Merge pull request #3 from TranslatorSRI/stub

Stub part 2

.github/workflows/dev.yml

@@ -0,0 +1,46 @@
+name: 'Pull Request Feedback'
+
+on:
+  pull_request:
+
+jobs:
+  test:
+    name: Run pytest
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v2
+
+      # Cache docker layers for faster build
+      - uses: satackey/[email protected]
+        # Ignore the failure of a step and avoid terminating the job.
+        continue-on-error: true
+
+      - name: Build
+        run: docker build -t appraiser-testing -f Dockerfile.test .
+
+      - name: Run tests and get output
+        run: |
+          echo 'TEST_OUTPUT<<EOF' >> $GITHUB_ENV
+          echo "$(docker run appraiser-testing)" >> $GITHUB_ENV
+          echo 'EOF' >> $GITHUB_ENV
+
+      - name: Exit if there are any test failures
+        run: '[[ $TEST_OUTPUT != *FAILED* ]]'
+
+  verify-lock:
+    name: Verify lockfiles are up to date
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v2
+
+      - name: Verify lockfiles
+        run: python manage.py verify_locked
+
+  check-format:
+    name: Check that code matches Black formatter
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable

Dockerfile.test

@@ -0,0 +1,21 @@
+FROM renciorg/renci-python-image:v0.0.1
+
+# Add image info
+LABEL org.opencontainers.image.source /github.com/TranslatorSRI/answer-appraiser
+
+# set up requirements
+WORKDIR /app
+
+# Normal requirements
+ADD requirements-lock.txt .
+RUN pip install -r requirements-lock.txt
+
+# Test requirements
+ADD requirements-test-lock.txt .
+RUN pip install -r requirements-test-lock.txt
+
+# Copy in files
+ADD . .
+
+# set up default command
+CMD pytest

app/ordering_components.py

@@ -19,15 +19,17 @@ def get_clinical_evidence(result, message, logger):
     # TODO Calculate clinical evidence
     return 0
 
+
 def get_novelty(result, message, logger):
     # TODO get novelty from novelty package
     return 0
-
+
+
 def get_ordering_components(message, logger):
     logger.debug(f"Computing scores for {len(message['results'])} results")
     for result in message.get("results") or []:
         result["ordering_components"] = {
             "confidence": get_confidence(result, message, logger),
             "clinical_evidence": get_clinical_evidence(result, message, logger),
-            "novelty": get_novelty(result, message, logger)
-        }
+            "novelty": get_novelty(result, message, logger),
+        }

app/server.py

@@ -8,12 +8,7 @@
 from starlette.middleware.cors import CORSMiddleware
 from uuid import uuid4
 
-from reasoner_pydantic import (
-    AsyncQuery,
-    AsyncQueryResponse,
-    Response,
-    Query
-)
+from reasoner_pydantic import AsyncQuery, AsyncQueryResponse, Response, Query
 
 from .logger import setup_logger, get_logger
 from .trapi import TRAPI
@@ -58,83 +53,64 @@
 
 APP.add_middleware(
     CORSMiddleware,
-    allow_origins=['*'],
+    allow_origins=["*"],
     allow_credentials=True,
     allow_methods=["*"],
     allow_headers=["*"],
 )
 
 EXAMPLE = {
-  "message": {
-      "query_graph": {
-          "nodes": {
-              "n0": {"ids": ["MESH:D008687"]},
-              "n1": {"categories": ["biolink:Disease"]}
-          },
-          "edges": {
-              "n0n1": {
-                  "subject": "n0",
-                  "object": "n1",
-                  "predicates": ["biolink:treats"]
-              }
-          }
-      },
-      "knowledge_graph": {
-          "nodes": {
-              "MESH:D008687": {
-                  "categories": ["biolink:SmallMolecule"],
-                  "name": "Metformin"
-              },
-              "MONDO:0005148": {
-                  "categories": [
-                      "biolink:Disease"
-                  ],
-                  "name": "type 2 diabetes mellitus"
-              }
-          },
-          "edges": {
-              "n0n1": {
-                  "subject": "MESH:D008687",
-                  "object": "MONDO:0005148",
-                  "predicate": "biolink:treats",
-                  "sources": [
-                      {
-                          "resource_id": "infores:kp0",
-                          "resource_role": "primary_knowledge_source"
-                      }
-                  ]
-              }
-          }
-      },
-      "results": [
-          {
-              "node_bindings": {
-                  "n0": [
-                      {
-                          "id": "MESH:D008687"
-                      }
-                  ],
-                  "n1": [
-                      {
-                          "id": "MONDO:0005148"
-                      }
-                  ]
-              },
-              "analyses": [
-                  {
-                      "resource_id": "kp0",
-                      "edge_bindings": {
-                          "n0n1": [
-                              {
-                                  "id": "n0n1"
-                              }
-                          ]
-                      }
-                  }
-              ]
-          }
-      ]
-  }
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "n0": {"ids": ["MESH:D008687"]},
+                "n1": {"categories": ["biolink:Disease"]},
+            },
+            "edges": {
+                "n0n1": {
+                    "subject": "n0",
+                    "object": "n1",
+                    "predicates": ["biolink:treats"],
+                }
+            },
+        },
+        "knowledge_graph": {
+            "nodes": {
+                "MESH:D008687": {
+                    "categories": ["biolink:SmallMolecule"],
+                    "name": "Metformin",
+                },
+                "MONDO:0005148": {
+                    "categories": ["biolink:Disease"],
+                    "name": "type 2 diabetes mellitus",
+                },
+            },
+            "edges": {
+                "n0n1": {
+                    "subject": "MESH:D008687",
+                    "object": "MONDO:0005148",
+                    "predicate": "biolink:treats",
+                    "sources": [
+                        {
+                            "resource_id": "infores:kp0",
+                            "resource_role": "primary_knowledge_source",
+                        }
+                    ],
+                }
+            },
+        },
+        "results": [
+            {
+                "node_bindings": {
+                    "n0": [{"id": "MESH:D008687"}],
+                    "n1": [{"id": "MONDO:0005148"}],
+                },
+                "analyses": [
+                    {"resource_id": "kp0", "edge_bindings": {"n0n1": [{"id": "n0n1"}]}}
+                ],
+            }
+        ],
+    }
 }
 
