From 26a6592dab535ce9574ea5ab70f6daa68c2484a9 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 19:17:33 -0700 Subject: [PATCH 1/7] Update to new python version --- R/zzz.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/zzz.R b/R/zzz.R index 28fe8121..ab55d54e 100644 --- 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") From 4b01a030bf0f49cd58ea4f6f41f5335d1eee63f7 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 21:15:08 -0700 Subject: [PATCH 2/7] Update python client --- DESCRIPTION | 1 + auto-man/Column.Rd | 2 +- auto-man/DockerRepository-class.Rd | 2 +- auto-man/DockerRepository.Rd | 13 +++++++------ auto-man/EntityViewSchema.Rd | 10 +--------- auto-man/File-class.Rd | 3 ++- auto-man/File.Rd | 4 +++- auto-man/Row-class.Rd | 2 +- auto-man/Row.Rd | 2 +- auto-man/RowSet-class.Rd | 2 +- auto-man/RowSet.Rd | 2 +- auto-man/Team-class.Rd | 2 +- auto-man/Team.Rd | 2 +- auto-man/synGetAnnotations.Rd | 4 +++- auto-man/synGetAvailableServices.Rd | 26 ++++++++++++++++++++++++++ auto-man/synGetMembershipStatus.Rd | 2 +- auto-man/synGetTeamOpenInvitations.Rd | 2 +- auto-man/synIsSynapseId.Rd | 25 +++++++++++++++++++++++++ auto-man/synLogin.Rd | 11 ++++------- auto-man/synService.Rd | 26 ++++++++++++++++++++++++++ auto-man/synSetPermissions.Rd | 13 +++++++++++-- auto-man/synTableQuery.Rd | 2 +- tools/installPythonClient.R | 4 ++-- 23 files changed, 122 insertions(+), 40 deletions(-) create mode 100644 auto-man/synGetAvailableServices.Rd create mode 100644 auto-man/synIsSynapseId.Rd create mode 100644 auto-man/synService.Rd diff --git a/DESCRIPTION b/DESCRIPTION index f7b64918..0cee4cdb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,6 +10,7 @@ Authors@R: c( Maintainer: Bruce Hoff 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/auto-man/Column.Rd b/auto-man/Column.Rd index 2a7189e2..b574e9a8 100644 --- 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 index 5ff3401c..d6c24bc7 100644 --- 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 index d2bdf3be..c97929ce 100644 --- 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 index 2897fa4c..17792d18 100644 --- 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 index 1928c8c8..e774ce73 100644 --- 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 index d1ea82fe..7fea385e 100644 --- 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 index f078938a..f3e2af83 100644 --- 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 index e757d3a4..2c2a38b3 100644 --- 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 index 0ee96186..a2e555f7 100644 --- 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 index 6b940706..0e1b9f8f 100644 --- 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 index b1be0728..2005a6ab 100644 --- 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 index 25edfe77..ae48a34a 100644 --- 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 index b05a6984..35aa6f4c 100644 --- 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 new file mode 100644 index 00000000..bf43b931 --- /dev/null +++ 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 index 5a84259f..2140ae12 100644 --- 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 index cb654264..779ce66b 100644 --- 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 new file mode 100644 index 00000000..db1e91ce --- /dev/null +++ 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 index 652ecb66..902ad19b 100644 --- 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 new file mode 100644 index 00000000..daac426e --- /dev/null +++ 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 index 676b8fad..e9b04ed0 100644 --- 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']) +%} +} diff --git a/auto-man/synTableQuery.Rd b/auto-man/synTableQuery.Rd index cb49b6de..3199ec80 100644 --- a/auto-man/synTableQuery.Rd +++ b/auto-man/synTableQuery.Rd @@ -16,7 +16,7 @@ Query a Synapse Table. synTableQuery(query, resultsAs=csv, offset=NULL, isConsistent=NULL, quoteCharacter=NULL, escapeCharacter=NULL, lineEnd=NULL, separator=NULL, header=NULL, includeRowIdAndRowVersion=NULL, downloadLocation=NULL) } \arguments{ -\item{query}{ query string in a \href{http://docs.synapse.org/rest/org/sagebionetworks/repo/web/controller/TableExamples.html}{SQL-like syntax }, for example\cr +\item{query}{ query string in a \href{https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/web/controller/TableExamples.html}{SQL-like syntax }, for example\cr "SELECT * from syn12345"} \item{resultsAs}{ select whether results are returned as a CSV file ("csv") or incrementally downloaded as\cr sets of rows ("rowset").} diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index a776104b..99d65f7c 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -5,7 +5,7 @@ # Author: bhoff ############################################################################### -PYTHON_CLIENT_VERSION <- '2.7.2' +PYTHON_CLIENT_VERSION <- '3.0.0' args <- commandArgs(trailingOnly = TRUE) baseDir<-args[1] @@ -17,5 +17,5 @@ print("*** Using Python Configuration:") reticulate::py_config() reticulate::py_run_string("import sys") reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python"))) -reticulate::py_install(c("requests<3", "pandas<1.5", "pysftp", "jinja2", "markupsafe")) +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) From f283e4a8f0d5f39175cb11b2b3aabdf167dad1d2 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 21:18:17 -0700 Subject: [PATCH 3/7] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0cee4cdb..683211f2 100644 --- 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 = "bruce.hoff@sagebase.org"), From 0e95be9f0cb41232c8b0afc0a3fb64e3bdbaf7b4 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 22:32:17 -0700 Subject: [PATCH 4/7] Add in R version to verify deployment --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 457c4806..9b3626ff 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -269,7 +269,7 @@ 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, 4.3.0] runs-on: ${{ matrix.os }} From aa2854be56e56d1c7ae6057944c2433cf73c0eb4 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 22:33:16 -0700 Subject: [PATCH 5/7] Update pip install --- .github/workflows/build.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9b3626ff..2fdd41ae 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -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: From 1223ea782b19e420601451560c82a8eae7e0d7c6 Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sat, 9 Sep 2023 22:52:47 -0700 Subject: [PATCH 6/7] Add in release changelog --- NEWS.md | 6 + docs/404.html | 2 +- docs/ISSUE_TEMPLATE.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/docker.html | 4 +- docs/articles/index.html | 2 +- docs/articles/manageSynapseCredentials.html | 4 +- docs/articles/synapser.html | 257 ++++++------------ docs/articles/systemDependencies.html | 4 +- docs/articles/tables.html | 16 +- docs/articles/troubleshooting.html | 89 +++++- docs/articles/upload.html | 4 +- docs/articles/views.html | 30 +- docs/authors.html | 6 +- docs/index.html | 28 +- docs/news/index.html | 16 +- docs/pkgdown.yml | 4 +- docs/reference/Activity-class.html | 2 +- docs/reference/Activity.html | 2 +- docs/reference/Column-class.html | 2 +- docs/reference/Column.html | 2 +- docs/reference/Dataset-class.html | 2 +- docs/reference/Dataset.html | 2 +- docs/reference/DockerRepository-class.html | 2 +- docs/reference/DockerRepository.html | 2 +- docs/reference/EntityViewSchema-class.html | 2 +- docs/reference/EntityViewSchema.html | 2 +- docs/reference/Evaluation-class.html | 2 +- docs/reference/Evaluation.html | 2 +- docs/reference/File-class.html | 2 +- docs/reference/File.html | 2 +- docs/reference/Folder-class.html | 2 +- docs/reference/Folder.html | 2 +- docs/reference/Link-class.html | 2 +- docs/reference/Link.html | 2 +- .../MaterializedViewSchema-class.html | 2 +- docs/reference/MaterializedViewSchema.html | 2 +- docs/reference/PartialRowset-class.html | 2 +- docs/reference/PartialRowset.html | 2 +- docs/reference/Project-class.html | 2 +- docs/reference/Project.html | 2 +- docs/reference/Row-class.html | 2 +- docs/reference/Row.html | 2 +- docs/reference/RowSet-class.html | 2 +- docs/reference/RowSet.html | 2 +- docs/reference/Schema-class.html | 2 +- docs/reference/Schema.html | 2 +- docs/reference/Submission-class.html | 2 +- docs/reference/Submission.html | 2 +- docs/reference/SubmissionStatus-class.html | 2 +- docs/reference/SubmissionStatus.html | 2 +- .../reference/SubmissionViewSchema-class.html | 2 +- docs/reference/SubmissionViewSchema.html | 2 +- docs/reference/Table.html | 2 +- docs/reference/Team-class.html | 2 +- docs/reference/Team.html | 2 +- docs/reference/TeamMember-class.html | 2 +- docs/reference/TeamMember.html | 2 +- docs/reference/UserGroupHeader-class.html | 2 +- docs/reference/UserGroupHeader.html | 2 +- docs/reference/UserProfile-class.html | 2 +- docs/reference/UserProfile.html | 2 +- docs/reference/Wiki-class.html | 2 +- docs/reference/Wiki.html | 2 +- docs/reference/as.list.html | 2 +- docs/reference/index.html | 6 +- docs/reference/nextElem.html | 2 +- docs/reference/synBuildTable.html | 2 +- docs/reference/synClearDownloadList.html | 2 +- docs/reference/synCreateColumn.html | 2 +- docs/reference/synCreateColumns.html | 2 +- .../synCreateExternalS3FileHandle.html | 2 +- .../reference/synCreateS3StorageLocation.html | 2 +- docs/reference/synCreateSnapshotVersion.html | 2 +- .../synCreateStorageLocationSetting.html | 2 +- docs/reference/synDelete.html | 2 +- docs/reference/synDeleteProvenance.html | 2 +- docs/reference/synDownloadTableColumns.html | 2 +- docs/reference/synFindEntityId.html | 2 +- docs/reference/synGet.html | 2 +- docs/reference/synGetAnnotations.html | 2 +- docs/reference/synGetChildren.html | 2 +- docs/reference/synGetColumn.html | 2 +- docs/reference/synGetColumns.html | 2 +- docs/reference/synGetConfigFile.html | 2 +- docs/reference/synGetDownloadList.html | 2 +- .../reference/synGetDownloadListManifest.html | 2 +- docs/reference/synGetEvaluation.html | 2 +- .../synGetEvaluationByContentSource.html | 2 +- docs/reference/synGetEvaluationByName.html | 2 +- docs/reference/synGetMembershipStatus.html | 2 +- .../synGetMyStorageLocationSetting.html | 2 +- docs/reference/synGetPermissions.html | 2 +- docs/reference/synGetProjectSetting.html | 2 +- docs/reference/synGetProvenance.html | 2 +- docs/reference/synGetStsStorageToken.html | 2 +- docs/reference/synGetSubmission.html | 2 +- docs/reference/synGetSubmissionBundles.html | 2 +- docs/reference/synGetSubmissionStatus.html | 2 +- docs/reference/synGetSubmissions.html | 2 +- docs/reference/synGetTableColumns.html | 2 +- docs/reference/synGetTeam.html | 2 +- docs/reference/synGetTeamMembers.html | 2 +- docs/reference/synGetTeamOpenInvitations.html | 2 +- docs/reference/synGetUserProfile.html | 2 +- docs/reference/synGetWiki.html | 2 +- docs/reference/synGetWikiAttachments.html | 2 +- docs/reference/synGetWikiHeaders.html | 2 +- docs/reference/synInvalidateAPIKey.html | 2 +- docs/reference/synInviteToTeam.html | 2 +- docs/reference/synIsCertified.html | 2 +- docs/reference/synLogin.html | 2 +- docs/reference/synLogout.html | 2 +- docs/reference/synMd5Query.html | 2 +- docs/reference/synMove.html | 2 +- docs/reference/synOnweb.html | 2 +- docs/reference/synPrintEntity.html | 2 +- docs/reference/synRemoveFromDownloadList.html | 2 +- docs/reference/synRestDELETE.html | 2 +- docs/reference/synRestGET.html | 2 +- docs/reference/synRestPOST.html | 2 +- docs/reference/synRestPUT.html | 2 +- .../synSendMembershipInvitation.html | 2 +- docs/reference/synSendMessage.html | 2 +- docs/reference/synSetAnnotations.html | 2 +- docs/reference/synSetEndpoints.html | 2 +- docs/reference/synSetPermissions.html | 2 +- docs/reference/synSetProvenance.html | 2 +- docs/reference/synSetStorageLocation.html | 2 +- docs/reference/synStore.html | 2 +- docs/reference/synSubmit.html | 2 +- docs/reference/synTableQuery.html | 2 +- docs/reference/synUpdateActivity.html | 2 +- docs/reference/synUploadFileHandle.html | 2 +- docs/reference/synapser-package.html | 2 +- 135 files changed, 370 insertions(+), 346 deletions(-) diff --git a/NEWS.md b/NEWS.md index 9c2f4bf2..7fce9caa 100644 --- 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/docs/404.html b/docs/404.html index f387370f..34bc5deb 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index a19f07c6..2d4d04cf 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5411cf91..1aad3d1e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/articles/docker.html b/docs/articles/docker.html index 1fcf9f09..e2b66100 100644 --- a/docs/articles/docker.html +++ b/docs/articles/docker.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.2.0 @@ -102,7 +102,7 @@

Docker

Bruce Hoff

-

2023-02-01

+

2023-09-09

Source: vignettes/docker.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 9b407ac2..af369750 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/articles/manageSynapseCredentials.html b/docs/articles/manageSynapseCredentials.html index dec6f0bf..1df32da3 100644 --- a/docs/articles/manageSynapseCredentials.html +++ b/docs/articles/manageSynapseCredentials.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.2.0 @@ -103,7 +103,7 @@

Manage Synapse Credentials

KimYen Ladia

-

2023-02-01

+

2023-09-09

Source: vignettes/manageSynapseCredentials.Rmd diff --git a/docs/articles/synapser.html b/docs/articles/synapser.html index fe9cff12..b8d84057 100644 --- a/docs/articles/synapser.html +++ b/docs/articles/synapser.html @@ -33,7 +33,7 @@ synapser - 1.0.0 + 1.2.0 @@ -102,7 +102,7 @@

Synapse R Client Overview

Bruce Hoff

-

2023-02-01

+

2023-09-09

Source: vignettes/synapser.Rmd @@ -218,7 +218,7 @@

Accessing DataView the entity’s metadata in the R console:

 print(fileEntity)
-## File(parentId='syn51038312', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpG52o0s/file156f930cb36ad', name='file156f930cb36ad', files=['file156f930cb36ad'], cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpG52o0s', etag='c22c30c1-ccb7-493b-a665-e5edeefa6fe1', concreteType='org.sagebionetworks.repo.model.FileEntity', createdOn='2023-02-02T02:15:24.818Z', dataFileHandleId='121216962', versionNumber=1, createdBy='3324230', modifiedOn='2023-02-02T02:15:24.974Z', modifiedBy='3324230', versionLabel='1', _file_handle={'id': '121216962', 'etag': 'db05364c-205e-460f-a79c-a679ca016da6', 'createdBy': '3324230', 'createdOn': '2023-02-02T02:15:25.000Z', 'modifiedOn': '2023-02-02T02:15:25.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'file156f930cb36ad', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/1c78e027-8a1a-49fc-832e-b927417b9e1f/file156f930cb36ad', 'isPreview': False, 'externalURL': None}, isLatestVersion=True, id='syn51038314', synapseStore=True)
+## File(name='filec7f2483a1da5', isLatestVersion=True, concreteType='org.sagebionetworks.repo.model.FileEntity', cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/Rtmp1fbwe6', modifiedOn='2023-09-10T05:47:56.465Z', versionLabel='1', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/Rtmp1fbwe6/filec7f2483a1da5', _file_handle={'id': '128471083', 'etag': '3c5bfff5-bca6-45f0-ab2e-aacad4b7c2d8', 'createdBy': '3324230', 'createdOn': '2023-09-10T05:47:56.000Z', 'modifiedOn': '2023-09-10T05:47:56.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'filec7f2483a1da5', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/f732db23-673e-4cd2-93fd-09561c8c485b/filec7f2483a1da5', 'isPreview': False, 'externalURL': None}, versionNumber=1, dataFileHandleId='128471083', createdOn='2023-09-10T05:47:56.272Z', id='syn52417540', modifiedBy='3324230', files=['filec7f2483a1da5'], etag='7750a89c-7606-4bcb-8e47-6c99da678425', createdBy='3324230', synapseStore=True, parentId='syn52417539')

This is one simple way to read in a small matrix (we load just the first few rows):

@@ -286,7 +286,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## [[1]]$id
-## [1] "syn51038316"
+## [1] "syn52417541"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -301,13 +301,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## [[1]]$createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T05:47:57.793Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T05:47:57.958Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -318,10 +318,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file156f930cb36ad"
+## [1] "filec7f2483a1da5"
 ## 
 ## [[2]]$id
-## [1] "syn51038314"
+## [1] "syn52417540"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -336,13 +336,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## [[2]]$createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T05:47:56.272Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T05:47:56.465Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -358,7 +358,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## [[1]]$id
-## [1] "syn51038316"
+## [1] "syn52417541"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -373,13 +373,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## [[1]]$createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T05:47:57.793Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T05:47:57.958Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -390,10 +390,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file156f930cb36ad"
+## [1] "filec7f2483a1da5"
 ## 
 ## [[2]]$id
-## [1] "syn51038314"
+## [1] "syn52417540"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -408,13 +408,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## [[2]]$createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T05:47:56.272Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T05:47:56.465Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -437,7 +437,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## $id
-## [1] "syn51038316"
+## [1] "syn52417541"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -452,13 +452,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## $createdOn
-## [1] "2023-02-02T02:15:25.912Z"
+## [1] "2023-09-10T05:47:57.793Z"
 ## 
 ## $modifiedOn
-## [1] "2023-02-02T02:15:26.070Z"
+## [1] "2023-09-10T05:47:57.958Z"
 ## 
 ## $createdBy
 ## [1] "3324230"
@@ -467,10 +467,10 @@ 
Organizing Data in a Project## [1] "3324230"
 ## 
 ## $name
-## [1] "file156f930cb36ad"
+## [1] "filec7f2483a1da5"
 ## 
 ## $id
-## [1] "syn51038314"
+## [1] "syn52417540"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -485,13 +485,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 51038312
+## [1] 52417539
 ## 
 ## $createdOn
-## [1] "2023-02-02T02:15:24.818Z"
+## [1] "2023-09-10T05:47:56.272Z"
 ## 
 ## $modifiedOn
-## [1] "2023-02-02T02:15:24.974Z"
+## [1] "2023-09-10T05:47:56.465Z"
 ## 
 ## $createdBy
 ## [1] "3324230"
@@ -524,7 +524,7 @@ 
Organizing Data in a Project= TRUE
 )
 ## Retrieving a deleted folder causes: Error in value[[3L]](cond): 404 Client Error: 
-## Entity syn51038316 is in trash can.
+## Entity syn52417541 is in trash can.

