Views

A view is a view of all entities (File, Folder, Project, Table, Docker Repository, View) within one or more Projects or Folders. Views can:

Provide a way of isolating or linking data based on similarities
Provide the ability to link entities together by their annotations
Allow view/editing entities attributes in bulk
Allow entities to be easily searched and queried

Preliminaries:

library(reticulate)
library(synapser)
## 
## TERMS OF USE NOTICE:
##   When using Synapse, remember that the terms and conditions of use require that you:
##   1) Attribute data contributors when discussing these data or results from these data.
##   2) Not discriminate, identify, or recontact individuals or groups represented by the data.
##   3) Use and contribute only data de-identified to HIPAA standards.
##   4) Redistribute data only under these same terms of use.
syn <- reticulate::import("synapseclient")
EntityViewType <- syn$EntityViewType
synLogin()
## NULL
# Create a new project
# use hex_digits to generate random string
hex_digits <- c(as.character(0:9), letters[1:6])
projectName <- sprintf("My unique project %s", paste0(sample(hex_digits, 32, replace = TRUE), collapse = ""))
project <- Project(projectName)
project <- synStore(project)

# Create some files
filePath <- tempfile()
connection <- file(filePath)
writeChar("this is the content of the first file", connection, eos = NULL)
close(connection)
file <- File(path = filePath, parent = project)
# Add some annotations
file$annotations = list(contributor = "UW", rank = "X")
file <- synStore(file)

filePath2 <- tempfile()
connection2 <- file(filePath2)
writeChar("this is the content of the second file", connection, eos = NULL)
close(connection2)
file2 <- File(path = filePath2, parent = project)
file2$annotations = list(contributor = "UW", rank = "X")
file2 <- synStore(file2)

Creating a View:

view <- EntityViewSchema(name = "my first file view",
                         columns = c(
                           Column(name = "contributor", columnType = "STRING"),
                           Column(name = "class", columnType = "STRING"),
                           Column(name = "rank", columnType = "STRING")),
                         parent = project$properties$id,
                         scopes = project$properties$id,
                         includeEntityTypes = c(EntityViewType$FILE, EntityViewType$FOLDER),
                         add_default_columns = TRUE)

view <- synStore(view)

We support the following entity type in a View:

EntityViewType
## <enum 'EntityViewType'>

To see the content of your newly created View, use synTableQuery():

queryResults <- synTableQuery(sprintf("select * from %s", view$properties$id))

data <- as.data.frame(queryResults)
data

##     ROW_ID ROW_VERSION                             ROW_ETAG          id
## 1 62283536           1 fc8f9520-9eac-4e86-9bb5-80827c26b91f syn62283536
## 2 62283537           1 85fa4ee1-e28f-4113-8486-a27b070de4e7 syn62283537
##               name description           createdOn createdBy
## 1 filec3d26300b69f        <NA> 2024-08-21 00:59:41   3434599
## 2 filec3d26e1406ab        <NA> 2024-08-21 00:59:42   3434599
##                                   etag          modifiedOn modifiedBy
## 1 fc8f9520-9eac-4e86-9bb5-80827c26b91f 2024-08-21 00:59:41    3434599
## 2 85fa4ee1-e28f-4113-8486-a27b070de4e7 2024-08-21 00:59:42    3434599
##                                                                  path type
## 1 My unique project 0fb1ce7d28c510effb6f19e613694b46/filec3d26300b69f file
## 2 My unique project 0fb1ce7d28c510effb6f19e613694b46/filec3d26e1406ab file
##   currentVersion    parentId benefactorId   projectId dataFileHandleId
## 1              1 syn62283535  syn62283535 syn62283535        146071347
## 2              1 syn62283535  syn62283535 syn62283535        146071348
##       dataFileName dataFileSizeBytes                   dataFileMD5Hex
## 1 filec3d26300b69f                37 47dfe7f5eaa49a5413c7b79b67ab9c43
## 2 filec3d26e1406ab                38 ba01e01b9e3ffea3ebef95efa62998b0
##                               dataFileConcreteType        dataFileBucket
## 1 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
## 2 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
##                                                     dataFileKey contributor
## 1 3434599/3ae1ce75-7edc-4c11-8ca2-23527177cf32/filec3d26300b69f          UW
## 2 3434599/ba98835c-e1ce-40cb-a111-b07f9fe35ecf/filec3d26e1406ab          UW
##   class rank
## 1  <NA>    X
## 2  <NA>    X

Updating Annotations using View

To update ‘class’ annotation for ‘file2’, simply update the view:

data["class"] <- c("V", "VI")
synStore(Table(view$properties$id, data))

The change in annotations is reflected in synGetAnnotations():

synGetAnnotations(file2$properties$id)

A unique etag is associated with every file that updates when changes are made to a file, including the contents, annotations, or metadata. Any updates pushed to Synapse will change an object’s etag.

data$etag

There may be cases where you want to update the annotations on a subset of files in a view. In order to preserve the etag, and thus the file history, you will need to store only the rows that have been modified.

data$contributor[1] <- c("Sage Bionetworks")
synStore(Table(view$properties$id, data[1,]))
## <synapseclient.table.CsvFileTable object at 0x7863a8c6fe80>

Update View’s Content

A view can contain different types of entity. To change the types of entity that will show up in a view:

view <- synGet(view$properties$id)
view$set_entity_types(list(EntityViewType$FILE))

A View is a Table. Please visit Tables vignettes to see how to change schema, update content, and other operations that can be done on View.

synDelete(project)
## NULL

Views

Tom Yu

2024-08-21

Views

Updating Annotations using View

Update View’s Content