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vcell_client.FieldDataResourceApi

All URIs are relative to https://vcell.cam.uchc.edu

Method	HTTP request	Description
advanced_create	POST /api/v1/fieldData/advancedCreate	Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.
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.
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.
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.
create_from_simulation	POST /api/v1/fieldData/createFromSimulation	Create new field data from existing simulation results.
delete	DELETE /api/v1/fieldData/delete/{fieldDataID}	Delete the selected field data.
get_all_ids	GET /api/v1/fieldData/IDs	Get all of the ids used to identify, and retrieve field data.
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.
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.

advanced_create

FieldDataSavedResults advanced_create(file=file, file_name=file_name, extent=extent, i_size=i_size, channel_names=channel_names, times=times, annotation=annotation, origin=origin)

Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.

Example

import time
import os
import vcell_client
from vcell_client.models.extent import Extent
from vcell_client.models.field_data_saved_results import FieldDataSavedResults
from vcell_client.models.i_size import ISize
from vcell_client.models.origin import Origin
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.FieldDataResourceApi(api_client)
    file = None # bytearray |  (optional)
    file_name = 'file_name_example' # str |  (optional)
    extent = vcell_client.Extent() # Extent |  (optional)
    i_size = vcell_client.ISize() # ISize |  (optional)
    channel_names = ['channel_names_example'] # List[str] |  (optional)
    times = [3.4] # List[float] |  (optional)
    annotation = 'annotation_example' # str |  (optional)
    origin = vcell_client.Origin() # Origin |  (optional)

    try:
        # Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.
        api_response = api_instance.advanced_create(file=file, file_name=file_name, extent=extent, i_size=i_size, channel_names=channel_names, times=times, annotation=annotation, origin=origin)
        print("The response of FieldDataResourceApi->advanced_create:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->advanced_create: %s\n" % e)

Parameters

Name	Type	Notes
file	bytearray	[optional]
file_name	str	[optional]
extent	Extent	[optional]
i_size	ISize	[optional]
channel_names	List[str]	[optional]
times	List[float]	[optional]
annotation	str	[optional]
origin	Origin	[optional]

Return type

FieldDataSavedResults

Authorization

openId

HTTP request headers

Content-Type: multipart/form-data
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
422	Unprocessable content submitted	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

analyze_file

FieldData analyze_file(file=file, file_name=file_name)

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.

Example

import time
import os
import vcell_client
from vcell_client.models.field_data import FieldData
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.FieldDataResourceApi(api_client)
    file = None # bytearray |  (optional)
    file_name = 'file_name_example' # str |  (optional)

    try:
        # 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.
        api_response = api_instance.analyze_file(file=file, file_name=file_name)
        print("The response of FieldDataResourceApi->analyze_file:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->analyze_file: %s\n" % e)

Parameters

Name	Type	Description	Notes
file	bytearray		[optional]
file_name	str		[optional]

Return type

FieldData

Authorization

openId

HTTP request headers

Content-Type: multipart/form-data
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
422	Unprocessable content submitted	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

copy_models_field_data

Dict[str, ExternalDataIdentifier] copy_models_field_data(source_model=source_model)

Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.

Example

import time
import os
import vcell_client
from vcell_client.models.external_data_identifier import ExternalDataIdentifier
from vcell_client.models.source_model import SourceModel
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.FieldDataResourceApi(api_client)
    source_model = vcell_client.SourceModel() # SourceModel |  (optional)

    try:
        # Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.
        api_response = api_instance.copy_models_field_data(source_model=source_model)
        print("The response of FieldDataResourceApi->copy_models_field_data:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->copy_models_field_data: %s\n" % e)

Parameters

Name	Type	Description	Notes
source_model	SourceModel		[optional]

Return type

Dict[str, ExternalDataIdentifier]

Authorization

openId

HTTP request headers

Content-Type: application/json
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
422	Unprocessable content submitted	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

create_from_file

FieldDataSavedResults create_from_file(file=file, field_data_name=field_data_name)

Submit a .zip or .tif file that converts into field data, with all defaults derived from the file submitted.

