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

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Files changed (25) hide show
  1. pymetadata/__init__.py +2 -1
  2. pymetadata/cache.py +1 -0
  3. pymetadata/chebi.py +1 -0
  4. pymetadata/console.py +1 -0
  5. pymetadata/core/annotation.py +1 -0
  6. pymetadata/core/creator.py +1 -0
  7. pymetadata/core/synonym.py +1 -0
  8. pymetadata/core/xref.py +1 -0
  9. pymetadata/examples/omex_example.py +1 -0
  10. pymetadata/identifiers/registry.py +2 -16
  11. pymetadata/log.py +1 -0
  12. pymetadata/metadata/kisao.py +10 -0
  13. pymetadata/omex.py +1 -1
  14. pymetadata/omex_v2.py +1 -0
  15. pymetadata/ontologies/ols.py +6 -9
  16. pymetadata/ontologies/ontology.py +2 -1
  17. pymetadata/resources/identifiers_registry.json +1082 -554
  18. pymetadata/unichem.py +7 -5
  19. {pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/METADATA +30 -39
  20. pymetadata-0.4.2.dist-info/RECORD +35 -0
  21. {pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/WHEEL +1 -1
  22. pymetadata-0.4.0.dist-info/RECORD +0 -35
  23. {pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/LICENSE +0 -0
  24. {pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/top_level.txt +0 -0
  25. {pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/zip-safe +0 -0
pymetadata/unichem.py CHANGED
@@ -6,6 +6,7 @@ Additional substance information based on inchikeys
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  https://www.ebi.ac.uk/unichem/info/webservices#GetSrcCpdIdsFromKey
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  https://www.ebi.ac.uk/unichem/rest/inchikey/AAOVKJBEBIDNHE-UHFFFAOYSA-N
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  """
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+
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  import urllib
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  from dataclasses import dataclass, field
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  from pathlib import Path
@@ -95,11 +96,12 @@ class UnichemQuery:
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  sources = {source.sourceID: source for source in sources_list}
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  # write cache
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- write_json_cache(
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- data=sources,
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- cache_path=unichem_sources_path,
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- json_encoder=DataclassJSONEncoder,
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- )
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+ if cache:
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+ write_json_cache(
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+ data=sources,
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+ cache_path=unichem_sources_path,
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+ json_encoder=DataclassJSONEncoder,
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+ )
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  return sources
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{pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: pymetadata
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- Version: 0.4.0
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+ Version: 0.4.2
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  Summary: pymetadata are python utilities for working with metadata.
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  Home-page: https://github.com/matthiaskoenig/pymetadata
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  Download-URL: https://pypi.org/project/pymetadata
@@ -17,38 +17,37 @@ Classifier: Development Status :: 4 - Beta
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  Classifier: Intended Audience :: Science/Research
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  Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
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  Classifier: Operating System :: OS Independent
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- Classifier: Programming Language :: Python :: 3.8
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  Classifier: Programming Language :: Python :: 3.9
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  Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: Implementation :: CPython
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  Classifier: Topic :: Scientific/Engineering
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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- Requires-Python: >=3.8
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+ Requires-Python: >=3.9
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  Description-Content-Type: text/x-rst
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  License-File: LICENSE
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  Requires-Dist: depinfo >=1.7
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- Requires-Dist: uuid >=1.30
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- Requires-Dist: lxml >=4.9
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- Requires-Dist: rich >=13.6
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+ Requires-Dist: lxml >=5.2
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+ Requires-Dist: rich >=13.7
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  Requires-Dist: requests >=2.31
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  Requires-Dist: zeep >=4.2.1
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- Requires-Dist: pronto >=2.5.5
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- Requires-Dist: fastobo >=0.12.2
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- Requires-Dist: jinja2 >=3.1.2
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+ Requires-Dist: pronto >=2.5.6
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+ Requires-Dist: fastobo >=0.12.3
