seer-pas-sdk 0.1.2__py3-none-any.whl → 0.2.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- seer_pas_sdk/auth/__init__.py +1 -77
- seer_pas_sdk/auth/auth.py +99 -0
- seer_pas_sdk/common/__init__.py +370 -72
- seer_pas_sdk/common/errors.py +5 -0
- seer_pas_sdk/common/groupanalysis.py +55 -0
- seer_pas_sdk/core/__init__.py +1 -1307
- seer_pas_sdk/core/sdk.py +2632 -0
- seer_pas_sdk/core/unsupported.py +1634 -0
- seer_pas_sdk/objects/__init__.py +3 -129
- seer_pas_sdk/objects/groupanalysis.py +30 -0
- seer_pas_sdk/objects/platemap.py +174 -0
- seer_pas_sdk/objects/volcanoplot.py +290 -0
- seer_pas_sdk-0.2.1.dist-info/METADATA +230 -0
- seer_pas_sdk-0.2.1.dist-info/RECORD +18 -0
- {seer_pas_sdk-0.1.2.dist-info → seer_pas_sdk-0.2.1.dist-info}/WHEEL +1 -1
- {seer_pas_sdk-0.1.2.dist-info → seer_pas_sdk-0.2.1.dist-info}/top_level.txt +0 -1
- seer_pas_sdk-0.1.2.dist-info/METADATA +0 -50
- seer_pas_sdk-0.1.2.dist-info/RECORD +0 -16
- tests/__init__.py +0 -0
- tests/conftest.py +0 -17
- tests/test_auth.py +0 -48
- tests/test_common.py +0 -99
- tests/test_objects.py +0 -91
- tests/test_sdk.py +0 -11
- {seer_pas_sdk-0.1.2.dist-info → seer_pas_sdk-0.2.1.dist-info/licenses}/LICENSE.txt +0 -0
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Metadata-Version: 2.4
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Name: seer-pas-sdk
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Version: 0.2.1
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Summary: SDK for Seer Proteograph Analysis Suite (PAS)
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Author-email: Ryan Sun <rsun@seer.bio>
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License:
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Apache License
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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END OF TERMS AND CONDITIONS
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Project-URL: Issues, https://github.com/seerbio/seer-pas-sdk/issues
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Keywords: seer,sdk,pas,mass spectrometry,proteomics
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Classifier: Development Status :: 4 - Beta
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Requires-Python: >=3.8
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Description-Content-Type: text/markdown
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License-File: LICENSE.txt
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Requires-Dist: boto3>=1.26.152
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Requires-Dist: botocore>=1.29.152
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Requires-Dist: pandas>=2.0.1
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Requires-Dist: numpy<2.0.0,>=1.5.3
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Requires-Dist: PyJWT>=2.8.0
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Requires-Dist: python-dotenv>=1.0.0
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Requires-Dist: Requests>=2.31.0
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Requires-Dist: tqdm>=4.65.0
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Dynamic: license-file
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# Seer PAS Python SDK
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[](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml)
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[](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml)
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This SDK permits interaction with the Seer Proteograph Analysis Suite using Python.
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## Installation
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```shell
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pip install seer-pas-sdk
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```
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## Usage
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To import and set up the SDK:
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```python
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from seer_pas_sdk import SeerSDK
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# Instantiate an SDK object with your credentials:
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sdk = SeerSDK(USERNAME, PASSWORD)
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```
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You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
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For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").
