DITTO API using FastAPI (#1)

* initial endpoint layout * readMe update * updates readme * annotations from API * copied scripts and configs for parsing and predictions * predictions are working * getting scores by transcript * working app so far * verifies if the variant info is actually valid * changelog and license * formatting changes using black * linting URL in header fix * changelog lint fix * adding __init__.py to src and utils * change query functionality to utils package * remove unused imports Co-authored-by: Brandon M Wilk <[email protected]> * adds python version to the readme Co-authored-by: Brandon M Wilk <[email protected]> * Update src/utils/query.py to remove unused import Co-authored-by: Brandon M Wilk <[email protected]> * Update README.md for linting Co-authored-by: James Scherer <[email protected]> * localhost link change * dead link workaround 1 * workaround 2 * removes dead code --------- Co-authored-by: Brandon M. Wilk <[email protected]> Co-authored-by: James Scherer <[email protected]>
uab-cgds-worthey · Jan 10, 2024 · f393450 · f393450
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diff --git a/.gitignore b/.gitignore
@@ -17,7 +17,6 @@ lib/
 lib64/
 parts/
 sdist/
-var/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -58,8 +57,9 @@ target/
 # DotEnv configuration
 .env
 
-# conda
+# conda/pip
 .conda
+ditto-api-env
 
 # Database
 *.db

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,10 +3,11 @@
 Here is a changelog format you could use. Feel free to choose a format that works for the repo.
 
 ```txt
-YYYY-MM-DD  John Doe
+2024-01-08  Tarun Mamidi
 
-* Big Change 1
-* Another Change 2
+* Added functionality from [DITTO-UI](https://github.com/uab-cgds-worthey/DITTO-UI) repo
+to query OpenCravat for annotations and make DITTO predictions.
+* Uses FastAPI
 ```
 
 ---
diff --git a/LICENSE b/LICENSE
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/README.md b/README.md
@@ -1,73 +1,65 @@
-# CGDS Repository Template [:pencil2: Edit this title]
+# DITTO-API
 
 <!-- markdown-link-check-disable -->
 [![Perform linting -
-Markdown](https://github.com/uab-cgds-worthey/cgds_repo_template/actions/workflows/linting.yml/badge.svg)](https://github.com/uab-cgds-worthey/cgds_repo_template/actions/workflows/linting.yml)
+Markdown](https://github.com/uab-cgds-worthey/DITTO-API/actions/workflows/linting.yml/badge.svg)](https://github.com/uab-cgds-worthey/DITTO-API/actions/workflows/linting.yml)
 <!-- markdown-link-check-enable -->
 
-:pencil2: Add description of the project here.
+***!!! For research purposes only !!!***
+
+Repo for querying DITTO predictions for variants using FastAPI.
 
 ## Requirements
 
-:pencil2: What are the requirements to install and run the project.
+Following are required:
+
+- [git](https://git-scm.com/downloads)
+- python3.7+  & [python virtual environment](https://docs.python.org/3/tutorial/venv.html)
+- pip3
 
 ## How to install
 
-:pencil2: Add installation instructions here.
+Installation simply requires fetching the source code.
 
-## How to run
+To fetch source code, change in to directory of your choice and run:
 
-:pencil2: Add run instructions here. This includes necessary configurations as well as the commands used.
-
-## Repo's directory structure
+```sh
+git clone https://github.com/uab-cgds-worthey/DITTO-API.git
+```
 
-The directory structure below shows the nature of files/directories used in this repo.
+Change in to root directory and run the command below to install environment:
 
 ```sh
-$ tree -a cgds_repo_template/
-cgds_repo_template
-├── CHANGELOG.md      <- Log of changes made
-│
-├── CONTRIBUTING.md   <- Contribution guidelines
-│
-├── LICENSE.md        <- License for the repo
-│
-├── README.md
-│
-├── .gitignore        <- Specifies intentionally untracked files to ignore by git
-│
-├── .editorconfig     <- Helps maintain consistent coding styles for multiple users working on the same project across
-│                        various editors and IDEs. See https://editorconfig.org/ for more info
-│
-├── .markdownlint.json  <- Markdown linting config
-│
-├── .pylintrc         <- Python linting config
-│
-├── configs           <- Dir to store config files. Conda env, requirements.txt, etc.
-│
-├── data              <- Dir structure from http://drivendata.github.io/cookiecutter-data-science. Please give it a read.
-│   ├── external      <- Data from third party sources
-│   ├── interim       <- Intermediate data that has been transformed
-│   ├── processed     <- The final, canonical datasets and results
-│   └── raw           <- The original, immutable data dump
-│
-├── notebooks         <- Dir to store Jupyter, R Markdown notebooks, etc.
-│
-├── src               <- Dir to store source code for use in this project
-│
-├── .github
-│   ├── ISSUE_TEMPLATE            <- Github issue templates
-│   │   ├── bug_report.md
-│   │   └── feature_request.md
-│   ├── PULL_REQUEST_TEMPLATE     <- Github PR templates
-│   │   └── pull_request_template.md
-│   └── workflows                 <- Github actions workflows for automated processes (eg. linting, etc)
-│       └── linting.yml
-│
-└── logs              <- Dir to store log files
+# Create an environment. Needed only the first time.
+python3 -m venv ditto-api-env
+source ditto-api-env/bin/activate
+pip3 install -r requirements.txt
+```
+
+## How to run
 
+Run the below command to activate the API
+
+```sh
+cd src
+uvicorn main:app --reload
 ```
 
+Test the app using this example as web address -
+<!-- markdown-link-check-disable -->
+<http://localhost:8000/docs>
+<!-- markdown-link-check-enable -->
+ and use this variant as example: 1-2406483-C-G
+
 ## Contributing
 
 We welcome contributions! [See the docs for guidelines](./CONTRIBUTING.md).
+
+## Contact information
+
+For issues, please send an email with clear description to
+
+|Name | Email |
+------|--------|
+Tarun Mamidi | <[email protected]>
+Brandon Wilk | <[email protected]>