[SYNR-1527] synapser release for version 2.1.0 (#337)

* upgraded synapseclient version to v4.4.0 * updated R version and package dependencies * added/extended reference documents for both new and modified functions * updated Github action to reflect most recent compatible R versions * resolved infinite recursion issues and package building failures on Ubuntu and Windows * update package description and changelog
Sage-Bionetworks · Aug 14, 2024 · d093605 · d093605
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -1,3 +1,4 @@
+
 # build and test synapser. Additionally deploys to  S3 RAN server on GitHub release.
 
 name: build
@@ -28,14 +29,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-13, windows-2022]
-        r: [4.1.3, 4.2.3, 4.3.1]
+        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]
 
     steps:
       - name: checkout
         uses: actions/checkout@v4
 
       - name: Set up Python Version
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -137,6 +138,10 @@ jobs:
       - name: linux-build-package
         if: ${{runner.os == 'linux'}}
         run: |
+          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
+          Rscript -e "reticulate::install_miniconda()"
+          echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+          Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
           R CMD build ./
           R CMD INSTALL ./ --library=$R_LIBS_USER --no-test-load
 
@@ -145,7 +150,7 @@ jobs:
       - name: mac-build-package
         if: ${{runner.os == 'macOS'}}
         run: |
-            Rscript -e "install.packages(c('remotes', 'reticulate'))"
+            Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
             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'))"
@@ -158,6 +163,11 @@ jobs:
         if: ${{runner.os == 'Windows'}}
         shell: bash
         run: |
+          echo "options(repos = c(CRAN = 'https://cloud.r-project.org'))" >> .Rprofile
+          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
+          Rscript -e "reticulate::install_python(version = '3.10.11')"
+          Rscript -e "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')"
+          Rscript -e "reticulate::use_virtualenv('r-reticulate')"
           R CMD build ./
           R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load --no-multiarch
 
@@ -193,7 +203,7 @@ jobs:
           echo "UPLOAD_NAME=$UPLOAD_NAME" >> $GITHUB_ENV
 
       - name: upload-artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{env.UPLOAD_NAME}}
           path: ${{env.ARTIFACT_NAME}}
@@ -236,7 +246,7 @@ jobs:
           echo "deploy_target=$DEPLOY_TARGET" >> $GITHUB_OUTPUT
 
       - name: download-artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
         with:
           path: deploy_artifacts
@@ -278,7 +288,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-13]
-        r: [4.1.3, 4.2.3, 4.3.1]
+        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]
 
     runs-on: ${{ matrix.os }}
 
@@ -290,7 +300,14 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
-
+
+      - name: setup-r-dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-version: 2
+          architecture: 'x64'
+
       - name: check-install
         shell: bash
         run: |
@@ -299,8 +316,9 @@ jobs:
           PACKAGE="synapser"
           echo "if (available.packages(repos='$RAN')['$PACKAGE','Version'] != '$VERSION_TO_CHECK') { quit(save = 'no', status = 1) }" > test.R
           echo "try(remove.packages('$PACKAGE'), silent=T)" >> test.R
-          echo "install.packages('reticulate', repos=c('https://cloud.r-project.org/'))" >> test.R
-          echo "reticulate::virtualenv_create('r-reticulate')" >> test.R
+          echo "install.packages('remotes', repos = 'https://cloud.r-project.org'); remotes::install_version('reticulate', version = '1.28', repos = 'https://cloud.r-project.org')" >> test.R
+          echo "reticulate::install_python(version = '3.10.11')" >> test.R
+          echo "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')" >> test.R
           echo "reticulate::use_virtualenv('r-reticulate')" >> test.R
           echo "install.packages('$PACKAGE', repos=c('$RAN', 'https://cloud.r-project.org/'))" >> test.R
           echo "library('$PACKAGE')" >> test.R

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,26 +1,28 @@
 Package: synapser
 Type: Package
 Title: R Language Bindings for Synapse API
-Version: 2.0.0
-Date: 2022-01-18
+Version: 2.1.0
+Date: 2024-07-31
 Authors@R: c(
-  person("Tom", "Yu", role = c("cre"), email = "[email protected]"),
+  person("Dan", "Lu", role = c("aut", "cre"), email = "[email protected]"),
+  person("Tom", "Yu", role = c("aut"), email = "[email protected]"),
   person("Bruce", "Hoff", role = c("aut"), email = "[email protected]"),
   person("Sage Bionetworks", role = c("cph"))
   )
-Maintainer: Bruce Hoff <[email protected]>
 BugReports: https://github.com/Sage-Bionetworks/synapser/issues
 Description: Provides R language bindings for Synapse RESTful web services.
 Encoding: UTF-8
 License: Apache License 2.0
 Imports:
   reticulate(>= 1.25),
+  reticulate(<= 1.28),
   methods,
   rjson,
   stats,
   utils
 Depends:
-  R(>= 4.0)
+  R(>= 4.1.3),
+  R(< 4.5)
 Remotes:
   [email protected]
 Suggests: pack, R6, testthat, knitr, rmarkdown

