diff --git a/README.md b/README.md
index 6e4363ea6693cde23a7828610b1ca78fe0a76587..4ebc592a32012598ccfb4854a5ae3bcc1abd7061 100644
--- a/README.md
+++ b/README.md
@@ -151,26 +151,36 @@ Follow these steps to initialize and manage a phenotype using `acmc`. In this ex
acmc phen init
```
+**Expected Output:**
+
+```bash
+[INFO] - Initialising Phenotype in directory: <path>/concepts-processing/workspace/phen
+[INFO] - Creating phen directory structure and config files
+[INFO] - Phenotype initialised successfully
+```
+
2. **Copy example medical code lists to the phenotype codes directory**
From the command prompt, copy medical code lists `/examples/codes`to the phenotype code directory:
- - [Download `res176-abdominal-pain.csv`](.//examples/codes/clinical-codes-org/Symptom%20code%20lists/Abdominal%20pain/res176-abdominal-pain.csv)
- - Alternatively, place your code lists in `./workspace/phen/codes`.
```bash
cp -r ./examples/codes/* ./workspace/phen/codes
```
+ - [Download `res176-abdominal-pain.csv`](.//examples/codes/clinical-codes-org/Symptom%20code%20lists/Abdominal%20pain/res176-abdominal-pain.csv)
+ - Alternatively, place your code lists in `./workspace/phen/codes`.
+
3. **Copy the example phenotype configuration file to the phenotype directory**
From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory:
- - [Download `config.json`](./examples/config.json)
- - Alternatively, place your own `config.json` file in `./workspace/phen`.
```bash
cp -r ./examples/config.json ./workspace/phen
```
+ - [Download `config.json`](./examples/config.json)
+ - Alternatively, place your own `config.json` file in `./workspace/phen`.
+
4. **Validate the phenotype configuration**
Use the followijng `acmc` command to validate the phenotype configuration to ensure it's correct:
@@ -179,15 +189,35 @@ cp -r ./examples/config.json ./workspace/phen
acmc phen validate
```
-Expected Output:
+**Expected Output:**
+
+```bash
+[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+```
+
+5. **Generate phenotype in Read2 code format**
+
+ Use the following `acmc` command to generate the phenotype in `read2` format:
+
+```bash
+acmc phen map -t read2
+```
-Once the command is executed, you should see output similar to this:
+**Expected Output:**
```bash
+[INFO] - Processing phenotype: <path>/concepts-processing/workspace/phen
[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
[INFO] - Phenotype validated successfully
+[INFO] - Processing read2 codes...
+[INFO] - Converting to target code type read2
+[INFO] - Saved mapped concepts to <path>/concepts-processing/workspace/phen/map/read2.csv
+[INFO] - Phenotype processed successfully
```
+The concept sets translating read2 to the acmc normalised CSV format will be stored in `./workspace/phen/concept-set/snomed/` in, e.g. `./workspace/phen/concept-set/read2/ABDO_PAIN.csv`.
+
6. **Publish phenotype at an initial version**
Use the following `acmc` command to publish the phenotype at an initial version:
@@ -196,6 +226,15 @@ Once the command is executed, you should see output similar to this:
acmc phen publish
```
+**Expected Output:**
+
+```bash
+[INFO] - Validating phenotype: /home/mjbonifa/datahdd/brcbat/derived_datasets/mjbonifa/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+[INFO] - New version: v1.0.3
+[INFO] - Phenotype published successfully
+```
+
7. **Generate phenotype in SNOWMED code format**
Generate the phenotype in `snomed` format:
@@ -204,6 +243,20 @@ Generate the phenotype in `snomed` format:
acmc phen map -t snomed
```
+**Expected Output:**
+
+```bash
+[INFO] - Processing phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+[INFO] - Processing read2 codes...
+[INFO] - Converting to target code type snomed
+[INFO] - Saved mapped concepts to <path>/concepts-processing/workspace/phen/map/snomed.csv
+[INFO] - Phenotype processed successfully
+```
+
+The concept sets translating read2 to snomed will be stored in acmc CSV format in `./workspace/phen/concept-set/snomed/`, e.g. `./workspace/phen/concept-set/snomed/ABDO_PAIN.csv`
+
8. **Get a copy of the previous version from the repo**
Use the following `acmc` command to retrieve a copy of the previous version (`v1.0.3`) from the repository:
@@ -212,14 +265,38 @@ acmc phen map -t snomed
acmc phen copy -v v1.0.3
```
+**Expected Output:**
+
+```bash
+[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+[INFO] - Copying repo <path>/concepts-processing/workspace/phen to <path>/concepts-processing/workspace/v1.0.3
+[INFO] - Checking out version v1.0.3...
+[INFO] - Phenotype copied successfully
+```
+
+A copy of the phenotype will be created in the directory `./workspace/v1.0.3`
+
9. **Compare the previous version `v1.0.3` with the latest version**
- Use the following `acmc` command to compare the previous version (`v1.0.3`) with the latest version in the repository:
+ Use the following `acmc` command to compare the previous version `v1.0.3` with the latest version in the repository:
```bash
acmc phen diff -old ./workspace/v1.0.3/
```
+**Expected Output:**
+
+```bash
+[INFO] - Validating phenotype: ./workspace/v1.0.3/
+[INFO] - Phenotype validated successfully
+[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+[INFO] - Phenotypes diff'd successfully
+```
+
+A report comparing the phenotype versions will be created in the workspace called './workspace/phen/v1.0.3_diff.md'
+
10. **Publish the phenotype at the next version**
Use the following `acmc` command to publish the phenotype at the next version:
@@ -228,6 +305,14 @@ acmc phen diff -old ./workspace/v1.0.3/
acmc phen publish
```
+**Expected Output:**
+
+```bash
+[INFO] - Validating phenotype: /home/mjbonifa/datahdd/brcbat/derived_datasets/mjbonifa/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
+[INFO] - New version: v1.0.4
+[INFO] - Phenotype published successfully
+```
## Usage
The `acmc` command-line tool provides various commands to interact with TRUD, OMOP, and Phenotype data. Below are the usage details for each command.
diff --git a/acmc/phen.py b/acmc/phen.py
index f36d64c42946ffa89943b559daceb1a1c8714fcf..e1ba3d6f64b162eab8e4a02136afc2079a6690f1 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -80,7 +80,7 @@ def init(phen_dir, remote_url):
# check if directory already exists and ask user if they want to recreate it
configure = False
if phen_path.exists() and phen_path.is_dir(): # Check if it exists and is a directory
- user_input = input(f"The phen directory '{phen_path}' already exists. Do you want to reinitialise? (yes/no): ").strip().lower()
+ user_input = input(f"The phen directory already exists. Do you want to reinitialise? (yes/no): ").strip().lower()
if user_input in ['yes', 'y']:
shutil.rmtree(phen_path)
configure = True;
@@ -599,7 +599,7 @@ def publish(phen_dir):
# set version and write to config file so consistent with repo version
next_minor_version = commit_count + 1
version = f"v{major_version}.{next_minor_version}"
- logger.info(f"New version: {version}")
+ logger.debug(f"New version: {version}")
config['concept_sets']['version'] = version
with open(config_path, "w", encoding="utf-8") as f:
json.dump(config, f, indent=4)
@@ -613,7 +613,7 @@ def publish(phen_dir):
if version in repo.tags:
raise Exception (f"Tag {version} already exists in repo {phen_path}")
repo.create_tag(version, message=f"Release {version}")
- logger.info(f"Created tag: {version}")
+ logger.info(f"New version: {version}")
# push to origin if a remote repo
try: