search-dragon

search-dragon Unified API Interface for ontology search APIs, OLS and UMLS.

Running the script locally or working on a branch?

1. Create and/or activate a virtual environment (recommended):

[Click here] for more on virtual environments.

```
# Step 1: cd into the directory to store the venv

# Step 2: run this code. It will create the virtual env named utils_venv in the current directory.
python3 -m venv utils_venv

# Step 3: run this code. It will activate the utils_venv environment
source utils_venv/bin/activate # On Windows: venv\Scripts\activate

# You are ready for installations! 
# If you want to deactivate the venv run:
deactivate
```

2. Install the package
   If working on a new feature it is possible to install a package version within the remote or local branch
   

   • Locutus Users
     
   1. If testing changes to search-dragon in locutus don't forget to deploy a locutus branch with the correct search-dragon version in the toml file!
      
   2. Any new env variables created, e.g. api keys, will need to be added to the locutus deployment files.

   Installation methods:

   Search-dragon should installed using the following command.
   pip install git+https://github.com/NIH-NCPI/search-dragon.git
   
   # This install command will ensure the proper version installed. Useful for troubleshooting purposes.
   pip install --force-reinstall --no-cache-dir git+https://github.com/NIH-NCPI/search-dragon.git
   
   # Installing a specific branch of search-dragon.
   pip install git+https://github.com/NIH-NCPI/search-dragon.git@{branch_name}
   
   # Use this method for local development. In the root dir of the cloned repo run this command to enact local changes. 
   pip install -e .

Dragon Search

Based on a CLI tool from DBT Utilities that Brenda has written, dragon_search provides the ability to do basic ontology searches using the same backed functionality that Locutus is currently using, though, adjusted for more general use.

Some example usages:

$ dragon_search -ak "lung|diabetes|heart" -o "HP,HPO,MONDO"

By default, the results are passed to the terminal via stdin and are displayed as a rich table.

If you want to write the results to a file, simply pass a filename for the results:

$ dragon_search -ak "HP:0000873|OMIM:616421" -f quick-onto-search.csv

When writing results to a file, logging is written to stdout. When writing to a stdout, logging is written to the file, 'logs/search.log'

Notes

API usage

• OLSSearchAPI
  • MapDragon tested
  
  
• OLSSearchAPICode
  • DBT tested.
  • This url is more reliable for searching on a code(HP:0003045)
  
  
• UMLSSearchAPI
  • MapDragon tested