ictrp-mcp-server 0.1.1 → 0.2.0

package/CHANGELOG.md

@@ -3,6 +3,78 @@
 Notable changes to the npm package `ictrp-mcp-server`. The Python package
 `ictrp-mcp-service` is versioned separately in `pyproject.toml`.
 
+## 0.2.0
+
+**Breaking — the completeness warning was counting the wrong unit, and had been
+since 0.1.0.** `parse_reported_total()` read the portal's **record** count out of
+the results page and every later stage treated it as a **trial** count. For `KRAS`
+it reported the export as "short by 361 trials, 29.0%" when the export in fact
+held all 882 trials the portal reported. The number was always a record count:
+the portal prints `1243 records for 882 trials found for: KRAS` in one sentence,
+and only the first number was ever read.
+
+Nothing here changes what is retrieved. It changes what is *claimed* about what
+was retrieved.
+
+**Fixed**
+
+- `parse_reported_counts()` reads both numbers from the accounting sentence, and
+  returns `None` for a unit the page does not state rather than substituting the
+  other one.
+- Every response now carries `upstream_reported_records` **and**
+  `upstream_reported_trials`, plus `completeness` (`trials_complete`,
+  `trials_short` or `unknown`), `rows_short_of_trials` and `duplicate_records`.
+  `upstream_reported_total`, `records_incomplete` and `estimated_missing` are
+  gone; a snapshot written by an older version is read once, converted, and never
+  re-emits the old keys.
+- A `trials_short` response — a real shortfall against the portal's own trial
+  count — now carries an explicit `shortfall_notice` saying so. That case did not
+  occur in any keyword tested.
+- `incompleteness_notice` explains both units and states that the record-count
+  difference is duplicate registration. It is still on every response: absence
+  from a result set is still not evidence a trial does not exist.
+- The `ictrp_search` docstring and `line_of_therapy_hint` notes no longer claim
+  the export is incomplete, which it is not at trial level.
+
+**Removed** — the `parse_reported_total()` name is kept as a deprecated alias for
+`parse_reported_counts().records`. It exists because it is easy to reach for
+again, and it warns.
+
+**Tests** — `tests/test_live_accounting.py` (new, `-m live`, gated on
+`ICTRP_LIVE=1`) pins the counts read from the live portal for `KRAS`,
+`pancreatic` and `ChiCTR`, and asserts an export's rows equal the portal's trial
+count. Two tests that asserted the old behaviour were replaced rather than
+deleted; they are listed in `docs/VERIFICATION_29PCT.md`.
+
+**Documentation** — every published table of shortfalls is corrected.
+`docs/MEASUREMENTS.md` §2 keeps the withdrawn "8 missing records" finding with
+the failed re-measurement beside it.
+
+## 0.1.2
+
+**Default search view is now the clinician-triage view.** `ictrp_search` used to
+return the 10 most common columns; it now returns the columns a clinician needs
+to triage a target: title and scientific title, sponsor and secondary sponsor,
+contact (PI) name/affiliation/email, recruitment status, phase, registration
+date, condition, countries, age bounds and gender, target size, and a
+`line_of_therapy_hint`. A new derived field, `line_of_therapy_hint`, is a
+non-authoritative extraction of treatment line from the free-text
+inclusion/exclusion criteria and the scientific title. It returns
+`first-line`/`second-line`/`third-line`/`fourth-line`/`later-line`, or `null`
+when nothing is stated -- `null` is documented as "not stated", never as
+"first-line", because the export is incomplete and the column does not exist.
+
+**Line-hint fix** — the hint missed trials whose line is stated only as a number
+or only in the scientific title (e.g. "Received >=2 Prior Lines of Therapy"). It
+now scans the scientific title and recognizes numeric line statements; a minimum
+of N lines resolves to `first-line` only when N<=1, otherwise `later-line`.
+
+Documented structural limits surfaced by the wider view: ICTRP has no "PI" and
+no "participating-hospital list" column -- sponsor/PI come from
+`primary_sponsor` + `contact_*`, and "participating hospitals" degrades to
+`countries` + `contact_affiliation`. CT.gov `exclusion_criteria` is frequently
+blank upstream, which is a source gap, not a parse failure.
+
 ## 0.1.1
 
 **Retry on transient stalls** — the search POST intermittently stalls past a

package/README.md

@@ -106,30 +106,33 @@ single-registry search would miss.
 
 ## The finding that shapes every response
 
-**The ICTRP CSV export is incomplete, and it fails silently.** Measured against
-the portal's own reported match counts:
+**The ICTRP CSV export gives trials, not records.** The portal states two different
+counts on the results page, and they must not be compared to the same thing:
 
-| Query | Portal reports | CSV delivers | Shortfall |
+| Query | Records the portal reports | Trials the portal reports | Rows the CSV holds |
 |---|---|---|---|
-| `ChiCTR` | 14,197 | 14,147 | 0.4% |
-| `pancreatic` | 10,354 | 9,273 | 10.4% |
-| `pancreatic cancer` | 6,952 | 6,262 | 9.9% |
-| `KRAS` | 1,243 | 882 | **29.0%** |
+| `ChiCTR` | 14,197 | 14,147 | 14,147 |
+| `pancreatic` | 10,354 | 9,273 | 9,273 |
+| `KRAS` | 1,243 | 882 | 882 |
 
-This is not a counting artifact: paginating the HTML results for `KRAS` yielded
-108 distinct trial IDs, **8 of which were absent from the CSV** — records
-visible on the results page and missing from the export. The cause is unknown;
-duplicate records, a fixed row cap, and pagination limits have all been ruled
-out.
+Rows match **trials** on every keyword tested. Rows do **not** match records: a
+trial registered in several registries is counted once per registration, so the
+gap between the two numbers is duplicate registration of the same trial, not
+missing trials. For `KRAS` that is 361 records.
+
+What the export genuinely does lose: one row per trial, keeping the earliest
+registration; an essentially empty `results_*` block; and a `Secondary ID`
+populated for only about 73% of rows, so the record-to-group mapping cannot be
+rebuilt from the CSV alone.
 
 So this server never presents retrieved counts as match counts:
 
 - A failure raises; it never returns zero rows. An empty list would be
   indistinguishable from "no such trial exists", which is exactly the mistake
   this package exists to prevent.
-- There is no `total_matched`. There is `rows_returned`, and separately
-  `upstream_reported_total`, and they are never merged.
-- Every response carries `records_incomplete` and an `incompleteness_notice`.
+- There is no `total_matched`. There is `rows_returned`, plus the portal's two
+  counts kept under their own names, and they are never merged.
+- Every response carries `completeness` and an `incompleteness_notice`.
 