In addition to simple data storage, Synapse entities can be annotated with key/value metadata, described in markdown documents (wikis), and linked together in provenance graphs to create a reproducible record of @@ -574,91 +574,6 @@

Annotating Synapse Entities## [1] 42
-

Type Conversions -

-

The core of the Synapser library is the python client. Reticulate is used to -translate R to Python and back.

-

These are the documented conversions from R to Python: Reticulate -Type Conversions

-

NA values in R do not have a direct equivalent in -Python. This has been a topic of great discussion. Synapser is not -trying to solve this. NA values in R are handled by -Reticulate per the implementation defined in Reticulate.

-

When working with R and Reticulate, NA values in types tables are -converted by Reticulate depending on the data type.

-

For numeric data types, NA values are converted to the corresponding -R value NA_real_. For integer data types, NA values are -converted to NA_integer_. For logical data types, NA values -are converted to NA_logical_. For character data types, NA -values are converted to NA_character_.

-

In addition, Reticulate also converts any values that cannot be -coerced to the specified data type to NA_character_.

-

Reticulate performs these conversions automatically.

-

When Reticulate converts R objects to Python objects, the NA values -in R types tables are converted to Python’s None.

-

R’s NA is a logical constant of length 1 which is used -to represent the absence of a value. In Python, the equivalent of -NA is None, which is a special constant used -to indicate the absence of a value.

-

Reticulate automatically converts NA values in R types -tables to None when converting R objects to Python. This -ensures that the data types and values remain consistent between the two -languages.

-

Examples:

-
    -
  • Reticulate converts logical NAs to Python -True, which convert back to TRUE in R
    • -
-
-na_logical = NA
-class(na_logical)
-## [1] "logical"
-na_py <- reticulate::r_to_py(na_logical)
-na_py
-## True
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] TRUE
-
-na_logical = c(T, F, NA)
-class(na_logical)
-## [1] "logical"
-na_py <- reticulate::r_to_py(na_logical)
-na_py
-## [True, False, True]
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1]  TRUE FALSE  TRUE
-
    -
  • Reticulate converts character NAs to Python strings, -which convert back to characters in R
    • -
-
-na_char = c("T", "F", NA)
-class(na_char)
-## [1] "character"
-na_py <- reticulate::r_to_py(na_char)
-na_py
-## ['T', 'F', 'NA']
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] "T"  "F"  "NA"
-
    -
  • Reticulate converts numeric NAs to Python -np.nan, which convert back to NA in R
    • -
-
-na_num = c(1538006762583, 1538006762584, NA)
-class(na_num)
-## [1] "numeric"
-na_py <- reticulate::r_to_py(na_num)
-na_py
-## [1538006762583.0, 1538006762584.0, nan]
-na_r <- reticulate::py_to_r(na_py)
-na_r
-## [1] 1.538007e+12 1.538007e+12           NA
-
-

Provenance

Synapse provides tools for tracking ‘provenance’, or the @@ -672,7 +587,7 @@

Provenance

Creating an activity object:

-
+
 act <- Activity(
   name = "clustering",
   description = "whizzy clustering",
@@ -682,18 +597,18 @@ 
Creating an activity object:
+
 act <- Activity(name = "clustering", description = "whizzy clustering")
 act$used(c("syn12345", "syn12346"))
 act$executed("syn4567")

 
The used and executed can reference entities in Synapse or URLs.

 
Entity examples:

-
+
   act$used("syn12345")
   act$used(project)
   act$used(target = "syn12345", targetVersion = 2)

 
URL examples:

-
+
   act$used("http://mydomain.com/my/awesome/data.RData")
   act$used(url = "http://mydomain.com/my/awesome/data.RData", name = "Awesome Data")
   act$used(url = "https://github.com/joe_hacker/code_repo", name = "Gnarly hacks", wasExecuted = TRUE)

@@ -703,7 +618,7 @@ 
Storing entities with provenance
 
The activity can be passed in when storing an Entity to set the
 Entity’s provenance:

-
+
 project <- synGet(project$properties$id)
 project <- synStore(project, activity = act)

 
We’ve now recorded that ‘project’ is the output of syn4567 applied to
@@ -715,14 +630,14 @@ 
Recording data sourceThe synStore() has shortcuts for specifying the used and executed
 lists directly. For example, when storing a data entity, it’s a good
 idea to record its source:

-
+
 project <- synStore(
   project,
   activityName = "data-r-us",
   activityDescription = "downloaded from data-r-us",
   used = "http://data-r-us.com/excellent/data.xyz")

 
For more information:

-
+
 ?Activity
 ?synDeleteProvenance

 

@@ -741,7 +656,7 @@ 
Wikis
 folder, file, etc). Text and graphics can be composed in markdown and
 rendered in the web view of the object.

 
Creating a Wiki

-
+
 project <- synGet(project$properties$id)
 content <- "
 # My Wiki Page
@@ -760,7 +675,7 @@ 
Wikis
              attachments = list(filePath))
 wiki <- synStore(wiki)

 
Updating a Wiki

-
+
 project <- synGet(project$properties$id)
 wiki <- synGetWiki(project)
 wiki.markdown <- "
@@ -772,7 +687,7 @@ 
Wikis
 
 wiki <- synStore(wiki)

 
For more information:

-
+
 ?Wiki
 ?synGetWiki

 

@@ -783,7 +698,7 @@ 
Evaluations
+
 eval <- Evaluation(
   name = sprintf("My unique evaluation created on %s", format(Sys.time(), "%a %b %d %H%M%OS4 %Y")),
   description = "testing",
@@ -792,22 +707,22 @@ 
Evaluations= "This evaluation only accepts files.")
 eval <- synStore(eval)

 
Retrieving the created Evaluation:

-
+
 eval <- synGetEvaluation(eval$id)
 eval
 ## {
-##   "contentSource": "syn51038321",
-##   "createdOn": "2023-02-02T02:15:38.350Z",
+##   "contentSource": "syn52417544",
+##   "createdOn": "2023-09-10T05:48:12.566Z",
 ##   "description": "testing",
-##   "etag": "ba59943c-7633-41b0-b1c7-cf395a2d2690",
-##   "id": "9615299",
-##   "name": "My unique evaluation created on Wed Feb 01 181538.1668 2023",
+##   "etag": "1da8272d-5b79-4e7b-930d-457d33e5bc25",
+##   "id": "9615411",
+##   "name": "My unique evaluation created on Sat Sep 09 224812.3255 2023",
 ##   "ownerId": "3324230",
 ##   "submissionInstructionsMessage": "This evaluation only accepts files.",
 ##   "submissionReceiptMessage": "Thank you for your submission!"
 ## }

 
Submitting a file to an existing Evaluation:

-
+
 # first create a file to submit
 filePath <- tempfile()
 connection <- file(filePath)
@@ -818,7 +733,7 @@ 
Evaluations# submit the created file
 submission <- synSubmit(eval, file)

 
List submissions:

-
+
 submissions <- synGetSubmissionBundles(eval)
 as.list(submissions)
 ## [[1]]
@@ -826,60 +741,60 @@ 
Evaluations## {
 ##   "contributors": [
 ##     {
-##       "createdOn": "2023-02-02T02:15:40.563Z",
+##       "createdOn": "2023-09-10T05:48:15.051Z",
 ##       "principalId": "3324230"
 ##     }
 ##   ],
-##   "createdOn": "2023-02-02T02:15:40.563Z",
-##   "entityBundleJSON": "{\"entity\":{\"name\":\"file156f93dd15047\",\"id\":\"syn51038326\",\"etag\":\"144a593a-46fa-4cf9-80e7-a9eb272b462f\",\"createdOn\":\"2023-02-02T02:15:40.020Z\",\"modifiedOn\":\"2023-02-02T02:15:40.169Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn51038321\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"121216980\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn51038326\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"121216980\",\"etag\":\"ed105c86-869d-4acf-a84c-2adadb1d15b4\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-02-02T02:15:40.000Z\",\"modifiedOn\":\"2023-02-02T02:15:40.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"file156f93dd15047\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/3e54a923-1a7a-426f-b298-40fd6b05fd5a/file156f93dd15047\",\"isPreview\":false}]}",
-##   "entityId": "syn51038326",
-##   "evaluationId": "9615299",
-##   "id": "9731868",
-##   "name": "file156f93dd15047",
+##   "createdOn": "2023-09-10T05:48:15.051Z",
+##   "entityBundleJSON": "{\"entity\":{\"name\":\"filec7f27aac4a73\",\"id\":\"syn52417545\",\"etag\":\"71bc491e-27d6-46be-b8be-9fbe54d58147\",\"createdOn\":\"2023-09-10T05:48:14.427Z\",\"modifiedOn\":\"2023-09-10T05:48:14.608Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn52417544\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"128471088\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn52417545\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"128471088\",\"etag\":\"6cfb8c95-5ea1-45b8-876d-5706031f82a2\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-09-10T05:48:14.000Z\",\"modifiedOn\":\"2023-09-10T05:48:14.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"filec7f27aac4a73\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/4463b495-99fe-4e36-be89-c93ac80f7536/filec7f27aac4a73\",\"isPreview\":false}]}",
+##   "entityId": "syn52417545",
+##   "evaluationId": "9615411",
+##   "id": "9740522",
+##   "name": "filec7f27aac4a73",
 ##   "userId": "3324230",
 ##   "versionNumber": 1
 ## }
 ## 
 ## [[1]][[2]]
 ## {
-##   "entityId": "syn51038326",
-##   "etag": "0df85dea-16a7-41f1-8402-3ba8fc5df2d6",
-##   "id": "9731868",
-##   "modifiedOn": "2023-02-02T02:15:40.563Z",
+##   "entityId": "syn52417545",
+##   "etag": "afcbbcc4-c338-47bd-b8b9-60ba6de89ae8",
+##   "id": "9740522",
+##   "modifiedOn": "2023-09-10T05:48:15.051Z",
 ##   "status": "RECEIVED",
 ##   "statusVersion": 0,
 ##   "submissionAnnotations": {},
 ##   "versionNumber": 1
 ## }

 
Retrieving submission by id:

-
+
 
Retrieving the submission status:

-
+
 submissionStatus <- synGetSubmissionStatus(submission)
 submissionStatus
 ## {
-##   "entityId": "syn51038326",
-##   "etag": "0df85dea-16a7-41f1-8402-3ba8fc5df2d6",
-##   "id": "9731868",
-##   "modifiedOn": "2023-02-02T02:15:40.563Z",
+##   "entityId": "syn52417545",
+##   "etag": "afcbbcc4-c338-47bd-b8b9-60ba6de89ae8",
+##   "id": "9740522",
+##   "modifiedOn": "2023-09-10T05:48:15.051Z",
 ##   "status": "RECEIVED",
 ##   "statusVersion": 0,
 ##   "submissionAnnotations": {},
 ##   "versionNumber": 1
 ## }

 
To view the annotations:

-
+
 submissionStatus$submissionAnnotations
 ## {}

 
To update an annotation:

-
+
 submissionStatus$annotations["doubleAnnos"] <- list(c("rank" = 3))
 synStore(submissionStatus)

 
Query an evaluation:

-
+
 queryString <- sprintf("query=select * from evaluation_%s LIMIT %s OFFSET %s'", eval$id, 10, 0)
 synRestGET(paste("/evaluation/submission/query?", URLencode(queryString), sep = ""))
 ## $headers
@@ -892,7 +807,7 @@ 
Evaluations## [1] 0

 
To learn more about writing an evaluation query, please see: http://docs.synapse.org/rest/GET/evaluation/submission/query.html

 
For more information, please see:

-
+
 ?synGetEvaluation
 ?synSubmit
 ?synGetSubmissionBundles
@@ -906,48 +821,48 @@ 
Sharing Access to Content
 
Retrieve the sharing setting on an entity:

-
+
 synGetPermissions(project, principalId = 273950)
 ## list()

 
The first time an entity is shared, an ACL object is created for that
 entity. Let’s make project public:

-
+
 acl <- synSetPermissions(project, principalId = 273949, accessType = list("READ"))
 acl
 ## $id
-## [1] "syn51038321"
+## [1] "syn52417544"
 ## 
 ## $creationDate
-## [1] "2023-02-02T02:15:31.181Z"
+## [1] "2023-09-10T05:48:04.799Z"
 ## 
 ## $etag
-## [1] "45bf1411-d081-4b88-a89c-7378d27f7ca7"
+## [1] "683b80f2-d8e1-4d08-b0e3-3363b1bc1eec"
 ## 
 ## $resourceAccess
 ## $resourceAccess[[1]]
 ## $resourceAccess[[1]]$principalId
-## [1] 273949
+## [1] 3324230
 ## 
 ## $resourceAccess[[1]]$accessType
-## [1] "READ"
+## [1] "CREATE"             "UPDATE"             "MODERATE"          
+## [4] "CHANGE_PERMISSIONS" "DOWNLOAD"           "DELETE"            
+## [7] "CHANGE_SETTINGS"    "READ"              
 ## 
 ## 
 ## $resourceAccess[[2]]
 ## $resourceAccess[[2]]$principalId
-## [1] 3324230
+## [1] 273949
 ## 
 ## $resourceAccess[[2]]$accessType
-## [1] "DELETE"             "CHANGE_PERMISSIONS" "CREATE"            
-## [4] "MODERATE"           "UPDATE"             "DOWNLOAD"          
-## [7] "CHANGE_SETTINGS"    "READ"

+## [1] "READ"

 
Now public can read:

-
+
 synGetPermissions(project, principalId = 273950)
 ## list()

-
+
 ?synGetPermissions
 ?synSetPermissions

-
+
 synDelete(project)
 ## NULL

 

@@ -962,7 +877,7 @@ 
Accessing the API Directly
 
These methods enable access to the Synapse REST(ish) API taking care
 of details like endpoints and authentication. See the REST API documentation.

-
+
 ?synRestGET
 ?synRestPOST
 ?synRestPUT
diff --git a/docs/articles/systemDependencies.html b/docs/articles/systemDependencies.html
index 2a199d33..f1cda30f 100644
--- a/docs/articles/systemDependencies.html
+++ b/docs/articles/systemDependencies.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -103,7 +103,7 @@ 
System Dependencies

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/systemDependencies.Rmd
       
diff --git a/docs/articles/tables.html b/docs/articles/tables.html
index a69b933d..75f96292 100644
--- a/docs/articles/tables.html
+++ b/docs/articles/tables.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -102,7 +102,7 @@
       
Tables

                         
Bruce Hoff

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/tables.Rmd
       
@@ -154,7 +154,7 @@ 
Tables
 
 table <- synBuildTable("My Favorite Genes", project, genes)
 table$schema
-## Schema(concreteType='org.sagebionetworks.repo.model.table.TableEntity', columnIds=[], columns_to_store=[{'name': 'Name', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Chromosome', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Start', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'End', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Strand', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'TranscriptionFactor', 'columnType': 'BOOLEAN', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Time', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}], parentId='syn51038332', name='My Favorite Genes')

+## Schema(name='My Favorite Genes', parentId='syn52417546', columnIds=[], concreteType='org.sagebionetworks.repo.model.table.TableEntity', columns_to_store=[{'name': 'Name', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Chromosome', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Start', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'End', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Strand', 'columnType': 'STRING', 'maximumSize': 30, 'defaultValue': '', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'TranscriptionFactor', 'columnType': 'BOOLEAN', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}, {'name': 'Time', 'columnType': 'INTEGER', 'concreteType': 'org.sagebionetworks.repo.model.table.ColumnModel'}])

 
synBuildTable creates a Table Schema based on the data
 and returns a Table object that can be stored in Synapse using
 synStore(). To create a custom Table Schema, defines the
@@ -186,7 +186,7 @@ 
Tables
 
 
We now have a table populated with data. Let’s try to query:

 
-results <- synTableQuery(sprintf("select * from %s where Chromosome='1' and Start < 41000 and End > 20000", tableId))

+results <- synTableQuery(sprintf('select * from %s where Chromosome=1 and Start < 41000 and "End" > 20000', tableId))

 
synTableQuery() downloads the data and saves it to a csv
 file at location:

 
@@ -225,7 +225,7 @@ 
Changing Data= c(F, F),
   Time = as.POSIXlt(c("2070-01-12 03:53:12.169", "2018-05-03 12:03:33.464"), tz = "UTC", format = "%Y-%m-%d %H:%M:%OS"))
 synStore(Table(tableId, moreGenes))
-## <synapseclient.table.CsvFileTable object at 0x12babe740>

+## <synapseclient.table.CsvFileTable object at 0x11fef9cf0>

 
For example, let’s update the names of some of our favorite
 genes:

 
@@ -367,14 +367,14 @@ 
Notes on Dates and Timesdf <- as.data.frame(results)
 df$Time <- as.POSIXlt("2015-07-04 05:22", tz = "UTC", format = "%Y-%m-%d %H:%M")
 synStore(Table(tableId, moreGenes))
-## <synapseclient.table.CsvFileTable object at 0x12bb405b0>

