napistu 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

tests/test_gaps.py

@@ -3,21 +3,32 @@ import numpy as np
 import warnings
 
 from napistu.sbml_dfs_core import SBML_dfs
-from napistu.constants import SBML_DFS
-from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.identifiers import Identifiers
-
+from napistu.source import Source
 from napistu.modify import gaps
+from napistu.constants import BQB
+from napistu.constants import IDENTIFIERS
+from napistu.constants import ONTOLOGIES
+from napistu.constants import MINI_SBO_FROM_NAME
+from napistu.constants import SBML_DFS
+from napistu.ingestion.constants import EXCHANGE_COMPARTMENT, COMPARTMENTS
 
 
 # Minimal compartments table
 def _create_sbml_dfs_missing_transport_rxns():
 
+    blank_id = Identifiers([])
+    blank_source = Source(init=True)
+
     compartments = pd.DataFrame(
         {
-            SBML_DFS.C_NAME: ["mitochondria", "nucleus", "cytosol"],
-            SBML_DFS.C_IDENTIFIERS: [None],
-            SBML_DFS.C_SOURCE: [None],
+            SBML_DFS.C_NAME: [
+                COMPARTMENTS.MITOCHONDRIA,
+                COMPARTMENTS.NUCLEUS,
+                EXCHANGE_COMPARTMENT,
+            ],
+            SBML_DFS.C_IDENTIFIERS: [blank_id],
+            SBML_DFS.C_SOURCE: [blank_source],
         },
         index=["c_mito", "c_nucl", "c_cytosol"],
     ).rename_axis(SBML_DFS.C_ID)
@@ -30,15 +41,15 @@ def _create_sbml_dfs_missing_transport_rxns():
                 Identifiers(
                     [
                         {
-                            "ontology": "uniprot",
-                            "identifier": "PFAKE1",
-                            "bqb": "BQB_IS",
-                            "url": None,
+                            IDENTIFIERS.ONTOLOGY: ONTOLOGIES.UNIPROT,
+                            IDENTIFIERS.IDENTIFIER: "PFAKE1",
+                            IDENTIFIERS.BQB: BQB.IS,
+                            IDENTIFIERS.URL: None,
                         }
                     ]
                 )
             ],
-            SBML_DFS.S_SOURCE: [None],
+            SBML_DFS.S_SOURCE: [blank_source],
         },
         index=["s_A"],
     ).rename_axis(SBML_DFS.S_ID)
@@ -49,7 +60,7 @@ def _create_sbml_dfs_missing_transport_rxns():
             SBML_DFS.SC_NAME: ["A [mitochondria]", "A [nucleus]"],
             SBML_DFS.S_ID: ["s_A", "s_A"],
             SBML_DFS.C_ID: ["c_mito", "c_nucl"],
-            SBML_DFS.SC_SOURCE: [None],
+            SBML_DFS.SC_SOURCE: [blank_source],
         },
         index=["sc_A_mito", "sc_A_nucl"],
     ).rename_axis(SBML_DFS.SC_ID)
@@ -58,8 +69,8 @@ def _create_sbml_dfs_missing_transport_rxns():
     reactions = pd.DataFrame(
         {
             SBML_DFS.R_NAME: ["A [mito] -> A [mito]", "A [nucl] -> A [nucl]"],
-            SBML_DFS.R_IDENTIFIERS: [None],
-            SBML_DFS.R_SOURCE: [None],
+            SBML_DFS.R_IDENTIFIERS: [blank_id],
+            SBML_DFS.R_SOURCE: [blank_source],
             SBML_DFS.R_ISREVERSIBLE: [True, True],
         },
         index=["r_A_mito", "r_A_nucl"],
@@ -105,7 +116,7 @@ def test_add_transportation_reactions():
 
     sbml_dfs = _create_sbml_dfs_missing_transport_rxns()
     sbml_dfs_w_transport = gaps.update_sbml_df_with_exchange(
-        np.array(["s_A"]), sbml_dfs, exchange_compartment="cytosol"
+        np.array(["s_A"]), sbml_dfs, exchange_compartment=EXCHANGE_COMPARTMENT
     )
     assert sbml_dfs_w_transport.reactions.shape[0] == 4, "Should add 2 reactions"
     assert sbml_dfs_w_transport.reactions[

tests/test_network_net_create.py

@@ -20,7 +20,7 @@ test_path = os.path.abspath(os.path.join(__file__, os.pardir))
 test_data = os.path.join(test_path, "test_data")
 
 sbml_path = os.path.join(test_data, "R-HSA-1237044.sbml")
-sbml_model = sbml.SBML(sbml_path).model
+sbml_model = sbml.SBML(sbml_path)
 sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
 
 

tests/test_network_precompute.py

@@ -18,7 +18,7 @@ sbml_path = os.path.join(test_path, "test_data", "reactome_glucose_metabolism.sb
 if not os.path.isfile(sbml_path):
     raise ValueError(f"{sbml_path} not found")
 
-sbml_model = sbml.SBML(sbml_path).model
+sbml_model = sbml.SBML(sbml_path)
 sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
 sbml_dfs.validate()
 

tests/test_ontologies_genodexito.py

@@ -1,4 +1,6 @@
 import pandas as pd
+import pytest
+
 from napistu.ontologies.genodexito import Genodexito
 from napistu.ontologies.constants import (
     GENODEXITO_DEFS,
@@ -7,6 +9,7 @@ from napistu.ontologies.constants import (
 )
 
 
+@pytest.skip_on_timeout(5)
 def test_genodexito_mapping_operations():
     """Test Genodexito mapping table creation and operations."""
     # Initialize with test mode and Python method to avoid R dependencies

tests/test_ontologies_mygene.py

@@ -1,7 +1,10 @@
+import pytest
+
 from napistu.ontologies.mygene import create_python_mapping_tables
 from napistu.ontologies.constants import INTERCONVERTIBLE_GENIC_ONTOLOGIES
 
 
+@pytest.skip_on_timeout(5)
 def test_create_python_mapping_tables_yeast():
     """Test create_python_mapping_tables with yeast species."""
     # Test with a subset of mappings to keep test runtime reasonable

tests/test_ontologies_renaming.py

@@ -1,14 +1,16 @@
 """Tests for the ontology aliases module."""
 
