This is the specification of the command sets for Synapse clients. The goal is to align the command sets for clients in different languages to ease users' transitions between languages. Additionally we define the organization of the file cache so that various clients arrange local copies of file consistently.
| Command | comments | R Syntax | Python Syntax | Command Line Syntax |
|---|---|---|---|---|
| 1 – Basic Level | ||||
| 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. | The specified file doesn't move or get copied at this time. | File(path="/path/to/file", name="foo", parentId="syn101") | ||
| Create a Synapse file handle in memory which will be a serialized version of an in-memory object. | The object is not serialized at this time. (We are hoping people will like calling the object a File, even though it takes an in-memory object as a parameter.) | File(obj=<obj ref>, name="foo", parentId="syn101") | ||
| TODO: File which is a URL, not be uploaded to Synapse, just linked. | ||||
| Create a Synapse Record in memory, specifying the paths to one or more files in the local file system, the name in Synapse, and the Folder in Synapse. This step 'stages' a Record to be sent to Synapse. | Files aren't moved or copied at this time. TODO: Should the files instead be set like attributes, using synSet()? | Record(paths=list("path1", "path2"), name="foo", parentId="syn101") | Record(paths=list("path1", "path2"), name="foo", parentId="syn101") | |
| Create a Folder or Project in memory. | Folder(name="foo", parentId="syn101") Project(name="foo", parentId="syn101") | |||
| Set an entity's attribute (property or annotation) in memory. Client first checks properties, then goes to annotations; setting to NULL deletes it | synSet(entity, name)<-value | entity.parentId="syn101" | ||
| Gets an entity's attribute value (property or annotation) from the object already in memory. If value is not set then NULL is returned. | (TODO: Do we need an isSet(entity, name) method?) | synGetAnnotationOrProperty(entity, name) (We obviously need a better name here.) | entity.name | |
| Create or update an entity (File, Folder, etc.) in Synapse. May also specify (1) whether a name collision in an attempted 'create' should become an 'update', (2) whether to 'force' a new version to be created, (3) the list of entities 'used' to generate this one, (4) the list of entities 'executed' to generate this one, (5) the name of the generation activity, and (6) the description of the generation activity. | synStore(entity, used, executed, activityName=NULL, activityDescription=NULL, createOrUpdate=T, forceVersion=T) | |||
| Get an entity (file, folder, etc.) from the Synapse server, with its attributes (properties, annotations) and, optionally, with its associated file(s). | synGet(id, version, downloadFile=T, load=T) | synapse.get(id, version, downloadFile=True, load=True) | synapse get ID -v NUMBER | |
| synGet(entity, downloadFile=T, load=T) | ||||
| Add a file to a Record entity in memory. | TODO: Can this be combined with synSet(record, ...)? | synAdd(record)<-"path/to/file" | record.add("/path/to/file") | |
| Add an in-memory object to a Record entity. | TODO: Can this be combined with synSet(record, ...)? | synAdd(record)<-object | ||
| Open the web browser to the page for this entity. | onWeb(entityId) / onWeb(entity) | |||
| 2 – Power User Level | ||||
| Execute query | TODO: pagination, e.g. the function returns an iterator. Look at current implementation in R client. | synQuery(queryString) | ||
| we talked about this, but is it needed? | synGetEntity() | |||
| we talked about this, but is it needed? | synStoreEntity() | |||
| Delete an entity, and all of its children (e.g. all Folders and Files within a Folder). | synDelete() | |||
| Retrieve the wiki for an entity | TODO: Is it a requirement that we retrieve attachments? If not, do we retrieve file handles? | synGetWiki(id, version) / synGetWiki(entity) | ||
| synStoreWiki() | ||||
| synGetAnnotations() | ||||
| synSetAnnotations() | ||||
| synGetProperties() | ||||
| Access properties, throwing exception if property is not defined. | synSetProperties() | |||
| synGetAnnotation() | ||||
| synSetAnnotation() | ||||
| Access property, throwing exception if property is not defined. | synGetProperty() | |||
| Access property, throwing exception if property is not defined. Setting to NULL deletes. | synSetProperty() | |||
| Create an Activity (provenance object) in memory. | Activity(name, description, used, executed) | |||
| Create or update the Activity in Synapse | synStoreActivity(activity) | |||
| Get the Activity which generated the given entity. | synGetActivity(entity) / synGetActivity(entityId) | |||
| Set the Activity which generated the given entity | synSetActivity(entity)<-activity | |||
| 3 – Web API Level | ||||
| Execute GET request | synRestGET(endpoint, uri) | |||
| Execute POST request | synRestPOST(endpoint, uri, body) | |||
| Execute PUT request | synRestPUT(endpoint, uri, body) | |||
| Execute DELETE request | synRestDELETE(endpoint, uri) |
Cache Design Principles
The function and design principles of the client-side file cache need to be made explicit:
The client has a file cache on the local file system. When an File or Record entity is fetched, if its associated files are fetched then they go into the cache.
When a file is added to an entity and pushed to Synapse, the local copy does not move. Thus there is no guarantee that the local file associated with an entity be in the download cache. (The entity must keep a reference to the local file handle.) (The arguments for this principle are: Moving large files could be expensive with wasteful duplication; the file might be a script that the user is editing.)
The files in the cache may be modified. That is, the client may not assume that a file in the cache is identical to the one in Synapse, even if the entity's e-tag has not changed. (TODO: How DOES the client know a file has been modified? One way is to keep a copy of the md5 in memory upon synGet or synStore, and compare when storing again.)
TODO: When the client does synGet() and the associated file(s) is/are in the cache already, how does it know whether to download again? One way is to compute the local file(s) md5(s) and compare to those in Synapse.
TODO: What if you add a script to a FIle entity, synStore(), exit, restart and synGet()? You now have two copies of the file, one in the cache and the original elsewhere. The user would like to keep editing the original and, upon synStore(), update again. How does the client know to associate the original? One solution: Client keeps a map of <Syn FileHandle> -> <local location> which gets saved upon exit and loaded upon start-up and which 'overlays' or 'amends' the default cache mapping.
TODO: read a remote file, edit it, lose session, then repeat 'loadEntity', keep editing local file, push/store entity what should happen?
TODO: how can we download a folder hierarchy and have that hierarchy reflected in the system? One approach is to mimic the situation in which we upload a folder hierarchy, keeping pointers to files which are outside of the cache. I.e. we download the files into a folder hierarchy outside of the normal cache and keep in-memory pointers to those file locations. In this case Synapse would hold the "truth" about the hierarchy, so the user would not be allowed to move things around locally without messing up the cache.