| Type: | Package |
| Title: | The Official SolveBio API Client |
| Version: | 2.15.1 |
| Date: | 2025-02-06 |
| Author: | Tobi Guennel [aut, cre] |
| Maintainer: | Tobi Guennel <tobi.guennel@precisionformedicine.com> |
| Description: | R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs. |
| URL: | https://github.com/solvebio/solvebio-r |
| Imports: | httr, jsonlite, mime |
| License: | MIT + file LICENSE |
| Collate: | solvebio.R annotation.R application.R beacon.R beacon_set.R dataset.R dataset_commit.R dataset_export.R dataset_field.R dataset_import.R dataset_migration.R dataset_template.R global_search.R object.R saved_query.R shiny.R task.R user.R utils.R vault.R zzz.R |
| RoxygenNote: | 7.3.2 |
| Encoding: | UTF-8 |
| Suggests: | testthat, shiny, shinyjs, openssl |
| NeedsCompilation: | no |
| Packaged: | 2025-02-14 14:20:48 UTC; davecap |
| Repository: | CRAN |
| Date/Publication: | 2025-02-14 23:00:02 UTC |
Annotator.annotate
Description
Annotate a data table/frame with additional fields.
Usage
Annotator.annotate(
records,
fields,
include_errors = FALSE,
raw = FALSE,
env = .solveEnv
)
Arguments
records |
The data table or data frame to annotate. |
fields |
The fields to add. |
include_errors |
Set to TRUE to include errors in the output (default: FALSE). |
raw |
Set to TRUE to return the raw response (default: FALSE). |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Annotator.annotate(records=tbl, fields=fields)
## End(Not run)
Application.all
Description
Retrieves the metadata about all application on SolveBio available to the current user.
Usage
Application.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Application.all()
## End(Not run)
Application.create
Description
Create a new SolveBio application.
Usage
Application.create(name, redirect_uris, env = .solveEnv, ...)
Arguments
name |
The name of the application. |
redirect_uris |
A list of space-separated OAuth2 redirect URIs. |
env |
(optional) Custom client environment. |
... |
(optional) Additional application attributes. |
References
Examples
## Not run:
Application.create(
name="My new application",
redirect_uris="http://localhost:3838/"
)
## End(Not run)
Application.delete
Description
Delete a specific application from SolveBio.
Usage
Application.delete(client_id, env = .solveEnv)
Arguments
client_id |
The client ID for the application. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Application.delete("abcd1234")
## End(Not run)
Application.retrieve
Description
Retrieves the metadata about a specific application SolveBio.
Usage
Application.retrieve(client_id, env = .solveEnv)
Arguments
client_id |
The client ID for the application. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Application.retrieve("abcd1234")
## End(Not run)
Application.update
Description
Updates the attributes of an existing application.
Usage
Application.update(client_id, env = .solveEnv, ...)
Arguments
client_id |
The client ID for the application. |
env |
(optional) Custom client environment. |
... |
Application attributes to change. |
References
Examples
## Not run:
Application.update(
"abcd1234",
name="New app name"
)
## End(Not run)
Beacon.all
Description
Retrieves the metadata about all beacons on SolveBio accessible to the current user.
Usage
Beacon.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Beacon.all()
## End(Not run)
Beacon.create
Description
Add a new beacon to an existing beacon set. The beacon set must already exist in order to add beacons.
Usage
Beacon.create(beacon_set_id, vault_object_id, title, env = .solveEnv, ...)
Arguments
beacon_set_id |
The ID of the parent beacon set. |
vault_object_id |
The ID of the vault object (i.e. dataset) queried by the beacon. |
title |
The title displayed for the beacon. |
env |
(optional) Custom client environment. |
... |
(optional) Additional beacon attributes (such as description and params). |
References
Examples
## Not run:
Beacon.create(
beacon_set_id="1234",
vault_object_id="1234567890",
title="My new beacon"
)
## End(Not run)
Beacon.delete
Description
Delete a specific beacon from SolveBio.
Usage
Beacon.delete(id, env = .solveEnv)
Arguments
id |
The ID of the beacon. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Beacon.delete("1234567890")
## End(Not run)
Beacon.query
Description
Query an individual beacon.
Usage
Beacon.query(id, query, entity_type, env = .solveEnv, ...)
Arguments
id |
The ID of the beacon. |
query |
The entity ID or query string. |
entity_type |
(optional) A valid SolveBio entity type. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Beacon.query(
id="1234",
query="BRCA2",
entity_type="gene"
)
## End(Not run)
Beacon.retrieve
Description
Retrieves the metadata about a specific beacon on SolveBio.
