set_option("mode.chained_assignment", None)
@@ -49,6 +39,26 @@ class PhenValidationException(Exception):
super().__init__(message)
self.validation_errors = validation_errors
+def construct_git_url(remote_url):
+ # check the url
+ parsed_url = urlparse(remote_url)
+
+ if "github.com" in parsed_url.netloc:
+ # get GitHub PAT from environment variable
+ auth = os.getenv("ACMC_GITHUB_PAT")
+ if not auth:
+ raise ValueError("GitHub PAT not found. Set the ACMC_GITHUB_PAT environment variable.")
+ else:
+ # get GitLab PAT from environment variable
+ auth = os.getenv("ACMC_GITLAB_PAT")
+ if not auth:
+ raise ValueError("GitLab PAT not found. Set the ACMC_GITLAB_PAT environment variable.")
+ auth = f"oauth2:{auth}"
+
+ # Construct the new URL with credentials
+ new_netloc = f"{auth}@{parsed_url.netloc}"
+ return urlunparse((parsed_url.scheme, new_netloc, parsed_url.path, parsed_url.params, parsed_url.query, parsed_url.fragment))
+
def init(phen_dir, remote_url):
"""Initial phenotype directory as git repo with standard structure"""
print(f"Initialising Phenotype in directory: {phen_dir}")
@@ -66,24 +76,25 @@ def init(phen_dir, remote_url):
else:
configure=True
- # configure the phen directories
+ # configure phen directories
if configure:
repo = None
- # remote then clone the repo
+ # if remote then clone the repo otherwise init a local repo
if remote_url != None:
- try:
- repo = git.cmd.Git()
- repo.clone(remote_url, phen_path)
- repo = git.Repo(phen_path)
- except Exception:
- raise Exception(f"Error: remote_url for the repo {remote_url} ")
+ # add PAT token to the URL
+ git_url = construct_git_url(remote_url)
+
+ # clone the repo
+ repo = git.cmd.Git()
+ repo.clone(git_url, phen_path)
+ repo = git.Repo(phen_path)
else:
- # local then create the directories and init
+ # local repo, create the directories and init
phen_path.mkdir(parents=True, exist_ok=True)
print(f"Phen directory '{phen_path}' has been created.")
repo = git.Repo.init(phen_path)
- # check if the phen path has already been configured which would be the case for remote clones
+ # if the phen path does not contain the config file then initialise the phen type
config_path = phen_path / CONFIG_FILE
if not config_path.exists():
print("Creating configuration files")
@@ -541,7 +552,6 @@ def publish(phen_dir):
# push to origin if a remote repo
try:
origin = repo.remotes.origin
- print(f"Remote 'origin' exists: {origin.url}")
origin.push(tags=True)
print("Changes pushed to 'origin'.")
except AttributeError:
diff --git a/trud.py b/trud.py
index a491684..cf758d2 100644
--- a/trud.py
+++ b/trud.py
@@ -271,6 +271,7 @@ def create_map_directories():
def install():
print(f"Installing TRUD")
+
# get TRUD api key from environment variable
api_key = os.getenv("ACMC_TRUD_API_KEY")
if not api_key:
@@ -347,7 +348,5 @@ def install():
item["extract"]()
print(f"Downloaded {release_ordinal} release(s) for item {item_id}.")
-
-
-
+
print(f"TRUD installation completed")
\ No newline at end of file
--
GitLab