diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 457c4806..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 @@ -120,8 +120,7 @@ jobs: shell: bash if: ${{runner.os == 'Windows'}} run: | - pip install pandas - pip install synapseclient + pip install 'synapseclient[pandas]' - uses: r-lib/actions/setup-r-dependencies@v2 with: @@ -201,7 +200,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: check-deployment-target id: check-deployment-target if: ${{github.event.action == 'published'}} @@ -234,7 +233,7 @@ jobs: # Before deoloying to RAN (which is an S3 bucket), authenticate to AWS using GitHub OIDC - name: Assume AWS Role - uses: aws-actions/configure-aws-credentials@v2 + uses: aws-actions/configure-aws-credentials@v3 with: aws-region: us-east-1 role-to-assume: arn:aws:iam::325565585839:role/sagebase-github-oidc-sage-bionetworks-synapser @@ -269,13 +268,13 @@ jobs: strategy: matrix: os: [ubuntu-22.04, windows-2022, macos-12] - r: [4.1.3, 4.2.2] + r: [4.1.3, 4.2.2, 4.3.1] runs-on: ${{ matrix.os }} steps: - name: checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: setup-r uses: r-lib/actions/setup-r@v2 diff --git a/DESCRIPTION b/DESCRIPTION index f7b64918..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"), @@ -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/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/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") 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/docs/404.html b/docs/404.html index 82938920..34bc5deb 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index 466250e9..2d4d04cf 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index cde16452..1aad3d1e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/docker.html b/docs/articles/docker.html index 6a390263..e2b66100 100644 --- a/docs/articles/docker.html +++ b/docs/articles/docker.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/index.html b/docs/articles/index.html index e9d2aa96..af369750 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/manageSynapseCredentials.html b/docs/articles/manageSynapseCredentials.html index 9392c3a9..1df32da3 100644 --- a/docs/articles/manageSynapseCredentials.html +++ b/docs/articles/manageSynapseCredentials.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/synapser.html b/docs/articles/synapser.html index f7452942..a6cbd0b9 100644 --- a/docs/articles/synapser.html +++ b/docs/articles/synapser.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 @@ -218,7 +218,7 @@

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

 print(fileEntity)
-## File(_file_handle={'id': '128470724', 'etag': '7ea66756-bbea-4827-a5d6-86d610952575', 'createdBy': '3324230', 'createdOn': '2023-09-10T01:52:04.000Z', 'modifiedOn': '2023-09-10T01:52:04.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'file335b64fd60c', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/a5f347b4-b614-4740-861f-29db3b84bff6/file335b64fd60c', 'isPreview': False, 'externalURL': None}, createdBy='3324230', modifiedBy='3324230', files=['file335b64fd60c'], synapseStore=True, cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpE2HGEb', path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpE2HGEb/file335b64fd60c', createdOn='2023-09-10T01:52:04.003Z', parentId='syn52417363', etag='d01545de-61aa-4fa3-a770-c7545a46e69e', concreteType='org.sagebionetworks.repo.model.FileEntity', versionNumber=1, id='syn52417364', isLatestVersion=True, modifiedOn='2023-09-10T01:52:04.176Z', name='file335b64fd60c', dataFileHandleId='128470724', versionLabel='1')
+## File(createdOn='2023-09-10T05:57:33.808Z', files=['filed50b25528b1'], modifiedBy='3324230', dataFileHandleId='128471129', etag='705f7ba2-ca7b-4028-bd37-056fbbeb0924', concreteType='org.sagebionetworks.repo.model.FileEntity', _file_handle={'id': '128471129', 'etag': '2e832a48-e232-41c2-8d53-37627e08be9a', 'createdBy': '3324230', 'createdOn': '2023-09-10T05:57:34.000Z', 'modifiedOn': '2023-09-10T05:57:34.000Z', 'concreteType': 'org.sagebionetworks.repo.model.file.S3FileHandle', 'contentType': 'application/octet-stream', 'contentMd5': '8465d33d9f407ef250ce519e92f300fb', 'fileName': 'filed50b25528b1', 'storageLocationId': 1, 'contentSize': 23, 'status': 'AVAILABLE', 'bucketName': 'proddata.sagebase.org', 'key': '3324230/e53a6758-78e2-426f-b531-bd85871086c2/filed50b25528b1', 'isPreview': False, 'externalURL': None}, modifiedOn='2023-09-10T05:57:34.009Z', isLatestVersion=True, path='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpoNRYtU/filed50b25528b1', synapseStore=True, name='filed50b25528b1', cacheDir='/var/folders/zl/j6z0kpys2gl7pwc1x63w0gwr001lqt/T/RtmpoNRYtU', id='syn52417559', createdBy='3324230', versionLabel='1', parentId='syn52417558', versionNumber=1)