Usage
Beacon.retrieve(id, env = .solveEnv)
Arguments
id |
The ID of the beacon. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Beacon.retrieve("1234")
## End(Not run)
Beacon.update
Description
Updates the attributes of an existing beacon.
Usage
Beacon.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the beacon to update. |
env |
(optional) Custom client environment. |
... |
Beacon attributes to change. |
References
Examples
## Not run:
Beacon.update(
id="1234",
title="New Beacon Title"
)
## End(Not run)
BeaconSet.all
Description
Retrieves the metadata about all beacon sets on SolveBio accessible to the current user.
Usage
BeaconSet.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
BeaconSet.all()
## End(Not run)
BeaconSet.create
Description
Create a new beacon set.
Usage
BeaconSet.create(title, description, is_shared = FALSE, env = .solveEnv, ...)
Arguments
title |
The title displayed for the beacon set. |
description |
(optional) An optional description for the new beacon set. |
is_shared |
If TRUE, everyone else in your account will be able to see and query the beacon set, but will not be able to edit it. (Default: FALSE) |
env |
(optional) Custom client environment. |
... |
(optional) Additional beacon set attributes. |
References
Examples
## Not run:
BeaconSet.create(
title="My new beacon set",
)
## End(Not run)
BeaconSet.delete
Description
Delete a specific beacon set (including all its beacons) from SolveBio.
Usage
BeaconSet.delete(id, env = .solveEnv)
Arguments
id |
The ID of the beacon set. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
BeaconSet.delete("1234")
## End(Not run)
BeaconSet.query
Description
Query a beacon set (i.e. all the beacons within a beacon set).
Usage
BeaconSet.query(id, query, entity_type, env = .solveEnv, ...)
Arguments
id |
The ID of the beacon set. |
query |
The entity ID or query string. |
entity_type |
(optional) A valid SolveBio entity type. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
BeaconSet.query(
id="1234",
query="BRCA2",
entity_type="gene"
)
## End(Not run)
BeaconSet.retrieve
Description
Retrieves the metadata about a specific beacon set on SolveBio.
Usage
BeaconSet.retrieve(id, env = .solveEnv)
Arguments
id |
The ID of the beacon set. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
BeaconSet.retrieve("1234")
## End(Not run)
BeaconSet.update
Description
Updates the attributes of an existing beacon set.
Usage
BeaconSet.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the beacon set to update. |
env |
(optional) Custom client environment. |
... |
Beacon set attributes to change. |
References
Examples
## Not run:
BeaconSet.update(
id="1234",
title="New Beacon Set Title"
)
## End(Not run)
Dataset.activity
Description
A helper function to get or follow the current activity on a dataset.
Usage
Dataset.activity(id, follow = TRUE, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset |
follow |
Follow active tasks until they complete. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.activity("1234567890")
## End(Not run)
Dataset.all
Description
Retrieves the metadata about datasets on SolveBio.
Usage
Dataset.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
Dataset.all()
## End(Not run)
Dataset.count
Description
Returns the total number of records for a given SolveBio dataset.
Usage
Dataset.count(id, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio dataset, or a Dataset object. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, limit, offset). |
References
Examples
## Not run:
dataset <- Dataset.get_by_full_path("solvebio:public:/ClinVar/3.7.4-2017-01-30/Variants-GRCh37")
Dataset.count(dataset)
Dataset.count(dataset, filters='[["gene_symbol", "BRCA2"]]')
## End(Not run)
Dataset.create
Description
Create an empty SolveBio dataset.
Usage
Dataset.create(vault_id, vault_parent_object_id, name, env = .solveEnv, ...)
Arguments
vault_id |
The ID of the vault. |
vault_parent_object_id |
The parent object (folder) ID in the vault. |
name |
The name of the dataset in the parent folder. |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset attributes. |
References
Examples
## Not run:
Dataset.create(vault_id=vault$id, vault_parent_object_id=NULL, name="My Dataset")
## End(Not run)
Dataset.data
Description
Returns one page of documents from a SolveBio dataset and processes the response.
Usage
Dataset.data(id, filters, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio dataset, or a Dataset object. |
filters |
(optional) Query filters. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
Dataset.data("1234567890")
## End(Not run)
Dataset.delete
Description
Delete a specific dataset from SolveBio.
Usage
Dataset.delete(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.delete("1234567890")
## End(Not run)
Dataset.disable_global_beacon
Description
Disables Global Beacon for the dataset.
Usage
Dataset.disable_global_beacon(id, env = .solveEnv)
Arguments
id |
The ID of a SolveBio dataset. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.disable_global_beacon("1234567890")
## End(Not run)
Dataset.enable_global_beacon
Description
Enables Global Beacon for the the dataset.
