| Name | udc JSON |
| Version |
0.3.3
JSON |
| download |
| home_page | |
| Summary | The Universal Data Client command-line tool |
| upload_time | 2023-06-08 13:43:54 |
| maintainer | |
| docs_url | None |
| author | Ernest Prabhakar |
| requires_python | >=3.10,<4.0 |
| license | |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# UDC
## The Universal Data Client
### What is UDC?
Universal Data is an open source initiative to build
a decentralized, cryptographically-secure ecosystem
containerizing both structured and unstructured data.
UDC is the initial (alpha) client for that system.
It currently supports both Quilt and Benchling URIs.
For example:
- `udc list "quilt+s3://quilt-example#package=examples/wellplates"`
- `udc patch "benchling+https://dtt.benchling.com?name=Update#type=Entry&id=etr_123"`
## Installation
NOTE: UDC requires Python 3.10 or higher.
You can check your version with `python3 --version`.
If you have an older version, you will need to update your environment to a
[newer version of Python](https://www.pythoncentral.io/how-to-update-python/).
### Production Package
From PyPi:
<!--pytest.mark.skip-->
```bash
python3 -m pip install udc # OR
python3 -m pip install --upgrade udc
which udc
```
## Development Branch
<!--pytest.mark.skip-->
```bash
python3 -m pip install git+https://github.com/data-yaml/udc.git@main
```
## Cloned
When cloned from [GitHub](https://github.com/data-yaml/udc):
```bash
poetry install
```
<--
```bash
alias udc="poetry run udc"
```
-->
## Usage
```bash
udc # prints help
```
### List contents of a specific package instance
```bash
udc list "quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2"
```
e.g.,
<!--pytest-codeblocks:expected-output-->
```bash
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=README.md"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=autoplate_H1N1.csv"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=data_products.ipynb"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=neutralisation-altair.json"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=neutralisation.json"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=quilt_summarize.json"
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=render.html"
```
### List all versions of a package
```bash
udc list "quilt+s3://quilt-example#package=examples/wellplates" | head -n 1
```
e.g.,
<!--pytest-codeblocks:expected-output-->
```bash
"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2c600f4c519efd5de868d5ef1e05ac92fcb0fa56044bb8c925c5f02"
```
### List all packages in a registry
```bash
udc list quilt+s3://quilt-example | head -n 1
```
e.g.,
<!--pytest-codeblocks:expected-output-->
```bash
"quilt+s3://quilt-example#package=akarve/amazon-reviews:latest"
```
### Get a package into a specific directory
You can also use `put` (replace) and `patch` (merge) if you have write access.
```bash
udc get "quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2" --dir /tmp/wellplates
```
Checking the download directory:
```bash
ls /tmp/wellplates
```
Should reveal the following output:
<!--pytest-codeblocks:expected-output-->
```bash
README.md
autoplate_H1N1.csv
data_products.ipynb
neutralisation-altair.json
neutralisation.json
quilt_summarize.json
render.html
```
## Development
### Testing
<!--pytest.mark.skip-->
```bash
make test
```
### Continuous Monitoring
<!--pytest.mark.skip-->
```bash
make watch
```
### Create Package
WARNING: Do this only if you are the maintainer of the package.
Be sure you to first set your [~/.pypirc](https://pypi.org/manage/account/) using `poetry config pypi-token.pypi <pypi-api-token>`
<!--pytest.mark.skip-->
```bash
# merge PR
make tag
make pypi
poetry publish
```
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"description": "# UDC\n\n## The Universal Data Client\n\n### What is UDC?\n\nUniversal Data is an open source initiative to build\na decentralized, cryptographically-secure ecosystem\ncontainerizing both structured and unstructured data.\n\nUDC is the initial (alpha) client for that system.\nIt currently supports both Quilt and Benchling URIs.\nFor example:\n\n- `udc list \"quilt+s3://quilt-example#package=examples/wellplates\"`\n- `udc patch \"benchling+https://dtt.benchling.com?name=Update#type=Entry&id=etr_123\"`\n\n## Installation\n\nNOTE: UDC requires Python 3.10 or higher.\nYou can check your version with `python3 --version`.\nIf you have an older version, you will need to update your environment to a\n[newer version of Python](https://www.pythoncentral.io/how-to-update-python/).\n\n### Production Package\n\nFrom PyPi:\n\n<!--pytest.mark.skip-->\n```bash\npython3 -m pip install udc # OR\npython3 -m pip install --upgrade udc\nwhich udc\n```\n\n## Development Branch\n\n<!--pytest.mark.skip-->\n```bash\npython3 -m pip install git+https://github.com/data-yaml/udc.git@main\n```\n\n## Cloned\n\nWhen cloned from [GitHub](https://github.com/data-yaml/udc):\n\n```bash\npoetry install\n```\n\n<--\n\n```bash\nalias udc=\"poetry run udc\"\n```\n-->\n\n## Usage\n\n```bash\nudc # prints help\n```\n\n### List contents of a specific package instance\n\n```bash\nudc list \"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2\"\n```\n\ne.g.,\n<!--pytest-codeblocks:expected-output-->\n```bash\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=README.md\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=autoplate_H1N1.csv\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=data_products.ipynb\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=neutralisation-altair.json\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=neutralisation.json\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=quilt_summarize.json\"\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2&path=render.html\"\n```\n\n### List all versions of a package\n\n```bash\nudc list \"quilt+s3://quilt-example#package=examples/wellplates\" | head -n 1\n```\n\ne.g.,\n<!--pytest-codeblocks:expected-output-->\n```bash\n\"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2c600f4c519efd5de868d5ef1e05ac92fcb0fa56044bb8c925c5f02\"\n```\n\n### List all packages in a registry\n\n```bash\nudc list quilt+s3://quilt-example | head -n 1\n```\n\ne.g.,\n<!--pytest-codeblocks:expected-output-->\n```bash\n\"quilt+s3://quilt-example#package=akarve/amazon-reviews:latest\"\n```\n\n### Get a package into a specific directory\n\nYou can also use `put` (replace) and `patch` (merge) if you have write access.\n\n```bash\nudc get \"quilt+s3://quilt-example#package=examples/wellplates@6782cf98a2\" --dir /tmp/wellplates\n```\n\nChecking the download directory:\n\n```bash\nls /tmp/wellplates\n```\n\nShould reveal the following output:\n<!--pytest-codeblocks:expected-output-->\n```bash\nREADME.md\nautoplate_H1N1.csv\ndata_products.ipynb\nneutralisation-altair.json\nneutralisation.json\nquilt_summarize.json\nrender.html\n```\n\n## Development\n\n### Testing\n\n<!--pytest.mark.skip-->\n```bash\nmake test\n```\n\n### Continuous Monitoring\n\n<!--pytest.mark.skip-->\n```bash\nmake watch\n```\n\n### Create Package\n\nWARNING: Do this only if you are the maintainer of the package.\n\nBe sure you to first set your [~/.pypirc](https://pypi.org/manage/account/) using `poetry config pypi-token.pypi <pypi-api-token>`\n\n<!--pytest.mark.skip-->\n```bash\n# merge PR\nmake tag\nmake pypi\npoetry publish\n```\n",
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