odm_api.XrefsetQueriesApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| create | POST /api/v1/xrefsets | Import a new xrefset file |
| delete_file | DELETE /api/v1/xrefsets/{id} | Delete a xrefset with all related data. Only users who uploaded the xrefset are allowed to delete it. |
| get_details_by_accession | GET /api/v1/xrefsets/{id}/metadata | Retrieve xrefset details |
| search_entries | GET /api/v1/xrefsets/entries | Retrieve a list of entries across all xrefsets for given sourceId and targetId |
| search_entries_within_file | GET /api/v1/xrefsets/{id}/entries | Retrieve a list of entries for the given xrefset and given sourceId and targetId |
create¶
XrefSetCreateResponse create(body=body)
Import a new xrefset file
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.xref_set_create_request import XrefSetCreateRequest
from odm_api.models.xref_set_create_response import XrefSetCreateResponse
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.XrefsetQueriesApi(api_client)
body = odm_api.XrefSetCreateRequest() # XrefSetCreateRequest | Request body for creating a new xrefset. ## Important: The length of 'sourceId' strings is limited to 255 characters. Ensure that the provided values adhere to this limitation to avoid data truncation. (optional)
try:
# Import a new xrefset file
api_response = api_instance.create(body=body)
print("The response of XrefsetQueriesApi->create:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling XrefsetQueriesApi->create: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| body | XrefSetCreateRequest | Request body for creating a new xrefset. ## Important: The length of 'sourceId' strings is limited to 255 characters. Ensure that the provided values adhere to this limitation to avoid data truncation. | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
| 201 | The objects were successfully created. The returned value is a list of created objects. | - |
| 400 | The object cannot be created. This error occurs when the supplied data or metadata are incorrect. Please 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). | - |
| 403 | Not enough permissions to work with the xrefset. | - |
| 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_file¶
delete_file(id)
Delete a xrefset with all related data. Only users who uploaded the xrefset are allowed to delete it.
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.XrefsetQueriesApi(api_client)
id = 'id_example' # str | xrefset ID
try:
# Delete a xrefset with all related data. Only users who uploaded the xrefset are allowed to delete it.
api_instance.delete_file(id)
except Exception as e:
print("Exception when calling XrefsetQueriesApi->delete_file: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | xrefset ID |
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 | Xrefset file successfully marked for deletion, mappings have been removed | - |
| 400 | Invalid data in the request. See the 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). | - |
| 403 | Not enough permissions to work with the xrefset. | - |
| 404 | The xrefset does not exist. | - |
| 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_details_by_accession¶
XrefSetMetadata get_details_by_accession(id)
Retrieve xrefset details
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.xref_set_metadata import XrefSetMetadata
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.XrefsetQueriesApi(api_client)
id = 'id_example' # str | xrefset ID
try:
# Retrieve xrefset details
api_response = api_instance.get_details_by_accession(id)
print("The response of XrefsetQueriesApi->get_details_by_accession:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling XrefsetQueriesApi->get_details_by_accession: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | xrefset ID |
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 | Object containing xrefset details, including user submitted metadata and system info | - |
| 400 | Invalid data in the request. See the 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). | - |
| 404 | The xrefset does not exist. | - |
| 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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search_entries¶
XrefSetSearchResult search_entries(source_id=source_id, target_id=target_id, cursor=cursor, page_limit=page_limit)
Retrieve a list of entries across all xrefsets for given sourceId and targetId
Conditions¶
It is possible to supply a list of values for "targetId" and "sourceId". If non-empty lists of values for "targetId" and "sourceId" are supplied, the following search rule is applied: (sourceId = "S1" OR .. sourceId = "Sn") AND (targetId = "T1" OR .. targetId = "Tm").
Important:¶
The length of 'sourceId' strings is limited to 255 characters. Ensure that the provided values adhere to this limitation to avoid data truncation.
