R API client for the Lamin API

Installation

To install directly from Github, use remotes:

if (!requireNamespace("remotes", quietly=TRUE)) {
    install.packages("remotes")
}
remotes::install_github("data-intuitive/laminr.api")

Usage

library(laminr.api)

api_url <- getOption("lamindb_current_instance")$api_url
instance_id <- getOption("lamindb_current_instance")$id
schema_id <- getOption("lamindb_current_instance")$schema_id

api_client <- ApiClient$new(base_path = api_url)

api <- DefaultApi$new(api_client = api_client)

Show API object:

api

<DefaultApi>
  Public:
    AddCollaboratorInstancesInstanceIdCollaboratorsAccountIdPut: function (instance_id, account_id, schema_id, role = "read", 
    AddCollaboratorInstancesInstanceIdCollaboratorsAccountIdPutWithHttpInfo: function (instance_id, account_id, schema_id, role = "read", 
    api_client: ApiClient, R6
    clone: function (deep = FALSE) 
    CreateInstanceInstancesPut: function (name, storage = "create-s3", schema_str = NULL, db_server_key = NULL, 
    CreateInstanceInstancesPutWithHttpInfo: function (name, storage = "create-s3", schema_str = NULL, db_server_key = NULL, 
    CreateRecordInstancesInstanceIdModulesModuleNameModelNamePut: function (instance_id, module_name, model_name, schema_id, body, 
    CreateRecordInstancesInstanceIdModulesModuleNameModelNamePutWithHttpInfo: function (instance_id, module_name, model_name, schema_id, body, 
    DeleteCollaboratorInstancesInstanceIdCollaboratorsAccountIdDelete: function (instance_id, account_id, authorization = NULL, data_file = NULL, 
    DeleteCollaboratorInstancesInstanceIdCollaboratorsAccountIdDeleteWithHttpInfo: function (instance_id, account_id, authorization = NULL, data_file = NULL, 
    DeleteInstanceInstancesInstanceIdDelete: function (instance_id, instance_name, authorization = NULL, data_file = NULL, 
    DeleteInstanceInstancesInstanceIdDeleteWithHttpInfo: function (instance_id, instance_name, authorization = NULL, data_file = NULL, 
    DeleteRecordInstancesInstanceIdModulesModuleNameModelNameUidDelete: function (instance_id, module_name, model_name, uid, schema_id, 
    DeleteRecordInstancesInstanceIdModulesModuleNameModelNameUidDeleteWithHttpInfo: function (instance_id, module_name, model_name, uid, schema_id, 
    GeneratePasswordInstancesInstanceIdDbPasswordGet: function (instance_id, authorization = NULL, data_file = NULL, 
    GeneratePasswordInstancesInstanceIdDbPasswordGetWithHttpInfo: function (instance_id, authorization = NULL, data_file = NULL, 
    GenerateUrlInstancesInstanceIdDbUrlGet: function (instance_id, authorization = NULL, data_file = NULL, 
    GenerateUrlInstancesInstanceIdDbUrlGetWithHttpInfo: function (instance_id, authorization = NULL, data_file = NULL, 
    GetInstanceStatisticsInstancesInstanceIdStatisticsGet: function (instance_id, schema_id, q = NULL, authorization = NULL, 
    GetInstanceStatisticsInstancesInstanceIdStatisticsGetWithHttpInfo: function (instance_id, schema_id, q = NULL, authorization = NULL, 
    GetNonEmptyTablesInstancesInstanceIdNonEmptyTablesGet: function (instance_id, schema_id, authorization = NULL, data_file = NULL, 
    GetNonEmptyTablesInstancesInstanceIdNonEmptyTablesGetWithHttpInfo: function (instance_id, schema_id, authorization = NULL, data_file = NULL, 
    GetRecordInstancesInstanceIdModulesModuleNameModelNameIdOrUidPost: function (instance_id, module_name, model_name, id_or_uid, schema_id, 
    GetRecordInstancesInstanceIdModulesModuleNameModelNameIdOrUidPostWithHttpInfo: function (instance_id, module_name, model_name, id_or_uid, schema_id, 
    GetRecordsInstancesInstanceIdModulesModuleNameModelNamePost: function (instance_id, module_name, model_name, schema_id, limit = 50, 
    GetRecordsInstancesInstanceIdModulesModuleNameModelNamePostWithHttpInfo: function (instance_id, module_name, model_name, schema_id, limit = 50, 
    GetRelationsInstancesInstanceIdSchemaModuleNameModelNameGet: function (module_name, model_name, instance_id, authorization = NULL, 
    GetRelationsInstancesInstanceIdSchemaModuleNameModelNameGetWithHttpInfo: function (module_name, model_name, instance_id, authorization = NULL, 
    GetSchemaInstancesInstanceIdSchemaGet: function (instance_id, authorization = NULL, data_file = NULL, 
    GetSchemaInstancesInstanceIdSchemaGetWithHttpInfo: function (instance_id, authorization = NULL, data_file = NULL, 
    GetValuesInstancesInstanceIdModulesModuleNameModelNameFieldsFieldPathPost: function (instance_id, module_name, model_name, field_path, schema_id, 
    GetValuesInstancesInstanceIdModulesModuleNameModelNameFieldsFieldPathPostWithHttpInfo: function (instance_id, module_name, model_name, field_path, schema_id, 
    GrantS3PermissionsStoragesS3BucketNamePermissionsPut: function (bucket_name, s3_permissions_request, aws_account_id = "767398070972", 
    GrantS3PermissionsStoragesS3BucketNamePermissionsPutWithHttpInfo: function (bucket_name, s3_permissions_request, aws_account_id = "767398070972", 
    GroupByInstancesInstanceIdModulesModuleNameModelNameGroupByPost: function (instance_id, module_name, model_name, schema_id, group_by_request_body, 
    GroupByInstancesInstanceIdModulesModuleNameModelNameGroupByPostWithHttpInfo: function (instance_id, module_name, model_name, schema_id, group_by_request_body, 
    initialize: function (api_client) 
    TransferOwnershipInstancesInstanceIdOwnerHandlePatch: function (instance_id, handle, schema_id, authorization = NULL, 
    TransferOwnershipInstancesInstanceIdOwnerHandlePatchWithHttpInfo: function (instance_id, handle, schema_id, authorization = NULL, 
    UpdateCollaboratorInstancesInstanceIdCollaboratorsAccountIdPatch: function (instance_id, account_id, role, authorization = NULL, 
    UpdateCollaboratorInstancesInstanceIdCollaboratorsAccountIdPatchWithHttpInfo: function (instance_id, account_id, role, authorization = NULL, 
    UpdateRecordInstancesInstanceIdModulesModuleNameModelNameUidPatch: function (instance_id, module_name, model_name, uid, schema_id, 
    UpdateRecordInstancesInstanceIdModulesModuleNameModelNameUidPatchWithHttpInfo: function (instance_id, module_name, model_name, uid, schema_id,

