diff --git a/README.md b/README.md
index 5dfb6cce5e92e99ced354cc462488fb9bfd6934d..2175c98051a9edc3ab93c8947c6cab233a955fe4 100644
--- a/README.md
+++ b/README.md
@@ -215,7 +215,7 @@ Expected Output:
Use the following `acmc` command to generate the phenotype in `read2` format:
```bash
-acmc phen map -t read2
+acmc phen map
```
Expected Output:
diff --git a/acmc/main.py b/acmc/main.py
index 89df65dda2d1da11eef38260f2d760a6bbf9846c..b702518e204a56d92a09bd97d0102cde67a78200 100644
--- a/acmc/main.py
+++ b/acmc/main.py
@@ -3,7 +3,7 @@ import logging
from pathlib import Path
import acmc
-from acmc import trud, omop, phen, logging_config as lc
+from acmc import trud, omop, phen, parse, logging_config as lc
# setup logging
logger = lc.setup_logger()
@@ -167,17 +167,8 @@ def main():
phen_map_parser.add_argument(
"-t",
"--target-coding",
- required=True,
- choices=["read2", "read3", "icd10", "snomed", "opcs4"],
- help="Specify the target coding (read2, read3, icd10, snomed, opcs4)",
- )
- phen_map_parser.add_argument(
- "-o",
- "--output",
- choices=["csv", "omop"],
- nargs="+", # allows one or more values
- default=["csv"], # default to CSV if not specified
- help="Specify output format(s): 'csv', 'omop', or both (default: csv)",
+ choices=parse.SUPPORTED_CODE_TYPES,
+ help=f"Specify the target coding {parse.SUPPORTED_CODE_TYPES}",
)
phen_map_parser.set_defaults(func=phen_map)
diff --git a/acmc/omop.py b/acmc/omop.py
index 4b8cc4c49868d990467d8cb52642a5689bc2823f..dd5a461dc7be73d19d3666490c892aa63382234f 100644
--- a/acmc/omop.py
+++ b/acmc/omop.py
@@ -16,7 +16,7 @@ logger = logging_config.setup_logger()
# constants
VOCAB_PATH = Path("./vocab/omop")
-OMOP_CDM_Version ="54"
+OMOP_CDM_Version = "54"
OMOP_DB_FILENAME = f"omop_{OMOP_CDM_Version}.sqlite"
DB_PATH = VOCAB_PATH / OMOP_DB_FILENAME
VERSION_FILE = "omop_version.yaml"
@@ -26,7 +26,7 @@ EXPORT_FILE = "omop_export.db"
vocabularies = {
"source": "OHDSI Athena",
"url": "https://athena.ohdsi.org/vocabulary/list",
- "cdm_version": OMOP_CDM_Version,
+ "cdm_version": OMOP_CDM_Version,
"version": "",
"vocabularies": [
{"id": 1, "name": "SNOMED"}, # No license required
diff --git a/acmc/parse.py b/acmc/parse.py
index ca5b3e1dc847994cab714142d1bfc946eb15bc64..798a10ba743f3d5e939e9ebd7037eb43bf21aaba 100644
--- a/acmc/parse.py
+++ b/acmc/parse.py
@@ -8,6 +8,9 @@ from acmc import trud, logging_config as lc
# setup logging
logger = lc.setup_logger()
+# Define allowed values
+SUPPORTED_CODE_TYPES = {"read2", "read3", "icd10", "snomed", "opcs4", "atc"}
+
class CodesError:
"""A class used in InvalidCodesException to report an error if a code parser check fails"""
diff --git a/acmc/phen.py b/acmc/phen.py
index a92bdb295986dbcec2dad4d4c9b8c46cb5f50a18..a9131b59ba704088478d7e697401707edb472468 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -70,6 +70,15 @@ CONFIG_SCHEMA = {
},
},
},
+ "map": {
+ "type": "list",
+ "schema": {
+ "type": "string",
+ "allowed": list(
+ parse.SUPPORTED_CODE_TYPES
+ ), # Ensure only predefined values are allowed
+ },
+ },
"concept_sets": {
"type": "list",
"required": True,
@@ -260,6 +269,7 @@ def init(phen_dir, remote_url):
"vocabulary_name": "",
"vocabulary_reference": "",
},
+ "translate": [],
"concept_sets": [],
}
}
@@ -603,7 +613,6 @@ def write_vocab_version(phen_path):
def map(phen_dir, target_code_type):
logger.info(f"Processing phenotype: {phen_dir}")
- logger.debug(f"Target coding format: {target_code_type}")
# Validate configuration
validate(phen_dir)
@@ -611,13 +620,33 @@ def map(phen_dir, target_code_type):
# initialise paths
phen_path = Path(phen_dir)
config_path = phen_path / CONFIG_FILE
- codes_path = phen_path / CODES_DIR
# load configuration
with config_path.open("r") as file:
