napistu 0.3.2.dev1__py3-none-any.whl → 0.3.3__py3-none-any.whl

napistu/ingestion/string.py

@@ -8,7 +8,6 @@ from napistu import sbml_dfs_core
 from napistu import source
 from napistu import utils
 from napistu.constants import BQB
-from napistu.constants import COMPARTMENTS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.ingestion import napistu_edgelist
 from napistu.ingestion.constants import SBML_SPECIES_DICT_IDENTIFIERS
@@ -28,6 +27,7 @@ from napistu.ingestion.constants import STRING_UPSTREAM_COMPARTMENT
 from napistu.ingestion.constants import STRING_UPSTREAM_NAME
 from napistu.ingestion.constants import STRING_URL_EXPRESSIONS
 from napistu.ingestion.constants import STRING_VERSION
+from napistu.ingestion.constants import GENERIC_COMPARTMENT
 from fs import open_fs
 
 logger = logging.getLogger(__name__)
@@ -297,7 +297,7 @@ def _build_interactor_edgelist(
     downstream_col_name: str = STRING_TARGET,
     add_reverse_interactions: bool = False,
     sbo_term: str = "interactor",
-    compartment: str = COMPARTMENTS["CELLULAR_COMPONENT"],
+    compartment: str = GENERIC_COMPARTMENT,
 ) -> pd.DataFrame:
     """Format STRING interactions as reactions."""
 

napistu/modify/gaps.py

@@ -15,18 +15,18 @@ from napistu import utils
 from napistu.network import net_create
 
 from napistu.constants import SBML_DFS
-from napistu.constants import COMPARTMENTS
 from napistu.constants import IDENTIFIERS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.constants import SBOTERM_NAMES
 from napistu.constants import SOURCE_SPEC
+from napistu.ingestion.constants import EXCHANGE_COMPARTMENT
 
 logger = logging.getLogger(__name__)
 
 
 def add_transportation_reactions(
     sbml_dfs: sbml_dfs_core.SBML_dfs,
-    exchange_compartment: str = COMPARTMENTS["CYTOSOL"],
+    exchange_compartment: str = EXCHANGE_COMPARTMENT,
 ) -> sbml_dfs_core.SBML_dfs:
     """
     Add transportation reactions to connect all forms of a protein across compartments.
@@ -73,7 +73,7 @@ def add_transportation_reactions(
 def update_sbml_df_with_exchange(
     species_needing_transport_rxns: np.ndarray,
     sbml_dfs: sbml_dfs_core.SBML_dfs,
-    exchange_compartment: str = COMPARTMENTS["CYTOSOL"],
+    exchange_compartment: str = EXCHANGE_COMPARTMENT,
 ) -> sbml_dfs_core.SBML_dfs:
     """
     Add transportation reactions between all locations of a set of molecular species by

napistu/sbml_dfs_core.py

@@ -13,6 +13,7 @@ from napistu import identifiers
 from napistu import sbml_dfs_utils
 from napistu import source
 from napistu import utils
+from napistu.ingestion import sbml
 from napistu.constants import SBML_DFS
 from napistu.constants import SBML_DFS_SCHEMA
 from napistu.constants import IDENTIFIERS
@@ -23,9 +24,6 @@ from napistu.constants import BQB_PRIORITIES
 from napistu.constants import ONTOLOGY_PRIORITIES
 from napistu.constants import BQB
 from napistu.constants import BQB_DEFINING_ATTRS
-from napistu.constants import COMPARTMENTS
-from napistu.constants import COMPARTMENT_ALIASES
-from napistu.constants import COMPARTMENTS_GO_TERMS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.constants import MINI_SBO_TO_NAME
 from napistu.constants import ONTOLOGIES
@@ -35,7 +33,9 @@ from napistu.constants import SBO_ROLES_DEFS
 from napistu.constants import ENTITIES_W_DATA
 from napistu.constants import ENTITIES_TO_ENTITY_DATA
 from napistu.constants import CHARACTERISTIC_COMPLEX_ONTOLOGIES
-from napistu.ingestion import sbml
+from napistu.ingestion.constants import GENERIC_COMPARTMENT
+from napistu.ingestion.constants import COMPARTMENT_ALIASES
+from napistu.ingestion.constants import COMPARTMENTS_GO_TERMS
 from fs import open_fs
 
 logger = logging.getLogger(__name__)
@@ -145,7 +145,7 @@ class SBML_dfs:
                 if ent in sbml_model:
                     setattr(self, ent, sbml_model[ent])
         else:
-            self = sbml.sbml_df_from_sbml(self, sbml_model)
+            self = sbml.sbml_dfs_from_sbml(self, sbml_model)
 
         for ent in SBML_DFS_SCHEMA.OPTIONAL_ENTITIES:
             # Initialize optional entities if not set
@@ -1421,8 +1421,8 @@ def filter_to_characteristic_species_ids(
     complexes and non-characteristic annotations such as pubmed references and
     homologues.
 
