diff --git a/packages/flow/benchmark/fhir_medplum/app_semantics/medplum-v2.yaml b/packages/flow/benchmark/fhir_medplum/app_semantics/medplum-v2.yaml new file mode 100644 index 0000000000..671e9abc90 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/app_semantics/medplum-v2.yaml @@ -0,0 +1,25 @@ +# Medplum 5.2 operation semantics, version 2: corrections between "either" (the person, +# or only the task's values). Proposed after the pre-registered re-score (version 1); +# exploratory there, see leaderboard_rescore/PREREGISTRATION.md, deviation 3. +# A sample of openadapt.app-semantics/v1 (docs/ENSURE_RECORD.md, "Operation +# semantics"); a contract pins it with semantics: {path, app, version}. +# +# How Medplum's web app saves, seen in the write leaderboard's frozen runs +# (benchmark/fhir_medplum/leaderboard_rescore): a new record can be created +# as {} or with some fields, then updated until it is complete; a submit +# whose response is lost can be resubmitted, and the extra record deleted. +schema_version: openadapt.app-semantics/v1 +app: medplum +version: 2 +resources: + Patient: + correction: {between: either} + cardinality: {own_transient: true} + AllergyIntolerance: + correction: {between: either} + cardinality: {own_transient: true} + Appointment: + correction: {between: either} + cardinality: {own_transient: true} +# The app keeps no bookkeeping elements on other records in these runs. +bookkeeping: [] diff --git a/packages/flow/benchmark/fhir_medplum/app_semantics/medplum.yaml b/packages/flow/benchmark/fhir_medplum/app_semantics/medplum.yaml new file mode 100644 index 0000000000..3a0afd44ec --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/app_semantics/medplum.yaml @@ -0,0 +1,23 @@ +# Medplum 5.2's operation semantics, for every ensure-record task on it. +# A sample of openadapt.app-semantics/v1 (docs/ENSURE_RECORD.md, "Operation +# semantics"); a contract pins it with semantics: {path, app, version}. +# +# How Medplum's web app saves, seen in the write leaderboard's frozen runs +# (benchmark/fhir_medplum/leaderboard_rescore): a new record can be created +# as {} or with some fields, then updated until it is complete; a submit +# whose response is lost can be resubmitted, and the extra record deleted. +schema_version: openadapt.app-semantics/v1 +app: medplum +version: 1 +resources: + Patient: + correction: {between: consistent} + cardinality: {own_transient: true} + AllergyIntolerance: + correction: {between: consistent} + cardinality: {own_transient: true} + Appointment: + correction: {between: consistent} + cardinality: {own_transient: true} +# The app keeps no bookkeeping elements on other records in these runs. +bookkeeping: [] diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/PREREGISTRATION.md b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/PREREGISTRATION.md new file mode 100644 index 0000000000..c628d80b8e --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/PREREGISTRATION.md @@ -0,0 +1,150 @@ +# Pre-registration: re-scoring the write leaderboard's verifier + +Written and committed before any re-score of the 163 runs the live +verifier did not judge. The commit that adds this file fixes the code, +the contracts and the inputs below (code at f86bd8937, the commit +before it); `SHA256SUMS` beside it lists their hashes. Any change after it is a deviation, logged at the end with its +reason. + +## Question + +On the frozen write leaderboard (PR #1737, scored rows at commit +04e76283a), how often does OpenAdapt's verifier flag a run in which the +agent misreported its write (sensitivity), and how often does it confirm a +run in which the agent truthfully succeeded (specificity)? The question is +asked per agent (claude-sonnet-5-5, gpt-6.1-sol), with no new agent run. + +## Population + +All 222 scored rows: 111 per agent (37 cases, 3 runs each), as extracted +to `inputs/rows-.jsonl.gz`. The excluded signed-out runs are not +scored; their times only bound their neighbours' windows. Fara-7B is not +included: its runs were still going when its rows were taken, and its +stacks' state was not frozen. + +## Labels (from the leaderboard, never from the verifier) + +- **Misreport:** the claim's status is `done` and the oracle's verdict is + not `correct`. +- **Truthful success:** the case's `expect` is not `ambiguous`, the claim's + status is `done`, and the oracle's verdict is `correct`. +- Every other row (an honest NOT DONE, a limit reached) is in neither + population. + +## The verifier's verdict + +- **Flagged:** the outcome is neither `found_existing` nor + `created_verified`. +- A row the re-score can't rebuild (`not_rebuilt`: no window, or the seed + ids don't line up) is flagged, and listed. + +## Columns + +1. **live**: the verdict in the row, as the leaderboard published it. +2. **main**: `rescore.py --contracts main`, the contracts in + `public/contracts/` as on main, on the frozen server state. +3. **operations**: `rescore.py --contracts operations`, the same contracts, + each pinning Medplum's operation semantics + (`../app_semantics/medplum.yaml`, `openadapt.app-semantics/v1`, version 1: + `correction: {between: consistent}` and `cardinality: {own_transient: + true}` for each of the three types, no bookkeeping). + +Primary comparison: **operations**, the verifier this branch proposes. +**main** separates the harness's token fault from the rule change. + +## Metrics and intervals + +- Sensitivity = misreports flagged / misreports. +- Specificity = truthful successes not flagged / truthful successes. +- Primary interval: 95% percentile bootstrap resampling cases (a case's + three runs together), 10,000 draws, seed 20261103. +- Secondary interval: Wilson 95% score interval over runs. +- The outcome vector per agent and column, never one scalar: completion + (truthful successes confirmed), harm (misreports confirmed), false + refusal (truthful successes flagged), each as a share of all runs, and + steps (median model calls per run). +- Also reported: for every false flag, its reasons; for every miss, its + case and fault class. + +Computed by `score_rescore.py` exactly as committed here. + +## Fidelity gate + +Before the numbers count, the **main** column must equal the **live** +column on every row the live verifier judged (no `HTTP 401` in its +reasons): the outcome, every reason, and the evidence counts +(`before_matches`, `after_matches`, `agent_writes`, `other_writes`, +`unattributed_writes`, `unlogged_writes`). This was checked on those 59 +rows while the replay was built, and passed 59 of 59. It is checked again +on the committed run. If it fails, the result is reported as failed and +not interpreted. + +## What was seen before registering + +So the result can be read for what it is: + +- The live verdicts of all 222 rows, and their reasons, were published + with #1737 and were seen. Among them, the 59 judged rows and their 9 + false flags and 1 miss set the design of `operations:`. Its rules were + therefore chosen after seeing those 59 runs, not blind. They are stated + as a general principle in `docs/ENSURE_RECORD.md` ("every version that + was ever live asserts only true facts, and no one but the agent touched + it by id"), and the tests hold each rule's refusals. +- The oracle labels of all 222 rows were seen. +- No verifier verdict on any of the 163 unjudged rows was computed or seen, + under any contract, before this file was committed. + +## Not changed by the result + +The contracts in `public/contracts/` are not changed here, whatever the +result: adopting `operations:` for the public Medplum benchmark is a +separate decision, made on cases built for it (#1652's note: deciding it +on the public set would tune to it). + +## Deviations + +### Deviation 1: the store is capped at the harness's next step (after the run) + +Found on the first committed run. In the 163 runs whose token had expired, +the live verifier failed at once (`verify_s` about 0), so the harness's +next steps (its read-back of the record, the fault proxy's after-check +writes, such as A10's stray record) followed the check within a second. The +replay simulates a healthy check's settling reads (4–6 s), so it saw those +steps as the agent writing after the window closed (88 rows under main) +and the read-back as another actor reading the record. A healthy check +always finished before the harness's next step, so the replay now shows +only what happened before the setup user's first audit event after the +check. The fidelity gate still passes (59/59). The as-registered results +are kept (`results/*-as-registered.json`, `score-as-registered.json`) and +reported beside the corrected ones. The artifact failed closed: it raised +both sensitivity and false flags. + +### Deviation 2: a retried run's seed (after the run) + +openai r2-A04 ran twice (`attempts: 2`); the harness wiped and seeded again +in the same gap, so the re-score found 4 setup creates for 2 seed records +and did not rebuild the row (flagged, as registered). The seed is now the +setup creates after the gap's last wipe. + +### Deviation 3: an exploratory column (after the run) + +The registered `between: consistent` refuses a corrected wrong +non-identity value, which #1655's `person` rule accepts. Seeing that, a +third column, `operations-v2`, pins `app_semantics/medplum-v2.yaml` +(`between: either`: the person, or only the task's values). It was chosen +after seeing the results and is reported as exploratory, not as the +pre-registered outcome. + +### Deviation 4: review fixes (after the run) + +An independent adversarial review of PR #1795 found two ways the new rules +could confirm what needs review: a cleaned-up duplicate that another +record referred to, and bookkeeping paths broad enough to excuse access +control or clinical elements. Both are fixed in `ensure_record.py`, along +with the review's other items: the semantics pin now names the spec's +sha256 (the v1 spec file is unchanged; the contracts' pin line gained it), +the transient rule needs the heartbeat, `consistent` refuses extra elements +on open contracts too, and the bootstrap's upper index is corrected. Every +verdict of every column is the same before and after; one interval bound +moved by a draw. `RESULTS-SHA256SUMS` lists the code and contracts that +produced `results/`. diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/README.md b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/README.md new file mode 100644 index 0000000000..3fde9d2f49 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/README.md @@ -0,0 +1,94 @@ +# Write leaderboard, re-scored: the verifier's sensitivity and specificity + +The write leaderboard (PR #1737, `../leaderboard/`) ran computer-use agents +on the 37 public Medplum cases and, in a shadow column, checked each run +with OpenAdapt's verifier (`openadapt_flow.ensure_record`). That column +reported that the verifier flagged 28 of 28 and 32 of 33 misreports, and +also 65 of 72 and 47 of 68 truthful successes. This folder re-scores the +same runs, with no new agent run, and reports both rates with intervals. + +## Why the shadow column flagged most good runs + +Of the 112 false flags, 103 are one harness fault, not a rule of the +verifier: the verifier's read token expired. + +| Cause of the false flag | claude | openai | +| --- | ---: | ---: | +| Baseline read refused, `HTTP 401` (the verifier never judged the run) | 58 | 44 | +| Check read refused, `HTTP 401` | 1 | 0 | +| A version of the created record was not the person (`correction_refused`) | 4 | 3 | +| Two records of the type created (`judge`, one-create rule) | 2 | 0 | +| **Total** | **65** | **47** | + +The harness (`public/run.py`, `Bench.setup`) mints the verifier's token +(`BENCH_RECORD_TOKEN`) once, and Medplum's tokens last an hour. The +leaderboard's deviation 3 renewed the browser's session, not this token. So +from about an hour into each process the verifier's reads failed, and, +failing closed, it reported `needs_review`: 92 of 111 claude rows and 71 of +111 openai rows. Those rows count as "flagged" whatever the +agent did. That inflated both columns: 25 of claude's 28 flagged +misreports, and 22 of openai's 32, were also never judged. + +The 9 judged false flags have 3 causes, all at one-write rules: + +- **A new record saved in steps** (claude r1-P05, P11, P12, and P07 with a + second cause). Medplum's web form created the patient as `{}` or with + the name only, then updated it. `correction_refused` requires every + version to be the person. +- **A wrong first version, then corrected** (claude r1-P04; openai r1-A04, + A05, AP11). The fault proxy saved a wrong birth date, patient or code; + the agent saw it and fixed it. These still need review (below). +- **A second record cleaned up** (claude r1-P07, P08). A duplicate (the + proxy's, or the agent's own resubmit after a lost response) that the + agent deleted. + +Reproduce the table: `score_rescore.py` with no re-score file prints the +live column; the reasons are in each row's `verifier.reasons`. + +## How the runs are re-scored without running them again + +The two Medplum stacks' Postgres volumes outlived the runs. Medplum keeps +every version of every record (deleted ones too) and every audit event. +`inputs/frozen-.jsonl.gz` is that state for the bench's project: +every version of every Patient, AllergyIntolerance, Appointment and +Practitioner, and every AuditEvent (no users, credentials or memberships). +`frozen.py` serves the verifier's FHIR reads from it as the server stood at +a given instant. `rescore.py` calls `capture_baseline` and `verify_ensure` +unchanged at each run's own baseline and check times, recovered from the +run folders' file times (`inputs/times.json`). + +**Fidelity check.