pymetadata 0.4.1__tar.gz → 0.4.4__tar.gz

{pymetadata-0.4.1/src/pymetadata.egg-info → pymetadata-0.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pymetadata
-Version: 0.4.1
+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
@@ -28,27 +28,26 @@ Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: depinfo>=1.7
-Requires-Dist: uuid>=1.30
-Requires-Dist: lxml>=4.9
-Requires-Dist: rich>=13.6
+Requires-Dist: lxml>=5.2
+Requires-Dist: rich>=13.7
 Requires-Dist: requests>=2.31
 Requires-Dist: zeep>=4.2.1
-Requires-Dist: pronto>=2.5.5
-Requires-Dist: fastobo>=0.12.2
-Requires-Dist: jinja2>=3.1.2
+Requires-Dist: pronto>=2.5.6
+Requires-Dist: fastobo>=0.12.3
+Requires-Dist: jinja2>=3.1
 Requires-Dist: xmltodict>=0.13.0
-Requires-Dist: pydantic>=2.4
+Requires-Dist: pydantic>=2.6
 Provides-Extra: development
-Requires-Dist: pip-tools>6.10; extra == "development"
-Requires-Dist: black>=24.1.1; extra == "development"
+Requires-Dist: pip-tools>=7.4.1; extra == "development"
+Requires-Dist: black>=24.3.0; extra == "development"
 Requires-Dist: bump2version>=1.0.1; extra == "development"
 Requires-Dist: isort>=5.13.2; extra == "development"
-Requires-Dist: tox>=4.12.1; extra == "development"
-Requires-Dist: flake8>=6.1.0; extra == "development"
+Requires-Dist: tox>=4.12.2; extra == "development"
+Requires-Dist: flake8>=7.0.0; extra == "development"
 Requires-Dist: flake8-mypy>=17.8.0; extra == "development"
-Requires-Dist: mypy>=1.8.0; extra == "development"
-Requires-Dist: pytest>=8.0.0; extra == "development"
-Requires-Dist: pytest-cov>=4.1.0; extra == "development"
+Requires-Dist: mypy>=1.9.0; extra == "development"
+Requires-Dist: pytest>=8.1.1; extra == "development"
+Requires-Dist: pytest-cov>=5.0.0; extra == "development"
 
 .. image:: https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png
    :align: left
@@ -56,36 +55,28 @@ Requires-Dist: pytest-cov>=4.1.0; extra == "development"
 
 pymetadata: python utilities for metadata and COMBINE archives
 ==============================================================
+|icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
 
-.. image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
+
+.. |icon1| image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
    :target: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD
    :alt: GitHub Actions CI/CD Status
-
-.. image:: https://img.shields.io/pypi/v/pymetadata.svg
+.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Current PyPI Version
-
-.. image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
+.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Supported Python Versions
-
-.. image:: https://img.shields.io/pypi/l/pymetadata.svg
+.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
    :target: http://opensource.org/licenses/LGPL-3.0
    :alt: GNU Lesser General Public License 3
-
-.. image:: https://codecov.io/gh/matthiaskoenig/pymetadata/branch/develop/graph/badge.svg
-   :target: https://codecov.io/gh/matthiaskoenig/pymetadata
-   :alt: Codecov
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
+.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
    :target: https://doi.org/10.5281/zenodo.5308801
    :alt: Zenodo DOI
-
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+.. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
    :alt: Black
-
-.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
+.. |icon7| image:: http://www.mypy-lang.org/static/mypy_badge.svg
    :target: http://mypy-lang.org/
    :alt: mypy
 
@@ -140,11 +131,14 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König is 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 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).
+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
 ============
@@ -165,8 +159,21 @@ Or via cloning the repository and installing via::
     cd pymetadata
     pip install -e .
 
+
 To install for development use::
 
     pip install -e .[development]
 
-© 2021-2022 Matthias König
+
+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-0.4.1 → pymetadata-0.4.4}/README.rst

@@ -4,36 +4,28 @@
 
 pymetadata: python utilities for metadata and COMBINE archives
 ==============================================================
+|icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
 
-.. image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
+
+.. |icon1| image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
    :target: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD
    :alt: GitHub Actions CI/CD Status
-
-.. image:: https://img.shields.io/pypi/v/pymetadata.svg
+.. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Current PyPI Version
-
-.. image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
+.. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
    :target: https://pypi.org/project/pymetadata/
    :alt: Supported Python Versions
-
-.. image:: https://img.shields.io/pypi/l/pymetadata.svg
+.. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
    :target: http://opensource.org/licenses/LGPL-3.0
    :alt: GNU Lesser General Public License 3
-
-.. image:: https://codecov.io/gh/matthiaskoenig/pymetadata/branch/develop/graph/badge.svg
-   :target: https://codecov.io/gh/matthiaskoenig/pymetadata
-   :alt: Codecov
-
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
+.. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
    :target: https://doi.org/10.5281/zenodo.5308801
    :alt: Zenodo DOI
-
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+.. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
    :alt: Black
-
-.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
+.. |icon7| image:: http://www.mypy-lang.org/static/mypy_badge.svg
    :target: http://mypy-lang.org/
    :alt: mypy
 