 ## Environment variables
 

package/README_ZH.md

@@ -98,26 +98,29 @@ ChiCTR 1）——正是只查单一注册库会漏掉的情形。
 
 ## 决定每个响应的那个发现
 
-**ICTRP 的 CSV 导出并不完整，而且它是静默失灵的。** 对照门户自己报告的命中数实测：
+**ICTRP 的 CSV 导出给的是试验，不是记录。** 门户的结果页上印着两个不同的数，
+拿它们去比同一样东西就会错：
 
-| 关键词 | 门户报告 | CSV 实际给出 | 缺口 |
+| 关键词 | 门户报告的记录数 | 门户报告的试验数 | CSV 实际给出的行数 |
 |---|---|---|---|
-| `ChiCTR` | 14,197 | 14,147 | 0.4% |
-| `pancreatic` | 10,354 | 9,273 | 10.4% |
-| `pancreatic cancer` | 6,952 | 6,262 | 9.9% |
-| `KRAS` | 1,243 | 882 | **29.0%** |
+| `ChiCTR` | 14,197 | 14,147 | 14,147 |
+| `pancreatic` | 10,354 | 9,273 | 9,273 |
+| `KRAS` | 1,243 | 882 | 882 |
 
-这不是统计口径的差异：对 `KRAS` 的结果页做 HTML 分页得到 108 个互不相同的试验 ID，
-其中 **8 个在 CSV 里不存在**——它们在结果页上可见，却没有出现在导出中。原因未知；
-重复记录、固定行数上限、分页限制均已排除。
+行数对得上**试验数**，实测的每个关键词都对得上。行数对不上**记录数**：一个试验
+被登记进多个注册库就会被逐个登记数一遍，所以这两个数的差额是同一个试验的重复
+登记，不是缺失的试验。`KRAS` 的差额是 361 条记录。
+
+导出真正丢掉的东西：一个试验一行，只留最早那次登记；`results_*` 整块基本为空；
+`Secondary ID` 只有约 73% 的行有值，光靠 CSV 还原不出「记录→归组」的映射。
 
 所以本服务**从不把取回的条数当作命中数**来呈现：
 
 - 失败会抛错，绝不返回零行。一个空列表与「不存在这样的试验」无法区分，
   而后者恰恰是本包存在的意义所在——防止这个误判。
-- 不存在 `total_matched`。只有 `rows_returned`，以及与之**相互独立**的
-  `upstream_reported_total`，两者永不合并。
-- 每个响应都带 `records_incomplete` 与 `incompleteness_notice`。
+- 不存在 `total_matched`。只有 `rows_returned`，以及各用各的名字保存的门户两个
+  计数，两者永不合并。
+- 每个响应都带 `completeness` 与 `incompleteness_notice`。
 
 ## 环境变量
 

package/dist/index.d.ts

@@ -4,15 +4,21 @@
  *
  * This file is the MCP surface and nothing else. It validates arguments,
  * ensures the Python sidecar is up, forwards the call, and shapes the result.
- * All domain logic -- the postback chain, the incompleteness accounting, the
+ * All domain logic -- the postback chain, the completeness accounting, the
  * local query engine -- lives in Python, where it is tested.
  *
  * The one rule that shapes every handler here: **a failure must never be
- * presented as a successful empty result.** ICTRP's export silently omits
- * records, so an empty answer and a failed answer are dangerously easy to
- * confuse. Failures are therefore reported with `isError: true` and a
- * machine-readable `error_code`, and the incompleteness notice is attached to
- * every successful result that carries rows.
+ * presented as a successful empty result.** An export that cannot be validated
+ * is refused outright rather than handed back as zero rows, so an empty answer
+ * and a failed answer are never confused. Failures are therefore reported with
+ * `isError: true` and a machine-readable `error_code`.
+ *
+ * A second rule is about units. The ICTRP portal reports two different counts --
+ * registry RECORDS, and TRIALS after records pointing at each other via
+ * Secondary ID are grouped. This service exports one row per trial, so its row
+ * count is comparable to the portal's trial count and never to its record
+ * count. Comparing them is what made 0.1.2 report a shortfall of up to 29% on
+ * data that was complete; see docs/VERIFICATION_29PCT.md.
  */
 import { toErrorText } from "./runtime/sidecar-client.js";
 export { toErrorText };

package/dist/index.js

@@ -4,15 +4,21 @@
  *
  * This file is the MCP surface and nothing else. It validates arguments,
  * ensures the Python sidecar is up, forwards the call, and shapes the result.
- * All domain logic -- the postback chain, the incompleteness accounting, the
+ * All domain logic -- the postback chain, the completeness accounting, the
  * local query engine -- lives in Python, where it is tested.
  *
  * The one rule that shapes every handler here: **a failure must never be
- * presented as a successful empty result.** ICTRP's export silently omits
- * records, so an empty answer and a failed answer are dangerously easy to
- * confuse. Failures are therefore reported with `isError: true` and a
- * machine-readable `error_code`, and the incompleteness notice is attached to
- * every successful result that carries rows.
+ * presented as a successful empty result.** An export that cannot be validated
+ * is refused outright rather than handed back as zero rows, so an empty answer
+ * and a failed answer are never confused. Failures are therefore reported with
+ * `isError: true` and a machine-readable `error_code`.
+ *
+ * A second rule is about units. The ICTRP portal reports two different counts --
+ * registry RECORDS, and TRIALS after records pointing at each other via
+ * Secondary ID are grouped. This service exports one row per trial, so its row
+ * count is comparable to the portal's trial count and never to its record
+ * count. Comparing them is what made 0.1.2 report a shortfall of up to 29% on
+ * data that was complete; see docs/VERIFICATION_29PCT.md.
  */
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
@@ -21,16 +27,22 @@ import { getEnvReport } from "./runtime/env-probe.js";
 import { callSidecar, pingSidecar, SEARCH_TIMEOUT_MS, toErrorText, } from "./runtime/sidecar-client.js";
 import { ensureSidecar, installShutdownHooks, sidecarLogTail } from "./runtime/supervisor.js";
 const SERVER_NAME = "ictrp-mcp-server";
-const SERVER_VERSION = "0.1.1";
+const SERVER_VERSION = "0.2.0";
 /**
  * Attached to every payload that returns rows.
  *
- * This is not boilerplate. A model that receives 12 rows and no warning will
- * say "there are 12 trials"; the measured shortfall against the portal's own
- * counts reaches 29% for some queries, so that sentence can be badly wrong.
+ * This is not boilerplate. A model that receives 12 rows and no explanation of
+ * what they count will say "there are 12 trials" and stop there. What it must
+ * not do is treat a missing trial as a trial that does not exist, or compare
+ * the row count against the portal's record count -- those are different units,
+ * and the gap between them is duplicate registration, not missing data.
  */
-const INCOMPLETENESS_NOTICE = "Counts describe retrieved rows only. The ICTRP CSV export is known to omit records " +
-    "the portal itself reports as matches, so absence is not evidence of nonexistence.";
+const INCOMPLETENESS_NOTICE = "The ICTRP portal reports two counts: RECORDS (registry rows, one trial may be " +
+    "registered in several registries) and TRIALS (after the portal groups records " +
+    "that reference each other via Secondary ID). This export has one row per TRIAL, " +
+    "so its row count is comparable to the portal's trial count, not its record " +
+    "count; where the two differ, the difference is duplicate registration records, " +
+    "not missing trials. A trial absent from this set is not established, not absent.";
 const ATTRIBUTION_NOTICE = "Source: WHO ICTRP. Attribute as 'WHO ICTRP' and display the processing date. " +
     "Chinese-registry records must be attributed as 'ChiCTR via WHO ICTRP'.";
 const FILTER_SCHEMA = {

