Merge pull request #322 from Sage-Bionetworks/update-to-new-py-client

Upgrade to python client 3.0.0
Sage-Bionetworks · Oct 31, 2023 · ce5c1f2 · ce5c1f2
2 parents 8b2d310 + 701438e
commit ce5c1f2
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -28,11 +28,11 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-12, macos-13, windows-2022]
-        r: [4.1.3, 4.2.3, 4.3.0]
+        r: [4.1.3, 4.2.3, 4.3.1]
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: setup-r
         uses: r-lib/actions/setup-r@v2
@@ -120,8 +120,7 @@ jobs:
         shell: bash
         if: ${{runner.os == 'Windows'}}
         run: |
-          pip install pandas
-          pip install synapseclient
+          pip install 'synapseclient[pandas]'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -201,7 +200,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: check-deployment-target
         id: check-deployment-target
         if: ${{github.event.action == 'published'}}
@@ -234,7 +233,7 @@ jobs:
 
         # Before deoloying to RAN (which is an S3 bucket), authenticate to AWS using GitHub OIDC
       - name: Assume AWS Role
-        uses: aws-actions/configure-aws-credentials@v2
+        uses: aws-actions/configure-aws-credentials@v3
         with:
           aws-region: us-east-1
           role-to-assume: arn:aws:iam::325565585839:role/sagebase-github-oidc-sage-bionetworks-synapser
@@ -269,13 +268,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-12]
-        r: [4.1.3, 4.2.2]
+        r: [4.1.3, 4.2.2, 4.3.1]
 
     runs-on: ${{ matrix.os }}
 
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: setup-r
         uses: r-lib/actions/setup-r@v2

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: synapser
 Type: Package
 Title: R Language Bindings for Synapse API
-Version: 1.1.0
+Version: 1.2.0
 Date: 2022-01-18
 Authors@R: c(
   person("Bruce", "Hoff", role = c("aut", "cre"), email = "[email protected]"),
@@ -10,6 +10,7 @@ Authors@R: c(
 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),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+## synapser 1.2.0
+
+### Improvements
+
+* Python synapsePythonClient dependency updated to 3.0.0
+
 ## synapser 1.1.0
 
 ### Improvements

diff --git a/R/zzz.R b/R/zzz.R
@@ -12,7 +12,7 @@
       # 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 <- '2.7.2'
+      PYTHON_CLIENT_VERSION <- '3.0.0'
       reticulate::py_install(c("requests", "pandas", "pysftp", "jinja2", "markupsafe"))
       reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T)
       reticulate::py_run_string("import synapseclient")

diff --git a/auto-man/Column.Rd b/auto-man/Column.Rd
@@ -22,7 +22,7 @@ Column(id=NULL, columnType=NULL, maximumSize=NULL, maximumListLength=NULL, name=
 \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://docs.synapse.org/rest/org/sagebionetworks/repo/model/table/ColumnType.html\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

diff --git a/auto-man/DockerRepository-class.Rd b/auto-man/DockerRepository-class.Rd
@@ -16,7 +16,7 @@ A Docker repository is a lightweight virtual machine image.
 NOTE: store()-ing a DockerRepository created in the Python client will always result in it being treated as a
 reference to an external Docker repository that is not managed by synapse.
 To upload a docker image that is managed by Synapse please use the official Docker client and read
- http://docs.synapse.org/articles/docker.html for instructions on uploading a Docker Image to Synapse
+https://help.synapse.org/docs/Synapse-Docker-Registry.2011037752.html for instructions on uploading a Docker Image to Synapse
 }
 \section{Methods}{
 \itemize{

diff --git a/auto-man/DockerRepository.Rd b/auto-man/DockerRepository.Rd
@@ -15,22 +15,23 @@ A Docker repository is a lightweight virtual machine image.
 NOTE: store()-ing a DockerRepository created in the Python client will always result in it being treated as a
 reference to an external Docker repository that is not managed by synapse.
 To upload a docker image that is managed by Synapse please use the official Docker client and read
- http://docs.synapse.org/articles/docker.html for instructions on uploading a Docker Image to Synapse
+https://help.synapse.org/docs/Synapse-Docker-Registry.2011037752.html for instructions on uploading a Docker Image to Synapse
 }
 \usage{
 DockerRepository(repositoryName=NULL, parent=NULL, properties=NULL, annotations=NULL, local_state=NULL)
 }
 \arguments{
 \item{repositoryName}{ the name of the Docker Repository. Usually in the format: [host[:port]/]path.\cr
- If host is not set, it will default to that of DockerHub. port can only be specified if the host is also specified.\cr
+                       If host is not set, it will default to that of DockerHub. port can only be specified\cr
+                       if the host is also specified.\cr
 }
-\item{parent}{ the parent project for the Docker repository\cr
+\item{parent}{         the parent project for the Docker repository\cr
 }
-\item{properties}{      A map of Synapse properties\cr
+\item{properties}{     A map of Synapse properties\cr
 }
-\item{annotations}{     A map of user defined annotations\cr
+\item{annotations}{    A map of user defined annotations\cr
 }
-\item{local_state}{     Internal use only}
+\item{local_state}{    Internal use only}
 }
 \value{
 An object of type DockerRepository

