Page Comparison

1 – Common functions

Create a Synapse file handle in memory, specifying the path to the file in the local file system, the name in Synapse, and the Folder in Synapse.  This step 'stages' a file to be sent to Synapse. Additional parameters (...) are interpreted as properties or annotations, in the manner of synSet(), defined below.  If 'synapseStore' is TRUE then file is uploaded to S3, else only the file location is saved.

Note:  synapseStore=T is not allowed if "path" is a URL rather than a local file path.

The specified file doesn't move or get copied.

File(path, parentId, synapseStore=T, ...)

example:

File(path="/path/to/file", parentId="syn101")

File(path, parentId, synapseStore=True, **kwargs)

example:

File('/foo/baz/bar.txt', 'syn123')

NA

Create a Synapse file handle in memory which will hold a serialized version of one or more in-memory objects.  Additional parameters (...) are interpreted as properties or annotations, in the manner of synSet(), defined below. If 'synapseStore' is TRUE then file is uploaded to S3, else only the file location is saved.

The object is not serialized at this time. 

(We are hoping people will like calling the object a File, even though it's a collecton of in-memory objects.)

File(parentId)

example:

file<-File(parentId="syn101")

file<-addObject(file, obj)

Will not be implemented in python.

NA

Create a Folder or Project in memory. Name and parentId are optional.

Folder(name=NULL, parentId=NULL, ...)

Project(name=NULL, ...)

example:
Folder(name="foo", parentId="syn101")

Folder(name="foo", parentId="syn101", **kwargs)

Project(name="foo", **kwargs)

Set an entity's attribute (property or annotation) in memory.  Client first checks properties, then goes to annotations; (setting to NULL deletes it in R, using DEL operator in python deletes it)

TODO:  we want to include files and (for R) in memory objects

synAnnot(entity, name)<-value

entity.parentId="syn101"

synapse update id --parentId syn101

Gets an entity's attribute value (property or annotation) from the object already in memory.

synAnnot(entity, name); returns NULL if undefined

entity.name; throws exception if value is undefined

Create or update an entity (File, Folder, etc.) in Synapse.  May also specify (1) the list of entities 'used' to generate this one, (2) the list of entities 'executed' to generate this one, (3) the name of the generation activity, and (4) the description of the generation activity, (5) whether a name collision in an attempted 'create' should become an 'update', (6) whether to 'force' a new version to be created, and (7) whether the data is restricted (which will put a download 'lock' on the data and contact the Synapse Access and Compliance team for review.

TODO:  Give some examples.

synStore(entity, used=NULL, executed=NULL, activityName=NULL, activityDescription=NULL, createOrUpdate=T, forceVersion=T, isRestricted=F)

synStore(entity, activity=NULL, createOrUpdate=T, forceVersion=T, isRestricted=F)

synapse.store(entity, used, executed, activityName=None, activityDescription=None, createOrUpdate=True, forceVersion=True, isRestricted=False)

synapse.store(entity, activity, createOrUpdate=True, forceVersion=True, isRestricted=False)

synapse create --name NAME --parentid PARENTID --description DESCRIPTION

--type TYPE

--file PATH

--update=T/F

--forceVersion=T/F

--annotations={foo=bar, bar=foo}

Delete an object from Synapse.  In the case of entities, move to the trash can.

synDelete(id)

synDelete(object)

synapse.delete(synid), synapse.delete(entity), synapse.delete(wiki), synapse.delete(evaluation), synapse.delete(activity) ##TODO, synapse.delete(submission)

Get an entity (file, folder, etc.) from the Synapse server, with its attributes (properties, annotations) and, optionally, with its associated file(s).  ifcollision is one of "keep.both", "keep.local", or "overwrite.local", telling the system what to do if a different file is found at the given local file location.

'download' and 'load' are ignored for objects other than Files.  If a downloadLocation is not provided a default location is used.  Collisions with existing files are handled according to the 'ifcollision' parameter.  Note, 'downloadLocation' must be a directory.

synGet(id, version, downloadFile=T, downloadLocation=NULL, ifcollision="keep.both", load=F)

synapse.get(id, version, downloadFile=True, downloadLocation=None, ifcollision="keep.both")

synapse get ID -v NUMBER

Get the downloaded location of the file associated with a File object.

If synGet was called with download=FALSE, getFilePath() NULL.

getFileLocation(file)

getFileURL(file)

file.path

file.url

TODO

Open the web browser to the page for this entity.

onWeb(entityId) / onWeb(entity)

synapse.onweb(entityId) / synapse.onweb(entity)

synapse onweb id

log-in

If fields are omitted, then values are retrieved from the configuration file or from cached API keys.

synapseLogin(username = "", password = "", sessionToken = "", apiKey = "", rememberMe = False)

synapseLogin()

synapse.login(email=None, password=None, sessionToken=None, apiKey=None, rememberMe=False, silent=False)

synapse.login()

synapse login -u USER -p PASSWORD

log-out

localOnly=T delete any local copies of sessionToken or apiKey

localOnly=F: -> (1) if client has sessionToken, then call "DELETE /session"; (2) do the localOnly part

synapseLogout(localOnly=F)

synapse.logout(local=False, clearCache=False)

synapse logout

invalidate API key

invlidate API key

invalidateAPIKey()

invalidateAPIKey()