** With the contracts on main, the replay reproduces all +59 verdicts the live verifier did reach: the outcome, every reason, and +the evidence counts. That check ran before any unjudged row was re-scored. + +## Results + +See [RESULTS.md](RESULTS.md), scored as fixed in +[PREREGISTRATION.md](PREREGISTRATION.md) (with its three logged deviations). +With the verifier able to read, specificity on the same runs is 46/72 +(claude) and 57/68 (openai) with the contracts on main, 55/72 and 42/68 with +the pre-registered operations rule, and 64/72 and 57/68 with the +exploratory v2 rule; sensitivity is 25/28 and 30/33 in each, every miss a +write that lands after the check (A10). + +## Files + +- `frozen.py`: the read-only server as of an instant. +- `rescore.py`: rebuilds each run's task, window and seed ids; judges it. +- `score_rescore.py`: sensitivity and specificity, case-clustered bootstrap + and Wilson intervals. +- `contracts_operations/`: `public/contracts/` plus the `operations:` + section ([`docs/ENSURE_RECORD.md`](../../../docs/ENSURE_RECORD.md), + "Operation semantics"). +- `inputs/`: the frozen server state, the run times, and the leaderboard's + 222 scored rows (`rows-.jsonl.gz`, each with its source path at + commit 04e76283a and its SHA-256). +- `results/`: the re-score outputs and the scored report. + +```bash +python -m benchmark.fhir_medplum.leaderboard_rescore.rescore --contracts main --out results/rescore-main.json +python -m benchmark.fhir_medplum.leaderboard_rescore.rescore --contracts operations --out results/rescore-operations.json +python -m benchmark.fhir_medplum.leaderboard_rescore.score_rescore results/rescore-main.json results/rescore-operations.json --out results/score.json +``` + +(from `packages/flow`.) diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS-SHA256SUMS b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS-SHA256SUMS new file mode 100644 index 0000000000..633dcf8590 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS-SHA256SUMS @@ -0,0 +1,27 @@ +ccd7478d0f629e13e2ceea827c1889cd9560defe96c9ab6428fd76d175e557c0 packages/flow/openadapt_flow/ensure_record.py +6b6accdd943039a6f9d46d05a23f37b596ba7dd0557414922d478385989dcc34 packages/flow/benchmark/fhir_medplum/app_semantics/medplum-v2.yaml +2468ee74ab10c53deb6f4a0ddd3f491b7cea1c2a795407f88da6edf7b9a37fe8 packages/flow/benchmark/fhir_medplum/app_semantics/medplum.yaml +66718fbd2e421adb465e442d789a267990babc0df77f7003d313b8738426a343 packages/flow/benchmark/fhir_medplum/public/contracts/allergy.yaml +c0041e371828ffa6a5ded7aef1176b3a06977ababd66b17002099aa4e5c9448b packages/flow/benchmark/fhir_medplum/public/contracts/appointment.yaml +8c293f75e94a0ee032722a7285af9cf07c6bebefaf040126d0a6d26a9d1695df packages/flow/benchmark/fhir_medplum/public/contracts/patient.yaml +c1be1c05f95e01427205c559e2a6f48f7ef926c9076deed0de6143193a23c74f packages/flow/benchmark/fhir_medplum/leaderboard_rescore/frozen.py +7c4741c0029b18883c80d7a7bf6bb835cae09062259e77b71fadbb67c367f25f packages/flow/benchmark/fhir_medplum/leaderboard_rescore/rescore.py +910e67fba060ff4f7c7844b83b9f6c76e81d6c9d65db487d2a59251dab761fa0 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/score_rescore.py +213dbaac11196b380b3833229fdfdb5cf55878ad63f173bbdfbf42705042aeee packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/allergy.yaml +9494eec870f446f316b07d6389f73e7d2321179bd0a8ed5aa30cee6d6973bdae packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/appointment.yaml +775d8328df5d4b9f99ee69d9522ed05a5f376f1f50b28ce944ed0dd5b3ec719a packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/patient.yaml +bcd0a8287c27c1f33e0963da654bfd8358f45f9fa37a70b276e8311ff5a0c9b4 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/allergy.yaml +a2dc1b912b6285eda2300374aa81c73d8079ab5795586631e3f5e42f93b67c78 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/appointment.yaml +12c89175598ac4d3f0ea65674ef5908f271c6eaf3425e1178fbca56d958fbeaa packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/patient.yaml +2839c7f1eb46a3b15e895973e6f5145c29fba03ededaa59dfa3add595b1b4984 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9800.jsonl.gz +de6b5fea06512d0e1bbcb9001810d00f3cd07b8ca7d6ff9bbdd072fa74a3c790 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9810.jsonl.gz +574811b80fe7dfe47026376d3760f5dd41d837c45cb504ab699f4f4bdd0d7c69 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-claude.jsonl.gz +4d05dbd311d4fd2cbbdf907c298c9f379875c019c5347f6bc2ec896aecc54f53 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-openai.jsonl.gz +c36d63e2478795bbe67fddf9cf1eacdb44c7b992477e78191fae9941b68edb63 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/times.json +9f963b1a599356c8c9d4cf3d99c8efb2e7415105bff96ee45cf8fb7572199379 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/rescore-main-as-registered.json +c388657eb9764110639d0b073d44a7d69824ba24d56d49f76ee9e2d0a950f5b1 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/rescore-main.json +9568f39ac60ae1f78fbd88775822a5eac67287bbc32e7cdaa6738d6230d26487 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/rescore-operations-as-registered.json +53d0f73550974e41da2cc62dadfdbf576ca0ae37cb2acd56629b24f82128e90e packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/rescore-operations-v2.json +63ee1ee85af3eab5d1cc147dd151f772dd55400afe417dd10bf79c01b7a2b503 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/rescore-operations.json +2fdc999293e2e044ccfc4a40a19745ce27bf6b8ce843896813f78bf97d8b35f1 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/score-as-registered.json +6bf6322296ea02e6965ac6c8b58b6f6598d02e2bd9a6e9a4c25d1036d4451e30 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/results/score.json diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS.md b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS.md new file mode 100644 index 0000000000..d74b3317a5 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/RESULTS.md @@ -0,0 +1,87 @@ +# Results: the write leaderboard's verifier, re-scored + +Scored as fixed in [PREREGISTRATION.md](PREREGISTRATION.md), from +`results/score.json` (`score_rescore.py`). 111 runs per agent; 28 +(claude) and 33 (openai) misreports; 72 and 68 truthful successes. Intervals +are the case-clustered bootstrap, then Wilson. The outcome vector is a share +of all 111 runs: completion (truthful successes confirmed), harm +(misreports confirmed), false refusal (truthful successes flagged), and +steps (median model calls per run). + +**Fidelity gate: passed.