diff --git a/auto-man/EntityViewSchema.Rd b/auto-man/EntityViewSchema.Rd
@@ -27,15 +27,7 @@ EntityViewSchema(name=NULL, columns=NULL, parent=NULL, scopes=NULL, type=NULL, i
 }
 \item{type}{                            This field is deprecated. Please use `includeEntityTypes`\cr
 }
-\item{includeEntityTypes}{              a list of entity types to include in the view. Supported entity types are:\cr
-                                            EntityViewType.FILE,\cr
-                                            EntityViewType.PROJECT,\cr
-                                            EntityViewType.TABLE,\cr
-                                            EntityViewType.FOLDER,\cr
-                                            EntityViewType.VIEW,\cr
-                                            EntityViewType.DOCKER\cr
-                                        If none is provided, the view will default to include EntityViewType.FILE.\cr
-}
+\item{includeEntityTypes}{              a list of entity types to include in the view. Supported entity types are:}
 \item{addDefaultViewColumns}{           If true, adds all default columns (e.g. name, createdOn, modifiedBy etc.)\cr
                                         Defaults to True.\cr
                                         The default columns will be added after a call to\cr

diff --git a/auto-man/File-class.Rd b/auto-man/File-class.Rd
@@ -14,7 +14,8 @@ File
 Represents a file in Synapse.
 
 When a File object is stored, the associated local file or its URL will be stored in Synapse. A File must have a
-path (or URL) and a parent.
+path (or URL) and a parent. By default, the name of the file in Synapse matches the filename, but by specifying
+the `name` attribute, the File Entity name can be different.
 }
 \section{Methods}{
 \itemize{

diff --git a/auto-man/File.Rd b/auto-man/File.Rd
@@ -13,7 +13,8 @@ Constructor for objects of type File
 Represents a file in Synapse.
 
 When a File object is stored, the associated local file or its URL will be stored in Synapse. A File must have a
-path (or URL) and a parent.
+path (or URL) and a parent. By default, the name of the file in Synapse matches the filename, but by specifying
+the `name` attribute, the File Entity name can be different.
 }
 \usage{
 File(path=NULL, parent=NULL, synapseStore=TRUE, properties=NULL, annotations=NULL, local_state=NULL, name=NULL, contentType=NULL, dataFileHandleId=NULL)
@@ -49,6 +50,7 @@ An object of type File
 
 \examples{
 %\dontrun{
+%    # The Entity name is derived from the path and is 'data.xyz'
 %    data = File('/path/to/file/data.xyz', parent=folder)
 %    data = syn.store(data)
 %}

diff --git a/auto-man/Row-class.Rd b/auto-man/Row-class.Rd
@@ -11,7 +11,7 @@ Row
 }
 \format{An R6 class object.}
 \description{
-A \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/table/Row.html}{row} in a Table.
+A \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/Row.html}{row} in a Table.
 }
 \section{Methods}{
 \itemize{

diff --git a/auto-man/Row.Rd b/auto-man/Row.Rd
@@ -10,7 +10,7 @@
 Constructor for objects of type Row
 }
 \description{
-A \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/table/Row.html}{row} in a Table.
+A \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/Row.html}{row} in a Table.
 }
 \usage{
 Row(values, rowId=NULL, versionNumber=NULL, etag=NULL)

diff --git a/auto-man/RowSet-class.Rd b/auto-man/RowSet-class.Rd
@@ -11,7 +11,7 @@ RowSet
 }
 \format{An R6 class object.}
 \description{
-A Synapse object of type \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/table/RowSet.html}{org.sagebionetworks.repo.model.table.RowSet    }.
+A Synapse object of type \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/RowSet.html}{org.sagebionetworks.repo.model.table.RowSet    }.
 }
 \section{Methods}{
 \itemize{

diff --git a/auto-man/RowSet.Rd b/auto-man/RowSet.Rd
@@ -10,7 +10,7 @@
 Constructor for objects of type RowSet
 }
 \description{
-A Synapse object of type \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/table/RowSet.html}{org.sagebionetworks.repo.model.table.RowSet    }.
+A Synapse object of type \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/RowSet.html}{org.sagebionetworks.repo.model.table.RowSet    }.
 }
 \usage{
 RowSet(columns=NULL, schema=NULL, headers=NULL, tableId=NULL, rows=NULL, etag=NULL)

diff --git a/auto-man/Team-class.Rd b/auto-man/Team-class.Rd
@@ -11,7 +11,7 @@ Team
 }
 \format{An R6 class object.}
 \description{
-Represents a \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/Team.html}{Synapse Team}.
+Represents a \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Team.html}{Synapse Team}.
 User definable fields are:
 }
 \section{Methods}{