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]]$id
-## [1] "syn52417365"
+## [1] "syn52417560"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -301,13 +301,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## [[1]]$createdOn
-## [1] "2023-09-10T01:52:05.690Z"
+## [1] "2023-09-10T05:57:35.816Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-09-10T01:52:05.840Z"
+## [1] "2023-09-10T05:57:36.006Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -318,10 +318,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file335b64fd60c"
+## [1] "filed50b25528b1"
 ## 
 ## [[2]]$id
-## [1] "syn52417364"
+## [1] "syn52417559"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -336,13 +336,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## [[2]]$createdOn
-## [1] "2023-09-10T01:52:04.003Z"
+## [1] "2023-09-10T05:57:33.808Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-09-10T01:52:04.176Z"
+## [1] "2023-09-10T05:57:34.009Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -358,7 +358,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## [[1]]$id
-## [1] "syn52417365"
+## [1] "syn52417560"
 ## 
 ## [[1]]$type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -373,13 +373,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[1]]$benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## [[1]]$createdOn
-## [1] "2023-09-10T01:52:05.690Z"
+## [1] "2023-09-10T05:57:35.816Z"
 ## 
 ## [[1]]$modifiedOn
-## [1] "2023-09-10T01:52:05.840Z"
+## [1] "2023-09-10T05:57:36.006Z"
 ## 
 ## [[1]]$createdBy
 ## [1] "3324230"
@@ -390,10 +390,10 @@ 
Organizing Data in a Project## 
 ## [[2]]
 ## [[2]]$name
-## [1] "file335b64fd60c"
+## [1] "filed50b25528b1"
 ## 
 ## [[2]]$id
-## [1] "syn52417364"
+## [1] "syn52417559"
 ## 
 ## [[2]]$type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -408,13 +408,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## [[2]]$benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## [[2]]$createdOn
-## [1] "2023-09-10T01:52:04.003Z"
+## [1] "2023-09-10T05:57:33.808Z"
 ## 
 ## [[2]]$modifiedOn
-## [1] "2023-09-10T01:52:04.176Z"
+## [1] "2023-09-10T05:57:34.009Z"
 ## 
 ## [[2]]$createdBy
 ## [1] "3324230"
@@ -437,7 +437,7 @@ 
Organizing Data in a Project## [1] "Data"
 ## 
 ## $id
-## [1] "syn52417365"
+## [1] "syn52417560"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.Folder"
@@ -452,13 +452,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## $createdOn
-## [1] "2023-09-10T01:52:05.690Z"
+## [1] "2023-09-10T05:57:35.816Z"
 ## 
 ## $modifiedOn
-## [1] "2023-09-10T01:52:05.840Z"
+## [1] "2023-09-10T05:57:36.006Z"
 ## 
 ## $createdBy
 ## [1] "3324230"
@@ -467,10 +467,10 @@ 
Organizing Data in a Project## [1] "3324230"
 ## 
 ## $name
-## [1] "file335b64fd60c"
+## [1] "filed50b25528b1"
 ## 
 ## $id
-## [1] "syn52417364"
+## [1] "syn52417559"
 ## 
 ## $type
 ## [1] "org.sagebionetworks.repo.model.FileEntity"
@@ -485,13 +485,13 @@ 
Organizing Data in a Project## [1] TRUE
 ## 
 ## $benefactorId
-## [1] 52417363
+## [1] 52417558
 ## 
 ## $createdOn
-## [1] "2023-09-10T01:52:04.003Z"
+## [1] "2023-09-10T05:57:33.808Z"
 ## 
 ## $modifiedOn
-## [1] "2023-09-10T01:52:04.176Z"
+## [1] "2023-09-10T05:57:34.009Z"
 ## 
 ## $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 syn52417365 is in trash can.
+## Entity syn52417560 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 @@ -711,12 +711,12 @@

Evaluationseval <- synGetEvaluation(eval$id) eval ## { -## "contentSource": "syn52417370", -## "createdOn": "2023-09-10T01:52:19.778Z", +## "contentSource": "syn52417563", +## "createdOn": "2023-09-10T05:57:50.610Z", ## "description": "testing", -## "etag": "ab96e0c7-14f2-4ca8-bc6e-343d23e97f9e", -## "id": "9615409", -## "name": "My unique evaluation created on Sat Sep 09 185219.5925 2023", +## "etag": "713fbeac-66a5-4cb4-a82b-e8429255ac60", +## "id": "9615412", +## "name": "My unique evaluation created on Sat Sep 09 225750.3941 2023", ## "ownerId": "3324230", ## "submissionInstructionsMessage": "This evaluation only accepts files.", ## "submissionReceiptMessage": "Thank you for your submission!" @@ -741,26 +741,26 @@

Evaluations## { ## "contributors": [ ## { -## "createdOn": "2023-09-10T01:52:22.150Z", +## "createdOn": "2023-09-10T05:57:52.987Z", ## "principalId": "3324230" ## } ## ], -## "createdOn": "2023-09-10T01:52:22.150Z", -## "entityBundleJSON": "{\"entity\":{\"name\":\"file335b1a36cede\",\"id\":\"syn52417371\",\"etag\":\"d842081b-7747-4d4d-908e-5ff7e1e903ce\",\"createdOn\":\"2023-09-10T01:52:21.570Z\",\"modifiedOn\":\"2023-09-10T01:52:21.734Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn52417370\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"128470731\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn52417371\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"128470731\",\"etag\":\"24c712b6-9809-468e-a4a1-f60d1a979b3a\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-09-10T01:52:21.000Z\",\"modifiedOn\":\"2023-09-10T01:52:21.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"file335b1a36cede\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/5076c7be-528c-412f-8abd-aa8cd1477038/file335b1a36cede\",\"isPreview\":false}]}", -## "entityId": "syn52417371", -## "evaluationId": "9615409", -## "id": "9740517", -## "name": "file335b1a36cede", +## "createdOn": "2023-09-10T05:57:52.987Z", +## "entityBundleJSON": "{\"entity\":{\"name\":\"filed50b5eab227e\",\"id\":\"syn52417564\",\"etag\":\"d5abdf9f-f6b6-474b-bf0f-0ffe90c7ad5b\",\"createdOn\":\"2023-09-10T05:57:52.407Z\",\"modifiedOn\":\"2023-09-10T05:57:52.580Z\",\"createdBy\":\"3324230\",\"modifiedBy\":\"3324230\",\"parentId\":\"syn52417563\",\"concreteType\":\"org.sagebionetworks.repo.model.FileEntity\",\"versionNumber\":1,\"versionLabel\":\"1\",\"isLatestVersion\":true,\"dataFileHandleId\":\"128471134\"},\"entityType\":\"file\",\"annotations\":{\"id\":\"syn52417564\",\"etag\":\"00000000-0000-0000-0000-000000000000\",\"annotations\":{}},\"fileHandles\":[{\"id\":\"128471134\",\"etag\":\"9cc8f980-b765-4ee1-808a-7ab6850fb824\",\"createdBy\":\"3324230\",\"createdOn\":\"2023-09-10T05:57:52.000Z\",\"modifiedOn\":\"2023-09-10T05:57:52.000Z\",\"concreteType\":\"org.sagebionetworks.repo.model.file.S3FileHandle\",\"contentType\":\"application/octet-stream\",\"contentMd5\":\"3f466b7f85d184292a68cea1c4f7cfc2\",\"fileName\":\"filed50b5eab227e\",\"storageLocationId\":1,\"contentSize\":27,\"status\":\"AVAILABLE\",\"bucketName\":\"proddata.sagebase.org\",\"key\":\"3324230/9a462b96-fd7c-4e20-9b85-907b46089142/filed50b5eab227e\",\"isPreview\":false}]}", +## "entityId": "syn52417564", +## "evaluationId": "9615412", +## "id": "9740524", +## "name": "filed50b5eab227e", ## "userId": "3324230", ## "versionNumber": 1 ## } ## ## [[1]][[2]] ## { -## "entityId": "syn52417371", -## "etag": "c3b2103e-5a41-4863-b798-7a4077c82aad", -## "id": "9740517", -## "modifiedOn": "2023-09-10T01:52:22.150Z", +## "entityId": "syn52417564", +## "etag": "321b6d29-eb9a-4dc5-bf58-0ff407b46224", +## "id": "9740524", +## "modifiedOn": "2023-09-10T05:57:52.987Z", ## "status": "RECEIVED", ## "statusVersion": 0, ## "submissionAnnotations": {}, @@ -776,10 +776,10 @@