-    Parameters
-    ----------
+        Parameters
+        ----------
     species_ids: pd.DataFrame
         A table of identifiers produced by sdbml_dfs.get_identifiers("species")
     max_complex_size: int
@@ -1812,8 +1812,8 @@ def export_sbml_dfs(
         If True then treat genes, transcript, and proteins as separate species. If False
         then treat them interchangeably.
 
-    Returns
-    -------
+        Returns
+        -------
     None
 
     """
@@ -2257,7 +2257,7 @@ def _sbml_dfs_from_edgelist_check_cspecies_merge(
 
 
 def _stub_compartments(
-    stubbed_compartment: str = "CELLULAR_COMPONENT",
+    stubbed_compartment: str = GENERIC_COMPARTMENT,
 ) -> pd.DataFrame:
     """Stub Compartments
 
@@ -2281,7 +2281,6 @@ def _stub_compartments(
             f"{stubbed_compartment} is not defined in constants.COMPARTMENTS_GO_TERMS"
         )
 
-    stubbed_compartment_name = COMPARTMENTS[stubbed_compartment]
     stubbed_compartment_id = COMPARTMENTS_GO_TERMS[stubbed_compartment]
 
     formatted_uri = identifiers.format_uri(
@@ -2294,7 +2293,7 @@ def _stub_compartments(
 
     compartments_df = pd.DataFrame(
         {
-            SBML_DFS.C_NAME: [stubbed_compartment_name],
+            SBML_DFS.C_NAME: [stubbed_compartment],
             SBML_DFS.C_IDENTIFIERS: [identifiers.Identifiers([formatted_uri])],
         }
     )
@@ -2507,9 +2506,9 @@ def validate_sbml_dfs_table(table_data: pd.DataFrame, table_name: str) -> None:
     table_name : str
         Name of the table in the SBML_dfs schema
 
-    Raises
-    ------
-    ValueError
+        Raises
+        ------
+        ValueError
         If table_name is not in schema or validation fails
     """
     if table_name not in SBML_DFS_SCHEMA.SCHEMA:
@@ -2533,8 +2532,8 @@ def _perform_sbml_dfs_table_validation(
     This function performs the actual validation checks for any table against its schema,
     regardless of whether it's part of an SBML_dfs object or standalone.
 
-    Parameters
-    ----------
+        Parameters
+        ----------
     table_data : pd.DataFrame
         The table data to validate
     table_schema : dict
@@ -2542,9 +2541,9 @@ def _perform_sbml_dfs_table_validation(
     table_name : str
         Name of the table (for error messages)
 
-    Raises
-    ------
-    ValueError
+        Raises
+        ------
+        ValueError
         If the table does not conform to its schema:
         - Not a DataFrame
         - Wrong index name

{napistu-0.3.2.dev1.dist-info → napistu-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.2.dev1
+Version: 0.3.3
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett

