odm_api.ExpressionIntegrationAsCuratorApi¶

All URIs are relative to http://localhost

Method	HTTP request	Description
create_expression_group_cell_group_link_as_curator	POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/cell/group/{targetId}	Create a link between a group of cell expression objects and a group of cell metadata.
create_expression_group_library_group_link_as_curator	POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId}	Create a link between a group of expression objects and a group of library objects
create_expression_group_preparation_group_link_as_curator	POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId}	Create a link between a group of expression objects and a group of preparation objects
create_expression_group_sample_group_link_as_curator	POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}	Create a link between a group of expression objects and a group of sample objects
create_expression_library_link_as_curator	POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId}	Create a link between an expression object and a library
create_expression_preparation_link_as_curator	POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId}	Create a link between an expression object and a preparation
create_expression_sample_link_as_curator	POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId}	Create a link between an expression object and a sample
delete_expression_group_library_group_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId}	Delete link between a group of expression objects and a group of library objects
delete_expression_group_preparation_group_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId}	Delete link between a group of expression objects and a group of preparation objects
delete_expression_group_sample_group_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}	Delete link between a group of expression objects and a group of sample objects
delete_expression_library_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId}	Delete link between an expression object and a library
delete_expression_preparation_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId}	Delete link between an expression object and a preparation
delete_expression_sample_link_as_curator	DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId}	Delete link between an expression object and a sample
get_expression_by_library_as_curator	GET /api/v1/as-curator/integration/link/expression/by/library/{id}	Retrieve expression run-level data by querying related library ID (accession)
get_expression_by_preparation	GET /api/v1/as-curator/integration/link/expression/by/preparation/{id}	Retrieve expression run-level data by querying related preparation ID (accession)
get_expression_by_sample_as_curator	GET /api/v1/as-curator/integration/link/expression/by/sample/{id}	Retrieve expression run-level data by querying related sample ID (accession)
get_expression_groups_by_study_as_curator	GET /api/v1/as-curator/integration/link/expression/group/by/study/{id}	Retrieve group metadata by querying study ID (accession)
get_expression_run_to_library_pairs_as_curator	GET /api/v1/as-curator/integration/link/expression/run-to-libraries/by/group/{id}	Retrieve run-library pairs by group id. Pagination is based on unique runs, not unique pairs.
get_expression_run_to_preparation_pairs_as_curator	GET /api/v1/as-curator/integration/link/expression/run-to-preparations/by/group/{id}	Retrieve run-preparation pairs by group id. Pagination is based on unique runs, not unique pairs.
get_expression_run_to_sample_pairs_as_curator	GET /api/v1/as-curator/integration/link/expression/run-to-samples/by/group/{id}	Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.

create_expression_group_cell_group_link_as_curator¶

create_expression_group_cell_group_link_as_curator(source_id, target_id)

Create a link between a group of cell expression objects and a group of cell metadata.

A cell expression object can be linked to one cell metadata object only.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the cell expression group object
    target_id = 'target_id_example' # str | The ID (accession) of the cell metadata group object

    try:
        # Create a link between a group of cell expression objects and a group of cell metadata.
        api_instance.create_expression_group_cell_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_group_cell_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the cell expression group object
target_id	str	The ID (accession) of the cell metadata group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
200	Some (not all) cell links were created.	-
204	All links were created.	-
400	Incorrect Cell or Expression group provided, see error message for details.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_group_library_group_link_as_curator¶

create_expression_group_library_group_link_as_curator(source_id, target_id)

Create a link between a group of expression objects and a group of library objects

Create a link between a group of expression objects and a group of library objects.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the library group object

    try:
        # Create a link between a group of expression objects and a group of library objects
        api_instance.create_expression_group_library_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_group_library_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the library group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
200	Some (not all) sample links created.	-
204	Link created.	-
400	Library group, signal group or libraries to link not found	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_group_preparation_group_link_as_curator¶

create_expression_group_preparation_group_link_as_curator(source_id, target_id)