EvaluationssubmissionStatus <- synGetSubmissionStatus(submission) submissionStatus ## { -## "entityId": "syn52417371", -## "etag": "c3b2103e-5a41-4863-b798-7a4077c82aad", -## "id": "9740517", -## "modifiedOn": "2023-09-10T01:52:22.150Z", +## "entityId": "syn52417564", +## "etag": "321b6d29-eb9a-4dc5-bf58-0ff407b46224", +## "id": "9740524", +## "modifiedOn": "2023-09-10T05:57:52.987Z", ## "status": "RECEIVED", ## "statusVersion": 0, ## "submissionAnnotations": {}, @@ -798,64 +798,13 @@

EvaluationsqueryString <- sprintf("query=select * from evaluation_%s LIMIT %s OFFSET %s'", eval$id, 10, 0) synRestGET(paste("/evaluation/submission/query?", URLencode(queryString), sep = "")) ## $headers -## [1] "scopeId" "entityId" "userId" "createdOn" -## [5] "versionNumber" "modifiedOn" "submitterAlias" "cancelControl" -## [9] "submitterId" "teamId" "name" "cancelRequested" -## [13] "objectId" "status" "canCancel" +## list() ## ## $rows -## $rows[[1]] -## $rows[[1]]$values -## $rows[[1]]$values[[1]] -## [1] "9615409" -## -## $rows[[1]]$values[[2]] -## [1] "syn52417371" -## -## $rows[[1]]$values[[3]] -## [1] "3324230" -## -## $rows[[1]]$values[[4]] -## [1] "1694310742150" -## -## $rows[[1]]$values[[5]] -## [1] "1" -## -## $rows[[1]]$values[[6]] -## [1] "1694310742150" -## -## $rows[[1]]$values[[7]] -## NULL -## -## $rows[[1]]$values[[8]] -## [1] "{\"submissionId\":\"9740517\",\"userId\":\"3324230\",\"canCancel\":false,\"cancelRequested\":false}" -## -## $rows[[1]]$values[[9]] -## [1] "3324230" -## -## $rows[[1]]$values[[10]] -## NULL -## -## $rows[[1]]$values[[11]] -## [1] "file335b1a36cede" -## -## $rows[[1]]$values[[12]] -## [1] "false" -## -## $rows[[1]]$values[[13]] -## [1] "9740517" -## -## $rows[[1]]$values[[14]] -## [1] "RECEIVED" -## -## $rows[[1]]$values[[15]] -## [1] "false" -## -## -## +## list() ## ## $totalNumberOfResults -## [1] 1 +## [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:

@@ -881,31 +830,31 @@ 
Sharing Access to Contentacl <- synSetPermissions(project, principalId = 273949, accessType = list("READ"))
 acl
 ## $id
-## [1] "syn52417370"
+## [1] "syn52417563"
 ## 
 ## $creationDate
-## [1] "2023-09-10T01:52:11.933Z"
+## [1] "2023-09-10T05:57:42.595Z"
 ## 
 ## $etag
-## [1] "6e48e9be-eb88-4ab9-b91b-271986469f72"
+## [1] "7205921e-0a24-4b73-a530-4e300bc36b63"
 ## 
 ## $resourceAccess
 ## $resourceAccess[[1]]
 ## $resourceAccess[[1]]$principalId
-## [1] 273949
+## [1] 3324230
 ## 
 ## $resourceAccess[[1]]$accessType
-## [1] "READ"
+## [1] "READ"               "CHANGE_SETTINGS"    "MODERATE"          
+## [4] "CREATE"             "CHANGE_PERMISSIONS" "DOWNLOAD"          
+## [7] "UPDATE"             "DELETE"            
 ## 
 ## 
 ## $resourceAccess[[2]]
 ## $resourceAccess[[2]]$principalId
-## [1] 3324230
+## [1] 273949
 ## 
 ## $resourceAccess[[2]]$accessType
-## [1] "CHANGE_SETTINGS"    "MODERATE"           "UPDATE"            
-## [4] "DOWNLOAD"           "CHANGE_PERMISSIONS" "READ"              
-## [7] "CREATE"             "DELETE"
+## [1] "READ"

Now public can read:

 synGetPermissions(project, principalId = 273950)
diff --git a/docs/articles/systemDependencies.html b/docs/articles/systemDependencies.html
index a2294ade..f1cda30f 100644
--- a/docs/articles/systemDependencies.html
+++ b/docs/articles/systemDependencies.html
@@ -33,7 +33,7 @@
       
       
         synapser
-        1.1.0
+        1.2.0
diff --git a/docs/articles/tables.html b/docs/articles/tables.html index 012e7d38..ad38134f 100644 --- a/docs/articles/tables.html +++ b/docs/articles/tables.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 @@ -154,7 +154,7 @@

