Dnanexus Integration

Data Operations

Quick Navigation

• Safety and lifecycle

• Transfer tool selection

• Small transfers

• Upload Agent

• Download Agent

• Python transfers

• Search and metadata

• Records and folders

• Cloning and archival

• Deletion

• Batch checklist

Safety Model

DNAnexus data objects live in projects or other data containers. Before a mutation:

1. Resolve the project to a project-... ID.

2. Resolve every path to an object ID.

3. Detect duplicate names.

4. Inspect state, archival state, size, and relevant metadata.

5. Confirm source/destination permissions and restrictions.

6. Show exact IDs and impact for deletion, cloning, archival, or egress.

Names and paths are convenient for humans but are not immutable identifiers. Use IDs in automation.

Object Lifecycle

Files use:

open → closing → closed

• open: parts/content can still be uploaded.

• closing: finalization is in progress; content cannot be read or written.

• closed: content is immutable and available to download/share.

Files must be closed before they can be read or cloned. They may be submitted as job inputs while open or closing, but the job remains waiting_on_input until closure. Open/closing files inactive for about 24 hours are considered abandoned and are later deleted by the platform.

When a data object closes, content plus types, details/links, and visibility become fixed. User-editable metadata such as name, properties, and tags can still be managed according to permissions.

Records may intentionally remain open when mutable structured details are required. Document this exception because open records weaken reproducibility.

Transfer Tool Selection

Use platform transfer agents when resumability and per-part integrity matter.

Small Transfers with dx

Upload:

dx upload "sample.fastq.gz" \
  --path "project-xxxx:/raw/sample.fastq.gz" \
  --property "sample_id=S001" \
  --tag "raw"

Download:

dx download "project-xxxx:/results/sample.bam" \
  --output "sample.bam"

Use quoted full paths. If a name is non-unique, use the object ID.

For scripts, use --brief or machine-readable output where supported instead of parsing human-formatted tables.

Current dx warns when a download or generated download URL targets a file flagged as malicious. Stop on that warning unless the user approves a containment procedure that prevents execution and protects the local system.

Upload Agent

Upload Agent is resumable and uses parallel connections. Important behavior:

• Uncompressed files are compressed by default.

• .gz is appended to the remote name.

• Already compressed inputs are not recompressed.

• --do-not-compress preserves the original bytes/name behavior.

• Repeating the same command resumes a matching incomplete transfer.

• --wait-on-close blocks until uploaded file objects are closed.

• Per-part Content-MD5 is verified by the platform.

Example:

ua \
  --project "project-xxxx" \
  --folder "/raw" \
  --wait-on-close \
  --progress \
  "sample.fastq.gz"

For an uncompressed file that must not be transformed:

ua \
  --project "project-xxxx" \
  --folder "/raw" \
  --do-not-compress \
  --wait-on-close \
  "reference.fa"

Do not run ua --env in captured output because it displays the active token. Treat any Upload Agent --auth-token value and the toolkit DX_SECURITY_CONTEXT as secrets.

Use --do-not-resume only when creating a deliberate second copy. Otherwise let the agent resume interrupted uploads.

Download Agent

Download Agent consumes a BZIP2-compressed JSON manifest. Use the manifest creation utility from the official dnanexus/dxda release and review its resolved file set before starting egress.

Download Agent checks the secret DX_API_TOKEN and otherwise falls back to ~/.dnanexus_config/environment.json. This is a Download Agent-specific variable; do not assume it configures Upload Agent, dx, or dxpy.

dx-download-agent download "manifest.json.bz2"
dx-download-agent progress "manifest.json.bz2"
dx-download-agent inspect "manifest.json.bz2"

inspect revalidates downloaded parts against manifest checksums. If a part is missing or corrupt, rerun download. Run inspect before retrying files that were moved, removed, or changed after a completed download; a bare download trusts its completion database and does not discover these changes by itself.

