odm_api.FlowCytometrySPoTAsCuratorApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| get_flow_cytometry_as_curator | GET /api/v1/as-curator/flow-cytometries/{id} | Retrieve a single sample flow cytometry by ID (accession) |
| get_flow_cytometry_by_version_as_curator | GET /api/v1/as-curator/flow-cytometries/{id}/versions/{version} | Retrieve a single sample flow cytometry by ID (accession) |
| get_flow_cytometry_data_as_curator | GET /api/v1/as-curator/flow-cytometries | Retrieve multiple flow cytometry data and metadata objects |
| get_flow_cytometry_group_as_curator | GET /api/v1/as-curator/flow-cytometries/group/{id} | Retrieve a single group object by ID (accession) |
| get_flow_cytometry_group_by_run_as_curator | GET /api/v1/as-curator/flow-cytometries/group/by/run/{id} | Retrieve a single group object by run ID (accession) |
| get_flow_cytometry_versions_as_curator | GET /api/v1/as-curator/flow-cytometries/{id}/versions | Retrieve a list of object versions by ID |
| search_flow_cytometry_groups_as_curator | GET /api/v1/as-curator/flow-cytometries/group | Retrieve groups that match a query |
| search_flow_cytometry_runs_as_curator | GET /api/v1/as-curator/flow-cytometries/runs/by/group/{id} | Retrieve run objects related to the given group |
| update_flow_cytometry_as_curator | PATCH /api/v1/as-curator/flow-cytometries/{id} | Update object metadata |
get_flow_cytometry_as_curator¶
GetFlowCytometryAsCurator200Response get_flow_cytometry_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
Retrieve a single sample flow cytometry by ID (accession)
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.get_flow_cytometry_as_curator200_response import GetFlowCytometryAsCurator200Response
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.FlowCytometrySPoTAsCuratorApi(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)
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 a single sample flow cytometry by ID (accession)
api_response = api_instance.get_flow_cytometry_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_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] |
| 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¶
GetFlowCytometryAsCurator200Response
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). | - |
| 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_flow_cytometry_by_version_as_curator¶
object get_flow_cytometry_by_version_as_curator(id, version, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
Retrieve a single sample flow cytometry by ID (accession)
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
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.FlowCytometrySPoTAsCuratorApi(api_client)
id = 'id_example' # str | Unique identifier (accession) of the object.
version = 'version_example' # str | Unique version 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)
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 a single sample flow cytometry by ID (accession)
api_response = api_instance.get_flow_cytometry_by_version_as_curator(id, version, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_by_version_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_by_version_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | Unique identifier (accession) of the object. | |
| version | str | Unique version 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] |
| 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¶
object
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). | - |
| 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_flow_cytometry_data_as_curator¶
FlowCytometryResponse get_flow_cytometry_data_as_curator(response_format=response_format, filter=filter, query=query, search_specific_terms=search_specific_terms, run_filter=run_filter, run_source_filter=run_source_filter, readout_type=readout_type, population=population, marker=marker, min_value=min_value, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields, page_limit=page_limit, cursor=cursor)
Retrieve multiple flow cytometry data and metadata objects
Retrieve all flow cytometry data and metadata objects that match a query.
Metadata full-text queries¶
Single words can be supplied as is, otherwise use speech marks (") to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (\).
Metadata filters¶
Metadata filters are key-value pairs joined by an operator. The = operator matches literal values/string. The != operator matches anything except the literal value/string. The < or > operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (").
Combinations¶
Metadata queries/filters for the same parameter can be combined with &&, AND, || and OR operators, using white-space to separate out the terms and operators. Parentheses ( ) can be used for complex expressions.
