Merge branch 'develop' into improvement/lint_typing

pori_python/ipr/connection.py

@@ -77,40 +77,62 @@ def upload_report(
         self, content: Dict, mins_to_wait: int = 5, async_upload: bool = False
     ) -> Dict:
         if async_upload:
+            # if async is used, the response for reports-async contains either 'jobStatus'
+            # or 'report'. jobStatus is no longer available once the report is successfully
+            # uploaded.
             initial_result = self.post("reports-async", content)
 
             report_id = initial_result["ident"]
 
+            def check_status_result(result):
+                if result.get("report", False):
+                    return "upload complete"
+                if result.get("jobStatus", False) and result["jobStatus"].get("state", False):
+                    return result["jobStatus"]["state"]
+                raise Exception(
+                    f"async report get returned with no report or jobStatus, or unexpected jobStatus type"
+                )
+
             def check_status(interval: int = 5, num_attempts: int = 5):
                 for i in range(num_attempts):
                     logger.info(f"checking report loading status in {interval} seconds")
                     time.sleep(interval)
                     current_status = self.get(f"reports-async/{report_id}")
 
-                    if current_status.get("ident", False):
+                    check_result = check_status_result(current_status)
+
+                    if check_result == "upload complete":
                         return current_status
 
-                    if current_status["state"] == "failed":
+                    if check_result == "failed":
                         raise Exception(
                             f'async report upload failed with reason: {current_status["failedReason"]}'
                         )
 
-                    if current_status["state"] not in ["active", "ready", "waiting", "completed"]:
+                    if check_result not in [
+                        "active",
+                        "ready",
+                        "waiting",
+                        "completed",
+                    ]:
                         raise Exception(
                             f"async report upload in unexpected state: {current_status}"
                         )
 
                 return current_status
 
             current_status = check_status()
+            check_result = check_status_result(current_status)
 
-            if current_status["state"] in ["active", "waiting"]:
+            if check_result in ["active", "waiting"]:
                 current_status = check_status(interval=30)
+                check_result = check_status_result(current_status)
 
-            if current_status["state"] in ["active", "waiting"]:
+            if check_result in ["active", "waiting"]:
                 current_status = check_status(interval=60, num_attempts=mins_to_wait)
+                check_result = check_status_result(current_status)
 
-            if current_status["state"] in ["active", "waiting"]:
+            if check_result in ["active", "waiting"]:
                 raise Exception(
                     f"async report upload taking longer than expected: {current_status}"
                 )

tests/test_ipr/test_upload.py

@@ -0,0 +1,127 @@
+import json
+import os
+import pandas as pd
+import pytest
+import sys
+import uuid
+from typing import Dict, Tuple, List
+from unittest.mock import MagicMock, patch
+
+from pori_python.ipr.connection import IprConnection
+from pori_python.ipr.main import command_interface
+from pori_python.ipr.types import IprGene
+
+from .constants import EXCLUDE_INTEGRATION_TESTS
+
+EXCLUDE_BCGSC_TESTS = os.environ.get("EXCLUDE_BCGSC_TESTS") == "1"
+EXCLUDE_ONCOKB_TESTS = os.environ.get("EXCLUDE_ONCOKB_TESTS") == "1"
+INCLUDE_UPLOAD_TESTS = os.environ.get("INCLUDE_UPLOAD_TESTS", 0) == "1"
+
+
+def get_test_spec():
+    ipr_spec = {"components": {"schemas": {"genesCreate": {"properties": {}}}}}
+    ipr_gene_keys = IprGene.__required_keys__ | IprGene.__optional_keys__
+    for key in ipr_gene_keys:
+        ipr_spec["components"]["schemas"]["genesCreate"]["properties"][key] = ""
+    return ipr_spec
+
+
+def get_test_file(name: str) -> str:
+    return os.path.join(os.path.dirname(__file__), "test_data", name)
+
+
+@pytest.fixture(scope="module")
+def loaded_report(tmp_path_factory) -> Dict:
+    mock = MagicMock()
+    json_file = tmp_path_factory.mktemp("inputs") / "content.json"
+    patient_id = f"TEST_{str(uuid.uuid4())}"
+    json_file.write_text(
+        json.dumps(
+            {
+                "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",
+            },
+            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",
+        ],
+    ):
+        with patch.object(IprConnection, "get_spec", return_value=get_test_spec()):
+            command_interface()
+
+    ipr_conn = IprConnection(
+        username=os.environ.get("IPR_USER", os.environ["USER"]),
+        password=os.environ["IPR_PASS"],
+        url=os.environ["IPR_TEST_URL"],
+    )
+    loaded_report = ipr_conn.get(uri=f"reports?searchText={patient_id}")
+    return (patient_id, loaded_report)
+
+
+def get_section(loaded_report, section_name):
+    ident = loaded_report[1]["reports"][0]["ident"]
+    ipr_conn = IprConnection(
+        username=os.environ.get("IPR_USER", os.environ["USER"]),
+        password=os.environ["IPR_PASS"],
+        url=os.environ["IPR_TEST_URL"],
+    )
+    return ipr_conn.get(uri=f"reports/{ident}/{section_name}")
+
+
+@pytest.mark.skipif(
+    not INCLUDE_UPLOAD_TESTS, reason="excluding tests of upload to live ipr instance"
+)
+@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"]