VariantSPoTAsCuratorApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| GetAllVariantsAsCurator | GET /api/v1/as-curator/variants | Retrieve multiple variant data and metadata objects |
| GetVariantAsCurator | GET /api/v1/as-curator/variants/{id} | Retrieve a single variant object by ID (itemId) |
| GetVariantByVersionAsCurator | GET /api/v1/as-curator/variants/{id}/versions/{version} | Retrieve a single variant object by run ID and its version |
| GetVariantGroupAsCurator | GET /api/v1/as-curator/variants/group/{id} | Retrieve a single variant group by ID (groupId) |
| GetVariantGroupByRunAsCurator | GET /api/v1/as-curator/variants/group/by/run/{id} | Retrieve a single group object by run ID (runId) |
| GetVariantVersionsAsCurator | GET /api/v1/as-curator/variants/{id}/versions | Retrieve a list of variant object versions by run ID (runId) |
| SearchGroupsAsCurator | GET /api/v1/as-curator/variants/group | Retrieve groups that match a query |
| SearchVariantRunsAsCurator | GET /api/v1/as-curator/variants/runs/by/group/{id} | Retrieve run objects related to the given group |
GetAllVariantsAsCurator¶
VariantResponse GetAllVariantsAsCurator(response_format = var.response_format, filter = var.filter, query = var.query, search_specific_terms = var.search_specific_terms, variant_region = var.variant_region, variant_feature = var.variant_feature, variant_id = var.variant_id, variant_filter = var.variant_filter, variant_info = var.variant_info, run_filter = var.run_filter, run_source_filter = var.run_source_filter, use_versions = var.use_versions, returned_metadata_fields = var.returned_metadata_fields, page_limit = var.page_limit, cursor = var.cursor)
Retrieve multiple variant data and metadata objects
Retrieve all variant 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¶
library(odmApi)
# Retrieve multiple variant data and metadata objects
#
# prepare function argument(s)
var_response_format <- ResponseFormat$new() # 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)
var_filter <- "filter_example" # character | Filter by variant metadata (key-value metadata pair(s)). E.g. `\"Variant Source\"=dbSNP`. (Optional)
var_query <- "query_example" # character | Search for variant objects via a full text query over all variant metadata. E.g. `dbSNP`. Queries matching dictionary terms are automatically expanded to include synonyms. (Optional)
var_search_specific_terms <- "search_specific_terms_example" # character | 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)
var_variant_region <- c("inner_example") # array[character] | Specify a chromosome interval to find genes between these positions. E.g. `2:233364596-233385916`. Multiple intervals can be provided as a list. (Optional)
var_variant_feature <- c("inner_example") # array[character] | Specify the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived. By providing the gene name, such as `TP53`, variants located within the same genomic region as the specified gene will be retrieved. Multiple genes can be provided as a list. (Optional)
var_variant_id <- c("inner_example") # array[character] | One or more specific variation IDs can be specified. E.g. `rs838705` (Optional)
var_variant_filter <- "variant_filter_example" # character | The parameter allows to retrieve gene variants based on the filters defined in the vcf file. If not specified, all variants are returned. 1. pass - return gene variants which passed all filters 2. noPass - return gene variants which failed one or more filters (Optional)
var_variant_info <- "variant_info_example" # character | Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(info.DB)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results. Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers, we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries. Combine multiple filters for `INFO` fields using `AND` (`&&`), `OR` (`||`) logical operators and parentheses (Optional)
var_run_filter <- c("inner_example") # array[character] | Autogenerated numeric ID that corresponds to a column and is used to link data from the same run to a sample. Multiple values can be provided as a list. (Optional)
var_run_source_filter <- c("inner_example") # array[character] | Column name from the file to which all data for a sample is related. Multiple values can be provided as a list to retrieve data from multiple columns. (Optional)
var_use_versions <- "use_versions_example" # character | 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)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | 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)
var_page_limit <- 56 # integer | 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)
var_cursor <- "cursor_example" # character | The page tag to resume results from (see paging above). (Optional)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetAllVariantsAsCurator(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, variant_region = var_variant_region, variant_feature = var_variant_feature, variant_id = var_variant_id, variant_filter = var_variant_filter, variant_info = var_variant_info, run_filter = var_run_filter, run_source_filter = var_run_source_filter, use_versions = var_use_versions, returned_metadata_fields = var_returned_metadata_fields, page_limit = var_page_limit, cursor = var_cursordata_file = "result.txt")
