generated client for current openapi.yaml

.github/workflows/python.yml

@@ -0,0 +1,38 @@
+# NOTE: This file is auto generated by OpenAPI Generator.
+# URL: https://openapi-generator.tech
+#
+# ref: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: vcell_api_client Python package
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          if [ -f test-requirements.txt ]; then pip install -r test-requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

.gitignore

@@ -50,7 +50,10 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
-.pytest_cache/
+venv/
+.venv/
+.python-version
+.pytest_cache
 
 # Translations
 *.mo
@@ -73,7 +76,7 @@ docs/_build/
 # PyBuilder
 target/
 
-# Jupyter Notebook
+#Ipython Notebook
 .ipynb_checkpoints
 
 # pyenv
@@ -112,3 +115,7 @@ ENV/
 
 # mkdocs build dir
 site/
+
+.gitlab-ci.yml
+
+.travis.yml

.openapi-generator-ignore

@@ -0,0 +1,23 @@
+# OpenAPI Generator Ignore
+# Generated by openapi-generator https://github.com/openapitools/openapi-generator
+
+# Use this file to prevent files from being overwritten by the generator.
+# The patterns follow closely to .gitignore or .dockerignore.
+
+# As an example, the C# client generator defines ApiClient.cs.
+# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line:
+#ApiClient.cs
+
+# You can match any string of characters against a directory, file or extension with a single asterisk (*):
+#foo/*/qux
+# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux
+
+# You can recursively match patterns against a directory, file or extension with a double asterisk (**):
+#foo/**/qux
+# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux
+
+# You can also negate patterns with an exclamation (!).
+# For example, you can ignore all files in a docs folder with the file extension .md:
+#docs/*.md
+# Then explicitly reverse the ignore rule for a single file:
+#!docs/README.md

.openapi-generator/FILES

@@ -0,0 +1,54 @@
+.github/workflows/python.yml
+.gitignore
+.gitlab-ci.yml
+.travis.yml
+README.md
+docs/AccesTokenRepresentationRecord.md
+docs/AdminResourceApi.md
+docs/BioModel.md
+docs/BioModelResourceApi.md
+docs/BiomodelRef.md
+docs/HelloWorldApi.md
+docs/HelloWorldMessage.md
+docs/Identity.md
+docs/MathmodelRef.md
+docs/Publication.md
+docs/PublicationResourceApi.md
+docs/Simulation.md
+docs/UserIdentityJSONSafe.md
+docs/UserLoginInfoForMapping.md
+docs/UserRegistrationInfo.md
+docs/UsersResourceApi.md
+git_push.sh
+pyproject.toml
+requirements.txt
+setup.cfg
+setup.py
+test-requirements.txt
+test/__init__.py
+tox.ini
+vcell_api_client/__init__.py
+vcell_api_client/api/__init__.py
+vcell_api_client/api/admin_resource_api.py
+vcell_api_client/api/bio_model_resource_api.py
+vcell_api_client/api/hello_world_api.py
+vcell_api_client/api/publication_resource_api.py
+vcell_api_client/api/users_resource_api.py
+vcell_api_client/api_client.py
+vcell_api_client/api_response.py
+vcell_api_client/configuration.py
+vcell_api_client/exceptions.py
+vcell_api_client/models/__init__.py
+vcell_api_client/models/acces_token_representation_record.py
+vcell_api_client/models/bio_model.py
+vcell_api_client/models/biomodel_ref.py
+vcell_api_client/models/hello_world_message.py
+vcell_api_client/models/identity.py
+vcell_api_client/models/mathmodel_ref.py
+vcell_api_client/models/publication.py
+vcell_api_client/models/simulation.py
+vcell_api_client/models/user_identity_json_safe.py
+vcell_api_client/models/user_login_info_for_mapping.py
+vcell_api_client/models/user_registration_info.py
+vcell_api_client/py.typed
+vcell_api_client/rest.py

