pymetadata 0.4.0__py2.py3-none-any.whl → 0.4.2__py2.py3-none-any.whl

pymetadata/__init__.py

@@ -1,8 +1,9 @@
 """pymetadata - Python utilities for metadata."""
+
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.4.0"
+__version__ = "0.4.2"
 
 
 program_name: str = "pymetadata"

pymetadata/cache.py

@@ -1,4 +1,5 @@
 """Caching of information."""
+
 import json
 from json.encoder import JSONEncoder
 from pathlib import Path

pymetadata/chebi.py

@@ -1,4 +1,5 @@
 """Module for working with chebi."""
+
 from pathlib import Path
 from pprint import pprint
 from typing import Any, Dict

pymetadata/console.py

@@ -1,4 +1,5 @@
 """Rich console for logging."""
+
 from rich import pretty
 from rich.console import Console
 from rich.theme import Theme

pymetadata/core/annotation.py

@@ -2,6 +2,7 @@
 
 Core data structure to store annotations.
 """
+
 import re
 import urllib
 from pprint import pprint

pymetadata/core/creator.py

@@ -1,4 +1,5 @@
 """Creator information."""
+
 from typing import Optional
 
 

pymetadata/core/synonym.py

@@ -1,4 +1,5 @@
 """Synonym information."""
+
 from dataclasses import dataclass
 
 

pymetadata/core/xref.py

@@ -1,4 +1,5 @@
 """Module for crossreferences (xref)."""
+
 import re
 from dataclasses import dataclass
 from typing import Dict

pymetadata/examples/omex_example.py

@@ -1,4 +1,5 @@
 """Example for reading and writing omex archives."""
+
 import zipfile
 from pathlib import Path
 

pymetadata/identifiers/registry.py

@@ -4,6 +4,7 @@ Helper tools to work with identifiers registry.
 https://identifiers.org/
 https://docs.identifiers.org/articles/api.html
 """
+
 from __future__ import annotations
 
 import inspect
@@ -186,18 +187,6 @@ def ols_namespaces() -> Dict[str, Namespace]:
             description="MONDO",
             namespaceEmbeddedInLui=True,
         ),
-        Namespace(
-            id=None,
-            prefix="stato",
-            pattern=r"^STATO:\d+$",
-            name="STATO",
-            description="STATO is the statistical methods ontology. It contains "
-            "concepts and properties related to statistical methods, "
-            "probability distributions and other concepts related to "
-            "statistical analysis, including relationships to study "
-            "designs and plots.",
-            namespaceEmbeddedInLui=True,
-        ),
         Namespace(
             id=None,
             prefix="atol",
@@ -348,7 +337,7 @@ class Registry:
         registry_path: Optional[Path] = None,
     ) -> Dict[str, Namespace]:
         """Update registry from identifiers.org webservice."""
-        logger.warning(f"Update registry: '{Registry.URL}' -> '{registry_path}'")
+        logger.info(f"Update registry from '{Registry.URL}'")
         response = requests.get(Registry.URL)
         namespaces = response.json()["payload"]["namespaces"]
 
@@ -373,9 +362,6 @@ class Registry:
             ns_dict[ns.prefix] = ns
 
         if custom_namespaces is not None:
-            logger.warning(
-                f"Adding custom namespaces: {sorted(custom_namespaces.keys())}"
-            )
             for key, ns in custom_namespaces.items():
                 if key in ns_dict:
                     logger.error(

pymetadata/log.py

@@ -2,6 +2,7 @@
 
 Using rich for output formating.
 """
+
 import logging
 
 from rich.logging import RichHandler

pymetadata/metadata/kisao.py

@@ -481,6 +481,8 @@ _terms = {
     "KISAO_0000695": "parameters for",
     "KISAO_0000696": "steady state root-finding problem",
     "KISAO_0000697": "SDE solver",
+    "KISAO_0000698": "particle coordinates",
+    "KISAO_0000699": "DAE Solver",
     "KISAO_0000800": "systems property",
     "KISAO_0000801": "concentration control coefficient matrix (unscaled)",
     "KISAO_0000802": "control coefficient (scaled)",
@@ -2455,6 +2457,14 @@ class KISAO(str, Enum):
     KISAO_0000697 = "KISAO_0000697"
     SDE_SOLVER = "KISAO_0000697"
 