+from unittest.mock import patch
+
 import pytest
 import pandas as pd
 from napistu import identifiers
-from napistu.constants import IDENTIFIERS, SBML_DFS
+from napistu.constants import IDENTIFIERS, SBML_DFS, ONTOLOGIES
 from napistu.ontologies import renaming
 
 
 @pytest.fixture
-def mock_sbml_dfs():
+def mock_sbml_dfs(sbml_dfs):
     """Create a mock SBML_dfs object for testing."""
     # Create a simple species DataFrame with identifiers
     s1_ids = identifiers.Identifiers(
@@ -39,32 +41,27 @@ def mock_sbml_dfs():
         ]
     )
 
+    s3_ids = identifiers.Identifiers([])
+
     species_df = pd.DataFrame(
-        {"s_name": ["gene1", "gene2"], SBML_DFS.S_IDENTIFIERS: [s1_ids, s2_ids]}
+        {
+            SBML_DFS.S_NAME: ["gene1", "gene2", "gene3"],
+            SBML_DFS.S_IDENTIFIERS: [s1_ids, s2_ids, s3_ids],
+        }
     )
 
-    # Create mock SBML_dfs object
-    class MockSBMLDfs:
-        def __init__(self):
-            self.species = species_df
-            self.schema = {"species": {"pk": "s_id", "id": SBML_DFS.S_IDENTIFIERS}}
-
-        def get_identifiers(self, table_name):
-            if table_name == SBML_DFS.SPECIES:
-                all_ids = []
-                for idx, row in self.species.iterrows():
-                    for id_dict in row[SBML_DFS.S_IDENTIFIERS].ids:
-                        all_ids.append({"s_id": idx, **id_dict})
-                return pd.DataFrame(all_ids)
-            return pd.DataFrame()
-
-    return MockSBMLDfs()
+    # Patch the species attribute only for the duration of the test
+    with patch.object(sbml_dfs, "species", new=species_df):
+        yield sbml_dfs  # All methods are real, only .species is patched
 
 
 def test_rename_species_ontologies_basic(mock_sbml_dfs):
     """Test basic alias updating functionality."""
     # Define test aliases
-    test_aliases = {"ncbi_entrez_gene": {"ncbigene"}, "uniprot": {"uniprot_id"}}
+    test_aliases = {
+        ONTOLOGIES.NCBI_ENTREZ_GENE: {"ncbigene"},
+        ONTOLOGIES.UNIPROT: {"uniprot_id"},
+    }
 
     # Update aliases
     renaming.rename_species_ontologies(mock_sbml_dfs, test_aliases)
@@ -73,11 +70,18 @@ def test_rename_species_ontologies_basic(mock_sbml_dfs):
     updated_ids = mock_sbml_dfs.get_identifiers(SBML_DFS.SPECIES)
 
     # Check that ontologies were updated correctly
-    assert "ncbi_entrez_gene" in set(updated_ids[IDENTIFIERS.ONTOLOGY])
-    assert "uniprot" in set(updated_ids[IDENTIFIERS.ONTOLOGY])
+    assert ONTOLOGIES.NCBI_ENTREZ_GENE in set(updated_ids[IDENTIFIERS.ONTOLOGY])
+    assert ONTOLOGIES.UNIPROT in set(updated_ids[IDENTIFIERS.ONTOLOGY])
     assert "ncbigene" not in set(updated_ids[IDENTIFIERS.ONTOLOGY])
     assert "uniprot_id" not in set(updated_ids[IDENTIFIERS.ONTOLOGY])
 
+    # verify that all the species have Identifiers object
+    for row in mock_sbml_dfs.species.itertuples():
+        val = getattr(row, SBML_DFS.S_IDENTIFIERS)
+        assert val is not None and isinstance(
+            val, identifiers.Identifiers
+        ), f"Bad value: {val} in row {row}"
+
 
 def test_rename_species_ontologies_no_overlap(mock_sbml_dfs):
     """Test that error is raised when no aliases overlap with data."""
@@ -93,7 +97,7 @@ def test_rename_species_ontologies_partial_update(mock_sbml_dfs):
     """Test that partial updates work correctly."""
     # Define aliases that only update some ontologies
     test_aliases = {
-        "ncbi_entrez_gene": {"ncbigene"}
+        ONTOLOGIES.NCBI_ENTREZ_GENE: {"ncbigene"}
         # Don't include uniprot_id mapping
     }
 
@@ -104,7 +108,7 @@ def test_rename_species_ontologies_partial_update(mock_sbml_dfs):
     updated_ids = mock_sbml_dfs.get_identifiers(SBML_DFS.SPECIES)
 
     # Check that only ncbigene was updated
-    assert "ncbi_entrez_gene" in set(updated_ids[IDENTIFIERS.ONTOLOGY])
+    assert ONTOLOGIES.NCBI_ENTREZ_GENE in set(updated_ids[IDENTIFIERS.ONTOLOGY])
     assert "uniprot_id" in set(
         updated_ids[IDENTIFIERS.ONTOLOGY]
     )  # Should remain unchanged