Get schema:

schema <- api$GetSchemaInstancesInstanceIdSchemaGet(instance_id)
names(schema)

[1] "core"   "bionty"

names(schema$core)

 [1] "run"                  "user"                 "param"                "ulabel"               "feature"              "storage"              "artifact"            
 [8] "transform"            "collection"           "featureset"           "paramvalue"           "featurevalue"         "runparamvalue"        "artifactulabel"      
[15] "collectionulabel"     "featuresetfeature"    "artifactfeatureset"   "artifactparamvalue"   "collectionartifact"   "artifactfeaturevalue"

Get record:

api$GetRecordInstancesInstanceIdModulesModuleNameModelNameIdOrUidPost(
  instance_id,
  "core",
  "artifact",
  "KBW89Mf7IGcekja2hADu",
  schema_id,
  include_foreign_keys = TRUE
)

$`_key_is_virtual`
[1] FALSE

$is_latest
[1] TRUE

$`_hash_type`
[1] "md5-n"

$updated_at
[1] "2024-07-12T12:40:48.837026+00:00"

$visibility
[1] 1

$type
[1] "dataset"

$created_at
[1] "2024-07-12T12:34:10.345829+00:00"

$run_id
[1] 27

$suffix
[1] ".h5ad"

$n_objects
NULL

$description
[1] "Myeloid compartment"

$uid
[1] "KBW89Mf7IGcekja2hADu"

$hash
[1] "SZ5tB0T4YKfiUuUkAL09ZA"

$transform_id
[1] 22

$storage_id
[1] 2

$version
[1] "2024-07-01"

$id
[1] 3659

$`_accessor`
[1] "AnnData"

$n_observations
[1] 51552

$created_by_id
[1] 1

$key
[1] "cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad"