Tables 
 table <- synBuildTable("My Favorite Genes", project, genes)
 table$schema
-## Schema(concreteType='org.sagebionetworks.repo.model.table.TableEntity', parentId='syn52417372', 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'}], name='My Favorite Genes', columnIds=[])
+## Schema(columnIds=[], concreteType='org.sagebionetworks.repo.model.table.TableEntity', parentId='syn52417565', name='My Favorite Genes', 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 @@ -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 0x125cdf430> +## <synapseclient.table.CsvFileTable object at 0x1268bdcf0>

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 0x125cdf580>
+## <synapseclient.table.CsvFileTable object at 0x126b50d90>

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 0x125d5d2d0>
+## <synapseclient.table.CsvFileTable object at 0x1268bf7f0>

Note that using POSIXlt is strongly preferred over POSIXct, because POSIXct does not store values with enough precision to reliably recover milliseconds. For more diff --git a/docs/articles/troubleshooting.html b/docs/articles/troubleshooting.html index d08f03bf..a00185eb 100644 --- a/docs/articles/troubleshooting.html +++ b/docs/articles/troubleshooting.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/upload.html b/docs/articles/upload.html index a6797d82..8892254a 100644 --- a/docs/articles/upload.html +++ b/docs/articles/upload.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/articles/views.html b/docs/articles/views.html index 3d0fb484..e1b16855 100644 --- a/docs/articles/views.html +++ b/docs/articles/views.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 @@ -200,17 +200,17 @@

Views data <- as.data.frame(queryResults) data ## ROW_ID ROW_VERSION ROW_ETAG id -## 1 52417381 1 4b6521d7-f314-4c67-9a64-0ddef6b6ca26 syn52417381 -## 2 52417382 1 43a889f5-a890-4d8a-8472-d0b7f5b0dbae syn52417382 +## 1 52417572 1 03d6cee4-35c4-4be7-9021-4b12f6eaa755 syn52417572 +## 2 52417573 1 ec739129-fea1-4901-bf71-2611930e94d2 syn52417573 ## name description createdOn createdBy -## 1 file36303670318 NA 2023-09-09 18:54:16 3324230 -## 2 file36305ffc1e66 NA 2023-09-09 18:54:17 3324230 +## 1 filed79d5e81ba3e NA 2023-09-09 22:59:50 3324230 +## 2 filed79d16ea6ceb NA 2023-09-09 22:59:51 3324230 ## etag modifiedOn modifiedBy type -## 1 4b6521d7-f314-4c67-9a64-0ddef6b6ca26 2023-09-09 18:54:18 3324230 file -## 2 43a889f5-a890-4d8a-8472-d0b7f5b0dbae 2023-09-09 18:54:18 3324230 file +## 1 03d6cee4-35c4-4be7-9021-4b12f6eaa755 2023-09-09 22:59:52 3324230 file +## 2 ec739129-fea1-4901-bf71-2611930e94d2 2023-09-09 22:59:52 3324230 file ## currentVersion parentId benefactorId projectId dataFileHandleId -## 1 1 syn52417380 syn52417380 syn52417380 128470769 -## 2 1 syn52417380 syn52417380 syn52417380 128470770 +## 1 1 syn52417571 syn52417571 syn52417571 128471165 +## 2 1 syn52417571 syn52417571 syn52417571 128471166 ## dataFileSizeBytes dataFileMD5Hex ## 1 37 47dfe7f5eaa49a5413c7b79b67ab9c43 ## 2 38 ba01e01b9e3ffea3ebef95efa62998b0 @@ -218,8 +218,8 @@

Views ## 1 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org ## 2 org.sagebionetworks.repo.model.file.S3FileHandle proddata.sagebase.org ## dataFileKey contributor -## 1 3324230/1707f7f0-0fe1-40c1-a732-089576539347/file36303670318 Sage -## 2 3324230/868c18c3-a1a7-4dd2-8067-a8d20addc0d6/file36305ffc1e66 UW +## 1 3324230/b4e57ee9-09e5-47eb-b0e7-f72a7286f57f/filed79d5e81ba3e Sage +## 2 3324230/a81a4d30-81bc-47b6-8990-021b9b790207/filed79d16ea6ceb 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 0x10e2cece0>
+## <synapseclient.table.CsvFileTable object at 0x11a6d1390>

Update View’s Content diff --git a/docs/authors.html b/docs/authors.html index dfe2cda3..d63da6f2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0

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

Citation

Hoff B (2023). synapser: R Language Bindings for Synapse API. -R package version 1.1.0, 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 1.1.0},
+  note = {R package version 1.2.0},
   url = {https://www.synapse.org},
 }
diff --git a/docs/index.html b/docs/index.html index 88a8edc7..68b99a3b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/news/index.html b/docs/news/index.html index 21e79c36..93b59ff6 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 @@ -78,6 +78,13 @@