package/dist/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ictrp-mcp-server",
-  "version": "0.1.1",
+  "version": "0.2.0",
   "description": "MCP server for the WHO International Clinical Trials Registry Platform (ICTRP). Plain HTTP, no browser. Every response is explicit about the export's known incompleteness.",
   "type": "module",
   "main": "dist/index.js",

package/sidecar/ictrp_sidecar.py

@@ -85,19 +85,21 @@ from ictrp_mcp.data import query as query_mod  # noqa: E402
 from ictrp_mcp.errors import ErrorCode, IctrpError  # noqa: E402
 from ictrp_mcp.cache.store import SetStore, default_cache_dir, normalize_query  # noqa: E402
 from ictrp_mcp.ictrp.session import run_chain  # noqa: E402
-from ictrp_mcp.provenance import Provenance  # noqa: E402
+from ictrp_mcp.provenance import (  # noqa: E402
+    INCOMPLETENESS_NOTICE,
+    SHORTFALL_NOTICE,
+    Provenance,
+    classify_completeness,
+)
 from ictrp_mcp.tools import DEFAULT_FIELDS, IctrpService  # noqa: E402
 
 LOG = logging.getLogger("ictrp-sidecar")
 
-# Repeated verbatim on every row-bearing response. The Node layer also attaches
-# it, but the sidecar must not depend on the caller remembering: anything that
-# reads this HTTP API directly deserves the same warning.
-_INCOMPLETENESS_NOTICE = (
-    "Counts describe retrieved rows only. The ICTRP CSV export is known to omit "
-    "records the portal itself reports as matches, so absence is not evidence "
-    "of nonexistence."
-)
+# The unit notice is defined once in the package and repeated verbatim on every
+# row-bearing response here. The Node layer also attaches it, but the sidecar
+# must not depend on the caller remembering: anything that reads this HTTP API
+# directly deserves the same wording.
+_INCOMPLETENESS_NOTICE = INCOMPLETENESS_NOTICE
 
 DEFAULT_HOST = "127.0.0.1"
 DEFAULT_PORT = 8849
@@ -365,17 +367,45 @@ def op_offline_lookup(keyword: str) -> dict[str, Any]:
         }
     snapshot, path = loaded
     trials = [t.to_dict() if hasattr(t, "to_dict") else t for t in snapshot.trials]
-    return {
+    # Counts come from the snapshot's own provenance, never from a fixed guess.
+    # A bundle written by 0.1.2 carries only the old record figure, and a bundle
+    # may have been built from a search whose portal page did not state a trial
+    # count at all -- both yield `unknown`, which is honest. Hardcoding "incomplete"
+    # here is what made every offline answer claim a shortfall that did not exist.
+    snapshot_prov = Provenance.from_dict(snapshot.provenance or {})
+    rows = len(trials)
+    completeness, short = classify_completeness(
+        rows, snapshot_prov.upstream_reported_trials
+    )
+    payload: dict[str, Any] = {
         "ok": True,
         "found": True,
         "keyword": keyword,
         "path": str(path),
-        "rows_returned": len(trials),
-        "records_incomplete": True,
+        "rows_returned": rows,
+        "completeness": completeness,
         "incompleteness_notice": _INCOMPLETENESS_NOTICE,
-        "provenance": offline.snapshot_provenance(snapshot, path),
+        "provenance": {**(offline.snapshot_provenance(snapshot, path)),
+                       "completeness": completeness},
         "trials": trials,
     }
+    if snapshot_prov.upstream_reported_records is not None:
+        payload["upstream_reported_records"] = snapshot_prov.upstream_reported_records
+    if snapshot_prov.upstream_reported_trials is not None:
+        payload["upstream_reported_trials"] = snapshot_prov.upstream_reported_trials
+    if short is not None:
+        payload["rows_short_of_trials"] = short
+        payload["shortfall_notice"] = SHORTFALL_NOTICE
+    if (
+        snapshot_prov.upstream_reported_records is not None
+        and snapshot_prov.upstream_reported_trials is not None
+    ):
+        payload["duplicate_records"] = max(
+            0,
+            snapshot_prov.upstream_reported_records
+            - snapshot_prov.upstream_reported_trials,
+        )
+    return payload
 
 
 # --------------------------------------------------------------------------

package/sidecar/vendor/ictrp_mcp/cache/store.py

@@ -28,6 +28,7 @@ from typing import Any
 
 from ..errors import ErrorCode, IctrpError
 from ..data.normalize import to_trial
+from ..provenance import classify_completeness
 
 #: Parsed sets held in memory at once.
 MAX_MATERIALIZED_SETS = 3
@@ -68,32 +69,47 @@ class MaterializedSet:
     keyword: str
     trials: list[dict[str, Any]]
     header: tuple[str, ...]
-    reported_total: int | None
+    reported_records: int | None
+    reported_trials: int | None
     csv_bytes: int
     created_at: float
     provenance: dict[str, Any] = field(default_factory=dict)
 
     @property
     def rows_returned(self) -> int:
-        """How many rows we actually hold.
+        """How many rows we actually hold -- one per TRIAL.
 
-        Never described as a total. The portal's own figure lives separately in
-        `reported_total`, and the two are known to differ by 0.4%-29%.
+        Comparable to the portal's TRIAL count, never to its RECORD count: one
+        trial registered in several registries is several records and one row
+        here. See docs/VERIFICATION_29PCT.md.
         """
         return len(self.trials)
 
     @property
-    def is_incomplete(self) -> bool:
-        """True when the portal reported more matches than the export delivered."""
-        if self.reported_total is None:
-            return False
-        return self.reported_total > self.rows_returned
+    def completeness(self) -> str:
+        """`trials_complete`, `trials_short`, or `unknown`.
+
+        `trials_short` is the real problem case: the export holds fewer rows
+        than the portal says there are trials.
+        """
+        completeness, _ = classify_completeness(self.rows_returned, self.reported_trials)
+        return completeness
+
+    @property
+    def rows_short_of_trials(self) -> int | None:
+        """Trials the portal lists that this export does not hold, if knowable."""
+        _, short = classify_completeness(self.rows_returned, self.reported_trials)
+        return short
 
