{laminr.api}: R Interface to the LaminDB API

Overview

The {laminr.api} package provides an low-level R interface to the LaminDB API. The package is not meant to be used directly by end-users, but is used by higher-level packages like {laminr}.

This package is mostly auto-generated from the OpenAPI specification of the LaminDB API using the OpenAPI Generator.

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)

# retrieve these values from ~/.lamin/current_instance.env
# after running `lamin connect <instance_id>`
api_url <- "https://us-east-1.api.lamin.ai/"
instance_id <- "037ba1e08d804f91a90275a47735076a"
schema_id <- "097186c3e91c01ced47aa3e01a3c1515"

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, 
    GetRelationCountsInstancesInstanceIdModulesModuleNameModelNameIdCountsGet: function (instance_id, module_name, model_name, id, schema_id, 
    GetRelationCountsInstancesInstanceIdModulesModuleNameModelNameIdCountsGetWithHttpInfo: function (instance_id, module_name, model_name, id, schema_id, 
    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" "wetlab"

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",
  "3TNCsZZcnIBv2WGb0001",
  schema_id,
  include_foreign_keys = TRUE
)

$n_objects
NULL

$uid
[1] "3TNCsZZcnIBv2WGb0001"

$hash
[1] "iETHP3Lw-tVqZxYAuEC-SA"

$storage_id
[1] 2

$version
NULL

$`_accessor`
[1] "AnnData"

$transform_id
[1] 163

$id
[1] 938

$created_at
[1] "2024-10-18T21:46:55.467982+00:00"

$description
[1] "10x reference adata, trusted cell type annotation"

$`_key_is_virtual`
[1] TRUE

$key
NULL

$updated_at
[1] "2024-10-18T21:58:06.010689+00:00"

$n_observations
[1] 70

$size
[1] 851664

$`_hash_type`
[1] "md5"

$created_by_id
[1] 9

$is_latest
[1] TRUE

$visibility
[1] 1

$type
[1] "dataset"

$run_id
[1] 305

$suffix
[1] ".h5ad"