pymetadata 0.4.2__tar.gz → 0.4.4__tar.gz

{pymetadata-0.4.2/src/pymetadata.egg-info → pymetadata-0.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pymetadata
-Version: 0.4.2
+Version: 0.4.4
 Summary: pymetadata are python utilities for working with metadata.
 Home-page: https://github.com/matthiaskoenig/pymetadata
 Download-URL: https://pypi.org/project/pymetadata
@@ -131,11 +131,14 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
-within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) 
-and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
-"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - 
-A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and 
+Matthias König (MK) was supported by the Federal Ministry of Education and Research 
+(BMBF, Germany) within the research network Systems Medicine of the Liver 
+(**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of 
+Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and 
+by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 
+QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection 
+- A Systems Medicine Approach) by grant number 436883643 and by grant number 
+465194077 (Priority Programme SPP 2311, Subproject SimLivA).
 
 Installation
 ============
@@ -156,8 +159,21 @@ Or via cloning the repository and installing via::
     cd pymetadata
     pip install -e .
 
+
 To install for development use::
 
     pip install -e .[development]
 
+
+Cache path
+==========
+`pymetadata` caches some information for faster retrieval. The cache path is set to::
+
+    CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
+
+To use a custom cache path use::
+
+    import pymetadata
+    pymetadata.CACHE_PATH = <cache_path>
+
 © 2021-2024 Matthias König

{pymetadata-0.4.2 → pymetadata-0.4.4}/README.rst

@@ -80,11 +80,14 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
-within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) 
-and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
-"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - 
-A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and 
+Matthias König (MK) was supported by the Federal Ministry of Education and Research 
+(BMBF, Germany) within the research network Systems Medicine of the Liver 
+(**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of 
+Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and 
+by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 
+QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection 
+- A Systems Medicine Approach) by grant number 436883643 and by grant number 
+465194077 (Priority Programme SPP 2311, Subproject SimLivA).
 
 Installation
 ============
@@ -105,8 +108,21 @@ Or via cloning the repository and installing via::
     cd pymetadata
     pip install -e .
 
+
 To install for development use::
 
     pip install -e .[development]
 
+
+Cache path
+==========
+`pymetadata` caches some information for faster retrieval. The cache path is set to::
+
+    CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
+
+To use a custom cache path use::
+
+    import pymetadata
+    pymetadata.CACHE_PATH = <cache_path>
+
 © 2021-2024 Matthias König

{pymetadata-0.4.2 → pymetadata-0.4.4}/setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.2
+current_version = 0.4.4
 commit = True
 tag = True
 parse = (?P<major>\d+)

{pymetadata-0.4.2 → pymetadata-0.4.4}/setup.py

@@ -4,4 +4,4 @@ from setuptools import setup  # type: ignore
 
 
 if __name__ == "__main__":
-    setup(version="0.4.2")
+    setup(version="0.4.4")

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.4.2"
+__version__ = "0.4.4"
 
 
 program_name: str = "pymetadata"
@@ -11,4 +11,4 @@ RESOURCES_DIR: Path = Path(__file__).parent / "resources"
 ENUM_DIR: Path = Path(__file__).parent / "metadata"
 
 CACHE_USE: bool = False
-CACHE_PATH: Path = RESOURCES_DIR / "cache"
+CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/cache.py

@@ -43,6 +43,7 @@ def write_json_cache(
     :param json_encoder: optional JSON encoder
     :return:
     """
+    cache_path.parent.mkdir(parents=True, exist_ok=True)
     with open(cache_path, "w") as fp:
         logger.info(f"Write cache: {cache_path}")
         if json_encoder:

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/chebi.py

@@ -2,18 +2,19 @@
 
 from pathlib import Path
 from pprint import pprint
-from typing import Any, Dict
+from typing import Any, Dict, Optional
 
 from zeep import Client
 
-from pymetadata import CACHE_PATH, CACHE_USE, RESOURCES_DIR, log
+import pymetadata
+from pymetadata import log
 from pymetadata.cache import DataclassJSONEncoder, read_json_cache, write_json_cache
 
 
 logger = log.get_logger(__name__)
 
-# client = Client('https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl')
-client = Client(str(RESOURCES_DIR / "chebi_webservice_wsdl.xml"))
+# FIXME: copy the file to the cache dir
+client = Client(str(pymetadata.RESOURCES_DIR / "chebi_webservice_wsdl.xml"))
 
 
 class ChebiQuery:
@@ -25,15 +26,19 @@ class ChebiQuery:
 
