Install synapser and rebuild documentation

Sage-Bionetworks · Feb 4, 2024 · 83e45d1 · 83e45d1
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diff --git a/NEWS.md b/NEWS.md
@@ -3,6 +3,8 @@
 ### Improvements
 
 * Python synapsePythonClient dependency updated to 4.0.0
+* You can only login via a Synapse Personal Access token now.  All other forms of authentication have been disabled for security purposes.
+* `synSetAnnotations` removed as it is not working as expected due to implementation in the Python API.
 
 ## synapser 1.3.0
 

diff --git a/R/PythonPkgWrapperUtils.R b/R/PythonPkgWrapperUtils.R
@@ -265,7 +265,6 @@ getFunctionInfo <- function(pyPkg,
   }
   # scrub the nulls
   functionInfo <- removeNulls(functionInfo)
-
   functionContainerName <- module
   if (!is.null(pySingletonName)) {
     functionContainerName <- pySingletonName

diff --git a/R/shared.R b/R/shared.R
@@ -45,8 +45,7 @@
   "putACLURI",
   "keys",
   "has_key",
-  "set_annotations",
-  "get_annotations"
+  "set_annotations"
 )
 
 .synapseClientClassFilter <- function(x) {

diff --git a/R/zzz.R b/R/zzz.R
@@ -22,7 +22,7 @@
   )
 
   reticulate::py_run_string(sprintf("synapserVersion = 'synapser/%s' ", utils::packageVersion("synapser")))
-  reticulate::py_run_string("synapseclient.USER_AGENT['User-Agent'] = synapserVersion + synapseclient.USER_AGENT['User-Agent']")
+  reticulate::py_run_string("synapseclient.USER_AGENT['User-Agent'] = synapserVersion + ' '+ synapseclient.USER_AGENT['User-Agent']")
   reticulate::py_run_string("synapseclient.core.config.single_threaded = True")
   reticulate::py_run_string("syn=synapseclient.Synapse(skip_checks=True)")
   # make syn available in the global environment

diff --git a/auto-man/Activity-class.Rd b/auto-man/Activity-class.Rd
@@ -12,12 +12,25 @@ Activity
 \format{An R6 class object.}
 \description{
 Represents the provenance of a Synapse Entity.
+
+Parameters:
+    name: Name of the Activity
+    description: A short text description of the Activity
+    used: Either a list of:
+
+        - [reference objects](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Reference.html) (e.g. [{'targetId':'syn123456', 'targetVersionNumber':1}])
+        - a list of Synapse Entities or Entity IDs
+        - a list of URL's
+    executed: A code resource that was executed to generate the Entity.
+    data: A dictionary representation of an Activity, with fields 'name', 'description' and 'used' (a list of reference objects)
+
+See also: The [W3C's provenance ontology](http://www.w3.org/TR/prov-o/)
 }
 \section{Methods}{
 \itemize{
 \item \code{Activity(name=NULL, description=NULL, used=NULL, executed=NULL, data=list())}: Constructor for \code{\link{Activity}}
 \item \code{executed(target=NULL, targetVersion=NULL, url=NULL, name=NULL)}: Add a code resource that was executed during the activity.\cr
-See synapseclient.activity.Activity.used
+See [synapseclient.activity.Activity.used][]
 \item \code{used(target=NULL, targetVersion=NULL, wasExecuted=NULL, url=NULL, name=NULL)}: Add a resource used by the activity.\cr
 \cr
 This method tries to be as permissive as possible. It accepts a string which might be a synapse ID or a URL,\cr
@@ -31,26 +44,26 @@ It is an error to specify both target/targetVersion parameters and url/name para
 To add multiple UsedEntities and UsedURLs, make a separate call for each or pass in a list.\cr
 \cr
 In case of conflicting settings for wasExecuted both inside an object and with a parameter, the parameter wins.\cr
-For example, this UsedURL will have wasExecuted set to False::\cr
+For example, this UsedURL will have wasExecuted set to False:\cr
 \cr
     activity.used({'url':'http://google.com', 'name':'Goog', 'wasExecuted':True}, wasExecuted=False)\cr
 \cr
-Entity examples::\cr
+Entity examples:\cr
 \cr
     activity.used('syn12345')\cr
     activity.used(entity)\cr
     activity.used(target=entity, targetVersion=2)\cr
     activity.used(codeEntity, wasExecuted=True)\cr
     activity.used({'reference':{'target':'syn12345', 'targetVersion':1}, 'wasExecuted':False})\cr
 \cr
-URL examples::\cr
+URL examples:\cr
 \cr
     activity.used('http://mydomain.com/my/awesome/data.RData')\cr
     activity.used(url='http://mydomain.com/my/awesome/data.RData', name='Awesome Data')\cr
     activity.used(url='https://github.com/joe_hacker/code_repo', name='Gnarly hacks', wasExecuted=True)\cr
     activity.used({'url':'https://github.com/joe_hacker/code_repo', 'name':'Gnarly hacks'}, wasExecuted=True)\cr
 \cr
-List example::\cr
+List example:\cr
 \cr
     activity.used(['syn12345', 'syn23456', entity,                           {'reference':{'target':'syn100009', 'targetVersion':2}, 'wasExecuted':True},                           'http://mydomain.com/my/awesome/data.RData'])
 }