+## <synapseclient.table.CsvFileTable object at 0x11ff40d90>

 
Dates may also be submitted in timestamp milliseconds:

 
 results <- synTableQuery(sprintf("select * from %s where Name='zap'", tableId))
 df <- as.data.frame(results)
 df$Time <- timestamp
 synStore(Table(tableId, moreGenes))
-## <synapseclient.table.CsvFileTable object at 0x12bb42140>

+## <synapseclient.table.CsvFileTable object at 0x11fefb7f0>

 
Note that using POSIXlt is strongly preferred over
 POSIXct, because POSIXct does not store values
 with enough precision to reliably recover milliseconds. For more
@@ -419,7 +419,7 @@ 
Table Attached Files# get the filehandle ids
 fileHandleIds <- lapply(files, function(f) f$id)
 newData["covers"] <- fileHandleIds
-## Warning in `[<-.data.frame`(`*tmp*`, "covers", value = list("121215793", :
+## Warning in `[<-.data.frame`(`*tmp*`, "covers", value = list("128470754", :
 ## provided 4 variables to replace 1 variables
 
 newTable <- synStore(Table(newSchema$properties$id, newData))

diff --git a/docs/articles/troubleshooting.html b/docs/articles/troubleshooting.html
index 7409bc0e..a00185eb 100644
--- a/docs/articles/troubleshooting.html
+++ b/docs/articles/troubleshooting.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -103,7 +103,7 @@ 
Troubleshooting

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/troubleshooting.Rmd
       
@@ -152,6 +152,91 @@ 
Using Synapser with reticulateSynapse
 Python client through reticulate.

 

+

+
Type Conversions
+

+
The core of the Synapser library is the python client. Reticulate is used to
+translate R to Python and back.

+
These are the documented conversions from R to Python: Reticulate
+Type Conversions

+
NA values in R do not have a direct equivalent in
+Python. This has been a topic of great discussion. Synapser is not
+trying to solve this. NA values in R are handled by
+Reticulate per the implementation defined in Reticulate.

+
When working with R and Reticulate, NA values in types tables are
+converted by Reticulate depending on the data type.

+
For numeric data types, NA values are converted to the corresponding
+R value NA_real_. For integer data types, NA values are
+converted to NA_integer_. For logical data types, NA values
+are converted to NA_logical_. For character data types, NA
+values are converted to NA_character_.

+
In addition, Reticulate also converts any values that cannot be
+coerced to the specified data type to NA_character_.

+
Reticulate performs these conversions automatically.

+
When Reticulate converts R objects to Python objects, the NA values
+in R types tables are converted to Python’s None.

+
R’s NA is a logical constant of length 1 which is used
+to represent the absence of a value. In Python, the equivalent of
+NA is None, which is a special constant used
+to indicate the absence of a value.

+
Reticulate automatically converts NA values in R types
+tables to None when converting R objects to Python. This
+ensures that the data types and values remain consistent between the two
+languages.

+
Examples:

+
    
+
  • Reticulate converts logical NAs to Python
+True, which convert back to TRUE in R
    • 
+

+
+na_logical = NA
+class(na_logical)
+## [1] "logical"
+na_py <- reticulate::r_to_py(na_logical)
+na_py
+## True
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] TRUE

+
+na_logical = c(T, F, NA)
+class(na_logical)
+## [1] "logical"
+na_py <- reticulate::r_to_py(na_logical)
+na_py
+## [True, False, True]
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1]  TRUE FALSE  TRUE

+
    
+
  • Reticulate converts character NAs to Python strings,
+which convert back to characters in R
    • 
+

+
+na_char = c("T", "F", NA)
+class(na_char)
+## [1] "character"
+na_py <- reticulate::r_to_py(na_char)
+na_py
+## ['T', 'F', 'NA']
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] "T"  "F"  "NA"

+
    
+
  • Reticulate converts numeric NAs to Python
+np.nan, which convert back to NA in R
    • 
+

+
+na_num = c(1538006762583, 1538006762584, NA)
+class(na_num)
+## [1] "numeric"
+na_py <- reticulate::r_to_py(na_num)
+na_py
+## [1538006762583.0, 1538006762584.0, nan]
+na_r <- reticulate::py_to_r(na_py)
+na_r
+## [1] 1.538007e+12 1.538007e+12           NA

+

 

   

 
diff --git a/docs/articles/upload.html b/docs/articles/upload.html
index 2405c00f..8892254a 100644
--- a/docs/articles/upload.html
+++ b/docs/articles/upload.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -103,7 +103,7 @@ 
File Upload

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/upload.Rmd
       
diff --git a/docs/articles/views.html b/docs/articles/views.html
index f9bdd3ce..e076efa1 100644
--- a/docs/articles/views.html
+++ b/docs/articles/views.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -103,7 +103,7 @@ 
Views

                         
KimYen
 Ladia

             
-            
2023-02-01

+            
2023-09-09

       
       Source: vignettes/views.Rmd
       
@@ -200,26 +200,26 @@ 
Views
 data <- as.data.frame(queryResults)
 data
 ##     ROW_ID ROW_VERSION                             ROW_ETAG          id
-## 1 51038357           1 31ff56cb-b476-4d8d-bb74-4a14d7ace68f syn51038357
-## 2 51038358           1 56d0f16e-e8ef-4293-9eb0-ba65001f0fdc syn51038358
-##                name description           createdOn createdBy
-## 1 file1583932d4a572          NA 2023-02-01 18:17:17   3324230
-## 2 file1583926b9f970          NA 2023-02-01 18:17:19   3324230
+## 1 52417553           1 2c0d0dde-f636-400e-b2d6-5a580f067d7b syn52417553
+## 2 52417554           1 7780b686-11cf-4710-b10d-a133dc52eb17 syn52417554
+##               name description           createdOn createdBy
+## 1  fileca573a99ef5          NA 2023-09-09 22:50:02   3324230
+## 2 fileca577502e8b3          NA 2023-09-09 22:50:04   3324230
 ##                                   etag          modifiedOn modifiedBy type
-## 1 31ff56cb-b476-4d8d-bb74-4a14d7ace68f 2023-02-01 18:17:19    3324230 file
-## 2 56d0f16e-e8ef-4293-9eb0-ba65001f0fdc 2023-02-01 18:17:20    3324230 file
+## 1 2c0d0dde-f636-400e-b2d6-5a580f067d7b 2023-09-09 22:50:04    3324230 file
+## 2 7780b686-11cf-4710-b10d-a133dc52eb17 2023-09-09 22:50:05    3324230 file
 ##   currentVersion    parentId benefactorId   projectId dataFileHandleId
-## 1              1 syn51038356  syn51038356 syn51038356        121217064
-## 2              1 syn51038356  syn51038356 syn51038356        121217065
+## 1              1 syn52417552  syn52417552 syn52417552        128471119
+## 2              1 syn52417552  syn52417552 syn52417552        128471120
 ##   dataFileSizeBytes                   dataFileMD5Hex
 ## 1                37 47dfe7f5eaa49a5413c7b79b67ab9c43
 ## 2                38 ba01e01b9e3ffea3ebef95efa62998b0
 ##                               dataFileConcreteType        dataFileBucket
 ## 1 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
 ## 2 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org
-##                                                      dataFileKey contributor
-## 1 3324230/094122c1-804d-4d5b-84dd-301746556a10/file1583932d4a572        Sage
-## 2 3324230/600e1433-6618-43ae-8970-cfc24033608a/file1583926b9f970          UW
+##                                                     dataFileKey contributor
+## 1  3324230/cce86a31-47f3-43f3-b666-3d6c0be4094c/fileca573a99ef5        Sage
+## 2 3324230/de3ad42c-f235-4bae-b294-0a23e91799dc/fileca577502e8b3          UW
 ##   class rank
 ## 1     V   NA
 ## 2    NA    X

@@ -246,7 +246,7 @@ 
Updating Annotations using View
 data$contributor[1] <- c("Sage Bionetworks")
 synStore(Table(view$properties$id, data[1,]))
-## <synapseclient.table.CsvFileTable object at 0x1134a1270>

+## <synapseclient.table.CsvFileTable object at 0x115009390>

 

 

 
Update View’s Content
diff --git a/docs/authors.html b/docs/authors.html
index daaac20b..d63da6f2 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -98,13 +98,13 @@ 
Citation

 
     
Hoff B (2023).
 synapser: R Language Bindings for Synapse API.
-R package version 1.0.0, https://www.synapse.org. 
+R package version 1.2.0, https://www.synapse.org. 
 

