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"tolerance": 0.0, "response": 3.2, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "b-2", "sourceRow": 2, "sourceTime": 240.0, "sourceTimeUnit": "min", "elapsedHours": 4.0, "rational": "4/1", "exactBinary64": true, "tolerance": 0.0, "response": 6.8, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] } } }, { "spec": { "id": "unresolved-and-partial-alignment", "description": "When one source has an anchor and the second is unresolved, timeAlignment stays not-established and elapsedHours remain null.", "sharedEventLabel": "Inoculation", "slotA": { "slotId": "slot-a", "label": "Anchored source", "inputHash": "sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "timeUnit": "h", "responseLabel": "OD600", "origin": "measured", "responseUnit": "OD600", "basis": "1 cm cuvette, unblanked", "receiptStatus": "not-supplied", "alignment": { "kind": "elapsed-from-declared-event", "anchorInSourceUnits": 0, "sourceTimeUnit": "h", "basis": "Recorded inoculation at 0 h" }, "readings": [ { "id": "a-1", "sourceRow": 1, "time": 0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "a-2", "sourceRow": 2, "time": 2, "response": 0.4, "role": "sample", "excluded": false, "exclusionReason": null } ] }, "slotB": { "slotId": "slot-b", "label": "Unresolved source", "inputHash": "sha256:bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb", "timeUnit": "min", "responseLabel": "OD600", "origin": "unspecified", "responseUnit": null, "basis": null, "receiptStatus": "not-supplied", "alignment": { "kind": "unresolved" }, "readings": [ { "id": "b-1", "sourceRow": 1, "time": 15, "response": 0.12, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "b-2", "sourceRow": 2, "time": 75, "response": 0.38, "role": "sample", "excluded": false, "exclusionReason": null } ] } }, "expected": { "method": { "id": "measured-comparison-time-alignment", "version": "1.0.0" }, "timeAlignment": "not-established", "responseBasis": "separate-panels", "conversionApplied": false, "modelParametersChanged": false, "commonElapsedExtentHours": null, "qualificationCodes": [ "raw-response-separate-axes", "elapsed-time-not-equivalence", "time-alignment-not-established", "unspecified-origin-retained" ], "slotA": { "slotId": "slot-a", "origin": "measured", "receiptStatus": "not-supplied", "sourceTimeUnit": "h", "enteredTimeExtent": [ 0.0, 2.0 ], "alignedElapsedExtentHours": null, "rows": [ { "id": "a-1", "sourceRow": 1, "sourceTime": 0.0, "sourceTimeUnit": "h", "elapsedHours": null, "rational": null, "exactBinary64": true, "tolerance": 0.0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "a-2", "sourceRow": 2, "sourceTime": 2.0, "sourceTimeUnit": "h", "elapsedHours": null, "rational": null, "exactBinary64": true, "tolerance": 0.0, "response": 0.4, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] }, "slotB": { "slotId": "slot-b", "origin": "unspecified", "receiptStatus": "not-supplied", "sourceTimeUnit": "min", "enteredTimeExtent": [ 15.0, 75.0 ], "alignedElapsedExtentHours": null, "rows": [ { "id": "b-1", "sourceRow": 1, "sourceTime": 15.0, "sourceTimeUnit": "min", "elapsedHours": null, "rational": null, "exactBinary64": true, "tolerance": 0.0, "response": 0.12, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "b-2", "sourceRow": 2, "sourceTime": 75.0, "sourceTimeUnit": "min", "elapsedHours": null, "rational": null, "exactBinary64": true, "tolerance": 0.0, "response": 0.38, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] } } }, { "spec": { "id": "mixed-origin-and-withheld-receipt", "description": "Measured source with estimated receipt paired with synthetic source carrying a withheld receipt retains both origins and historical receipt statuses.", "sharedEventLabel": "Inoculation", "slotA": { "slotId": "slot-a", "label": "Measured shake-flask", "inputHash": "sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "timeUnit": "h", "responseLabel": "OD600", "origin": "measured", "responseUnit": "OD600", "basis": "1 cm cuvette, unblanked", "receiptStatus": "historical-estimated", "alignment": { "kind": "elapsed-from-declared-event", "anchorInSourceUnits": 0, "sourceTimeUnit": "h", "basis": "Inoculation at 0 h" }, "readings": [ { "id": "a-1", "sourceRow": 1, "time": 0, "response": 