From 4aff257e6715f8bb41f1aa245017c7ee8d199e75 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Fri, 21 Feb 2025 13:00:22 +0000
Subject: [PATCH] moved full usage to docs as we now have an example
---
README.md | 137 -------------------------------------------------
docs/index.md | 139 +++++++++++++++++++++++++++++++++++++++++++++++++-
2 files changed, 138 insertions(+), 138 deletions(-)
diff --git a/README.md b/README.md
index 2962927..b3259d7 100644
--- a/README.md
+++ b/README.md
@@ -153,8 +153,6 @@ Expected output:
[INFO] - OMOP installation completed
```
----
-
## **Example Usage**
Follow these steps to initialize and manage a phenotype using `acmc`. In this example, we use a source concept code list for the Concept Set `Abdominal Pain` created from [ClinicalCodes.org](ClinicalCodes.org). The source concept codes are is read2. We genereate versioned phenotypes for read2 and then translate to snomed with a another version.
@@ -329,141 +327,6 @@ Expected Output:
[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.
-
-### General Syntax
-
-```bash
-acmc [OPTIONS] COMMAND [SUBCOMMAND] [ARGUMENTS]
-```
-
-Where:
-- `[OPTIONS]` are global options that apply to all commands (e.g., `--debug`, `--version`).
-- `[COMMAND]` is the top-level command (e.g., `trud`, `omop`, `phen`).
-- `[SUBCOMMAND]` refers to the specific operation within the command (e.g., `install`, `validate`).
-
-### Global Options
-
-- `--version`: Display the acmc tool version number
-- `--debug`: Enable debug mode for more verbose logging.
-
-### Commands
-
-#### TRUD Command
-
-The `trud` command is used for installing NHS TRUD vocabularies.
-
-- **Install TRUD**
-
- Install clinically assurred TRUD medical code mappings:
-
- ```bash
- acmc trud install
- ```
-
-#### OMOP Command
-
-The `omop` command is used for installing OMOP vocabularies.
-
-- **Install OMOP**
-
- Install vocabularies in a local OMOP database:
-
- ```bash
- acmc omop install -d <OMOP_DIRECTORY_PATH> -v <OMOP_VERSION>
- ```
-
- - `-d`, `--omop-dir`: (Optional) Directory path to extracted OMOP downloads, default is `./build/omop`
- - `-v`, `--version`: OMOP vocabularies release version.
-
-- **Clear OMOP**
-
- Clear data from the local OMOP database:
-
- ```bash
- acmc omop clear
- ```
-
-- **Delete OMOP**
-
- Delete the local OMOP database:
-
- ```bash
- acmc omop delete
- ```
-
-#### PHEN Command
-
-The `phen` command is used phenotype-related operations.
-
-- **Initialize Phenotype**
-
- Initialize a phenotype directory locally or from a remote git repository:
-
- ```bash
- acmc phen init -d <PHENOTYPE_DIRECTORY> -r <REMOTE_URL>
- ```
-
- - `-d`, `--phen-dir`: (Optional) Directory to write phenotype configuration (the default is ./build/phen).
- - `-r`, `--remote_url`: (Optional) URL to a remote git repository.
-
-- **Validate Phenotype**
-
- Validate the phenotype configuration:
-
- ```bash
- acmc phen validate -d <PHENOTYPE_DIRECTORY>
- ```
-
- - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-
-- **Map Phenotype**
-
- Process phenotype mapping and specify the target coding and output format:
-
- ```bash
- 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`).
- - `-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**
-
- Publish a phenotype configuration, committing all changes and tagging with a new version number. If the phenotype has been initialised from a remote git URL, then the commit and new version tag will be pushed to the remote repo:
-
- ```bash
- acmc phen publish -d <PHENOTYPE_DIRECTORY>
- ```
-
- - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-
-- **Copy Phenotype Configuration**
-
- Copy a phenotype configuration from a source directory to a target directory at a specific version. This is used when wanting to compare versions of phenotypes using the `acmc phen diff` command:
-
- ```bash
- acmc phen copy -d <PHENOTYPE_DIRECTORY> -td <TARGET_DIRECTORY> -v <PHENOTYPE_VERSION>
- ```
-
- - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
- - `-td`, `--target-dir`: (Optional) Directory to copy the phenotype configuration to, (the default is ./build).
- - `-v`, `--version`: The phenotype version to copy.
-
-- **Compare Phenotype Configurations**
-
- Compare a a new phenotype version with pervious version of a phenotype:
-
- ```bash
- acmc phen diff -d <NEW_PHENOTYPE_DIRECTORY> -old <OLD_PHENOTYPE_DIRECTORY>
- ```
-
- - `-d`, `--phen-dir`: (Optional) Directory of current phenotype configuration (the default is ./build/phen).