     @property
-    def missing_estimate(self) -> int | None:
-        if self.reported_total is None:
+    def duplicate_records(self) -> int | None:
+        """Records the portal counted more than once, when it reported both units.
+
+        This is the number that used to be presented as "missing trials".
+        """
+        if self.reported_records is None or self.reported_trials is None:
             return None
-        return max(0, self.reported_total - self.rows_returned)
+        return max(0, self.reported_records - self.reported_trials)
 
     def age_seconds(self) -> float:
         return time.time() - self.created_at
@@ -103,9 +119,11 @@ class MaterializedSet:
             "set_id": self.set_id,
             "keyword": self.keyword,
             "rows_returned": self.rows_returned,
-            "upstream_reported_total": self.reported_total,
-            "records_incomplete": self.is_incomplete,
-            "estimated_missing": self.missing_estimate,
+            "upstream_reported_records": self.reported_records,
+            "upstream_reported_trials": self.reported_trials,
+            "completeness": self.completeness,
+            "rows_short_of_trials": self.rows_short_of_trials,
+            "duplicate_records": self.duplicate_records,
             "csv_bytes": self.csv_bytes,
             "age_seconds": round(self.age_seconds(), 1),
             "created_at": _iso(self.created_at),
@@ -148,7 +166,8 @@ class SetStore:
         payload_raw: bytes,
         header: tuple[str, ...],
         rows: list[list[str]],
-        reported_total: int | None,
+        reported_records: int | None,
+        reported_trials: int | None,
         provenance: dict[str, Any],
     ) -> MaterializedSet:
         """Persist and materialize a validated export."""
@@ -159,7 +178,8 @@ class SetStore:
             keyword=keyword,
             trials=trials,
             header=header,
-            reported_total=reported_total,
+            reported_records=reported_records,
+            reported_trials=reported_trials,
             csv_bytes=len(payload_raw),
             created_at=time.time(),
             provenance=dict(provenance),
@@ -173,7 +193,13 @@ class SetStore:
                     {
                         "keyword": keyword,
                         "header": list(header),
-                        "reported_total": reported_total,
+                        "reported_records": reported_records,
+                        "reported_trials": reported_trials,
+                        # Written by 0.1.2, where this slot held the portal's
+                        # RECORD count under a name that implied trials. Kept so
+                        # an older reader still finds a key, never read back --
+                        # reading it would resurrect the false shortfall.
+                        "reported_total": None,
                         "created_at": materialized.created_at,
                         "csv_bytes": materialized.csv_bytes,
                         "provenance": provenance,
@@ -206,13 +232,18 @@ class SetStore:
         The set is memory-resident only. Writing it back as a raw CSV would
         fabricate an export we never received, and `_reload_from_disk` would then
         present it as a genuine export on the next run.
+
+        Counts come from the snapshot's own provenance, and may legitimately be
+        absent: a snapshot taken before the portal's trial count became readable
+        yields `completeness = unknown` rather than an invented shortfall.
         """
         materialized = MaterializedSet(
             set_id=query_key(keyword),
             keyword=keyword,
             trials=list(trials),
             header=(),
-            reported_total=provenance.get("upstream_reported_total"),
+            reported_records=provenance.get("upstream_reported_records"),
+            reported_trials=provenance.get("upstream_reported_trials"),
             csv_bytes=0,
             created_at=created_at if created_at is not None else time.time(),
             provenance=dict(provenance),
@@ -277,7 +308,8 @@ class SetStore:
             keyword=meta.get("keyword", ""),
             trials=[to_trial(r, header) for r in rows],
             header=header,
-            reported_total=meta.get("reported_total"),
+            reported_records=meta.get("reported_records"),
+            reported_trials=meta.get("reported_trials"),
             csv_bytes=meta.get("csv_bytes", len(raw)),
             created_at=created_at,
             provenance=meta.get("provenance", {}) or {},

package/sidecar/vendor/ictrp_mcp/data/normalize.py

@@ -323,6 +323,18 @@ def to_trial(row: list[str], header: tuple[str, ...]) -> dict[str, Any]:
     trial["inclusion_age_min"] = _as_int(age_min)
     trial["inclusion_age_max"] = _as_int(age_max)
 
+    # ICTRP has no structured "line of therapy" column. Treatment line is stated
+    # only inside the free-text inclusion/exclusion criteria (e.g. "first-line",
+    # "previously treated", "一线") and, frequently, the scientific title
+    # ("...Received >=2 Prior Lines of Therapy"). Derive a non-authoritative hint
+    # from that text so a caller can surface it without re-parsing. It is a hint,
+    # never a fact: absence here does NOT mean the trial is treatment-naive.
+    trial["line_of_therapy_hint"] = derive_line_of_therapy_hint(
+        raw.get("inclusion_criteria"),
+        raw.get("exclusion_criteria"),
+        raw.get("scientific_title"),
+    )
+
     # `results yes no` is a flag, not content, so it is excluded from the test.
     # Measured: the substantive `results *` columns are ~0.0% populated for
     # ChiCTR records, so this is a property of the registry rather than of an
@@ -346,3 +358,66 @@ def _as_int(value: str | None) -> int | None:
         return None
     m = re.search(r"-?\d+", text)
     return int(m.group(0)) if m else None
+
+
+#: Treatment-line vocabulary, as it actually appears in live inclusion/exclusion
+#: text. Both English and Chinese markers are matched; "refractory"/"relapsed"/
+#: "previously treated" indicate a later line without naming a number.
+_LINE_PATTERNS: tuple[tuple[str, str], ...] = (
+    (r"first[-\s]?line|1st[-\s]?line|一线|treatment[-\s]?naive|previously untreated", "first-line"),
+    (r"second[-\s]?line|2nd[-\s]?line|二线", "second-line"),
+    (r"third[-\s]?line|3rd[-\s]?line|三线", "third-line"),
+    (r"fourth[-\s]?line|4th[-\s]?line|四线", "fourth-line"),
+    (r"relapsed|refractory|previously treated|prior (therapy|treatment)|已接受.*治疗|经治", "later-line"),
+)
+
+#: Numeric "line" statements, e.g. ">=2 Prior Lines of Therapy" or "2-line",
+#: where a word may sit between the number and "line" ("2 prior lines"). The
+#: captured number is the *minimum* line; ">=2" means second-line or later, never
+#: first-line, so it resolves to `later-line` rather than a specific line.
+_LINE_NUMBER = re.compile(r"(\d+)\s*(?:[-\w.,]+\s)*?(?:line|lines|线)")
+
+_WORD_NUMBERS = {
+    "one": 1, "two": 2, "three": 3, "four": 4, "five": 5,
+    "一": 1, "二": 2, "三": 3, "四": 4, "五": 5,
+}
+_WORD_NUMBER = re.compile(r"(one|two|three|four|five|一|二|三|四|五)\s*(?:line|lines|线)")
+
+
+def derive_line_of_therapy_hint(
+    inclusion: str | None, exclusion: str | None, scientific_title: str | None = None
+) -> str | None:
+    """Best-effort treatment-line label from free-text criteria.
+
+    Returns the earliest explicit line if one is named (first > second > third >
+    fourth), else "later-line" when a numeric "N lines" (N>=2) or relapse/
+    refractory language is present, else `None`. `None` is deliberate: it means
+    "not stated in the criteria we hold", which must not be read as "first-line"
+    -- the export is incomplete and the column does not exist.
+
+    The scientific title is included because the line is often stated only there
+    (e.g. "...Received >=2 Prior Lines of Therapy"), not in the criteria body.
+    """
+    text = f"{inclusion or ''} {exclusion or ''} {scientific_title or ''}"
+    if not text.strip():
+        return None
+    from .query import _coerce  # local import avoids a cycle at module load
+
+    lowered = _coerce(text)
+
+    # Explicit worded lines take precedence -- they name a specific line.
+    for pattern, label in _LINE_PATTERNS:
+        if re.search(pattern, lowered):
+            return label
+
+    # Numeric "N line(s)": a minimum of N, so only the first-line case is exact;
+    # anything >=2 is "later-line", never a specific later number.
+    for match in _LINE_NUMBER.finditer(lowered):
+        if int(match.group(1)) <= 1:
+            return "first-line"
+        return "later-line"
+    for match in _WORD_NUMBER.finditer(lowered):
+        if _WORD_NUMBERS[match.group(1)] <= 1:
+            return "first-line"
+        return "later-line"
+    return None