Changelog

Source: NEWS.md +
+

synapser 1.2.0

+
+

Improvements

+
  • Python synapsePythonClient dependency updated to 3.0.0
    • +
+

synapser 1.1.0

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 888a1650..802446da 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,5 +10,5 @@ articles: troubleshooting: troubleshooting.html upload: upload.html views: views.html -last_built: 2023-09-10T01:51Z +last_built: 2023-09-10T05:56Z diff --git a/docs/reference/Activity-class.html b/docs/reference/Activity-class.html index aea1fc05..2c1016f4 100644 --- a/docs/reference/Activity-class.html +++ b/docs/reference/Activity-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0
diff --git a/docs/reference/Activity.html b/docs/reference/Activity.html index aa330fb7..3708f4fc 100644 --- a/docs/reference/Activity.html +++ b/docs/reference/Activity.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0
diff --git a/docs/reference/Column-class.html b/docs/reference/Column-class.html index 16823b7c..e02d5ebc 100644 --- a/docs/reference/Column-class.html +++ b/docs/reference/Column-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Column.html b/docs/reference/Column.html index aeeddfa5..9bffd746 100644 --- a/docs/reference/Column.html +++ b/docs/reference/Column.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Dataset-class.html b/docs/reference/Dataset-class.html index dd48cd1b..42c7de6c 100644 --- a/docs/reference/Dataset-class.html +++ b/docs/reference/Dataset-class.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Dataset.html b/docs/reference/Dataset.html index 77d8fa33..f033a590 100644 --- a/docs/reference/Dataset.html +++ b/docs/reference/Dataset.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/DockerRepository-class.html b/docs/reference/DockerRepository-class.html index 84e359f8..34154c13 100644 --- a/docs/reference/DockerRepository-class.html +++ b/docs/reference/DockerRepository-class.html @@ -20,7 +20,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/DockerRepository.html b/docs/reference/DockerRepository.html index 3c0795e8..abb6070a 100644 --- a/docs/reference/DockerRepository.html +++ b/docs/reference/DockerRepository.html @@ -20,7 +20,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/EntityViewSchema-class.html b/docs/reference/EntityViewSchema-class.html index d1c5b281..4971e146 100644 --- a/docs/reference/EntityViewSchema-class.html +++ b/docs/reference/EntityViewSchema-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/EntityViewSchema.html b/docs/reference/EntityViewSchema.html index 03cfbfd8..0af502b5 100644 --- a/docs/reference/EntityViewSchema.html +++ b/docs/reference/EntityViewSchema.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Evaluation-class.html b/docs/reference/Evaluation-class.html index b763fade..9f8d1182 100644 --- a/docs/reference/Evaluation-class.html +++ b/docs/reference/Evaluation-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Evaluation.html b/docs/reference/Evaluation.html index f49e69ed..0459e946 100644 --- a/docs/reference/Evaluation.html +++ b/docs/reference/Evaluation.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/File-class.html b/docs/reference/File-class.html index 734825fc..054c5199 100644 --- a/docs/reference/File-class.html +++ b/docs/reference/File-class.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/File.html b/docs/reference/File.html index 2e367037..374bb0c5 100644 --- a/docs/reference/File.html +++ b/docs/reference/File.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Folder-class.html b/docs/reference/Folder-class.html index 52efd030..4de4aefb 100644 --- a/docs/reference/Folder-class.html +++ b/docs/reference/Folder-class.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Folder.html b/docs/reference/Folder.html index 3c2fa886..16493151 100644 --- a/docs/reference/Folder.html +++ b/docs/reference/Folder.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Link-class.html b/docs/reference/Link-class.html index 8fa74035..02373f10 100644 --- a/docs/reference/Link-class.html +++ b/docs/reference/Link-class.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Link.html b/docs/reference/Link.html index 1dda25a4..2403007f 100644 --- a/docs/reference/Link.html +++ b/docs/reference/Link.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/MaterializedViewSchema-class.html b/docs/reference/MaterializedViewSchema-class.html index 68158414..866ed9b1 100644 --- a/docs/reference/MaterializedViewSchema-class.html +++ b/docs/reference/MaterializedViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/MaterializedViewSchema.html b/docs/reference/MaterializedViewSchema.html index 4c1c5ee3..9ed5d38a 100644 --- a/docs/reference/MaterializedViewSchema.html +++ b/docs/reference/MaterializedViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/PartialRowset-class.html b/docs/reference/PartialRowset-class.html index cc20e27e..9e7401a7 100644 --- a/docs/reference/PartialRowset-class.html +++ b/docs/reference/PartialRowset-class.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/PartialRowset.html b/docs/reference/PartialRowset.html index 0d230eb9..97ed53bc 100644 --- a/docs/reference/PartialRowset.html +++ b/docs/reference/PartialRowset.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Project-class.html b/docs/reference/Project-class.html index c530ef20..adb86728 100644 --- a/docs/reference/Project-class.html +++ b/docs/reference/Project-class.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Project.html b/docs/reference/Project.html index 78a512e2..8a5332a7 100644 --- a/docs/reference/Project.html +++ b/docs/reference/Project.html @@ -19,7 +19,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Row-class.html b/docs/reference/Row-class.html index 2662783e..d7e1e55e 100644 --- a/docs/reference/Row-class.html +++ b/docs/reference/Row-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Row.html b/docs/reference/Row.html index 76b8ee32..d327c5c2 100644 --- a/docs/reference/Row.html +++ b/docs/reference/Row.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/RowSet-class.html b/docs/reference/RowSet-class.html index 03720b1f..e2d901e2 100644 --- a/docs/reference/RowSet-class.html +++ b/docs/reference/RowSet-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/RowSet.html b/docs/reference/RowSet.html index c4d217ac..9d03cbe7 100644 --- a/docs/reference/RowSet.html +++ b/docs/reference/RowSet.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Schema-class.html b/docs/reference/Schema-class.html index 531242cc..0547bf6a 100644 --- a/docs/reference/Schema-class.html +++ b/docs/reference/Schema-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Schema.html b/docs/reference/Schema.html index 4e284683..dfbc6ea8 100644 --- a/docs/reference/Schema.html +++ b/docs/reference/Schema.