libica 3.2__tar.gz → 3.3__tar.gz

libica-3.3/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020-2026 UMCCR and Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

libica-3.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: libica
+Version: 3.3
+Summary: Python SDK for Illumina BioInsight Platform Core
+Home-page: https://github.com/umccr/libica
+Author: UMCCR and Contributors
+Author-email: services@umccr.org
+License: MIT
+Project-URL: Bug Tracker, https://github.com/umccr/libica/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: python-dateutil
+Requires-Dist: urllib3
+Requires-Dist: pydantic
+Requires-Dist: typing-extensions
+Provides-Extra: dev
+Requires-Dist: pipdeptree; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: setuptools; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: pdoc3; extra == "dev"
+Requires-Dist: mkdocs; extra == "dev"
+Requires-Dist: mkdocs-material; extra == "dev"
+Requires-Dist: openapi-spec-validator; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: detect-secrets; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ggshield; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: mockito; extra == "test"
+Requires-Dist: tox; extra == "test"
+Requires-Dist: nose2; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# libica
+
+[![Pull Request Build Status](https://github.com/umccr/libica/workflows/Pull%20Request%20Build/badge.svg)](https://github.com/umccr/libica/actions) 
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/libica?style=flat)](https://pypistats.org/packages/libica) 
+[![PyPI](https://img.shields.io/pypi/v/libica?style=flat)](https://pypi.org/project/libica) 
+[![PyPI - License](https://img.shields.io/pypi/l/libica?style=flat)](https://opensource.org/licenses/MIT)
+
+Python SDK to programmatically call Illumina BioInsight Platform Core Genomic (multi-omics) data platform and BioInformatics web services.
+
+- ICA API: https://help.ica.illumina.com/reference/r-api
+- Install through ``pip`` like so:
+```commandline
+pip install libica
+```
+
+## Overview
+
+- Tested for Python 3.11, 3.12, 3.13, 3.14
+- SDK Guide: [PyDoc](https://umccr.github.io/libica/libica/)
+- User Guide: https://umccr.github.io/libica/
+
+## Roadmap
+
+- See [changelog](https://github.com/umccr/libica/blob/main/CHANGELOG.md) and [closed milestones](https://github.com/umccr/libica/milestones?state=closed)
+- See opening [milestones](https://github.com/umccr/libica/milestones) for current planning and next SDK release
+
+## Release
+
+There are two SDK Python packages, namely `v2` and `v3`. If you are a new starter, please use `v3` SDK package. If you are an existing user, please upgrade to `v3` when you can. Most of the time, this should be straight forward with minor tuning to application code. Since `v3` release, the SDK `v2` package will now enter into maintenance mode and deprecate by 2026 Oct.
+
+## Example
+
+- See the [examples](https://github.com/umccr/libica/tree/main/examples) directory for some example scripts
+- See [wrapica](https://github.com/umccr/wrapica) and [icav2-cli-plugins](https://github.com/umccr/icav2-cli-plugins) for client application that build on top of SDK
+
+## Notice
+
+- MIT License and DISCLAIMER
+- [The Advanced Genomics Collaboration (TAGC)](https://www.tagcaustralia.com)

libica-3.3/README.md

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+# libica
+
+[![Pull Request Build Status](https://github.com/umccr/libica/workflows/Pull%20Request%20Build/badge.svg)](https://github.com/umccr/libica/actions) 
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/libica?style=flat)](https://pypistats.org/packages/libica) 
+[![PyPI](https://img.shields.io/pypi/v/libica?style=flat)](https://pypi.org/project/libica) 
+[![PyPI - License](https://img.shields.io/pypi/l/libica?style=flat)](https://opensource.org/licenses/MIT)
+
+Python SDK to programmatically call Illumina BioInsight Platform Core Genomic (multi-omics) data platform and BioInformatics web services.
+
+- ICA API: https://help.ica.illumina.com/reference/r-api
+- Install through ``pip`` like so:
+```commandline
+pip install libica
+```
+
+## Overview
+
+- Tested for Python 3.11, 3.12, 3.13, 3.14
+- SDK Guide: [PyDoc](https://umccr.github.io/libica/libica/)
+- User Guide: https://umccr.github.io/libica/
+
+## Roadmap
+
+- See [changelog](https://github.com/umccr/libica/blob/main/CHANGELOG.md) and [closed milestones](https://github.com/umccr/libica/milestones?state=closed)
+- See opening [milestones](https://github.com/umccr/libica/milestones) for current planning and next SDK release
+
+## Release
+
+There are two SDK Python packages, namely `v2` and `v3`. If you are a new starter, please use `v3` SDK package. If you are an existing user, please upgrade to `v3` when you can. Most of the time, this should be straight forward with minor tuning to application code. Since `v3` release, the SDK `v2` package will now enter into maintenance mode and deprecate by 2026 Oct.
+
+## Example
+
+- See the [examples](https://github.com/umccr/libica/tree/main/examples) directory for some example scripts
+- See [wrapica](https://github.com/umccr/wrapica) and [icav2-cli-plugins](https://github.com/umccr/icav2-cli-plugins) for client application that build on top of SDK
+
+## Notice
+
+- MIT License and DISCLAIMER
+- [The Advanced Genomics Collaboration (TAGC)](https://www.tagcaustralia.com)

