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aind-data-access-api-0.2.1
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مشاهده بیشترتوضیحات
API to interact with a few AIND databases
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | aind-data-access-api-0.2.1 |
| نام | aind-data-access-api |
| نسخه کتابخانه | 0.2.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Allen Institute for Neural Dynamics |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/aind-data-access-api/ |
| مجوز | MIT |
# aind-data-access-api
[](LICENSE)
[](https://github.com/semantic-release/semantic-release)
API to interact with a few AIND databases.
## Usage
We have two primary databases. A Document store to keep unstructured json documents, and a relational database to store structured tables.
### Document Store
We have some convenience methods to interact with our Document Store. You can create a client by explicitly setting credentials, or downloading from AWS Secrets Manager.
```
from aind_data_access_api.credentials import DocumentStoreCredentials
from aind_data_access_api.document_store import Client
# Method one assuming user, password, and host are known
ds_client = Client(
credentials=DocumentStoreCredentials(
username="user",
password="password",
host="host",
database="metadata",
),
collection_name="data_assets",
)
# Method two if you have permissions to AWS Secrets Manager
ds_client = Client(
credentials=DocumentStoreCredentials(
aws_secrets_name="aind/data/access/api/document_store/metadata"
),
collection_name="data_assets",
)
# To get all records
response = list(ds_client.retrieve_data_asset_records())
# To get a list of filtered records:
response = list(ds_client.retrieve_data_asset_records({"subject.subject_id": "123456"}))
```
### RDS Tables
We have some convenience methods to interact with our Relational Database. You can create a client by explicitly setting credentials, or downloading from AWS Secrets Manager.
```
from aind_data_access_api.credentials import RDSCredentials
from aind_data_access_api.rds_tables import Client
# Method one assuming user, password, and host are known
ds_client = Client(
credentials=RDSCredentials(
username="user",
password="password",
host="host",
database="metadata",
),
collection_name="data_assets",
)
# Method two if you have permissions to AWS Secrets Manager
ds_client = Client(
credentials=RDSCredentials(
aws_secrets_name="aind/data/access/api/rds_tables"
),
)
# To retrieve a table as a pandas dataframe
df = ds_client.read_table(table_name="spike_sorting_urls")
# Can also pass in a custom sql query
df = ds_client.read_table(query="SELECT * FROM spike_sorting_urls")
# It's also possible to save a pandas dataframe as a table. Please check internal documentation for more details.
ds_client.overwrite_table_with_df(df, table_name)
```
## Installation
To use the software, it can be installed from PyPI.
```bash
pip install aind-data-access-api
```
To develop the code, clone repo and run
```bash
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:
```bash
coverage run -m unittest discover && coverage report
```
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
```bash
interrogate .
```
- Use **flake8** to check that code is up to standards (no unused imports, etc.):
```bash
flake8 .
```
- Use **black** to automatically format the code into PEP standards:
```bash
black .
```
- Use **isort** to automatically sort import statements:
```bash
isort .
```
### Pull requests
For internal members, please create a branch. For external members, please fork the repository 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:
```text
<type>(<scope>): <short summary>
```
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
- **build**: Changes that affect build tools 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 bugfix
- **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
### Semantic Release
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
| Commit message | Release type |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
### Documentation
To generate the rst files source files for documentation, run
```bash
sphinx-apidoc -o doc_template/source/ src
```
Then to create the documentation HTML files, run
```bash
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).
نیازمندی
| مقدار | نام |
|---|---|
| - | boto3 |
| - | black |
| - | coverage |
| - | flake8 |
| - | interrogate |
| - | isort |
| - | Sphinx |
| - | furo |
| - | aind-data-access-api[full] |
| - | aind-data-access-api[secrets] |
| - | pandas |
| - | psycopg2-binary |
| - | pydantic |
| - | pymongo |
| - | SQLAlchemy |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl aind-data-access-api-0.2.1:
pip install aind-data-access-api-0.2.1.whl
نصب پکیج tar.gz aind-data-access-api-0.2.1:
pip install aind-data-access-api-0.2.1.tar.gz