Fix #51, better handling cache path

.zenodo.json

@@ -8,7 +8,7 @@
       "name": "König, Matthias"
     }
   ],
-  "description": "<p><code>pymetadata</code> is a collection of python utilities for working with metadata in the context of COMBINE standards with source code available from available from <a href=\"https://github.com/matthiaskoenig/pymetadata\">https://github.com/matthiaskoenig/pymetadata</a></p>\n<p>Features include among others<ul><li>annotation classes and helpers</li></ul></p>\n<p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/pymetadata/issues\">open an issue</a></p>\n<h2>Funding</h2><p>Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (<strong>LiSyM</strong>, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 <strong><a href=\"https://qualiperf.de\">QuaLiPerF</a></strong> (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).</p>",
+  "description": "<p><code>pymetadata</code> is a collection of python utilities for working with metadata in the context of COMBINE standards with source code available from available from <a href=\"https://github.com/matthiaskoenig/pymetadata\">https://github.com/matthiaskoenig/pymetadata</a></p><p>Features include among others<ul><li>annotation classes and helpers</li></ul></p><p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/pymetadata/issues\">open an issue</a></p><h2>Funding</h2><p>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).</p>",
   "access_right": "open",
   "license": "LGPL-3.0",
   "keywords": [

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

release-notes/0.4.3.md

@@ -0,0 +1,9 @@
+# Release notes for pymetadata 0.4.3
+![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
+- better handling of resources and cache
+- customization of cache path via setting `pymetadata.CACHE_PATH`

src/pymetadata/__init__.py

@@ -11,4 +11,4 @@
 ENUM_DIR: Path = Path(__file__).parent / "metadata"
 
 CACHE_USE: bool = False
-CACHE_PATH: Path = RESOURCES_DIR / "cache"
+CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"

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)
 

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)

src/pymetadata/identifiers/registry.py

@@ -16,7 +16,8 @@
 
 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 @@ def __init__(
         :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:

src/pymetadata/ontologies/ols.py

@@ -12,7 +12,8 @@
 
 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