From 1e099555a32d3d30fa569f08168c531b4145b7f6 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 6 Mar 2025 08:49:37 +0000
Subject: [PATCH] (refactor) Changed codes to concepts directory for alignment
with OMOP. Closes #52
---
acmc/phen.py | 16 ++++++++--------
.../Where this code list comes from .docx | Bin
.../res52-cardiovascular-events-icd10.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
.../Abdominal pain/res176-abdominal-pain.csv | 0
.../Falls/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
.../Neuropathic pain/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
.../Symptom code lists/Stress/res175-stress.csv | 0
.../hanlon/Hanlon_drug_read_codes.csv | 0
.../hanlon/MM_code_names.csv | 0
.../hanlon/Read_codes_for_diagnoses.csv | 0
.../Read_codes_for_drug_mm_count_diagnoses.csv | 0
tests/test_acmc.py | 6 +++---
29 files changed, 11 insertions(+), 11 deletions(-)
rename examples/{codes => concepts}/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx (100%)
rename examples/{codes => concepts}/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv (100%)
rename examples/{codes => concepts}/hanlon/Hanlon_drug_read_codes.csv (100%)
rename examples/{codes => concepts}/hanlon/MM_code_names.csv (100%)
rename examples/{codes => concepts}/hanlon/Read_codes_for_diagnoses.csv (100%)
rename examples/{codes => concepts}/hanlon/Read_codes_for_drug_mm_count_diagnoses.csv (100%)
diff --git a/acmc/phen.py b/acmc/phen.py
index 4ef51e6..86675bf 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -29,12 +29,12 @@ pd.set_option("mode.chained_assignment", None)
PHEN_DIR = "phen"
DEFAULT_PHEN_PATH = Path("./workspace") / PHEN_DIR
-CODES_DIR = "codes"
+CONCEPTS_DIR = "concepts"
MAP_DIR = "map"
CONCEPT_SET_DIR = "concept-set"
CSV_PATH = Path(CONCEPT_SET_DIR) / "csv"
OMOP_PATH = Path(CONCEPT_SET_DIR) / "omop"
-DEFAULT_PHEN_DIR_LIST = [CODES_DIR, MAP_DIR, CONCEPT_SET_DIR]
+DEFAULT_PHEN_DIR_LIST = [CONCEPTS_DIR, MAP_DIR, CONCEPT_SET_DIR]
CONFIG_FILE = "config.yaml"
VOCAB_VERSION_FILE = "vocab_version.yaml"
@@ -327,10 +327,10 @@ def validate(phen_dir):
f"Error: phen configuration file '{config_path}' does not exist."
)
- codes_path = phen_path / CODES_DIR
- if not codes_path.is_dir():
+ concepts_path = phen_path / CONCEPTS_DIR
+ if not concepts_path.is_dir():
raise FileNotFoundError(
- f"Error: source codes directory {source_codes_dir} does not exist."
+ f"Error: source concepts directory {concepts_path} does not exist."
)
# Calidate the directory is a git repo
@@ -384,7 +384,7 @@ def validate(phen_dir):
# check codes definition
for item in phenotype["concept_sets"]:
# check concepte code file exists
- concept_code_file_path = codes_path / item["file"]["path"]
+ concept_code_file_path = concepts_path / item["file"]["path"]
if not concept_code_file_path.exists():
validation_errors.append(
f"Coding file {str(concept_code_file_path.resolve())} does not exist"
@@ -683,7 +683,7 @@ def map(phen_dir, target_code_type):
def map_target_code_type(phen_path, phenotype, target_code_type):
logger.debug(f"Target coding format: {target_code_type}")
- codes_path = phen_path / CODES_DIR
+ concepts_path = phen_path / CONCEPTS_DIR
# Create output dataframe
out = pd.DataFrame([])
code_errors = []
@@ -693,7 +693,7 @@ def map_target_code_type(phen_path, phenotype, target_code_type):
logger.debug(f"--- {concept_set['file']} ---")
# Load code file
- codes_file_path = Path(codes_path / concept_set["file"]["path"])
+ codes_file_path = Path(concepts_path / concept_set["file"]["path"])
df = read_table_file(codes_file_path)
# process structural actions
diff --git a/examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv b/examples/concepts/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
rename to examples/concepts/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
diff --git a/examples/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv b/examples/concepts/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
rename to examples/concepts/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Falls/res178-fall.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Fatigue/res175-fatigue.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx b/examples/concepts/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
rename to examples/concepts/clinical-codes-org/Symptom code lists/Stress/Where this code list comes from .docx
diff --git a/examples/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv b/examples/concepts/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
similarity index 100%
rename from examples/codes/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
rename to examples/concepts/clinical-codes-org/Symptom code lists/Stress/res175-stress.csv
diff --git a/examples/codes/hanlon/Hanlon_drug_read_codes.csv b/examples/concepts/hanlon/Hanlon_drug_read_codes.csv
similarity index 100%
rename from examples/codes/hanlon/Hanlon_drug_read_codes.csv
rename to examples/concepts/hanlon/Hanlon_drug_read_codes.csv
diff --git a/examples/codes/hanlon/MM_code_names.csv b/examples/concepts/hanlon/MM_code_names.csv
similarity index 100%
rename from examples/codes/hanlon/MM_code_names.csv
rename to examples/concepts/hanlon/MM_code_names.csv
diff --git a/examples/codes/hanlon/Read_codes_for_diagnoses.csv b/examples/concepts/hanlon/Read_codes_for_diagnoses.csv
similarity index 100%
rename from examples/codes/hanlon/Read_codes_for_diagnoses.csv
rename to examples/concepts/hanlon/Read_codes_for_diagnoses.csv
diff --git a/examples/codes/hanlon/Read_codes_for_drug_mm_count_diagnoses.csv b/examples/concepts/hanlon/Read_codes_for_drug_mm_count_diagnoses.csv
similarity index 100%
rename from examples/codes/hanlon/Read_codes_for_drug_mm_count_diagnoses.csv
rename to examples/concepts/hanlon/Read_codes_for_drug_mm_count_diagnoses.csv
diff --git a/tests/test_acmc.py b/tests/test_acmc.py
index 4b7e82d..a9bda40 100644
--- a/tests/test_acmc.py
+++ b/tests/test_acmc.py
@@ -5,7 +5,7 @@ import shutil
import logging
from pathlib import Path
-from acmc import trud, omop, main, logging_config as lc
+from acmc import trud, omop, main, phen, logging_config as lc
# setup logging
lc.setup_logger()
@@ -71,7 +71,7 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
with caplog.at_level(logging.DEBUG):
# validate phenotype
# copy examples across
- shutil.rmtree(phen_path / "codes")
+ shutil.rmtree(phen_path / phen.CONCEPTS_DIR)
ex_path = Path("./examples").resolve()
for item in ex_path.iterdir():
source = ex_path / item.name
@@ -182,7 +182,7 @@ def test_diff(tmp_dir, monkeypatch, caplog):
main.main()
# copy example codes
- shutil.rmtree(phen_path / "codes")
+ shutil.rmtree(phen_path / phen.CONCEPTS_DIR)
ex_path = Path("./examples").resolve()
for item in ex_path.iterdir():
source = ex_path / item.name
--
GitLab