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,35 @@
+## synapser 2.1.0
+
+### Improvements
+
+* Upgraded to the synapsePythonClient v4.4.0.
+* Now support R 4.4.1.
+* The data upload and download algorithm in synapsePythonClient have been revamped for enhanced stability, reliability, and performance.
+* Updated reference documents and code examples for both new and modified functions. 
+
+#### New Functions
+* `synCreateTeam` and `synDeleteTeam` have been added to manage team. 
+* `synRestGetAsync`, `synRestDeleteAsync`, `synRestPostAsync` and `synRestPutAsync` have been added to allow interaction with Synapse server utilizing [asynchronous](https://python-docs.synapse.org/reference/oop/models_async/) models.
+
+#### Minor behavior changes: 
+* Credentials passed by command line argument will now be evaluated before credentials stored in the `~/.synapseConfig` file.
+* Using syn123.version notation is now supported with `synGet` and `synSetProvenance`.
+* File entities will no longer have their version incremented during no-op changes. Only when file content, or fields on the file has been updated will a version number be incremented.
+* New parameters have been added to allow more features: 
+  + Defining the project alias used in project url is now supported in `Project`.
+  + Setting the annotations on the entity is now supported in `synStore`.
+  + The MD5 of the file can now be used when creating S3 file handle in `synCreateExternalS3FileHandle`. 
+
+
+For more changes, please view the [Release Notes](https://python-docs.synapse.org/news/) on the Python client documentation.
+
 ## 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.
+* `rememberMe` has been deprecated in `synLogin`. 
 * `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/).
 

diff --git a/R/table.R b/R/table.R
@@ -124,7 +124,7 @@
   df <- data.frame(
     Map(.convertToRType, list = df, synapseType = types),
     stringsAsFactors = F)
-
+  
   # The Map function mangles column names (which are in the Schema), so let's fix them
   colnames(df) <- .extractColumnNames(columnSchema)
   df
@@ -137,7 +137,7 @@
   df <- data.frame(
     Map(.convertToSynapseType, list = df, synapseType = types),
     stringsAsFactors = F)
-
+  
   # The Map function mangles column names (which are in the Schema), so let's fix them
   colnames(df) <- .extractColumnNames(columnSchema)
   df
@@ -181,4 +181,4 @@
   } else {
     .saveToCsv(values, file)
   }
-}
+}
diff --git a/R/zzz.R b/R/zzz.R
@@ -12,28 +12,28 @@
       # 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 <- '4.0.0'
+      PYTHON_CLIENT_VERSION <- '4.4.0'
       # 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("pandas>=1.5,<=2.0.3", "jinja2", "markupsafe","numpy<=1.24.4"))
       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.core.config.single_threaded = True")
-  reticulate::py_run_string("syn=synapseclient.Synapse(skip_checks=True)")
+  reticulate::py_run_string("syn=synapseclient.Synapse(skip_checks=True, debug=False)")
   # make syn available in the global environment
   syn <<- reticulate::py_eval("syn")
-
+  
   .addPythonAndFoldersToSysPath(system.file(package = "synapser"))
   .defineRPackageFunctions()
   # .defineOverloadFunctions() must come AFTER .defineRPackageFunctions()
   # because it redefines selected generic functions
   .defineOverloadFunctions()
-
+  
   # mute Python warnings
   reticulate::py_run_string("import warnings")
   reticulate::py_run_string("warnings.filterwarnings('ignore')")
@@ -57,7 +57,6 @@
                     assignEnumCallback = .assignEnumCallback,
                     functionFilter = .synapseClassFunctionFilter,
                     functionPrefix = "syn",
-                    transformReturnObject = .objectDefinitionHelper,
                     pySingletonName = "syn")
   # exposing all supporting classes except for Synapse itself and some selected classes.
   generateRWrappers(pyPkg = "synapseclient",
@@ -73,23 +72,25 @@
                     assignEnumCallback = .assignEnumCallback,
                     functionFilter = .cherryPickTableFunctionFilter,
                     classFilter = .removeAllClassesClassFilter,
-                    functionPrefix = "syn",
-                    transformReturnObject = .objectDefinitionHelper)
+                    functionPrefix = "syn")
 }
 
