A view is a view of all entities (File, Folder, Project, Table, Docker Repository, View) within one or more Projects or Folders. Views can:
Preliminaries:
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.
synLogin()
## Welcome, test!
## 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)
file <- synStore(file)
## ################################################## Uploading file to Synapse storage ##################################################
Uploading [--------------------]0.00% 0.0bytes/37.0bytes file86104a1ec12b
Uploading [####################]100.00% 37.0bytes/37.0bytes (31.0bytes/s) file86104a1ec12b Done...
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 <- synStore(file2)
## ################################################## Uploading file to Synapse storage ##################################################
Uploading [--------------------]0.00% 0.0bytes/38.0bytes file8610291c1411
Uploading [####################]100.00% 38.0bytes/38.0bytes (67.4bytes/s) file8610291c1411 Done...
# add some annotations
synSetAnnotations(file, list(contributor = "Sage", class = "V"))
## $class
## $class[[1]]
## [1] "V"
##
##
## $contributor
## $contributor[[1]]
## [1] "Sage"
synSetAnnotations(file2, list(contributor = "UW", rank = "X"))
## $rank
## $rank[[1]]
## [1] "X"
##
##
## $contributor
## $contributor[[1]]
## [1] "UW"Creating a View:
view <- EntityViewSchema(name = "my first file view",
columns = c(
Column(name = "contributor", columnType = "STRING"),
Column(name = "class", columnType = "STRING"),
Column(name = "rank", columnType = "STRING")),
parent = project$properties$id,
scopes = project$properties$id,
includeEntityTypes = c(EntityViewType$FILE, EntityViewType$FOLDER),
add_default_columns = TRUE)
view <- synStore(view)
##
[####################]100.00% 1/1 Done...We support the following entity type in a View:
EntityViewType
## $DOCKER
## EntityViewType.DOCKER
##
## $FILE
## EntityViewType.FILE
##
## $FOLDER
## EntityViewType.FOLDER
##
## $PROJECT
## EntityViewType.PROJECT
##
## $TABLE
## EntityViewType.TABLE
##
## $VIEW
## EntityViewType.VIEWTo see the content of your newly created View, use synTableQuery():
queryResults <- synTableQuery(sprintf("select * from %s", view$properties$id))
##
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 834.0bytes/834.0bytes (502.1kB/s) SYNAPSE_TABLE_QUERY_2926613.csv Done...
data <- as.data.frame(queryResults)
data
## ROW_ID ROW_VERSION ROW_ETAG id
## 1 11769481 1 4836e928-7466-44a7-8764-0b80b0de8dc3 syn11769481
## 2 11769482 1 c12a41f9-bd78-434b-98a3-c9739e4d459f syn11769482
## name createdOn createdBy
## 1 file86104a1ec12b 2021-04-28 22:02:16 3336368
## 2 file8610291c1411 2021-04-28 22:02:18 3336368
## etag type currentVersion parentId
## 1 4836e928-7466-44a7-8764-0b80b0de8dc3 file 1 syn11769480
## 2 c12a41f9-bd78-434b-98a3-c9739e4d459f file 1 syn11769480
## benefactorId projectId modifiedOn modifiedBy dataFileHandleId
## 1 syn11769480 syn11769480 2021-04-28 22:02:19 3336368 2926611
## 2 syn11769480 syn11769480 2021-04-28 22:02:19 3336368 2926612
## dataFileSizeBytes dataFileMD5Hex contributor class rank
## 1 37 47dfe7f5eaa49a5413c7b79b67ab9c43 Sage V <NA>
## 2 38 ba01e01b9e3ffea3ebef95efa62998b0 UW <NA> XTo update ‘class’ annotation for ‘file2’, simply update the view:
The change in annotations is reflected in synGetAnnotations():
synGetAnnotations(file2$properties$id)A unique etag is associated with every file that updates when changes are made to a file, including the contents, annotations, or metadata. Any updates pushed to Synapse will change an object’s etag.
data$etagThere 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,]))
##
Uploading [--------------------]0.00% 0.0bytes/555.0bytes file861036131520
Uploading [####################]100.00% 555.0bytes/555.0bytes (503.7bytes/s) file861036131520 Done...
[####################]100.00% 1/1 Done...
## <synapseclient.table.CsvFileTable object at 0x143ff3080>A view can contain different types of entity. To change the types of entity that will show up in a view:
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