synStore: synStore

In Sage-Bionetworks/synapser: R Language Bindings for Synapse API

synStore

Description

Creates a new Entity or updates an existing Entity, uploading any files in the process.

Usage

synStore(obj, createOrUpdate=TRUE, forceVersion=TRUE, versionLabel=NULL, isRestricted=FALSE, activity=NULL, used=NULL, executed=NULL, activityName=NULL, activityDescription=NULL, set_annotations=TRUE)

Arguments

obj	A Synapse Entity, Evaluation, or Wiki.
used	Optional. The Entity, Synapse ID, or URL used to create the object (can also be a list of these.
executed	Optional. The Entity, Synapse ID, or URL representing code executed to create the object (can also be a list of these).
activity	Optional. Activity object specifying the user's provenance.
activityName	Optional. Activity name to be used in conjunction with used and executed.
activityDescription	Optional. Activity description to be used in conjunction with used and executed.
createOrUpdate	Optional. Indicates whether the method should automatically perform an update if the 'obj' conflicts with an existing Synapse object. Defaults to TRUE.
forceVersion	Optional. Indicates whether the method should increment the version of the object even if nothing has changed. Defaults to TRUE.
versionLabel	Optional. Arbitrary string used to label the version.
isRestricted	Optional.If set to TRUE, an email will be sent to the Synapse access control team to start the process of adding terms-of-use or review board approval for this entity. You will be contacted with regards to the specific data being restricted and the requirements of access. Defaults to FALSE.
set_annotations	If TRUE, set the annotations on the entity. If FALSE, do not set the annotations. Defaults to TRUE.

Value

A Synapse Entity, Evaluation, or Wiki

Examples

## Not run: 
# Create a new project

project <- Project('My uniquely named project')
project <- synStore(project)

# Adding files with provenance:
#
# A synapse entity *syn1906480* contains data
# entity *syn1917825* contains code
#
activity <- Activity('Fancy Processing',
                      description='No seriously, really fancy processing',
                      used=c('syn1906480', 'http://data_r_us.com/fancy/data.txt'),
                      executed='syn1917825')
file <- File('/path/to/data/file.xyz', description='Fancy new data', parent=project)
file <- synStore(file, activity=activity)

# Evaluation
eval <- Evaluation(name =sprintf("My unique evaluation created on %s", format(Sys.time(), "%a %b %d %H%M%OS4 %Y")), 
                   description = "testing",
                   contentSource = project$properties$id,
                   submissionReceiptMessage = "Thank you for your submission!",
                   submissionInstructionsMessage = "This evaluation only accepts files.")
eval <- synStore(eval)

# Wiki
content <- "
# My Wiki Page

Here is a description of my **fantastic** project!
"
wiki = Wiki(title='My Wiki Page',
            owner=project,
            markdown=content,
            attachments=list('/path/to/logo.png'))
wiki <- synStore(wiki)

## End(Not run)

Sage-Bionetworks/synapser documentation built on Aug. 23, 2024, 11:07 a.m.