odm_api.ExpressionIntegrationAsUserApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| get_expression_by_library_as_user | GET /api/v1/as-user/integration/link/expression/by/library/{id} | Retrieve expression run-level data by querying related library ID (accession) |
| get_expression_by_preparation_as_user | GET /api/v1/as-user/integration/link/expression/by/preparation/{id} | Retrieve expression run-level data by querying related preparation ID (accession) |
| get_expression_by_sample_as_user | GET /api/v1/as-user/integration/link/expression/by/sample/{id} | Retrieve expression run-level data by querying related sample ID (accession) |
| get_expression_groups_by_study_as_user | GET /api/v1/as-user/integration/link/expression/group/by/study/{id} | Retrieve group metadata by querying study ID (accession) |
| get_expression_run_to_library_pairs_as_user | GET /api/v1/as-user/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_user | GET /api/v1/as-user/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_user | GET /api/v1/as-user/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. |
get_expression_by_library_as_user¶
ListResponse get_expression_by_library_as_user(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.ExpressionIntegrationAsUserApi(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_user(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 ExpressionIntegrationAsUserApi->get_expression_by_library_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_by_library_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_by_preparation_as_user¶
ListResponse get_expression_by_preparation_as_user(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.ExpressionIntegrationAsUserApi(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_as_user(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 ExpressionIntegrationAsUserApi->get_expression_by_preparation_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_by_preparation_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_by_sample_as_user¶
ListResponse get_expression_by_sample_as_user(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.ExpressionIntegrationAsUserApi(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_user(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 ExpressionIntegrationAsUserApi->get_expression_by_sample_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_by_sample_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_groups_by_study_as_user¶
List[MetadataWithId] get_expression_groups_by_study_as_user(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.ExpressionIntegrationAsUserApi(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_user(id, response_format=response_format, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields)
print("The response of ExpressionIntegrationAsUserApi->get_expression_groups_by_study_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_groups_by_study_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_run_to_library_pairs_as_user¶
ListResponse get_expression_run_to_library_pairs_as_user(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.ExpressionIntegrationAsUserApi(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_user(id, page_limit=page_limit, page_offset=page_offset)
print("The response of ExpressionIntegrationAsUserApi->get_expression_run_to_library_pairs_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_run_to_library_pairs_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_run_to_preparation_pairs_as_user¶
ListResponse get_expression_run_to_preparation_pairs_as_user(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.ExpressionIntegrationAsUserApi(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_user(id, page_limit=page_limit, page_offset=page_offset)
print("The response of ExpressionIntegrationAsUserApi->get_expression_run_to_preparation_pairs_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_run_to_preparation_pairs_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]
get_expression_run_to_sample_pairs_as_user¶
ListResponse get_expression_run_to_sample_pairs_as_user(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.ExpressionIntegrationAsUserApi(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_user(id, page_limit=page_limit, page_offset=page_offset)
print("The response of ExpressionIntegrationAsUserApi->get_expression_run_to_sample_pairs_as_user:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling ExpressionIntegrationAsUserApi->get_expression_run_to_sample_pairs_as_user: %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¶
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. | - |
[Back to top] [Back to API list] [Back to Model list] [Back to README]