jinko-protocol

Jinkō Protocol SDK Workflows

Use this skill for protocol-design mechanics through the SDK. Keep the separation of concerns explicit: the model defines treatment-regimen functions and inputs; the protocol instantiates those inputs per arm.

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.

Separation Of Concerns

• Protocol designs only override component values, with different override values per arm.
• Dosing functionality is defined at the model level: schedule parameterization, dose parameterization, treatment activation/deactivation through categorical parameters, route or administration mode through categorical parameters, and any formulas that interpret those inputs.
• In the model, define the treatment-regimen function and its input components.
• In the protocol, assign values to those inputs, as if instantiating that function for each arm.
• If a needed override key does not exist as a model input, switch to jinko-model first and add the model component or dosing logic there.

Core Rules

• Prefer client.create_protocol_design(arms, model=model) when a model is available.
• Use client.create_protocol_design_from_csv(csv_file_path=...) when arms come from a spreadsheet. Use the canonical metadata columns arm, control, active, and weight. The platform maps all other columns to overrides. This path does not accept a model argument; link a model with client.create_protocol_design(...) instead if that is required. See assets/toy_protocol_arms.csv for an example file and references/protocol-design.md for the SDK call.
• Link protocol designs to a model when possible so the protocol design carries the model snapshot reference.
• The override key must target a protocol-runnable model input, such as Dose or route in the toy model.
• Solving times are overridable per arm through the tMax and tStep keys, as assets/protocol.json shows. Use this when arms need different time horizons or different output resolution, for example when one reported figure runs to 7 days at hourly resolution and another runs to 56 days at daily resolution.
• Use formulas as strings, for example "1.0", "iv", or "PT24H" depending on the target component.
• Include control relationships when comparing arms; use armControl to identify the comparator arm.
• Edit individual arms on an existing design with protocol.arms (get, create, set_control, set_active, set_weight, set_override, delete, compare_overrides), not by replacing the raw design payload.
• Require explicit confirmation or script --apply before creating or updating project items.

Project Folder Hygiene

• Prefer creating protocol designs 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 SDK creation calls that support it.

Bundled Assets

• assets/toy_protocol_arms.json: three arms with two routes and three doses. The iv route repeats across two arms.
• assets/toy_protocol_arms.csv: the same three arms in CSV form, one row per arm, for use with create_protocol_design_from_csv.
• assets/protocol.json: subset of the OpenAPI schema for protocol arm shape.

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.create_protocol_design: creates a three-arm protocol design, optionally linked to a model.
• jinko.cli.create_protocol_design_from_csv: creates a protocol design from a CSV file of arms.
• jinko.cli.edit_protocol_design_arms: upserts arms and overrides on an existing protocol design via the arms mutator service. It retains arms and overrides omitted from the input; use explicit protocol.arms.delete(...) or arm.remove_override(...) calls for removals.
• jinko.cli.inspect_protocol_design: prints protocol content or a concise arm summary.

Examples:

python -m jinko.cli.create_protocol_design --model-sid cm-...
python -m jinko.cli.create_protocol_design --model-sid cm-... --apply
python -m jinko.cli.create_protocol_design --model-sid cm-... --folder 2026-06-15-regimens --create-folder --apply
python -m jinko.cli.create_protocol_design_from_csv --csv skills/jinko-protocol/assets/toy_protocol_arms.csv --apply
python -m jinko.cli.edit_protocol_design_arms --protocol-design-sid pd-... --arms skills/jinko-protocol/assets/toy_protocol_arms.json --apply
python -m jinko.cli.inspect_protocol_design --protocol-design-sid pd-... --summary

Arm Shape

Each arm should include:

• armName: stable arm identifier.
• armOverrides: list of { "key": "<model-input-id>", "formula": "<arm-specific-value>" } entries.
• armIsActive: usually true for active arms.
• armWeight: usually 1 unless weighted simulations are intentional (for calibration).
• armControl: null for the comparator arm, or another arm name for arms compared against a control.

Default toy arms:

• iv_low_dose: Dose=1.0, route=iv, no control arm.
• po_mid_dose: Dose=2.0, route=po, controlled by iv_low_dose.
• iv_high_dose: Dose=3.0, route=iv, controlled by iv_low_dose.

Reference Routing

• Read references/protocol-design.md for separation of concerns and SDK patterns.
• Read assets/protocol.json when validating arm payload shape.