Fix github actions and update to 2.0.0 synapser to use 4.0.0 python c…

…lient (#328) * Fix actions * Bump macos-13 * Setup python * Update actions * Pin version * Update to 2.0.0 * only use mac * Try to install miniconda * Add in remotes installation * Install remotes and reticulate * Install synapser and rebuild documentation * Update vignettes and authors * Add to news and fix markdown * Update test dockerfile * Add ubuntu and linux back in the mix * Revise and add in all documentation
Sage-Bionetworks · Feb 4, 2024 · 8ee91ce · 8ee91ce
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -27,14 +27,18 @@ jobs:
 
     strategy:
       matrix:
-        # os: [ubuntu-22.04, macos-12, macos-13, windows-2022]
         os: [ubuntu-22.04, macos-13, windows-2022]
         r: [4.1.3, 4.2.3, 4.3.1]
 
     steps:
       - name: checkout
         uses: actions/checkout@v4
 
+      - name: Set up Python Version
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
       - name: setup-r
         uses: r-lib/actions/setup-r@v2
         with:
@@ -92,8 +96,8 @@ jobs:
           echo "package_version=$PACKAGE_VERSION" >> $GITHUB_OUTPUT
           echo "r_minor_version=$R_MINOR_VERSION" >> $GITHUB_OUTPUT
 
-      - name: setup-r-mac-12
-        if: ${{matrix.os == 'macos-12'}}
+      - name: setup-r-mac-13
+        if: ${{matrix.os == 'macos-13'}}
         run: |
           R_LIBS_USER=${GITHUB_WORKSPACE}/R_LIBS
           rm -rf R_LIBS_USER
@@ -102,6 +106,7 @@ jobs:
 
           echo "R=R" >> $GITHUB_ENV
 
+
       - name: install-test-config
         shell: bash
         run: |
@@ -140,6 +145,10 @@ jobs:
       - name: mac-build-package
         if: ${{runner.os == 'macOS'}}
         run: |
+            Rscript -e "install.packages(c('remotes', 'reticulate'))"
+            Rscript -e "reticulate::install_miniconda()"
+            echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+            Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
             R CMD build ./
             R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,11 @@
 Package: synapser
 Type: Package
 Title: R Language Bindings for Synapse API
-Version: 1.3.0
+Version: 2.0.0
 Date: 2022-01-18
 Authors@R: c(
-  person("Bruce", "Hoff", role = c("aut", "cre"), email = "[email protected]"),
+  person("Tom", "Yu", role = c("cre"), email = "[email protected]"),
+  person("Bruce", "Hoff", role = c("aut"), email = "[email protected]"),
   person("Sage Bionetworks", role = c("cph"))
   )
 Maintainer: Bruce Hoff <[email protected]>

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+## synapser 2.0.0
+
+### 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.
+* For more changes, please view the 3.2.0 and 4.0.0 changes on the [Python client documentation](https://python-docs.synapse.org/news/).
+
 ## synapser 1.3.0
 
 ### Improvements

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
@@ -12,16 +12,17 @@
       # Ideally we would source tools/installPythonClient.R to not
       # have to duplicate the synapseclient install code
       # system2(paste("Rscript ", getwd(), "/tools/installPythonClient.R ", getwd(), sep=""))
-      PYTHON_CLIENT_VERSION <- '3.1.1'
-      reticulate::virtualenv_create('r-reticulate')
-      reticulate::use_virtualenv('r-reticulate')
+      PYTHON_CLIENT_VERSION <- '4.0.0'
+      # reticulate::virtualenv_create('r-reticulate')
+      # reticulate::use_virtualenv('r-reticulate')
       reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe"))
       reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
+      reticulate::py_run_string("import synapseclient")
     }
   )
 
   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