Before a large download:

• Confirm local free space.

• Confirm data egress approval and cost.

• Confirm download restrictions/TRE policy.

• Check that all files are live and closed.

• Review the manifest for unexpected projects or PHI.

• Use a token that remains valid for the expected transfer duration.

Do not place an API token in a Docker command line or committed compose file.

Python Upload and Download

from pathlib import Path

import dxpy

project_id = "project-xxxx"
Path("downloads").mkdir(parents=True, exist_ok=True)

remote = dxpy.upload_local_file(
    "sample.fastq.gz",
    project=project_id,
    folder="/raw",
    properties={"sample_id": "S001"},
    tags=["raw"],
    wait_on_close=True,
    show_progress=True,
)

dxpy.download_dxfile(
    remote,
    str(Path("downloads") / "sample.fastq.gz"),
    project=project_id,
    show_progress=True,
)

project on download is also a billing/context hint. Pass it when the same file has copies in multiple projects or the billing context matters.

Read a remote file as a stream:

import dxpy

with dxpy.open_dxfile("file-xxxx", project="project-xxxx") as stream:
    first_chunk = stream.read(1024)

DXFile.open_file() is not a current dxpy method; use dxpy.open_dxfile().

Search

CLI

dx find data \
  --class file \
  --path "project-xxxx:/results" \
  --name "*.bam" \
  --name-mode glob

Use dx find data --help from the installed toolkit for current filter flags.

dxpy

import dxpy

results = dxpy.find_data_objects(
    classname="file",
    project="project-xxxx",
    folder="/results",
    recurse=True,
    name="*.bam",
    name_mode="glob",
    state="closed",
    archival_state="live",
    describe={
        "fields": {
            "name": True,
            "size": True,
            "created": True,
            "archivalState": True,
            "properties": True,
        }
    },
    limit=500,
)

for result in results:
    print(result["id"], result["describe"]["name"])

Critical semantics:

• Default name_mode is "exact".

• Use "glob" for * and ?.

• Use "regexp" only with a reviewed, bounded pattern.

• Results are generators and dxpy handles API pagination.

• Without limit, dxpy can traverse the full result set.

• Keep explicit SDK limit at most 1000 in dxpy 0.415.0: it is forwarded as the initial API page size. For larger bounded sets, apply itertools.islice to the generator with limit omitted.

• describe adds API work and may expose metadata; request only needed fields.

• archival_state requires a file class plus project/folder scope.

The API defaults to pages of at most 1000. DNAnexus documents a 200 API calls/second account limit; implement bounded concurrency and exponential backoff rather than flooding the service.

Metadata

Properties are string key/value pairs; tags are strings.

import dxpy

file_obj = dxpy.DXFile("file-xxxx", project="project-xxxx")
file_obj.set_properties(
    {
        "sample_id": "S001",
        "pipeline_version": "2.4.1",
    }
)
file_obj.add_tags(["validated", "release-2026-07"])
file_obj.rename("S001.aligned.bam")

Avoid direct identifiers in tags/properties when projects contain PHI. Follow the organization's approved metadata model.

Metadata updates affect discovery and provenance. Review overwrite semantics before replacing a full property/detail mapping. set_properties() changes the supplied keys; passing None for a key removes that property. set_details() replaces the entire details value on an open object. Use a closed record for immutable scientific provenance.

Records

Create a closed immutable record:

import dxpy

record = dxpy.new_dxrecord(
    project="project-xxxx",
    folder="/metadata",
    name="run-001",
    types=["RunMetadata"],
    details={
        "pipeline": "rna-seq",
        "pipeline_version": "2.4.1",
    },
    close=True,
)

Create an open record only when continued mutation is required:

record = dxpy.new_dxrecord(
    project="project-xxxx",
    name="mutable-status",
    details={"state": "queued"},
    close=False,
)
record.set_details({"state": "running"})
record.close()

Closing fixes details and links. For append-only provenance, prefer creating a new versioned record instead of mutating a shared open record.

