pymetadata 0.5.2__py3-none-any.whl → 0.5.4__py3-none-any.whl

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Files changed (16) hide show
  1. pymetadata/__init__.py +1 -1
  2. pymetadata/chebi.py +21 -29
  3. pymetadata/core/annotation.py +4 -1
  4. pymetadata/examples/cache_path_example.py +0 -1
  5. pymetadata/identifiers/registry.py +11 -33
  6. pymetadata/metadata/eco.py +1246 -1340
  7. pymetadata/metadata/kisao.py +83 -26
  8. pymetadata/metadata/sbo.py +131 -378
  9. pymetadata/ontologies/ontology.py +6 -5
  10. pymetadata/resources/templates/ontology_enum.pytemplate +0 -2
  11. pymetadata/unichem.py +2 -2
  12. {pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/METADATA +6 -7
  13. {pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/RECORD +15 -16
  14. {pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/licenses/LICENSE +1 -1
  15. pymetadata/resources/chebi_webservice_wsdl.xml +0 -509
  16. {pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/WHEEL +0 -0
pymetadata/ontologies/ontology.py CHANGED
@@ -26,6 +26,7 @@ from pronto.relationship import Relationship as ProntoRelationship
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  from pronto.term import Term as ProntoTerm
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  from pymetadata import ENUM_DIR, RESOURCES_DIR, log
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+ from pymetadata.console import console
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  logger = log.get_logger(__name__)
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@@ -51,18 +52,18 @@ class OntologyFile:
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  @property
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  def path(self) -> Path:
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  """Path of ontology file."""
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- return RESOURCES_DIR / "ontologies" / f"{self.id.lower()}.{self.format}.gz"
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+ return RESOURCES_DIR / "ontologies" / f"{self.id.lower()}.{self.format.value}.gz"
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  @property
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  def filename(self) -> str:
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  """Filename of ontology file.
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- :return: ontolgoy filename
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+ :return: ontology filename
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  :rtype: str
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  """
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- data = str(self.path)
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- print(data)
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- return data
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+ name = str(self.path)
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+ console.print(name)
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+ return name
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  _ontology_files: List[OntologyFile] = [
pymetadata/resources/templates/ontology_enum.pytemplate CHANGED
@@ -57,5 +57,3 @@ __all__ = [
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  "{{ontology_id}}",
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  "{{ontology_id}}Type",
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  ]
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-
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-
pymetadata/unichem.py CHANGED
@@ -130,7 +130,7 @@ class UnichemQuery:
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  xrefs: List[CrossReference] = []
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  if data:
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  if "error" in data:
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- logger.error(f"No xrefs for inchikey: '{inchikey}'")
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+ logger.warning(f"No xrefs for inchikey: '{inchikey}'")
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  return []
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  # process data
@@ -138,7 +138,7 @@ class UnichemQuery:
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  for item in data:
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  source_id: int = int(item["src_id"])
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  if source_id not in self.sources:
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- if source_id != 40:
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+ if source_id not in {40, 49, 50}:
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  # number 40 is missing from definitions
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  logger.error(
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  f"No UniChem source for source id '{source_id}', in item "
{pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pymetadata
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- Version: 0.5.2
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+ Version: 0.5.4
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  Summary: pymetadata are python utilities for working with metadata.
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  Author-email: Matthias König <konigmatt@googlemail.com>
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  Maintainer-email: Matthias König <konigmatt@googlemail.com>
@@ -27,7 +27,6 @@ Requires-Dist: pydantic>=2.10.4
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  Requires-Dist: requests>=2.32.3
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  Requires-Dist: rich>=13.9.4
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  Requires-Dist: xmltodict>=0.14.2
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- Requires-Dist: zeep>=4.3.1
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  Provides-Extra: dev
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  Requires-Dist: bump-my-version>=0.29.0; extra == 'dev'
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  Requires-Dist: mypy>=1.9.0; extra == 'dev'
@@ -49,15 +48,15 @@ Description-Content-Type: text/markdown
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  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
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  pymetadata is a collection of python utilities for working with
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- metadata in the context of COMBINE standards with source code available from
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+ metadata in the context of COMBINE standards with source code available from
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  [https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
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  Features include among others
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- - COMBINE archive version 1 support (OMEX)
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+ - [core](src/pymetadata/core)COMBINE archive version 1 support (OMEX)
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  - annotation classes and helpers
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  - SBO and KISAO ontology enums
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-
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+
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  If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
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  # Documentation
@@ -75,10 +74,10 @@ Contributions are always welcome! Please read the [contributing guidelines](http
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  - Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
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  # Funding
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- 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).