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.xref_set_search_result import XrefSetSearchResult
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.XrefsetQueriesApi(api_client)
source_id = ['source_id_example'] # List[str] | Supply sourceId in the format \"sourceId\". For transcript-gene mapping this is gene ID, e.g. \"ENSG00000146648\" (optional)
target_id = ['target_id_example'] # List[str] | Supply targetId in the format \"targetId\". For transcript-gene mapping this is transcript ID, e.g. \"ENST00000617423.4\" (optional)
cursor = 'cursor_example' # str | The page tag to resume results from (see paging above). (optional)
page_limit = 56 # int | This parameter determines the number of results to retrieve per page, with the default set at 2000. (optional)
try:
# Retrieve a list of entries across all xrefsets for given sourceId and targetId
api_response = api_instance.search_entries(source_id=source_id, target_id=target_id, cursor=cursor, page_limit=page_limit)
print("The response of XrefsetQueriesApi->search_entries:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling XrefsetQueriesApi->search_entries: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| source_id | List[str] | Supply sourceId in the format \"sourceId\". For transcript-gene mapping this is gene ID, e.g. \"ENSG00000146648\" | [optional] |
| target_id | List[str] | Supply targetId in the format \"targetId\". For transcript-gene mapping this is transcript ID, e.g. \"ENST00000617423.4\" | [optional] |
| cursor | str | The page tag to resume results from (see paging above). | [optional] |
| page_limit | int | This parameter determines the number of results to retrieve per page, with the default set at 2000. | [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 | Json object with the cursor and json array of retrieved xrefset data. Response entries are ordered by xrefset ID and then by source ID. | - |
| 400 | Invalid data in the request. See the 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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search_entries_within_file¶
XrefSetSearchResult search_entries_within_file(id, source_id=source_id, target_id=target_id, cursor=cursor, page_limit=page_limit)
Retrieve a list of entries for the given xrefset and given sourceId and targetId
Conditions¶
It is possible to supply a list of values for "targetId" and "sourceId". If non-empty lists of values for "targetId" and "sourceId" are supplied, the following search rule is applied: (sourceId = "S1" OR .. sourceId = "Sn") AND (targetId = "T1" OR .. targetId = "Tm").
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.xref_set_search_result import XrefSetSearchResult
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.XrefsetQueriesApi(api_client)
id = 'id_example' # str | xrefset ID
source_id = ['source_id_example'] # List[str] | Supply sourceId in the format \"sourceId\". For transcript-gene mapping this is gene ID, e.g. \"ENSG00000146648\" (optional)
target_id = ['target_id_example'] # List[str] | Supply targetId in the format \"targetId\". For transcript-gene mapping this is transcript ID, e.g. \"ENST00000617423.4\" (optional)
cursor = 'cursor_example' # str | The page tag to resume results from (see paging above). (optional)
page_limit = 56 # int | This parameter determines the number of results to retrieve per page, with the default set at 2000. (optional)
try:
# Retrieve a list of entries for the given xrefset and given sourceId and targetId
api_response = api_instance.search_entries_within_file(id, source_id=source_id, target_id=target_id, cursor=cursor, page_limit=page_limit)
print("The response of XrefsetQueriesApi->search_entries_within_file:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling XrefsetQueriesApi->search_entries_within_file: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | xrefset ID | |
| source_id | List[str] | Supply sourceId in the format \"sourceId\". For transcript-gene mapping this is gene ID, e.g. \"ENSG00000146648\" | [optional] |
| target_id | List[str] | Supply targetId in the format \"targetId\". For transcript-gene mapping this is transcript ID, e.g. \"ENST00000617423.4\" | [optional] |
| cursor | str | The page tag to resume results from (see paging above). | [optional] |
| page_limit | int | This parameter determines the number of results to retrieve per page, with the default set at 2000. | [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 | Json object with the cursor and json array of retrieved xrefset data. Response entries are ordered by xrefset ID and then by source ID. | - |
| 400 | Invalid data in the request. See the 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). | - |
| 404 | The xrefset does not exist. | - |
| 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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