Usage
Dataset.enable_global_beacon(id, env = .solveEnv)
Arguments
id |
The ID of a SolveBio dataset. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.enable_global_beacon("1234567890")
## End(Not run)
Dataset.facets
Description
Retrieves aggregated statistics or term counts for one or more fields in a SolveBio dataset. Returns a list of data frames, one for each requested facet.
Usage
Dataset.facets(id, facets, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio dataset, or a Dataset object. |
facets |
A list of one or more field facets. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, limit, offset). |
References
Examples
## Not run:
Dataset.facets("1234567890", list("clinical_significance", "gene_symbol"))
## End(Not run)
Dataset.fields
Description
Retrieves the list of fields and field metadata for a dataset.
Usage
Dataset.fields(id, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio dataset, or a Dataset object. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
Dataset.fields("1234567890")
## End(Not run)
Dataset.get_by_full_path
Description
A helper function to get a dataset by its full path.
Usage
Dataset.get_by_full_path(full_path, env = .solveEnv)
Arguments
full_path |
A valid full path to a dataset. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.get_by_full_path("solvebio:public:/ClinVar/3.7.4-2017-01-30/Variants-GRCh37")
## End(Not run)
Dataset.get_global_beacon_status
Description
Retrieves the global beacon status for the dataset.
Usage
Dataset.get_global_beacon_status(
id,
raise_on_disabled = FALSE,
env = .solveEnv
)
Arguments
id |
The ID of a SolveBio dataset. |
raise_on_disabled |
Whether to raise an exception if Global Beacon is disabled or to return NULL. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.get_global_beacon_status("1234567890")
## End(Not run)
Dataset.get_or_create_by_full_path
Description
A helper function to get or create a dataset by its full path.
Usage
Dataset.get_or_create_by_full_path(full_path, env = .solveEnv, ...)
Arguments
full_path |
A valid full path to a dataset. |
env |
(optional) Custom client environment. |
... |
Additional dataset creation parameters. |
References
Examples
## Not run:
Dataset.get_or_create_by_full_path("MyVault:/folder/sub-folder/dataset")
## End(Not run)
Dataset.query
Description
Queries a SolveBio dataset and returns an R data frame containing all records. Returns a single page of results otherwise (default).
Usage
Dataset.query(
id,
paginate = FALSE,
use_field_titles = TRUE,
env = .solveEnv,
...
)
Arguments
id |
The ID of a SolveBio dataset, or a Dataset object. |
paginate |
When set to TRUE, retrieves all records (memory permitting). |
use_field_titles |
(optional) Use field title instead of field name for query. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, limit, offset). |
References
Examples
## Not run:
Dataset.query("12345678790", paginate=TRUE)
## End(Not run)
Dataset.retrieve
Description
Retrieves the metadata about a specific dataset from SolveBio.
Usage
Dataset.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.retrieve("1234567890")
## End(Not run)
Dataset.template
Description
Retrieves the template for a dataset.
Usage
Dataset.template(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Dataset.template("1234567890")
## End(Not run)
Dataset.update
Description
Updates the attributes of an existing dataset.
Usage
Dataset.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the dataset to update. |
env |
(optional) Custom client environment. |
... |
Dataset attributes to change. |
References
Examples
## Not run:
Dataset.update(
id="1234",
name="New Dataset Name",
)
## End(Not run)
DatasetCommit.all
Description
Retrieves the metadata about all dataset commits on SolveBio.
Usage
DatasetCommit.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetCommit.all()
## End(Not run)
DatasetCommit.delete
Description
Deletes a specific dataset commit on SolveBio.
Usage
DatasetCommit.delete(id, env = .solveEnv)
Arguments
id |
String The ID or full name of a SolveBio dataset commit. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetCommit.delete(<ID>)
## End(Not run)
DatasetCommit.retrieve
Description
Retrieves the metadata about a specific dataset commit on SolveBio.
Usage
DatasetCommit.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset commit. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetCommit.retrieve(<ID>)
## End(Not run)
DatasetExport.all
Description
Retrieves the metadata about all dataset exports on SolveBio.
Usage
DatasetExport.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetExport.all()
## End(Not run)
DatasetExport.create
Description
Create a new dataset export.
Usage
DatasetExport.create(
dataset_id,
format = "json",
params = list(),
follow = FALSE,
env = .solveEnv,
...
)
Arguments
dataset_id |
The target dataset ID. |
format |
(optional) The export format (default: json). |
params |
(optional) Query parameters for the export. |
follow |
(default: FALSE) Follow the export task until it completes. |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset export parameters. |
References
Examples
## Not run:
DatasetExport.create(dataset_id=<ID>, format='json', params=list(fields=c("field_1"), limit=100))
## End(Not run)
DatasetExport.delete
Description
Deletes a specific dataset export on SolveBio.