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Submission-class.html b/docs/reference/Submission-class.html index cd45f0f7..a0fe7149 100644 --- a/docs/reference/Submission-class.html +++ b/docs/reference/Submission-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Submission.html b/docs/reference/Submission.html index 19bd3821..f43a0a56 100644 --- a/docs/reference/Submission.html +++ b/docs/reference/Submission.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/SubmissionStatus-class.html b/docs/reference/SubmissionStatus-class.html index 27245462..39bbce40 100644 --- a/docs/reference/SubmissionStatus-class.html +++ b/docs/reference/SubmissionStatus-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/SubmissionStatus.html b/docs/reference/SubmissionStatus.html index 7f14fae1..9a937016 100644 --- a/docs/reference/SubmissionStatus.html +++ b/docs/reference/SubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/SubmissionViewSchema-class.html b/docs/reference/SubmissionViewSchema-class.html index c764eb78..3beb5539 100644 --- a/docs/reference/SubmissionViewSchema-class.html +++ b/docs/reference/SubmissionViewSchema-class.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/SubmissionViewSchema.html b/docs/reference/SubmissionViewSchema.html index adfe345d..b0316314 100644 --- a/docs/reference/SubmissionViewSchema.html +++ b/docs/reference/SubmissionViewSchema.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Table.html b/docs/reference/Table.html index 48ccde2f..1c693594 100644 --- a/docs/reference/Table.html +++ b/docs/reference/Table.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Team-class.html b/docs/reference/Team-class.html index cd65bc00..573b191e 100644 --- a/docs/reference/Team-class.html +++ b/docs/reference/Team-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Team.html b/docs/reference/Team.html index 8ef22316..22e14d53 100644 --- a/docs/reference/Team.html +++ b/docs/reference/Team.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/TeamMember-class.html b/docs/reference/TeamMember-class.html index 608ea1d4..faf9f99f 100644 --- a/docs/reference/TeamMember-class.html +++ b/docs/reference/TeamMember-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/TeamMember.html b/docs/reference/TeamMember.html index 566dc8ba..48c16c9b 100644 --- a/docs/reference/TeamMember.html +++ b/docs/reference/TeamMember.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/UserGroupHeader-class.html b/docs/reference/UserGroupHeader-class.html index 4fc59390..3d2ed336 100644 --- a/docs/reference/UserGroupHeader-class.html +++ b/docs/reference/UserGroupHeader-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/UserGroupHeader.html b/docs/reference/UserGroupHeader.html index e0d3b781..967427fb 100644 --- a/docs/reference/UserGroupHeader.html +++ b/docs/reference/UserGroupHeader.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/UserProfile-class.html b/docs/reference/UserProfile-class.html index 00f8da89..5391bfde 100644 --- a/docs/reference/UserProfile-class.html +++ b/docs/reference/UserProfile-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/UserProfile.html b/docs/reference/UserProfile.html index 6bb0cdc1..9c5ae24c 100644 --- a/docs/reference/UserProfile.html +++ b/docs/reference/UserProfile.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Wiki-class.html b/docs/reference/Wiki-class.html index 685bbd57..6678c6e9 100644 --- a/docs/reference/Wiki-class.html +++ b/docs/reference/Wiki-class.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/Wiki.html b/docs/reference/Wiki.html index 2273cd19..e1c89296 100644 --- a/docs/reference/Wiki.html +++ b/docs/reference/Wiki.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/as.list.html b/docs/reference/as.list.html index 063af7b7..d9b14059 100644 --- a/docs/reference/as.list.html +++ b/docs/reference/as.list.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index f0a130db..c8c22584 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 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 92f2b895..4c5a775f 100644 --- a/docs/reference/nextElem.html +++ b/docs/reference/nextElem.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synBuildTable.html b/docs/reference/synBuildTable.html index 561840ec..cc07f99d 100644 --- a/docs/reference/synBuildTable.html +++ b/docs/reference/synBuildTable.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synClearDownloadList.html b/docs/reference/synClearDownloadList.html index aee01f8f..ae44d5cc 100644 --- a/docs/reference/synClearDownloadList.html +++ b/docs/reference/synClearDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateColumn.html b/docs/reference/synCreateColumn.html index bd7d1ce3..46df0290 100644 --- a/docs/reference/synCreateColumn.html +++ b/docs/reference/synCreateColumn.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateColumns.html b/docs/reference/synCreateColumns.html index 349af277..edeba87c 100644 --- a/docs/reference/synCreateColumns.html +++ b/docs/reference/synCreateColumns.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateExternalS3FileHandle.html b/docs/reference/synCreateExternalS3FileHandle.html index 0b7da2df..3b74784c 100644 --- a/docs/reference/synCreateExternalS3FileHandle.html +++ b/docs/reference/synCreateExternalS3FileHandle.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateS3StorageLocation.html b/docs/reference/synCreateS3StorageLocation.html index 30a1008d..25969f3e 100644 --- a/docs/reference/synCreateS3StorageLocation.html +++ b/docs/reference/synCreateS3StorageLocation.html @@ -21,7 +21,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateSnapshotVersion.html b/docs/reference/synCreateSnapshotVersion.html index b1538e0a..0bf8dc3a 100644 --- a/docs/reference/synCreateSnapshotVersion.html +++ b/docs/reference/synCreateSnapshotVersion.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synCreateStorageLocationSetting.html b/docs/reference/synCreateStorageLocationSetting.html index 3560314b..081dd77b 100644 --- a/docs/reference/synCreateStorageLocationSetting.html +++ b/docs/reference/synCreateStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synDelete.html b/docs/reference/synDelete.html index 16fb518a..6336ded9 100644 --- a/docs/reference/synDelete.html +++ b/docs/reference/synDelete.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synDeleteProvenance.html b/docs/reference/synDeleteProvenance.html index d332c6b9..93bd6dd0 100644 --- a/docs/reference/synDeleteProvenance.html +++ b/docs/reference/synDeleteProvenance.