`onecodex` client library v1.1.0

New

Added
updated_at
to
Analyses
schema
onecodex.models.Workflows
(a type of
onecodex.models.Analyses
) for Custom Workflows (https://docs.onecodex.com/en/collections/9673389-your-authored-workflows-on-one-codex)
Added
Jobs.run()
for running analyses including Workflows
onecodex.models.Assets
for querying and creating Workflow assets
Analyses.await_completion()
blocks until an analysis reaches a terminal state using adaptive polling.
onecodex analyses await <analysis_id>
CLI command, with
--timeout
,
--initial-interval
, and
--max-interval
options. Also available as
onecodex await <analysis_id>
for backward compatibility.
Analyses.logs()
fetches the job run logs for an analysis, with an optional
tail
parameter to limit the output to the last N lines.
onecodex analyses logs <analysis_id>
CLI command, with
--tail
to limit the number of log lines returned (defaults to 1000). Only available for custom workflow runs.
Jobs.create()
and
Jobs.update()
for creating and updating custom jobs from the Python client.
assets=[...]
accepts
Assets
instances directly;
dependencies=[{"job": parent_job, "output_dir": "..."}]
accepts
Jobs
instances directly.
onecodex jobs create
and
onecodex jobs update <job_id>
CLI commands.
onecodex download samples
accepts
-s
/
--sample
(repeatable) to download specific samples by ID. Mutually exclusive with
--project
and
--tags
.
onecodex jobs run
accepts
--args-json
to pass runtime arguments as a JSON object, preserving non-string types (integers, floats, booleans, arrays, objects).
-a
/
--arg
only supports string values; use
--args-json
when a job argument expects another type. Mutually exclusive with
-a
/
--arg
.
ocx.Jobs.get("...").details()
for retrieving CPU/memory/script/etc for Custom Workflows.

Changed

ApiRef
now accepts any object with a
field_uri
attribute (e.g. resource model instances), in addition to the existing
$ref
/
$uri
dict shapes. This lets users pass fetched resources directly into create/update calls.
OneCodexBase.create()
now validates kwargs against the schema declared in
_allowed_methods["create"]
(when one is set), mirroring how
update()
already worked. Surfaces server error messages instead of failing on response parsing.

Fixed

plot_pcoa
no longer flips axis orientation between runs; PCoA eigenvector signs are now pinned so the entry with the largest absolute value on each axis is positive.
CLI commands that take One Codex IDs (
onecodex samples
,
analyses
,
classifications
,
panels
,
workflows
,
documents download
,
jobs run
/
update
,
upload --sample-id
,
download samples --sample
) now validate the format up front and fail with a helpful error instead of an opaque 404.