result <- api_instance$GetAllVariantsAsCurator(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, variant_region = var_variant_region, variant_feature = var_variant_feature, variant_id = var_variant_id, variant_filter = var_variant_filter, variant_info = var_variant_info, run_filter = var_run_filter, run_source_filter = var_run_source_filter, use_versions = var_use_versions, returned_metadata_fields = var_returned_metadata_fields, page_limit = var_page_limit, cursor = var_cursor)
dput(result)
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 | character | Filter by variant metadata (key-value metadata pair(s)). E.g. `\"Variant Source\"=dbSNP`. | [optional] |
| query | character | Search for variant objects via a full text query over all variant metadata. E.g. `dbSNP`. Queries matching dictionary terms are automatically expanded to include synonyms. | [optional] |
| search_specific_terms | character | 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] |
| variant_region | list( character ) | Specify a chromosome interval to find genes between these positions. E.g. `2:233364596-233385916`. Multiple intervals can be provided as a list. | [optional] |
| variant_feature | list( character ) | Specify the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived. By providing the gene name, such as `TP53`, variants located within the same genomic region as the specified gene will be retrieved. Multiple genes can be provided as a list. | [optional] |
| variant_id | list( character ) | One or more specific variation IDs can be specified. E.g. `rs838705` | [optional] |
| variant_filter | Enum [pass, noPass] | The parameter allows to retrieve gene variants based on the filters defined in the vcf file. If not specified, all variants are returned. 1. pass - return gene variants which passed all filters 2. noPass - return gene variants which failed one or more filters | [optional] |
| variant_info | character | Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(info.DB)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results. Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers, we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries. Combine multiple filters for `INFO` fields using `AND` (`&&`), `OR` (` | |
| run_filter | list( character ) | Autogenerated numeric ID that corresponds to a column and is used to link data from the same run to a sample. Multiple values can be provided as a list. | [optional] |
| run_source_filter | list( character ) | Column name from the file to which all data for a sample is related. Multiple values can be provided as a list to retrieve data from multiple columns. | [optional] |
| use_versions | character | 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 | Enum [minimal_data, extended_data_included, original_data_included] | 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 | integer | 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 | character | 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 variant data. | - |
| 400 | Variant 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. | - |
GetVariantAsCurator¶
GetVariantAsCurator200Response GetVariantAsCurator(id, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single variant object by ID (itemId)
Example¶
library(odmApi)
# Retrieve a single variant object by ID (itemId)
#
# prepare function argument(s)
var_id <- "id_example" # character | Variant object unique identifier (itemId).
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetVariantAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetVariantAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Variant object unique identifier (itemId). | |
| 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 | Enum [minimal_data, extended_data_included, original_data_included] | 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¶
GetVariantAsCurator200Response
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. | - |
GetVariantByVersionAsCurator¶
object GetVariantByVersionAsCurator(id, version, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single variant object by run ID and its version
Example¶
library(odmApi)
# Retrieve a single variant object by run ID and its version
#
# prepare function argument(s)
var_id <- "id_example" # character | Variant object run ID (runId).
var_version <- "version_example" # character | Unique version of the variant object.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetVariantByVersionAsCurator(var_id, var_version, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetVariantByVersionAsCurator(var_id, var_version, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Variant object run ID (runId). | |
| version | character | Unique version of the variant 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 | Enum [minimal_data, extended_data_included, original_data_included] | 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. | - |
GetVariantGroupAsCurator¶
VariantMetadataWithId GetVariantGroupAsCurator(id, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single variant group by ID (groupId)
Example¶
library(odmApi)
# Retrieve a single variant group by ID (groupId)
#
# prepare function argument(s)
var_id <- "id_example" # character | Variant group identifier (groupId).