$size
[1] 691757462

Documentation for API Endpoints

All URIs are relative to http://localhost

Class	Method	HTTP request	Description
DefaultApi	AddCollaboratorInstancesInstanceIdCollaboratorsAccountIdPut	PUT /instances/{instance_id}/collaborators/{account_id}	Add Collaborator
DefaultApi	CreateInstanceInstancesPut	PUT /instances	Create Instance
DefaultApi	CreateRecordInstancesInstanceIdModulesModuleNameModelNamePut	PUT /instances/{instance_id}/modules/{module_name}/{model_name}	Create Record
DefaultApi	DeleteCollaboratorInstancesInstanceIdCollaboratorsAccountIdDelete	DELETE /instances/{instance_id}/collaborators/{account_id}	Delete Collaborator
DefaultApi	DeleteInstanceInstancesInstanceIdDelete	DELETE /instances/{instance_id}	Delete Instance
DefaultApi	DeleteRecordInstancesInstanceIdModulesModuleNameModelNameUidDelete	DELETE /instances/{instance_id}/modules/{module_name}/{model_name}/{uid}	Delete Record
DefaultApi	GeneratePasswordInstancesInstanceIdDbPasswordGet	GET /instances/{instance_id}/db/password	Generate Password
DefaultApi	GenerateUrlInstancesInstanceIdDbUrlGet	GET /instances/{instance_id}/db/url	Generate Url
DefaultApi	GetInstanceStatisticsInstancesInstanceIdStatisticsGet	GET /instances/{instance_id}/statistics	Get Instance Statistics
DefaultApi	GetNonEmptyTablesInstancesInstanceIdNonEmptyTablesGet	GET /instances/{instance_id}/non_empty_tables	Get Non Empty Tables
DefaultApi	GetRecordInstancesInstanceIdModulesModuleNameModelNameIdOrUidPost	POST /instances/{instance_id}/modules/{module_name}/{model_name}/{id_or_uid}	Get Record
DefaultApi	GetRecordsInstancesInstanceIdModulesModuleNameModelNamePost	POST /instances/{instance_id}/modules/{module_name}/{model_name}	Get Records
DefaultApi	GetRelationsInstancesInstanceIdSchemaModuleNameModelNameGet	GET /instances/{instance_id}/schema/{module_name}/{model_name}	Get Relations
DefaultApi	GetSchemaInstancesInstanceIdSchemaGet	GET /instances/{instance_id}/schema	Get Schema
DefaultApi	GetValuesInstancesInstanceIdModulesModuleNameModelNameFieldsFieldPathPost	POST /instances/{instance_id}/modules/{module_name}/{model_name}/fields/{field_path}	Get Values
DefaultApi	GrantS3PermissionsStoragesS3BucketNamePermissionsPut	PUT /storages/s3/{bucket_name}/permissions	Grant S3 Permissions
DefaultApi	GroupByInstancesInstanceIdModulesModuleNameModelNameGroupByPost	POST /instances/{instance_id}/modules/{module_name}/{model_name}/group-by	Group By
DefaultApi	TransferOwnershipInstancesInstanceIdOwnerHandlePatch	PATCH /instances/{instance_id}/owner/{handle}	Transfer Ownership
DefaultApi	UpdateCollaboratorInstancesInstanceIdCollaboratorsAccountIdPatch	PATCH /instances/{instance_id}/collaborators/{account_id}	Update Collaborator
DefaultApi	UpdateRecordInstancesInstanceIdModulesModuleNameModelNameUidPatch	PATCH /instances/{instance_id}/modules/{module_name}/{model_name}/{uid}	Update Record

Documentation for Models

Documentation for Authorization

Endpoints do not require authorization.

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
.github/workflows		.github/workflows
.openapi-generator		.openapi-generator
R		R
docs		docs
man		man
tests		tests
.Rbuildignore		.Rbuildignore
.gitignore		.gitignore
.lintr		.lintr
.openapi-generator-ignore		.openapi-generator-ignore
DESCRIPTION		DESCRIPTION
LICENSE.md		LICENSE.md
NAMESPACE		NAMESPACE
README.md		README.md
README.qmd		README.qmd
git_push.sh		git_push.sh
update_package.sh		update_package.sh

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R API client for the Lamin API

Installation

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Documentation for Models

Documentation for Authorization

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R API client for the Lamin API

Installation

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Documentation for API Endpoints

Documentation for Models

Documentation for Authorization

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