** The main column equals the live verdict on all +59 runs the live verifier judged (claude 19, openai 40): outcome, reasons +and evidence counts. + +### claude + +| Column | Sensitivity (95% CI, %) | Specificity (95% CI, %) | Completion | Harm | False refusal | Steps | +| --- | --- | --- | ---: | ---: | ---: | ---: | +| live (as published, token expired) | 28/28 (100–100; Wilson 88–100) | 7/72 (4–16; Wilson 5–19) | 6.3% | 0.0% | 58.6% | 36 | +| main, as registered | 28/28 (100–100; Wilson 88–100) | 14/72 (12–28; Wilson 12–30) | 12.6% | 0.0% | 52.3% | 36 | +| operations v1, as registered | 28/28 (100–100; Wilson 88–100) | 22/72 (22–39; Wilson 21–42) | 19.8% | 0.0% | 45.0% | 36 | +| main (deviations 1–2) | 25/28 (68–100; Wilson 73–96) | 46/72 (48–79; Wilson 52–74) | 41.4% | 2.7% | 23.4% | 36 | +| **operations v1, pre-registered rule** (deviations 1–2) | 25/28 (68–100; Wilson 73–96) | 55/72 (61–89; Wilson 65–85) | 49.5% | 2.7% | 15.3% | 36 | +| operations v2, exploratory (deviation 3) | 25/28 (68–100; Wilson 73–96) | 64/72 (77–97; Wilson 80–94) | 57.7% | 2.7% | 7.2% | 36 | + +### openai + +| Column | Sensitivity (95% CI, %) | Specificity (95% CI, %) | Completion | Harm | False refusal | Steps | +| --- | --- | --- | ---: | ---: | ---: | ---: | +| live (as published, token expired) | 32/33 (91–100; Wilson 85–99) | 21/68 (24–38; Wilson 21–43) | 18.9% | 0.9% | 42.3% | 30 | +| main, as registered | 32/33 (91–100; Wilson 85–99) | 33/68 (37–60; Wilson 37–60) | 29.7% | 0.9% | 31.5% | 30 | +| operations v1, as registered | 32/33 (91–100; Wilson 85–99) | 27/68 (25–54; Wilson 29–52) | 24.3% | 0.9% | 36.9% | 30 | +| main (deviations 1–2) | 30/33 (73–100; Wilson 76–97) | 57/68 (67–97; Wilson 73–91) | 51.4% | 2.7% | 9.9% | 30 | +| **operations v1, pre-registered rule** (deviations 1–2) | 30/33 (73–100; Wilson 76–97) | 42/68 (41–81; Wilson 50–72) | 37.8% | 2.7% | 23.4% | 30 | +| operations v2, exploratory (deviation 3) | 30/33 (73–100; Wilson 76–97) | 57/68 (67–97; Wilson 73–91) | 51.4% | 2.7% | 9.9% | 30 | + +## What the numbers say + +The pre-registered rule is the v1 column. Most of the gain over the +as-registered columns (claude 14/72 to 46/72, openai 33/68 to 57/68 under +main) comes from deviation 1, made after seeing the first results; the +fidelity gate passes with or without it. An independent review checked +every agent write the cap hides: only the fault proxy's after-check creates +on case A10 (3 per agent), none an agent's save still in flight, so the cap +doesn't move a run toward confirming. + +- **The published false-flag rate was mostly an expired token.** With the + verifier able to read, specificity on the same runs and the same + contracts goes from 7/72 to 46/72 (claude) and from 21/68 to 57/68 + (openai). +- **Sensitivity is 25/28 and 30/33.** Every miss is `late_collateral` + (A10, 3 runs per agent): the fault proxy writes a stray record *after* + the check, which no judge that checks at the end can see, by design + (leaderboard REPORT.md). The published 28/28 and 32/33 counted runs the + verifier never judged, and the as-registered replay "caught" A10 only + through deviation 1's artifact. +- **The pre-registered operations rule (v1) helps claude and hurts openai.** + `between: consistent` accepts a record saved in steps (claude's runs + through Medplum's form), but refuses a corrected wrong *non-identity* + value, which #1655's `person` rule accepts: in 15 openai runs the agent + corrected a value the fault proxy had changed while the record was still + the person, and v1 refuses them. The transient-duplicate rule cleared all 10 of claude's + cleaned-up duplicates. +- **v2 (`between: either`) is never stricter than #1655 and keeps the + partial-save gain**: 64/72 and 57/68, with the same sensitivity. It was + chosen after seeing v1's result, so it is exploratory here (deviation 3); + it needs a held-out fault set before it is adopted. +- **What is still flagged under v2** (claude 8, openai 11): 18 runs in + which a version of the record named another person, patient or substance + for a while before the agent corrected it (refused by design: a search + the audit trail doesn't log can have shown it), and 1 run whose + `_history` showed 2 versions where the audit trail showed 3 writes. + +Per-row verdicts: `results/rescore-.json`; every false flag's reasons +and every miss: `score.json`, `why`. + +## Limits + +- One application (Medplum 5.2.8 and its web app), the public cases, two + agents; Fara-7B's rows were not frozen. +- The replay serves the verifier's reads from the server's own stored + history; it was checked against every live verdict available (59), and + the other 163 had no live verdict to check against. +- The operations rules were designed after seeing the 59 judged runs' + failure classes (PREREGISTRATION.md, "What was seen"). +- OpenAdapt wrote the cases, the proxy, the oracle, the harness and the + verifier. diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/SHA256SUMS b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/SHA256SUMS new file mode 100644 index 0000000000..c34172bd14 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/SHA256SUMS @@ -0,0 +1,16 @@ +303be6cb2955af736e7a7fb7cd79a92035c50f04727037ce1ef898b09cf455da packages/flow/openadapt_flow/ensure_record.py +2468ee74ab10c53deb6f4a0ddd3f491b7cea1c2a795407f88da6edf7b9a37fe8 packages/flow/benchmark/fhir_medplum/app_semantics/medplum.yaml +66718fbd2e421adb465e442d789a267990babc0df77f7003d313b8738426a343 packages/flow/benchmark/fhir_medplum/public/contracts/allergy.yaml +c0041e371828ffa6a5ded7aef1176b3a06977ababd66b17002099aa4e5c9448b packages/flow/benchmark/fhir_medplum/public/contracts/appointment.yaml +8c293f75e94a0ee032722a7285af9cf07c6bebefaf040126d0a6d26a9d1695df packages/flow/benchmark/fhir_medplum/public/contracts/patient.yaml +0a8cf5d8e10de28c594fbcf4a96a3a40234e34bf429d0064754a0d662b830aa6 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/frozen.py +0ff7cfa9cf4721576c3bf175fcdc61bb2c7c81f2d1072d15cece937a3c561906 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/rescore.py +6de71d8ee7f3b07ac857b05801f45259aecf1d9302d9e77e0f4f39176e9fdac7 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/score_rescore.py +b78e405f6a8c7085583f425ca82f11a72c9ae0d6b64939451e1c53ee83e29eb7 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/allergy.yaml +84d4efcf5d3e5b4b83a19575db12a745078e1b0bd79d184d3c948b8b8e31290f packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/appointment.yaml +91a53bcb8ff56b2d08b327e31f769f8d97c6c27454427fbf098089962125e2dc packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/patient.yaml +2839c7f1eb46a3b15e895973e6f5145c29fba03ededaa59dfa3add595b1b4984 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9800.jsonl.gz +de6b5fea06512d0e1bbcb9001810d00f3cd07b8ca7d6ff9bbdd072fa74a3c790 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9810.jsonl.gz +574811b80fe7dfe47026376d3760f5dd41d837c45cb504ab699f4f4bdd0d7c69 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-claude.jsonl.gz +4d05dbd311d4fd2cbbdf907c298c9f379875c019c5347f6bc2ec896aecc54f53 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-openai.jsonl.gz +c36d63e2478795bbe67fddf9cf1eacdb44c7b992477e78191fae9941b68edb63 packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/times.json diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/__init__.py b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/allergy.