Merge pull request #376 from monarch-initiative/375-error-when-a-phev…

…al-result-cannot-be-found

375 error when a pheval result cannot be found

src/pheval/analyse/disease_prioritisation_analysis.py

@@ -38,11 +38,16 @@ def assess_disease_prioritisation(
         for _i, row in df.iterrows():
             result = (
                 self.conn.execute(
-                    f"SELECT * FROM '{standardised_disease_result_path}' "
-                    f"WHERE contains_entity_function(CAST(COALESCE(disease_identifier, '') AS VARCHAR),"
-                    f" '{row['disease_identifier']}') "
-                    f"OR contains_entity_function(CAST(COALESCE(disease_name, '') AS VARCHAR), "
-                    f"'{row['disease_name']}')"
+                    (
+                        f"SELECT * FROM '{standardised_disease_result_path}' "
+                        f"WHERE contains_entity_function(CAST(COALESCE(disease_identifier, '') AS VARCHAR),"
+                        f" '{row['disease_identifier']}') "
+                        f"OR contains_entity_function(CAST(COALESCE(disease_name, '') AS VARCHAR), "
+                        f"'{row['disease_name']}')"
+                    )
+                    if standardised_disease_result_path.exists()
+                    and standardised_disease_result_path.stat().st_size > 0
+                    else "SELECT NULL WHERE FALSE"
                 )
                 .fetchdf()
                 .to_dict(orient="records")
@@ -56,9 +61,15 @@ def assess_disease_prioritisation(
                     f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
                     (disease_match, primary_key),
                 )
+            elif len(result) == 0:
+                relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_disease_result_path), RankedPhEvalDiseaseResult
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_disease_result_path), RankedPhEvalDiseaseResult
+                )
+                if standardised_disease_result_path.exists()
+                else []
             ),
             relevant_ranks,
         )

src/pheval/analyse/gene_prioritisation_analysis.py

@@ -36,11 +36,16 @@ def assess_gene_prioritisation(
         for _i, row in df.iterrows():
             result = (
                 self.conn.execute(
-                    f"SELECT * FROM '{standardised_gene_result_path}' "
-                    f"WHERE contains_entity_function(CAST(COALESCE(gene_identifier, '') AS VARCHAR),"
-                    f" '{row['gene_identifier']}') "
-                    f"OR contains_entity_function(CAST(COALESCE(gene_symbol, '') AS VARCHAR), "
-                    f"'{row['gene_symbol']}')"
+                    (
+                        f"SELECT * FROM '{standardised_gene_result_path}' "
+                        f"WHERE contains_entity_function(CAST(COALESCE(gene_identifier, '') AS VARCHAR), "
+                        f"'{row['gene_identifier']}') "
+                        f"OR contains_entity_function(CAST(COALESCE(gene_symbol, '') AS VARCHAR), "
+                        f"'{row['gene_symbol']}')"
+                    )
+                    if standardised_gene_result_path.exists()
+                    and standardised_gene_result_path.stat().st_size > 0
+                    else "SELECT NULL WHERE FALSE"
                 )
                 .fetchdf()
                 .to_dict(orient="records")
@@ -53,9 +58,15 @@ def assess_gene_prioritisation(
                     f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
                     (gene_match, primary_key),
                 )
+            if not result:
+                relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_gene_result_path), RankedPhEvalGeneResult
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_gene_result_path), RankedPhEvalGeneResult
+                )
+                if standardised_gene_result_path.exists()
+                else []
             ),
             relevant_ranks,
         )

src/pheval/analyse/variant_prioritisation_analysis.py

@@ -44,12 +44,16 @@ def assess_variant_prioritisation(
             )
             result = (
                 self.conn.execute(
-                    f"SELECT * FROM '{standardised_variant_result_path}' "
-                    f"WHERE "
-                    f"chromosome == '{causative_variant.chrom}' AND "
-                    f"start == {causative_variant.pos} AND "
-                    f"ref == '{causative_variant.ref}' AND "
-                    f"alt == '{causative_variant.alt}'"
+                    (
+                        f"SELECT * FROM '{standardised_variant_result_path}' "
+                        f"WHERE "
+                        f"chromosome == '{causative_variant.chrom}' AND "
+                        f"start == {causative_variant.pos} AND "
+                        f"ref == '{causative_variant.ref}' AND "
+                        f"alt == '{causative_variant.alt}'"
+                    )
+                    if standardised_variant_result_path.exists()
+                    else "SELECT NULL WHERE FALSE"
                 )
                 .fetchdf()
                 .to_dict(orient="records")
@@ -66,10 +70,15 @@ def assess_variant_prioritisation(
                     f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
                     (variant_match, primary_key),
                 )
-
+            elif len(result) == 0:
+                relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_variant_result_path), RankedPhEvalVariantResult
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_variant_result_path), RankedPhEvalVariantResult
+                )
+                if standardised_variant_result_path.exists()
+                else []
             ),
             relevant_ranks,
         )

tests/test_analysis.py

@@ -1,7 +1,7 @@
 import unittest
 from copy import copy
 from pathlib import Path
-from unittest.mock import patch
+from unittest.mock import MagicMock, patch
 
 import duckdb
 
@@ -130,9 +130,13 @@ def test_assess_gene_with_threshold_meets_cutoff(self):
         )
 
     def test_assess_gene_prioritisation_no_threshold(self):
+        mock_path = MagicMock(spec=Path)
+        mock_path.exists.return_value = True
+        mock_path.stat.return_value.st_size = 100
+        mock_path.__str__.return_value = "result"
         self.db_connector.add_contains_function()
         self.assess_gene_prioritisation.assess_gene_prioritisation(
-            "result",
+            mock_path,
             Path("/path/to/phenopacket_1.json"),
             self.binary_classification_stats,
         )
@@ -150,7 +154,7 @@ def test_assess_gene_prioritisation_no_threshold(self):
                 true_positives=1,
                 true_negatives=3,
                 false_positives=0,
-                false_negatives=0,
+                false_negatives=1,
                 labels=[1, 0, 0, 0],
                 scores=[0.8764, 0.5777, 0.5777, 0.3765],
             ),
@@ -282,9 +286,13 @@ def test_assess_variant_with_threshold_meets_cutoff(self):
         )
 
     def test_assess_variant_prioritisation(self):
+        mock_path = MagicMock(spec=Path)
+        mock_path.exists.return_value = True
+        mock_path.stat.return_value.st_size = 100
+        mock_path.__str__.return_value = "result"
         self.db_connector.add_contains_function()
         self.assess_variant_prioritisation.assess_variant_prioritisation(
-            "result",
+            mock_path,
             Path("/path/to/phenopacket_1.json"),
             self.binary_classification_stats,
         )
@@ -318,7 +326,7 @@ def test_assess_variant_prioritisation(self):
                 true_positives=0,
                 true_negatives=0,
                 false_positives=2,
-                false_negatives=1,
+                false_negatives=2,
                 labels=[0, 0, 1],
                 scores=[0.0484, 0.0484, 0.0484],
             ),
@@ -439,9 +447,13 @@ def test_assess_disease_with_threshold_meets_cutoff(self):
         )
 
     def test_assess_disease_prioritisation(self):
+        mock_path = MagicMock(spec=Path)
+        mock_path.exists.return_value = True
+        mock_path.stat.return_value.st_size = 100
+        mock_path.__str__.return_value = "result"
         self.db_connector.add_contains_function()
         self.assess_disease_prioritisation.assess_disease_prioritisation(
-            "result",
+            mock_path,
             Path("/path/to/phenopacket_1.json"),
             self.binary_classification_stats,
         )