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seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
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seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
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seer_pas_sdk/auth/auth.py,sha256=C9XQWg2dScHcvvypqnjmluRlH-GEuc4D9rYyG9_OnN0,2965
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seer_pas_sdk/common/__init__.py,sha256=jA5qm-t9x3qXMp5Q6v7vV2kZdLw32-lnbtf0fPY4lIw,22482
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seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
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seer_pas_sdk/common/groupanalysis.py,sha256=DxB-gbQfYzl7p9MTYWDIqghcH-IeakzdYdrRZrlIHek,1730
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seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
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seer_pas_sdk/core/sdk.py,sha256=fUbskM4zxhVkK8i9lt6dJJi32ss4KVO3ZNOF3OB1S7c,97689
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seer_pas_sdk/core/unsupported.py,sha256=FqaJrkctNIStr1YTyV2nZc4qmgje3yza221z4Y28zpM,59908
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seer_pas_sdk/objects/__init__.py,sha256=HJLS6sOr7DfzdI14fv5dWcITEj5QQsKcdfED3YNvUrY,107
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seer_pas_sdk/objects/groupanalysis.py,sha256=x3D_5NmYBoPDilNCQqUoCFARIfIeUq4FBY3_N6u8tfM,994
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seer_pas_sdk/objects/platemap.py,sha256=8IvJPAecs_e_FyqibzhCw-O4zjCFnf-zMUp_5krTEsg,5864
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seer_pas_sdk/objects/volcanoplot.py,sha256=tKuCWDIdoO8FLJlhpXhuwHn0aMYnvudTugxAslDXyGs,9357
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seer_pas_sdk-0.2.1.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
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seer_pas_sdk-0.2.1.dist-info/METADATA,sha256=qD8N0JVJ5AKlzsDy2N8d56rNoef0QFh8hvWAjx-rMJY,13421
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seer_pas_sdk-0.2.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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seer_pas_sdk-0.2.1.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
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seer_pas_sdk-0.2.1.dist-info/RECORD,,
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Metadata-Version: 2.1
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Name: seer-pas-sdk
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Version: 0.1.2
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Summary: SDK for Seer Proteograph Analysis Suite (PAS)
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Home-page: https://github.com/seerbio/seer-pas-sdk
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Author: Agam Jolly
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Author-email: ajolly@seer.bio
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Project-URL: Bug Tracker, https://github.com/seerbio/seer-pas-sdk/issues
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Classifier: Programming Language :: Python :: 3
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Classifier: Operating System :: OS Independent
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Requires-Python: >=3.6
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Description-Content-Type: text/markdown
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License-File: LICENSE.txt
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Requires-Dist: boto3==1.26.152
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Requires-Dist: botocore==1.29.152
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Requires-Dist: pandas==2.0.1
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Requires-Dist: numpy<2.0.0,>=1.5.3
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Requires-Dist: PyJWT==2.8.0
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Requires-Dist: python-dotenv==1.0.0
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Requires-Dist: Requests==2.31.0
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Requires-Dist: tqdm==4.65.0
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# Seer PAS Python SDK
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[](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml)
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[](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml)
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This SDK permits interaction with the Seer Proteograph Analysis Suite using Python.
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## Installation
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```shell
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pip install seer-pas-sdk
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```
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## Usage
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To import and set up the SDK:
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```python
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from seer_pas_sdk import SeerSDK
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# Instantiate an SDK object with your credentials:
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sdk = SeerSDK(USERNAME, PASSWORD)
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```
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You can then use the SDK's functions to create, query, or retrieve projects, plates, samples, and analyses.
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For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").
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seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
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seer_pas_sdk/auth/__init__.py,sha256=DZcbkYel11GvIn-iiutt9UOVfj9URZ_f89QMHhyGfRg,2277
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seer_pas_sdk/common/__init__.py,sha256=QnBup2dT6okt62Yjdhik4DmLf36Ozgv6KybdvFAULaA,12260
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seer_pas_sdk/core/__init__.py,sha256=J8dAiYsvNbc11zN1mgp7KqjHSVPw9CVwI-uc85UHw5s,47488
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seer_pas_sdk/objects/__init__.py,sha256=DosquJu2-XvDjVj4JFKoXa0DBVS8OroYCDeS5Np4U8Q,3693
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tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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tests/conftest.py,sha256=nu5Qu8CHwgJEwFpLQ0iX8e5csz4HGIC2oe50AdkA2Ms,317
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tests/test_auth.py,sha256=np4XXbEzoSFf-zXKaZQFL4Ry1ehMtjbXtHG3J6D-zzc,933
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tests/test_common.py,sha256=3VgHPbeLVJCh8V0kBGMvkhTKMd6sN_eLJF3AgvbyH0I,3433
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tests/test_objects.py,sha256=BcQtE8CbGUAnFlbkwsaJalUV6D8WbdwN2aWiQddh3k4,2521
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tests/test_sdk.py,sha256=ZNfsRAe_YHIXfteVugfkcds_lmYb0emIfDbJz7jpqR4,239
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seer_pas_sdk-0.1.2.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
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seer_pas_sdk-0.1.2.dist-info/METADATA,sha256=VuuOZGQuA6LaN6MgYSZEHKBJXKRuVZxXNDFLLM63shk,1716
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seer_pas_sdk-0.1.2.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
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seer_pas_sdk-0.1.2.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
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seer_pas_sdk-0.1.2.dist-info/RECORD,,
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tests/__init__.py
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tests/conftest.py
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"""