libica-3.3/libica/openapi/v2/__init__.py

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+# flake8: noqa
+
+"""
+    Platform Core Rest API
+
+    This API can be used to interact with Illumina BioInsight Platform Core.<br> <h2>Authentication</h2> <p> Authentication to the  API can be done in multiple ways:<br> <ul><li>For the entire API, except for the POST /tokens endpoint: API-key + JWT</li> <li>Only for the POST /tokens endpoint: API-key + Basic Authentication</li></ul> </p> <p> <h4>API-key</h4> API keys are managed within the Illumina portal where you can manage your profile after you have logged on. The API-key has to be provided in the X-API-Key header parameter when executing API calls to Platform Core. In the background, a JWT will be requested at the IDP of Illumina to create a session. A good practice is to not use the API-key for every API call, but to first generate a JWT and to use that for authentication in subsequent calls.<br> </p> <p> <h4>JWT</h4> To avoid using an API-key for each call, we recommend to request a JWT via the POST /tokens endpoint  using this API-key. The JWT will expire after a pre-configured period specified by a tenant administrator through the IAM console in the Illumina portal. The JWT is the preferred way for authentication.<br>A not yet expired, still valid JWT could be refreshed using the POST /tokens:refresh endpoint.<br>Refreshing the JWT is not possible if the JWT was generated by using an API-key.<br> </p> <p> <h4>Basic Authentication</h4> Basic authentication is only supported by the POST /tokens endpoint for generating a JWT. Use \"Basic base64encoded(emailaddress:password)\" in the \"Authorization\" header parameter for this authentication method. In case having access to multiple tenants using the same email-address, also provide the \"tenant\" request parameter to indicate what tenant you would like to request a JWT for. </p> <p> <h2>Compression</h2> If the API client provides request header 'Accept-Encoding' with value 'gzip', then the API applies GZIP compression on the JSON response. This significantly reduces the size and thus the download time of the response, which results in faster end-to-end API calls. In case of compression, the API also provides response header 'Content-Encoding' with value 'gzip', as indication for the client that decompression is required. </p>   # noqa: E501
+
+    The version of the OpenAPI document: 3
+    Generated by: https://openapi-generator.tech
+"""
+
+
+__version__ = "1.0.0"
+
+# import ApiClient
+from libica.openapi.v2.api_client import ApiClient
+
+# import Configuration
+from libica.openapi.v2.configuration import Configuration
+
+# import exceptions
+from libica.openapi.v2.exceptions import OpenApiException
+from libica.openapi.v2.exceptions import ApiAttributeError
+from libica.openapi.v2.exceptions import ApiTypeError
+from libica.openapi.v2.exceptions import ApiValueError
+from libica.openapi.v2.exceptions import ApiKeyError
+from libica.openapi.v2.exceptions import ApiException

