Merge pull request #111 from ExposuresProvider/add-testing

This PR adds a test suite in Python for CAM-KP-API to cam-pipeline. Some of this code has been moved over from https://github.com/ExposuresProvider/cam-kp-api and the rest has been newly written for this. There are three tests here: - test_api.py: test the Automat-CAM-KP API endpoints. - test_examples.py: tests the example files in `examples/`. - test_curies.py: test a set of CURIEs to see if Automat-CAM-KP has information or not about them. This currently includes failing tests from #101 I tried to move over the integration tests from CAM-KP-API, but I couldn't work out the easiest way to figure out how to move them over as a Scala project. I think these Python tests are easier to read and maintain, but I'm happy to be proved wrong. Closes #94
ExposuresProvider · Feb 13, 2024 · 0cb6dab · 0cb6dab
2 parents b158f1e + c539c74
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diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,4 @@
+# Used only by the Python testing code in `tests/`.
+pytest
+requests
+black
diff --git a/tests/examples/chemicals-affected-by-prcd.json b/tests/examples/chemicals-affected-by-prcd.json
@@ -0,0 +1,42 @@
+{
+  "meta": {
+    "description": "Chemicals affected by gene Photoreceptor Disc Component (PRCD, NCBIGene:768206)"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "gene": {
+            "categories": [
+              "biolink:Gene"
+            ],
+            "ids": [
+              "NCBIGene:768206"
+            ]
+          },
+          "chemical": {
+            "categories": [
+              "biolink:ChemicalEntity"
+            ]
+          }
+        },
+        "edges": {
+          "t_edge": {
+            "object": "gene",
+            "subject": "chemical",
+            "predicates": [
+              "biolink:affects"
+            ],
+            "knowledge_type": "inferred"
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 17
+    }
+  ]
+}
diff --git a/tests/examples/chemicals-decreasing-ncbigene-1956.json b/tests/examples/chemicals-decreasing-ncbigene-1956.json
@@ -0,0 +1,43 @@
+{
+  "meta": {
+    "description": "Chemicals decreasing the activity of epidermal growth factor receptor (NCBIGene:1956)"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "name": "Chemical Entity",
+            "categories": [
+              "biolink:ChemicalEntity"
+            ]
+          },
+          "n1": {
+            "name": "EGFR",
+            "ids": [
+              "NCBIGene:1956"
+            ],
+            "categories": [
+              "biolink:Gene"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "subject": "n1",
+            "object": "n0",
+            "predicates": [
+              "biolink:affects"
+            ]
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 35
+    }
+  ]
+}
diff --git a/tests/examples/genes-affecting-genes-found-in-leukocytes.json b/tests/examples/genes-affecting-genes-found-in-leukocytes.json
@@ -0,0 +1,53 @@
+{
+  "meta": {
+    "description": "Find genes that affect the activity of ‘GPR35’, specifically occurring within leukocytes (CL:0000738)"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "categories": [
+              "biolink:GeneOrGeneProduct"
+            ]
+          },
+          "n1": {
+            "categories": [
+              "biolink:GeneOrGeneProduct"
+            ]
+          },
+          "n2": {
+            "categories": [
+              "biolink:AnatomicalEntity"
+            ],
+            "ids": [
+              "CL:0000738"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "subject": "n0",
+            "object": "n1",
+            "predicates": [
+              "biolink:affects"
+            ]
+          },
+          "e1": {
+            "subject": "n1",
+            "object": "n2",
+            "predicates": [
+              "biolink:overlaps"
+            ]
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 5
+    }
+  ]
+}
diff --git a/tests/examples/genetic-pathway-positive-control.json b/tests/examples/genetic-pathway-positive-control.json
@@ -0,0 +1,35 @@
+{
+  "meta": {
+    "description": "Half the genetic pathway 'positive control' from the June 2022 Relay at https://docs.google.com/presentation/d/1V_K_bgyLWEP2neTdM0TD7Bs-GtJUmqCt8p6BzWTv96s/edit?pli=1#slide=id.p"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "ids": [
+              "NCBIGene:5468"
+            ]
+          },
+          "n1": {
+            "categories": [
+              "biolink:BiologicalProcess"
+            ]
+          }
+        },
+        "edges": {
+          "e01": {
+            "object": "n0",
+            "subject": "n1"
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 8
+    }
+  ]
+}
diff --git a/tests/examples/molecular-activity-with-valproic-acid-as-input.json b/tests/examples/molecular-activity-with-valproic-acid-as-input.json
@@ -0,0 +1,44 @@
+{
+  "meta": {
+    "description": "Molecular activity that has valproic acid (PUBCHEM.COMPOUND:3121) as an input"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "categories": [
+              "biolink:MolecularActivity"
+            ]
+          },
+          "n1": {
+            "ids": [
+              "PUBCHEM.COMPOUND:3121"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "subject": "n0",
+            "object": "n1",
+            "predicates": [
+              "biolink:has_input"
+            ]
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 1
+    },
+    {
+      "type": "ExpectedNodeResults",
+      "node": "n0",
+      "resultEquals": ["GO:0005488"],
+      "description": "Expected binding (GO:0005488) to have valproic acid (PUBCHEM.COMPOUND:3121) as an input."
