Artifact Outputs

Use artifact outputs when a module produces files that need to survive beyond the Python process, such as structures, ranked poses, reports, images, or summary JSON.

Local runs: structure3d sources

In biosimulant labs serve, point a structure3d visual at a file with source.path:

def visualize(self):
    return {
        "render": "structure3d",
        "data": {
            "title": "Top ranked complex",
            "format": "pdb",
            "source": {
                "kind": "artifact",
                "artifact_id": "top-complex",
                "path": str(self.top_complex_pdb),
            },
        },
    }

When Labs Serve collects run results, it resolves path. If the file exists, it records the file as a run artifact and sets source.url to /api/runs/{run_id}/artifacts/{artifact_id}. If artifact_id is missing, one is derived from the path. A source.url you set yourself is left unchanged.

Remote runs: the structure_artifacts output

Remote runs on the hosted platform also read a module output named structure_artifacts. This is a platform convention. The open-source package does not act on it.

Emit a record whose value holds fields ending in _file, either directly or under a payload key:

def outputs(self):
    return {
        "structure_artifacts": biosim.SignalSpec.record(
            schema={"payload": "json"},
            description="Files produced by the docking run.",
        )
    }
 
def execute(self, inputs, *, context):
    ...
    return {
        "structure_artifacts": {
            "payload": {
                "docking_output_file": str(self.output_pdbqt),
                "top_complex_file": str(self.top_complex_pdb),
                "pose_summary_file": str(self.pose_summary_json),
            }
        }
    }

For each *_file value that points at an existing file, the remote executor uploads the file with its size and SHA-256 hash and replaces the path in the run results with an artifact reference. Paths that do not exist are skipped. If a structure3d visual uses the same source.path, its artifact_id is reused.

Return each file separately. Do not return directories as *_file values. A non-file field such as prediction_dir can name the folder that groups them.

Common roles include:

See Also

• BioSignal & Metadata
• Visualization Contract
• Labs Serve UI