config = yaml.safe_load(file)
phenotype = config["phenotype"]
+ if len(phenotype["map"]) == 0:
+ raise ValueError(f"No map codes defined in the phenotype configuration")
+
+ if target_code_type is not None and target_code_type not in phenotype["map"]:
+ raise ValueError(
+ f"Target code type {target_code_type} not in phenotype configuration map {phenotype['map']}"
+ )
+
+ if target_code_type is not None:
+ map_target_code_type(phen_path, phenotype, target_code_type)
+ else:
+ for t in phenotype["map"]:
+ map_target_code_type(phen_path, phenotype, t)
+
+ logger.info(f"Phenotype processed successfully")
+
+
+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
# Create output dataframe
out = pd.DataFrame([])
code_errors = []
@@ -717,7 +746,7 @@ def map(phen_dir, target_code_type):
write_vocab_version(phen_path)
- logger.info(f"Phenotype processed successfully")
+ logger.info(f"Phenotype processed target code type {target_code_type}")
def publish(phen_dir):
diff --git a/docs/usage.md b/docs/usage.md
index 1527165ea12c7f7d696f8ba70c011c35eb2e92a5..57271cf0f12b54054159c184e56c0e00d38da5f4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -96,9 +96,8 @@ The `phen` command is used phenotype-related operations.
acmc phen map -d <PHENOTYPE_DIRECTORY> -t <TARGET_CODING> -o <OUTPUT_FORMAT>
```
- - `-t`, `--target-coding`: Specify the target coding (e.g., `read2`, `read3`, `icd10`, `snomed`, `opcs4`).
+ - `-t`, `--target-coding`: (Optional) Specify the target coding (e.g., `read2`, `read3`, `icd10`, `snomed`, `opcs4`).
- `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
- - `-o`, `--output`: Output format(s) (`csv`, `omop`, or both), default is 'csv'.
- **Publish Phenotype Configuration**
diff --git a/examples/config1.yaml b/examples/config1.yaml
index 19fd9c686ff25da888c1f7ce39d122ebc6b479db..09d0e807b3ff433682ea69a0642bebdec87bdd1e 100644
--- a/examples/config1.yaml
+++ b/examples/config1.yaml
@@ -4,6 +4,9 @@ phenotype:
vocabulary_id: "ACMC_Example_1"
vocabulary_name: "ACMC example 1 phenotype"
vocabulary_reference: "https://git.soton.ac.uk/meldb/concepts-processing/-/tree/main/examples"
+ map:
+ - "read2"
+ - "read3"
concept_sets:
- name: "ABDO_PAIN"
file:
diff --git a/examples/config2.yaml b/examples/config2.yaml
index 33d6df4eb06d24fc4f7e2e6940b56bfec50ead37..4c6252efb6fa4c7eec6520ddfc963e40d32e9ccc 100644
--- a/examples/config2.yaml
+++ b/examples/config2.yaml
@@ -4,6 +4,9 @@ phenotype:
vocabulary_id: "ACMC_Example_2"
vocabulary_name: "ACMC example 2 phenotype"
vocabulary_reference: "https://www.it-innovation.soton.ac.uk/projects/meldb/concept-processing/example"
+ map:
+ - "read2"
+ - "read3"
concept_sets:
- name: "CVD_EVENTS"
file:
diff --git a/examples/config3.yaml b/examples/config3.yaml
index 926ab602479bc7a83af4a39ff584cee14daccdce..764d7d8dd614132d4fed584d42b824a45694be9d 100644
--- a/examples/config3.yaml
+++ b/examples/config3.yaml
@@ -4,6 +4,10 @@ phenotype:
vocabulary_id: "ACMC_Example_3"
vocabulary_name: "ACMC example 3 phenotype"
vocabulary_reference: "https://www.it-innovation.soton.ac.uk/projects/meldb/concept-processing/example"
+ map:
+ - "read2"
+ - "read3"
+ - "snomed"
concept_sets:
- name: "CVD_EVENTS"
file:
diff --git a/tests/test_acmc.py b/tests/test_acmc.py
index 6533847661e2c1b64a9194613fb5280bed5c1013..c4cb94efcc2630ff0285489525049d0fa41ab047 100644
--- a/tests/test_acmc.py
+++ b/tests/test_acmc.py
@@ -91,7 +91,7 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
assert "Phenotype validated successfully" in caplog.text
# map phenotype
- for code_type in ["read2", "read3", "snomed"]:
+ for code_type in ["read2", "read3"]:
with caplog.at_level(logging.DEBUG):
monkeypatch.setattr(
sys,