+    }
+  ]
+}
diff --git a/tests/examples/proteins-that-interact-with-pyruvate.json b/tests/examples/proteins-that-interact-with-pyruvate.json
@@ -0,0 +1,44 @@
+{
+  "meta": {
+    "description": "Named things related to pyruvate (PUBCHEM.COMPOUND:107735)"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "categories": [
+              "biolink:Protein"
+            ]
+          },
+          "n1": {
+            "ids": [
+              "PUBCHEM.COMPOUND:107735"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "subject": "n0",
+            "object": "n1",
+            "predicates": [
+              "biolink:interacts_with"
+            ]
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 6
+    },
+    {
+      "type": "ExpectedNodeResults",
+      "node": "n0",
+      "resultEquals": ["UniProtKB:P21796", "UniProtKB:P26297", "UniProtKB:Q9BYZ2", "UniProtKB:Q1EHB4",
+        "UniProtKB:P11498", "UniProtKB:Q8N695"]
+    }
+  ]
+}
diff --git a/tests/examples/what-gene-product-is-part-of-the-plasma-membrane.json b/tests/examples/what-gene-product-is-part-of-the-plasma-membrane.json
@@ -0,0 +1,41 @@
+{
+  "meta": {
+    "description": "What gene or gene product is part of the plasma membrane?"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "categories": [
+              "biolink:GeneOrGeneProduct"
+            ]
+          },
+          "n1": {
+            "categories": [
+              "biolink:AnatomicalEntity"
+            ],
+            "ids": [
+              "GO:0005886"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "subject": "n0",
+            "object": "n1",
+            "predicates": [
+              "biolink:part_of"
+            ]
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 10
+    }
+  ]
+}
diff --git a/tests/examples/what-regulates-mapk-activity.json b/tests/examples/what-regulates-mapk-activity.json
@@ -0,0 +1,44 @@
+{
+  "meta": {
+    "description": "What regulates MAP kinase activity (GO:0004707)?"
+  },
+  "query": {
+    "message": {
+      "query_graph": {
+        "nodes": {
+          "n0": {
+            "categories": [
+              "biolink:NamedThing"
+            ]
+          },
+          "n1": {
+            "ids": [
+              "GO:0004707"
+            ]
+          }
+        },
+        "edges": {
+          "e0": {
+            "predicates": [
+              "biolink:regulates"
+            ],
+            "subject": "n0",
+            "object": "n1"
+          }
+        }
+      }
+    }
+  },
+  "assertions": [
+    {
+      "type": "ExpectedResultCounts",
+      "min": 85
+    },
+    {
+      "type": "ExpectedNodeResults",
+      "node": "n0",
+      "resultIncludes": ["GO:0004708", "GO:0004709"],
+      "description": "MAP kinase activity (GO:0004707) is regulated by MAP kinase kinase activity (GO:0004708) and MAP kinase kinase kinase activity (GO:0004709)"
+    }
+  ]
+}