Usage
DatasetExport.delete(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset export. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetExport.delete(<ID>)
## End(Not run)
DatasetExport.get_download_url
Description
Helper method to get the download URL for a dataset export.
Usage
DatasetExport.get_download_url(id, env = .solveEnv)
Arguments
id |
The ID of the dataset export. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetExport.get_download_url("1234567890")
## End(Not run)
DatasetExport.retrieve
Description
Retrieves the metadata about a specific dataset export on SolveBio.
Usage
DatasetExport.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset export. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetExport.retrieve(<ID>)
## End(Not run)
DatasetField.all
Description
Retrieves the metadata about all dataset fields on SolveBio.
Usage
DatasetField.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetField.all()
## End(Not run)
DatasetField.create
Description
Create a new dataset field.
Usage
DatasetField.create(dataset_id, name, data_type = "auto", env = .solveEnv, ...)
Arguments
dataset_id |
The dataset ID. |
name |
The name of the dataset field. |
data_type |
(optional) The data type for the field (default: auto). |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset import attributes. |
References
Examples
## Not run:
DatasetField.create(dataset_id=<ID>, name="my_field", title="My Field", data_type="string")
## End(Not run)
DatasetField.facets
Description
Returns the facets for a given dataset field.
Usage
DatasetField.facets(id, env = .solveEnv, ...)
Arguments
id |
String The ID of a dataset field. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
DatasetField.facets(691)
## End(Not run)
DatasetField.retrieve
Description
Retrieves the metadata about a specific dataset field.
Usage
DatasetField.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a dataset field. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetField.retrieve(691)
## End(Not run)
DatasetField.update
Description
Updates the attributes of an existing dataset field. NOTE: The data_type of a field cannot be changed.
Usage
DatasetField.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the dataset field to update. |
env |
(optional) Custom client environment. |
... |
Dataset field attributes to change. |
References
Examples
## Not run:
DatasetField.update(
id="1234",
title="New Field Title"
)
## End(Not run)
DatasetImport.all
Description
Retrieves the metadata about all dataset imports on SolveBio.
Usage
DatasetImport.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetImport.all()
## End(Not run)
DatasetImport.create
Description
Create a new dataset import. Either an object_id, manifest, or data_records is required.
Usage
DatasetImport.create(dataset_id, commit_mode = "append", env = .solveEnv, ...)
Arguments
dataset_id |
The target dataset ID. |
commit_mode |
(optional) The commit mode (default: append). |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset import attributes. |
References
Examples
## Not run:
DatasetImport.create(dataset_id=<ID>, upload_id=<ID>)
## End(Not run)
DatasetImport.delete
Description
Deletes a specific dataset import on SolveBio.
Usage
DatasetImport.delete(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset import. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetImport.delete(<ID>)
## End(Not run)
DatasetImport.retrieve
Description
Retrieves the metadata about a specific dataset import on SolveBio.
Usage
DatasetImport.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset import. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetImport.retrieve(<ID>)
## End(Not run)
DatasetMigration.all
Description
Retrieves the metadata about all dataset migrations on SolveBio.
Usage
DatasetMigration.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetMigration.all()
## End(Not run)
DatasetMigration.create
Description
Create a new dataset migration.
Usage
DatasetMigration.create(
source_id,
target_id,
commit_mode = "append",
source_params = NULL,
target_fields = NULL,
include_errors = FALSE,
env = .solveEnv,
...
)
Arguments
source_id |
The source dataset ID. |
target_id |
The target dataset ID. |
commit_mode |
(optional) The commit mode (default: append). |
source_params |
(optional) The query parameters used on the source dataset. |
target_fields |
(optional) A list of valid dataset fields to add or override in the target dataset. |
include_errors |
(optional) If TRUE, a new field (_errors) will be added to each record containing expression evaluation errors (default: FALSE). |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset migration attributes. |
References
Examples
## Not run:
DatasetMigration.create(dataset_id=<ID>, upload_id=<ID>)
## End(Not run)
DatasetMigration.delete
Description
Deletes specific dataset migration on SolveBio.
Usage
DatasetMigration.delete(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset migration. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetMigration.delete(<ID>)
## End(Not run)
DatasetMigration.retrieve
Description
Retrieves the metadata about a specific dataset migration on SolveBio.
Usage
DatasetMigration.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset migration. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetMigration.retrieve(<ID>)
## End(Not run)
DatasetTemplate.all
Description
Retrieves the metadata about all dataset templates on SolveBio.
Usage
DatasetTemplate.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
DatasetTemplate.all()
## End(Not run)
DatasetTemplate.create
Description
Create a SolveBio dataset template.