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+ Requires-Dist: jinja2 >=3.1
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  Requires-Dist: xmltodict >=0.13.0
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- Requires-Dist: pydantic >=2.4
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+ Requires-Dist: pydantic >=2.6
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  Provides-Extra: development
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- Requires-Dist: pip-tools >6.5.1 ; extra == 'development'
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- Requires-Dist: black >=22.1.0 ; extra == 'development'
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+ Requires-Dist: pip-tools >=7.4.1 ; extra == 'development'
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+ Requires-Dist: black >=24.3.0 ; extra == 'development'
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  Requires-Dist: bump2version >=1.0.1 ; extra == 'development'
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- Requires-Dist: isort >=5.10 ; extra == 'development'
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- Requires-Dist: tox >=3.25 ; extra == 'development'
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- Requires-Dist: flake8 >=4.0.1 ; extra == 'development'
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+ Requires-Dist: isort >=5.13.2 ; extra == 'development'
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+ Requires-Dist: tox >=4.12.2 ; extra == 'development'
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+ Requires-Dist: flake8 >=7.0.0 ; extra == 'development'
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  Requires-Dist: flake8-mypy >=17.8.0 ; extra == 'development'
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- Requires-Dist: mypy >=0.931 ; extra == 'development'
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- Requires-Dist: pytest >=7.0.1 ; extra == 'development'
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- Requires-Dist: pytest-cov >=3.0.0 ; extra == 'development'
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+ Requires-Dist: mypy >=1.9.0 ; extra == 'development'
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+ Requires-Dist: pytest >=8.1.1 ; extra == 'development'
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+ Requires-Dist: pytest-cov >=5.0.0 ; extra == 'development'
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  .. image:: https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png
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  :align: left
@@ -56,36 +55,28 @@ Requires-Dist: pytest-cov >=3.0.0 ; extra == 'development'
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  pymetadata: python utilities for metadata and COMBINE archives
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  ==============================================================
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+ |icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
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- .. image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
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+
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+ .. |icon1| image:: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD/badge.svg
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  :target: https://github.com/matthiaskoenig/pymetadata/workflows/CI-CD
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  :alt: GitHub Actions CI/CD Status
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-
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- .. image:: https://img.shields.io/pypi/v/pymetadata.svg
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+ .. |icon2| image:: https://img.shields.io/pypi/v/pymetadata.svg
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  :target: https://pypi.org/project/pymetadata/
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  :alt: Current PyPI Version
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-
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- .. image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
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+ .. |icon3| image:: https://img.shields.io/pypi/pyversions/pymetadata.svg
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  :target: https://pypi.org/project/pymetadata/
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  :alt: Supported Python Versions
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-
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- .. image:: https://img.shields.io/pypi/l/pymetadata.svg
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+ .. |icon4| image:: https://img.shields.io/pypi/l/pymetadata.svg
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  :target: http://opensource.org/licenses/LGPL-3.0
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  :alt: GNU Lesser General Public License 3
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-
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- .. image:: https://codecov.io/gh/matthiaskoenig/pymetadata/branch/develop/graph/badge.svg
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- :target: https://codecov.io/gh/matthiaskoenig/pymetadata
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- :alt: Codecov
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-
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- .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
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+ .. |icon5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg
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  :target: https://doi.org/10.5281/zenodo.5308801
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  :alt: Zenodo DOI
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-
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- .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