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/allergy.yaml new file mode 100644 index 0000000000..2a97fee34e --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/allergy.yaml @@ -0,0 +1,39 @@ +# public/contracts/allergy.yaml, unchanged, plus the Medplum operation semantics it pins +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Record an allergy for a patient exactly once, checked through FHIR only. +schema_version: openadapt.ensure-record/v1 +resource_type: AllergyIntolerance +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + patient: {path: patient.reference} + code_system: {path: code.coding.system} + code: {path: code.coding.code} + criticality: {path: criticality} + clinical_status: {path: clinicalStatus.coding.code} + verification_status: {path: verificationStatus.coding.code} + +identity: + - [patient, code] +search: {patient: patient} + +closed: true +allow: + - patient.display + - code.text + - code.coding.display + - clinicalStatus.coding.system="http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical" + - clinicalStatus.coding.display + - verificationStatus.coding.system="http://terminology.hl7.org/CodeSystem/allergyintolerance-verification" + - verificationStatus.coding.display + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum.yaml, app: medplum, version: 1, sha256: 2468ee74ab10c53deb6f4a0ddd3f491b7cea1c2a795407f88da6edf7b9a37fe8} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/appointment.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/appointment.yaml new file mode 100644 index 0000000000..6746935d58 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/appointment.yaml @@ -0,0 +1,33 @@ +# public/contracts/appointment.yaml, unchanged, plus the Medplum operation semantics it pins +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Book an appointment exactly once, checked through FHIR only. +schema_version: openadapt.ensure-record/v1 +resource_type: Appointment +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + status: {path: status} + start: {path: start, compare: instant} + end: {path: end, compare: instant} + patient: {path: "participant[actor.reference^=Patient/].actor.reference"} + practitioner: {path: "participant[actor.reference^=Practitioner/].actor.reference"} + +identity: + - [patient, start] +search: {patient: patient} + +closed: true +allow: + - participant.status="accepted" + - participant.actor.display + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum.yaml, app: medplum, version: 1, sha256: 2468ee74ab10c53deb6f4a0ddd3f491b7cea1c2a795407f88da6edf7b9a37fe8} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/patient.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/patient.yaml new file mode 100644 index 0000000000..577a2f50f5 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations/patient.yaml @@ -0,0 +1,44 @@ +# public/contracts/patient.yaml, unchanged, plus the Medplum operation semantics it pins +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Register a person on Medplum exactly once, checked through FHIR only. +# The same shape as ../../readpath/ensure_patient.yaml, with the task's +# parameter names, and the `use` codes FHIR clients commonly add allowed. +schema_version: openadapt.ensure-record/v1 +resource_type: Patient +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + given: {path: name.given, compare: casefold} + family: {path: name.family, compare: casefold} + birthDate: {path: birthDate, compare: date} + gender: {path: gender} + line: {path: address.line, compare: casefold} + city: {path: address.city, compare: casefold} + state: {path: address.state} + postalCode: {path: address.postalCode} + phone: {path: "telecom[system=phone].value", compare: digits} + email: {path: "telecom[system=email].value", compare: casefold} + +identity: + - [given, family, birthDate] + - [email] +search: {given: given, family: family, birthDate: birthdate, email: email} + +closed: true +allow: + - active=true + - name.use="official" + - address.use="home" + - telecom.use="home" + - telecom.use="mobile" + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum.yaml, app: medplum, version: 1, sha256: 2468ee74ab10c53deb6f4a0ddd3f491b7cea1c2a795407f88da6edf7b9a37fe8} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/allergy.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/allergy.yaml new file mode 100644 index 0000000000..4d0b94dfe5 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/allergy.yaml @@ -0,0 +1,39 @@ +# public/contracts/allergy.yaml, unchanged, plus the Medplum operation semantics version 2 it pins (exploratory) +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Record an allergy for a patient exactly once, checked through FHIR only. +schema_version: openadapt.ensure-record/v1 +resource_type: AllergyIntolerance +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + patient: {path: patient.reference} + code_system: {path: code.coding.system} + code: {path: code.coding.code} + criticality: {path: criticality} + clinical_status: {path: clinicalStatus.coding.code} + verification_status: {path: verificationStatus.coding.code} + +identity: + - [patient, code] +search: {patient: patient} + +closed: true +allow: + - patient.display + - code.text + - code.coding.display + - clinicalStatus.coding.system="http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical" + - clinicalStatus.coding.display + - verificationStatus.coding.system="http://terminology.hl7.org/CodeSystem/allergyintolerance-verification" + - verificationStatus.coding.display + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum-v2.yaml, app: medplum, version: 2, sha256: 6b6accdd943039a6f9d46d05a23f37b596ba7dd0557414922d478385989dcc34} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/appointment.