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+ 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).
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  # Installation
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- `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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+ `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
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  can be installed via
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  ```bash
{pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/RECORD RENAMED
@@ -1,19 +1,19 @@
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- pymetadata/__init__.py,sha256=35mfW854dCAnEdVYlCj4WPTTQiU-v_XXB7B0VnUPS6M,357
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+ pymetadata/__init__.py,sha256=jesaxsDSp7xbL8JFTMU_pSdcTcYx1NdgzY_XV8wgoD0,357
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  pymetadata/cache.py,sha256=tQuMIcd1cOfO0dvODQMG92_IrHqgswPfshhFjtl7Pd0,1409
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- pymetadata/chebi.py,sha256=EH8sYRx7af3Hi1O8x5Tvj_T9cawGVMtlYp_4B3L8tHY,2730
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+ pymetadata/chebi.py,sha256=P9OWSf8fzcjfMscPG8LORMNnFRUye-Ai-Y3NiGyG0uc,2822
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  pymetadata/console.py,sha256=ouDYOx_81ndvtMW5GVrut71uzPC5xlvibGu9N5YdbRA,332
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  pymetadata/log.py,sha256=3uRVMYolalrS0PVWS_4qSme8RYhot3_W2ad1JopI88g,664
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  pymetadata/omex.py,sha256=ZFsX9Xbh8sgT1UeBpKMgdrOh2PGTxrH2IAdYo_R9xc0,29927
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  pymetadata/omex_v2.py,sha256=HZBg_wmQWixweOZG3qVj2zqG_o1x9Ljxy-JEP6-ZFhM,584
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  pymetadata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- pymetadata/unichem.py,sha256=slxTabar1ZdZQUyTyRloiWKxD92ixnDGsJ2xk3alrTo,6878
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+ pymetadata/unichem.py,sha256=SCdljAA6dsR3DrD_OrjRoXIMhgwVV-MiXoCiNMVo_-0,6894
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  pymetadata/core/__init__.py,sha256=VWZCD9TgSGldzdtXoarvp_2oUHKXQkC1T-VUSvMLwNA,28
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- pymetadata/core/annotation.py,sha256=PO2dyjgDP91J6JcJ2i3CzvdSd-6I0-3lAeTaaRd_cyY,13695
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+ pymetadata/core/annotation.py,sha256=aAkgWzx-Qmp2fUO3Qn-yq0-Ht3fEiwaR1yAlqXvvQJ4,13742
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  pymetadata/core/creator.py,sha256=0_z0HPhO2Tq8FnAED_4kuVzUiPfm_tYMiZSvyw73Aho,1307
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  pymetadata/core/synonym.py,sha256=-2_1ouSWAtQK5eZv2-p6CIJgYZX4xGKua-09ubBg5uo,155
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  pymetadata/core/xref.py,sha256=qlUfAb5wk4bOwPiUCEV0s9gIWVdWf5yup1W8UxR5uHY,1594
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  pymetadata/examples/__init__.py,sha256=LHY-XmQoiBxoHQW9mQN1_fUYnpfkALuRsdxDXU9sIeU,31
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- pymetadata/examples/cache_path_example.py,sha256=f1-uvvIO28voxpehIvlXuWybNsAkAldmS70Bd77Cb78,377
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+ pymetadata/examples/cache_path_example.py,sha256=WGDiwVmRO47r2k19y3mtyQGYD74NgTfiK6V4Cm8kaEQ,376
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  pymetadata/examples/omex_example.py,sha256=z8fKyI1z5NMze8DdTfGYvG0rxzinFk61ruiT6NDdcT4,1403
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  pymetadata/examples/test.omex,sha256=uVrkDrA59F0S6TpQOk_UulDO-pTu0nU3f6zmaWI7zi4,26219
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  pymetadata/examples/results/test_from_files.omex,sha256=wFBnU3v8uUiKkh4RcvMBWSUuaKtSCixQMwwZtbwEiZE,1807
@@ -25,18 +25,17 @@ pymetadata/examples/results/testomex/models/omex_comp_flat.xml,sha256=3avaqyiP07