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synDownloadTableColumns.html b/docs/reference/synDownloadTableColumns.html index 52d749d9..21ce5f48 100644 --- a/docs/reference/synDownloadTableColumns.html +++ b/docs/reference/synDownloadTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synFindEntityId.html b/docs/reference/synFindEntityId.html index edcd0620..97089e14 100644 --- a/docs/reference/synFindEntityId.html +++ b/docs/reference/synFindEntityId.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGet.html b/docs/reference/synGet.html index 0cddaf4f..d34cbf18 100644 --- a/docs/reference/synGet.html +++ b/docs/reference/synGet.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetAnnotations.html b/docs/reference/synGetAnnotations.html index 64f8deed..fdbf58bd 100644 --- a/docs/reference/synGetAnnotations.html +++ b/docs/reference/synGetAnnotations.html @@ -20,7 +20,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetChildren.html b/docs/reference/synGetChildren.html index e41fdf83..942d7368 100644 --- a/docs/reference/synGetChildren.html +++ b/docs/reference/synGetChildren.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetColumn.html b/docs/reference/synGetColumn.html index 3992acd4..e0ff631a 100644 --- a/docs/reference/synGetColumn.html +++ b/docs/reference/synGetColumn.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetColumns.html b/docs/reference/synGetColumns.html index afae92c2..21ff0d23 100644 --- a/docs/reference/synGetColumns.html +++ b/docs/reference/synGetColumns.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetConfigFile.html b/docs/reference/synGetConfigFile.html index 8022fc40..d0dc6ad3 100644 --- a/docs/reference/synGetConfigFile.html +++ b/docs/reference/synGetConfigFile.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetDownloadList.html b/docs/reference/synGetDownloadList.html index 444a79a2..132540a8 100644 --- a/docs/reference/synGetDownloadList.html +++ b/docs/reference/synGetDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetDownloadListManifest.html b/docs/reference/synGetDownloadListManifest.html index 38495118..50c88549 100644 --- a/docs/reference/synGetDownloadListManifest.html +++ b/docs/reference/synGetDownloadListManifest.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluation.html b/docs/reference/synGetEvaluation.html index 26f5273b..ff72cd87 100644 --- a/docs/reference/synGetEvaluation.html +++ b/docs/reference/synGetEvaluation.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluationByContentSource.html b/docs/reference/synGetEvaluationByContentSource.html index 66e96cf1..4dd816e3 100644 --- a/docs/reference/synGetEvaluationByContentSource.html +++ b/docs/reference/synGetEvaluationByContentSource.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetEvaluationByName.html b/docs/reference/synGetEvaluationByName.html index 0d6758ab..4ecd74e1 100644 --- a/docs/reference/synGetEvaluationByName.html +++ b/docs/reference/synGetEvaluationByName.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetMembershipStatus.html b/docs/reference/synGetMembershipStatus.html index 36ad5706..63a4c662 100644 --- a/docs/reference/synGetMembershipStatus.html +++ b/docs/reference/synGetMembershipStatus.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetMyStorageLocationSetting.html b/docs/reference/synGetMyStorageLocationSetting.html index 1388e152..54c3cee6 100644 --- a/docs/reference/synGetMyStorageLocationSetting.html +++ b/docs/reference/synGetMyStorageLocationSetting.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetPermissions.html b/docs/reference/synGetPermissions.html index 24e94e24..144ddb52 100644 --- a/docs/reference/synGetPermissions.html +++ b/docs/reference/synGetPermissions.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetProjectSetting.html b/docs/reference/synGetProjectSetting.html index 04dd670c..7611c224 100644 --- a/docs/reference/synGetProjectSetting.html +++ b/docs/reference/synGetProjectSetting.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetProvenance.html b/docs/reference/synGetProvenance.html index 76f0d311..8e4aa76a 100644 --- a/docs/reference/synGetProvenance.html +++ b/docs/reference/synGetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetStsStorageToken.html b/docs/reference/synGetStsStorageToken.html index 9038fa91..b32611a0 100644 --- a/docs/reference/synGetStsStorageToken.html +++ b/docs/reference/synGetStsStorageToken.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetSubmission.html b/docs/reference/synGetSubmission.html index b3f02b03..7833ba8d 100644 --- a/docs/reference/synGetSubmission.html +++ b/docs/reference/synGetSubmission.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissionBundles.html b/docs/reference/synGetSubmissionBundles.html index 4f6e6f3f..768d30ea 100644 --- a/docs/reference/synGetSubmissionBundles.html +++ b/docs/reference/synGetSubmissionBundles.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissionStatus.html b/docs/reference/synGetSubmissionStatus.html index 36a6f572..69767797 100644 --- a/docs/reference/synGetSubmissionStatus.html +++ b/docs/reference/synGetSubmissionStatus.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetSubmissions.html b/docs/reference/synGetSubmissions.html index 60b5b01a..53d42c9c 100644 --- a/docs/reference/synGetSubmissions.html +++ b/docs/reference/synGetSubmissions.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetTableColumns.html b/docs/reference/synGetTableColumns.html index 981b662b..180d1fd6 100644 --- a/docs/reference/synGetTableColumns.html +++ b/docs/reference/synGetTableColumns.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetTeam.html b/docs/reference/synGetTeam.html index e274c92f..0051cfa4 100644 --- a/docs/reference/synGetTeam.html +++ b/docs/reference/synGetTeam.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetTeamMembers.html b/docs/reference/synGetTeamMembers.html index c02fe079..904199f0 100644 --- a/docs/reference/synGetTeamMembers.html +++ b/docs/reference/synGetTeamMembers.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetTeamOpenInvitations.html b/docs/reference/synGetTeamOpenInvitations.html index 33f1e511..0f70fb96 100644 --- a/docs/reference/synGetTeamOpenInvitations.html +++ b/docs/reference/synGetTeamOpenInvitations.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetUserProfile.html b/docs/reference/synGetUserProfile.html index f1e45a0e..c0aae181 100644 --- a/docs/reference/synGetUserProfile.html +++ b/docs/reference/synGetUserProfile.