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`conftest.py` -- common fixtures and other pytest config
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"""
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import pytest
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from seer_pas_sdk import PlateMap
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@pytest.fixture
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def platemap():
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"""A very basic platemap"""
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return PlateMap(
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ms_file_name=["test.msfile"],
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sample_name=["TEST_sample_name"],
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sample_id=["TEST0"],
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)
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tests/test_auth.py
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import pytest
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from seer_pas_sdk.auth import Auth
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@pytest.fixture
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def password():
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return "XXX_fake_password"
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@pytest.fixture
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def username():
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return "XXX_fake_user"
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@pytest.fixture(
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params=[
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*Auth._instances.keys(),
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*Auth._instances.values(),
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"https://secure-https-url.example/",
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]
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)
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def valid_instance(request):
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return request.param
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def test_valid_instance(username, password, valid_instance):
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Auth(
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username=username,
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password=password,
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instance=valid_instance,
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)
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@pytest.fixture(
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params=["XX", "http://insecure-http-url.example/", "my-favorite-instance"]
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)
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def invalid_instance(request):
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return request.param
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def test_invalid_instance(username, password, invalid_instance):
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with pytest.raises(ValueError):
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Auth(
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username=username,
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password=password,
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instance=invalid_instance,
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)
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tests/test_common.py
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import pytest
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from seer_pas_sdk.common import *
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@pytest.fixture
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def mock_sample(platemap):
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"""A file name in our mock platemap"""
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idx = 0
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return (
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platemap.ms_file_name[idx],
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platemap.sample_name[idx],
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platemap.sample_id[idx],
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)
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@pytest.fixture(scope="function")
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def platemap_file(platemap, tmpdir):
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"""Our mock platemap, as a file"""
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outfile = tmpdir / "test_platemap.csv"
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platemap.to_csv(outfile)
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yield outfile
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# Clean up test file
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outfile.remove()
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def test_get_sample_info(platemap_file, mock_sample):
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"""Test that get_sample_info correctly parses the platemap file"""
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filename, sample_name, sample_id = mock_sample
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plate_id = "TEST_plate_id"
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ms_data_files = {filename}
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space = "TEST_space_id"
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res = get_sample_info(
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plate_id=plate_id,
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ms_data_files=ms_data_files,
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plate_map_file=platemap_file,
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space=space,
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sample_description_file=None, # TODO: test sample description file
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)
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assert len(res) == 1
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for sampleinfo in res:
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assert sampleinfo["plateID"] == plate_id
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assert sampleinfo["sampleName"] == sample_name
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assert sampleinfo["sampleID"] == sample_id
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assert sampleinfo["sampleUserGroup"] == space
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def test_get_sample_info_missing_file(platemap_file):
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"""Test that get_sample_info raises an exception if a file doesn't exist"""
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plate_id = "TEST_plate_id"
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ms_data_files = {"XXX_file_does_not_exist"}
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space = "TEST_space_id"
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with pytest.raises(ValueError):
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res = get_sample_info(
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plate_id=plate_id,
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ms_data_files=ms_data_files,
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plate_map_file=platemap_file,
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space=space,
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)
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def test_camel_case():
