Merge branch 'feat/DEVSU-2349-add-async-and-sync-upload-test' of http…

…s://github.com/bcgsc/pori_python into refactor/lint_unify_types
bcgsc · Jul 19, 2024 · 9c1e70c · 9c1e70c
2 parents e53c510 + 36b8eda
commit 9c1e70c
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Showing 2 changed files with 103 additions and 63 deletions.
diff --git a/pori_python/ipr/main.py b/pori_python/ipr/main.py
@@ -74,7 +74,10 @@ def command_interface() -> None:
     parser.add_argument("--graphkb_url", default=None)
     parser.add_argument("--log_level", default="info", choices=LOG_LEVELS.keys())
     parser.add_argument(
-        "--therapeutics", default=False, help="Generate therapeutic options", action="store_true"
+        "--therapeutics",
+        default=False,
+        help="Generate therapeutic options",
+        action="store_true",
     )
     parser.add_argument(
         "--skip_comments",
@@ -83,7 +86,9 @@ def command_interface() -> None:
         help="Turn off generating the analyst comments section of the report",
     )
     parser.add_argument(
-        "-o", "--output_json_path", help="path to a JSON to output the report upload body"
+        "-o",
+        "--output_json_path",
+        help="path to a JSON to output the report upload body",
     )
     parser.add_argument(
         "-w",
@@ -365,7 +370,10 @@ def ipr_report(
     logger.info(f"annotating {len(structural_variants)} structural variants")
     gkb_matches.extend(
         annotate_positional_variants(
-            graphkb_conn, structural_variants, kb_disease_match, show_progress=interactive
+            graphkb_conn,
+            structural_variants,
+            kb_disease_match,
+            show_progress=interactive,
         )
     )
     logger.debug(f"\tgkb_matches: {len(gkb_matches)}")
@@ -381,7 +389,10 @@ def ipr_report(
     logger.info(f"annotating {len(expression_variants)} expression variants")
     gkb_matches.extend(
         annotate_expression_variants(
-            graphkb_conn, expression_variants, kb_disease_match, show_progress=interactive
+            graphkb_conn,
+            expression_variants,
+            kb_disease_match,
+            show_progress=interactive,
         )
     )
     logger.debug(f"\tgkb_matches: {len(gkb_matches)}")
@@ -418,7 +429,10 @@ def ipr_report(
     if generate_comments:
         comments = {
             "comments": summarize(
-                graphkb_conn, gkb_matches, disease_name=kb_disease_match, variants=all_variants
+                graphkb_conn,
+                gkb_matches,
+                disease_name=kb_disease_match,
+                variants=all_variants,
             )
         }
     else:

diff --git a/tests/test_ipr/test_upload.py b/tests/test_ipr/test_upload.py
@@ -31,62 +31,78 @@ def get_test_file(name: str) -> str:
 