Usage
DatasetTemplate.create(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Dataset template attributes. |
References
Examples
## Not run:
DatasetTemplate.create(name="My Dataset Template")
## End(Not run)
DatasetTemplate.delete
Description
Deletes a specific dataset template on SolveBio.
Usage
DatasetTemplate.delete(id, env = .solveEnv)
Arguments
id |
String The ID or full name of a SolveBio dataset template. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetTemplate.delete(<ID>)
## End(Not run)
DatasetTemplate.retrieve
Description
Retrieves the metadata about a specific dataset template on SolveBio.
Usage
DatasetTemplate.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio dataset template. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
DatasetTemplate.retrieve(<ID>)
## End(Not run)
DatasetTemplate.update
Description
Updates the attributes of an existing dataset template.
Usage
DatasetTemplate.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the dataset template to update. |
env |
(optional) Custom client environment. |
... |
Dataset template attributes to change. |
References
Examples
## Not run:
DatasetTemplate.update(
id="1234",
name="New Template Name",
)
## End(Not run)
Expression.evaluate
Description
Evaluate a SolveBio expression.
Usage
Expression.evaluate(
expression,
data_type = "string",
is_list = FALSE,
data = NULL,
raw = FALSE,
env = .solveEnv
)
Arguments
expression |
The SolveBio expression string. |
data_type |
The data type to cast the expression result (default: string). |
is_list |
Set to TRUE if the result is expected to be a list (default: FALSE). |
data |
Variables used in the expression (default: NULL). |
raw |
Set to TRUE to return the raw response (default: FALSE). |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Expression.evaluate("1 + 1", data_type="integer", is_list=FALSE)
## End(Not run)
GlobalSearch.facets
Description
Performs a Global Search based on provided filters, entities, queries, and returns an R data frame containing the facets results from API response.
Usage
GlobalSearch.facets(facets, env = .solveEnv, ...)
Arguments
facets |
Facets list. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, entities, query). |
References
Examples
## Not run:
GlobalSearch.facets(facets="study")
## End(Not run)
GlobalSearch.request
Description
Performs a single Global Search API request with the provided filters, queries and entities. A single request will only retrieve one page of results (based on the 'limit' parameter). Use 'GlobalSearch.search()' to retrieve all pages of results. Returns the full API response (containing attributes: results, vaults, subjects, subjects_count, total)
Usage
GlobalSearch.request(query = NULL, filters, entities, env = .solveEnv, ...)
Arguments
query |
(optional) Advanced search query. |
filters |
(optional) Low-level filter specification. |
entities |
(optional) Low-level entity specification. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
# No filters are applied
GlobalSearch.request()
# Global Beacon search
GlobalSearch.request(entities = '[["gene","BRCA2"]]')
# Type filter (only vaults)
GlobalSearch.request(filters = '[{"and":[["type__in",["vault"]]]}]')
# Advanced search
GlobalSearch.request(query = "fuji")
# Multiple filters and entities
GlobalSearch.request(
entities = '[["gene","BRCA2"]]',
filters = '[{
"and": [
{"and": [
["created_at__range",["2021-11-28","2021-12-28"]]]},
["type__in",["dataset"]]
]
}]'
)
## End(Not run)
GlobalSearch.search
Description
Performs a Global Search based on provided filters, entities, queries, and returns an R data frame containing results from API response. Returns a single page of results otherwise (default).
Usage
GlobalSearch.search(paginate = FALSE, env = .solveEnv, ...)
Arguments
paginate |
When set to TRUE, retrieves all records (memory permitting). |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, entities, query, limit, offset). |
References
Examples
## Not run:
# No filters applied
GlobalSearch.search()
#Global Beacon search
GlobalSearch.search(entities = '[["gene","BRCA2"]]')
GlobalSearch.search(filters = '[{"and":[["type__in",["vault"]]]}]')
# Advanced search
GlobalSearch.search(query = "fuji")
## End(Not run)
GlobalSearch.subjects
Description
Performs a Global Search based on provided filters, entities, queries, and returns an R data frame containing subjects from API response.
Usage
GlobalSearch.subjects(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, entities, query, limit, offset). |
References
Examples
## Not run:
GlobalSearch.subjects(entities = '[["gene","BRCA2"]]')
## End(Not run)
GlobalSearch.subjects_count
Description
Performs a Global Search based on provided filters, entities, queries, and returns the total number of subjects from API response.
Usage
GlobalSearch.subjects_count(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, entities, query, limit, offset). |
References
Examples
## Not run:
GlobalSearch.subjects_count(entities = '[["gene","BRCA2"]]')
## End(Not run)
Object.all
Description
Retrieves the metadata about all objects on SolveBio accessible to the current user.