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assert camel_case("my favorite") == "myFavorite"
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assert camel_case("my Favorite") == "myFavorite"
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assert camel_case("My favorite") == "myFavorite"
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assert camel_case("My Favorite") == "myFavorite"
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assert camel_case("snake_case") == "snakeCase"
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assert camel_case("snake_Case") == "snakeCase"
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assert camel_case("Snake_case") == "snakeCase"
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assert camel_case("Snake_Case") == "snakeCase"
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assert camel_case("camelcase") == "camelcase"
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assert camel_case("camelCase") == "camelcase"
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assert camel_case("Camelcase") == "camelcase"
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assert camel_case("CamelCase") == "camelcase"
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assert camel_case("kebab-case") == "kebabCase"
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assert camel_case("kebab-Case") == "kebabCase"
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assert camel_case("Kebab-case") == "kebabCase"
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assert camel_case("Kebab-Case") == "kebabCase"
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# Corner cases:
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assert camel_case("two\nlines") == "two\nLines"
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assert camel_case("two\nLines") == "two\nLines"
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assert camel_case("Two\nlines") == "two\nLines"
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assert camel_case("Two\nLines") == "two\nLines"
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assert camel_case("über コンピュータコード") == "überコンピュータコード"
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assert camel_case("über コンピュータコード") == "überコンピュータコード"
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assert camel_case("Über コンピュータコード") == "überコンピュータコード"
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assert camel_case("Über コンピュータコード") == "überコンピュータコード"
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assert camel_case("clap👏back") == "clap👏Back"
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assert camel_case("clap👏Back") == "clap👏Back"
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assert camel_case("Clap👏back") == "clap👏Back"
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assert camel_case("Clap👏Back") == "clap👏Back"
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from io import StringIO
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import pandas as pd
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import pytest
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from seer_pas_sdk.objects import PlateMap
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def test_toofew_items():
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"""Test passing too few items to one or more attributes"""
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filenames = ["test_0.msfile", "test_1.msfile"]
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samplenames = ["TEST_sample_name"]
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platemap = PlateMap(
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ms_file_name=filenames.copy(), # prevent mutating shared state
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sample_name=samplenames.copy(), # prevent mutating shared state
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)
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assert len(platemap.ms_file_name) == len(filenames)
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assert len(platemap.sample_name) == len(filenames)
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for i in range(len(platemap.sample_name)):
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assert (platemap.sample_name[i] == None) == (i >= len(samplenames))
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def test_toomany_items():
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with pytest.raises(ValueError):
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PlateMap(
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ms_file_name=["test.msfile"],
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sample_name=["TEST_sample_name_0", "TEST_sample_name_1"],
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)
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def test_platemap_to_dict(platemap):
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res = platemap.to_dict()
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assert isinstance(res, dict)
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for k in res:
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assert len(res[k]) == platemap.length
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def test_platemap_to_df(platemap):
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res = platemap.to_df()
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assert isinstance(res, pd.DataFrame)
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assert len(res) == platemap.length
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for k in res.columns:
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assert len(res[k]) == platemap.length
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def test_platemap_to_csv_str(platemap):
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res = platemap.to_csv()
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assert isinstance(res, str)
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assert len(StringIO(res).readlines()) == platemap.length + 1
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59
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# Re-parse CSV with Pandas for additional checks
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df = pd.read_csv(StringIO(res))
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61
|
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assert len(df) == platemap.length
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for k in df.columns:
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assert len(df[k]) == platemap.length
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def test_platemap_to_csv_file(platemap, tmpdir):
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|
-
outfile = tmpdir / "test.csv"
|
|
69
|
-
res = platemap.to_csv(outfile)
|
|
70
|
-
|
|
71
|
-
with open(outfile, "r") as f:
|
|
72
|
-
assert len(f.readlines()) == platemap.length + 1
|
|
73
|
-
|
|
74
|
-
# Re-parse CSV with Pandas for additional checks
|
|
75
|
-
f.seek(0)
|
|
76
|
-
df = pd.read_csv(f)
|
|
77
|
-
|
|
78
|
-
assert len(df) == platemap.length
|
|
79
|
-
for k in df.columns:
|
|
80
|
-
assert len(df[k]) == platemap.length
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
def test_mutate_defaults():
|
|
84
|
-
"""Test that default values in the construtor aren't shared mutable instances"""
|
|
85
|
-
|
|
86
|
-
# Force extension of default (empty) values by creating a platemap with 2 samples
|
|
87
|
-
platemap_0 = PlateMap(["test_0.msfile", "test_1.msfile"])
|
|
88
|
-
|
|
89
|
-
# Now create a platemap with fewer samples; this will trigger an error if the default
|
|
90
|
-
# values were mutated by the first call.
|
|
91
|
-
platemap_1 = PlateMap(["test_0.msfile"])
|
tests/test_sdk.py
DELETED
|
File without changes
|