{napistu-0.3.2.dev1.dist-info → napistu-0.3.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/__main__.py,sha256=PbzIsFAoFHNQuSyi-ql-D7tQLEOuqgmTcgk0PY-OGeU,28636
 napistu/consensus.py,sha256=UbKKSLP1O46e3Rk8d_aqNlhRHeR3sZRztAgIm7-XK6Y,69960
-napistu/constants.py,sha256=Wb1eir8DKSAjukNPknNkKTS4kQSqZjTcTjFaOYNyrC8,15317
+napistu/constants.py,sha256=M-zGc85bo1DDRe7uvyeEMUoD9Qf59Qz53nx4R6PwHvk,12483
 napistu/identifiers.py,sha256=wsVriQdvPllA5uvh5CiREklA2tYW2MIB14dV7CPaMVU,34003
 napistu/indices.py,sha256=E_djN1XWc6l1lrFw_QnQXfZTKYTaUv8-jFPP7cHkY5A,9780
-napistu/sbml_dfs_core.py,sha256=5t2TYQeuvZeBqR3_eX0oEfAVHyaWSYMLkEO7zmSpo4Y,91779
+napistu/sbml_dfs_core.py,sha256=TUPp2nzaxRWkHKsXrbFzgp0_p5CzEGAmA5cg3dOUm84,91794
 napistu/sbml_dfs_utils.py,sha256=LJo6WWTrmnE58ZLDuibeeHk88uCdfunWdja7XxdZpps,11525
 napistu/source.py,sha256=9uUJrkY4jHaKlzz5nNcQQ8wUAep2pfqhlHxHw1hmEkI,13648
 napistu/utils.py,sha256=TcholWrFbRSu_sn9ODMA8y2YyAhekEKZjwf4S0WQNzI,33241
@@ -17,7 +17,7 @@ napistu/gcs/downloads.py,sha256=SvGv9WYr_Vt3guzyz1QiAuBndeKPTBtWSFLj1-QbLf4,6348
 napistu/gcs/utils.py,sha256=eLSsvewWJdCguyj2k0ozUGP5BTemaE1PZg41Z3aY5kM,571
 napistu/ingestion/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/ingestion/bigg.py,sha256=q0HeVSO6pFftbrxxVfFGUtMvCoak9Wi9ngMggRfjFjo,4364
-napistu/ingestion/constants.py,sha256=JmIefW8qektzpJr5t0GBtcAq-4bVLougTrOAegm5bl8,5410
+napistu/ingestion/constants.py,sha256=9UP47VImZ11q0kz17N3EJg2155USqLewwNWyKpA-cbA,8089
 napistu/ingestion/gtex.py,sha256=X0hSC1yrpf4xSJWFhpeNcnHwJzKDII2MvjfUqYA0JN8,3720
 napistu/ingestion/hpa.py,sha256=R27ExrryKQ4Crxv9ATXmBJCa-yd01TMOrDjkeBhIQac,5054
 napistu/ingestion/identifiers_etl.py,sha256=6ppDUA6lEZurdmVbiFLOUzphYbr-hndMhtqsQnq_yAc,5009
@@ -25,8 +25,8 @@ napistu/ingestion/napistu_edgelist.py,sha256=eVT9M7gmdBuGHcAYlvkD_zzvTtyzXufKWjw
 napistu/ingestion/obo.py,sha256=AQkIPWbjA464Lma0tx91JucWkIwLjC7Jgv5VHGRTDkE,9601
 napistu/ingestion/psi_mi.py,sha256=5eJjm7XWogL9oTyGqR52kntHClLwLsTePKqCvUGyi-w,10111
 napistu/ingestion/reactome.py,sha256=Hn9X-vDp4o_HK-OtaQvel3vJeZ8_TC1-4N2rruK9Oks,7099
-napistu/ingestion/sbml.py,sha256=muLTo-LTeL9lvvdEOjnSg82PQM2jpRExkK0UyF1qea8,20262
-napistu/ingestion/string.py,sha256=8igOC3j8cPdG_pMl14Z2OZsbvHUldPTJOJOUD7IJ-Mc,11676
+napistu/ingestion/sbml.py,sha256=N7neMwjTEF7OMhAcNvQJ29V_d3PqMLjLOZqvJTlK9q0,24743
+napistu/ingestion/string.py,sha256=YSWqaKm3I8bOixzvSA8fU4yfR2izddPYs4qJiqwjbxk,11678
 napistu/ingestion/trrust.py,sha256=ccjZc_eF3PdxxurnukiEo_e0-aKc_3z22NYbaJBtHdY,9774
 napistu/ingestion/yeast.py,sha256=bwFBNxRq-dLDaddgBL1hpfZj0eQ56nBXyR_9n0NZT9Y,5233
 napistu/matching/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
@@ -54,7 +54,7 @@ napistu/mcp/utils.py,sha256=WB4c6s8aPZLgi_Wvhhq0DE8Cnz2QGff0V8hrF1feVRg,1296
 napistu/modify/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/modify/constants.py,sha256=H6K6twzPlxt0yp6QLAxIx0Tp8YzYhtKKXPdmXi5V_QQ,3689
 napistu/modify/curation.py,sha256=sQeSO53ZLdn14ww2GSKkoP0vJnDpAoSWb-YDjUf5hDQ,21743
-napistu/modify/gaps.py,sha256=nhoo30iQai16NzYYfHQ4PE42psWp5hA20Oq7yae1pzw,26743
+napistu/modify/gaps.py,sha256=qprylC2BbSk_vPWayYPVT8lwURXDMOlW5zNLV_wMFZ4,26755
 napistu/modify/pathwayannot.py,sha256=xuBSMDFWbg_d6-Gzv0Td3Q5nnFTa-Qzic48g1b1AZtQ,48081
 napistu/modify/uncompartmentalize.py,sha256=U5X4Q7Z-YIkC8_711x3sU21vTVdv9rKfauwz4JNzl6c,9690
 napistu/network/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
@@ -81,7 +81,7 @@ napistu/rpy2/rids.py,sha256=AfXLTfTdonfspgAHYO0Ph7jSUWv8YuyT8x3fyLfAqc8,3413
 napistu/scverse/__init__.py,sha256=Lgxr3iMQAkTzXE9BNz93CndNP5djzerLvmHM-D0PU3I,357
 napistu/scverse/constants.py,sha256=0iAkhyJUIeFGHdLLU3fCaEU1O3Oix4qAsxr3CxGTjVs,653
 napistu/scverse/loading.py,sha256=jqiE71XB-wdV50GyZrauFNY0Lai4bX9Fm2Gv80VR8t8,27016
-napistu-0.3.2.dev1.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.3.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/conftest.py,sha256=XVkd0tQywhnf2cgab7fIjBo3NlaTVX3cO8HaRS2jIwM,3190
 tests/test_consensus.py,sha256=3dJvvPsPG7bHbw_FY4Pm647N_Gt_Ud9157OKYfPCUd4,9502
@@ -115,7 +115,7 @@ tests/test_ontologies_renaming.py,sha256=k7bQzP24zG7W3fpULwk1me2sOWEWlxylr4Mhx1_
 tests/test_pathwayannot.py,sha256=bceosccNy9tgxQei_7j7ATBSSvBSxOngJvK-mAzR_K0,3312
 tests/test_rpy2_callr.py,sha256=UVzXMvYN3wcc-ikDIjH2sA4BqkbwiNbMm561BcbnbD4,2936
 tests/test_rpy2_init.py,sha256=APrNt9GEQV9va3vU5k250TxFplAoWFc-FJRFhM2GcDk,5927
-tests/test_sbml.py,sha256=-Lxr_Iu7zl15c98NLG-ty9d1V9lLYHsieKbU_s96F6s,471
+tests/test_sbml.py,sha256=f25zj1NogYrmLluvBDboLameTuCiQ309433Qn3iPvhg,1483
 tests/test_sbml_dfs_core.py,sha256=z2dYl5-3ZvIsEeK_sHxm8VtWSdL81Eljz_9aeedlM6U,16806
 tests/test_sbml_dfs_utils.py,sha256=onFWdhrTix30XR1-CMrMXld37BYxEGi6TZrweugLDzI,505
 tests/test_sbo.py,sha256=x_PENFaXYsrZIzOZu9cj_Wrej7i7SNGxgBYYvcigLs0,308
@@ -126,8 +126,8 @@ tests/test_uncompartmentalize.py,sha256=nAk5kfAVLU9a2VWe2x2HYVcKqj-EnwmwddERIPRa
 tests/test_utils.py,sha256=JRJFmjDNZpjG59a-73JkTyGqa_a7Z8d0fE2cZt0CRII,22580
 tests/utils.py,sha256=SoWQ_5roJteFGcMaOeEiQ5ucwq3Z2Fa3AAs9iXHTsJY,749
 tests/test_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-napistu-0.3.2.dev1.dist-info/METADATA,sha256=go09DE0iiD9UQmhyGSTdq2iGLGgODt84uZ9vKbridIg,3418
-napistu-0.3.2.dev1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.2.dev1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.2.dev1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.2.dev1.dist-info/RECORD,,
+napistu-0.3.3.dist-info/METADATA,sha256=Y5HCnBOuVO0Rvc1S-P3llVgWJSeBR1hes6UTt0cyhB4,3413
+napistu-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.3.3.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.3.3.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.3.3.dist-info/RECORD,,