diff --git a/auto-man/Activity.Rd b/auto-man/Activity.Rd
@@ -11,20 +11,29 @@ Constructor for objects of type Activity
 }
 \description{
 Represents the provenance of a Synapse Entity.
+
+Parameters:
+    name: Name of the Activity
+    description: A short text description of the Activity
+    used: Either a list of:
+
+        - [reference objects](https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Reference.html) (e.g. [{'targetId':'syn123456', 'targetVersionNumber':1}])
+        - a list of Synapse Entities or Entity IDs
+        - a list of URL's
+    executed: A code resource that was executed to generate the Entity.
+    data: A dictionary representation of an Activity, with fields 'name', 'description' and 'used' (a list of reference objects)
+
+See also: The [W3C's provenance ontology](http://www.w3.org/TR/prov-o/)
 }
 \usage{
 Activity(name=NULL, description=NULL, used=NULL, executed=NULL, data=list())
 }
 \arguments{
-\item{name}{        name of the Activity\cr
-}
-\item{description}{ a short text description of the Activity\cr
-}
-\item{used}{        Either a list of:}
-\item{executed}{    A code resource that was executed to generate the Entity.\cr
-}
-\item{data}{        A dictionary representation of an Activity, with fields 'name', 'description' and 'used'\cr
-                    (a list of reference objects)}
+\item{name}{}
+\item{description}{}
+\item{used}{}
+\item{executed}{}
+\item{data}{}
 }
 \value{
 An object of type Activity

diff --git a/auto-man/Column-class.Rd b/auto-man/Column-class.Rd
@@ -11,12 +11,40 @@ Column
 }
 \format{An R6 class object.}
 \description{
-Defines a column to be used in a table Schema
-EntityViewSchema.
+Defines a column to be used in a table [Schema][synapseclient.table.Schema]
+[EntityViewSchema][synapseclient.table.EntityViewSchema].
+
+Attributes:
+    id:                An immutable ID issued by the platform
+    columnType:        The column type determines the type of data that can be stored in a column. It can be any
+                       of:
+
+        - `STRING`
+        - `DOUBLE`
+        - `INTEGER`
+        - `BOOLEAN`
+        - `DATE`
+        - `FILEHANDLEID`
+        - `ENTITYID`
+        - `LINK`
+        - `LARGETEXT`
+        - `USERID`
+
+        For more information, please see:
+        <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html>
+    maximumSize:       A parameter for columnTypes with a maximum size. For example, ColumnType.STRINGs have a
+                       default maximum size of 50 characters, but can be set to a `maximumSize` of 1 to 1000
+                       characters.
+    maximumListLength: Required if using a columnType with a "_LIST" suffix. Describes the maximum number of
+                       values that will appear in that list. Value range 1-100 inclusive. Default 100
+    name:              The display name of the column
+    enumValues:        Columns type of STRING can be constrained to an enumeration values set on this list.
+    defaultValue:      The default value for this column. Columns of type FILEHANDLEID and ENTITYID are not
+                       allowed to have default values.
 }
 \section{Methods}{
 \itemize{
-\item \code{Column(id=NULL, columnType=NULL, maximumSize=NULL, maximumListLength=NULL, name=NULL, enumValues=NULL, defaultValue=NULL)}: Constructor for \code{\link{Column}}
+\item \code{Column()}: Constructor for \code{\link{Column}}
 }
 }
 
