vjcitn/terraClientR
R Package Client for FireCloud

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docs/LibraryApi.md

docs/LibraryApi.md
In vjcitn/terraClientR: R Package Client for FireCloud

LibraryApi

All URIs are relative to http://localhost

Method | HTTP request | Description ------------- | ------------- | ------------- DataIngest | POST /duos/structuredData | Data Use Search ingest DuosAutocomplete | GET /duos/autocomplete/{queryTerm} | Passes through to DUOS' autocomplete method to select ontology terms of disease type that match the query term. DuosConsentOrspId | GET /api/duos/consent/orsp/{orspId} | Find Consent by ORSP ID DuosResearchPurposeQuery | POST /duos/researchPurposeQuery | Generates an ElasticSearch clause for filtering by research purpose FindDocuments | POST /api/library/search | searches published library datasets GetDiscoverableGroups | GET /api/library/{workspaceNamespace}/{workspaceName}/discoverableGroups | get the groups that can discover this library dataset GetLibraryMetadata | GET /api/library/{workspaceNamespace}/{workspaceName}/metadata | get the entire metadata for a library dataset Groups | GET /api/library/groups | returns groups that can be used for discoverable datasets PopulateSuggest | GET /api/library/populate/suggest/{field} | suggestions for populating a field PublishLibraryWorkspace | POST /api/library/{workspaceNamespace}/{workspaceName}/published | publish the workspace in the Library PutLibraryMetadata | PUT /api/library/{workspaceNamespace}/{workspaceName}/metadata | put the entire metadata for a library dataset ReindexAll | POST /api/library/admin/reindex | deletes and rebuilds the entire index of published library datasets SearchSuggest | POST /api/library/suggest | search suggestions UnpublishLibraryWorkspace | DELETE /api/library/{workspaceNamespace}/{workspaceName}/published | unpublish the workspace in the Library UpdateDiscoverableGroups | PUT /api/library/{workspaceNamespace}/{workspaceName}/discoverableGroups | set the groups that can discover this library dataset

DataIngest

DataIngest(body)

Data Use Search ingest

The ingest API will take the answers to consent questions and return the elasticsearch structure to persist with the data reference.

Example

library(openapi)

var.body <- structuredDataRequest$new("generalResearchUse_example", "healthMedicalBiomedicalUseRequired_example", list("diseaseUseRequired_example"), "commercialUseProhibited_example", "forProfitUseProhibited_example", "methodsResearchProhibited_example", "aggregateLevelDataProhibited_example", "controlsUseProhibited_example", "genderUseRequired_example", "pediatricResearchRequired_example", "irbRequired_example", "prefix_example") # StructuredDataRequest | Structured Data Request

#Data Use Search ingest
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DataIngest(var.body)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- body | StructuredDataRequest| Structured Data Request |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 500 | Internal Server Error | - |

DuosAutocomplete

DuosAutocomplete(query.term)

Passes through to DUOS' autocomplete method to select ontology terms of disease type that match the query term.

Example

library(openapi)

var.query.term <- 'query.term_example' # character | The query term (word fragment) which the service should try and complete.

#Passes through to DUOS' autocomplete method to select ontology terms of disease type that match the query term. 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DuosAutocomplete(var.query.term)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- query.term | character| The query term (word fragment) which the service should try and complete. |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Array of results. | - | | 500 | Internal Server Error | - |

DuosConsentOrspId

Consent DuosConsentOrspId(orsp.id)

Find Consent by ORSP ID

Example

library(openapi)

var.orsp.id <- 'orsp.id_example' # character | Finds the consent for the provided ORSP ID.

#Find Consent by ORSP ID
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$DuosConsentOrspId(var.orsp.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- orsp.id | character| Finds the consent for the provided ORSP ID. |

Return type

Consent

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Consent | - | | 400 | The consent associated with the provided name has not been approved. | - | | 401 | Invalid authorization, must be a FireCloud user. | - | | 404 | The consent associated with the provided name could not be found. | - | | 500 | Internal Server Error | - |

DuosResearchPurposeQuery

DuosResearchPurposeQuery(body)

Generates an ElasticSearch clause for filtering by research purpose

Example

library(openapi)

var.body <- ResearchPurposeRequest$new(list("DS_example"), "NMDS_example", "NCTRL_example", "NAGR_example", "POA_example", "NCU_example", "prefix_example") # ResearchPurposeRequest | Research Purpose Request

#Generates an ElasticSearch clause for filtering by research purpose
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DuosResearchPurposeQuery(var.body)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- body | ResearchPurposeRequest| Research Purpose Request |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | JSON of ES filter clause | - |

FindDocuments

FindDocuments(search.params=var.search.params)

searches published library datasets

Example

library(openapi)

var.search.params <- SearchTermRef$new("searchString_example", TODO, ResearchPurpose$new(list("DS_example"), "NMDS_example", "NCTRL_example", "NAGR_example", "POA_example", "NCU_example"), TODO, 123, 123, "sortField_example", "sortDirection_example") # SearchTermRef | Search terms and pagination parameters

#searches published library datasets 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$FindDocuments(search.params=var.search.params)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- search.params | SearchTermRef| Search terms and pagination parameters | [optional]

