This examples sets up a phenotype workspace environment, installs dependencies, configures necessary files, and validates and maps phenotypes to read2.
1.**Clone the Git Repository:**
```sh
git clone <repository_url>
```
This copies the remote repository to your local machine.
2.**Navigate to the Project Directory:**
```sh
cd concepts-processing
```
Moves into the cloned repository's directory.
3.**Create a Virtual Environment:**
```sh
py -m venv venv
```
This sets up an Virtual Python environment named `venv`.
4.**Upgrade `pip`:**
```sh
python -m pip install--upgrade pip
```
Ensures you have the latest version of `pip`, which helps manage dependencies.
5.**Install the Required Package (`acmc`):**
```sh
pip install acmc
```
Installs `acmc`, which is likely a package required for processing concepts.
6.**Initialize a Phenotype Project:**
```sh
acmc phen init
```
Sets up the workspace file strucutre for working with phenotype concepts. An example phenotype project is created within the `phen` sub-folder.
7.**Download TRUD Data:**
Downloads necessary TRUD (Terminology Reference Data) files, for concept verification and translation.
1. **Register at TRUD**
Registry your account with TRUD at [NHS TRUD](https://isd.digital.nhs.uk/trud/user/guest/group/0/account/form).
2. **Subscribe and Accept Licenses**: Subscribe to the following data files:
- [OPCS-4.10 Data Files](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/10/items/119/releases)
After subscribing, you'll receive an API key once your request is approved (usually within a few hours).
3. **Get TRUD API KEY**
Copy your API key from [NHS TRUD Account Management](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/account/manage) and store it securely.
4. **Add TRUD API KEY to as an environment variable**
To set the environment variable temporarily (for the current session), run:
On macOS/Linux:
```bash
export ACMC_TRUD_API_KEY="your_api_key_here"
```
On Windows (Command Prompt or PowerShell):
```bash
setx ACMC_TRUD_API_KEY "your_api_key_here"
```
5. **Install TRUD within ACMC**
```sh
acmc trud install
```
8.**Create Phenotype Configuration:**
Modify the `config.yml` file as needed for your project settings.
For more information on see the [configuration file documentation](https://acmc.readthedocs.io/en/latest/#configuration-file).
9.**Validate the Phenotype Configuration:**
Use the followijng `acmc` command to validate the phenotype configuration to ensure it's correct:
```sh
acmc phen validate -d workspace\phen
```
Checks that the phenotype definitions are correctly structured and valid.