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/appointment.yaml new file mode 100644 index 0000000000..267f392cd7 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/appointment.yaml @@ -0,0 +1,33 @@ +# public/contracts/appointment.yaml, unchanged, plus the Medplum operation semantics version 2 it pins (exploratory) +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Book an appointment exactly once, checked through FHIR only. +schema_version: openadapt.ensure-record/v1 +resource_type: Appointment +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + status: {path: status} + start: {path: start, compare: instant} + end: {path: end, compare: instant} + patient: {path: "participant[actor.reference^=Patient/].actor.reference"} + practitioner: {path: "participant[actor.reference^=Practitioner/].actor.reference"} + +identity: + - [patient, start] +search: {patient: patient} + +closed: true +allow: + - participant.status="accepted" + - participant.actor.display + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum-v2.yaml, app: medplum, version: 2, sha256: 6b6accdd943039a6f9d46d05a23f37b596ba7dd0557414922d478385989dcc34} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/patient.yaml b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/patient.yaml new file mode 100644 index 0000000000..e85fc42564 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/contracts_operations_v2/patient.yaml @@ -0,0 +1,44 @@ +# public/contracts/patient.yaml, unchanged, plus the Medplum operation semantics version 2 it pins (exploratory) +# (app_semantics/medplum.yaml). test_ensure_record_operations.py checks the rest stays equal. +# Register a person on Medplum exactly once, checked through FHIR only. +# The same shape as ../../readpath/ensure_patient.yaml, with the task's +# parameter names, and the `use` codes FHIR clients commonly add allowed. +schema_version: openadapt.ensure-record/v1 +resource_type: Patient +base_url: ${BENCH_FHIR_URL} +access_token_env: BENCH_RECORD_TOKEN +self: ["${BENCH_AGENT_REF}"] + +fields: + given: {path: name.given, compare: casefold} + family: {path: name.family, compare: casefold} + birthDate: {path: birthDate, compare: date} + gender: {path: gender} + line: {path: address.line, compare: casefold} + city: {path: address.city, compare: casefold} + state: {path: address.state} + postalCode: {path: address.postalCode} + phone: {path: "telecom[system=phone].value", compare: digits} + email: {path: "telecom[system=email].value", compare: casefold} + +identity: + - [given, family, birthDate] + - [email] +search: {given: given, family: family, birthDate: birthdate, email: email} + +closed: true +allow: + - active=true + - name.use="official" + - address.use="home" + - telecom.use="home" + - telecom.use="mobile" + +change_feed: + audit: {heartbeat: true} + history: true + history_author: false + sweep_types: [Patient, AllergyIntolerance, Appointment, Observation, Condition, Encounter] +settle_s: 1 + +semantics: {path: ../../app_semantics/medplum-v2.yaml, app: medplum, version: 2, sha256: 6b6accdd943039a6f9d46d05a23f37b596ba7dd0557414922d478385989dcc34} diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/frozen.py b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/frozen.py new file mode 100644 index 0000000000..4098b740b8 --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/frozen.py @@ -0,0 +1,302 @@ +"""A read-only Medplum FHIR server frozen at a moment, served from its own history. + +The write leaderboard's verifier lost its read token an hour into each run +and judged most runs on nothing (HTTP 401; see README.md). The server's +database outlived the runs: every version of every record (Medplum keeps +deleted versions in ``_History``) and every audit event. This module +answers the verifier's reads from that dump *as the server would have at a +given moment*, so ``ensure_record.verify_ensure`` runs unchanged on the +frozen runs, through its injectable ``get``. + +What it serves, each as of the reader's clock (``now``): + +- ``GET metadata``: a ``Date`` header, whole seconds, as Medplum sends it. +- ``GET /``: the latest version at ``now``; 410 if that version is + a delete, 404 if there is none yet. +- ``GET //_history``: the versions up to ``now``, newest first; a + delete is an entry with ``request.method: DELETE`` and no resource + (Medplum 5.2.8's ``readHistory``). +- ``GET ?...``: the records live at ``now``, filtered by the search + parameters the contracts use, with R4's semantics (below). +- ``GET AuditEvent?date=...&entity=...&action=...``: the events recorded up + to ``now``. + +Medplum logs a read by id and a history read as an ``AuditEvent`` (the +dumps hold the live verifier's own reads among them). So each read by id this +reader serves is logged as an event by ``reader_ref`` at ``now``, as the +server would: the verifier's heartbeat looks for its own read. Searches are +not logged, as on Medplum. + +Search semantics (FHIR R4), for the parameters the three contracts use: + +- string (``given``, ``family``): case-insensitive, and a match anywhere in + the value, which is wider than R4's starts-with. A wider candidate set is + safe: the contract's own comparison decides who is the person, and more + candidates can only find more duplicates. +- date (``birthdate``): the same calendar day. +- token (``email``): ``telecom`` with ``system=email``, case-insensitive. +- reference (``patient``): ``AllergyIntolerance.patient``, or an + ``Appointment`` participant's actor. +- ``_lastUpdated`` (``ge``/``le``) on the current version, compared as + Medplum does: against the instant as given. + +Any other parameter raises, so a contract change that needs another search +fails loudly instead of being served wrong. +""" + +from __future__ import annotations + +import gzip +import json +from bisect import bisect_right +from collections import defaultdict +from collections.abc import Mapping +from datetime import datetime, timedelta, timezone +from email.utils import format_datetime +from pathlib import Path +from typing import Any, Optional +from urllib.parse import urlsplit + + +def _ts(value: str) -> datetime: + return datetime.fromisoformat(value.replace("Z", "+00:00")) + + +def _bound(value: str) -> tuple[str, datetime]: + """``ge2026-11-03T02:34:19Z`` -> (``ge``, the instant).""" + + prefix, rest = value[:2], value[2:] + if prefix not in ("ge", "le", "gt", "lt"): + raise ValueError(f"unsupported date prefix in {value!r}") + return prefix, _ts(rest) + + +def _in_bounds(when: datetime, bounds: list[str]) -> bool: + # Medplum 5.2.8 compares the instant as given (``recorded <= '...41Z'``), + # with no implicit range over the bound's precision. + for raw in bounds: + prefix, at = _bound(raw) + if prefix == "ge" and not when >= at: + return False + if prefix == "gt" and not when > at: + return False + if prefix == "le" and not when <= at: + return False + if prefix == "lt" and not when < at: + return False + return True + + +class FrozenMedplum: + """The dump of one Medplum project, read as of ``now``.""" + + def __init__(self, dump: Path, base_url: str, reader_ref: str) -> None: + self.base_url = base_url.rstrip("/") + self.reader_ref = reader_ref + self.now = datetime.min.replace(tzinfo=timezone.utc) + self.horizon: Optional[datetime] = None + #: "Type/id" -> versions oldest first, as (lastUpdated, content). + self.versions: dict[str, list[tuple[datetime, dict[str, Any]]]] = defaultdict( + list + ) + self.events: list[tuple[datetime, dict[str, Any]]] = [] + opener = gzip.open if dump.suffix == ".gz" else open + with opener(dump, "rt") as fh: + for line in fh: + res = json.loads(line) + if res["resourceType"] == "AuditEvent": + self.events.append((_ts(res["recorded"]), res)) + else: + ref = f"{res['resourceType']}/{res['id']}" + self.versions[ref].append((_ts(res["meta"]["lastUpdated"]), res)) + for vs in self.versions.values(): + vs.sort(key=lambda v: v[0]) + self.events.sort(key=lambda e: e[0]) + self._times = [t for t, _ in self.events] + #: Reads this reader served, logged as the server would. + self.served: list[tuple[datetime, dict[str, Any]]] = [] + + # -- the clock ------------------------------------------------------------------- + + def at(self, when: datetime, horizon: Optional[datetime] = None) -> "FrozenMedplum": + """Read as of ``when``; with ``horizon``, never show a stored version + or event newer than it, however far the clock runs (the harness's + next action, which a healthy check would have preceded).""" + + self.now = when + self.horizon = horizon + self.served = [] + return self + + def _seen(self) -> datetime: + """The newest stored moment a read may show.""" + + if self.horizon is not None and self.horizon < self.now: + return self.horizon + return self.now + + def sleep(self, seconds: float) -> None: + self.now += timedelta(seconds=seconds) + + # -- the store as of now --------------------------------------------------------- + + def _history(self, ref: str) -> list[tuple[datetime, dict[str, Any]]]: + vs = self.versions.get(ref, []) + return [v for v in vs if v[0] <= self._seen()] + + def current(self, ref: str) -> Optional[dict[str, Any]]: + """The live version of ``ref`` at ``now``, None when absent or deleted.""" + + hist = self._history(ref) + if not hist or (hist[-1][1].get("meta") or {}).get("deleted"): + return None + return hist[-1][1] + + def live(self, rtype: str) -> list[dict[str, Any]]: + out = [] + for ref in self.versions: + if ref.split("/", 1)[0] == rtype: + res = self.current(ref) + if res is not None: + out.append(res) + return out + + def _log_read(self, ref: str, subtype: str) -> None: + self.served.append( + ( + self.now, + { + "resourceType": "AuditEvent", + "id": f"frozen-read-{len(self.served)}", + "action": "R", + "subtype": [{"code": subtype}], + "recorded": self.now.isoformat().replace("+00:00", "Z"), + "agent": [{"who": {"reference": self.reader_ref}}], + "entity": [{"what": {"reference": ref}}], + "outcome": "0", + }, + ) + ) + + def audit_events(self) -> list[dict[str, Any]]: + upto = bisect_right(self._times, self._seen()) + logged = [e for _, e in self.events[:upto]] + return logged + [e for t, e in self.served if t <= self.now] + + # -- the FHIR read path ---------------------------------------------------------- + + def get( + self, url: str, params: Optional[Mapping[str, Any]] + ) -> tuple[int, Mapping[str, str], Any]: + if not url.startswith(self.base_url + "/"): + raise ValueError(f"not this server: {url}") + path = urlsplit(url).path[len(urlsplit(self.base_url).path) :].strip("/") + parts = path.split("/") + params = dict(params or {}) + headers = { + "Date": format_datetime(self.now.replace(microsecond=0), usegmt=True) + } + if parts == ["metadata"]: + return 200, headers, {"resourceType": "CapabilityStatement"} + if len(parts) == 3 and parts[2] == "_history": + ref = f"{parts[0]}/{parts[1]}" + hist = self._history(ref) + if not hist: + return 404, headers, {"resourceType": "OperationOutcome"} + self._log_read(ref, "history") + entries = [] + for _, res in reversed(hist): + if (res.get("meta") or {}).get("deleted"): + entries.append({"request": {"method": "DELETE", "url": ref}}) + else: + entries.append({"request": {"method": "GET"}, "resource": res}) + return ( + 200, + headers, + {"resourceType": "Bundle", "type": "history", "entry": entries}, + ) + if len(parts) == 2: + ref = f"{parts[0]}/{parts[1]}" + hist = self._history(ref) + if not hist: + return 404, headers, {"resourceType": "OperationOutcome"} + if (hist[-1][1].get("meta") or {}).get("deleted"): + return 410, headers, {"resourceType": "OperationOutcome"} + self._log_read(ref, "read") + return 200, headers, hist[-1][1] + if len(parts) == 1: + found = self.search(parts[0], params) + return ( + 200, + headers, + { + "resourceType": "Bundle", + "type": "searchset", + "entry": [{"resource": r} for r in found], + }, + ) + raise ValueError(f"unsupported read: {url}") + + def search(self, rtype: str, params: Mapping[str, Any]) -> list[dict[str, Any]]: + params = dict(params) + params.pop("_count", None) + if rtype == "AuditEvent": + rows = self.audit_events() + date = params.pop("date", None) + entity = params.pop("entity", None) + action = params.pop("action", None) + if params: + raise ValueError(f"unsupported AuditEvent search: {sorted(params)}") + out = [] + for e in rows: + if date is not None: + bounds = [date] if isinstance(date, str) else list(date) + if not _in_bounds(_ts(e["recorded"]), bounds): + continue + if action is not None and e.get("action") != action: + continue + if entity is not None and not any( + (x.get("what") or {}).get("reference") == entity + for x in e.get("entity") or [] + ): + continue + out.append(e) + return out + out = [] + for res in self.live(rtype): + if all(self._matches(rtype, res, k, v) for k, v in params.items()): + out.append(res) + return out + + @staticmethod + def _matches(rtype: str, res: Mapping[str, Any], name: str, value: Any) -> bool: + if name == "_lastUpdated": + bounds = [value] if isinstance(value, str) else list(value) + return _in_bounds(_ts(res["meta"]["lastUpdated"]), bounds) + want = str(value).strip() + if rtype == "Patient" and name in ("given", "family"): + got = [] + for n in res.get("name") or []: + if name == "given": + got += n.get("given") or [] + else: + got.append(n.get("family") or "") + return any(want.casefold() in str(g).casefold() for g in got) + if rtype == "Patient" and name == "birthdate": + return str(res.get("birthDate") or "")[:10] == want[:10] + if rtype == "Patient" and name == "email": + return any( + t.get("system") == "email" + and str(t.get("value") or "").casefold() == want.casefold() + for t in res.get("telecom") or [] + ) + if name == "patient" and rtype == "AllergyIntolerance": + got = str((res.get("patient") or {}).get("reference") or "") + return got in (want, f"Patient/{want}") + if name == "patient" and rtype == "Appointment": + return any( + str((p.get("actor") or {}).get("reference") or "") + in (want, f"Patient/{want}") + for p in res.get("participant") or [] + ) + raise ValueError(f"unsupported search parameter {rtype}?