Create a link between a group of expression objects and a group of preparation objects

Create a link between a group of expression objects and a group of preparation objects.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the preparation group object

    try:
        # Create a link between a group of expression objects and a group of preparation objects
        api_instance.create_expression_group_preparation_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_group_preparation_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the preparation group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
200	Some (not all) sample links created.	-
204	Link created.	-
400	Preparation group, signal group or preparations to link not found	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_group_sample_group_link_as_curator¶

create_expression_group_sample_group_link_as_curator(source_id, target_id, linking_attribute=linking_attribute)

Create a link between a group of expression objects and a group of sample objects

Create a link between a group of expression objects and a group of sample objects.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Users can specify a custom metadata field for linking omics data to samples via the “linkingAttribute” parameter, if not specified the “Sample Source ID“ sample metadata attribute will be used by default.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the sample group object
    linking_attribute = 'linking_attribute_example' # str | Metadata field containing sample IDs to link omics data to samples. The template applied to the study must contain this field in the sample section. (optional)

    try:
        # Create a link between a group of expression objects and a group of sample objects
        api_instance.create_expression_group_sample_group_link_as_curator(source_id, target_id, linking_attribute=linking_attribute)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_group_sample_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the sample group object
linking_attribute	str	Metadata field containing sample IDs to link omics data to samples. The template applied to the study must contain this field in the sample section.	[optional]

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
200	Not all signal data were linked to the samples.	-
204	All signal data were linked to the samples from the specified sample group.	-
400	Sample group, signal group or samples to the link were not found, or the specified linking attribute was not found.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_library_link_as_curator¶

create_expression_library_link_as_curator(source_id, target_id)

Create a link between an expression object and a library

Create a link between an expression object and a library.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the library object

    try:
        # Create a link between an expression object and a library
        api_instance.create_expression_library_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_library_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the library object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link created.	-
400	Link cannot be created.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_preparation_link_as_curator¶

create_expression_preparation_link_as_curator(source_id, target_id)

Create a link between an expression object and a preparation

Create a link between an expression object and a preparation.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the preparation object

    try:
        # Create a link between an expression object and a preparation
        api_instance.create_expression_preparation_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_preparation_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the preparation object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link created.	-
400	Link cannot be created.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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create_expression_sample_link_as_curator¶

create_expression_sample_link_as_curator(source_id, target_id)

Create a link between an expression object and a sample

Create a link between an expression object and a sample.

An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created. Expression objects of the same group can only be linked to objects of the same study.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the sample object

    try:
        # Create a link between an expression object and a sample
        api_instance.create_expression_sample_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->create_expression_sample_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the sample object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link created.	-
400	Link cannot be created.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_group_library_group_link_as_curator¶

delete_expression_group_library_group_link_as_curator(source_id, target_id)

Delete link between a group of expression objects and a group of library objects

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the library group object

    try:
        # Delete link between a group of expression objects and a group of library objects
        api_instance.delete_expression_group_library_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_group_library_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the library group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_group_preparation_group_link_as_curator¶

delete_expression_group_preparation_group_link_as_curator(source_id, target_id)

Delete link between a group of expression objects and a group of preparation objects

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the preparation group object

    try:
        # Delete link between a group of expression objects and a group of preparation objects
        api_instance.delete_expression_group_preparation_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_group_preparation_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the preparation group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_group_sample_group_link_as_curator¶

delete_expression_group_sample_group_link_as_curator(source_id, target_id)

Delete link between a group of expression objects and a group of sample objects

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the group of run-level objects (corresponding to a GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the sample group object

    try:
        # Delete link between a group of expression objects and a group of sample objects
        api_instance.delete_expression_group_sample_group_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_group_sample_group_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the group of run-level objects (corresponding to a GCT file)
target_id	str	The ID (accession) of the sample group object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_library_link_as_curator¶

delete_expression_library_link_as_curator(source_id, target_id)