.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.1.0

README.md

@@ -24,3 +24,143 @@ Client library to connect to VCell remote API
 ## Credits
 
 This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [waynerv/cookiecutter-pypackage](https://github.com/waynerv/cookiecutter-pypackage) project template.
+
+## Background
+
+This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
+
+- API version: 1.0.1
+- Package version: 0.1.0
+- Build package: org.openapitools.codegen.languages.PythonClientCodegen
+For more information, please visit [http://exampleurl.com/contact](http://exampleurl.com/contact)
+
+## Requirements.
+
+Python 3.9+
+
+## Installation & Usage
+### pip install
+
+If the python package is hosted on a repository, you can install directly using:
+
+```sh
+pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git
+```
+(you may need to run `pip` with root permission: `sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git`)
+
+Then import the package:
+```python
+import vcell_api_client
+```
+
+### Setuptools
+
+Install via [Setuptools](http://pypi.python.org/pypi/setuptools).
+
+```sh
+python setup.py install --user
+```
+(or `sudo python setup.py install` to install the package for all users)
+
+Then import the package:
+```python
+import vcell_api_client
+```
+
+### Tests
+
+Execute `pytest` to run the tests.
+
+## Getting Started
+
+Please follow the [installation procedure](#installation--usage) and then run the following:
+
+```python
+
+import time
+import vcell_api_client
+from vcell_api_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to https://vcellapi-test.cam.uchc.edu
+# See configuration.py for a list of all supported configuration parameters.
+configuration = vcell_api_client.Configuration(
+    host = "https://vcellapi-test.cam.uchc.edu"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+
+# Enter a context with an instance of the API client
+with vcell_api_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = vcell_api_client.AdminResourceApi(api_client)
+
+    try:
+        # Get usage summary
+        api_response = api_instance.get_usage()
+        print("The response of AdminResourceApi->get_usage:\n")
+        pprint(api_response)
+    except ApiException as e:
+        print("Exception when calling AdminResourceApi->get_usage: %s\n" % e)
+
+```
+
+## Documentation for API Endpoints
+
+All URIs are relative to *https://vcellapi-test.cam.uchc.edu*
+
+Class | Method | HTTP request | Description
+------------ | ------------- | ------------- | -------------
+*AdminResourceApi* | [**get_usage**](docs/AdminResourceApi.md#get_usage) | **GET** /api/v1/admin/usage | Get usage summary
+*BioModelResourceApi* | [**delete_bio_model**](docs/BioModelResourceApi.md#delete_bio_model) | **DELETE** /api/v1/bioModel/{bioModelID} | Delete the BioModel from VCell's database.
+*BioModelResourceApi* | [**get_biomodel_by_id**](docs/BioModelResourceApi.md#get_biomodel_by_id) | **GET** /api/v1/bioModel/{bioModelID} | Get BioModel information in JSON format by ID.
+*BioModelResourceApi* | [**upload_bio_model**](docs/BioModelResourceApi.md#upload_bio_model) | **POST** /api/v1/bioModel/upload_bioModel | Upload the BioModel to VCell database. Returns BioModel ID.
+*HelloWorldApi* | [**get_hello_world**](docs/HelloWorldApi.md#get_hello_world) | **GET** /api/v1/helloworld | Get hello world message.
+*PublicationResourceApi* | [**create_publication**](docs/PublicationResourceApi.md#create_publication) | **POST** /api/v1/publications | Create publication
+*PublicationResourceApi* | [**delete_publication**](docs/PublicationResourceApi.md#delete_publication) | **DELETE** /api/v1/publications/{id} | Delete publication
+*PublicationResourceApi* | [**get_publication_by_id**](docs/PublicationResourceApi.md#get_publication_by_id) | **GET** /api/v1/publications/{id} | Get publication by ID
+*PublicationResourceApi* | [**get_publications**](docs/PublicationResourceApi.md#get_publications) | **GET** /api/v1/publications | Get all publications
+*PublicationResourceApi* | [**update_publication**](docs/PublicationResourceApi.md#update_publication) | **PUT** /api/v1/publications | Create publication
+*UsersResourceApi* | [**forgot_legacy_password**](docs/UsersResourceApi.md#forgot_legacy_password) | **POST** /api/v1/users/forgotLegacyPassword | The end user has forgotten the legacy password they used for VCell, so they will be emailed it.
+*UsersResourceApi* | [**get_legacy_api_token**](docs/UsersResourceApi.md#get_legacy_api_token) | **POST** /api/v1/users/bearerToken | Get token for legacy API
+*UsersResourceApi* | [**get_mapped_user**](docs/UsersResourceApi.md#get_mapped_user) | **GET** /api/v1/users/mappedUser | Get mapped VCell identity
+*UsersResourceApi* | [**get_me**](docs/UsersResourceApi.md#get_me) | **GET** /api/v1/users/me | Get current user
+*UsersResourceApi* | [**map_new_user**](docs/UsersResourceApi.md#map_new_user) | **POST** /api/v1/users/newUser | create vcell user
+*UsersResourceApi* | [**map_user**](docs/UsersResourceApi.md#map_user) | **POST** /api/v1/users/mapUser | map vcell user
+*UsersResourceApi* | [**unmap_user**](docs/UsersResourceApi.md#unmap_user) | **PUT** /api/v1/users/unmapUser/{userName} | remove vcell identity mapping
+
+
+## Documentation For Models
+
+ - [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
+ - [BioModel](docs/BioModel.md)
+ - [BiomodelRef](docs/BiomodelRef.md)
+ - [HelloWorldMessage](docs/HelloWorldMessage.md)
+ - [Identity](docs/Identity.md)
+ - [MathmodelRef](docs/MathmodelRef.md)
+ - [Publication](docs/Publication.md)
+ - [Simulation](docs/Simulation.md)
+ - [UserIdentityJSONSafe](docs/UserIdentityJSONSafe.md)
+ - [UserLoginInfoForMapping](docs/UserLoginInfoForMapping.md)
+ - [UserRegistrationInfo](docs/UserRegistrationInfo.md)
+
+
+<a id="documentation-for-authorization"></a>
+## Documentation For Authorization
+
+
+Authentication schemes defined for the API:
+<a id="openId"></a>
+### openId
+
+
+
+## Author
+
+[email protected]
+
+

docs/AccesTokenRepresentationRecord.md

@@ -0,0 +1,32 @@
+# AccesTokenRepresentationRecord
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**token** | **str** |  | [optional] 
+**creation_date_seconds** | **int** |  | [optional] 
+**expire_date_seconds** | **int** |  | [optional] 
+**user_id** | **str** |  | [optional] 
+**user_key** | **str** |  | [optional] 
+
+## Example
+
+```python
+from vcell_api_client.models.acces_token_representation_record import AccesTokenRepresentationRecord
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AccesTokenRepresentationRecord from a JSON string
+acces_token_representation_record_instance = AccesTokenRepresentationRecord.from_json(json)
+# print the JSON string representation of the object
+print AccesTokenRepresentationRecord.to_json()
+
+# convert the object into a dict
+acces_token_representation_record_dict = acces_token_representation_record_instance.to_dict()
+# create an instance of AccesTokenRepresentationRecord from a dict
+acces_token_representation_record_form_dict = acces_token_representation_record.from_dict(acces_token_representation_record_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+