Example

import time
import os
import vcell_client
from vcell_client.models.field_data_saved_results import FieldDataSavedResults
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.FieldDataResourceApi(api_client)
    file = None # bytearray |  (optional)
    field_data_name = 'field_data_name_example' # str |  (optional)

    try:
        # Submit a .zip or .tif file that converts into field data, with all defaults derived from the file submitted.
        api_response = api_instance.create_from_file(file=file, field_data_name=field_data_name)
        print("The response of FieldDataResourceApi->create_from_file:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->create_from_file: %s\n" % e)

Parameters

Name	Type	Description	Notes
file	bytearray		[optional]
field_data_name	str		[optional]

Return type

FieldDataSavedResults

Authorization

openId

HTTP request headers

Content-Type: multipart/form-data
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
422	Unprocessable content submitted	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

create_from_simulation

create_from_simulation(sim_key_reference=sim_key_reference, job_index=job_index, new_field_data_name=new_field_data_name)

Create new field data from existing simulation results.

Example

import time
import os
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.FieldDataResourceApi(api_client)
    sim_key_reference = 'sim_key_reference_example' # str |  (optional)
    job_index = 56 # int |  (optional)
    new_field_data_name = 'new_field_data_name_example' # str |  (optional)

    try:
        # Create new field data from existing simulation results.
        api_instance.create_from_simulation(sim_key_reference=sim_key_reference, job_index=job_index, new_field_data_name=new_field_data_name)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->create_from_simulation: %s\n" % e)

Parameters

Name	Type	Notes
sim_key_reference	str	[optional]
job_index	int	[optional]
new_field_data_name	str	[optional]

Return type

void (empty response body)

Authorization

openId

HTTP request headers

Content-Type: application/x-www-form-urlencoded
Accept: application/json

HTTP response details

Status code	Description	Response headers
201	Created	-
401	Not Authenticated	-
403	Not Allowed	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

delete

delete(field_data_id)

Delete the selected field data.

Example

import time
import os
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.FieldDataResourceApi(api_client)
    field_data_id = 'field_data_id_example' # str | 

    try:
        # Delete the selected field data.
        api_instance.delete(field_data_id)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->delete: %s\n" % e)

Parameters

Name	Type	Description	Notes
field_data_id	str

Return type

void (empty response body)

Authorization

openId

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
204	No Content	-
401	Not Authenticated	-
403	Not Allowed	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

get_all_ids

List[FieldDataReference] get_all_ids()

Get all of the ids used to identify, and retrieve field data.

Example

import time
import os
import vcell_client
from vcell_client.models.field_data_reference import FieldDataReference
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.FieldDataResourceApi(api_client)

    try:
        # Get all of the ids used to identify, and retrieve field data.
        api_response = api_instance.get_all_ids()
        print("The response of FieldDataResourceApi->get_all_ids:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->get_all_ids: %s\n" % e)

Parameters

This endpoint does not need any parameter.

Return type

List[FieldDataReference]

Authorization

openId

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

get_shape_from_id

FieldDataShape get_shape_from_id(field_data_id)

Get the shape of the field data. That is it's size, origin, extent, times, and data identifiers.

Example

import time
import os
import vcell_client
from vcell_client.models.field_data_shape import FieldDataShape
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.FieldDataResourceApi(api_client)
    field_data_id = 'field_data_id_example' # str | 

    try:
        # Get the shape of the field data. That is it's size, origin, extent, times, and data identifiers.
        api_response = api_instance.get_shape_from_id(field_data_id)
        print("The response of FieldDataResourceApi->get_shape_from_id:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->get_shape_from_id: %s\n" % e)

Parameters

Name	Type	Description	Notes
field_data_id	str

Return type

FieldDataShape

Authorization

openId

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
404	Not found	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

save

FieldDataSavedResults save(field_data=field_data)

Take the generated field data, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.

Example

import time
import os
import vcell_client
from vcell_client.models.field_data import FieldData
from vcell_client.models.field_data_saved_results import FieldDataSavedResults
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.FieldDataResourceApi(api_client)
    field_data = vcell_client.FieldData() # FieldData |  (optional)

    try:
        # Take the generated field data, and save it to the server. User may adjust the analyzed file before uploading to edit defaults.
        api_response = api_instance.save(field_data=field_data)
        print("The response of FieldDataResourceApi->save:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling FieldDataResourceApi->save: %s\n" % e)

Parameters

Name	Type	Description	Notes
field_data	FieldData		[optional]

Return type

FieldDataSavedResults

Authorization

openId

HTTP request headers

Content-Type: application/json
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	OK	-
401	Not Authenticated	-
403	Not Allowed	-
422	Unprocessable content submitted	-
500	Data Access Exception	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]