pymetadata 0.5.3__tar.gz → 0.5.4__tar.gz

{pymetadata-0.5.3 → pymetadata-0.5.4}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.5.3"
+current_version = "0.5.4"
 commit = true
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]

pymetadata-0.5.4/.python-version

@@ -0,0 +1 @@
+3.13

{pymetadata-0.5.3 → pymetadata-0.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymetadata
-Version: 0.5.3
+Version: 0.5.4
 Summary: pymetadata are python utilities for working with metadata.
 Author-email: Matthias König <konigmatt@googlemail.com>
 Maintainer-email: Matthias König <konigmatt@googlemail.com>
@@ -27,7 +27,6 @@ Requires-Dist: pydantic>=2.10.4
 Requires-Dist: requests>=2.32.3
 Requires-Dist: rich>=13.9.4
 Requires-Dist: xmltodict>=0.14.2
-Requires-Dist: zeep>=4.3.1
 Provides-Extra: dev
 Requires-Dist: bump-my-version>=0.29.0; extra == 'dev'
 Requires-Dist: mypy>=1.9.0; extra == 'dev'

{pymetadata-0.5.3 → pymetadata-0.5.4}/pyproject.toml

@@ -40,7 +40,6 @@ dependencies = [
 	"lxml>=5.3",
 	"rich>=13.9.4",
 	"requests>=2.32.3",
-	"zeep>=4.3.1",
 	"pronto>=2.5.8",
 	"fastobo>=0.12.3",
 	"jinja2>=3.1.5",

pymetadata-0.5.4/release-notes/0.5.4.md

@@ -0,0 +1,11 @@
+# Release notes for pymetadata 0.5.4
+![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+We are pleased to release the next version of pymetadata including the
+following changes:
+
+## Features & fixes
+- bugfix for annotations with "/"
+- fixing webservices for Chebi 2.0 (#61)
+
+Your pymetadata team

{pymetadata-0.5.3 → pymetadata-0.5.4}/src/pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.5.3"
+__version__ = "0.5.4"
 
 
 program_name: str = "pymetadata"

{pymetadata-0.5.3 → pymetadata-0.5.4}/src/pymetadata/chebi.py

@@ -1,28 +1,19 @@
 """Module for working with chebi."""
 
 from pathlib import Path
-from pprint import pprint
 from typing import Any, Dict, Optional
-
-from zeep import Client
-
+import requests
 
 import pymetadata
 from pymetadata import log
 from pymetadata.cache import DataclassJSONEncoder, read_json_cache, write_json_cache
+from pymetadata.console import console
 
 logger = log.get_logger(__name__)
 
-# FIXME: copy the file to the cache dir
-client = Client(str(pymetadata.RESOURCES_DIR / "chebi_webservice_wsdl.xml"))
-
 
 class ChebiQuery:
-    """Class to query information from ChEBI.
-
-    An overview over available methods:
-        python -mzeep https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl
-    """
+    """Class to query information from ChEBI."""
 
     @staticmethod
     def query(
@@ -52,27 +43,28 @@ class ChebiQuery:
 
         # fetch and cache data
         if not data:
-            try:
-                result = client.service.getCompleteEntity(chebi)
-                # print(result)
-            except Exception:
+            response = requests.get(
+                url=f"https://www.ebi.ac.uk/chebi/backend/api/public/compounds/?chebi_ids={chebi}"
+            )
+            if response.status_code == 200:
+                result = response.json()
+            else:
                 logger.error(f"CHEBI information could not be retrieved for: {chebi}")
                 return dict()
 
-            # parse formula
-            formula = None
-            formulae = result["Formulae"]
-            if formulae:
-                formula = formulae[0]["data"]
-
+            result = result[chebi]["data"]
+            chemical_data = result["chemical_data"]
+            default_structure = result["default_structure"]
             data = {
                 "chebi": chebi,
-                "name": result["chebiAsciiName"],
+                "name": result["ascii_name"],
                 "definition": result["definition"],
-                "formula": formula,
-                "charge": result["charge"],
-                "mass": result["mass"],
-                "inchikey": result["inchiKey"],
+                "formula": chemical_data["formula"] if chemical_data else None,
+                "charge": chemical_data["charge"] if chemical_data else None,
+                "mass": chemical_data["mass"] if chemical_data else None,
+                "inchikey": default_structure["standard_inchi_key"]
+                if default_structure
+                else None,
             }
 
             logger.info(f"Write chebi: {chebi_path}")
@@ -86,7 +78,7 @@ class ChebiQuery:
 if __name__ == "__main__":
     chebis = ["CHEBI:2668", "CHEBI:138366", "CHEBI:9637", "CHEBI:155897"]
     for chebi in chebis:
-        print(chebi)
+        console.rule(chebi, align="left", style="bold white")
         d = ChebiQuery.query(chebi=chebi, cache=False)
-        pprint(d)
+        console.print(d)
         d = ChebiQuery.query(chebi=chebi, cache=True)

{pymetadata-0.5.3 → pymetadata-0.5.4}/src/pymetadata/core/annotation.py

@@ -98,6 +98,8 @@ class RDFAnnotation:
                     f"{resource} does not conform to "
                     f"http(s)://identifiers.org/collection/id or http(s)://identifiers.org/id",
                 )
+
+        # handle urns
         elif resource.startswith("urn:miriam:"):
             match3 = MIRIAM_URN_PATTERN.match(resource)
             if match3:
@@ -113,13 +115,14 @@ class RDFAnnotation:
         else:
             # handle short notation
             tokens = resource.split("/")
-            if len(tokens) == 2:
+            if len(tokens) > 1:
                 self.collection = tokens[0]
                 self.term = "/".join(tokens[1:])
             elif len(tokens) == 1 and ":" in tokens[0]:
                 self.collection = tokens[0].split(":")[0].lower()
                 self.term = tokens[0]
 
+            # validation
             if len(tokens) < 2 and not self.collection:
                 logger.error(
                     f"Resource `{resource}` could not be split in collection and term. "

{pymetadata-0.5.3 → pymetadata-0.5.4}/tests/core/test_annotation.py

@@ -124,6 +124,11 @@ rdf_annotation_data = [
         "CHEBI:000012",
         "RDFAnnotation(BQB.IS|chebi|CHEBI:000012)",
     ),
+    (
+        BQB.IS,
+        "doi/10.3389/fphar.2025.1686415",
+        "RDFAnnotation(BQB.IS|doi|10.3389/fphar.2025.1686415)",
+    ),
 ]