aiagents4pharma 1.46.0__tar.gz → 1.46.1__tar.gz

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.46.0
+Version: 1.46.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/aiagents4pharma/talk2biomodels/api/__init__.py

@@ -2,4 +2,4 @@
 This file is used to import the modules in the package.
 """
 
-from . import kegg, ols, uniprot
+from . import ols, uniprot

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/aiagents4pharma/talk2biomodels/tests/test_api.py

@@ -2,7 +2,6 @@
 Test cases for Talk2Biomodels.
 """
 
-from ..api.kegg import fetch_from_api, fetch_kegg_names
 from ..api.ols import fetch_from_ols
 from ..api.uniprot import search_uniprot_labels
 
@@ -30,32 +29,3 @@ def test_fetch_from_ols():
     assert isinstance(label_2, str), f"Expected string, got {type(label_2)}"
     assert label_1 == "plasma membrane"
     assert label_2.startswith("Error: 404")
-
-
-def test_fetch_kegg_names():
-    """
-    Test the fetch_kegg_names function.
-    """
-    ids = ["C00001", "C00002"]
-    results = fetch_kegg_names(ids)
-    assert results["C00001"] == "H2O"
-    assert results["C00002"] == "ATP"
-
-    # Try with an empty list
-    results = fetch_kegg_names([])
-    assert not results
-
-
-def test_fetch_from_api():
-    """
-    Test the fetch_from_api function.
-    """
-    base_url = "https://rest.kegg.jp/get/"
-    query = "C00001"
-    entry_data = fetch_from_api(base_url, query)
-    assert entry_data.startswith("ENTRY       C00001")
-
-    # Try with an invalid query
-    query = "C0000Q"
-    entry_data = fetch_from_api(base_url, query)
-    assert not entry_data

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -126,7 +126,7 @@ def test_all_species_annotations(make_graph):
     Here, we test the tool with three models since they have different use cases:
         - model 12 contains a species with no URL provided.
         - model 20 contains a species without description.
-        - model 56 contains a species with database outside of KEGG, UniProt, and OLS.
+        - model 56 contains a species with database outside of UniProt, and OLS.
 
     We are testing a condition where the user asks for annotations
     of all species in a specific model.

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -19,7 +19,6 @@ from langgraph.prebuilt import InjectedState
 from langgraph.types import Command
 from pydantic import BaseModel, Field
 
-from ..api.kegg import fetch_kegg_annotations
 from ..api.ols import search_ols_labels
 from ..api.uniprot import search_uniprot_labels
 
@@ -298,8 +297,6 @@ class GetAnnotationTool(BaseTool):
         for ols_ontology_abbreviation in ols_ontology_abbreviations:
             if ols_ontology_abbreviation + "/" in link:
                 link = link.replace(f"{ols_ontology_abbreviation}/", "")
-        if "kegg.compound" in link:
-            link = link.replace("kegg.compound/", "kegg.compound:")
         return link
 
     def _fetch_descriptions(self, data: list[dict[str, str]]) -> dict[str, str]:
@@ -338,14 +335,8 @@ class GetAnnotationTool(BaseTool):
                 )
                 for identifier in identifiers:
                     results[identifier] = annotations.get(database, {}).get(identifier, "-")
-            elif database == "kegg.compound":
-                data = [
-                    {"Id": identifier, "Database": "kegg.compound"} for identifier in identifiers
-                ]
-                annotations = fetch_kegg_annotations(data)
-                for identifier in identifiers:
-                    results[identifier] = annotations.get(database, {}).get(identifier, "-")
             else:
+                # For any other database types, do not fetch; mark as unknown
                 for identifier in identifiers:
                     results[identifier] = "-"
         return results

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/package-lock.json

@@ -10,7 +10,7 @@
 				"@semantic-release/github": "^11.0.1",
 				"semantic-release": "^24.0.0"
 			},
-			"version": "1.46.0"
+			"version": "1.46.1"
 		},
 		"node_modules/@babel/code-frame": {
 			"version": "7.26.2",
@@ -11110,5 +11110,5 @@
 			"dev": true
 		}
 	},
-	"version": "1.46.0"
+	"version": "1.46.1"
 }