     @staticmethod
     def query(
-        chebi: str, cache: bool = CACHE_USE, cache_path: Path = CACHE_PATH
+        chebi: str, cache: Optional[bool] = None, cache_path: Optional[Path] = None
     ) -> Dict:
         """Query additional ChEBI information."""
 
         if not chebi:
             return dict()
+        if cache is None:
+            cache = pymetadata.CACHE_USE
+        if cache_path is None:
+            cache_path = pymetadata.CACHE_PATH
 
         # caching
-        chebi_base_path = cache_path / "chebi"
+        chebi_base_path = Path(cache_path) / "chebi"
         if not chebi_base_path.exists():
             chebi_base_path.mkdir(parents=True)
 

pymetadata-0.4.4/src/pymetadata/examples/cache_path_example.py

@@ -0,0 +1,15 @@
+"""Example for customizing the cache path."""
+
+from pathlib import Path
+
+import pymetadata
+from pymetadata.chebi import ChebiQuery
+
+
+pymetadata.CACHE_PATH = Path.home() / ".cache" / "pymetadata"
+
+if __name__ == "__main__":
+
+    chebis = ["CHEBI:2668", "CHEBI:138366", "CHEBI:9637", "CHEBI:155897"]
+    for chebi in chebis:
+        d = ChebiQuery.query(chebi=chebi, cache=True)

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/identifiers/registry.py

@@ -16,7 +16,8 @@ from typing import Any, Dict, List, Optional
 
 import requests
 
-from pymetadata import RESOURCES_DIR, log
+import pymetadata
+from pymetadata import CACHE_PATH, log
 from pymetadata.cache import DataclassJSONEncoder, read_json_cache, write_json_cache
 
 
@@ -298,7 +299,6 @@ class Registry:
 
     def __init__(
         self,
-        registry_path: Path = RESOURCES_DIR / "identifiers_registry.json",
         cache_duration: int = 24,
         cache: bool = True,
     ):
@@ -308,13 +308,13 @@ class Registry:
         :param cache_duration: Duration of caching in hours.
         :param cache: boolean flag to stop caching
         """
-        self.registry_path = registry_path
+        self.registry_path = pymetadata.CACHE_PATH / "identifiers_registry.json"
 
         # check if update needed
         if cache:
             if os.path.exists(self.registry_path):
                 registry_age = (
-                    time.time() - os.path.getmtime(registry_path)
+                    time.time() - os.path.getmtime(self.registry_path)
                 ) / 3600  # [hr]
                 update = registry_age > cache_duration
             else:

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/ontologies/ols.py

@@ -12,7 +12,8 @@ from typing import Any, Dict, List, Optional
 
 import requests
 
-from pymetadata import CACHE_PATH, CACHE_USE, log
+import pymetadata
+from pymetadata import log
 from pymetadata.cache import read_json_cache, write_json_cache
 from pymetadata.identifiers.registry import Registry
 
@@ -76,13 +77,18 @@ class OLSQuery:
     def __init__(
         self,
         ontologies: List[OLSOntology],
-        cache_path: Path = CACHE_PATH,
-        cache: bool = CACHE_USE,
+        cache_path: Optional[Path] = None,
+        cache: Optional[bool] = None,
     ):
         """Initialize OLSQuery."""
         self.ontologies: Dict[str, OLSOntology] = {
             ontology.name: ontology for ontology in ontologies
         }
+        if not cache_path:
+            cache_path = pymetadata.CACHE_PATH
+        if not cache:
+            cache = pymetadata.CACHE_USE
+
         self.cache_path = cache_path / "ols"
         self.cache = cache
 

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata/unichem.py

@@ -14,7 +14,8 @@ from typing import Dict, List, Optional
 
 import requests
 
-from pymetadata import CACHE_PATH, CACHE_USE, log
+import pymetadata
+from pymetadata import log
 from pymetadata.cache import DataclassJSONEncoder, read_json_cache, write_json_cache
 from pymetadata.core.xref import CrossReference
 
@@ -59,27 +60,27 @@ class UnichemQuery:
 
     sources: Dict[int, UnichemSource] = {}
 
-    def __init__(self, cache_path: Path = CACHE_PATH, cache: bool = CACHE_USE):
+    def __init__(self, cache_path: Optional[Path] = None, cache: Optional[bool] = None):
         """Initialize UnichemQuery."""
+        if cache_path is None:
+            cache_path = pymetadata.CACHE_PATH
+        if cache is None:
+            cache = pymetadata.CACHE_USE
+
         self.cache_path: Path = cache_path
         self.cache: bool = cache
 
         if not self.sources:
-            self.sources = self.get_sources(
-                cache_path=self.cache_path, cache=self.cache
-            )
+            self.sources = self.get_sources()
 
