Tutorial purpose | Prerequisites | 1. Create a new project | 2. Print stored attributes about your project | 3. Get an existing project | Clean Up | References used in this tutorial
Package: synapser 3.0.0
Dan Lu
synapser: R Language Bindings for Synapse API
Provides R language bindings for the 'Synapse' platform <https://www.synapse.org>, a collaborative research platform from Sage Bionetworks for sharing data, tracking analyses, and managing provenance. Supports authentication, uploading and downloading files, managing projects, folders, tables, views, annotations, and access permissions. Built on the official 'Synapse' 'Python' client ('synapseclient') via the 'reticulate' package.
Authors:
synapser_3.0.0.tar.gz
synapser_3.0.0.zip(r-4.7-any)synapser_3.0.0.zip(r-4.6-any)synapser_3.0.0.zip(r-4.5-any)
synapser_3.0.0.tgz(r-4.6-any)synapser_3.0.0.tgz(r-4.5-any)
synapser_3.0.0.tar.gz(r-4.7-any)synapser_3.0.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
synapser/json (API)
| # Install 'synapser' in R: |
| install.packages('synapser', repos = c('https://sage-bionetworks.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sage-bionetworks/synapser/issues
Pkgdown/docs site:https://r-docs.synapse.org
Last updated from:c74ced761d (on SYNR-1649-upgrade-pythonclient-4-14). Checks:6 WARNING, 1 OK, 1 ERROR, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 189 | ||
| source / vignettes | OK | 287 | ||
| linux-release | WARNING | 190 | ||
| macos-release | WARNING | 206 | ||
| macos-oldrel | WARNING | 194 | ||
| windows-devel | ERROR | 285 | ||
| windows-release | WARNING | 286 | ||
| windows-oldrel | WARNING | 212 | ||
| wasm-release | FAIL | 104 |
Exports:.addPythonAndFoldersToSysPath.assignEnumCallback.buildExamplesRdContent.buildMethodsListContent.checkForUpdate.cherryPickTableFunctionFilter.cleanExampleBody.convertInlineCode.convertMarkdownLinks.convertMkdocstringsCrossRefs.convertPOSIXToCharacterTimestamp.convertToRType.convertToRTypeFromSchema.convertToSynapseType.convertToSynapseTypeFromSchema.createFormalArgs.defineOperationsFallbacks.defineOverloadFunctions.defineRPackageFunctions.ensureMetaCols.escapeRdPercent.extractColumnNames.extractColumnTypes.formatDefaultValueForUsage.functionalMethodDispatch.functionalMethodIsClassLevel.functionNameMappingSynapse.functionNameMappingSynapseclientModels.gateway.getGateway.googleSectionHeaderPattern.initPyPkgInfo.isClassLevelFunctionalMethod.isVersionOutOfDate.modelClassesToInclude.modelClassMethodsToOmit.modelsFunctionFilter.modelsFunctionNamesToOmit.NAMESPACE.operationsClassesToInclude.operationsClassFilter.operationsFunctionNames.operationsFunctionNamesFilter.operationsUnsupportedModelMethods.parseArgSectionBody.printVersionOutOfDateWarnings.rAuthMessage.readCsv.readCsvBasedOnSchema.removeAllClassesClassFilter.removeAllFunctionsFunctionFilter.removeEmptyRdSections.replaceAuthMessage.resolveCrossRefRName.retagShortClassName.saveToCsv.saveToCsvWithSchema.sectionsWithHeader.sectionText.setGenericCallback.simplifyVersion.splitGoogleStyleSections.storeArgText.stripCodeFenceMarkers.synapseClassFunctionFilter.synapseClassMethodsToInclude.synapseModelClassFilterActivityActivityOptionsaddPrefixAgentAgentPromptAgentSessionapplyFunctionNameMappingas.listautoGenerateClassesautoGenerateClassesWithFunctionalInterfaceautoGenerateEnumautoGenerateFunctionsautoGenerateRdFilescapitalizeFirstLettercleanUpStackTraceColumncreateClassRdContentcreateFunctionRdContentcreateMethodContentDatasetDatasetCollectiondefineClassMethoddefineConstructordefineEnumdefineFunctiondefineFunctionalClassMethoddetermineArgsAndKwArgsDownloadListItemEntityRefEntityViewEvaluationFileFileOptionsFolderformatArgsForArgumentSectiongenerateFunctionalInterfaceInfogenerateRdFilesgenerateRWrappersgetClassInfogetDescriptiongetEnumInfogetErrorsgetExampleSectionsgetFunctionInfogetNotegetReturnedinsertLatexNewLinesJSONSchemaJsonSubColumnLinkLinkOptionsMaterializedViewnextElemOrganizationparseArgDescriptionsFromDetailsProjectpyVerbiageToLatexremoveNullssnakeToCamelStorageLocationStorageLocationTypeStoreContainerOptionsStoreFileOptionsStoreGridOptionsStoreJSONSchemaOptionsStoreTableOptionsSubmissionSubmissionBundleSubmissionStatusSubmissionViewsynAddColumnsynAddItemsynBatchUpdateSubmissionStatusessynBindSchemasynCancelsynChangeMetadatasynCopysynCreatesynDeletesynDeleteColumnsynDeleteInvitationsynDeletePermissionssynDeleteProjectSettingsynDeleteRowssynDisassociateActivityFromEntitysynDownloadListAddsynDownloadListClearsynDownloadListFilessynDownloadListManifestsynDownloadListRemovesynFindEntityIdsynFlattenFileListsynFromUrisynGenerateSyncManifestsynGetsynGetAclsynGetAllEvaluationssynGetAllSubmissionStatusessynGetAttachmentsynGetAttachmentHandlessynGetAttachmentPreviewsynGetAvailableEvaluationssynGetBodysynGetChatHistorysynGetEvaluationsByProjectsynGetEvaluationSubmissionBundlessynGetEvaluationSubmissionssynGetFromIdsynGetFromNamesynGetFromParentsynGetFromPathsynGetFromUsernamesynGetInvalidValidationsynGetJsonSchemassynGetMarkdownFilesynGetOpenInvitationssynGetPermissionssynGetProjectSettingsynGetSchemasynGetSchemaDerivedKeyssynGetSchemaValidationStatisticssynGetSessionsynGetStsStorageTokensynGetSubmissionCountsynGetTeamMemberssynGetUserMembershipStatussynGetUserSubmissionBundlessynGetUserSubmissionssynGetVersionssynIndexFilesForMigrationsynInviteToTeamsynIsCertifiedsynIsSynapseIdsynListsynListAclsynLoginsynLogoutsynMapDirectoryToAllContainedFilessynMd5QuerysynMigrateIndexedFilessynOnwebsynPrintEntitysynPromptsynQuerysynQueryPartMasksynReformatAttachmentFileNamesynRegistersynRemoveItemsynReorderColumnsynRestDeletesynRestGetsynRestoresynRestPostsynRestPutsynSendMessagesynSetEndpointssynSetPermissionssynSetPropertiessynSetStorageLocationsynSnapshotsynStartsynStartSessionsynStoresynStoreRowssynSyncFromSynapsesynSyncToSynapsesynUnbindSchemasynUnzipGzippedFilesynUpdatesynUpdateAclsynUpdateRowssynUpsertRowssynValidateSchemasynWalkTableTableOptionsTeamusageUsedEntityUsedURLUserPreferenceUserProfileVirtualTableWikiHeaderWikiHistorySnapshotWikiOrderHintWikiPagewriteContent
Dependencies:herejsonlitelatticeMatrixpngrappdirsRcppRcppTOMLreticulaterjsonrlangrprojrootwithr
Project
Last update: 2026-10-29
Started: 2026-09-30
Tables
Tutorial purpose | Prerequisites | 1. Creating a table | Initial setup | Example data | Loading data | 2. Querying for data | 3. Changing Data | Appending new rows | Updating existing rows | Upserting (Update or Insert) rows | 4. Changing Table Structure | 5. Deleting Table Rows & Tables | Working with dates and datetimes | Storing timezone-aware datetimes (recommended) | Storing naive datetimes | Storing dates without a time of day | Loading date columns from a CSV | Querying datetime data back | Clean Up
Last update: 2026-10-29
Started: 2017-08-14
Datasets
Tutorial Purpose | Prerequisites | 1. Get the ID of your Synapse project | 2. Create your Dataset | 3. Add files to the dataset | 4. Retrieve the dataset | 5. Query the dataset | 6. Add a custom column to the dataset | 7. Save a snapshot of the dataset | References
Last update: 2026-10-28
Started: 2026-10-21
Access Control
Core Concepts | Access Control Lists (ACLs) | Benefactors and Inheritance | Permission Types | Special Principal IDs | Common Use Cases | Research Collaboration | Hierarchical Access Control | Data Governance | Best Practices | Security Considerations | Learn More | API References
Last update: 2026-10-21
Started: 2026-10-02
Dataset Collections
Tutorial Purpose | Prerequisites | 1. Get the ID of your Synapse project | 2. Create your Dataset Collection | 3. Add Datasets to the Dataset Collection | 4. Retrieve the Dataset Collection | 5. Add a custom column to the Dataset Collection | 6. Query the Dataset Collection | 7. Save a snapshot of the Dataset Collection | References
Last update: 2026-10-21
Started: 2026-09-30
Domain Models of Synapse
Overview | Entity | Projects | Folders | Files | Annotations | Activity/Provenance
Last update: 2026-10-21
Started: 2026-10-01
Downloading data by Synapse ID
Tutorial Purpose | Prerequisites | 1. Build a mapping of Synapse IDs to download directories | 2. Download all files | References used in this tutorial
Last update: 2026-10-21
Started: 2026-10-02
Downloading data in bulk
Tutorial Purpose | Prerequisites | 1. Download all files/folder from a project | First let's set up some constants we'll use in this script | Next we'll create an instance of the Project we are going to sync | Finally we'll sync the project from synapse to your local machine | 2. Control manifest CSV generation during download | 3. Download all files/folders for a specific folder within the project | 4. Loop over all files/folders on the project/folder object instances | References used in this tutorial
Last update: 2026-10-21
Started: 2026-10-02
EntityViews
