aind-metadata-service

REST service to retrieve metadata from databases.

Installation

Server Installation

Can be pip installed using pip install aind-metadata-service[server].

Installing pyodbc.

You may need to install unixodbc-dev. You can follow this https://learn.microsoft.com/en-us/sql/connect/odbc/linux-mac/installing-the-microsoft-odbc-driver-for-sql-server?view=sql-server-ver16 for instructions depending on your os.

You may need to run docker system prune before building the docker image if you're getting erros running apt-get:


#10 23.69 Err:1 http://deb.debian.org/debian bullseye/main amd64 libodbc1 amd64 2.3.6-0.1+b1
#10 23.69   Could not connect to debian.map.fastlydns.net:80 (146.75.42.132). - connect (111: Connection refused) Unable to connect to deb.debian.org:http:


### Client Installation

Can be pip installed with `pip install aind-metadata-service[client]`

### For Development

In the root directory, run

pip install -e .[dev]


## Contributing

### Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:

coverage run -m unittest discover && coverage report


- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:

interrogate .


- Use **flake8** to check that code is up to standards (no unused imports, etc.):

flake8 .


- Use **black** to automatically format the code into PEP standards:

black .


- Use **isort** to automatically sort import statements:

isort .


### Pull requests

For internal members, please create a branch. For external members, please fork the repo and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:

(): ``` where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of: - **build**: Changes that affect the build system or external dependencies (example scopes: pyproject.toml, setup.py) - **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml) - **docs**: Documentation only changes - **feat**: A new feature - **fix**: A bug fix - **perf**: A code change that improves performance - **refactor**: A code change that neither fixes a bug nor adds a feature - **test**: Adding missing tests or correcting existing tests ### Documentation To generate the rst files source files for documentation, run ``` sphinx-apidoc -o doc_template/source/ src ``` Then to create the documentation html files, run ``` sphinx-build -b html doc_template/source/ doc_template/build/html ``` More info on sphinx installation can be found here: https://www.sphinx-doc.org/en/master/usage/installation.html ### Responses There are 6 possible status code responses for aind-metadata-service: - **200**: successfully retrieved valid data without any problems. - **406**: successfully retrieved some data, but failed to validate against pydantic models. - **404**: found no data that matches query. - **300**: queried the server, but more items were returned than expected. - **503**: failed to connect to labtracks/sharepoint servers. - **500**: successfully connected to labtracks/sharepoint, but some other server error occurred. These status codes are defined in StatusCodes enum in response_handler.py

AllenNeuralDynamics / aind-metadata-service

readme

aind-metadata-service

Installation

Server Installation