Folders

import dxpy

project = dxpy.DXProject("project-xxxx")
project.new_folder("/analysis/run-001/results", parents=True)
listing = project.list_folder(
    "/analysis/run-001",
    describe={"fields": {"name": True, "state": True}},
)

Move exact IDs:

project.move(
    "/analysis/run-001/final",
    objects=["file-xxxx", "record-yyyy"],
)

Never use a broad recursive operation until the folder listing and count have been shown to the user.

Cloning

import dxpy

source = dxpy.DXFile("file-xxxx", project="project-source")
clone = source.clone(
    project="project-destination",
    folder="/imports",
)
print(clone.get_id())

Requirements and caveats:

• Source object must be closed.

• VIEW or higher is needed on the source.

• UPLOAD or higher is needed on the destination.

• Source and destination must be in the same region. Cloning preserves the data object ID; do not treat it as a new globally unique object.

• Restricted projects/TREs can forbid cloning.

• Databases cannot be cloned.

• Hidden linked objects may be cloned with their visible parent.

• Archive transitions can block cloning.

• Cross-billTo cloning of archived data requires live objects.

• The clone is independent; removing the source does not remove the clone.

Use dx cp for project-to-project copies when folder structure is the primary interface:

dx cp \
  "project-source:/results" \
  "project-destination:/imports"

Confirm source, destination, file count, and billing entity first.

Archival

Archive and unarchive are billable/storage-affecting operations and may take time:

dx archive "project-xxxx:/old-results/sample.bam"
dx unarchive "project-xxxx:/old-results/sample.bam"

Before archiving:

• Check whether active workflows, collaborators, or published outputs need it.

• Check all copies and billing behavior.

• Confirm the target is a file or intended folder.

Before unarchiving:

• Confirm retrieval cost and required completion time.

• Avoid launching dependent jobs until files return to live.

Programmatic wrappers exist as dxpy.api.project_archive() and dxpy.api.project_unarchive(), but prefer the CLI for one-off human-reviewed operations.

Deletion

Data removal is irreversible on the platform. Removing a visible object can also remove orphaned hidden linked objects.

Safe sequence:

1. List the exact IDs.

2. Describe each object.

3. Confirm project, folder, size, state, and linked-object impact.

4. Ask for confirmation.

5. Remove by ID.

6. Verify absence and record an audit note outside the deleted data.

Project controls are distinct:

• protected=true restricts project-data deletion to project administrators; when false, contributors can also delete.

• destroyProtected=true blocks destruction of the entire project regardless of requester permissions until an authorized administrator clears it.

• Project destruction removes every object. It fails while jobs are active unless terminateJobs=true, which force-terminates them.

Never clear destroyProtected, set terminateJobs=true, or destroy a project as an implicit extension of an object-deletion request. Each requires separate explicit authorization after listing active jobs, project protections, billing context, and total data impact.

Python:

import dxpy

project = dxpy.DXProject("project-xxxx")
project.remove_objects(["file-xxxx"], force=False)

Recursive folder removal:

project.remove_folder("/obsolete/run-001", recurse=True, force=False)

This is dangerous. Removing / recursively deletes all container contents. Never generate or execute that operation.

The API removes at most 10,000 objects per folder-removal request. Do not automatically loop partial deletion without rechecking the remaining scope.

Project deletion, permission changes, and delegated overrideProjectAccess deletion require separate explicit authorization.

Batch Operation Checklist

• Bound result count and concurrency.

• Materialize and review the target ID list before mutation.

• Preserve a machine-readable manifest of source IDs and destinations.

• Make operations restartable/idempotent.

• Do not treat duplicate names as one object.

• Check file state after upload.

• Validate transfer integrity.

• Capture failures without logging credentials or sensitive metadata.

• Reconcile completed, skipped, and failed IDs.

• Respect service limits and use exponential backoff.