diff --git a/README.md b/README.md index 3f05d1fe4df9f0807693099e55852a3826a6d606..f0c7138b995c093040828b0366fdcdfc310ce964 100644 --- a/README.md +++ b/README.md @@ -51,22 +51,25 @@ The tool supports verification and mapping across various diagnostic coding form - **ATC Codes:** Maintained by WHO and used internationally for medication classification. ## Installation +1. **Setup Conda Enviroment:** Download and Install Python Enviroment. Follow insturctions to install minicoda from [https://docs.conda.io/en/latest/miniconda.html](https://docs.conda.io/en/latest/miniconda.html). + - Run the following command to recreate the environment: `conda env create -f conda.yaml`. + - Activate the environment: `conda activate base` -1. **Sign Up:** Register at [NHS TRUD](https://isd.digital.nhs.uk/trud/user/guest/group/0/account/form) and accept the following licenses: +2. **Sign Up:** Register at [NHS TRUD](https://isd.digital.nhs.uk/trud/user/guest/group/0/account/form) and accept the following licenses: - [NHS Read Browser](https://isd.digital.nhs.uk/trud/users/guest/filters/2/categories/9/items/8/releases) - [NHS Data Migration](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/9/items/9/releases) - [ICD10 Edition 5 XML](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/categories/28/items/259/releases) - [OPCS-4.10 Data Files](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/10/items/119/releases) <!-- - [BNF/Snomed Mapping data.xlsx](https://www.nhsbsa.nhs.uk/prescription-data/understanding-our-data/bnf-snomed-mapping) --> -2. **Obtain API Key:** Retrieve your API key from [NHS TRUD Account Management](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/account/manage). +3. **Obtain API Key:** Retrieve your API key from [NHS TRUD Account Management](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/account/manage). -3. **Install TRUD:** Download and Install NHS TRUD medical code resources. +4. **Install TRUD:** Download and Install NHS TRUD medical code resources. Executing the script using the command: `python trud_api.py --key <API_KEY>`. Processed tables will be saved as `.parquet` files in the `maps/processed/` directory. - *Note: NHS TRUD defines one-way mappings and does <b>NOT ADVISE</b> reversing the mappings. If you still wish to reverse these into two-way mappings, duplicate the given `.parquet` table and reverse the filename (e.g. `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`)* -4. ***Optional: Install OMOP Database:** Download and install OMOP vocabularies from [Athena OHDSI](https://athena.ohdsi.org/vocabulary/list). +5. ***Optional: Install OMOP Database:** Download and install OMOP vocabularies from [Athena OHDSI](https://athena.ohdsi.org/vocabulary/list). - Required vocabularies include: - 1) SNOMED - 2) ICD9CM diff --git a/conda.yaml b/conda.yaml index 75f66e2fcdbb0b51a207b9f2f8120ed32f691b45..cc563eaa7013f3cee3142089ab0655e91d5dd6be 100644 --- a/conda.yaml +++ b/conda.yaml @@ -154,7 +154,7 @@ dependencies: - cfgv==3.3.1 - click==8.0.3 - cloudpickle==2.0.0 - - cramjam==2.7.0 + - cramjam==2.8.0 - databricks-cli==0.16.2 - distlib==0.3.4 - docker==5.0.3 @@ -162,20 +162,20 @@ dependencies: - fastparquet==2023.10.1 - filelock==3.4.2 - flask==2.0.2 - - fsspec==2023.10.0 + - fsspec==2023.12.2 - gitdb==4.0.9 - gitpython==3.1.24 - gunicorn==20.1.0 - identify==2.4.2 - itsdangerous==2.0.1 - jmespath==0.10.0 - - lxml==4.9.3 + - lxml==5.3.0 - minio==7.1.2 - mlflow==1.22.0 - nodeenv==1.6.0 - - numpy==1.26.1 + - numpy==1.26.3 - openpyxl==3.1.2 - - pandas==2.1.2 + - pandas==2.1.4 - platformdirs==2.4.1 - pre-commit==2.16.0 - prometheus-flask-exporter==0.18.7 @@ -191,7 +191,7 @@ dependencies: - tabulate==0.8.9 - toml==0.10.2 - typing-extensions==4.0.1 - - tzdata==2023.3 + - tzdata==2023.4 - virtualenv==20.13.0 - werkzeug==2.0.2 prefix: /opt/conda