 
 @pytest.fixture(scope="module")
-def loaded_report(tmp_path_factory) -> Dict:
-    mock = MagicMock()
+def loaded_reports(tmp_path_factory) -> Dict:
     json_file = tmp_path_factory.mktemp("inputs") / "content.json"
+    async_json_file = tmp_path_factory.mktemp("inputs") / "async_content.json"
     patient_id = f"TEST_{str(uuid.uuid4())}"
-    json_file.write_text(
-        json.dumps(
+    async_patient_id = f"TEST_ASYNC_{str(uuid.uuid4())}"
+    json_contents = {
+        "comparators": [
+            {"analysisRole": "expression (disease)", "name": "1"},
+            {"analysisRole": "expression (primary site)", "name": "2"},
+            {"analysisRole": "expression (biopsy site)", "name": "3"},
             {
-                "comparators": [
-                    {"analysisRole": "expression (disease)", "name": "1"},
-                    {"analysisRole": "expression (primary site)", "name": "2"},
-                    {"analysisRole": "expression (biopsy site)", "name": "3"},
-                    {"analysisRole": "expression (internal pancancer cohort)", "name": "4"},
-                ],
-                "patientId": patient_id,
-                "project": "TEST",
-                "expressionVariants": json.loads(
-                    pd.read_csv(get_test_file("expression.short.tab"), sep="\t").to_json(
-                        orient="records"
-                    )
-                ),
-                "smallMutations": json.loads(
-                    pd.read_csv(get_test_file("small_mutations.short.tab"), sep="\t").to_json(
-                        orient="records"
-                    )
-                ),
-                "copyVariants": json.loads(
-                    pd.read_csv(get_test_file("copy_variants.short.tab"), sep="\t").to_json(
-                        orient="records"
-                    )
-                ),
-                "structuralVariants": json.loads(
-                    pd.read_csv(get_test_file("fusions.tab"), sep="\t").to_json(orient="records")
-                ),
-                "kbDiseaseMatch": "colorectal cancer",
+                "analysisRole": "expression (internal pancancer cohort)",
+                "name": "4",
             },
+        ],
+        "patientId": patient_id,
+        "project": "TEST",
+        "expressionVariants": json.loads(
+            pd.read_csv(get_test_file("expression.short.tab"), sep="\t").to_json(orient="records")
+        ),
+        "smallMutations": json.loads(
+            pd.read_csv(get_test_file("small_mutations.short.tab"), sep="\t").to_json(
+                orient="records"
+            )
+        ),
+        "copyVariants": json.loads(
+            pd.read_csv(get_test_file("copy_variants.short.tab"), sep="\t").to_json(
+                orient="records"
+            )
+        ),
+        "structuralVariants": json.loads(
+            pd.read_csv(get_test_file("fusions.tab"), sep="\t").to_json(orient="records")
+        ),
+        "kbDiseaseMatch": "colorectal cancer",
+    }
+    json_file.write_text(
+        json.dumps(
+            json_contents,
             allow_nan=False,
         )
     )
-    with patch.object(
-        sys,
-        "argv",
-        [
-            "ipr",
-            "--username",
-            os.environ.get("IPR_USER", os.environ["USER"]),
-            "--password",
-            os.environ["IPR_PASS"],
-            "--ipr_url",
-            os.environ["IPR_TEST_URL"],
-            "--graphkb_url",
-            os.environ.get("GRAPHKB_URL", False),
-            "--content",
-            str(json_file),
-            "--therapeutics",
-        ],
-    ):
+
+    json_contents["patientId"] = async_patient_id
+    async_json_file.write_text(
+        json.dumps(
+            json_contents,
+            allow_nan=False,
+        )
+    )
+
+    argslist = [
+        "ipr",
+        "--username",
+        os.environ.get("IPR_USER", os.environ["USER"]),
+        "--password",
+        os.environ["IPR_PASS"],
+        "--ipr_url",
+        os.environ["IPR_TEST_URL"],
+        "--graphkb_url",
+        os.environ.get("GRAPHKB_URL", False),
+        "--therapeutics",
+    ]
+
+    sync_argslist = argslist.copy()
+    sync_argslist.extend(["--content", str(json_file)])
+    with patch.object(sys, "argv", sync_argslist):
+        with patch.object(IprConnection, "get_spec", return_value=get_test_spec()):
+            command_interface()
+
+    async_argslist = argslist.copy()
+    async_argslist.extend(["--content", str(async_json_file), "--async_upload"])
+    with patch.object(sys, "argv", async_argslist):
         with patch.object(IprConnection, "get_spec", return_value=get_test_spec()):
             command_interface()
 
@@ -96,7 +112,12 @@ def loaded_report(tmp_path_factory) -> Dict:
         url=os.environ["IPR_TEST_URL"],
     )
     loaded_report = ipr_conn.get(uri=f"reports?searchText={patient_id}")
-    return (patient_id, loaded_report)
+    async_loaded_report = ipr_conn.get(uri=f"reports?searchText={async_patient_id}")
+
+    return {
+        "sync": (patient_id, loaded_report),
+        "async": (async_patient_id, async_loaded_report),
+    }
 
 
 def get_section(loaded_report, section_name):
@@ -114,11 +135,16 @@ def get_section(loaded_report, section_name):
 )
 @pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding long running integration tests")
 class TestCreateReport:
-    def test_patient_id_loaded_once(self, loaded_report: Tuple) -> None:
-        patient_id = loaded_report[0]
-        assert loaded_report[1]["total"] == 1
-        assert loaded_report[1]["reports"][0]["patientId"] == patient_id
-
-    def test_analyst_comments_loaded(self, loaded_report: Tuple) -> None:
-        section = get_section(loaded_report, "summary/analyst-comments")
-        assert section["comments"]
+    def test_patient_id_loaded_once(self, loaded_reports) -> None:
+        sync_patient_id = loaded_reports["sync"][0]
+        assert loaded_reports["sync"][1]["total"] == 1
+        assert loaded_reports["sync"][1]["reports"][0]["patientId"] == sync_patient_id
+        async_patient_id = loaded_reports["async"][0]
+        assert loaded_reports["async"][1]["total"] == 1
+        assert loaded_reports["async"][1]["reports"][0]["patientId"] == async_patient_id
+
+    def test_analyst_comments_loaded(self, loaded_reports) -> None:
+        sync_section = get_section(loaded_reports["sync"], "summary/analyst-comments")
+        assert sync_section["comments"]
+        async_section = get_section(loaded_reports["async"], "summary/analyst-comments")
+        assert async_section["comments"]