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Matching datasets | - |

GetDiscoverableGroups

array[character] GetDiscoverableGroups(workspace.namespace, workspace.name)

get the groups that can discover this library dataset

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name

#get the groups that can discover this library dataset 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetDiscoverableGroups(var.workspace.namespace, var.workspace.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |

Return type

array[character]

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | The groups that can discover the dataset | - | | 403 | Insufficient permissions | - | | 404 | Workspace not found | - | | 500 | Error | - |

GetLibraryMetadata

object GetLibraryMetadata(workspace.namespace, workspace.name)

get the entire metadata for a library dataset

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name

#get the entire metadata for a library dataset 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetLibraryMetadata(var.workspace.namespace, var.workspace.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |

Return type

object

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 404 | Workspace not found | - | | 500 | Rawls Internal Error | - |

Groups

array[character] Groups()

returns groups that can be used for discoverable datasets

Example

library(openapi)


#returns groups that can be used for discoverable datasets 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Groups()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[character]

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Names of the allowed groups | - |

PopulateSuggest

PopulateSuggest(field, q)

suggestions for populating a field

Example

library(openapi)

var.field <- 'field_example' # character | the property to get suggestions for
var.q <- 'q_example' # character | the initial text to complete

#suggestions for populating a field 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$PopulateSuggest(var.field, var.q)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- field | character| the property to get suggestions for | q | character| the initial text to complete |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Field specific suggestions | - | | 400 | Bad Request, specified field that was not configured for suggestions | - |

PublishLibraryWorkspace

Workspace PublishLibraryWorkspace(workspace.namespace, workspace.name)

publish the workspace in the Library

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name

#publish the workspace in the Library 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PublishLibraryWorkspace(var.workspace.namespace, var.workspace.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |

Return type

Workspace

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 204 | Dataset already in requested published state | - | | 403 | You must be the workspace owner and library curator to publish a workspace to the library | - | | 500 | Rawls Internal Error | - |

PutLibraryMetadata

Workspace PutLibraryMetadata(workspace.namespace, workspace.name, library.metadata.json, validate=var.validate)

put the entire metadata for a library dataset

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.library.metadata.json <- NULL # object | Library metadata
var.validate <- 'validate_example' # character | Should the payload be validated? Validation is always enabled for published datasets and defaults to false for unpublished datasets. 

#put the entire metadata for a library dataset 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PutLibraryMetadata(var.workspace.namespace, var.workspace.name, var.library.metadata.json, validate=var.validate)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | library.metadata.json | object| Library metadata | validate | character| Should the payload be validated? Validation is always enabled for published datasets and defaults to false for unpublished datasets. | [optional]

Return type

Workspace

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 404 | Workspace not found | - | | 500 | Rawls Internal Error | - |

ReindexAll

LibraryBulkIndexResponse ReindexAll()

deletes and rebuilds the entire index of published library datasets

Example

library(openapi)


#deletes and rebuilds the entire index of published library datasets 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ReindexAll()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

LibraryBulkIndexResponse

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Indexing Success | - | | 204 | No published datasets exist to index | - | | 500 | Indexing Error | - |

SearchSuggest

SearchSuggest(search.params=var.search.params)

search suggestions

Example

library(openapi)

var.search.params <- SearchTermRef$new("searchString_example", TODO, ResearchPurpose$new(list("DS_example"), "NMDS_example", "NCTRL_example", "NAGR_example", "POA_example", "NCU_example"), TODO, 123, 123, "sortField_example", "sortDirection_example") # SearchTermRef | Search terms and pagination parameters

#search suggestions 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$SearchSuggest(search.params=var.search.params)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- search.params | SearchTermRef| Search terms and pagination parameters | [optional]

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Search suggestions, with highlighting | - |

UnpublishLibraryWorkspace

Workspace UnpublishLibraryWorkspace(workspace.namespace, workspace.name)

unpublish the workspace in the Library

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name

#unpublish the workspace in the Library 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UnpublishLibraryWorkspace(var.workspace.namespace, var.workspace.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |

Return type

Workspace

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 403 | You must be the workspace owner and library curator to unpublish a workspace from the library | - | | 500 | Rawls Internal Error | - |

UpdateDiscoverableGroups

Workspace UpdateDiscoverableGroups(workspace.namespace, workspace.name, discoverable.groups)

set the groups that can discover this library dataset

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.discoverable.groups <- list("property_example") # array[character] | Json array of group names, or empty array for no restrictions

#set the groups that can discover this library dataset 
api.instance <- LibraryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateDiscoverableGroups(var.workspace.namespace, var.workspace.name, var.discoverable.groups)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | discoverable.groups | list( character )| Json array of group names, or empty array for no restrictions |

Return type

Workspace

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | The workspace, after assigning groups to be able to discover the dataset | - | | 400 | Invalid input | - | | 403 | Insufficient permissions to change catalog permissions (must be owner or have grant or catalog with access to the workspace) | - | | 404 | Workspace, user or group not found | - | | 500 | Error | - |



vjcitn/terraClientR documentation built on Dec. 23, 2021, 4:07 p.m.

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