     
@Manual{,
   title = {synapser: R Language Bindings for Synapse API},
   author = {Bruce Hoff},
   year = {2023},
-  note = {R package version 1.0.0},
+  note = {R package version 1.2.0},
   url = {https://www.synapse.org},
 }

 
diff --git a/docs/index.html b/docs/index.html
index 48844361..68b99a3b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
       
     

 
@@ -174,7 +174,7 @@ 
On Windows
python --version

+
python --version

 
 
  • Note If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.
    • 
 
@@ -185,17 +185,17 @@ 
    On macOS
 
  • 
 
    Both python 2x and 3x can stay installed in a MAC. Mac comes with python 2x version. To check the default python version in your MAC, open the terminal and type
    
-
    python --version
-python3 --version
    
+
    python --version
+python3 --version
    
 
    • 
 
  • If you don’t then go ahead and install it with the installer. Go the the python’s official site here.
    • 
 
  • 
 
    Now restart the terminal and check again with both commands python —version
    
-
    python3 --version
    
+
    python3 --version
    
 
    • 
 
  • 
 
    Or use to install last version
    
-
    brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python
    
+
    brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python
    
 
    • 
 
 
    
@@ -205,29 +205,29 @@ 
    On Linux
 
  • 
 
    Add the repository and update
    
-
    sudo add-apt-repository ppa:deadsnakes/ppa
-sudo apt-get update
    
+
    sudo add-apt-repository ppa:deadsnakes/ppa
+sudo apt-get update
    
 
    • 
 
  • 
 
    Update the package list
    
-
    apt-get update
    
+
    apt-get update
    
 
    • 
 
  • 
 
    Verify the updated Python packages list
    
-
    apt list | grep python3.10
    
+
    apt list | grep python3.10
    
 
    • 
 
  • 
 
    Install the Python 3.10 package using apt-get
    
-
    sudo apt-get install python3.10
    
+
    sudo apt-get install python3.10
    
 
    • 
 
  • 
 
    Add Python 3.8 & Python 3.10 to update-alternatives
    
-
    sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
-sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2
    
+
    sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
+sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2
    
 
    • 
 
  • 
 
    Update Python 3 for point to Python 3.10
    
-
    sudo update-alternatives --config python3
    
+
    sudo update-alternatives --config python3
    
 
    • 
 
 
    
diff --git a/docs/news/index.html b/docs/news/index.html
index 69138517..93b59ff6 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       
       
         synapser
-        1.0.0
+        1.2.0
    @@ -78,6 +78,20 @@

    Changelog

    Source: NEWS.md
    +
    +

    synapser 1.2.0

    +
    +

    Improvements

    +
    • Python synapsePythonClient dependency updated to 3.0.0
      • +
    +
    +
    +

    synapser 1.1.0

    +
    +

    Improvements

    +
    • Python synapsePythonClient dependency updated to 2.7.2
      • +
    +

    synapser 1.0.0

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 278a3317..ed8ca41d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.19.2 +pandoc: 3.1.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -10,5 +10,5 @@ articles: troubleshooting: troubleshooting.html upload: upload.html views: views.html -last_built: 2023-02-02T02:14Z +last_built: 2023-09-10T05:47Z diff --git a/docs/reference/Activity-class.html b/docs/reference/Activity-class.html index e4b79f01..2c1016f4 100644 --- a/docs/reference/Activity-class.html +++ b/docs/reference/Activity-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0
    diff --git a/docs/reference/Activity.html b/docs/reference/Activity.html index 13376aaa..3708f4fc 100644 --- a/docs/reference/Activity.html +++ b/docs/reference/Activity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0
    diff --git a/docs/reference/Column-class.html b/docs/reference/Column-class.html index ec830991..e02d5ebc 100644 --- a/docs/reference/Column-class.html +++ b/docs/reference/Column-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Column.html b/docs/reference/Column.html index 9e6a8533..9bffd746 100644 --- a/docs/reference/Column.html +++ b/docs/reference/Column.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Dataset-class.html b/docs/reference/Dataset-class.html index 49948172..42c7de6c 100644 --- a/docs/reference/Dataset-class.html +++ b/docs/reference/Dataset-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Dataset.html b/docs/reference/Dataset.html index ac2afe69..f033a590 100644 --- a/docs/reference/Dataset.html +++ b/docs/reference/Dataset.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/DockerRepository-class.html b/docs/reference/DockerRepository-class.html index 3218ac16..34154c13 100644 --- a/docs/reference/DockerRepository-class.html +++ b/docs/reference/DockerRepository-class.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/DockerRepository.html b/docs/reference/DockerRepository.html index 932860d8..abb6070a 100644 --- a/docs/reference/DockerRepository.html +++ b/docs/reference/DockerRepository.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/EntityViewSchema-class.html b/docs/reference/EntityViewSchema-class.html index b685454d..4971e146 100644 --- a/docs/reference/EntityViewSchema-class.html +++ b/docs/reference/EntityViewSchema-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/EntityViewSchema.html b/docs/reference/EntityViewSchema.html index c5556f7c..0af502b5 100644 --- a/docs/reference/EntityViewSchema.html +++ b/docs/reference/EntityViewSchema.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Evaluation-class.html b/docs/reference/Evaluation-class.html index 2022e847..9f8d1182 100644 --- a/docs/reference/Evaluation-class.html +++ b/docs/reference/Evaluation-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Evaluation.html b/docs/reference/Evaluation.html index 698f095e..0459e946 100644 --- a/docs/reference/Evaluation.html +++ b/docs/reference/Evaluation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/File-class.html b/docs/reference/File-class.html index 9e091b03..054c5199 100644 --- a/docs/reference/File-class.html +++ b/docs/reference/File-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/File.html b/docs/reference/File.html index ab78af40..374bb0c5 100644 --- a/docs/reference/File.html +++ b/docs/reference/File.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Folder-class.html b/docs/reference/Folder-class.html index c1528651..4de4aefb 100644 --- a/docs/reference/Folder-class.html +++ b/docs/reference/Folder-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Folder.html b/docs/reference/Folder.html index 32015ce0..16493151 100644 --- a/docs/reference/Folder.html +++ b/docs/reference/Folder.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Link-class.html b/docs/reference/Link-class.html index bec06a9d..02373f10 100644 --- a/docs/reference/Link-class.html +++ b/docs/reference/Link-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Link.html b/docs/reference/Link.html index b455763a..2403007f 100644 --- a/docs/reference/Link.html +++ b/docs/reference/Link.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/MaterializedViewSchema-class.html b/docs/reference/MaterializedViewSchema-class.html index 478a379c..866ed9b1 100644 --- a/docs/reference/MaterializedViewSchema-class.html +++ b/docs/reference/MaterializedViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/MaterializedViewSchema.html b/docs/reference/MaterializedViewSchema.html index ebf56413..9ed5d38a 100644 --- a/docs/reference/MaterializedViewSchema.html +++ b/docs/reference/MaterializedViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/PartialRowset-class.html b/docs/reference/PartialRowset-class.html index f938ad85..9e7401a7 100644 --- a/docs/reference/PartialRowset-class.html +++ b/docs/reference/PartialRowset-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/PartialRowset.html b/docs/reference/PartialRowset.html index 6ca9ed98..97ed53bc 100644 --- a/docs/reference/PartialRowset.html +++ b/docs/reference/PartialRowset.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Project-class.html b/docs/reference/Project-class.html index 89a22a62..adb86728 100644 --- a/docs/reference/Project-class.html +++ b/docs/reference/Project-class.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Project.html b/docs/reference/Project.html index 24f3967a..8a5332a7 100644 --- a/docs/reference/Project.html +++ b/docs/reference/Project.html @@ -19,7 +19,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Row-class.html b/docs/reference/Row-class.html index 4a010004..d7e1e55e 100644 --- a/docs/reference/Row-class.html +++ b/docs/reference/Row-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Row.html b/docs/reference/Row.html index 6a44103a..d327c5c2 100644 --- a/docs/reference/Row.html +++ b/docs/reference/Row.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/RowSet-class.html b/docs/reference/RowSet-class.html index 02be4049..e2d901e2 100644 --- a/docs/reference/RowSet-class.html +++ b/docs/reference/RowSet-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/RowSet.html b/docs/reference/RowSet.html index b6fb3f39..9d03cbe7 100644 --- a/docs/reference/RowSet.html +++ b/docs/reference/RowSet.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Schema-class.html b/docs/reference/Schema-class.html index 0a93b3aa..0547bf6a 100644 --- a/docs/reference/Schema-class.html +++ b/docs/reference/Schema-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Schema.html b/docs/reference/Schema.html index a236e62e..dfbc6ea8 100644 --- a/docs/reference/Schema.html +++ b/docs/reference/Schema.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Submission-class.html b/docs/reference/Submission-class.html index 0bd0baf2..a0fe7149 100644 --- a/docs/reference/Submission-class.html +++ b/docs/reference/Submission-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Submission.html b/docs/reference/Submission.html index 475ccd0e..f43a0a56 100644 --- a/docs/reference/Submission.html +++ b/docs/reference/Submission.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/SubmissionStatus-class.html b/docs/reference/SubmissionStatus-class.html index 9a2810b3..39bbce40 100644 --- a/docs/reference/SubmissionStatus-class.html +++ b/docs/reference/SubmissionStatus-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/SubmissionStatus.html b/docs/reference/SubmissionStatus.html index 50fb81fb..9a937016 100644 --- a/docs/reference/SubmissionStatus.html +++ b/docs/reference/SubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/SubmissionViewSchema-class.html b/docs/reference/SubmissionViewSchema-class.html index c7bd4a79..3beb5539 100644 --- a/docs/reference/SubmissionViewSchema-class.html +++ b/docs/reference/SubmissionViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/SubmissionViewSchema.html b/docs/reference/SubmissionViewSchema.html index 7d8a0b11..b0316314 100644 --- a/docs/reference/SubmissionViewSchema.html +++ b/docs/reference/SubmissionViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Table.html b/docs/reference/Table.html index 5cbbb641..1c693594 100644 --- a/docs/reference/Table.html +++ b/docs/reference/Table.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Team-class.html b/docs/reference/Team-class.html index 500afc21..573b191e 100644 --- a/docs/reference/Team-class.html +++ b/docs/reference/Team-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Team.html b/docs/reference/Team.html index 1ed208a5..22e14d53 100644 --- a/docs/reference/Team.html +++ b/docs/reference/Team.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/TeamMember-class.html b/docs/reference/TeamMember-class.html index 9b1f9861..faf9f99f 100644 --- a/docs/reference/TeamMember-class.html +++ b/docs/reference/TeamMember-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/TeamMember.html b/docs/reference/TeamMember.html index 22992a15..48c16c9b 100644 --- a/docs/reference/TeamMember.html +++ b/docs/reference/TeamMember.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/UserGroupHeader-class.html b/docs/reference/UserGroupHeader-class.html index f25f02c7..3d2ed336 100644 --- a/docs/reference/UserGroupHeader-class.html +++ b/docs/reference/UserGroupHeader-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/UserGroupHeader.html b/docs/reference/UserGroupHeader.html index 4e1c9ba1..967427fb 100644 --- a/docs/reference/UserGroupHeader.html +++ b/docs/reference/UserGroupHeader.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/UserProfile-class.html b/docs/reference/UserProfile-class.html index cd99c82f..5391bfde 100644 --- a/docs/reference/UserProfile-class.html +++ b/docs/reference/UserProfile-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/UserProfile.html b/docs/reference/UserProfile.html index 84e22870..9c5ae24c 100644 --- a/docs/reference/UserProfile.html +++ b/docs/reference/UserProfile.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Wiki-class.html b/docs/reference/Wiki-class.html index ace95fde..6678c6e9 100644 --- a/docs/reference/Wiki-class.html +++ b/docs/reference/Wiki-class.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/Wiki.html b/docs/reference/Wiki.html index 56181211..e1c89296 100644 --- a/docs/reference/Wiki.html +++ b/docs/reference/Wiki.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/as.list.html b/docs/reference/as.list.html index 4f74f1ba..d9b14059 100644 --- a/docs/reference/as.list.html +++ b/docs/reference/as.list.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index d57d6ec7..c8c22584 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 @@ -273,6 +273,10 @@