Delete link between an expression object and a library

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the library object

    try:
        # Delete link between an expression object and a library
        api_instance.delete_expression_library_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_library_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the library object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_preparation_link_as_curator¶

delete_expression_preparation_link_as_curator(source_id, target_id)

Delete link between an expression object and a preparation

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the preparation object

    try:
        # Delete link between an expression object and a preparation
        api_instance.delete_expression_preparation_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_preparation_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the preparation object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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delete_expression_sample_link_as_curator¶

delete_expression_sample_link_as_curator(source_id, target_id)

Delete link between an expression object and a sample

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
    target_id = 'target_id_example' # str | The ID (accession) of the sample object

    try:
        # Delete link between an expression object and a sample
        api_instance.delete_expression_sample_link_as_curator(source_id, target_id)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->delete_expression_sample_link_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
source_id	str	The ID (accession) of the run-level object (corresponding to the column in a VCG/GCT file)
target_id	str	The ID (accession) of the sample object

Return type¶

void (empty response body)

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: Not defined

HTTP response details¶

Status code	Description	Response headers
204	Link deleted.	-
400	Link cannot be deleted.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_by_library_as_curator¶

ListResponse get_expression_by_library_as_curator(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)

Retrieve expression run-level data by querying related library ID (accession)

Versioning¶

Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

Example usage: useVersions=* (query all versions, including those without CHAIN_IDs) useVersions=v2 (query the second version. If there is no second version then the data file is not queried) useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) ) useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version) useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.models.response_format import ResponseFormat
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    response_format = odm_api.ResponseFormat() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (optional)
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)
    use_versions = 'use_versions_example' # str | Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:  \\* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>` (optional)
    returned_metadata_fields = 'returned_metadata_fields_example' # str | The parameter defines amount of metadata attributes to return:  1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (optional)

    try:
        # Retrieve expression run-level data by querying related library ID (accession)
        api_response = api_instance.get_expression_by_library_as_curator(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_by_library_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_by_library_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
response_format	ResponseFormat	Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries.	[optional]
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]
use_versions	str	Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`	[optional]
returned_metadata_fields	str	The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json, text/tab-separated-values

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_by_preparation¶

ListResponse get_expression_by_preparation(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)

Retrieve expression run-level data by querying related preparation ID (accession)

Versioning¶

Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

Example usage: useVersions=* (query all versions, including those without CHAIN_IDs) useVersions=v2 (query the second version. If there is no second version then the data file is not queried) useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) ) useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version) useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.models.response_format import ResponseFormat
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    response_format = odm_api.ResponseFormat() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (optional)
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)
    use_versions = 'use_versions_example' # str | Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:  \\* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>` (optional)
    returned_metadata_fields = 'returned_metadata_fields_example' # str | The parameter defines amount of metadata attributes to return:  1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (optional)

    try:
        # Retrieve expression run-level data by querying related preparation ID (accession)
        api_response = api_instance.get_expression_by_preparation(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_by_preparation:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_by_preparation: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
response_format	ResponseFormat	Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries.	[optional]
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]
use_versions	str	Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`	[optional]
returned_metadata_fields	str	The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json, text/tab-separated-values

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_by_sample_as_curator¶

ListResponse get_expression_by_sample_as_curator(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)

Retrieve expression run-level data by querying related sample ID (accession)