diff --git a/auto-man/Column.Rd b/auto-man/Column.Rd
@@ -10,33 +10,42 @@
 Constructor for objects of type Column
 }
 \description{
-Defines a column to be used in a table Schema
-EntityViewSchema.
+Defines a column to be used in a table [Schema][synapseclient.table.Schema]
+[EntityViewSchema][synapseclient.table.EntityViewSchema].
+
+Attributes:
+    id:                An immutable ID issued by the platform
+    columnType:        The column type determines the type of data that can be stored in a column. It can be any
+                       of:
+
+        - `STRING`
+        - `DOUBLE`
+        - `INTEGER`
+        - `BOOLEAN`
+        - `DATE`
+        - `FILEHANDLEID`
+        - `ENTITYID`
+        - `LINK`
+        - `LARGETEXT`
+        - `USERID`
+
+        For more information, please see:
+        <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html>
+    maximumSize:       A parameter for columnTypes with a maximum size. For example, ColumnType.STRINGs have a
+                       default maximum size of 50 characters, but can be set to a `maximumSize` of 1 to 1000
+                       characters.
+    maximumListLength: Required if using a columnType with a "_LIST" suffix. Describes the maximum number of
+                       values that will appear in that list. Value range 1-100 inclusive. Default 100
+    name:              The display name of the column
+    enumValues:        Columns type of STRING can be constrained to an enumeration values set on this list.
+    defaultValue:      The default value for this column. Columns of type FILEHANDLEID and ENTITYID are not
+                       allowed to have default values.
 }
 \usage{
-Column(id=NULL, columnType=NULL, maximumSize=NULL, maximumListLength=NULL, name=NULL, enumValues=NULL, defaultValue=NULL)
+Column()
 }
 \arguments{
-\item{id}{optional named parameter:                   An immutable ID issued by the platform\cr
-}
-\item{columnType}{optional named parameter:         The column type determines the type of data that can be stored in a column. It can be any\cr
-                          of: "STRING", "DOUBLE", "INTEGER", "BOOLEAN", "DATE", "FILEHANDLEID", "ENTITYID", "LINK",\cr
-                          "LARGETEXT", "USERID". For more information, please see:\cr
-                          https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html\cr
-}
-\item{maximumSize}{optional named parameter:        A parameter for columnTypes with a maximum size. For example, ColumnType.STRINGs have a\cr
-                          default maximum size of 50 characters, but can be set to a maximumSize of 1 to 1000\cr
-                          characters.\cr
-}
-\item{maximumListLength}{optional named parameter:  Required if using a columnType with a "_LIST" suffix. Describes the maximum number of\cr
-                          values that will appear in that list. Value range 1-100 inclusive. Default 100\cr
-}
-\item{name}{optional named parameter:               The display name of the column\cr
-}
-\item{enumValues}{optional named parameter:         Columns type of STRING can be constrained to an enumeration values set on this list.\cr
-}
-\item{defaultValue}{optional named parameter:       The default value for this column. Columns of type FILEHANDLEID and ENTITYID are not\cr
-                          allowed to have default values.}
+
 }
 \value{
 An object of type Column