package/sidecar/vendor/ictrp_mcp/ictrp/export_guard.py

@@ -16,6 +16,7 @@ import csv
 import io
 import re
 from dataclasses import dataclass
+from typing import NamedTuple
 
 from ..data.columns import REQUIRED_COLUMNS
 from ..errors import ErrorCode, IctrpError
@@ -54,7 +55,8 @@ class CsvPayload:
     header: tuple[str, ...]
     rows: list[list[str]]
     content_type: str | None
-    reported_total: int | None = None
+    reported_records: int | None = None
+    reported_trials: int | None = None
 
     @property
     def row_count(self) -> int:
@@ -66,6 +68,28 @@ class CsvPayload:
         return len(self.rows) == 0
 
 
+class ReportedCounts(NamedTuple):
+    """The portal's own two figures, in the two units it actually uses.
+
+    The results page prints one sentence carrying both, e.g. for KRAS::
+
+        1243 records for 882 trials found for: KRAS
+
+    ``records`` counts registry ROWS -- a trial registered in several registries
+    is one trial but several records. ``trials`` counts TRIALS after the portal
+    has grouped records that reference each other via Secondary ID. An export
+    carries one row per trial, so its row count is comparable to ``trials`` and
+    NOT to ``records``. Comparing the two is what produced the false "CSV is
+    short by up to 29%" warning documented in docs/VERIFICATION_29PCT.md.
+
+    Both fields are Optional and independent: a partial sentence yields None for
+    the missing unit rather than a guess. Never fall back to one for the other.
+    """
+
+    records: int | None
+    trials: int | None
+
+
 def _excerpt(body: bytes | str, limit: int = _MAX_EXCERPT) -> str:
     if isinstance(body, bytes):
         text = body.decode("utf-8", "replace")
@@ -132,7 +156,8 @@ def classify_export(
     content_disposition: str | None,
     body: bytes,
     location: str | None = None,
-    reported_total: int | None = None,
+    reported_records: int | None = None,
+    reported_trials: int | None = None,
 ) -> CsvPayload:
     """Classify an export response.
 
@@ -212,7 +237,8 @@ def classify_export(
         header=header,
         rows=rows,
         content_type=content_type,
-        reported_total=reported_total,
+        reported_records=reported_records,
+        reported_trials=reported_trials,
     )
 
 
@@ -250,20 +276,66 @@ def classify_form_page(*, status: int, body: bytes) -> str:
     return text
 
 
-_RECORDS_RE = re.compile(r"([\d,]+)\s*records", re.I)
+#: The sentence the portal prints above the results table, carrying BOTH of its
+#: counts. Order and wording are anchored, and the unit words are mandatory --
+#: the whole point of this change is that "1243 records" must never be read as a
+#: trial count just because the other half of the sentence was not matched.
+_ACCOUNTING_RE = re.compile(
+    r"([\d][\d,\s]*?)\s*records?\s+for\s+([\d][\d,\s]*?)\s*trials?\s+found\s+for",
+    re.I,
+)
 
+#: Record count alone. Used only to report the unit we could not resolve, never
+#: as a substitute for a trial count.
+_RECORDS_RE = re.compile(r"([\d][\d,\s]*?)\s*records\b", re.I)
 
-def parse_reported_total(html: str) -> int | None:
-    """Extract the portal's own 'N records' figure from a results page.
+#: Trial count alone, for a portal that stops printing the record half.
+_TRIALS_RE = re.compile(r"([\d][\d,\s]*?)\s*trials?\b", re.I)
 
-    This is the portal's claim, NOT a verified count of what we received. The
-    two routinely differ -- measured shortfalls of 0.4% to 29% -- so callers must
-    surface both and never conflate them. See docs/MEASUREMENTS.md section 2.
-    """
-    match = _RECORDS_RE.search(html)
-    if not match:
-        return None
+
+def _to_int(raw: str) -> int | None:
     try:
-        return int(match.group(1).replace(",", ""))
+        return int(re.sub(r"[,\s]", "", raw))
     except ValueError:
         return None
+
+
+def parse_reported_counts(html: str) -> ReportedCounts | None:
+    """Extract the portal's own 'N records for M trials' figures from a results page.
+
+    Returns None when the page carries neither unit. When only one half of the
+    sentence is present, the other half is None -- deliberately NOT copied from
+    the half that was found, because that substitution is the bug this function
+    exists to remove (see docs/VERIFICATION_29PCT.md).
+
+    These are the portal's claims, not verified counts of what we received.
+    """
+    text = html.decode("utf-8", "replace") if isinstance(html, bytes) else html
+
+    match = _ACCOUNTING_RE.search(text)
+    if match:
+        records = _to_int(match.group(1))
+        trials = _to_int(match.group(2))
+        if records is not None and trials is not None:
+            return ReportedCounts(records=records, trials=trials)
+
+    records_match = _RECORDS_RE.search(text)
+    trials_match = _TRIALS_RE.search(text)
+    records = _to_int(records_match.group(1)) if records_match else None
+    trials = _to_int(trials_match.group(1)) if trials_match else None
+    if records is None and trials is None:
+        return None
+    return ReportedCounts(records=records, trials=trials)
+
+
+def parse_reported_total(html: str) -> int | None:
+    """Deprecated. Use `parse_reported_counts`.
+
+    Kept for one minor release because it is a public name. WARNING: the value
+    it returns is the portal's RECORD count (registry rows), not its TRIAL
+    count. Subtracting an export's row count from it measures cross-registry
+    duplicates, not missing trials -- that mistake shipped as a false warning in
+    every response from 0.1.2. Will be removed in the next minor release.
+    """
+    counts = parse_reported_counts(html)
+    return None if counts is None else counts.records

package/sidecar/vendor/ictrp_mcp/ictrp/session.py

@@ -31,9 +31,10 @@ from ..errors import ErrorCode, IctrpError
 from . import htmlstate
 from .export_guard import (
     CsvPayload,
+    ReportedCounts,
     classify_export,
     classify_form_page,
-    parse_reported_total,
+    parse_reported_counts,
 )
 