+    # particle coordinates
+    KISAO_0000698 = "KISAO_0000698"
+    PARTICLE_COORDINATES = "KISAO_0000698"
+
+    # DAE Solver
+    KISAO_0000699 = "KISAO_0000699"
+    DAE_SOLVER = "KISAO_0000699"
+
     # systems property
     KISAO_0000800 = "KISAO_0000800"
     SYSTEMS_PROPERTY = "KISAO_0000800"

pymetadata/omex.py

@@ -33,7 +33,7 @@ logger = log.get_logger(__name__)
 __all__ = ["EntryFormat", "ManifestEntry", "Manifest", "Omex"]
 
 
-IDENTIFIERS_PREFIX = "http://identifiers.org/combine.specifications:"
+IDENTIFIERS_PREFIX = "http://identifiers.org/combine.specifications/"
 PURL_PREFIX = "https://purl.org/NET/mediatypes/"
 
 

pymetadata/omex_v2.py

@@ -2,6 +2,7 @@
 
 See https://docs.google.com/document/d/1-UDgY5lQ6tv4mZILZzol-PvCoAYW8yr2Ydn1OxcHMjM/edit#
 """
+
 from typing import List, Optional
 
 from pydantic import BaseModel

pymetadata/ontologies/ols.py

@@ -4,6 +4,7 @@ This uses the EMBL-EBI Ontology Lookup Service
 https://www.ebi.ac.uk/ols4
 
 """
+
 import urllib.parse
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -79,13 +80,13 @@ class OLSQuery:
         cache: bool = CACHE_USE,
     ):
         """Initialize OLSQuery."""
-        self.ontologies = {
+        self.ontologies: Dict[str, OLSOntology] = {
             ontology.name: ontology for ontology in ontologies
-        }  # type: Dict[str, OLSOntology]
+        }
         self.cache_path = cache_path / "ols"
         self.cache = cache
 
-        if not self.cache_path.exists():
+        if cache and not self.cache_path.exists():
             self.cache_path.mkdir(parents=True)
 
     def get_iri(self, ontology: str, term: str) -> str:
@@ -136,11 +137,6 @@ class OLSQuery:
         # double urlencode iri for OLS
         urliri = urllib.parse.quote(iri, safe="")
         urliri = urllib.parse.quote(urliri, safe="")
-        # urliri = iri.replace(":", "%253A")
-        # urliri = urliri.replace("/", "%252F")
-
-        # term_id = term.split(":")[-1]
-        # url = ols_pattern.replace('{$id}', term_id)
         cache_path = self.cache_path / f"{urliri}.json"
         data: Dict[str, Any] = {}
         if self.cache:
@@ -176,7 +172,8 @@ class OLSQuery:
                 else:
                     data["errors"] = []
                     data["warnings"] = []
-                    write_json_cache(data=data, cache_path=cache_path)  # type: ignore
+                    if self.cache:
+                        write_json_cache(data=data, cache_path=cache_path)  # type: ignore
 
         return data
 

pymetadata/ontologies/ontology.py

@@ -5,6 +5,7 @@ Special ontologies are provided as enums.
 
 Uses the OWL links provided on OLS4 to download the ontologies.
 """
+
 import gzip
 import importlib
 import re
@@ -290,7 +291,7 @@ def try_ontology_import(ontology_id: str) -> None:
 
 if __name__ == "__main__":
     # download latest versions
-    # update_ontology_files()
+    update_ontology_files()
 
     # test loading of OWL files
     # ofile: OntologyFile