From 6c1beb0ba859b5cdf16d2a9b8b09bbb2418f3a6d Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Fri, 21 Feb 2025 12:14:30 +0000
Subject: [PATCH] updated readme with expected output
---
README.md | 11 ++++++++---
acmc/logging_config.py | 7 ++++---
acmc/main.py | 1 -
3 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index 55e9c9f..88c6e64 100644
--- a/README.md
+++ b/README.md
@@ -154,6 +154,8 @@ acmc phen init
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
@@ -162,6 +164,8 @@ cp -r ./examples/codes/* ./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
@@ -175,12 +179,13 @@ cp -r ./examples/config.json ./workspace/phen
acmc phen validate
```
-5. **Generate phenotype in read2 code format**
+ **Expected Output:**
- Use the followijng `acmc` command to generate the phenotype in `read2` format:
+ Once the command is executed, you should see output similar to this:
```bash
-acmc phen map -t read2
+[INFO] - Validating phenotype: <path>/concepts-processing/workspace/phen
+[INFO] - Phenotype validated successfully
```
6. **Publish phenotype at an initial version**
diff --git a/acmc/logging_config.py b/acmc/logging_config.py
index 5af1bc6..b9bb42e 100644
--- a/acmc/logging_config.py
+++ b/acmc/logging_config.py
@@ -31,11 +31,12 @@ def setup_logger(log_level=logging.INFO):
stream_handler.setLevel(logging.INFO)
# Create a formatter for how the log messages should look
- formatter = logging.Formatter('%(asctime)s - - %(levelname)s - %(message)s')
# Add the formatter to both handlers
- file_handler.setFormatter(formatter)
- stream_handler.setFormatter(formatter)
+ file_formatter = logging.Formatter('%(asctime)s - - %(levelname)s - %(message)s')
+ file_handler.setFormatter(file_formatter)
+ stream_formatter = logging.Formatter('[%(levelname)s] - %(message)s')
+ stream_handler.setFormatter(stream_formatter)
# Add the handlers to the logger
logger.addHandler(file_handler)
diff --git a/acmc/main.py b/acmc/main.py
index 72a055f..43fd39d 100644
--- a/acmc/main.py
+++ b/acmc/main.py
@@ -194,7 +194,6 @@ def main():
lc.set_log_level(logging.DEBUG)
# Call the function associated with the command
- logger.info("ACMC Tool")
args.func(args)
if __name__ == "__main__":
--
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