0.08, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "a-2", "sourceRow": 2, "time": 1, "response": 0.16, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "a-3", "sourceRow": 3, "time": 2, "response": 0.32, "role": "sample", "excluded": false, "exclusionReason": null } ] }, "slotB": { "slotId": "slot-b", "label": "Synthetic nonpositive example", "inputHash": "sha256:bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb", "timeUnit": "h", "responseLabel": "OD600", "origin": "synthetic", "responseUnit": "OD600", "basis": "1 cm cuvette, unblanked", "receiptStatus": "historical-withheld-nonpositive", "alignment": { "kind": "elapsed-from-declared-event", "anchorInSourceUnits": 0, "sourceTimeUnit": "h", "basis": "Synthetic start at 0 h" }, "readings": [ { "id": "b-1", "sourceRow": 1, "time": 0, "response": 0.0, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "b-2", "sourceRow": 2, "time": 1, "response": -0.02, "role": "sample", "excluded": false, "exclusionReason": null } ] }, "simulationReference": { "included": true } }, "expected": { "method": { "id": "measured-comparison-time-alignment", "version": "1.0.0" }, "timeAlignment": "elapsed-from-declared-event", "responseBasis": "separate-panels", "conversionApplied": false, "modelParametersChanged": false, "commonElapsedExtentHours": [ 0.0, 2.0 ], "qualificationCodes": [ "raw-response-separate-axes", "elapsed-time-not-equivalence", "synthetic-source-retained", "simulation-reference-qualification" ], "slotA": { "slotId": "slot-a", "origin": "measured", "receiptStatus": "historical-estimated", "sourceTimeUnit": "h", "enteredTimeExtent": [ 0.0, 2.0 ], "alignedElapsedExtentHours": [ 0.0, 2.0 ], "rows": [ { "id": "a-1", "sourceRow": 1, "sourceTime": 0.0, "sourceTimeUnit": "h", "elapsedHours": 0.0, "rational": "0/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.08, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "a-2", "sourceRow": 2, "sourceTime": 1.0, "sourceTimeUnit": "h", "elapsedHours": 1.0, "rational": "1/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.16, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "a-3", "sourceRow": 3, "sourceTime": 2.0, "sourceTimeUnit": "h", "elapsedHours": 2.0, "rational": "2/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.32, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] }, "slotB": { "slotId": "slot-b", "origin": "synthetic", "receiptStatus": "historical-withheld-nonpositive", "sourceTimeUnit": "h", "enteredTimeExtent": [ 0.0, 1.0 ], "alignedElapsedExtentHours": [ 0.0, 1.0 ], "rows": [ { "id": "b-1", "sourceRow": 1, "sourceTime": 0.0, "sourceTimeUnit": "h", "elapsedHours": 0.0, "rational": "0/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.0, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "b-2", "sourceRow": 2, "sourceTime": 1.0, "sourceTimeUnit": "h", "elapsedHours": 1.0, "rational": "1/1", "exactBinary64": true, "tolerance": 0.0, "response": -0.02, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] } } }, { "spec": { "id": "same-source-witness-warning", "description": "Two slots carrying the same scientific-input hash emit same-source-input-hash qualification.", "sharedEventLabel": "Inoculation", "slotA": { "slotId": "slot-a", "label": "Dataset copy 1", "inputHash": "sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "timeUnit": "h", "responseLabel": "OD600", "origin": "measured", "responseUnit": "OD600", "basis": "1 cm cuvette, unblanked", "receiptStatus": "not-supplied", "alignment": { "kind": "elapsed-from-declared-event", "anchorInSourceUnits": 0, "sourceTimeUnit": "h", "basis": "Anchor at 0 h" }, "readings": [ { "id": "a-1", "sourceRow": 1, "time": 0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "a-2", "sourceRow": 2, "time": 1, "response": 0.2, "role": "sample", "excluded": false, "exclusionReason": null } ] }, "slotB": { "slotId": "slot-b", "label": "Dataset copy 2", "inputHash": "sha256:aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", "timeUnit": "h", "responseLabel": "OD600", "origin": "measured", "responseUnit": "OD600", "basis": "1 cm cuvette, unblanked", "receiptStatus": "not-supplied", "alignment": { "kind": "elapsed-from-declared-event", "anchorInSourceUnits": 1, "sourceTimeUnit": "h", "basis": "Shifted anchor at 