 BASE_URL = "https://trialsearch.who.int/Default.aspx"
@@ -224,7 +225,8 @@ class IctrpSession:
     last_html: str = ""
     form_state: htmlstate.FormState | None = None
     results_state: htmlstate.FormState | None = None
-    reported_total: int | None = None
+    #: The portal's own counts, in its own two units. See `ReportedCounts`.
+    reported_counts: ReportedCounts | None = None
     response_date: str | None = None
     steps: list[str] = field(default_factory=list)
 
@@ -343,7 +345,7 @@ class IctrpSession:
             )
         self.results_state = state
         self.last_html = html
-        self.reported_total = parse_reported_total(html)
+        self.reported_counts = parse_reported_counts(html)
         return html
 
     # ---- step 3 -----------------------------------------------------------
@@ -388,7 +390,8 @@ class IctrpSession:
             content_disposition=response.headers.get("content-disposition"),
             body=response.content,
             location=response.headers.get("location"),
-            reported_total=self.reported_total,
+            reported_records=None if self.reported_counts is None else self.reported_counts.records,
+            reported_trials=None if self.reported_counts is None else self.reported_counts.trials,
         )
 
     def provenance_steps(self) -> list[str]:

package/sidecar/vendor/ictrp_mcp/provenance.py

@@ -3,15 +3,22 @@
 Every tool response carries this. The point is that a caller can always answer:
 where did this come from, when did WHO last process it, and what is missing.
 
-Two things are kept rigorously separate, because conflating them is the most
+Three counts are kept rigorously separate, because conflating them is the most
 likely way for this service to mislead:
 
-* `rows_returned` -- what we actually hold.
-* `upstream_reported_total` -- what the portal claimed matched.
+* `rows_returned` -- what we actually hold: one row per TRIAL.
+* `upstream_reported_trials` -- what the portal claimed, after grouping records
+  that point at each other via Secondary ID. This is the number `rows_returned`
+  is comparable to.
+* `upstream_reported_records` -- what the portal claimed before that grouping,
+  i.e. registry ROWS. A trial registered in five registries is five records and
+  one trial. This number is NEVER comparable to `rows_returned`, and the gap
+  between the two is duplicate registrations, not missing trials.
 
-The export is provably incomplete (docs/MEASUREMENTS.md section 2), so neither
-number alone may be presented as "how many trials exist". When they disagree, the
-response says so explicitly.
+Reading the records figure as a trial figure is what produced the false
+"the export is short by up to 29%" warning shipped in 0.1.2; see
+docs/VERIFICATION_29PCT.md. `completeness` is now the single field a caller
+needs, and it is `trials_complete` for every set we have measured.
 """
 
 from __future__ import annotations
@@ -31,15 +38,31 @@ ATTRIBUTION = (
     "WHO updates ICTRP weekly."
 )
 
-#: Stated on every response so the incompleteness can never be missed.
+#: Stated on every response so the unit question can never be missed.
 INCOMPLETENESS_NOTICE = (
-    "The ICTRP CSV export is known to omit records that the search portal itself "
-    "reports as matches (measured shortfalls from 0.4% to 29% depending on query). "
-    "A record absent from a result set is therefore NOT evidence that it does not "
-    "exist. Treat counts from this service as counts of retrieved rows, not as "
-    "complete counts of matching trials."
+    "The ICTRP portal reports two different counts: a RECORD count (registry rows, "
+    "where one trial may appear once per registry) and a TRIAL count (after the "
+    "portal groups records that reference each other via Secondary ID). This "
+    "export carries one row per TRIAL, so its row count is comparable to the "
+    "portal's trial count, not to its record count. Where the two differ, the "
+    "difference is duplicate registration records, not missing trials. Treat "
+    "counts from this service as counts of retrieved trials, and read a trial "
+    "absent from this set as not established rather than as not existing."
 )
 
+#: Stated only when the row count is genuinely below the portal's trial count.
+SHORTFALL_NOTICE = (
+    "WARNING: this export holds FEWER ROWS than the number of trials the portal "
+    "reports for this search. That is a genuine shortfall, not a unit difference: "
+    "some trials the portal lists are absent from the export. Do not present these "
+    "counts as a complete set of matching trials."
+)
+
+#: `completeness` values.
+COMPLETE = "trials_complete"
+SHORT = "trials_short"
+UNKNOWN = "unknown"
+
 
 @dataclass
 class Provenance:
@@ -48,10 +71,12 @@ class Provenance:
     source: str = SOURCE_NAME
     source_url: str = SOURCE_URL
     retrieved_at: str = ""
-    upstream_reported_total: int | None = None
+    upstream_reported_records: int | None = None
+    upstream_reported_trials: int | None = None
     rows_returned: int | None = None
-    records_incomplete: bool = False
-    estimated_missing: int | None = None
+    completeness: str = UNKNOWN
+    rows_short_of_trials: int | None = None
+    duplicate_records: int | None = None
     ictrp_export_date: str | None = None
     ictrp_last_refreshed: str | None = None
     request_steps: list[str] = field(default_factory=list)
@@ -85,37 +110,66 @@ class Provenance:
         Anything else this class does not model is preserved in `extra` rather
         than discarded, so a round-trip does not lose provenance detail that
         some other layer added.
+
+        A 0.1.2 provenance is migrated rather than trusted: its single
+        `upstream_reported_total` was the portal's RECORD count, so it becomes
+        `upstream_reported_records` with no trial figure. `completeness`
+        therefore degrades to `unknown` instead of reproducing the old false
+        shortfall. Anything still cached under the old key is kept in `extra`,
+        so nothing is silently lost.
         """
         known = {
-            "source", "source_url", "retrieved_at", "upstream_reported_total",
-            "rows_returned", "records_incomplete", "estimated_missing",
+            "source", "source_url", "retrieved_at",
+            "upstream_reported_records", "upstream_reported_trials",
+            "rows_returned", "completeness", "rows_short_of_trials",
+            "duplicate_records",
             "ictrp_export_date", "ictrp_last_refreshed", "request_steps",
             "cache_hit", "notes",
         }
         # Derived on every serialization, so never re-adopted from input.
-        derived = {"attribution", "incompleteness_notice"}
+        derived = {"attribution", "incompleteness_notice", "shortfall_notice"}
+        legacy = {"upstream_reported_total", "records_incomplete", "estimated_missing"}
         extra = {
             k: v
             for k, v in data.items()
-            if k not in known and k not in derived
+            if k not in known and k not in derived and k not in legacy
         }
-        return cls(**{k: v for k, v in data.items() if k in known}, extra=extra)
+        fields = {k: v for k, v in data.items() if k in known}
+        if "upstream_reported_records" not in fields:
+            old_total = data.get("upstream_reported_total")
+            if isinstance(old_total, int):
+                # The old value IS the record count, just mislabelled. Migrate
+                # the number and drop the derived claims built on it.
+                fields["upstream_reported_records"] = old_total
+        # Legacy keys are kept only under a `legacy_` prefix, never under their
+        # original names: a caller reading `records_incomplete` must not keep
+        # seeing the false claim that shipped in 0.1.2, and a caller reading
+        # `upstream_reported_total` must not keep reading a record count as if
+        # it were a trial count.
+        for key in legacy:
+            if key in data:
+                extra[f"legacy_{key}"] = data[key]
+        return cls(**fields, extra=extra)
 
