Views

KimYen Ladia

2023-09-09

Source: vignettes/views.Rmd

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)
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 <- synStore(file2)

# add some annotations
synSetAnnotations(file, list(contributor = "Sage", class = "V"))
## $class
## [1] "V"
## 
## $contributor
## [1] "Sage"
synSetAnnotations(file2, list(contributor = "UW", rank = "X"))
## $rank
## [1] "X"
## 
## $contributor
## [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)

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 52417572           1 03d6cee4-35c4-4be7-9021-4b12f6eaa755 syn52417572
## 2 52417573           1 ec739129-fea1-4901-bf71-2611930e94d2 syn52417573
##               name description           createdOn createdBy
## 1 filed79d5e81ba3e          NA 2023-09-09 22:59:50   3324230
## 2 filed79d16ea6ceb          NA 2023-09-09 22:59:51   3324230
##                                   etag          modifiedOn modifiedBy type
## 1 03d6cee4-35c4-4be7-9021-4b12f6eaa755 2023-09-09 22:59:52    3324230 file
## 2 ec739129-fea1-4901-bf71-2611930e94d2 2023-09-09 22:59:52    3324230 file
##   currentVersion    parentId benefactorId   projectId dataFileHandleId
## 1              1 syn52417571  syn52417571 syn52417571        128471165
## 2              1 syn52417571  syn52417571 syn52417571        128471166
##   dataFileSizeBytes                   dataFileMD5Hex
## 1                37 47dfe7f5eaa49a5413c7b79b67ab9c43
## 2                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 3324230/b4e57ee9-09e5-47eb-b0e7-f72a7286f57f/filed79d5e81ba3e        Sage
## 2 3324230/a81a4d30-81bc-47b6-8990-021b9b790207/filed79d16ea6ceb          UW
##   class rank
## 1     V   NA
## 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 0x11a6d1390>

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