Usage
Object.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Object.all()
## End(Not run)
Object.create
Description
Create a SolveBio object.
Usage
Object.create(
vault_id,
parent_object_id,
object_type,
filename,
env = .solveEnv,
...
)
Arguments
vault_id |
The target vault ID. |
parent_object_id |
The ID of the parent object (folder) or NULL for the vault root. |
object_type |
The type of object (i.e. "folder"). |
filename |
The filename (i.e. the name) of the object. |
env |
(optional) Custom client environment. |
... |
(optional) Additional object attributes. |
References
Examples
## Not run:
Object.create(
vault_id="1234567890",
parent_object_id=NULL,
object_type="folder",
filename="My Folder"
)
## End(Not run)
Object.data
Description
Returns one page of documents from a SolveBio file (object) and processes the response.
Usage
Object.data(id, filters, col.names = NULL, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio file (vault object). |
filters |
(optional) Query filters. |
col.names |
(optional) Force data frame column name ordering. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
Object.data("1234567890")
## End(Not run)
Object.delete
Description
Delete a specific object from SolveBio.
Usage
Object.delete(id, env = .solveEnv)
Arguments
id |
The ID of the object. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.delete("1234567890")
## End(Not run)
Object.disable_global_beacon
Description
Disables Global Beacon for the specified dataset.
Usage
Object.disable_global_beacon(id, env = .solveEnv)
Arguments
id |
The ID of a SolveBio dataset. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.disable_global_beacon("1234567890")
## End(Not run)
Object.enable_global_beacon
Description
Enables Global Beacon for the specified dataset.
Usage
Object.enable_global_beacon(id, env = .solveEnv)
Arguments
id |
The ID of a SolveBio dataset. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.enable_global_beacon("1234567890")
## End(Not run)
Object.fields
Description
Retrieves the list of fields for a file (JSON, CSV, or TSV).
Usage
Object.fields(id, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio file (vault object). |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
Object.fields("1234567890")
## End(Not run)
Object.get_by_full_path
Description
A helper function to get an object on SolveBio by its full path.
Usage
Object.get_by_full_path(full_path, env = .solveEnv, ...)
Arguments
full_path |
The full path to the object. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Object.get_by_full_path("solvebio:public:/ClinVar")
## End(Not run)
Object.get_by_path
Description
A helper function to get an object on SolveBio by its path. Used as a pass-through function from some Vault methods.
Usage
Object.get_by_path(path, env = .solveEnv, ...)
Arguments
path |
The path to the object, relative to a vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Object.get_by_path("/ClinVar")
## End(Not run)
Object.get_download_url
Description
Helper method to get the download URL for a file object.
Usage
Object.get_download_url(id, env = .solveEnv)
Arguments
id |
The ID of the object. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.get_download_url("1234567890")
## End(Not run)
Object.get_global_beacon_status
Description
Retrieves the global beacon status for the specified dataset.
Usage
Object.get_global_beacon_status(id, raise_on_disabled = FALSE, env = .solveEnv)
Arguments
id |
The ID of a SolveBio dataset. |
raise_on_disabled |
Whether to raise an exception if Global Beacon is disabled or to return NULL. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.get_global_beacon_status("1234567890")
Object.get_global_beacon_status("1234567890", raise_on_disabled=TRUE)
## End(Not run)
Object.get_or_upload_file
Description
Upload a local file to a vault on SolveBio only if it does not yet exist (by name, at the provided path). The vault path provided is the parent directory for uploaded file. Accepts the same arguments as 'Object.upload_file'.
Usage
Object.get_or_upload_file(
local_path,
vault_id,
vault_path,
filename,
env = .solveEnv
)
Arguments
local_path |
The path to the local file |
vault_id |
The SolveBio vault ID |
vault_path |
The remote path in the vault |
filename |
(optional) The filename for the uploaded file in the vault (default: the basename of the local_path) |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.get_or_upload_file("my_file.json.gz", vault$id, "/parent/directory/")
## End(Not run)
Object.query
Description
Queries a SolveBio file (vault object) and returns an R data frame containing all records. Returns a single page of results otherwise (default).
Usage
Object.query(id, paginate = FALSE, env = .solveEnv, ...)
Arguments
id |
The ID of a SolveBio file (vault object). |
paginate |
When set to TRUE, retrieves all records (memory permitting). |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. filters, limit, offset). |
References
Examples
## Not run:
Object.query("12345678790", paginate=TRUE)
## End(Not run)
Object.retrieve
Description
Retrieves the metadata about a specific object on SolveBio.
