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