-    @classmethod
-    def get_sources(
-        cls, cache_path: Path = CACHE_PATH, cache: bool = CACHE_USE
-    ) -> Dict[int, UnichemSource]:
+    def get_sources(self) -> Dict[int, UnichemSource]:
         """Retrieve or query the sources."""
 
         sources: Dict[int, UnichemSource]
-        unichem_sources_path = cache_path / "unichem_sources.json"
+        unichem_sources_path = self.cache_path / "unichem_sources.json"
 
         data: Dict
-        if cache and unichem_sources_path.exists():
+        if self.cache and unichem_sources_path.exists():
             data = read_json_cache(unichem_sources_path)
             sources = {int(k): UnichemSource(**v) for k, v in data.items()}
         else:
@@ -96,7 +97,7 @@ class UnichemQuery:
             sources = {source.sourceID: source for source in sources_list}
 
             # write cache
-            if cache:
+            if self.cache:
                 write_json_cache(
                     data=sources,
                     cache_path=unichem_sources_path,
@@ -174,8 +175,10 @@ class UnichemQuery:
 
 
 if __name__ == "__main__":
+    pymetadata.CACHE_PATH = Path.home() / ".cache" / "pymetadata"
+
     # query sources
-    sources = UnichemQuery.get_sources()
+    sources = UnichemQuery().get_sources()
 
     # query xrefs
     inchikey = "NGBFQHCMQULJNZ-UHFFFAOYSA-N"

{pymetadata-0.4.2 → pymetadata-0.4.4/src/pymetadata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pymetadata
-Version: 0.4.2
+Version: 0.4.4
 Summary: pymetadata are python utilities for working with metadata.
 Home-page: https://github.com/matthiaskoenig/pymetadata
 Download-URL: https://pypi.org/project/pymetadata
@@ -131,11 +131,14 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
-within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) 
-and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
-"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - 
-A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and 
+Matthias König (MK) was supported by the Federal Ministry of Education and Research 
+(BMBF, Germany) within the research network Systems Medicine of the Liver 
+(**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of 
+Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and 
+by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 
+QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection 
+- A Systems Medicine Approach) by grant number 436883643 and by grant number 
+465194077 (Priority Programme SPP 2311, Subproject SimLivA).
 
 Installation
 ============
@@ -156,8 +159,21 @@ Or via cloning the repository and installing via::
     cd pymetadata
     pip install -e .
 
+
 To install for development use::
 
     pip install -e .[development]
 
+
+Cache path
+==========
+`pymetadata` caches some information for faster retrieval. The cache path is set to::
+
+    CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
+
+To use a custom cache path use::
+
+    import pymetadata
+    pymetadata.CACHE_PATH = <cache_path>
+
 © 2021-2024 Matthias König

{pymetadata-0.4.2 → pymetadata-0.4.4}/src/pymetadata.egg-info/SOURCES.txt

@@ -24,6 +24,7 @@ src/pymetadata/core/creator.py
 src/pymetadata/core/synonym.py
 src/pymetadata/core/xref.py
 src/pymetadata/examples/__init__.py
+src/pymetadata/examples/cache_path_example.py
 src/pymetadata/examples/omex_example.py
 src/pymetadata/identifiers/__init__.py
 src/pymetadata/identifiers/miriam.py
@@ -36,7 +37,6 @@ src/pymetadata/ontologies/__init__.py
 src/pymetadata/ontologies/ols.py
 src/pymetadata/ontologies/ontology.py
 src/pymetadata/resources/chebi_webservice_wsdl.xml
-src/pymetadata/resources/identifiers_registry.json
 src/pymetadata/resources/templates/ontology_enum.pytemplate
 tests/test_chebi.py
 tests/test_ols.py

{pymetadata-0.4.2 → pymetadata-0.4.4}/tests/test_unichem.py

@@ -9,11 +9,11 @@ from pymetadata.unichem import UnichemQuery, UnichemSource
 def test_get_sources(tmp_path: Path) -> None:
     """Test retrieving sources."""
     cache_path: Path = tmp_path
-    sources = UnichemQuery.get_sources(cache=True, cache_path=cache_path)
+    sources = UnichemQuery(cache=True, cache_path=cache_path).get_sources()
     assert sources
     assert (cache_path / "unichem_sources.json").exists()
 
-    sources = UnichemQuery.get_sources(cache=True, cache_path=cache_path)
+    sources = UnichemQuery(cache=True, cache_path=cache_path).get_sources()
     assert sources