diff --git a/auto-man/Team.Rd b/auto-man/Team.Rd
@@ -10,7 +10,7 @@
 Constructor for objects of type Team
 }
 \description{
-Represents a \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/model/Team.html}{Synapse Team}.
+Represents a \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/Team.html}{Synapse Team}.
 User definable fields are:
 }
 \usage{

diff --git a/auto-man/synGetAnnotations.Rd b/auto-man/synGetAnnotations.Rd
@@ -10,8 +10,10 @@
 synGetAnnotations
 }
 \description{
-.. deprecated:: 2.1.0
 deprecated and replaced with get_annotations
+
+.. deprecated:: 2.1.0
+   deprecated and replaced with get_annotations
 }
 \usage{
 synGetAnnotations(entity, version=NULL)

diff --git a/auto-man/synGetAvailableServices.Rd b/auto-man/synGetAvailableServices.Rd
@@ -0,0 +1,26 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{synGetAvailableServices}
+\alias{synGetAvailableServices}
+\docType{methods}
+\title{
+synGetAvailableServices
+}
+\description{
+Get available Synapse services
+This is a beta feature and is subject to change
+}
+\usage{
+synGetAvailableServices()
+}
+\arguments{
+
+}
+\value{
+
+}
+
+
diff --git a/auto-man/synGetMembershipStatus.Rd b/auto-man/synGetMembershipStatus.Rd
@@ -11,7 +11,7 @@ synGetMembershipStatus
 }
 \description{
 Retrieve a user's Team Membership Status bundle.
-https://docs.synapse.org/rest/GET/team/id/member/principalId/membershipStatus.html
+https://rest-docs.synapse.org/rest/GET/team/id/member/principalId/membershipStatus.html
 }
 \usage{
 synGetMembershipStatus(userid, team, user=NULL)

diff --git a/auto-man/synGetTeamOpenInvitations.Rd b/auto-man/synGetTeamOpenInvitations.Rd
@@ -11,7 +11,7 @@ synGetTeamOpenInvitations
 }
 \description{
 Retrieve the open requests submitted to a Team
-https://docs.synapse.org/rest/GET/team/id/openInvitation.html
+https://rest-docs.synapse.org/rest/GET/team/id/openInvitation.html
 }
 \usage{
 synGetTeamOpenInvitations(team)

diff --git a/auto-man/synIsSynapseId.Rd b/auto-man/synIsSynapseId.Rd
@@ -0,0 +1,25 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{synIsSynapseId}
+\alias{synIsSynapseId}
+\docType{methods}
+\title{
+synIsSynapseId
+}
+\description{
+Checks if given synID is valid (attached to actual entity?)
+}
+\usage{
+synIsSynapseId(syn_id)
+}
+\arguments{
+\item{syn_id}{}
+}
+\value{
+
+}
+
+
diff --git a/auto-man/synLogin.Rd b/auto-man/synLogin.Rd
@@ -12,13 +12,10 @@ synLogin
 \description{
 Valid combinations of login() arguments:
 
-- email/username and password (**WILL BE DEPRECATED**)
-
-- email/username and apiKey (Base64 encoded string) (**WILL BE DEPRECATED**)
-
-- authToken
-
-- sessionToken (**DEPRECATED**)
+    - email/username and password
+    - email/username and apiKey (Base64 encoded string)
+    - authToken
+    - sessionToken (**DEPRECATED**)
 
 If no login arguments are provided or only username is provided, login() will attempt to log in using
  information from these sources (in order of preference):

diff --git a/auto-man/synService.Rd b/auto-man/synService.Rd
@@ -0,0 +1,26 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{synService}
+\alias{synService}
+\docType{methods}
+\title{
+synService
+}
+\description{
+Get available Synapse services
+This is a beta feature and is subject to change
+}
+\usage{
+synService(service_name)
+}
+\arguments{
+\item{service_name}{}
+}
+\value{
+
+}
+
+
diff --git a/auto-man/synSetPermissions.Rd b/auto-man/synSetPermissions.Rd
@@ -19,7 +19,8 @@ synSetPermissions(entity, principalId=NULL, accessType=c("READ", "DOWNLOAD"), mo
 \arguments{
 \item{entity}{              An Entity or Synapse ID to modify\cr
 }
-\item{principalId}{         Identifier of a user or group\cr
+\item{principalId}{         Identifier of a user or group. '273948' is for all registered Synapse users\cr
+                            and '273949' is for public access.\cr
 }
 \item{accessType}{          Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE,\cr
                             DELETE, CHANGE_PERMISSIONS\cr
@@ -36,4 +37,12 @@ synSetPermissions(entity, principalId=NULL, accessType=c("READ", "DOWNLOAD"), mo
  an Access Control List object
 }
 
-
+ 
+\examples{
+%\dontrun{
+%    # Grant all registered users download access
+%    syn.setPermissions('syn1234','273948',['READ','DOWNLOAD'])
+%    # Grant the public view access
+%    syn.setPermissions('syn1234','273949',['READ'])
+%}
+}