Usage
Object.retrieve(id, env = .solveEnv)
Arguments
id |
The ID of the object. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.retrieve("1234567890")
## End(Not run)
Object.update
Description
Updates the attributes of an existing vault object.
Usage
Object.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault to update. |
env |
(optional) Custom client environment. |
... |
Object attributes to change. |
References
Examples
## Not run:
Object.update(
id="1234",
filename="New Name",
)
## End(Not run)
Object.upload_file
Description
Upload a local file to a vault on SolveBio. The vault path provided is the parent directory for uploaded file.
Usage
Object.upload_file(local_path, vault_id, vault_path, filename, env = .solveEnv)
Arguments
local_path |
The path to the local file |
vault_id |
The SolveBio vault ID |
vault_path |
The remote path in the vault |
filename |
(optional) The filename for the uploaded file in the vault (default: the basename of the local_path) |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Object.upload_file("my_file.json.gz", vault$id, "/parent/directory/")
## End(Not run)
SavedQuery.all
Description
Retrieves the all saved queries on SolveBio.
Usage
SavedQuery.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. page). |
References
Examples
## Not run:
SavedQuery.all()
## End(Not run)
SavedQuery.create
Description
Create a SolveBio saved query.
Usage
SavedQuery.create(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Saved query attributes. |
References
Examples
## Not run:
SavedQuery.create(name="My Dataset Template")
## End(Not run)
SavedQuery.delete
Description
Deletes a specific saved query on SolveBio.
Usage
SavedQuery.delete(id, env = .solveEnv)
Arguments
id |
String The ID of the SolveBio saved query. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
SavedQuery.delete(<ID>)
## End(Not run)
SavedQuery.retrieve
Description
Retrieves a specific saved query on SolveBio by ID.
Usage
SavedQuery.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio saved query. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
SavedQuery.retrieve(<ID>)
## End(Not run)
SavedQuery.update
Description
Updates the attributes of an existing saved query.
Usage
SavedQuery.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the saved query to update. |
env |
(optional) Custom client environment. |
... |
Saved query attributes to change. |
References
Examples
## Not run:
SavedQuery.update(
id="1234",
name="New query Name",
)
## End(Not run)
Task.all
Description
Retrieves the metadata about all tasks on SolveBio accessible to the current user.
Usage
Task.all(env = .solveEnv, ...)
Arguments
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters. |
References
Examples
## Not run:
Task.all()
## End(Not run)
Task.follow
Description
A helper function to follow a specific task until it gets completed.
Usage
Task.follow(id, env = .solveEnv, interval = 2)
Arguments
id |
String The ID of a task. |
env |
(optional) Custom client environment. |
interval |
2. Delay in seconds between each completion status query |
Value
the task object
References
Examples
## Not run:
Task.follow("1234567890")
## End(Not run)
Task.retrieve
Description
Retrieves the metadata about a specific task on SolveBio.
Usage
Task.retrieve(id, env = .solveEnv)
Arguments
id |
The ID of a task. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Task.retrieve("1234567890")
## End(Not run)
User.retrieve
Description
Retrieves information about the current user.
Usage
User.retrieve(env = .solveEnv)
Arguments
env |
(optional) Custom client environment. |
References
Examples
## Not run:
User.retrieve()
## End(Not run)
Vault.all
Description
Retrieves the metadata about all accessible vaults.
Usage
Vault.all(..., env = .solveEnv)
Arguments
... |
(optional) Additional query parameters (e.g. limit, offset). |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Vault.all()
## End(Not run)
Vault.create
Description
Create a new SolveBio vault.
Usage
Vault.create(name, env = .solveEnv, ...)
Arguments
name |
The unique name of the vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional vault attributes. |
References
Examples
## Not run:
Vault.create(name="my-domain:MyVault")
## End(Not run)
Vault.create_dataset
Description
Create a new dataset in a vault.
Usage
Vault.create_dataset(id, path, name, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
path |
The path to the dataset, within the vault. |
name |
The name (filename) for the dataset. |
env |
(optional) Custom client environment. |
... |
(optional) Additional dataset creation parameters. |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.create_dataset(vault$id, path="/", name="My Dataset")
## End(Not run)
Vault.create_folder
Description
Create a new folder in a vault.
Usage
Vault.create_folder(id, path, recursive = FALSE, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
path |
The path to the folder, within the vault. |
recursive |
Create all parent directories that do not yet exist (default: FALSE). |
env |
(optional) Custom client environment. |
... |
(optional) Additional folder creation parameters. |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.create_folder(vault$id, "/My Folder")
## End(Not run)
Vault.datasets
Description
Retrieves all datasets in a specific vault.