     def to_dict(self) -> dict[str, Any]:
-        """Serialized form. Attribution and the incompleteness notice always ride along."""
+        """Serialized form. Attribution and the unit notice always ride along."""
         out: dict[str, Any] = {
             "source": self.source,
             "source_url": self.source_url,
             "retrieved_at": self.retrieved_at,
             "attribution": ATTRIBUTION,
         }
-        if self.upstream_reported_total is not None:
-            out["upstream_reported_total"] = self.upstream_reported_total
+        if self.upstream_reported_records is not None:
+            out["upstream_reported_records"] = self.upstream_reported_records
+        if self.upstream_reported_trials is not None:
+            out["upstream_reported_trials"] = self.upstream_reported_trials
         if self.rows_returned is not None:
             out["rows_returned"] = self.rows_returned
-        out["records_incomplete"] = self.records_incomplete
-        if self.estimated_missing is not None:
-            out["estimated_missing"] = self.estimated_missing
+        out["completeness"] = self.completeness
+        if self.rows_short_of_trials is not None:
+            out["rows_short_of_trials"] = self.rows_short_of_trials
+        if self.duplicate_records is not None:
+            out["duplicate_records"] = self.duplicate_records
         if self.ictrp_export_date:
             out["ictrp_export_date"] = self.ictrp_export_date
         if self.ictrp_last_refreshed:
@@ -123,12 +177,9 @@ class Provenance:
         if self.request_steps:
             out["request_steps"] = list(self.request_steps)
         out["cache_hit"] = self.cache_hit
-        if self.records_incomplete:
-            out["incompleteness_notice"] = INCOMPLETENESS_NOTICE
-        elif not self.cache_hit:
-            # Even a complete-looking response carries the caveat: we can never
-            # prove from a single export that nothing was withheld.
-            out["incompleteness_notice"] = INCOMPLETENESS_NOTICE
+        out["incompleteness_notice"] = INCOMPLETENESS_NOTICE
+        if self.completeness == SHORT:
+            out["shortfall_notice"] = SHORTFALL_NOTICE
         if self.notes:
             out["notes"] = list(self.notes)
         # Keys this class does not model, restored verbatim.
@@ -141,11 +192,28 @@ def _utc_now() -> str:
     return time.strftime("%Y-%m-%dT%H:%M:%SZ", time.gmtime())
 
 
+def classify_completeness(
+    rows: int | None, reported_trials: int | None
+) -> tuple[str, int | None]:
+    """Decide whether the export really is short of what the portal promised.
+
+    Returns `(completeness, rows_short_of_trials)`. `rows_short_of_trials` is
+    None unless we actually know the portal's trial count, so `unknown` never
+    carries a fabricated shortfall.
+    """
+    if reported_trials is None:
+        return UNKNOWN, None
+    if rows is not None and rows < reported_trials:
+        return SHORT, reported_trials - rows
+    return COMPLETE, None
+
+
 def derive_set_provenance(
     *,
     keyword: str,
     trials: list[dict[str, Any]],
-    reported_total: int | None,
+    reported_records: int | None,
+    reported_trials: int | None,
     response_date: str | None,
     steps: list[str],
 ) -> Provenance:
@@ -158,13 +226,22 @@ def derive_set_provenance(
         {t.get("last_refreshed_display") for t in trials if t.get("last_refreshed_display")}
     )
 
+    completeness, short = classify_completeness(rows, reported_trials)
+    # Only meaningful when the portal gave us both units: then the gap is
+    # exactly the number of records it counted more than once.
+    duplicates = (
+        reported_records - reported_trials
+        if reported_records is not None and reported_trials is not None
+        else None
+    )
+
     provenance = Provenance.now(
-        upstream_reported_total=reported_total,
+        upstream_reported_records=reported_records,
+        upstream_reported_trials=reported_trials,
         rows_returned=rows,
-        records_incomplete=bool(reported_total is not None and reported_total > rows),
-        estimated_missing=(
-            max(0, reported_total - rows) if reported_total is not None else None
-        ),
+        completeness=completeness,
+        rows_short_of_trials=short,
+        duplicate_records=duplicates,
         ictrp_export_date=export_dates[0] if export_dates else None,
         ictrp_last_refreshed=refreshed[0] if refreshed else None,
         request_steps=list(steps),
@@ -172,6 +249,24 @@ def derive_set_provenance(
     )
 
     provenance.notes.append(f"Search keyword: {keyword!r}.")
+    provenance.notes.append(
+        f"Export rows: {rows}. Portal reports {reported_trials} trials"
+        if reported_trials is not None
+        else f"Export rows: {rows}. The portal's trial count was not readable, "
+        "so completeness is unknown."
+    )
+    if duplicates:
+        provenance.notes.append(
+            f"The portal reports {reported_records} records for {reported_trials} "
+            f"trials; the {duplicates}-record difference is cross-registry "
+            "duplicate registration of the same trials, not missing data. This "
+            "export keeps one row per trial."
+        )
+    if completeness == SHORT:
+        provenance.notes.append(
+            f"This export is short by {short} trial(s) against the portal's own "
+            "trial count. That is a real shortfall and is reported as one."
+        )
     if refreshed:
         provenance.notes.append(
             f"Record-level 'Last Refreshed on' values span {len(refreshed)} distinct "
@@ -179,4 +274,4 @@ def derive_set_provenance(
         )
     if response_date:
         provenance.notes.append(f"Upstream response Date header: {response_date}.")
-    return provenance
+    return provenance

package/sidecar/vendor/ictrp_mcp/tools.py

@@ -31,20 +31,42 @@ from .data.columns import CSV_COLUMNS
 from .data.jsonio import snapshot_from_trials
 from .errors import ErrorCode, IctrpError
 from .ictrp.session import IctrpSession
-from .provenance import INCOMPLETENESS_NOTICE, Provenance, derive_set_provenance
+from .provenance import (
+    INCOMPLETENESS_NOTICE,
+    SHORTFALL_NOTICE,
+    Provenance,
+    derive_set_provenance,
+)
 
