Merge pull request #6 from BioPack-team/tests

Add tests + fixes

Author: tokebe

.vscode/settings.json

@@ -1,3 +1,8 @@
 {
-  "python.languageServer": "None"
+  "python.languageServer": "None",
+  "python.testing.pytestArgs": [
+    "tests"
+  ],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true,
 }

pyproject.toml

@@ -58,18 +58,18 @@ reasoner-pydantic = { git = "https://github.com/tokebe/reasoner-pydantic" }
 [tool.taskipy.tasks]
 # Code work
 hook = "pre-commit install"
-lint = 'ruff check src/retriever'
+lint = 'ruff check src'
 'lint:stats' = 'task lint --statistics'
 'lint:watch' = 'task lint --watch'
 'lint:fix' = 'task lint --fix'
 
-typecheck = 'basedpyright src/retriever'
+typecheck = 'basedpyright src'
 'typecheck:watch' = 'task typecheck --watch'
 
-format = 'ruff format --diff src/retriever'
-'format:fix' = 'ruff format src/retriever'
+format = 'ruff format --diff src'
+'format:fix' = 'ruff format src'
 
-test = 'pytest --cov=src --cov-config=pyproject.toml'
+test = 'pytest --cov=src --cov-config=pyproject.toml --cov-report term-missing'
 
 fixup = """
 echo 'Linting...' &&
@@ -155,6 +155,9 @@ include = ["src/*"]
 line-length = 88
 indent-width = 4
 
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D", "PLR2004"]
+
 [tool.ruff.lint]
 select = [
     # All of these were carefully chosen, see https://docs.astral.sh/ruff/rules
@@ -223,6 +226,9 @@ line_length = 88
 [tool.deptry]
 extend_exclude = ["locustfile.py", "tests"]
 
+[tool.pytest.ini_options]
+norecursedirs=["utils"]
+
 [tool.coverage.run]
 branch = true
 relative_files = true

src/retriever/utils/trapi.py

@@ -175,6 +175,7 @@ def update_kgraph(kgraph: KnowledgeGraphDict, new: KnowledgeGraphDict) -> None:
     for edge_id, edge in new["edges"].items():
         if edge_id not in kgraph["edges"]:
             kgraph["edges"][edge_id] = edge
+            continue
         update_edge(kgraph["edges"][edge_id], edge)
 
 
@@ -222,15 +223,20 @@ def prune_kg(
     for result in results:
         for node_binding_set in result["node_bindings"].values():
             bound_nodes.update([str(binding["id"]) for binding in node_binding_set])
-        # Only ever one analysis so we can use next(iter())
-        for edge_binding_set in next(iter(result["analyses"]))[
-            "edge_bindings"
-        ].values():
-            bound_edges.update([str(binding["id"]) for binding in edge_binding_set])
+        for analysis in result["analyses"]:
+            for edge_binding_set in analysis["edge_bindings"].values():
+                bound_edges.update([str(binding["id"]) for binding in edge_binding_set])
 
+    checked_edges = set[str]()
     edges_to_check = list(bound_edges)
     while len(edges_to_check) > 0:
         edge_id = edges_to_check.pop()
+
+        # Avoid infinite loops if edge and aux graph reference each other
+        if edge_id in checked_edges:
+            continue
+        checked_edges.add(edge_id)
+
         edge = kgraph["edges"][edge_id]
 
         bound_edges.add(edge_id)