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vcell-api

VCell API

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: 1.0.1
  • Package version: 1.0.0
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen For more information, please visit https://vcell.org

Requirements.

Python 3.7+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

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:

import vcell_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import vcell_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import time
import vcell_client
from vcell_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://vcell.cam.uchc.edu
# See configuration.py for a list of all supported configuration parameters.
configuration = vcell_client.Configuration(
    host = "https://vcell.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_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = vcell_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://vcell.cam.uchc.edu

Class Method HTTP request Description
AdminResourceApi get_usage GET /api/v1/admin/usage Get usage summary
BioModelResourceApi delete_bio_model DELETE /api/v1/bioModel/{bioModelID} Delete the BioModel from VCell's database.
BioModelResourceApi get_bio_model GET /api/v1/bioModel/{bioModelID} Get BioModel.
BioModelResourceApi get_bio_model_summaries GET /api/v1/bioModel/summaries Return BioModel summaries.
BioModelResourceApi get_bio_model_summary GET /api/v1/bioModel/{bioModelID}/summary All of the text based information about a BioModel (summary, version, publication status, etc...), but not the actual BioModel itself.
BioModelResourceApi get_bio_model_vcml GET /api/v1/bioModel/{bioModelID}/vcml_download Get the BioModel in VCML format.
BioModelResourceApi get_summaries_container GET /api/v1/bioModel/summariesContainer
BioModelResourceApi save_bio_model POST /api/v1/bioModel Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
ExportResourceApi export_n5 POST /api/v1/export/N5
ExportResourceApi export_status GET /api/v1/export/status
FieldDataResourceApi advanced_create POST /api/v1/fieldData/advancedCreate Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.
FieldDataResourceApi analyze_file POST /api/v1/fieldData/analyzeFile Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and return field data. Color mapped images not supported (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
FieldDataResourceApi copy_models_field_data POST /api/v1/fieldData/copyModelsFieldData Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.
FieldDataResourceApi create_from_file POST /api/v1/fieldData/createFromFile Submit a .zip or .tif file that converts into field data, with all defaults derived from the file submitted.
FieldDataResourceApi create_from_simulation POST /api/v1/fieldData/createFromSimulation Create new field data from existing simulation results.
FieldDataResourceApi delete DELETE /api/v1/fieldData/delete/{fieldDataID} Delete the selected field data.
FieldDataResourceApi get_all_ids GET /api/v1/fieldData/IDs Get all of the ids used to identify, and retrieve field data.
FieldDataResourceApi get_shape_from_id GET /api/v1/fieldData/shape/{fieldDataID} Get the shape of the field data. That is it's size, origin, extent, times, and data identifiers.
FieldDataResourceApi save POST /api/v1/fieldData/save Take the generated field data, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
GeometryResourceApi delete_geometry DELETE /api/v1/geometry/{id}
GeometryResourceApi get_geometry_summaries GET /api/v1/geometry/summaries
GeometryResourceApi get_geometry_summary GET /api/v1/geometry/summary/{id}
GeometryResourceApi get_geometry_vcml GET /api/v1/geometry/{id}
GeometryResourceApi save_geometry POST /api/v1/geometry
HelloWorldApi get_hello_world GET /api/v1/helloworld Get hello world message.
MathModelResourceApi delete_math_model DELETE /api/v1/mathModel/{id}
MathModelResourceApi get_summaries GET /api/v1/mathModel/summaries
MathModelResourceApi get_summary GET /api/v1/mathModel/summary/{id}
MathModelResourceApi get_vcml GET /api/v1/mathModel/{id}
MathModelResourceApi save_math_model POST /api/v1/mathModel
PublicationResourceApi create_publication POST /api/v1/publications Create publication
PublicationResourceApi delete_publication DELETE /api/v1/publications/{id} Delete publication
PublicationResourceApi get_publication_by_id GET /api/v1/publications/{id} Get publication by ID
PublicationResourceApi get_publications GET /api/v1/publications Get all publications
PublicationResourceApi update_publication PUT /api/v1/publications Update publication
SimulationResourceApi get_simulation_status GET /api/v1/Simulation/{simID}/simulationStatus Get the status of simulation running
SimulationResourceApi start_simulation POST /api/v1/Simulation/{simID}/startSimulation Start a simulation.
SimulationResourceApi stop_simulation POST /api/v1/Simulation/{simID}/stopSimulation Stop a simulation.
SolverResourceApi get_fv_solver_input_from_sbml POST /api/v1/solver/getFVSolverInput Retrieve finite volume input from SBML spatial model.
SolverResourceApi get_fv_solver_input_from_vcml POST /api/v1/solver/getFVSolverInputFromVCML Retrieve finite volume input from SBML spatial model.
UsersResourceApi 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_guest_legacy_api_token POST /api/v1/users/guestBearerToken Method to get legacy tokens for guest users
UsersResourceApi get_legacy_api_token POST /api/v1/users/bearerToken Get token for legacy API
UsersResourceApi get_mapped_user GET /api/v1/users/mappedUser Get mapped VCell identity
UsersResourceApi get_me GET /api/v1/users/me Get current user
UsersResourceApi map_new_user POST /api/v1/users/newUser create vcell user
UsersResourceApi map_user POST /api/v1/users/mapUser map vcell user
UsersResourceApi process_magic_link GET /api/v1/users/processMagicLink Process the magic link and map the user
UsersResourceApi request_recovery_email POST /api/v1/users/requestRecoveryEmail request a recovery email to link a VCell account.
UsersResourceApi unmap_user PUT /api/v1/users/unmapUser/{userName} remove vcell identity mapping
VCImageResourceApi delete_image_vcml DELETE /api/v1/image/{id}
VCImageResourceApi get_image_summaries GET /api/v1/image/summaries
VCImageResourceApi get_image_summary GET /api/v1/image/summary/{id}
VCImageResourceApi get_image_vcml GET /api/v1/image/{id}
VCImageResourceApi save_image_vcml POST /api/v1/image

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

openId

Author

vcell_support@uchc.com