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetVariantGroupAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetVariantGroupAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Variant group identifier (groupId). | |
| 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 | Enum [minimal_data, extended_data_included, original_data_included] | 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. | - |
GetVariantGroupByRunAsCurator¶
VariantMetadataWithId GetVariantGroupByRunAsCurator(id, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single group object by run ID (runId)
Example¶
library(odmApi)
# Retrieve a single group object by run ID (runId)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (runId) of the run.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetVariantGroupByRunAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetVariantGroupByRunAsCurator(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (runId) of the run. | |
| 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 | Enum [minimal_data, extended_data_included, original_data_included] | 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. | - |
GetVariantVersionsAsCurator¶
array[CommitInfo] GetVariantVersionsAsCurator(id)
Retrieve a list of variant object versions by run ID (runId)
Example¶
library(odmApi)
# Retrieve a list of variant object versions by run ID (runId)
#
# prepare function argument(s)
var_id <- "id_example" # character | Variant object run ID (runId).
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetVariantVersionsAsCurator(var_iddata_file = "result.txt")
result <- api_instance$GetVariantVersionsAsCurator(var_id)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Variant object run ID (runId). |
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. | - |
SearchGroupsAsCurator¶
ListResponse SearchGroupsAsCurator(response_format = var.response_format, filter = var.filter, query = var.query, search_specific_terms = var.search_specific_terms, returned_metadata_fields = var.returned_metadata_fields, use_versions = var.use_versions, page_offset = var.page_offset, page_limit = var.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 return all results iterate through pages using pageOffset values of n*pageLimit until the resultsExhausted response field is true. ## List operation This endpoint can be called with no query parameter. Doing so returns a list of all data objects.
Example¶
library(odmApi)
# Retrieve groups that match a query
#
# prepare function argument(s)
var_response_format <- ResponseFormat$new() # 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)
var_filter <- "filter_example" # character | Filter by variant metadata (key-value metadata pair(s)). E.g. `\"Variant Source\"=dbSNP`. (Optional)
var_query <- "query_example" # character | Search for variant objects via a full text query over all variant metadata. E.g. `dbSNP`. Queries matching dictionary terms are automatically expanded to include synonyms. (Optional)
var_search_specific_terms <- "search_specific_terms_example" # character | 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)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | 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)
var_use_versions <- "use_versions_example" # character | 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)
var_page_offset <- 56 # integer | 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)
var_page_limit <- 56 # integer | 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)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$SearchGroupsAsCurator(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, returned_metadata_fields = var_returned_metadata_fields, use_versions = var_use_versions, page_offset = var_page_offset, page_limit = var_page_limitdata_file = "result.txt")
result <- api_instance$SearchGroupsAsCurator(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, returned_metadata_fields = var_returned_metadata_fields, use_versions = var_use_versions, page_offset = var_page_offset, page_limit = var_page_limit)
dput(result)
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 | character | Filter by variant metadata (key-value metadata pair(s)). E.g. `\"Variant Source\"=dbSNP`. | [optional] |
| query | character | Search for variant objects via a full text query over all variant metadata. E.g. `dbSNP`. Queries matching dictionary terms are automatically expanded to include synonyms. | [optional] |
| search_specific_terms | character | 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] |
| returned_metadata_fields | Enum [minimal_data, extended_data_included, original_data_included] | 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] |
| use_versions | character | 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] |
| page_offset | integer | 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 | integer | 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. | - |
SearchVariantRunsAsCurator¶
RunsResponse SearchVariantRunsAsCurator(id, cursor = var.cursor, page_limit = var.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¶
library(odmApi)
# Retrieve run objects related to the given group
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_cursor <- "cursor_example" # character | The page tag to resume results from (see paging above). (Optional)
var_page_limit <- 56 # integer | 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)
api_instance <- VariantSPoTAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$SearchVariantRunsAsCurator(var_id, cursor = var_cursor, page_limit = var_page_limitdata_file = "result.txt")
result <- api_instance$SearchVariantRunsAsCurator(var_id, cursor = var_cursor, page_limit = var_page_limit)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| cursor | character | The page tag to resume results from (see paging above). | [optional] |
| page_limit | integer | 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. | - |