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Copy file name to clipboardExpand all lines: .github/ISSUE_TEMPLATE/new-source.md
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You can do some of these tasks in parallel, specially if you need to wait for approval, but it's good to keep in mind the intended order:
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*[ ] Make a branch in [ShareYourCloning_LinkML](https://github.com/genestorian/ShareYourCloning_LinkML) where you implement the new source (see extra docs in there) on how to do this.
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*[ ] Add your branch as a dependency (via commit id) using poetry in this repository, to update `shareyourcloning-linkml` dependency in `pyproject.toml`:
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*[ ] Make a branch in [OpenCloning_LinkML](https://github.com/genestorian/OpenCloning_LinkML) where you implement the new source (see extra docs in there) on how to do this.
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*[ ] Add your branch as a dependency (via commit id) using poetry in this repository, to update `opencloning-linkml` dependency in `pyproject.toml`:
* [ ] Implement the new sourcein a branch in this repository. You will need to add a new endpoint in`main.py` and a new class in`pydantic_models.py` that will handle the new source. You can use the existing sources as a template. Note that you can add extra validation or methods (see examples as well).
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* [ ] Write tests forthe new sourcein`tests/test_endpoints.py`. You can use the existing tests as a template.
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* [ ] Once the tests pass, merge the PR of the new sourcein [ShareYourCloning_LinkML] and make a release of the `shareyourcloning-linkml` package.
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* [ ] Once the tests pass, merge the PR of the new sourcein [OpenCloning_LinkML] and make a release of the `opencloning-linkml` package.
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* [ ] Update the dependency in the branch of this repository repository to the new version.
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```bash
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# Get version from https://pypi.org/project/shareyourcloning-linkml/
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# Get version from https://pypi.org/project/opencloning-linkml/
* [ ] Implement the frontend functionality in a branch, following [the frontend wiki](https://github.com/manulera/ShareYourCloning_frontend/wiki/Checklist-%E2%80%90--adding-a-source).
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* [ ] Implement the frontend functionality in a branch, following [the frontend wiki](https://github.com/manulera/OpenCloning_frontend/wiki/Checklist-%E2%80%90--adding-a-source).
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* [ ] Make tests for the frontend functionality.
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* [ ] Merge the PR in this repository into master.
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* [ ] Update the backend submodule in the frontend repository to the latest master.
This API is part of a bigger application, before going further, please go to the [main project readme](https://github.com/manulera/ShareYourCloning), where you can find an introduction.
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This API is part of a bigger application, before going further, please go to the [main project readme](https://github.com/manulera/OpenCloning), where you can find an introduction.
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This python API is built with [FastAPI](https://fastapi.tiangolo.com/) and is for *in silico* cloning.
This API provides a series of entry points. The API documentation can be accessed [here](https://shareyourcloning.api.genestorian.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://shareyourcloning.api.genestorian.org/](https://shareyourcloning.api.genestorian.org/).
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This API provides a series of entry points. The API documentation can be accessed [here](https://OpenCloning.api.genestorian.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/).
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## Getting started
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If you want to quickly set up a local instance of the frontend and backend of the application, check [getting started in 5 minutes](https://github.com/manulera/ShareYourCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
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If you want to quickly set up a local instance of the frontend and backend of the application, check [getting started in 5 minutes](https://github.com/manulera/OpenCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
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### Running locally
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# Activate the virtual environment
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source .venv/bin/activate
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# Install the package from github (will be in pypi at some point)
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pip install shareyourcloning
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pip install opencloning
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# Run the API (uvicorn should be installed in the virtual environment)
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uvicorn shareyourcloning.main:app
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uvicorn opencloning.main:app
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```
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### Running locally if you want to contribute
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```bash
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# The --reload argument will reload the API if you make changes to the code
Then you should be able to open the API docs at [http://127.0.0.1:8000/docs](http://127.0.0.1:8000/docs) to know that your API is working.
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### Running locally with docker :whale:
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If you want to serve the full site (backend and frontend) with docker, check [getting started in 5 minutes](https://github.com/manulera/ShareYourCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
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If you want to serve the full site (backend and frontend) with docker, check [getting started in 5 minutes](https://github.com/manulera/OpenCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
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If you want to serve only the backend from a docker container, an image is available at [manulera/shareyourcloningbackend](https://hub.docker.com/r/manulera/shareyourcloningbackend). The image is built from the Dockerfile in the root of this repository and exposes the port 3000. To run it:
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If you want to serve only the backend from a docker container, an image is available at [manulera/opencloningbackend](https://hub.docker.com/r/manulera/opencloningbackend). The image is built from the Dockerfile in the root of this repository and exposes the port 3000. To run it:
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```bash
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docker build -t manulera/shareyourcloningbackend.
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docker run -d --name backendcontainer -p 8000:8000 manulera/shareyourcloningbackend
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docker build -t manulera/opencloningbackend.
