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The effect of this architecture is that repeated uploads or downloads of an entity's file are avoided when the local copy is not modified. This strategy does not avoid repeated downloads of an entity's file to a variety of local folders. We feel that the potential efficiency gains of doing this are outweighed by the complexity of tracking multiple, mutable copies of a file.
File Usage Examples
Example 1: Create File
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entity wrapping local file, save to Synapse, retrieve
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, and save again
synStore()
synGet()
getFileLocation()
"/Users/johndoe/Downloads/myscript.txt"
# retrieve for additional editing (no location specified), and save again
# retrieve once more, no location specified
Example 2: Retrieve File from Synapse given entity ID
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project<-(name="myproject")
# 'synStore' will either create the project or retrieve it if it already exists
project<-synStore(project)
pid<-propertyValue(project, "id")
file <- File(path="~/myproject/genotypedata.csv", name="genotypedata", parentId=pid)
# 'synStore' will upload the file to Synapse
# locally we record that the uploaded file is available at ~/myproject/genotypedata.csv
file <- synStore(file)
# we can get the ID of the file in Synapse
fileId <- propertyValue(file, "id")
# ----- Now assume a new session (perhaps a different user)
# at first we have only the Synapse file ID
fileId <- "synXXXXX"
file <-synGet(fileId, load=F)
# client recognizes that local copy exists, avoiding repeated download
getFileLocation(file)
> "~/myproject/genotypedata.csv"
# now change something, e.g. add an annotation...
synAnnot(file, "data type")<-"genotype"
# ... and save. the client determines that the file is unchanged so does not upload again
file <-synStore(file)
# we can also download to a specific location
fileCopy<-synGet(fileId, downloadLocation="~/scratch/", load=F)
getFileLocation(fileCopy)
> "~/scratch/genotypedata.csv"
# we now have two copies on the local file system
Example 2: Link to File on web, then download
project<-(name="myproject")
project<-synStore(project)
pid<-propertyValue(project, "id")
# we use 'synapseStore=F' to indicate that we only wish to link
file <- File(path="ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/matrix/GSExxxx_RAW.tar", synapseStore=F, name="genotypedata", parentId=pid)
# Synapse stores the metadata, but does not upload the file
file <- synStore(file)
# we can get the ID of the file in Synapse
fileId <- propertyValue(file, "id")
# synGet downloads the file to a default location
file <-synGet(fileId, load=F)
getFileLocation(file)
> "~/.synapseCache/GSExxxx_RAW.tar"
# now change the meta data and save
synAnnot(file, "data type")<-"gene expression"
# synStore does not upload the file
file<-synStore(file)
Command Set
We conceptual divide the client commands into three levels (1) Common functions, (2) Advanced functions and (3) low-level Web API functions. The first collection of commands captures the majority of functionality of interest to users. The second collection rounds out the functionality with less frequently used functions. The third set comprises simple, low level wrappers around the Synapse web service interface. By including this third set users can access web services in advance of having specialized commands in the analytic clients.
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