tests/test_sbml.py

@@ -1,17 +1,48 @@
 from __future__ import annotations
 
-import pandas as pd
 from napistu import sbml_dfs_core
 from napistu.ingestion import sbml
+import pytest
+from pydantic import ValidationError
 
 
 def test_sbml_dfs(sbml_path):
     sbml_model = sbml.SBML(sbml_path)
-    _ = sbml_model.model
+    _ = sbml_dfs_core.SBML_dfs(sbml_model)
 
-    dfs = sbml_dfs_core.SBML_dfs(sbml_model)
-    dfs.validate()
 
-    assert type(dfs.get_cspecies_features()) is pd.DataFrame
-    assert type(dfs.get_species_features()) is pd.DataFrame
-    assert type(dfs.get_identifiers("species")) is pd.DataFrame
+def test_compartment_aliases_validation_positive():
+    """
+    Tests that a valid compartment aliases dictionary passes validation.
+    """
+    valid_aliases = {
+        "extracellular": ["ECM", "extracellular space"],
+        "cytosol": ["cytoplasm"],
+    }
+    # This should not raise an exception
+    sbml.CompartmentAliasesValidator.model_validate(valid_aliases)
+
+
+def test_compartment_aliases_validation_negative():
+    """
+    Tests that an invalid compartment aliases dictionary raises a ValidationError.
+    """
+    invalid_aliases = {
+        "extracellular": ["ECM"],
+        "not_a_real_compartment": ["fake"],
+    }
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate(invalid_aliases)
+
+
+def test_compartment_aliases_validation_bad_type():
+    """
+    Tests that a validation error is raised for incorrect data types.
+    """
+    # Test with a non-dict input
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate(["extracellular"])
+
+    # Test with incorrect value types in the dictionary
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate({"extracellular": "ECM"})