- - `-old`, `--phen-dir-old`: (Required) Directory of old phenotype version)
-
## License
diff --git a/docs/index.md b/docs/index.md
index d5c1620..4ef8d11 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -34,4 +34,141 @@ The tool supports verification and mapping across diagnostic coding formats belo
Processed resources will be saved in the `build/maps/processed/` directory.
-*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
\ No newline at end of file
+*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
+
+
+
+## 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.
+
+### General Syntax
+
+```bash
+acmc [OPTIONS] COMMAND [SUBCOMMAND] [ARGUMENTS]
+```
+
+Where:
+- `[OPTIONS]` are global options that apply to all commands (e.g., `--debug`, `--version`).
+- `[COMMAND]` is the top-level command (e.g., `trud`, `omop`, `phen`).
+- `[SUBCOMMAND]` refers to the specific operation within the command (e.g., `install`, `validate`).
+
+### Global Options
+
+- `--version`: Display the acmc tool version number
+- `--debug`: Enable debug mode for more verbose logging.
+
+### Commands
+
+#### TRUD Command
+
+The `trud` command is used for installing NHS TRUD vocabularies.
+
+- **Install TRUD**
+
+ Install clinically assurred TRUD medical code mappings:
+
+ ```bash
+ acmc trud install
+ ```
+
+#### OMOP Command
+
+The `omop` command is used for installing OMOP vocabularies.
+
+- **Install OMOP**
+
+ Install vocabularies in a local OMOP database:
+
+ ```bash
+ acmc omop install -d <OMOP_DIRECTORY_PATH> -v <OMOP_VERSION>
+ ```
+
+ - `-d`, `--omop-dir`: (Optional) Directory path to extracted OMOP downloads, default is `./build/omop`
+ - `-v`, `--version`: OMOP vocabularies release version.
+
+- **Clear OMOP**
+
+ Clear data from the local OMOP database:
+
+ ```bash
+ acmc omop clear
+ ```
+
+- **Delete OMOP**
+
+ Delete the local OMOP database:
+
+ ```bash
+ acmc omop delete
+ ```
+
+#### PHEN Command
+
+The `phen` command is used phenotype-related operations.
+
+- **Initialize Phenotype**
+
+ Initialize a phenotype directory locally or from a remote git repository:
+
+ ```bash
+ acmc phen init -d <PHENOTYPE_DIRECTORY> -r <REMOTE_URL>
+ ```
+
+ - `-d`, `--phen-dir`: (Optional) Directory to write phenotype configuration (the default is ./build/phen).
+ - `-r`, `--remote_url`: (Optional) URL to a remote git repository.
+
+- **Validate Phenotype**
+
+ Validate the phenotype configuration:
+
+ ```bash
+ acmc phen validate -d <PHENOTYPE_DIRECTORY>
+ ```
+
+ - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+
+- **Map Phenotype**
+
+ Process phenotype mapping and specify the target coding and output format:
+
+ ```bash
+ 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`).
+ - `-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**
+
+ Publish a phenotype configuration, committing all changes and tagging with a new version number. If the phenotype has been initialised from a remote git URL, then the commit and new version tag will be pushed to the remote repo:
+
+ ```bash
+ acmc phen publish -d <PHENOTYPE_DIRECTORY>
+ ```
+
+ - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+
+- **Copy Phenotype Configuration**
+
+ Copy a phenotype configuration from a source directory to a target directory at a specific version. This is used when wanting to compare versions of phenotypes using the `acmc phen diff` command:
+
+ ```bash
+ acmc phen copy -d <PHENOTYPE_DIRECTORY> -td <TARGET_DIRECTORY> -v <PHENOTYPE_VERSION>
+ ```
+
+ - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+ - `-td`, `--target-dir`: (Optional) Directory to copy the phenotype configuration to, (the default is ./build).
+ - `-v`, `--version`: The phenotype version to copy.
+
+- **Compare Phenotype Configurations**
+
+ Compare a a new phenotype version with pervious version of a phenotype:
+
+ ```bash
+ acmc phen diff -d <NEW_PHENOTYPE_DIRECTORY> -old <OLD_PHENOTYPE_DIRECTORY>
+ ```
+
+ - `-d`, `--phen-dir`: (Optional) Directory of current phenotype configuration (the default is ./build/phen).
+ - `-old`, `--phen-dir-old`: (Required) Directory of old phenotype version)
\ No newline at end of file
--
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