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docker run -d --name backendcontainer -p 8000:8000 manulera/opencloningbackend
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```
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If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://shareyourcloning.api.genestorian.org/](https://shareyourcloning.api.genestorian.org/))
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If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/))
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```bash
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docker pull manulera/shareyourcloningbackend
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docker run -d --name backendcontainer -p 8000:8000 manulera/shareyourcloningbackend
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docker pull manulera/opencloningbackend
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docker run -d --name backendcontainer -p 8000:8000 manulera/opencloningbackend
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```
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The api will be running at `http://localhost:8000`, so you should be able to access the docs at [http://localhost:8000/docs](http://localhost:8000/docs).
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### Connecting to the frontend
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If you want to receive requests from the [frontend](https://github.com/manulera/ShareYourCloning_frontend), or from another web application you may have to include the url of the frontend application in the CORS exceptions. By default, if you run the dev server with `uvicorn shareyourcloning.main:app --reload --reload-exclude='.venv'`, the backend will accept requests coming from `http://localhost:3000`, which is the default address of the frontend dev server (ran with `yarn start`).
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If you want to receive requests from the [frontend](https://github.com/manulera/OpenCloning_frontend), or from another web application you may have to include the url of the frontend application in the CORS exceptions. By default, if you run the dev server with `uvicorn opencloning.main:app --reload --reload-exclude='.venv'`, the backend will accept requests coming from `http://localhost:3000`, which is the default address of the frontend dev server (ran with `yarn start`).
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If you want to change the allowed origins, you can do so via env variables (comma-separated). e.g.:
Similarly, the frontend should be configured to send requests to the backend address, [see here](https://github.com/manulera/ShareYourCloning_frontend#connecting-to-the-backend).
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Similarly, the frontend should be configured to send requests to the backend address, [see here](https://github.com/manulera/OpenCloning_frontend#connecting-to-the-backend).
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#### Serving the frontend from the backend
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You may prefer to handle everything from a single server. You can do so by:
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* Build the [frontend](https://github.com/manulera/ShareYourCloning_frontend) with `yarn build`.
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* Build the [frontend](https://github.com/manulera/OpenCloning_frontend) with `yarn build`.
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* Copy the folder `build` from the frontend to the root directory of the backend, and rename it to `frontend`.
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* Set the environment variable `SERVE_FRONTEND=1` when running the backend. By default this will remove all allowed origins, but you can still set them with `ALLOWED_ORIGINS`.
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* Set the value of `backendUrl` in `frontend/config.js` to `/`.
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* Now, when you go to the root of the backend (e.g. `http://localhost:8000`), you should receive the frontend instead of the greeting page of the API.
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You can see how this is done in this [docker image](https://github.com/manulera/ShareYourCloning/blob/master/Dockerfile) and [docker-compose file](https://github.com/manulera/ShareYourCloning/blob/master/docker-compose.yml).
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You can see how this is done in this [docker image](https://github.com/manulera/OpenCloning/blob/master/Dockerfile) and [docker-compose file](https://github.com/manulera/OpenCloning/blob/master/docker-compose.yml).
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## Contributing :hammer_and_wrench:
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Check [contribution guidelines in the main repository](https://github.com/manulera/ShareYourCloning/blob/master/CONTRIBUTING.md) for general guidelines.
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Check [contribution guidelines in the main repository](https://github.com/manulera/OpenCloning/blob/master/CONTRIBUTING.md) for general guidelines.
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For more specific tasks:
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* Creating a new type of source: follow the [new source issue template](.github/ISSUE_TEMPLATE/new-source.md). You can create an issue like that [here](https://github.com/manulera/ShareYourCloning_backend/issues/new?assignees=&labels=new-source&projects=&template=new-source.md&title=New+source%3A+%3Cname-of-source%3E).
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* Creating a new type of source: follow the [new source issue template](.github/ISSUE_TEMPLATE/new-source.md). You can create an issue like that [here](https://github.com/manulera/OpenCloning_backend/issues/new?assignees=&labels=new-source&projects=&template=new-source.md&title=New+source%3A+%3Cname-of-source%3E).
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## Running the tests locally
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by looking at the `RecordStubRoute` class in `api_config_utils.py`. To run the dev server and record stubs:
Copy file name to clipboardExpand all lines: examples/snapgene_history/readme.md
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The equivalent history is built with ShareYourCloning with the script `build_history.py`, and stored as json in `history.json`. The only difference in this case is that ase1 is loaded directly from GenBank instead of loaded from a file (I actually loaded from GenBank with SnapGene, but it does not register this in the history).
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The equivalent history is built with OpenCloning with the script `build_history.py`, and stored as json in `history.json`. The only difference in this case is that ase1 is loaded directly from GenBank instead of loaded from a file (I actually loaded from GenBank with SnapGene, but it does not register this in the history).
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