PreparationIntegrationAsUserApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| GetPreparationBySampleAsUser | GET /api/v1/as-user/integration/link/preparation/by/sample/{id} | Retrieve preparation metadata by querying related sample ID (accession) |
| GetPreparationGroupsByStudyAsUser | GET /api/v1/as-user/integration/link/preparation/group/by/study/{id} | Retrieve group metadata by querying study ID (accession) |
| GetPreparationLinksToSamplesAsUser | GET /api/v1/as-user/integration/link/preparation/preparations-to-samples/by/group/{id} | Retrieve run-sample pairs by group id. Pagination is based on unique preparations, not unique pairs. |
| GetPreparationsBySamplesAsUser | GET /api/v1/as-user/integration/link/preparations/by/samples | Retrieve preparation metadata by querying related samples |
GetPreparationBySampleAsUser¶
array[object] GetPreparationBySampleAsUser(id, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve preparation metadata by querying related sample ID (accession)
Example¶
library(odmApi)
# Retrieve preparation metadata by querying related sample ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- PreparationIntegrationAsUserApi$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$GetPreparationBySampleAsUser(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetPreparationBySampleAsUser(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 (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 | 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¶
array[object]
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json, text/tab-separated-values
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetPreparationGroupsByStudyAsUser¶
array[MetadataWithId] GetPreparationGroupsByStudyAsUser(id, response_format = var.response_format)
Retrieve group metadata by querying study ID (accession)
Example¶
library(odmApi)
# Retrieve group metadata by querying study ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
api_instance <- PreparationIntegrationAsUserApi$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$GetPreparationGroupsByStudyAsUser(var_id, response_format = var_response_formatdata_file = "result.txt")
result <- api_instance$GetPreparationGroupsByStudyAsUser(var_id, response_format = var_response_format)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | 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] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is the object. | - |
| 400 | The supplied object ID is invalid. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetPreparationLinksToSamplesAsUser¶
ListResponse GetPreparationLinksToSamplesAsUser(id, page_limit = var.page_limit, page_offset = var.page_offset)
Retrieve run-sample pairs by group id. Pagination is based on unique preparations, not unique pairs.
Paging For performance reasons this endpoint returns results in \"pages\" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using pageOffset values of n * pageLimit until a page returns fewer results than the page limit, which indicates there are no more results.¶
Example¶
library(odmApi)
# Retrieve run-sample pairs by group id. Pagination is based on unique preparations, not unique pairs.
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_page_limit <- 56 # integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (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)
api_instance <- PreparationIntegrationAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetPreparationLinksToSamplesAsUser(var_id, page_limit = var_page_limit, page_offset = var_page_offsetdata_file = "result.txt")
result <- api_instance$GetPreparationLinksToSamplesAsUser(var_id, page_limit = var_page_limit, page_offset = var_page_offset)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| page_limit | integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). | [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] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 404 | No object exists with the given ID. | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetPreparationsBySamplesAsUser¶
ListResponse GetPreparationsBySamplesAsUser(response_format = var.response_format, filter = var.filter, query = var.query, search_specific_terms = var.search_specific_terms, page_limit = var.page_limit, page_offset = var.page_offset, returned_metadata_fields = var.returned_metadata_fields)
Retrieve preparation metadata by querying related samples
Retrieve preparation metadata objects whose linked sample metadata matches all supplied conditions. ## Conditions It is possible to supply conditions for: 1. Samples (full-text or metadata key-value pair) 2. Parent studies (full-text or metadata key-value pair) 3. Linked variant objects (list of data key-value pairs) 4. Linked flow cytometry objects (list of data key-value pairs) 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs) ## 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 (\"). ## Data queries Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (\"). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. ## 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.
Example¶
library(odmApi)
# Retrieve preparation metadata by querying related samples
#
# 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 sample metadata (key-value metadata pair(s)). E.g. `\"Species or strain\"=\"Homo sapiens\"` (Optional)
var_query <- "query_example" # character | Search for objects via a full-text query over all sample metadata fields. E.g. `Clozapine`. 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_page_limit <- 56 # integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (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_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 <- PreparationIntegrationAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetPreparationsBySamplesAsUser(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, page_limit = var_page_limit, page_offset = var_page_offset, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetPreparationsBySamplesAsUser(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, page_limit = var_page_limit, page_offset = var_page_offset, returned_metadata_fields = var_returned_metadata_fields)
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 sample metadata (key-value metadata pair(s)). E.g. `\"Species or strain\"=\"Homo sapiens\"` | [optional] |
| query | character | Search for objects via a full-text query over all sample metadata fields. E.g. `Clozapine`. 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] |
| page_limit | integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). | [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] |
| 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, text/tab-separated-values
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 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. | - |