diff --git a/auto-man/Dataset-class.Rd b/auto-man/Dataset-class.Rd
@@ -11,24 +11,80 @@ Dataset
 }
 \format{An R6 class object.}
 \description{
-A Dataset is an Entity that defines a
+A Dataset is an [Entity][synapseclient.entity.Entity] that defines a
 flat list of entities as a tableview (a.k.a. a "dataset").
+
+Attributes:
+    name:          The name for the Dataset object
+    description:   User readable description of the schema
+    columns:       A list of [Column][synapseclient.table.Column] objects or their IDs
+    parent:        The Synapse Project to which this Dataset belongs
+    properties:    A map of Synapse properties
+    annotations:   A map of user defined annotations
+    dataset_items: A list of items characterized by entityId and versionNumber
+    folder:        A list of Folder IDs
+    local_state:   Internal use only
 }
 \section{Methods}{
 \itemize{
-\item \code{Dataset(name=NULL, columns=NULL, parent=NULL, properties=NULL, addDefaultViewColumns=TRUE, addAnnotationColumns=TRUE, ignoredAnnotationColumnNames=list(), annotations=NULL, local_state=NULL, dataset_items=NULL, folders=NULL, force=FALSE, description=NULL, folder=NULL)}: Constructor for \code{\link{Dataset}}
-\item \code{addColumn(column)}: 
-\item \code{addColumns(columns)}: 
-\item \code{add_folder(folder, force=TRUE)}: 
-\item \code{add_folders(folders, force=TRUE)}: 
-\item \code{add_item(dataset_item, force=TRUE)}: 
-\item \code{add_items(dataset_items, force=TRUE)}: 
-\item \code{add_scope(entities)}: 
+\item \code{Dataset(name=NULL, columns=NULL, parent=NULL, properties=NULL, addDefaultViewColumns=TRUE, addAnnotationColumns=TRUE, ignoredAnnotationColumnNames=list(), annotations=NULL, local_state=NULL, dataset_items=NULL, folders=NULL, force=FALSE)}: Constructor for \code{\link{Dataset}}
+\item \code{addColumn(column)}: Store the column\cr
+\cr
+Arguments:\cr
+    column: A column object or its ID\cr
+\cr
+Raises:\cr
+    ValueError: If the given column is not a string, integer or [Column][synapseclient.table.Column] object
+\item \code{addColumns(columns)}: Add columns\cr
+\cr
+Arguments:\cr
+    columns: A list of column objects or their ID
+\item \code{add_folder(folder, force=TRUE)}: Add a folder\cr
+\cr
+Arguments:\cr
+    folder: A single Synapse Folder ID\cr
+    force:  Force add items from folder
+\item \code{add_folders(folders, force=TRUE)}: Add folders\cr
+\cr
+Arguments:\cr
+    folders: A list of Synapse Folder IDs\cr
+    force:   Force add items from folders
+\item \code{add_item(dataset_item, force=TRUE)}: Add a dataset item\cr
+\cr
+Arguments:\cr
+    dataset_item: A single dataset item\cr
+    force:        Force add item\cr
+\cr
+Raises:\cr
+    ValueError: If duplicate item is found\cr
+    ValueError: The item is not a DatasetItem
+\item \code{add_items(dataset_items, force=TRUE)}: Add items\cr
+\cr
+Arguments:\cr
+    dataset_items: A list of dataset items\cr
+    force:         Force add items
+\item \code{add_scope(entities)}: Add scope\cr
+\cr
+Arguments:\cr
+    entities: A [Project][synapseclient.entity.Project], [Folder][synapseclient.entity.Folder],\cr
+              [Evaluation][synapseclient.evaluation.Evaluation] object or its ID, can also be a list of them
 \item \code{empty()}: 
 \item \code{has_columns()}: Does this schema have columns specified?
-\item \code{has_item(item_id)}: 
-\item \code{removeColumn(column)}: 
-\item \code{remove_item(item_id)}: 
+\item \code{has_item(item_id)}: Check if has dataset item\cr
+\cr
+Arguments:\cr
+    item_id: A single dataset item Synapse ID
+\item \code{removeColumn(column)}: Remove column\cr
+\cr
+Arguments:\cr
+    column: A column object or its ID\cr
+\cr
+Raises:\cr
+    ValueError: If the given column is not a string, integer or [Column][synapseclient.table.Column] object
+\item \code{remove_item(item_id)}: Remove item\cr
+\cr
+Arguments:\cr
+    item_id: A single dataset item Synapse ID
 }
 }