1 h" }, "readings": [ { "id": "a-1", "sourceRow": 1, "time": 0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null }, { "id": "a-2", "sourceRow": 2, "time": 1, "response": 0.2, "role": "sample", "excluded": false, "exclusionReason": null } ] } }, "expected": { "method": { "id": "measured-comparison-time-alignment", "version": "1.0.0" }, "timeAlignment": "elapsed-from-declared-event", "responseBasis": "separate-panels", "conversionApplied": false, "modelParametersChanged": false, "commonElapsedExtentHours": [ -1.0, 1.0 ], "qualificationCodes": [ "raw-response-separate-axes", "elapsed-time-not-equivalence", "same-source-input-hash" ], "slotA": { "slotId": "slot-a", "origin": "measured", "receiptStatus": "not-supplied", "sourceTimeUnit": "h", "enteredTimeExtent": [ 0.0, 1.0 ], "alignedElapsedExtentHours": [ 0.0, 1.0 ], "rows": [ { "id": "a-1", "sourceRow": 1, "sourceTime": 0.0, "sourceTimeUnit": "h", "elapsedHours": 0.0, "rational": "0/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "a-2", "sourceRow": 2, "sourceTime": 1.0, "sourceTimeUnit": "h", "elapsedHours": 1.0, "rational": "1/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.2, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] }, "slotB": { "slotId": "slot-b", "origin": "measured", "receiptStatus": "not-supplied", "sourceTimeUnit": "h", "enteredTimeExtent": [ 0.0, 1.0 ], "alignedElapsedExtentHours": [ -1.0, 0.0 ], "rows": [ { "id": "a-1", "sourceRow": 1, "sourceTime": 0.0, "sourceTimeUnit": "h", "elapsedHours": -1.0, "rational": "-1/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.1, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false }, { "id": "a-2", "sourceRow": 2, "sourceTime": 1.0, "sourceTimeUnit": "h", "elapsedHours": 0.0, "rational": "0/1", "exactBinary64": true, "tolerance": 0.0, "response": 0.2, "role": "sample", "excluded": false, "exclusionReason": null, "plotted": true, "hollow": false } ] } } } ], "refusalCases": [ { "id": "refuse-malformed-comparison-payload", "fault": "top-level kind is not 'measured-comparison' or unknown key is present", "expectedCode": "malformed-comparison-payload" }, { "id": "refuse-aggregate-byte-limit-exceeded", "fault": "serialized comparison payload exceeds 2,000,000 UTF-8 bytes", "expectedCode": "aggregate-byte-limit-exceeded" }, { "id": "refuse-aggregate-reading-limit-exceeded", "fault": "combined readings across slotA and slotB exceed 4,000 rows", "expectedCode": "aggregate-reading-limit-exceeded" }, { "id": "refuse-invalid-growth-review-payload", "fault": "slot imported payload fails readGrowthReviewPayload structural check", "expectedCode": "invalid-growth-review-payload" }, { "id": "refuse-source-input-hash-mismatch", "fault": "slot imported.source.inputHash does not match contentHashLight(growthInput(imported.growth))", "expectedCode": "source-input-hash-mismatch" }, { "id": "refuse-synthetic-origin-downgrade", "fault": "imported synthetic dataset has arrival context origin changed to 'measured' or 'unspecified'", "expectedCode": "synthetic-origin-downgrade-refused" }, { "id": "refuse-invalid-time-alignment-unit", "fault": "alignment sourceTimeUnit ('min') does not match slot growth.settings.timeUnit ('h')", "expectedCode": "invalid-time-alignment-unit" }, { "id": "refuse-nonfinite-time-anchor", "fault": "alignment anchorInSourceUnits is NaN, Infinity, or produces non-finite elapsedHours", "expectedCode": "nonfinite-time-anchor" }, { "id": "refuse-missing-time-alignment-basis", "fault": "alignment kind is 'elapsed-from-declared-event' but basis or sharedEventLabel is blank", "expectedCode": "missing-time-alignment-basis" }, { "id": "refuse-invalid-simulation-reference-schema", "fault": "simulation reference result schema is not bioreactor-simulator.recorded-simulation v1", "expectedCode": "invalid-simulation-reference-schema" }, { "id": "refuse-simulation-reference-hash-mismatch", "fault": "simulation reference ResultSnapshot or InputSnapshot contentHash fails verification", "expectedCode": "simulation-reference-hash-mismatch" }, { "id": "refuse-unsupported-simulation-reference-output", "fault": "simulation reference RunView has unlisted null RQ where OUR !== 0 or mismatched series length", "expectedCode": "unsupported-simulation-reference-output" } ] }