@@ -88,11 +80,14 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 Funding
 =======
-Matthias König is 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 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).
+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
 ============
@@ -113,8 +108,21 @@ Or via cloning the repository and installing via::
     cd pymetadata
     pip install -e .
 
+
 To install for development use::
 
     pip install -e .[development]
 
-© 2021-2022 Matthias König
+
+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-0.4.1 → pymetadata-0.4.4}/setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.1
+current_version = 0.4.4
 commit = True
 tag = True
 parse = (?P<major>\d+)
@@ -52,19 +52,18 @@ zip_safe = True
 python_requires = >=3.9
 install_requires = 
 	depinfo>=1.7
-	uuid>=1.30
-	lxml>=4.9
-	rich>=13.6
+	lxml>=5.2
+	rich>=13.7
 	requests>=2.31
 	zeep>=4.2.1
-	pronto>=2.5.5
-	fastobo>=0.12.2
-	jinja2>=3.1.2
+	pronto>=2.5.6
+	fastobo>=0.12.3
+	jinja2>=3.1
 	xmltodict>=0.13.0
-	pydantic>=2.4
+	pydantic>=2.6
 tests_require = 
-	tox>=3.27
-	pytest
+	tox>=4.14.2
+	pytest>=8.1.1
 packages = find:
 package_dir = 
 	= src
@@ -81,16 +80,16 @@ where = src
 
 [options.extras_require]
 development = 
-	pip-tools>6.10
-	black>=24.1.1
+	pip-tools>=7.4.1
+	black>=24.3.0
 	bump2version>=1.0.1
 	isort>=5.13.2
-	tox>=4.12.1
-	flake8>=6.1.0
+	tox>=4.12.2
+	flake8>=7.0.0
 	flake8-mypy>=17.8.0
-	mypy>=1.8.0
-	pytest>=8.0.0
-	pytest-cov>=4.1.0
+	mypy>=1.9.0
+	pytest>=8.1.1
+	pytest-cov>=5.0.0
 
 [bdist_wheel]
 universal = 1

{pymetadata-0.4.1 → pymetadata-0.4.4}/setup.py

@@ -4,4 +4,4 @@ from setuptools import setup  # type: ignore
 
 
 if __name__ == "__main__":
-    setup(version="0.4.1")
+    setup(version="0.4.4")

{pymetadata-0.4.1 → pymetadata-0.4.4}/src/pymetadata/__init__.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 __author__ = "Matthias Koenig"
-__version__ = "0.4.1"
+__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-0.4.1 → 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-0.4.1 → 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-0.4.1 → 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
 
 
@@ -187,18 +188,6 @@ 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",
@@ -310,7 +299,6 @@ class Registry:
 
     def __init__(
         self,
-        registry_path: Path = RESOURCES_DIR / "identifiers_registry.json",
         cache_duration: int = 24,
         cache: bool = True,
     ):
@@ -320,13 +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:
@@ -349,7 +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"]
 
@@ -374,9 +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-0.4.1 → pymetadata-0.4.4}/src/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-0.4.1 → pymetadata-0.4.4}/src/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-0.4.1 → 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
 
@@ -76,17 +77,22 @@ 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 = {
+        self.ontologies: Dict[str, OLSOntology] = {
             ontology.name: ontology for ontology in ontologies
-        }  # type: Dict[str, OLSOntology]
+        }
+        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
 
-        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:
@@ -137,11 +143,6 @@ 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:
@@ -177,7 +178,8 @@ 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-0.4.1 → pymetadata-0.4.4}/src/pymetadata/ontologies/ontology.py

@@ -291,7 +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

{pymetadata-0.4.1 → 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:
@@ -96,11 +97,12 @@ class UnichemQuery:
             sources = {source.sourceID: source for source in sources_list}
 
             # write cache
-            write_json_cache(
-                data=sources,
-                cache_path=unichem_sources_path,
-                json_encoder=DataclassJSONEncoder,
-            )
+            if self.cache:
+                write_json_cache(
+                    data=sources,
+                    cache_path=unichem_sources_path,
+                    json_encoder=DataclassJSONEncoder,
+                )
 
         return sources
 
@@ -173,8 +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"