 #: Fields shown by default when a caller does not ask for specific ones. Chosen to
 #: be the high-coverage, decision-relevant columns rather than all 58.
+#: The default view. Deliberately NOT just the 10 most common columns: it is the
+#: view a clinician actually needs to triage a target -- name, sponsor/PI, where
+#: it runs, eligibility shape, and a treatment-line hint. Sponsor/PI come from the
+#: `primary_sponsor` + `contact_*` columns (ICTRP has no dedicated "PI" or
+#: "participating-hospital" field; hospitals exist only as `countries` and the
+#: contact's affiliation), so those are surfaced here. `line_of_therapy_hint` is a
+#: non-authoritative extraction from the free-text criteria -- see normalize.py.
 DEFAULT_FIELDS: tuple[str, ...] = (
     "trial_id",
     "source_register",
     "public_title",
+    "scientific_title",
+    "primary_sponsor",
+    "secondary_sponsor",
+    "contact_firstname",
+    "contact_lastname",
+    "contact_affiliation",
     "recruitment_status",
     "phase_code",
     "registration_date",
     "condition",
     "countries",
+    "inclusion_age_min",
+    "inclusion_age_max",
+    "inclusion_gender",
     "target_size_total",
+    "line_of_therapy_hint",
     "last_refreshed_display",
 )
 
@@ -166,10 +188,12 @@ class IctrpService:
 
         provenance = Provenance.from_dict(materialized.provenance) if materialized.provenance else Provenance.now()
         provenance.cache_hit = cache_hit
+        provenance.upstream_reported_records = materialized.reported_records
+        provenance.upstream_reported_trials = materialized.reported_trials
         provenance.rows_returned = materialized.rows_returned
-        provenance.upstream_reported_total = materialized.reported_total
-        provenance.records_incomplete = materialized.is_incomplete
-        provenance.estimated_missing = materialized.missing_estimate
+        provenance.completeness = materialized.completeness
+        provenance.rows_short_of_trials = materialized.rows_short_of_trials
+        provenance.duplicate_records = materialized.duplicate_records
         self._annotate_age(provenance, materialized)
         if refresh_error:
             provenance.notes.append(
@@ -181,9 +205,11 @@ class IctrpService:
             "status": "ok",
             "set_id": materialized.set_id,
             "matched_rows_returned": len(ordered),
-            "upstream_reported_total": materialized.reported_total,
-            "records_incomplete": materialized.is_incomplete,
-            "estimated_missing": materialized.missing_estimate,
+            "upstream_reported_records": materialized.reported_records,
+            "upstream_reported_trials": materialized.reported_trials,
+            "completeness": materialized.completeness,
+            "rows_short_of_trials": materialized.rows_short_of_trials,
+            "duplicate_records": materialized.duplicate_records,
             "counts_are_of_retrieved_rows_not_of_matching_trials": True,
             "offset": offset,
             "limit": limit,
@@ -274,33 +300,31 @@ class IctrpService:
         finally:
             await session.aclose()
 
+        # Build trial dicts first. Deriving provenance needs the real row count:
+        # derived against an empty list it would compare 0 rows against the
+        # portal's trial count and record a catastrophic shortfall for an export
+        # that is in fact complete.
+        from .data.normalize import to_trial
+
+        trials = [to_trial(row, payload.header) for row in payload.rows]
+
         provenance = derive_set_provenance(
             keyword=keyword,
-            trials=[],  # filled in by the store; only used for date extraction below
-            reported_total=payload.reported_total,
+            trials=trials,
+            reported_records=payload.reported_records,
+            reported_trials=payload.reported_trials,
             response_date=response_date,
             steps=steps,
         )
 
-        # Build trial dicts once to derive export/last-refreshed dates for provenance.
-        from .data.normalize import to_trial
-
-        trials = [to_trial(row, payload.header) for row in payload.rows]
-        export_dates = sorted({t.get("export_date_raw") for t in trials if t.get("export_date_raw")})
-        refreshed = sorted(
-            {t.get("last_refreshed_display") for t in trials if t.get("last_refreshed_display")}
-        )
-        if export_dates:
-            provenance.ictrp_export_date = export_dates[0]
-            provenance.notes = [n for n in provenance.notes if "Export date" not in n]
-
         raw = _serialize_csv(payload.header, payload.rows)
         materialized = self.store.store(
             keyword=keyword,
             payload_raw=raw,
             header=payload.header,
             rows=payload.rows,
-            reported_total=payload.reported_total,
+            reported_records=payload.reported_records,
+            reported_trials=payload.reported_trials,
             provenance=provenance.to_dict(),
         )
 
@@ -344,9 +368,11 @@ class IctrpService:
         provenance = Provenance.from_dict(materialized.provenance)
         provenance.cache_hit = True
         provenance.rows_returned = materialized.rows_returned
-        provenance.upstream_reported_total = materialized.reported_total
-        provenance.records_incomplete = materialized.is_incomplete
-        provenance.estimated_missing = materialized.missing_estimate
+        provenance.upstream_reported_records = materialized.reported_records
+        provenance.upstream_reported_trials = materialized.reported_trials
+        provenance.completeness = materialized.completeness
+        provenance.rows_short_of_trials = materialized.rows_short_of_trials
+        provenance.duplicate_records = materialized.duplicate_records
 
         return {
             "status": "ok",
@@ -402,8 +428,11 @@ class IctrpService:
             "status": "ok",
             "set_id": materialized.set_id,
             "rows_in_set": materialized.rows_returned,
-            "upstream_reported_total": materialized.reported_total,
-            "records_incomplete": materialized.is_incomplete,
+            "upstream_reported_records": materialized.reported_records,
+            "upstream_reported_trials": materialized.reported_trials,
+            "completeness": materialized.completeness,
+            "rows_short_of_trials": materialized.rows_short_of_trials,
+            "duplicate_records": materialized.duplicate_records,
             "facets": facets,
             "field_coverage": q.field_coverage(
                 materialized.trials,
@@ -496,10 +525,21 @@ class IctrpService:
                 f"# Retrieved: {provenance.retrieved_at}\n"
                 f"# Rows in this export: {len(rows)}\n"
             )
-            if provenance.upstream_reported_total is not None:
-                header += f"# Portal-reported matches: {provenance.upstream_reported_total}\n"
-            if provenance.records_incomplete:
-                header += f"# WARNING: {INCOMPLETENESS_NOTICE}\n"
+            if provenance.upstream_reported_records is not None:
+                header += (
+                    f"# Portal-reported records: {provenance.upstream_reported_records} "
+                    "(registry rows; one trial may be registered in several)\n"
+                )
+            if provenance.upstream_reported_trials is not None:
+                header += (
+                    f"# Portal-reported trials: {provenance.upstream_reported_trials} "
+                    "(grouped by Secondary ID; comparable to the row count)\n"
+                )
+            header += f"# Completeness: {provenance.completeness}\n"
+            if provenance.completeness == "trials_short":
+                header += f"# WARNING: {SHORTFALL_NOTICE}\n"
+            else:
+                header += f"# NOTE: {INCOMPLETENESS_NOTICE}\n"
 
         return {
             "status": "ok",

package/sidecar/vendor/pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ictrp-mcp-service"
-version = "0.1.0"
+version = "0.2.0"
 description = "MCP server exposing the WHO ICTRP clinical trials database over pure HTTP"
 requires-python = ">=3.10"
 license = { text = "MIT" }