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 together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.flow_cytometry_response import FlowCytometryResponse
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.FlowCytometrySPoTAsCuratorApi(api_client)
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)
filter = 'filter_example' # str | Filter by flow cytometry metadata (key-value metadata pair(s)). E.g. `Organ=blood`. (optional)
query = 'query_example' # str | Search for flow cytometry objects via a full text query over all flow cytometry metadata. Queries matching dictionary terms are automatically expanded to include synonyms. (optional)
search_specific_terms = True # bool | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. (optional)
run_filter = ['run_filter_example'] # List[str] | Autogenerated numeric ID that identifies a set of rows related to one run and is used to link data from the run to a sample. Multiple values can be provided as a list. (optional)
run_source_filter = ['run_source_filter_example'] # List[str] | Sample name from the file which allows retrieval of all the rows related to the sample. Multiple values can be provided as a list. (optional)
readout_type = 'readout_type_example' # str | Required value of \"Readout type\" column. E.g.: `Count`, `Median` (optional)
population = 'population_example' # str | Value of \"Cell Population\" column. E.g.: `\"total cells\"`, `CD45+,live/CD45+`, `CD3+`. Note that if this value contains special characters like `/` which is used as a URI path separator, such characters should be escaped manually before sending request. For example, `/` should be escaped as `%2F`. (optional)
marker = 'marker_example' # str | Marker value. E.g.: `PD1`, `BV786` (optional)
min_value = 3.4 # float | Minimum threshold (inclusive) for returned expression values. (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)
page_limit = 56 # int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. (optional)
cursor = 'cursor_example' # str | The page tag to resume results from (see paging above). (optional)
try:
# Retrieve multiple flow cytometry data and metadata objects
api_response = api_instance.get_flow_cytometry_data_as_curator(response_format=response_format, filter=filter, query=query, search_specific_terms=search_specific_terms, run_filter=run_filter, run_source_filter=run_source_filter, readout_type=readout_type, population=population, marker=marker, min_value=min_value, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields, page_limit=page_limit, cursor=cursor)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_data_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_data_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| 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] |
| filter | str | Filter by flow cytometry metadata (key-value metadata pair(s)). E.g. `Organ=blood`. | [optional] |
| query | str | Search for flow cytometry objects via a full text query over all flow cytometry metadata. Queries matching dictionary terms are automatically expanded to include synonyms. | [optional] |
| search_specific_terms | bool | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. | [optional] |
| run_filter | List[str] | Autogenerated numeric ID that identifies a set of rows related to one run and is used to link data from the run to a sample. Multiple values can be provided as a list. | [optional] |
| run_source_filter | List[str] | Sample name from the file which allows retrieval of all the rows related to the sample. Multiple values can be provided as a list. | [optional] |
| readout_type | str | Required value of \"Readout type\" column. E.g.: `Count`, `Median` | [optional] |
| population | str | Value of \"Cell Population\" column. E.g.: `\"total cells\"`, `CD45+,live/CD45+`, `CD3+`. Note that if this value contains special characters like `/` which is used as a URI path separator, such characters should be escaped manually before sending request. For example, `/` should be escaped as `%2F`. | [optional] |
| marker | str | Marker value. E.g.: `PD1`, `BV786` | [optional] |
| min_value | float | Minimum threshold (inclusive) for returned expression values. | [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] |
| page_limit | int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. | [optional] |
| cursor | str | The page tag to resume results from (see paging above). | [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 | Retrieved Flow Cytometry data. | - |
| 400 | Flow Cytometry data 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_flow_cytometry_group_as_curator¶
MetadataWithId get_flow_cytometry_group_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
Retrieve a single group object by ID (accession)
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.FlowCytometrySPoTAsCuratorApi(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)
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 a single group object by ID (accession)
api_response = api_instance.get_flow_cytometry_group_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_group_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_group_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] |
| 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). | - |
| 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_flow_cytometry_group_by_run_as_curator¶
MetadataWithId get_flow_cytometry_group_by_run_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
Retrieve a single group object by run ID (accession)
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.FlowCytometrySPoTAsCuratorApi(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)
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 a single group object by run ID (accession)
api_response = api_instance.get_flow_cytometry_group_by_run_as_curator(id, response_format=response_format, returned_metadata_fields=returned_metadata_fields)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_group_by_run_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_group_by_run_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] |
| 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). | - |
| 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_flow_cytometry_versions_as_curator¶
List[CommitInfo] get_flow_cytometry_versions_as_curator(id)
Retrieve a list of object versions by ID
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.commit_info import CommitInfo
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.FlowCytometrySPoTAsCuratorApi(api_client)
id = 'id_example' # str | Unique identifier (accession) of the object.
try:
# Retrieve a list of object versions by ID
api_response = api_instance.get_flow_cytometry_versions_as_curator(id)
print("The response of FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_versions_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->get_flow_cytometry_versions_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | Unique identifier (accession) of the object. |
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 list of object versions. | - |
| 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_flow_cytometry_groups_as_curator¶
ListResponse search_flow_cytometry_groups_as_curator(response_format=response_format, filter=filter, query=query, search_specific_terms=search_specific_terms, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields, page_offset=page_offset, page_limit=page_limit)
Retrieve groups that match a query
Retrieve all group metadata objects that match a query.