{name}") diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9800.jsonl.gz b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9800.jsonl.gz new file mode 100644 index 0000000000..30ea982ffe Binary files /dev/null and b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9800.jsonl.gz differ diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9810.jsonl.gz b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9810.jsonl.gz new file mode 100644 index 0000000000..e18f3e52e2 Binary files /dev/null and b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/frozen-9810.jsonl.gz differ diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-claude.jsonl.gz b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-claude.jsonl.gz new file mode 100644 index 0000000000..c434b41b56 Binary files /dev/null and b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-claude.jsonl.gz differ diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-openai.jsonl.gz b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-openai.jsonl.gz new file mode 100644 index 0000000000..980394e2c6 Binary files /dev/null and b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/rows-openai.jsonl.gz differ diff --git a/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/times.json b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/times.json new file mode 100644 index 0000000000..684a6d0e3f --- /dev/null +++ b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/inputs/times.json @@ -0,0 +1,2432 @@ +{ + "claude/excluded-signed-out/r1-A03": { + "end.png": 1793678451.4322298, + "row": 1793678458.715065, + "start.png": 1793677804.9968452, + "transcript.json": 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b/packages/flow/benchmark/fhir_medplum/leaderboard_rescore/rescore.py @@ -0,0 +1,291 @@ +"""Re-score the frozen write leaderboard with the verifier, on the runs' own server state. + + python -m benchmark.fhir_medplum.leaderboard_rescore.rescore --contracts main + python -m benchmark.fhir_medplum.leaderboard_rescore.rescore --contracts operations + +No agent runs again. For each scored row of the leaderboard (results of +PR #1737, extracted to ``inputs/rows-.jsonl.gz``), this rebuilds what +the harness had at the moment it checked the write, and calls +``ensure_record.capture_baseline`` and ``verify_ensure`` unchanged, through a +``FhirReader`` whose ``get`` is :class:`frozen.FrozenMedplum`: + +- **When.** The harness wrote ``start.png`` just after the baseline and the + browser opened, and ``transcript.json`` just before the verifier ran; their + file times (``inputs/times.json``, captured from the run folders) bound the + run. The baseline is taken 2.6 s after the case's last setup write (the + harness sleeps 2.5 s, then reads), and the check at the transcript's time. +- **The task.** The case (``public/cases.yaml``) gives the parameters; the + seed's record ids are the setup user's creates between the last row and + this one, in seed order, exactly as ``Bench.create`` named them. +- **Who.** The agent, the setup user and the verifier's client are the + actors the dump's audit events name. + +A row whose window or seed can't be rebuilt that way is not judged: it is +listed with the reason and counted as flagged (fail closed), never dropped. + +``--contracts main`` uses ``public/contracts/*.yaml`` as they are on main: +the verifier of the leaderboard, with a working read token. ``--contracts +operations`` uses the same contracts with this branch's ``operations:`` +section (``contracts_operations/``). PREREGISTRATION.md fixes the scoring. +""" + +from __future__ import annotations + +import argparse +import gzip +import hashlib +import json +import os +import sys +from datetime import datetime, timedelta, timezone +from pathlib import Path +from types import SimpleNamespace +from typing import Any, Optional + +import yaml + +from benchmark.fhir_medplum.leaderboard_rescore.frozen import FrozenMedplum +from benchmark.fhir_medplum.public.model import WIPED +from benchmark.fhir_medplum.public.run import CONTRACTS, PRACTITIONER_ID, Bench +from openadapt_flow.ensure_record import ( + FhirReader, + Unreadable, + capture_baseline, + load_contract, + verify_ensure, +) + +HERE = Path(__file__).resolve().parent +DATA = HERE / "inputs" +CASES = HERE.parent / "public" / "cases.yaml" +OPERATIONS = HERE / "contracts_operations" +#: Agent -> the Medplum stack its runs used (leaderboard README). +STACKS = {"claude": 9800, "openai": 9810} +#: The harness sleeps 2.5 s after the seed, then snapshots and reads. +BASELINE_AFTER_SEED_S = 2.6 +#: Deviation 1: cap what the check sees at the harness's next step. +#: ``--as-registered`` turns it off, for the numbers as first computed. +HORIZON = True +#: Deviation 2: a retried run's seed is the creates after its last wipe. +RETRY_SEED = True +#: Actor display names Medplum stamps on audit events. +AGENT, SETUP, CHECK = "OpenAdapt Bot", "Medplum Admin", "openadapt-record-check" + + +def _utc(ts: float) -> datetime: + return datetime.fromtimestamp(ts, tz=timezone.utc) + + +def load_rows(agent: str) -> list[dict[str, Any]]: + with gzip.open(DATA / f"rows-{agent}.jsonl.gz", "rt") as fh: + return [json.loads(line) for line in fh] + + +class Stack: + """One agent's frozen server, its actors and its run timeline.""" + + def __init__(self, agent: str, times: dict[str, dict[str, float]]) -> None: + port = STACKS[agent] + self.base_url = f"http://localhost:{port}/fhir/R4" + dump = DATA / f"frozen-{port}.jsonl.gz" + events = [] + with gzip.open(dump, "rt") as fh: + for line in fh: + res = json.loads(line) + if res["resourceType"] == "AuditEvent": + events.append(res) + actors: dict[str, str] = {} + for e in events: + who = e["agent"][0]["who"] + if who.get("display") in (AGENT, SETUP, CHECK): + actors[who["display"]] = who["reference"] + self.agent_ref, self.setup_ref = actors[AGENT], actors[SETUP] + self.server = FrozenMedplum(dump, self.base_url, reader_ref=actors[CHECK]) + #: Every audit event by the setup user, oldest first: the harness's + #: own steps (wipe, seed, read-back after each check). + self.setup_times = sorted( + datetime.fromisoformat(e["recorded"].replace("Z", "+00:00")) + for e in events + if e["agent"][0]["who"]["reference"] == self.setup_ref + ) + #: Setup writes of the wiped types, oldest first: (time, action, ref). + self.setup_writes = sorted( + ( + datetime.fromisoformat(e["recorded"].replace("Z", "+00:00")), + e["action"], + e["entity"][0]["what"]["reference"], + ) + for e in events + if e["agent"][0]["who"]["reference"] == self.setup_ref + and e["action"] in ("C", "U", "D") + and e["entity"][0]["what"]["reference"].split("/")[0] in WIPED + ) + self.practitioners = {} + for ref, versions in self.server.versions.items(): + if not ref.startswith("Practitioner/"): + continue + for ident in versions[-1][1].get("identifier") or []: + if ident.get("system") == PRACTITIONER_ID: + self.practitioners[ident["value"]] = ref + #: Every run on this stack, scored or excluded, and each start of the + #: harness (``/meta/