    All functions as.list()

    as.list

    + +

    generateRWrappers()

    + +

    Generate R wrappers for Python classes and functions

    nextElem()

    diff --git a/docs/reference/nextElem.html b/docs/reference/nextElem.html index dcb02284..4c5a775f 100644 --- a/docs/reference/nextElem.html +++ b/docs/reference/nextElem.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synBuildTable.html b/docs/reference/synBuildTable.html index 0f573332..cc07f99d 100644 --- a/docs/reference/synBuildTable.html +++ b/docs/reference/synBuildTable.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synClearDownloadList.html b/docs/reference/synClearDownloadList.html index 0d8bf3fe..ae44d5cc 100644 --- a/docs/reference/synClearDownloadList.html +++ b/docs/reference/synClearDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateColumn.html b/docs/reference/synCreateColumn.html index 786f8f33..46df0290 100644 --- a/docs/reference/synCreateColumn.html +++ b/docs/reference/synCreateColumn.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateColumns.html b/docs/reference/synCreateColumns.html index 00990157..edeba87c 100644 --- a/docs/reference/synCreateColumns.html +++ b/docs/reference/synCreateColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateExternalS3FileHandle.html b/docs/reference/synCreateExternalS3FileHandle.html index c8edca6a..3b74784c 100644 --- a/docs/reference/synCreateExternalS3FileHandle.html +++ b/docs/reference/synCreateExternalS3FileHandle.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateS3StorageLocation.html b/docs/reference/synCreateS3StorageLocation.html index 077cc998..25969f3e 100644 --- a/docs/reference/synCreateS3StorageLocation.html +++ b/docs/reference/synCreateS3StorageLocation.html @@ -21,7 +21,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateSnapshotVersion.html b/docs/reference/synCreateSnapshotVersion.html index dc1a2c5e..0bf8dc3a 100644 --- a/docs/reference/synCreateSnapshotVersion.html +++ b/docs/reference/synCreateSnapshotVersion.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synCreateStorageLocationSetting.html b/docs/reference/synCreateStorageLocationSetting.html index 4dbbe640..081dd77b 100644 --- a/docs/reference/synCreateStorageLocationSetting.html +++ b/docs/reference/synCreateStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synDelete.html b/docs/reference/synDelete.html index dcc93024..6336ded9 100644 --- a/docs/reference/synDelete.html +++ b/docs/reference/synDelete.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synDeleteProvenance.html b/docs/reference/synDeleteProvenance.html index 08567dd9..93bd6dd0 100644 --- a/docs/reference/synDeleteProvenance.html +++ b/docs/reference/synDeleteProvenance.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synDownloadTableColumns.html b/docs/reference/synDownloadTableColumns.html index 5c1d1521..21ce5f48 100644 --- a/docs/reference/synDownloadTableColumns.html +++ b/docs/reference/synDownloadTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synFindEntityId.html b/docs/reference/synFindEntityId.html index babda132..97089e14 100644 --- a/docs/reference/synFindEntityId.html +++ b/docs/reference/synFindEntityId.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGet.html b/docs/reference/synGet.html index 2a8e89f7..d34cbf18 100644 --- a/docs/reference/synGet.html +++ b/docs/reference/synGet.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetAnnotations.html b/docs/reference/synGetAnnotations.html index 3bd067e5..fdbf58bd 100644 --- a/docs/reference/synGetAnnotations.html +++ b/docs/reference/synGetAnnotations.html @@ -20,7 +20,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetChildren.html b/docs/reference/synGetChildren.html index aeafb19c..942d7368 100644 --- a/docs/reference/synGetChildren.html +++ b/docs/reference/synGetChildren.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetColumn.html b/docs/reference/synGetColumn.html index 937f72e4..e0ff631a 100644 --- a/docs/reference/synGetColumn.html +++ b/docs/reference/synGetColumn.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetColumns.html b/docs/reference/synGetColumns.html index af760f45..21ff0d23 100644 --- a/docs/reference/synGetColumns.html +++ b/docs/reference/synGetColumns.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetConfigFile.html b/docs/reference/synGetConfigFile.html index 28240c35..d0dc6ad3 100644 --- a/docs/reference/synGetConfigFile.html +++ b/docs/reference/synGetConfigFile.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetDownloadList.html b/docs/reference/synGetDownloadList.html index 95756c14..132540a8 100644 --- a/docs/reference/synGetDownloadList.html +++ b/docs/reference/synGetDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetDownloadListManifest.html b/docs/reference/synGetDownloadListManifest.html index 8e897f11..50c88549 100644 --- a/docs/reference/synGetDownloadListManifest.html +++ b/docs/reference/synGetDownloadListManifest.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluation.html b/docs/reference/synGetEvaluation.html index 08f2a609..ff72cd87 100644 --- a/docs/reference/synGetEvaluation.html +++ b/docs/reference/synGetEvaluation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluationByContentSource.html b/docs/reference/synGetEvaluationByContentSource.html index 74c10882..4dd816e3 100644 --- a/docs/reference/synGetEvaluationByContentSource.html +++ b/docs/reference/synGetEvaluationByContentSource.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluationByName.html b/docs/reference/synGetEvaluationByName.html index 6c8a91d5..4ecd74e1 100644 --- a/docs/reference/synGetEvaluationByName.html +++ b/docs/reference/synGetEvaluationByName.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetMembershipStatus.html b/docs/reference/synGetMembershipStatus.html index cd81d52d..63a4c662 100644 --- a/docs/reference/synGetMembershipStatus.html +++ b/docs/reference/synGetMembershipStatus.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetMyStorageLocationSetting.html b/docs/reference/synGetMyStorageLocationSetting.html index aa639afd..54c3cee6 100644 --- a/docs/reference/synGetMyStorageLocationSetting.html +++ b/docs/reference/synGetMyStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetPermissions.html b/docs/reference/synGetPermissions.html index 45ff3bb5..144ddb52 100644 --- a/docs/reference/synGetPermissions.html +++ b/docs/reference/synGetPermissions.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetProjectSetting.html b/docs/reference/synGetProjectSetting.html index 09b2ae7b..7611c224 100644 --- a/docs/reference/synGetProjectSetting.html +++ b/docs/reference/synGetProjectSetting.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetProvenance.html b/docs/reference/synGetProvenance.html index fbe0f738..8e4aa76a 100644 --- a/docs/reference/synGetProvenance.html +++ b/docs/reference/synGetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetStsStorageToken.html b/docs/reference/synGetStsStorageToken.html index cf5e76ab..b32611a0 100644 --- a/docs/reference/synGetStsStorageToken.html +++ b/docs/reference/synGetStsStorageToken.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetSubmission.html b/docs/reference/synGetSubmission.html index 37fa62c8..7833ba8d 100644 --- a/docs/reference/synGetSubmission.html +++ b/docs/reference/synGetSubmission.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissionBundles.html b/docs/reference/synGetSubmissionBundles.html index d443563b..768d30ea 100644 --- a/docs/reference/synGetSubmissionBundles.html +++ b/docs/reference/synGetSubmissionBundles.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissionStatus.html b/docs/reference/synGetSubmissionStatus.html index 5b91077c..69767797 100644 --- a/docs/reference/synGetSubmissionStatus.html +++ b/docs/reference/synGetSubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissions.html b/docs/reference/synGetSubmissions.html index 807a44e0..53d42c9c 100644 --- a/docs/reference/synGetSubmissions.html +++ b/docs/reference/synGetSubmissions.