Tutorial purpose | Prerequisites | 1. Find the Synapse ID of your project | 2. Create an EntityView with Columns | 3. Query the EntityView | 4. Update rows in the EntityView | 5. Update the scope of your EntityView | 6. Update the types of Entities included in your EntityView | Results | References used in this tutorial
Last update: 2026-10-21
Started: 2026-09-30
Evaluations
Tutorial purpose | Prerequisites | 1. Create and update an Evaluation on Synapse | 2. Update the ACL of an Evaluation on Synapse | 3. Retrieve and delete all Evaluations from a given Project | References
Last update: 2026-10-21
Started: 2026-09-30
Files
Overview | Prerequisites | 1. Upload several files to Synapse | First, retrieve the project and folders created in the Folders vignette | Next let's create all of the File objects to upload content | 2. Print stored attributes about your files | 3. List all Folders and Files within my project | Results | Clean Up | References used in this tutorial
Last update: 2026-10-21
Started: 2026-09-30
Folders
Overview | Load the package and log in | Prerequisites | 1. Create a new folder | 2. Print stored attributes about your folder | 3. Create 2 sub-folders | Results | Clean Up | References used in this tutorial
Last update: 2026-10-21
Started: 2026-09-30
Installation
Prerequisites | Install SynapseR from GitHub | A specific release, by its tag (for example, 2.1.5) | Install R | SynapseR Installation (WIP) | Install from RStudio | Install from R | Step-by-Step Installation with Dependency Management | Prerequisites: Verify Python Installation | R Installation Steps | Alternative Simple Installation | Troubleshooting | (Optional) Managing Python | Option 1: Using pyenv (Recommended) | Install pyenv | Configure pyenv | Install and set Python 3.10 | Option 2: Official Python Installer (Alternative)
Last update: 2026-10-21
Started: 2024-02-04
Properties and annotations
Properties and annotations, implementation details | Properties and annotations are kept separate | Setting properties and annotations
Last update: 2026-10-21
Started: 2026-10-01
Sharing Settings (ACL Management)
Sharing Settings (ACL Management) in Synapse | Tutorial Purpose | Prerequisites | Understanding Permission Types | Special Principal IDs | Permission Inheritance and Benefactors | Benefactor Concept | Default Inheritance Behavior | Applying Permissions to Other Entities | 1. Set Up and Get Project | 2. Create a main folder to set custom sharing settings | 3. Examine Current Permissions | 4. Get ACL for Specific Principal | 5. Set Custom Permissions | 6. Create Sub-folder with Different Permissions | 7. List All ACLs | 8. Advanced Permission Management | 9. Remove Permissions | 10. Delete Entire ACLs | 11. Final Overview | Key Concepts Covered | Inheritance vs Local ACLs | Permission Management Functions | Best Practices | Common Use Cases | Research Collaboration | Data Sharing | Hierarchical Access | References used in this tutorial
Last update: 2026-10-21
Started: 2026-10-01
Structuring Your Synapse Project
Permissions Management | Project Structure | Top Level Folder Names | Flattened Data Layout Example | Hierarchy Data Layout Example | File Views | Creating the File View | Uploading annotations with manifests | An example: ELITE portal
Last update: 2026-10-21
Started: 2026-10-01
Submissions, SubmissionStatuses, SubmissionBundles
What are Submissions? | Key Concepts | How Submissions Work | Related Objects | What You'll Learn | Tutorial Purpose | Prerequisites | 1. Participating in a Synapse challenge | Initial setup | 1. Make a submission to an existing evaluation queue on Synapse | 2. Fetch your existing submission | 3. Count your submissions | 4. Fetch all of your submissions from an existing evaluation queue on Synapse | 5. Check the status of your submission | 6. Cancel your submission | 2. Organizing a Synapse challenge | 1. Annotate a submission to score it | 2. Batch-update submission statuses | 3. Fetch the submission bundles for an evaluation queue | 4. Allow cancellation of submissions | 5. Delete submissions | References
Last update: 2026-10-21
Started: 2026-09-30
Synapse R Client Overview
Overview | Installation | Connecting to Synapse | Accessing Data | Organizing Data in a Project | Annotating Synapse Entities | Provenance | Tables | Wikis | Evaluations | Sharing Access to Content | File Views | Accessing the API Directly | Synapse Utilities | More information
Last update: 2026-10-21
Started: 2017-08-04
Troubleshooting
