Removed json test files

tests/query_planner/test_query_planner.py

@@ -7,7 +7,7 @@
 
 from tests.helpers.context import \
     with_registry_overlay, with_norm_overlay
-from tests.helpers.utils import load_kps, generate_kps, validate_template, \
+from tests.helpers.utils import generate_kps, validate_template, \
     time_and_display, query_graph_from_string, \
     kps_from_string, plan_template_from_string
 from tests.helpers.logger import assert_no_level
@@ -22,8 +22,6 @@
 from strider.config import settings
 from strider.util import standardize_graph_lists
 
-cwd = Path(__file__).parent
-
 # Switch prefix path before importing server
 settings.kpregistry_url = "http://registry"
 settings.normalizer_url = "http://normalizer"
@@ -335,16 +333,30 @@ async def test_plan_double_loop(caplog):
     assert_no_level(caplog, logging.WARNING)
 
 
-ex1_kps = load_kps(cwd / "ex1_kps.json")
-
-
 @pytest.mark.asyncio
-@with_registry_overlay(settings.kpregistry_url, ex1_kps)
+@with_registry_overlay(
+    settings.kpregistry_url,
+    kps_from_string(
+        """
+        kp0 biolink:Disease -biolink:treated_by-> biolink:Drug
+        kp1 biolink:Drug -biolink:affects-> biolink:Gene
+        kp2 biolink:MolecularEntity -biolink:decreases_abundance_of-> biolink:GeneOrGeneProduct
+        kp3 biolink:Disease -biolink:treated_by-> biolink:MolecularEntity
+        """
+    )
+)
 @with_norm_overlay(settings.normalizer_url)
 async def test_plan_ex1(caplog):
     """ Test that we get a good plan for our first example """
-    with open(cwd / "ex1_qg.json", "r") as f:
-        qg = json.load(f)
+    qg = query_graph_from_string(
+        """
+        n0(( category biolink:MolecularEntity ))
+        n1(( id MONDO:0005148 ))
+        n2(( category biolink:GeneOrGeneProduct ))
+        n1-- biolink:treated_by -->n0
+        n0-- biolink:affects_abundance_of -->n2
+        """
+    )
     await prepare_query_graph(qg)
 
     plans = await generate_plans(qg)
@@ -601,8 +613,21 @@ async def test_planning_performance_typical_example():
     We should be able to do better on performance using our filtering methods.
     """
 
-    with open(cwd / "ex2_qg.json", "r") as f:
-        qg = json.load(f)
+    qg = query_graph_from_string(
+        """
+        n0(( id MONDO:0005737 ))
+        n1(( category biolink:BiologicalProcessOrActivity ))
+        n2(( category biolink:AnatomicalEntity ))
+        n3(( category biolink:PhenotypicFeature ))
+        n4(( category biolink:PhenotypicFeature ))
+        n5(( id MONDO:6801 ))
+        n0-- biolink:related_to -->n1
+        n1-- biolink:related_to -->n2
+        n2-- biolink:related_to -->n3
+        n3-- biolink:related_to -->n4
+        n4-- biolink:related_to -->n5
+        """
+    )
     await prepare_query_graph(qg)
 
     async def testable_generate_plans():

tests/server/test_server.py

@@ -26,8 +26,6 @@
 
 setup_logger()
 
-cwd = Path(__file__).parent
-
 DEFAULT_PREFIXES = {
     "biolink:Disease": ["MONDO", "DOID"],
     "biolink:ChemicalSubstance": ["CHEBI", "MESH"],
@@ -61,8 +59,16 @@
 )
 async def test_solve_ex1():
     """Test solving the ex1 query graph"""
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
     # Create query
     q = Query(
@@ -89,8 +95,8 @@ async def test_solve_ex1():
                     n1 MONDO:0005148
                     n2 HP:0004324
                 edge_bindings:
-                    e01 CHEBI:6801-MONDO:0005148
-                    e12 MONDO:0005148-HP:0004324
+                    n0n1 CHEBI:6801-MONDO:0005148
+                    n1n2 MONDO:0005148-HP:0004324
                 """
             ],
         },
@@ -158,11 +164,19 @@ async def test_duplicate_results():
     }
 )
 async def test_solve_missing_predicate():
-    """Test solving the ex1 query graph, in which one of the predicates is missing. """
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    """Test solving a query graph, in which one of the predicates is missing. """
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
-    del QGRAPH['edges']['e01']['predicate']
+    del QGRAPH['edges']['n0n1']['predicate']
 
     # Create query
     q = Query(
@@ -195,8 +209,16 @@ async def test_solve_missing_predicate():
 )
 async def test_solve_missing_category():
     """Test solving the ex1 query graph, in which one of the categories is missing. """
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
     del QGRAPH['nodes']['n0']['category']
 
@@ -356,8 +378,16 @@ async def test_solve_loop(caplog):
 )
 async def test_log_level_param():
     """Test that changing the log level changes the output """
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
     # Create query
     q = Query(
@@ -403,10 +433,18 @@ async def test_log_level_param():
         """
     }
 )
-async def test_plan_ex1():
+async def test_plan_endpoint():
     """Test /plan endpoint"""
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
     # Create query
     q = Query(
@@ -422,8 +460,8 @@ async def test_plan_ex1():
     plan = output[0]
 
     # Two steps in the plan each with KPs to contact
-    assert len(plan['n0-e01-n1']) == 2
-    assert len(plan['n1-e12-n2']) == 1
+    assert len(plan['n0-n0n1-n1']) == 2
+    assert len(plan['n1-n1n2-n2']) == 1
 
 
 @pytest.mark.asyncio
@@ -464,8 +502,16 @@ async def test_kp_500():
     Test that when a KP returns a 500 error we add
     a message to the log but continue running
     """
-    with open(cwd / "ex1_qg.json", "r") as f:
-        QGRAPH = json.load(f)
+    QGRAPH = query_graph_from_string(
+        """
+        n0(( id CHEBI:6801 ))
+        n0(( category biolink:ChemicalSubstance ))
+        n1(( category biolink:Disease ))
+        n2(( category biolink:PhenotypicFeature ))
+        n0-- biolink:treats -->n1
+        n1-- biolink:has_phenotype -->n2
+        """
+    )
 
     # Create query
     q = Query(