Sources and Version Baseline

Verification

Last verified: 2026-09-30

The dxpy symbols/signatures, CLI help, and bundled offline helpers were executed locally against the pinned SDK. Platform contracts and the remaining release versions were reviewed in current official documentation/source. Transfers, builds, launches, and compiler/Nextflow execution examples are illustrative; no authenticated or billable end-to-end run was performed. The current dxCompiler release is established by its tagged release, because the develop changelog still labels the 0.6.4 download-agent change as unreleased.

Version-specific examples in this skill are pinned for reproducibility. Before upgrading, inspect release notes, run scripts/inspect_dxpy.py, and rebuild/test apps in a non-production project.

Documentation Index and Releases

• [DNAnexus documentation index (llms.txt)](https://documentation.dnanexus.com/llms.txt)
• DNAnexus 2026 release notes
• Downloads
• [Index of dx commands](https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities.md)
• dx-toolkit GitHub repository
• dx-toolkit changelog
• dxpy on PyPI
• Generated Python API reference

The release notes are date-versioned by platform deployment. The skill baseline incorporates:

• 2026-09-22: dx-toolkit 415.0 Nextflow offline mode
• 2026-09-15: CLI login default expiration aligned to 18 hours
• 2026-08-18: normal login sessions shortened to two hours idle, 18 hours absolute
• 2026-08-11: user API tokens blocked for UKB RAP; dxCompiler 2.18.0 / dxda 0.6.4
• 2026-08-04: rebuild Nextflow applets to pick up upload-recovery fixes
• 2026-07-21: dx-toolkit 410.0 malicious-file download warning
• 2026-07-14: strengthened session/password controls
• 2026-06-23: dxCompiler 2.17.0 authenticated WDL imports
• 2026-06-09: file download API securityStatus
• 2026-05-19: dxCompiler resource-retry support
• 2026-03-17: automatic upgrade on insufficient-resource retry
• 2026-02-03: retired instance type validation
• 2026-01-27: dynamic instance type selection

Authentication

• Login and Logout
• Environment Variables
• dx-toolkit environment bootstrap
• API Authentication
• API Protocols and Errors

Key current points:

• Environment variables override saved CLI configuration.
• dx env displays token material.
• Tokens without explicit expiry default to one month.
• Token revocation terminates associated active jobs/transfers.
• New normal-policy login sessions expire after two hours idle and at most 18 hours after issuance; org policies may be stricter.
• User API tokens can be scoped to selected projects and access levels.
• User-generated API tokens cannot access UKB RAP resources.

Apps and Applets

• Introduction to Building Apps
• Developer Quickstart
• [App Metadata (dxapp.json)](https://documentation.dnanexus.com/developer/apps/app-metadata.md)
• I/O and Run Specifications
• App Execution Environment
• Apps API
• Applets, Jobs, and Entry Points API
• App Permissions
• Types of Errors
• Developing Apps and Applets FAQ

Dependencies:

• Dependency management
• Python packages in Ubuntu 24.04 AEE
• Asset Build Process
• Docker Images

Data and Projects

• Uploading and Downloading Files
• [dx upload](https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/small-sets-of-files/uploading-using-dx.md)
• [dx download](https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/small-sets-of-files/downloading-using-dx.md)
• Upload Agent
• Download Agent
• Download Agent repository
• Download Agent 0.6.4 release
• dxFUSE 1.6.1 release
• Data Object Lifecycle
• Records API
• Files API
• Data Object Metadata
• Folders and Deletion
• Cloning
• Project Permissions and Sharing
• Project API Methods
• Project Data Access Controls
• Search API
• Service Limits

Execution and Workflows

• Running Apps and Workflows
• Running Apps and Applets
• Running Workflows
• Monitoring Executions
• Job Lifecycle
• Execution Cost and Spending Limits
• Running Analyses API
• Workflows and Analyses API
• Building and Running Workflows
• Importing Workflows

WDL, CWL, and Nextflow

• dxCompiler repository
• dxCompiler 2.18.0 release
• dxCompiler release notes
• Running Nextflow Pipelines

Check these sources together. Platform documentation describes supported integration behavior; compiler/tool release notes describe version-specific language and runtime changes.

API Audit Coverage

• Authentication/protocol: Bearer header, JSON POST body, API version header, project-scoped tokens, session expiry, revocation, and UKB RAP restriction.
• /system/findDataObjects, /system/findExecutions, and /system/findProjects: request filters, results/next response shape, cursor continuation, per-page limits, and SDK generator limits.
• File create/upload/close/describe/download and record create/getDetails/ setDetails/close: SDK signatures and official lifecycle/transfer contracts. Object rename/setProperties/addTags and project clone/newFolder/listFolder/ move/removeObjects/removeFolder/archive/unarchive were checked against the metadata, container, and project API references. No mutations were executed.
• /app/new, /applet/new, app/applet/workflow run, /job/new, job/analysis describe and terminate: source manifest versus API payload, accepted classes/access/version values, resource-selector compatibility, return IDs, states, output references, timeout, retry, and cost controls. SDK waits were reviewed in 0.415.0 source; DXAnalysis.wait_on_done() can raise while partially_failed is still nonterminal.

Corrected Legacy Patterns

The previous skill version contained examples that should not be copied:

Refresh Procedure

When updating this skill:

1. Check PyPI for the current dxpy release and Python requirement.
2. Read platform release notes since the verification date.
3. Read dx-toolkit and dxCompiler release notes.
4. Run:

bash uv run --with "dxpy==<new-version>" \ "scripts/inspect_dxpy.py" --strict

1. Compare dx build --help, dx run --help, and search command help.
2. Test dxapp.json validation and a minimal build in a sandbox project.
3. Test representative file, job, analysis, WDL/CWL, and Nextflow workflows.
4. Update the date/version table and skill metadata.version.

Do not update examples from memory alone.