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/package.json

@@ -26,5 +26,5 @@
 			]
 		]
 	},
-	"version": "1.46.0"
+	"version": "1.46.1"
 }

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.1}/pyproject.toml

@@ -85,7 +85,7 @@ dependencies = [
   "cloudscraper==1.2.71",
   "azure-identity==1.24.0",
 ]
-version = "1.46.0"
+version = "1.46.1"
 
 [project.optional-dependencies]
 dev = [
@@ -133,7 +133,7 @@ extension-pkg-allow-list = ["pcst_fast"]
 disable = ["R0801", "R0902", "W0221", "W0122"]
 
 [tool.ruff]
-target-version = "1.46.0"
+target-version = "1.46.1"
 line-length = 100
 
 [tool.ruff.lint]
@@ -155,7 +155,7 @@ ignore = [
 "__init__.py" = ["F401"]
 
 [tool.mypy]
-python_version = "1.46.0"
+python_version = "1.46.1"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true

aiagents4pharma-1.46.0/aiagents4pharma/talk2biomodels/api/kegg.py

@@ -1,87 +0,0 @@
-"""
-This module contains the API for fetching Kegg database
-"""
-
-import re
-
-import requests
-
-
-def fetch_from_api(base_url: str, query: str) -> str:
-    """Fetch data from the given API endpoint."""
-    try:
-        response = requests.get(base_url + query, timeout=10)
-        response.raise_for_status()
-        return response.text
-    except requests.exceptions.RequestException as e:
-        print(f"Error fetching data for query {query}: {e}")
-        return ""
-
-
-def fetch_kegg_names(ids: list[str], batch_size: int = 10) -> dict[str, str]:
-    """
-    Fetch the names of multiple KEGG entries using the KEGG REST API in batches.
-
-    Args:
-        ids (List[str]): List of KEGG IDs.
-        batch_size (int): Maximum number of IDs to include in a single request.
-
-    Returns:
-        Dict[str, str]: A mapping of KEGG IDs to their names.
-    """
-    if not ids:
-        return {}
-
-    base_url = "https://rest.kegg.jp/get/"
-    entry_name_map = {}
-
-    # Process IDs in batches
-    for i in range(0, len(ids), batch_size):
-        batch = ids[i : i + batch_size]
-        query = "+".join(batch)
-        entry_data = fetch_from_api(base_url, query)
-
-        # if not entry_data:
-        #     continue
-        entries = entry_data.split("///")
-        for entry in entries:
-            if not entry.strip():
-                continue
-            lines = entry.strip().split("\n")
-            entry_line = next((line for line in lines if line.startswith("ENTRY")), None)
-            name_line = next((line for line in lines if line.startswith("NAME")), None)
-
-            # if not entry_line and not name_line:
-            #     continue
-            entry_id = entry_line.split()[1]
-            # Split multiple names in the NAME field and clean them
-            names = [
-                re.sub(r"[^a-zA-Z0-9\s]", "", name).strip()
-                for name in name_line.replace("NAME", "").strip().split(";")
-            ]
-            # Join cleaned names into a single string
-            entry_name_map[entry_id] = " ".join(names).strip()
-
-    return entry_name_map
-
-
-def fetch_kegg_annotations(
-    data: list[dict[str, str]], batch_size: int = 10
-) -> dict[str, dict[str, str]]:
-    """Fetch KEGG entry descriptions grouped by database type."""
-    grouped_data = {}
-    for entry in data:
-        db_type = entry["Database"].lower()
-        grouped_data.setdefault(db_type, []).append(entry["Id"])
-
-    results = {}
-    for db_type, ids in grouped_data.items():
-        results[db_type] = fetch_kegg_names(ids, batch_size=batch_size)
-
-    return results
-
-
-# def get_protein_name_or_label(data: List[Dict[str, str]],
-#                               batch_size: int = 10) -> Dict[str, Dict[str, str]]:
-#     """Fetch descriptions for KEGG-related identifiers."""
-#     return fetch_kegg_annotations(data, batch_size=batch_size)