Versioning¶

Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

Example usage: useVersions=* (query all versions, including those without CHAIN_IDs) useVersions=v2 (query the second version. If there is no second version then the data file is not queried) useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) ) useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version) useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.models.response_format import ResponseFormat
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    response_format = odm_api.ResponseFormat() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (optional)
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)
    use_versions = 'use_versions_example' # str | Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:  \\* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>` (optional)
    returned_metadata_fields = 'returned_metadata_fields_example' # str | The parameter defines amount of metadata attributes to return:  1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (optional)

    try:
        # Retrieve expression run-level data by querying related sample ID (accession)
        api_response = api_instance.get_expression_by_sample_as_curator(id, response_format=response_format, page_limit=page_limit, page_offset=page_offset, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_by_sample_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_by_sample_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
response_format	ResponseFormat	Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries.	[optional]
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]
use_versions	str	Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`	[optional]
returned_metadata_fields	str	The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json, text/tab-separated-values

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_groups_by_study_as_curator¶

List[MetadataWithId] get_expression_groups_by_study_as_curator(id, response_format=response_format, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)

Retrieve group metadata by querying study ID (accession)

Versioning¶

Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

Example usage: useVersions=* (query all versions, including those without CHAIN_IDs) useVersions=v2 (query the second version. If there is no second version then the data file is not queried) useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) ) useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version) useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.metadata_with_id import MetadataWithId
from odm_api.models.response_format import ResponseFormat
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    response_format = odm_api.ResponseFormat() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (optional)
    use_versions = 'use_versions_example' # str | Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:  \\* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>` (optional)
    returned_metadata_fields = 'returned_metadata_fields_example' # str | The parameter defines amount of metadata attributes to return:  1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (optional)

    try:
        # Retrieve group metadata by querying study ID (accession)
        api_response = api_instance.get_expression_groups_by_study_as_curator(id, response_format=response_format, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_groups_by_study_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_groups_by_study_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
response_format	ResponseFormat	Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries.	[optional]
use_versions	str	Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax: \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`	[optional]
returned_metadata_fields	str	The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.	[optional]

Return type¶

List[MetadataWithId]

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is the object.	-
400	The supplied object ID is invalid.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_run_to_library_pairs_as_curator¶

ListResponse get_expression_run_to_library_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)

Retrieve run-library pairs by group id. Pagination is based on unique runs, not unique pairs.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)

    try:
        # Retrieve run-library pairs by group id. Pagination is based on unique runs, not unique pairs.
        api_response = api_instance.get_expression_run_to_library_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_run_to_library_pairs_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_run_to_library_pairs_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
404	No object exists with the given ID.	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_run_to_preparation_pairs_as_curator¶

ListResponse get_expression_run_to_preparation_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)

Retrieve run-preparation pairs by group id. Pagination is based on unique runs, not unique pairs.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)

    try:
        # Retrieve run-preparation pairs by group id. Pagination is based on unique runs, not unique pairs.
        api_response = api_instance.get_expression_run_to_preparation_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_run_to_preparation_pairs_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_run_to_preparation_pairs_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
404	No object exists with the given ID.	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_expression_run_to_sample_pairs_as_curator¶

ListResponse get_expression_run_to_sample_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)

Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.

Paging¶

For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.list_response import ListResponse
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ExpressionIntegrationAsCuratorApi(api_client)
    id = 'id_example' # str | Unique identifier (accession) of the object.
    page_limit = 56 # int | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (optional)
    page_offset = 56 # int | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results  starting from the 101st result. The default value is 0. (optional)

    try:
        # Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
        api_response = api_instance.get_expression_run_to_sample_pairs_as_curator(id, page_limit=page_limit, page_offset=page_offset)
        print("The response of ExpressionIntegrationAsCuratorApi->get_expression_run_to_sample_pairs_as_curator:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ExpressionIntegrationAsCuratorApi->get_expression_run_to_sample_pairs_as_curator: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
id	str	Unique identifier (accession) of the object.
page_limit	int	Maximum number of results to return. This value must be between 0 and 2000 (inclusive).	[optional]
page_offset	int	Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0.	[optional]

Return type¶

ListResponse

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json

HTTP response details¶

Status code	Description	Response headers
200	The request was successful. The returned value is a list of objects.	-
400	Entities cannot be retrieved.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
404	No object exists with the given ID.	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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