Add test for organometallic pubchem structures;

INCHI-1-TEST/tests/test_executable/test_organometallics_pubchem.py

@@ -0,0 +1,72 @@
+import pytest
+from pathlib import Path
+from helpers import parse_inchi_from_executable_output
+from sdf_pipeline.utils import read_records_from_gzipped_sdf
+import tempfile
+
+
+@pytest.fixture
+def sdf_path():
+    return (
+        Path(__file__)
+        .parent.absolute()
+        .joinpath("data/organometallic_structures_pubchem.sdf.gz")
+    )
+
+
+def test_organometallics_pubchem(sdf_path, run_inchi_exe):
+    exectuable_results = [
+        run_inchi_exe(mol, "-RecMet") for mol in read_records_from_gzipped_sdf(sdf_path)
+    ]
+    inchis = [
+        parse_inchi_from_executable_output(result.output)
+        for result in exectuable_results
+    ]
+    assert all(inchis)
+
+
+@pytest.mark.skip(reason="used to get statistics and insights")
+def test_organometallics_pubchem_statistics(sdf_path, run_inchi_exe):
+    error_ids = []
+    inchis = {}
+    inchi_ids = []
+    error_mols = []
+    errors = {}
+    mol_counter = 0
+
+    for mol in read_records_from_gzipped_sdf(sdf_path):
+        mol_counter += 1
+        result = run_inchi_exe(mol, "-RecMet")
+        inchi = parse_inchi_from_executable_output(result.output)
+
+        id = mol.split("\n")[0]
+        if inchi == "":
+            error_ids.append(id)
+            error_mols.append(mol)
+            for line in result.stderr.splitlines():
+                if line.startswith("Error"):
+                    errors[id] = line
+        else:
+            inchi_ids.append(id)
+            inchis[id] = inchi
+
+    with open(f"{tempfile.gettempdir()}/inchis.txt", "w") as f:
+        for id, inchi in inchis.items():
+            f.write(f"{id}: {inchi}\n")
+
+    with open(f"{tempfile.gettempdir()}/inchi_ids.txt", "w") as f:
+        for id in inchi_ids:
+            f.write(f"{id}\n")
+
+    with open(f"{tempfile.gettempdir()}/error_ids.txt", "w") as f:
+        for id in error_ids:
+            f.write(f"{id}\n")
+
+    with open(f"{tempfile.gettempdir()}/error_mols.sdf", "w") as f:
+        for mol in error_mols:
+            f.write(f"{mol}$$$$\n")
+
+    with open(f"{tempfile.gettempdir()}/errors.txt", "w") as f:
+        for id, error in errors.items():
+            f.write(f"{id}: {error}\n")
+    print(f"{len(inchis)}/{mol_counter} InChIs converted.")