Metadata full-text queries¶
Single words can be supplied as is, otherwise use speech marks (") to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (\).
Metadata filters¶
Metadata filters are key-value pairs joined by an operator. The = operator matches literal values/string. The != operator matches anything except the literal value/string. The < or > operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (").
Combinations¶
Metadata queries/filters for the same parameter can be combined with &&, AND, || and OR operators, using white-space to separate out the terms and operators. Parentheses ( ) can be used for complex expressions.
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.
List operation¶
This endpoint can be called with no query parameter. Doing so returns a list of all data objects.
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.FlowCytometrySPoTAsCuratorApi(api_client)
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)
filter = 'filter_example' # str | Filter by flow cytometry metadata (key-value metadata pair(s)). E.g. `Organ=blood`. (optional)
query = 'query_example' # str | Search for flow cytometry objects via a full text query over all flow cytometry metadata. Queries matching dictionary terms are automatically expanded to include synonyms. (optional)
search_specific_terms = True # bool | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. (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)
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)
page_limit = 56 # int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. (optional)
try:
# Retrieve groups that match a query
api_response = api_instance.search_flow_cytometry_groups_as_curator(response_format=response_format, filter=filter, query=query, search_specific_terms=search_specific_terms, use_versions=use_versions, returned_metadata_fields=returned_metadata_fields, page_offset=page_offset, page_limit=page_limit)
print("The response of FlowCytometrySPoTAsCuratorApi->search_flow_cytometry_groups_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->search_flow_cytometry_groups_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| 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] |
| filter | str | Filter by flow cytometry metadata (key-value metadata pair(s)). E.g. `Organ=blood`. | [optional] |
| query | str | Search for flow cytometry objects via a full text query over all flow cytometry metadata. Queries matching dictionary terms are automatically expanded to include synonyms. | [optional] |
| search_specific_terms | bool | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. | [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] |
| 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] |
| page_limit | int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 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 | The request was successful. The returned value is a list of objects. | - |
| 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). | - |
| 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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search_flow_cytometry_runs_as_curator¶
RunsResponse search_flow_cytometry_runs_as_curator(id, cursor=cursor, page_limit=page_limit)
Retrieve run objects related to the given group
Paging¶
For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
Example¶
- Api Key Authentication (Access-token):
- Api Key Authentication (Genestack-API-Token):
import odm_api
from odm_api.models.runs_response import RunsResponse
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.FlowCytometrySPoTAsCuratorApi(api_client)
id = 'id_example' # str | Unique identifier (accession) of the object.
cursor = 'cursor_example' # str | The page tag to resume results from (see paging above). (optional)
page_limit = 56 # int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. (optional)
try:
# Retrieve run objects related to the given group
api_response = api_instance.search_flow_cytometry_runs_as_curator(id, cursor=cursor, page_limit=page_limit)
print("The response of FlowCytometrySPoTAsCuratorApi->search_flow_cytometry_runs_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->search_flow_cytometry_runs_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | Unique identifier (accession) of the object. | |
| cursor | str | The page tag to resume results from (see paging above). | [optional] |
| page_limit | int | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 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 | 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). | - |
| 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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update_flow_cytometry_as_curator¶
object update_flow_cytometry_as_curator(id, body=body)
Update object metadata
Basic operation¶
The object metadata is updated using the supplied map of attribute names to attribute values. There are three cases:
1. The attribute name does not already exist in the object metadata. In this case, the attribute and value are added to the object metadata.
2. The attribute name already exists in the object metadata. In this case, the value is updated.
3. The attribute value is null.In this case, the attribute is removed from the object metadata.
Attribute values¶
The attribute values are intelligently parsed as booleans, integers, etc.
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.FlowCytometrySPoTAsCuratorApi(api_client)
id = 'id_example' # str | Unique identifier (accession) of the object.
body = None # object | Metadata in the form of `{key: value, key2: value2, ...}` (optional)
try:
# Update object metadata
api_response = api_instance.update_flow_cytometry_as_curator(id, body=body)
print("The response of FlowCytometrySPoTAsCuratorApi->update_flow_cytometry_as_curator:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FlowCytometrySPoTAsCuratorApi->update_flow_cytometry_as_curator: %s\n" % e)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | str | Unique identifier (accession) of the object. | |
| body | object | Metadata in the form of `{key: value, key2: value2, ...}` | [optional] |
Return type¶
object
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 | The objects was successfully created. The returned value is the updated object, along with any warnings. | - |
| 400 | The supplied object ID or metadata 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). | - |
| 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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