 ASYNC_EXAMPLE = {
@@ -148,18 +124,19 @@ async def async_appraise(message, callback, logger: logging.Logger):
         get_ordering_components(message, logger)
     except Exception:
         logger.error(f"Something went wrong while appraising: {traceback.format_exc()}")
-    try:    
+    try:
         logger.info(f"Posting to callback {callback}")
         async with httpx.AsyncClient(timeout=httpx.Timeout(timeout=600.0)) as client:
             res = await client.post(callback, json=message)
             logger.info(f"Posted to {callback} with code {res.status_code}")
     except Exception as e:
         logger.error(f"Unable to post to callback {callback}.")
 
+
 @APP.post("/async_get_appraisal", response_model=AsyncQueryResponse)
 async def get_appraisal(
     background_tasks: BackgroundTasks,
-    query: AsyncQuery = Body(..., example=ASYNC_EXAMPLE)
+    query: AsyncQuery = Body(..., example=ASYNC_EXAMPLE),
 ):
     """Appraise Answers"""
     qid = str(uuid4())[:8]
@@ -169,28 +146,34 @@ async def get_appraisal(
     message = query_dict["message"]
     if not message.get("results"):
         logger.warning("No results given.")
-        return JSONResponse(content={"status": "Rejected",
-                                     "description": "No Results.",
-                                     "job_id": qid}, status_code=400)
+        return JSONResponse(
+            content={"status": "Rejected", "description": "No Results.", "job_id": qid},
+            status_code=400,
+        )
     callback = query_dict["callback"]
     background_tasks.add_task(async_appraise, message, callback, logger)
-    return JSONResponse(content={"status": "Accepted",
-                                 "description": f"Appraising answers. Will send response to {callback}",
-                                 "job_id": qid}, status_code=200)
+    return JSONResponse(
+        content={
+            "status": "Accepted",
+            "description": f"Appraising answers. Will send response to {callback}",
+            "job_id": qid,
+        },
+        status_code=200,
+    )
+
 
 @APP.post("/get_appraisal", response_model=Response)
-async def sync_get_appraisal(
-    query: Query = Body(..., example=EXAMPLE)
-):
+async def sync_get_appraisal(query: Query = Body(..., example=EXAMPLE)):
     qid = str(uuid4())[:8]
     query_dict = query.dict()
     log_level = query_dict.get("log_level") or "WARNING"
     logger = get_logger(qid, log_level)
     message = query_dict["message"]
     if not message.get("results"):
-        return JSONResponse(content={"status": "Rejected",
-                                     "description": "No Results.",
-                                     "job_id": qid}, status_code=400)
+        return JSONResponse(
+            content={"status": "Rejected", "description": "No Results.", "job_id": qid},
+            status_code=400,
+        )
     try:
         get_ordering_components(message, logger)
     except Exception:

app/trapi.py

@@ -65,10 +65,10 @@ def openapi(self) -> Dict[str, Any]:
             "externalDocs": {
                 "description": "The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url",
                 "url": "https://github.com/NCATSTranslator/translator_extensions/blob/production/x-trapi/",
-            }
+            },
         }
         openapi_schema["info"]["contact"] = self.contact
         openapi_schema["info"]["termsOfService"] = self.terms_of_service
 
         self.openapi_schema = openapi_schema
-        return self.openapi_schema
+        return self.openapi_schema

manage.py

@@ -35,8 +35,8 @@ def test(extra_args):
     and then exits.
     """
     command = """\
-    docker build -t workflow-runner-testing -f Dockerfile.test .
-    docker run -it workflow-runner-testing\
+    docker build -t appraiser-testing -f Dockerfile.test .
+    docker run -it appraiser-testing\
     """
     run_command(command + extra_args)
 

tests/test_server.py

@@ -4,11 +4,12 @@
 
 testclient = TestClient(APP)
 
+
 def test_sync_get_appraisal_400():
     """Test calling /query endpoint."""
     response = testclient.post(
         "/sync_get_appraisal",
         json={"message": {}},
     )
     response_json = response.json()
-    assert response_json["status"] == "Rejected"
+    assert response_json["status"] == "Rejected"