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  pymetadata/examples/results/testomex/models/omex_minimal.xml,sha256=r6FDgMu4rEXR2H_EKyQlSh4JkisH1Yu2clVkqKarPOI,6619
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  pymetadata/identifiers/__init__.py,sha256=6Jd-w9Izl_wpWKV8IMBv7rW0Aq067V2czu00LNfPTL8,34
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  pymetadata/identifiers/miriam.py,sha256=pa7lB1_C2cKRUuojFPvxAQ6yDI_ZQNjGEoYMb1395pY,982
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- pymetadata/identifiers/registry.py,sha256=FzajEoFXlywtAqhGQ2YpxkViAoBRXZM5P82J6ZOHyPc,13081
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+ pymetadata/identifiers/registry.py,sha256=B2LgtNhGyEwL_X-PlwmrJy4IWUuOQPN6-54L-WZs8xk,12152
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  pymetadata/metadata/__init__.py,sha256=wrZtmqudWwyxJXrsHoTx235ooDepKgiia8kHKiIZO4Y,154
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- pymetadata/metadata/eco.py,sha256=wsF-nRuXdI5Fm8T1e8wWYFtBPgzQ9ap2zIkH3nXjab4,662767
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- pymetadata/metadata/kisao.py,sha256=oI3zuCDhDmA-aK5pWLhNJu1Y0XgBvI6IpmLlEnymgdo,89273
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- pymetadata/metadata/sbo.py,sha256=rJEtdhOP5YUY1i8-6drWsglDmayFEpWVA2h2t3fjLCo,141756
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+ pymetadata/metadata/eco.py,sha256=5htFnOP7y5EKVJujTcuUvGQWHiBBjpQBrKl5Z0wN41g,704651
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+ pymetadata/metadata/kisao.py,sha256=W8ZrG79zRUftOLIIvuSSIp-b33YtLhJqifYF40v7jv4,91588
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+ pymetadata/metadata/sbo.py,sha256=x8Sg6k4VhqkcFF_NjBRF_RixCYIwJvUAz2YSuq-77HU,139787
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  pymetadata/ontologies/__init__.py,sha256=vIpTqwqrhOAOYfnavWBQL149dNMAPv-OE5IyloYQCrQ,18
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  pymetadata/ontologies/ols.py,sha256=lKmhRMKuEx29QAZsxCRlzUwH48CGtl8YKM2AcsiDFVk,6814
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- pymetadata/ontologies/ontology.py,sha256=cnAgXzxPn3XxZ8FUAMuSAH0eOGio-YK1Enzy3ZuKzcc,9100
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- pymetadata/resources/chebi_webservice_wsdl.xml,sha256=0AEgcZ48bk4L6l3jO5-6BIVwfTr4yXnRZCtXue5NyHo,23846
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+ pymetadata/ontologies/ontology.py,sha256=-3_AAq-HxRBOZReuLb3dj56HPPFUXsW22ULwaYQLIBc,9153
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  pymetadata/resources/ontologies/README.md,sha256=h1LIKpr42-s0RzwpCufkR_YJ2nWiwOapZX_frRXk3Qg,163
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- pymetadata/resources/templates/ontology_enum.pytemplate,sha256=fK7SBTVfRzVk-z_6wiZ_9MDbTNSlEpGGellRoliGqac,1674
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- pymetadata-0.5.2.dist-info/METADATA,sha256=d39G-Arr7ZINSjkrXQg5JxHqurwMItj8dmwOAP0Vc0w,4943
40
- pymetadata-0.5.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
41
- pymetadata-0.5.2.dist-info/licenses/LICENSE,sha256=bIHEDEMiQfVe9c81lFP7Q9hsCOmEuj2c_m50LuotsMM,1058
42
- pymetadata-0.5.2.dist-info/RECORD,,
37
+ pymetadata/resources/templates/ontology_enum.pytemplate,sha256=nona0KbGoFumgJo2v_J-pcTniXveiTGb8bz-1rMoDR8,1672
38
+ pymetadata-0.5.4.dist-info/METADATA,sha256=0U53rnyuNU9DAru79B-TAmujpzBCzvFbYTYEg5iCIxE,4936
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+ pymetadata-0.5.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
40
+ pymetadata-0.5.4.dist-info/licenses/LICENSE,sha256=4oZhYj-TN8e6NrD0wup4nJfQUH9zX0v3gz43xN6F2hs,1059
41
+ pymetadata-0.5.4.dist-info/RECORD,,
{pymetadata-0.5.2.dist-info → pymetadata-0.5.4.dist-info}/licenses/LICENSE RENAMED
@@ -4,4 +4,4 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
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  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
7
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.