Troubleshooting (WIP) | Build Synapser | Build Synapser when creating vignettes | Dependency Conflicts (rjson/reticulate) | Python Version Compatibility | R Version Compatibility | Troubleshooting R Version Issues: | Using Synapser with reticulate | Type Conversions | Poisoned cache and endswith error
Last update: 2026-10-21
Started: 2019-01-23
Uploading data in bulk
Tutorial Purpose | Prerequisites | 1. Set up constants | 2. Create a manifest CSV file to upload data in bulk | 3. Upload the data in bulk | 4. Add an annotation to our manifest file | 5. Create an Activity/Provenance | References used in this tutorial
Last update: 2026-10-21
Started: 2026-10-02
Virtual Tables
Tutorial purpose | Prerequisites | 1. Log in, get your project, and create tables with data | 2. Create and query a basic Virtual Table | 3. Create a Virtual Table with column selection | 4. Create a Virtual Table with filtering | 5. Create a Virtual Table with ordering | 6. Create a Virtual Table with aggregation | Clean Up | References
Last update: 2026-10-21
Started: 2026-09-30
Wikis
Overview | Prerequisites | 1. Create a Wiki page | Initial setup | 2. Update a Wiki page | 3. Restore a Wiki page to a previous version | 4. Get a Wiki page | 5. Create a sub-Wiki page | 6. Create a Wiki page from markdown | Create a Wiki page directly from a string | Create a Wiki page from a markdown file | 7. Download Wiki page markdown | Download the markdown file URL for a Wiki page | Download the markdown file for a Wiki page created from plain text | Download the markdown file for a Wiki page created from a markdown file | 8. Create Wiki pages with attachments | Create a Wiki page with attachments | 9. Retrieve attachment handles and URLs, and download attachments and previews | Get attachment handles | Get attachment URL without downloading | Download an attachment file | Get attachment preview URL | Download an attachment preview | 10. Retrieve Wiki page hierarchy using WikiHeader | 11. Access Wiki version history using WikiHistorySnapshot | 12. Get, set, and update Wiki page ordering using WikiOrderHint | Get the current order hint | Set the Wiki order hint | Update Wiki order hint | 13. Delete Wiki pages | Where to go next
Last update: 2026-10-21
Started: 2026-09-30
Migrating to synapser 3.0
Who this guide is for | Why upgrade now | Why this release is not backwards compatible | What you gain in 3.0 | Before you upgrade | Four patterns to relearn | 1. Instance-first, then pipe | 2. Properties are no longer nested under $properties and synSetProperties | 3. Arguments are snake_case, matching the Python client exactly | 4. Mutation goes through synSetProperties(), then an explicit synStore() | Side-by-side reference: common operations | Removed functions | Renamed or restructured | Not currently exposed in 3.0 | New in 3.0: capabilities that didn't exist before | Richer access control | Container traversal and sync | JSON Schema binding and validation | Known pitfall: integer literals | Worked example: before and after | Where to go next
Last update: 2026-10-02
Started: 2026-10-02
Manifest CSV
Manifest file format | Required fields for upload | Standard fields | Metadata fields (ignored during upload) | Annotations | Multiple values of annotations per key | Dates in the manifest file | Manifest sources | Example manifest file | References
Last update: 2026-10-01
Started: 2026-10-01
Configuration
.synapseConfig sections | [default] and [profile ] | [sftp://hostname] | [https://s3.amazonaws.com/bucket_name] | [cache] | [debug] | [endpoints] | [transfer]
Last update: 2026-09-30
Started: 2026-09-30
Data Upload, Download, and Delete
Overview | Key differences from the legacy API: | Load the package | Login | Create a Project | Create a Folder | Upload a File | Version the file | Add, Update and Remove Annotations | Add annotations to a file | Update annotations of a file | Remove annotations of a file | Download a File | Download a Specific Version | Clean Up
Last update: 2026-09-30
Started: 2026-09-30
Authentication
Prerequisites | One Time Login | Use .synapseConfig | Editing the ~/.synapseConfig file | Transitioning from One Profile to Multiple | Logging in with your ~/.synapseConfig file | Logging in via R | For more information, see:
Last update: 2026-09-30
Started: 2026-09-30
Docker
Last update: 2026-04-16
Started: 2017-11-20
System Dependencies
Required System Dependencies | Python Version Requirements | Ubuntu Installation | Redhat Installation
Last update: 2026-04-16
Started: 2018-08-17