-.objectDefinitionHelper <- function(object) {
-  if (methods::is(object, "CsvFileTable")) {
-    # reading from csv
-    # Removed due to Error in unlockBinding("asDataFrame", object) : no binding for "asDataFrame"
-    # unlockBinding("asDataFrame", object)
-    object$asDataFrame <- function() {
-      .readCsvBasedOnSchema(object)
-    }
-    # Removed due to Error in lockBinding("asDataFrame", object) : no binding for "asDataFrame"
-    # lockBinding("asDataFrame", object)
-  }
-  object
-}
+# TODO: This section is removed since it causes the infinite recursion 
+# issue when reading downloaded entity to a dataframe. Revisit this
+# when deprecating PythonEmbedInR code
+# .objectDefinitionHelper <- function(object) {
+#   if (methods::is(object, "CsvFileTable")) {
+#     # reading from csv
+#     # Removed due to Error in unlockBinding("asDataFrame", object) : no binding for "asDataFrame"
+#     # unlockBinding("asDataFrame", object)
+#     object$asDataFrame <- function() {
+#       .readCsvBasedOnSchema(object)
+#     }
+#     # Removed due to Error in lockBinding("asDataFrame", object) : no binding for "asDataFrame"
+#     # lockBinding("asDataFrame", object)
+#   }
+#   object
+# }
 
 .onAttach <- function(libname, pkgname) {
   tou <- "\nTERMS OF USE NOTICE:
@@ -98,7 +99,7 @@
   2) Not discriminate, identify, or recontact individuals or groups represented by the data.
   3) Use and contribute only data de-identified to HIPAA standards.
   4) Redistribute data only under these same terms of use.\n"
-
+  
   .checkForUpdate()
   packageStartupMessage(tou)
 }
@@ -128,7 +129,7 @@
       Table(schema, file)
     }
   )
-
+  
   methods::setMethod(
     f = "synBuildTable",
     signature = c("ANY", "ANY", "data.frame"),
@@ -144,10 +145,10 @@
     f = "as.data.frame",
     signature = c(x = "CsvFileTable"),
     definition = function(x) {
-      x$asDataFrame()
+      .readCsvBasedOnSchema(x)
     }
   )
-
+  
   methods::setClass("GeneratorWrapper")
   methods::setMethod(
     f = "as.list",
@@ -156,19 +157,19 @@
       x$asList()
     }
   )
-
+  
   methods::setGeneric(
     name = "nextElem",
     def = function(x) {
       standardGeneric("nextElem")
     }
   )
-
+  
   methods::setMethod(
     f = "nextElem",
     signature = c(x = "GeneratorWrapper"),
     definition = function(x) {
       x$nextElem()
     }
   )
-}
+}
diff --git a/auto-man/Project-class.Rd b/auto-man/Project-class.Rd
@@ -18,13 +18,14 @@ Projects in Synapse must be uniquely named. Trying to create a project with a na
 
 Attributes:
     name: The name of the project
+    alias: The project alias for use in friendly project urls.
     properties: A map of Synapse properties
     annotations: A map of user defined annotations
     local_state: Internal use only
 }
 \section{Methods}{
 \itemize{
-\item \code{Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL)}: Constructor for \code{\link{Project}}
+\item \code{Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL, alias=NULL)}: Constructor for \code{\link{Project}}
 \item \code{local_state(state=NULL)}: Set or get the object's internal state, excluding properties, or annotations.\cr
 \cr
 Arguments:\cr

diff --git a/auto-man/Project.Rd b/auto-man/Project.Rd
@@ -17,18 +17,20 @@ Projects in Synapse must be uniquely named. Trying to create a project with a na
 
 Attributes:
     name: The name of the project
+    alias: The project alias for use in friendly project urls.
     properties: A map of Synapse properties
     annotations: A map of user defined annotations
     local_state: Internal use only
 }
 \usage{
-Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL)
+Project(name=NULL, properties=NULL, annotations=NULL, local_state=NULL, alias=NULL)
 }
 \arguments{
 \item{name}{}
 \item{properties}{}
 \item{annotations}{}
 \item{local_state}{}
+\item{alias}{}
 }
 \value{
 An object of type Project