fix(prisma): repair tests stale since 81cbe53 — OA-service fetch_pmc + extraction-template guard (closes #658, refs #657)

tests/prisma/test_fetch.py

@@ -5,6 +5,8 @@ from __future__ import annotations
 import hashlib
 from unittest.mock import MagicMock
 
+import httpx
+
 from prisma.fetch import (
     PendingItem,
     _altcha_bootstrap,
@@ -140,17 +142,39 @@ class TestFetchUnpaywall:
 
 
 class TestFetchPmc:
+    _OA_HIT = (
+        '<OA><records><record id="PMC12345">'
+        '<link format="pdf" href="ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/aa/bb/main.PMC12345.pdf" />'
+        "</record></records></OA>"
+    )
+    _OA_MISS = '<OA><error code="idIsNotOpenAccess">identifier not OA</error></OA>'
+
+    def _client(self, body, seen):
+        def handler(request):
+            seen.append(str(request.url))
+            return httpx.Response(200, text=body)
+
+        return httpx.Client(transport=httpx.MockTransport(handler))
+
     def test_with_prefix(self):
-        assert (
+        seen: list[str] = []
-            fetch_pmc(MagicMock(), "PMC12345")
+        url = fetch_pmc(self._client(self._OA_HIT, seen), "PMC12345")
-            == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12345/pdf/"
+        assert url == (
+            "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/aa/bb/main.PMC12345.pdf"
         )
+        assert "oa/oa.fcgi" in seen[0] and "id=PMC12345" in seen[0]
 
     def test_without_prefix(self):
-        assert (
+        seen: list[str] = []
-            fetch_pmc(MagicMock(), "12345")
+        url = fetch_pmc(self._client(self._OA_HIT, seen), "12345")
-            == "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12345/pdf/"
+        assert url == (
+            "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/aa/bb/main.PMC12345.pdf"
         )
+        assert "id=PMC12345" in seen[0]
+
+    def test_not_open_access(self):
+        seen: list[str] = []
+        assert fetch_pmc(self._client(self._OA_MISS, seen), "PMC12345") is None
 
     def test_empty(self):
         assert fetch_pmc(MagicMock(), "") is None

tests/prisma/test_stages_exercise.py

@@ -117,9 +117,15 @@ class TestEligRun:
 
 class TestExtBuildCall:
     def test_returns_call(self):
+        from prisma.tools import build_extract_tool
+
         project = MagicMock()
-        project.extraction_template = "template"
+        project.name = "test"
-        call = ext_build(project, "# Item")
+        project.extraction_template = (
+            "- **population** — study population\n- **outcome** — primary outcome"
+        )
+        tool = build_extract_tool(project.extraction_template, project=project.name)
+        call = ext_build(project, "# Item", tool)
         assert len(call.messages) == 3
 
 
@@ -136,7 +142,9 @@ class TestExtRun:
         provider = MagicMock()
         project = MagicMock()
         project.name = "test"
-        project.extraction_template = "t"
+        project.extraction_template = (
+            "- **population** — study population\n- **outcome** — primary outcome"
+        )
         with Db(path) as db:
             stats = ext_run(db, provider, project, storage_dir=Path(tmp_path))
         assert stats["extracted"] == 0
@@ -158,7 +166,9 @@ class TestExtRun:
 
             project = MagicMock()
             project.name = "test"
-            project.extraction_template = "t"
+            project.extraction_template = (
+                "- **population** — study population\n- **outcome** — primary outcome"
+            )
 
             stats = ext_run(db, provider, project, storage_dir=Path(tmp_path))
         assert stats["extracted"] == 1
@@ -171,6 +181,9 @@ class TestExtRun:
             provider = MagicMock()
             project = MagicMock()
             project.name = "test"
+            project.extraction_template = (
+                "- **population** — study population\n- **outcome** — primary outcome"
+            )
 
             stats = ext_run(db, provider, project, storage_dir=Path(tmp_path))
         assert stats["errors"] == 1