Merge branch 'develop'

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: synapseClient
 Type: Package
 Title: Synapse R Client from Sage Bionetworks
-Version: 0.21
-ReleaseNotes: This version introduces the 'synapseExecute' function, which creates provenance records while running code.
-Date: 2013-03-20
+Version: 0.22
+ReleaseNotes: Upgrade for compliance with Synapse back-end.
+Date: 2013-04-01
 Author@R: c(
 	person("Bruce", "Hoff", email="[email protected]", role="aut"),
 	person("Chris", "Bare", email="[email protected]", role="aut"),

NAMESPACE

@@ -10,6 +10,13 @@ useDynLib(synapseClient)
 
 export(onWeb) ##,attach, detach)
 
+## public methods introduced with v 0.22, ...
+export(
+  File,
+  synGet,
+  synStore
+)
+
 ## S3 utility methods
 export(
   synapseResetEndpoints, 
@@ -33,7 +40,7 @@ export(
 export(as.environment.EnhancedEnvironment,as.environment.GlobalCache, as.list.SimplePropertyOwner, 
 as.list.SynapseAnnotations, as.list.TypedPropertyStore, as.environment.EnhancedEnvironment,
 length.EnhancedEnvironment, names.CachingObjectOwner, names.EnhancedEnvironment, names.LocationableWithoutBinaries,
-names.Locationable,FileEntity,getPackageName.EnhancedEnvironment, getPackageName.ArchiveOwner,
+names.Locationable,File,getPackageName.EnhancedEnvironment, getPackageName.ArchiveOwner,
   as.environment.ArchiveOwner, edit.Code, names.Entity,
 
   names.QueryResult,

R/AAAschema.R

@@ -60,8 +60,6 @@ defineEntityClass <-
 
   if("org.sagebionetworks.repo.model.Locationable" %in% implements) {
     contains <- "Locationable"
-  } else if ("org.sagebionetworks.repo.model.FileEntity" %in% implements) {
-    contains <- "FileEntity"
   } else{
     contains <- "Entity"
   }
@@ -75,6 +73,16 @@ defineEntityClass <-
       ),
       package=package
   )
+
+  # now add the new class to the list of defined ones
+  addToEntityTypeMap(className=name, jsonSchemaName=which)
+}
+
+addToEntityTypeMap<-function(className, jsonSchemaName) {
+  synapseEntityTypeMap<-.getCache("synapseEntityTypeMap")
+  if (is.null(synapseEntityTypeMap)) synapseEntityTypeMap<-list()
+  synapseEntityTypeMap[[jsonSchemaName]]<-className
+  .setCache("synapseEntityTypeMap", synapseEntityTypeMap)
 }
 
 defineEntityConstructors <-

R/AllClasses.R

@@ -6,7 +6,7 @@
 
 ##
 ## NOTE: this constructor is defined here because it is used in the definition of
-## the Entity, FileEntity and Locationable classes
+## the Entity and Locationable classes
 ##
 setGeneric(
   name = "SynapseProperties",
@@ -470,4 +470,3 @@ setRefClass(
         }
     )
 )
-

R/AllGenerics.R

@@ -5,11 +5,18 @@
 
 setGeneric(
   name="Activity",
-  def = function(activity, ...){
+  def = function(activity, ...) {
     standardGeneric("Activity")
   }
 )
 
+setGeneric(
+  name="File",
+  def = function(filePathParam, synapseStoreParam, ...) {
+    standardGeneric("File")
+  }
+)
+
 setGeneric(
   name = "cacheEntity",
   def = function(entity){
@@ -195,7 +202,6 @@ setGeneric(
   }
 )
 
-
 setGeneric(
   name = "deleteEntity",
   def = function(entity){
@@ -289,13 +295,6 @@ setGeneric(
   }
 )
 
-setGeneric(
-  name = "FileEntity",
-  def = function(entity){
-    standardGeneric("FileEntity")
-  }
-)
-
 setGeneric(
   name = "Code",
   def = function(entity, ...){
@@ -822,4 +821,3 @@ setGeneric(
   }
 )
 
-

R/AllMgetFileCache.R

@@ -25,10 +25,3 @@ setMethod(
   }
 )
 
-setMethod(
-  f = "getFileCache",
-  signature = signature("missing", "missing", "FileCacheFactory"),
-  definition = function(factory){
-    getFileCache(tempfile(), "load", factory)
-  }
-)

R/Entity.R

@@ -282,17 +282,19 @@ setMethod(
   }
 )
 
-setMethod(
-  f = "updateEntity",
-  signature = "Entity",
-  definition = function(entity)
+updateEntityMethod<-function(entity, forceVersion)
   {
     if(is.null(entity$properties$id))
       stop("entity ID was null so could not update. use createEntity instead.")
 
     annots <- entity@annotations
     updateUri<-entity$properties$uri
 
+    if (missing("forceVersion")) forceVersion=FALSE
+    if (forceVersion) {
+      updateUri <-sprintf("%s/version", updateUri)
+    }
+
     generatingActivity <- generatedBy(entity)
     if (!is.null(generatingActivity)) {
       generatingActivity <-storeEntity(generatingActivity)
@@ -324,8 +326,16 @@ setMethod(
     cacheEntity(ee)
 
     ee
-  }
+}
+
+setMethod(
+  f = "updateEntity",
+  signature = signature("Entity"),
+#  signature = signature("Entity", "missing"),
+  definition = function(entity) {updateEntityMethod(entity)}
 )
+
+
 
 setMethod(
   f = "downloadEntity",
@@ -375,17 +385,21 @@ setMethod(
   }
 )
 
+storeEntityMethod<-function(entity, forceVersion) {
+  if (missing("forceVersion")) forceVersion=FALSE
+  if (is.null(propertyValue(entity, "id"))) {
+    entity <- createEntity(entity)
+  }
+  else {
+    entity <- updateEntityMethod(entity, forceVersion)
+  }
+}
+
 setMethod(
   f = "storeEntity",
-  signature= "Entity",
-  definition = function(entity) {
-    if (is.null(propertyValue(entity, "id"))) {
-      entity <- createEntity(entity)
-    }
-    else {
-      entity <- updateEntity(entity)
-    }
-  }
+#  signature= signature("Entity", "missing"),
+  signature= signature("Entity"),
+  definition = function(entity){storeEntityMethod(entity)}
 )
 
 #####