Usage
Vault.datasets(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.datasets(vault$id)
## End(Not run)
Vault.delete
Description
Delete a specific vault from SolveBio. This operation cannot be undone.
Usage
Vault.delete(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio vault. |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Vault.delete("1")
## End(Not run)
Vault.files
Description
Retrieves all files in a specific vault.
Usage
Vault.files(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.files(vault$id)
## End(Not run)
Vault.folders
Description
Retrieves all folders in a specific vault.
Usage
Vault.folders(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.folders(vault$id)
## End(Not run)
Vault.get_by_full_path
Description
Retrieves a specific vault by its full path (domain:vault).
Usage
Vault.get_by_full_path(full_path, verbose = TRUE, env = .solveEnv)
Arguments
full_path |
The full path of a SolveBio vault. |
verbose |
Print warning/error messages (default: TRUE). |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Vault.get_by_full_path("SolveBio:Public")
## End(Not run)
Vault.get_or_create_by_full_path
Description
Retrieves or creates a specific vault by its full path (domain:vault).
Usage
Vault.get_or_create_by_full_path(full_path, env = .solveEnv, ...)
Arguments
full_path |
The full path of a SolveBio vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional parameters. |
References
Examples
## Not run:
Vault.get_or_create_by_full_path("My New Vault")
## End(Not run)
Vault.get_personal_vault
Description
Retrieves the current users"s personal, private vault.
Usage
Vault.get_personal_vault(env = .solveEnv)
Arguments
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Vault.get_personal_vault()
## End(Not run)
Vault.objects
Description
Retrieves all objects in a specific vault.
Usage
Vault.objects(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.objects(vault$id)
## End(Not run)
Vault.retrieve
Description
Retrieves the metadata about a specific SolveBio vault.
Usage
Vault.retrieve(id, env = .solveEnv)
Arguments
id |
String The ID of a SolveBio vault |
env |
(optional) Custom client environment. |
References
Examples
## Not run:
Vault.retrieve("1234567890")
## End(Not run)
Vault.search
Description
Search for objects in a specific vault.
Usage
Vault.search(id, query, env = .solveEnv, ...)
Arguments
id |
The ID of the vault. |
query |
The search query. |
env |
(optional) Custom client environment. |
... |
(optional) Additional query parameters (e.g. limit, offset). |
References
Examples
## Not run:
vault = Vault.get_personal_vault()
Vault.search('test')
## End(Not run)
Vault.update
Description
Updates the attributes of an existing vault.
Usage
Vault.update(id, env = .solveEnv, ...)
Arguments
id |
The ID of the vault to update. |
env |
(optional) Custom client environment. |
... |
Vault attributes to change. |
References
Examples
## Not run:
Vault.update(
id="1234",
name="New Vault Name",
)
## End(Not run)
createEnv
Description
Create a new SolveBio environment.
Usage
createEnv(token, token_type = "Token", host = .solveEnv$host)
Arguments
token |
A SolveBio API key or OAuth2 token |
token_type |
SolveBio token type (default: Token) |
host |
(optional) The SolveBio API host (default: https://api.solvebio.com) |
References
Examples
## Not run:
env <- createEnv("MyAPIkey")
User.retrieve(env = myEnv)
## End(Not run)
login
Description
Store and verify your SolveBio credentials.
Usage
login(api_key, api_host, env = .solveEnv)
Arguments
api_key |
Your SolveBio API key |
api_host |
SolveBio API host (default: https://api.solvebio.com) |
env |
(optional) The R environment used to store API credentials. |
References
Examples
## Not run:
login()
## End(Not run)
protectedServer
Description
Wraps an existing Shiny server in an OAuth2 flow.
Usage
protectedServer(
server,
client_id,
client_secret = NULL,
base_url = "https://my.solvebio.com"
)
Arguments
server |
Your original Shiny server function. |
client_id |
Your application's client ID. |
client_secret |
(optional) Your application's client secret. |
base_url |
(optional) Override the default login host (default: https://my.solvebio.com). |
References
Examples
## Not run:
protectedServer(
server=server,
client_id="abcd1234"
)
## End(Not run)
protectedServerUI
Description
Returns ShinyJS-compatible JS code to support cookie-based token storage.
Usage
protectedServerJS()
References
Examples
## Not run:
jscookie_src <- "https://cdnjs.cloudflare.com/ajax/libs/js-cookie/2.2.0/js.cookie.js"
ui <- fluidPage(
shiny::tags$head(
shiny::tags$script(src = jscookie_src)
),
useShinyjs(),
extendShinyjs(text = solvebio::protectedServerJS(),
functions = c("enableCookieAuth", "getCookie", "setCookie", "rmCookie"))
)
## End(Not run)