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Skillsjinko-trial

jinko-trial

Data & analytics

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Updated 10-16 07:23

About this skill

Jinkō Trial SDK Workflows

Use this skill for trial setup, sanity checks, run/poll, and result download. Keep creation of upstream assets in their dedicated skills: jinko-model, jinko-vpop, jinko-protocol, jinko-data-table, and jinko-output-set (simple and advanced output sets).

PREREQUISITE: This skill needs an initialized jinko-sdk connection and an SDK satisfying its metadata.requires_sdk range. Run the jinko-sdk-setup skill (../jinko-sdk-setup/SKILL.md) and proceed only once its check passes. A session code can be exchanged only once, so call get_session_code again before this skill's own SDK process. If that skill is not found, install it from novainsilico/jinko-skills.

Minimum Trial

A minimum trial is composed of:

  • A computational model.
  • Solving options, using the model defaults unless an override is explicitly provided.
  • A simple output set, defined as the list of component time series that should be saved and visualized. Use model.time_dependent_ids() as the default output ids when the user has not specified ids.

Optional trial inputs:

  • Vpop.
  • Protocol design.
  • Data table design(s).
  • Advanced output set/scoring design.

Sanity Constraints

Do not launch while trial sanity reports errors. Always confirm this by calling trial.sanity() — not by re-running standalone checks from upstream skills (validate_scoring_formula, client.validate_scoring_condition, scoring_design.diagnostics, etc.). Those checks only validate an asset in isolation; they cannot see how it behaves once bound to this concrete trial. trial.sanity() is the same trial-context check the Jinkō UI runs before launch and is the source of truth for launch-readiness — see references/trial-setup.md for the pre-launch workflow and errors after standalone validation passed troubleshooting.

Typical constraints surfaced by trial sanity:

  • The computational model cannot have sanity errors.
  • All descriptors in the protocol must correspond to model components.
  • All descriptors in the vpop must correspond to model components.
  • All descriptors in data-table obsId columns must correspond to model components.
  • All data-table armScope values must correspond to protocol arms when a protocol is used.
  • The advanced output set (scoring design) must resolve cleanly against this trial's model outputs and simple output set — this can fail here (ADVANCED_OUTPUTS_ERRORS) even when jinko-output-set's standalone validation passed.

If sanity errors are reported, show them and ask whether the user wants help fixing the upstream asset.

Core SDK Methods

  • Create simple output set: client.create_simple_output_set(model, model.time_dependent_ids()) unless explicit output ids were requested. See jinko-output-set for measure shapes and advanced output sets (constraints/scalars/objectives).
  • Create trial: client.create_trial(model, data_tables=..., vpop=..., protocol=..., simple_output_set=..., advanced_output_set=...).
  • Edit solving options after creation with trial.edit_solving_options({...}), passing only the options to change. Partial solving_* arguments at creation raise ValueError. Use trial.get_solving_options() to inspect raw ISO 8601 duration strings, or trial.get_solving_options(duration_format="timedelta") for timedelta values. For focused edits, use trial.set_solving_times(t_max=timedelta(days=28), t_step="P1D") with either representation.
  • Pre-launch sanity check (required before run()): trial.sanity() — returns a raw dict (the JSON response, not a typed object) with one component report per key (model, protocol, vpop, outputSet for the simple output set, scorings for the advanced output set, dataTables, solvingTimes), each with ["sanity"]["errors"]/["sanity"]["warnings"] and ["sanity"]["componentsSanity"] for per-component detail.
  • Run trial: trial.run().
  • Poll: trial.wait_until_completed(timeout=1800).
  • Discover time series: trial.output_ids().
  • Discover scalars and arms: trial.results.summary().
  • Download time series as pandas when available: trial.results.timeseries({...}).to_dataframe().
  • Download scalars as pandas when available: trial.results.scalars([...]).to_dataframe().
  • Without pandas, use TabularDownload.raw_bytes; result payloads may be CSV or zipped CSV.
  • Calculated plot data, read-only and typed: trial.results.aggregate_scalars(...), aggregate_timeseries(...), tornado_sensitivity(...), survival_analysis(...), scalars_per_population(...) (scatter). Filters and groups both come from the descriptor handles (age.gte(18), sex.in_levels([...]), auc.group_by_quantiles(4), sex.group_by_levels()), plus trial.results.group_by_arm(). No import beyond JinkoClient is needed. Query the trial directly and do not create a TrialVisualization just to read data. Each response has a to_dataframe() method (requires pandas) that returns a tidy frame. By default, draw the frames with the Jinkō plot style (jinko.plotting; requires matplotlib and pandas in the active Python environment), which matches the web app plots: see references/trial-plots.md. The same filter and group vocabulary configures a stored visualization in jinko-trial-viz.
  • Ignore every time series and scalar whose id starts with __jinko. These are platform telemetry, such as __jinkoSolvingTime, __jinkoAllocationMiB, and __jinkoNumSteps. They differ between any two runs of the same trial and carry no scientific meaning, so exclude them before comparing results, reporting agreement, or computing any metric.

When data tables are attached, pass them through the supported data_tables= argument. Require each data table to report metadata.public.validForFitnessFunction is True before creating the trial; reject False, missing, and malformed values.

Project Folder Hygiene

  • Prefer creating output sets and trials inside a dedicated Jinkō folder instead of the project root. At the start of a workflow, ask for or propose a folder name, for example YYYY-MM-DD-<experiment-name>.
  • Reuse an existing exact-match folder when possible: client.get_folder_by_name(name, exact_match_only=True).
  • If the folder does not exist, create it only after user confirmation or when a script is run with --apply.
  • Resolve one folder object or folder id, then pass folder=folder to trial creation calls. For simple output sets, create them first and then move them with output_set.move_to_folder(folder).

Retry And Reuse Hygiene

  • For one user request, keep one named local setup script and update it rather than creating run_v2.py, run_v3.py, and similar copies.
  • When a trial or output set fails validation, inspect and repair the existing item first. Re-run trial.sanity() after the repair.
  • Create a new trial or output set only when the user requests an independent scenario, the existing item is immutable/incompatible, or a repair would destroy a result the user asked to preserve. State the reason when creating a replacement.

SDK Scripts

These are on PATH as console scripts once the SDK is installed, and also runnable via python -m as shown below.

  • jinko.cli.find_completed_trial_results: lists trials, finds the first completed one, prints its summary, and downloads TimeSeries and Scalar results to pandas DataFrames.
  • jinko.cli.setup_and_run_trial: creates a simple output set, creates a trial from model plus optional assets, sanity-checks, optionally runs, polls, and optionally downloads results.

Examples:

python -m jinko.cli.find_completed_trial_results --limit 20 --output-dir trial-results
python -m jinko.cli.setup_and_run_trial --model-sid cm-...
python -m jinko.cli.setup_and_run_trial --model-sid cm-... --output-id Drug
python -m jinko.cli.setup_and_run_trial --model-sid cm-... --output-id Drug --folder 2026-06-15-trial-run --create-folder --apply --run
python -m jinko.cli.setup_and_run_trial --model-sid cm-... --output-id Drug --vpop-sid vp-... --protocol-design-sid pd-... --data-table-sid dt-... --apply --run --download-results

Reference Routing

  • Read references/trial-setup.md for trial creation, the safe pre-launch sanity-check workflow, and troubleshooting ADVANCED_OUTPUTS_ERRORS/"The following advanced outputs have errors".
  • Read references/trial-results.md for completed-trial discovery and result downloads.
  • Read references/trial-plots.md to draw plot data as figures in the Jinkō style: time series, scalar distributions, tornado, survival, and scatter.