libica-3.3/libica/openapi/v2/api/analysis_storage_api.py

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+"""
+    Platform Core Rest API
+
+    This API can be used to interact with Illumina BioInsight Platform Core.<br> <h2>Authentication</h2> <p> Authentication to the  API can be done in multiple ways:<br> <ul><li>For the entire API, except for the POST /tokens endpoint: API-key + JWT</li> <li>Only for the POST /tokens endpoint: API-key + Basic Authentication</li></ul> </p> <p> <h4>API-key</h4> API keys are managed within the Illumina portal where you can manage your profile after you have logged on. The API-key has to be provided in the X-API-Key header parameter when executing API calls to Platform Core. In the background, a JWT will be requested at the IDP of Illumina to create a session. A good practice is to not use the API-key for every API call, but to first generate a JWT and to use that for authentication in subsequent calls.<br> </p> <p> <h4>JWT</h4> To avoid using an API-key for each call, we recommend to request a JWT via the POST /tokens endpoint  using this API-key. The JWT will expire after a pre-configured period specified by a tenant administrator through the IAM console in the Illumina portal. The JWT is the preferred way for authentication.<br>A not yet expired, still valid JWT could be refreshed using the POST /tokens:refresh endpoint.<br>Refreshing the JWT is not possible if the JWT was generated by using an API-key.<br> </p> <p> <h4>Basic Authentication</h4> Basic authentication is only supported by the POST /tokens endpoint for generating a JWT. Use \"Basic base64encoded(emailaddress:password)\" in the \"Authorization\" header parameter for this authentication method. In case having access to multiple tenants using the same email-address, also provide the \"tenant\" request parameter to indicate what tenant you would like to request a JWT for. </p> <p> <h2>Compression</h2> If the API client provides request header 'Accept-Encoding' with value 'gzip', then the API applies GZIP compression on the JSON response. This significantly reduces the size and thus the download time of the response, which results in faster end-to-end API calls. In case of compression, the API also provides response header 'Content-Encoding' with value 'gzip', as indication for the client that decompression is required. </p>   # noqa: E501
+
+    The version of the OpenAPI document: 3
+    Generated by: https://openapi-generator.tech
+"""
+
+
+import re  # noqa: F401
+import sys  # noqa: F401
+
+from libica.openapi.v2.api_client import ApiClient, Endpoint as _Endpoint
+from libica.openapi.v2.model_utils import (  # noqa: F401
+    check_allowed_values,
+    check_validations,
+    date,
+    datetime,
+    file_type,
+    none_type,
+    validate_and_convert_types
+)
+from libica.openapi.v2.model.analysis_storage_list_v3 import AnalysisStorageListV3
+from libica.openapi.v2.model.problem import Problem
+
+
+class AnalysisStorageApi(object):
+    """NOTE: This class is auto generated by OpenAPI Generator
+    Ref: https://openapi-generator.tech
+
+    Do not edit the class manually.
+    """
+
+    def __init__(self, api_client=None):
+        if api_client is None:
+            api_client = ApiClient()
+        self.api_client = api_client
+        self.get_analysis_storage_options_endpoint = _Endpoint(
+            settings={
+                'response_type': (AnalysisStorageListV3,),
+                'auth': [
+                    'ApiKeyAuth',
+                    'JwtAuth'
+                ],
+                'endpoint_path': '/api/analysisStorages',
+                'operation_id': 'get_analysis_storage_options',
+                'http_method': 'GET',
+                'servers': None,
+            },
+            params_map={
+                'all': [
+                ],
+                'required': [],
+                'nullable': [
+                ],
+                'enum': [
+                ],
+                'validation': [
+                ]
+            },
+            root_map={
+                'validations': {
+                },
+                'allowed_values': {
+                },
+                'openapi_types': {
+                },
+                'attribute_map': {
+                },
+                'location_map': {
+                },
+                'collection_format_map': {
+                }
+            },
+            headers_map={
+                'accept': [
+                    'application/problem+json',
+                    'application/vnd.illumina.v3+json'
+                ],
+                'content_type': [],
+            },
+            api_client=api_client
+        )
+
+    def get_analysis_storage_options(
+        self,
+        **kwargs
+    ):
+        """Retrieve the list of analysis storage options.  # noqa: E501
+
+        This endpoint only returns V3 items. Use the search project analysis storage endpoint to get V4 items.  # noqa: E501
+        This method makes a synchronous HTTP request by default. To make an
+        asynchronous HTTP request, please pass async_req=True
+
+        >>> thread = api.get_analysis_storage_options(async_req=True)
+        >>> result = thread.get()
+
+
+        Keyword Args:
+            _return_http_data_only (bool): response data without head status
+                code and headers. Default is True.
+            _preload_content (bool): if False, the urllib3.HTTPResponse object
+                will be returned without reading/decoding response data.
+                Default is True.
+            _request_timeout (int/float/tuple): timeout setting for this request. If
+                one number provided, it will be total request timeout. It can also
+                be a pair (tuple) of (connection, read) timeouts.
+                Default is None.
+            _check_input_type (bool): specifies if type checking
+                should be done one the data sent to the server.
+                Default is True.
+            _check_return_type (bool): specifies if type checking
+                should be done one the data received from the server.
+                Default is True.
+            _spec_property_naming (bool): True if the variable names in the input data
+                are serialized names, as specified in the OpenAPI document.
+                False if the variable names in the input data
+                are pythonic names, e.g. snake case (default)
+            _content_type (str/None): force body content-type.
+                Default is None and content-type will be predicted by allowed
+                content-types and body.
+            _host_index (int/None): specifies the index of the server
+                that we want to use.
+                Default is read from the configuration.
+            async_req (bool): execute request asynchronously
+
+        Returns:
+            AnalysisStorageListV3
+                If the method is called asynchronously, returns the request
+                thread.
+        """
+        kwargs['async_req'] = kwargs.get(
+            'async_req', False
+        )
+        kwargs['_return_http_data_only'] = kwargs.get(
+            '_return_http_data_only', True
+        )
+        kwargs['_preload_content'] = kwargs.get(
+            '_preload_content', True
+        )
+        kwargs['_request_timeout'] = kwargs.get(
+            '_request_timeout', None
+        )
+        kwargs['_check_input_type'] = kwargs.get(
+            '_check_input_type', True
+        )
+        kwargs['_check_return_type'] = kwargs.get(
+            '_check_return_type', True
+        )
+        kwargs['_spec_property_naming'] = kwargs.get(
+            '_spec_property_naming', False
+        )
+        kwargs['_content_type'] = kwargs.get(
+            '_content_type')
+        kwargs['_host_index'] = kwargs.get('_host_index')
+        return self.get_analysis_storage_options_endpoint.call_with_http_info(**kwargs)
+