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetTableColumns.html b/docs/reference/synGetTableColumns.html index a328036b..180d1fd6 100644 --- a/docs/reference/synGetTableColumns.html +++ b/docs/reference/synGetTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetTeam.html b/docs/reference/synGetTeam.html index 96a632e9..0051cfa4 100644 --- a/docs/reference/synGetTeam.html +++ b/docs/reference/synGetTeam.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetTeamMembers.html b/docs/reference/synGetTeamMembers.html index 8325209c..904199f0 100644 --- a/docs/reference/synGetTeamMembers.html +++ b/docs/reference/synGetTeamMembers.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetTeamOpenInvitations.html b/docs/reference/synGetTeamOpenInvitations.html index 69eb3dc1..0f70fb96 100644 --- a/docs/reference/synGetTeamOpenInvitations.html +++ b/docs/reference/synGetTeamOpenInvitations.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetUserProfile.html b/docs/reference/synGetUserProfile.html index 61b715b2..c0aae181 100644 --- a/docs/reference/synGetUserProfile.html +++ b/docs/reference/synGetUserProfile.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetWiki.html b/docs/reference/synGetWiki.html index e1bcbae6..3c6bf586 100644 --- a/docs/reference/synGetWiki.html +++ b/docs/reference/synGetWiki.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetWikiAttachments.html b/docs/reference/synGetWikiAttachments.html index 8dfd2c7a..8fa725ee 100644 --- a/docs/reference/synGetWikiAttachments.html +++ b/docs/reference/synGetWikiAttachments.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synGetWikiHeaders.html b/docs/reference/synGetWikiHeaders.html index 1aed301c..939be639 100644 --- a/docs/reference/synGetWikiHeaders.html +++ b/docs/reference/synGetWikiHeaders.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synInvalidateAPIKey.html b/docs/reference/synInvalidateAPIKey.html index d974e1c2..ed7424f9 100644 --- a/docs/reference/synInvalidateAPIKey.html +++ b/docs/reference/synInvalidateAPIKey.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synInviteToTeam.html b/docs/reference/synInviteToTeam.html index bd359d07..5fbef550 100644 --- a/docs/reference/synInviteToTeam.html +++ b/docs/reference/synInviteToTeam.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synIsCertified.html b/docs/reference/synIsCertified.html index 44b095ab..331c648c 100644 --- a/docs/reference/synIsCertified.html +++ b/docs/reference/synIsCertified.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synLogin.html b/docs/reference/synLogin.html index 3c4cfc6f..7ad2ff8b 100644 --- a/docs/reference/synLogin.html +++ b/docs/reference/synLogin.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synLogout.html b/docs/reference/synLogout.html index 00847b5c..644c74ce 100644 --- a/docs/reference/synLogout.html +++ b/docs/reference/synLogout.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synMd5Query.html b/docs/reference/synMd5Query.html index 0a6be8a4..bdc2f35b 100644 --- a/docs/reference/synMd5Query.html +++ b/docs/reference/synMd5Query.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synMove.html b/docs/reference/synMove.html index db7a5ceb..f535e96c 100644 --- a/docs/reference/synMove.html +++ b/docs/reference/synMove.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synOnweb.html b/docs/reference/synOnweb.html index d482d8c6..29bca56b 100644 --- a/docs/reference/synOnweb.html +++ b/docs/reference/synOnweb.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synPrintEntity.html b/docs/reference/synPrintEntity.html index 59f1cd55..7bf104a6 100644 --- a/docs/reference/synPrintEntity.html +++ b/docs/reference/synPrintEntity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synRemoveFromDownloadList.html b/docs/reference/synRemoveFromDownloadList.html index 6a0f5192..d793c3e6 100644 --- a/docs/reference/synRemoveFromDownloadList.html +++ b/docs/reference/synRemoveFromDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synRestDELETE.html b/docs/reference/synRestDELETE.html index e7cc4797..c820c18c 100644 --- a/docs/reference/synRestDELETE.html +++ b/docs/reference/synRestDELETE.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synRestGET.html b/docs/reference/synRestGET.html index 957cef88..f409c2b7 100644 --- a/docs/reference/synRestGET.html +++ b/docs/reference/synRestGET.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synRestPOST.html b/docs/reference/synRestPOST.html index 37451566..e39925b9 100644 --- a/docs/reference/synRestPOST.html +++ b/docs/reference/synRestPOST.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synRestPUT.html b/docs/reference/synRestPUT.html index 897cda5d..239ba1d8 100644 --- a/docs/reference/synRestPUT.html +++ b/docs/reference/synRestPUT.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSendMembershipInvitation.html b/docs/reference/synSendMembershipInvitation.html index 96a346a9..a81536de 100644 --- a/docs/reference/synSendMembershipInvitation.html +++ b/docs/reference/synSendMembershipInvitation.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSendMessage.html b/docs/reference/synSendMessage.html index befd27c7..a2a4f598 100644 --- a/docs/reference/synSendMessage.html +++ b/docs/reference/synSendMessage.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSetAnnotations.html b/docs/reference/synSetAnnotations.html index a578114e..504dc11d 100644 --- a/docs/reference/synSetAnnotations.html +++ b/docs/reference/synSetAnnotations.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSetEndpoints.html b/docs/reference/synSetEndpoints.html index 5aff31a8..94bbbe49 100644 --- a/docs/reference/synSetEndpoints.html +++ b/docs/reference/synSetEndpoints.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSetPermissions.html b/docs/reference/synSetPermissions.html index 1eca59db..6b06bf67 100644 --- a/docs/reference/synSetPermissions.html +++ b/docs/reference/synSetPermissions.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSetProvenance.html b/docs/reference/synSetProvenance.html index dda8f5a3..49d81512 100644 --- a/docs/reference/synSetProvenance.html +++ b/docs/reference/synSetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSetStorageLocation.html b/docs/reference/synSetStorageLocation.html index e83b2c5a..746ed9d1 100644 --- a/docs/reference/synSetStorageLocation.html +++ b/docs/reference/synSetStorageLocation.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synStore.html b/docs/reference/synStore.html index 5de68679..9affa116 100644 --- a/docs/reference/synStore.html +++ b/docs/reference/synStore.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synSubmit.html b/docs/reference/synSubmit.html index 5190f067..5183adfd 100644 --- a/docs/reference/synSubmit.html +++ b/docs/reference/synSubmit.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synTableQuery.html b/docs/reference/synTableQuery.html index 66f767f1..75ce6634 100644 --- a/docs/reference/synTableQuery.html +++ b/docs/reference/synTableQuery.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synUpdateActivity.html b/docs/reference/synUpdateActivity.html index 91853ff6..e3df5f51 100644 --- a/docs/reference/synUpdateActivity.html +++ b/docs/reference/synUpdateActivity.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synUploadFileHandle.html b/docs/reference/synUploadFileHandle.html index 32751bf9..4779f468 100644 --- a/docs/reference/synUploadFileHandle.html +++ b/docs/reference/synUploadFileHandle.html @@ -18,7 +18,7 @@ synapser - 1.0.0 + 1.2.0 diff --git a/docs/reference/synapser-package.html b/docs/reference/synapser-package.html index d9515e2c..1ddfb2eb 100644 --- a/docs/reference/synapser-package.html +++ b/docs/reference/synapser-package.html @@ -17,7 +17,7 @@ synapser - 1.0.0 + 1.2.0 From 701438ed6b9c80fd3eb9149cf7274aa5619f913b Mon Sep 17 00:00:00 2001 From: thomasyu888 Date: Sun, 10 Sep 2023 09:01:58 -0700 Subject: [PATCH 7/7] Upgrade actions --- .github/workflows/build.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2fdd41ae..d57b5dd9 100644 --- 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 @@ -200,7 +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'}} @@ -233,7 +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 @@ -268,13 +268,13 @@ jobs: strategy: matrix: os: [ubuntu-22.04, windows-2022, macos-12] - r: [4.1.3, 4.2.2, 4.3.0] + 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