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetWiki.html b/docs/reference/synGetWiki.html index ef481555..3c6bf586 100644 --- a/docs/reference/synGetWiki.html +++ b/docs/reference/synGetWiki.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetWikiAttachments.html b/docs/reference/synGetWikiAttachments.html index 43833d82..8fa725ee 100644 --- a/docs/reference/synGetWikiAttachments.html +++ b/docs/reference/synGetWikiAttachments.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synGetWikiHeaders.html b/docs/reference/synGetWikiHeaders.html index 852da150..939be639 100644 --- a/docs/reference/synGetWikiHeaders.html +++ b/docs/reference/synGetWikiHeaders.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synInvalidateAPIKey.html b/docs/reference/synInvalidateAPIKey.html index 4c0c7e14..ed7424f9 100644 --- a/docs/reference/synInvalidateAPIKey.html +++ b/docs/reference/synInvalidateAPIKey.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synInviteToTeam.html b/docs/reference/synInviteToTeam.html index 4b91850a..5fbef550 100644 --- a/docs/reference/synInviteToTeam.html +++ b/docs/reference/synInviteToTeam.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synIsCertified.html b/docs/reference/synIsCertified.html index 26eb1f15..331c648c 100644 --- a/docs/reference/synIsCertified.html +++ b/docs/reference/synIsCertified.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synLogin.html b/docs/reference/synLogin.html index 818758d5..7ad2ff8b 100644 --- a/docs/reference/synLogin.html +++ b/docs/reference/synLogin.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synLogout.html b/docs/reference/synLogout.html index a6d2d7a7..644c74ce 100644 --- a/docs/reference/synLogout.html +++ b/docs/reference/synLogout.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synMd5Query.html b/docs/reference/synMd5Query.html index d31fcf1f..bdc2f35b 100644 --- a/docs/reference/synMd5Query.html +++ b/docs/reference/synMd5Query.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synMove.html b/docs/reference/synMove.html index ce381c2d..f535e96c 100644 --- a/docs/reference/synMove.html +++ b/docs/reference/synMove.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synOnweb.html b/docs/reference/synOnweb.html index f11c682a..29bca56b 100644 --- a/docs/reference/synOnweb.html +++ b/docs/reference/synOnweb.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synPrintEntity.html b/docs/reference/synPrintEntity.html index 019d1862..7bf104a6 100644 --- a/docs/reference/synPrintEntity.html +++ b/docs/reference/synPrintEntity.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synRemoveFromDownloadList.html b/docs/reference/synRemoveFromDownloadList.html index b2b98096..d793c3e6 100644 --- a/docs/reference/synRemoveFromDownloadList.html +++ b/docs/reference/synRemoveFromDownloadList.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synRestDELETE.html b/docs/reference/synRestDELETE.html index 51a310de..c820c18c 100644 --- a/docs/reference/synRestDELETE.html +++ b/docs/reference/synRestDELETE.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synRestGET.html b/docs/reference/synRestGET.html index ad7eedec..f409c2b7 100644 --- a/docs/reference/synRestGET.html +++ b/docs/reference/synRestGET.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synRestPOST.html b/docs/reference/synRestPOST.html index 0b4b6237..e39925b9 100644 --- a/docs/reference/synRestPOST.html +++ b/docs/reference/synRestPOST.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synRestPUT.html b/docs/reference/synRestPUT.html index c64dfab6..239ba1d8 100644 --- a/docs/reference/synRestPUT.html +++ b/docs/reference/synRestPUT.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSendMembershipInvitation.html b/docs/reference/synSendMembershipInvitation.html index d8b8884a..a81536de 100644 --- a/docs/reference/synSendMembershipInvitation.html +++ b/docs/reference/synSendMembershipInvitation.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSendMessage.html b/docs/reference/synSendMessage.html index 2c9f2431..a2a4f598 100644 --- a/docs/reference/synSendMessage.html +++ b/docs/reference/synSendMessage.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSetAnnotations.html b/docs/reference/synSetAnnotations.html index a56eda43..504dc11d 100644 --- a/docs/reference/synSetAnnotations.html +++ b/docs/reference/synSetAnnotations.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSetEndpoints.html b/docs/reference/synSetEndpoints.html index 74702bb8..94bbbe49 100644 --- a/docs/reference/synSetEndpoints.html +++ b/docs/reference/synSetEndpoints.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSetPermissions.html b/docs/reference/synSetPermissions.html index fae30bd4..6b06bf67 100644 --- a/docs/reference/synSetPermissions.html +++ b/docs/reference/synSetPermissions.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSetProvenance.html b/docs/reference/synSetProvenance.html index 3cdc5c95..49d81512 100644 --- a/docs/reference/synSetProvenance.html +++ b/docs/reference/synSetProvenance.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSetStorageLocation.html b/docs/reference/synSetStorageLocation.html index 8cd04849..746ed9d1 100644 --- a/docs/reference/synSetStorageLocation.html +++ b/docs/reference/synSetStorageLocation.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synStore.html b/docs/reference/synStore.html index 204a2248..9affa116 100644 --- a/docs/reference/synStore.html +++ b/docs/reference/synStore.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synSubmit.html b/docs/reference/synSubmit.html index 6a650237..5183adfd 100644 --- a/docs/reference/synSubmit.html +++ b/docs/reference/synSubmit.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synTableQuery.html b/docs/reference/synTableQuery.html index 0de9d51c..75ce6634 100644 --- a/docs/reference/synTableQuery.html +++ b/docs/reference/synTableQuery.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synUpdateActivity.html b/docs/reference/synUpdateActivity.html index eb33b445..e3df5f51 100644 --- a/docs/reference/synUpdateActivity.html +++ b/docs/reference/synUpdateActivity.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synUploadFileHandle.html b/docs/reference/synUploadFileHandle.html index cd9cbf3c..4779f468 100644 --- a/docs/reference/synUploadFileHandle.html +++ b/docs/reference/synUploadFileHandle.html @@ -18,7 +18,7 @@ synapser - 1.1.0 + 1.2.0 diff --git a/docs/reference/synapser-package.html b/docs/reference/synapser-package.html index 2401f011..1ddfb2eb 100644 --- a/docs/reference/synapser-package.html +++ b/docs/reference/synapser-package.html @@ -17,7 +17,7 @@ synapser - 1.1.0 + 1.2.0 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)