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+ .. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
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  :target: https://github.com/ambv/black
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  :alt: Black
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-
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- .. image:: http://www.mypy-lang.org/static/mypy_badge.svg
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+ .. |icon7| image:: http://www.mypy-lang.org/static/mypy_badge.svg
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  :target: http://mypy-lang.org/
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  :alt: mypy
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@@ -140,11 +131,11 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
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  Funding
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  =======
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- Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
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+ Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany)
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  within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054)
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- and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
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+ and is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
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  "`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection -
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- A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
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+ A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA), and
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  Installation
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  ============
@@ -169,4 +160,4 @@ To install for development use::
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  pip install -e .[development]
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- © 2021-2022 Matthias König
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+ © 2021-2024 Matthias König
pymetadata-0.4.2.dist-info/RECORD ADDED
@@ -0,0 +1,35 @@
1
+ pymetadata/__init__.py,sha256=ExrWsLL5kayU0yfVHH1PfHIik4UXV32B4IRr1NNKesQ,343
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+ pymetadata/cache.py,sha256=sEJu0D-Dua4aTEaTQfMscT9Gv71r5uXddqca9iv5FHs,1352
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+ pymetadata/chebi.py,sha256=LphWaLhDTlLfcb-Fw8_eP-mkQu-Dg3qVmO13JvTtE9Q,2610
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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=SrviUHCEchbDm3jf4hYrqSLifvA9v-QN5WY9SlAatD4,29867
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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=1cII_ltk0J56Mz3h4EXHz3mgfIxpc6G_AgT91LyCtK4,6804
10
+ pymetadata/core/__init__.py,sha256=VWZCD9TgSGldzdtXoarvp_2oUHKXQkC1T-VUSvMLwNA,28
11
+ pymetadata/core/annotation.py,sha256=PO2dyjgDP91J6JcJ2i3CzvdSd-6I0-3lAeTaaRd_cyY,13695
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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/omex_example.py,sha256=D1LI0ILG8r26yVdaF5IUqqh7TTe5ueIXCnUF41dd9zY,1418
17
+ pymetadata/identifiers/__init__.py,sha256=6Jd-w9Izl_wpWKV8IMBv7rW0Aq067V2czu00LNfPTL8,34
18
+ pymetadata/identifiers/miriam.py,sha256=pa7lB1_C2cKRUuojFPvxAQ6yDI_ZQNjGEoYMb1395pY,982
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+ pymetadata/identifiers/registry.py,sha256=QOZFm6kFMx8NSFNwtHa2tpUL2jNoeZq4qdMDEjwhX2U,13110
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+ pymetadata/metadata/__init__.py,sha256=7O7rPwJwW9_uHuvIs6IvQZiQz4MngZSV9Nu7SYL9eA8,102
21
+ pymetadata/metadata/eco.py,sha256=wsF-nRuXdI5Fm8T1e8wWYFtBPgzQ9ap2zIkH3nXjab4,662767
22
+ pymetadata/metadata/kisao.py,sha256=oI3zuCDhDmA-aK5pWLhNJu1Y0XgBvI6IpmLlEnymgdo,89273
23
+ pymetadata/metadata/sbo.py,sha256=rJEtdhOP5YUY1i8-6drWsglDmayFEpWVA2h2t3fjLCo,141756
24
+ pymetadata/ontologies/__init__.py,sha256=vIpTqwqrhOAOYfnavWBQL149dNMAPv-OE5IyloYQCrQ,18
25
+ pymetadata/ontologies/ols.py,sha256=F3vtM8sc879ETyE4yykuAuMJ3hm1jIGxQpvXa3eRAkQ,6672
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+ pymetadata/ontologies/ontology.py,sha256=1TGraeTlKdBmGfU3GCwiHHuq8OSQcM-DU8asoZ7q9-E,9140
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+ pymetadata/resources/chebi_webservice_wsdl.xml,sha256=0AEgcZ48bk4L6l3jO5-6BIVwfTr4yXnRZCtXue5NyHo,23846
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+ pymetadata/resources/identifiers_registry.json,sha256=NcfQoyg6KKUMNHTa76zxSFLiALLTt9yUEKiAO576YOk,2097405
29
+ pymetadata/resources/templates/ontology_enum.pytemplate,sha256=fK7SBTVfRzVk-z_6wiZ_9MDbTNSlEpGGellRoliGqac,1674
30
+ pymetadata-0.4.2.dist-info/LICENSE,sha256=2n6rt7r999OuXp8iOqW9we7ORaxWncIbOwN1ILRGR2g,7651
31
+ pymetadata-0.4.2.dist-info/METADATA,sha256=O8OEU9UFoyCgqP0tPaRHMT21QYhB_XS3exF8kHpuxbg,6713
32
+ pymetadata-0.4.2.dist-info/WHEEL,sha256=DZajD4pwLWue70CAfc7YaxT1wLUciNBvN_TTcvXpltE,110
33
+ pymetadata-0.4.2.dist-info/top_level.txt,sha256=6X2ZP7y4yuvIEbAghdb6NuNxw9mykRIdV9hdgVIibpY,11
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+ pymetadata-0.4.2.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
35
+ pymetadata-0.4.2.dist-info/RECORD,,
{pymetadata-0.4.0.dist-info → pymetadata-0.4.2.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.41.2)
2
+ Generator: bdist_wheel (0.43.0)
3
3
  Root-Is-Purelib: true
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4
  Tag: py2-none-any
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5
  Tag: py3-none-any
pymetadata-0.4.0.dist-info/RECORD DELETED
@@ -1,35 +0,0 @@
1
- pymetadata/__init__.py,sha256=IvsCDuGufUijmZJhwD7a3TeTP_T468NOyHgn8E7h8NA,342
2
- pymetadata/cache.py,sha256=ulPQKn6TXSe2ElfyO7abOUztI3j4SoweGh2Bav3q8Jg,1351
3
- pymetadata/chebi.py,sha256=O9UEHha260QuVNIJBqGk_FNDCn2vTPfJ2jluR5A6c4g,2609
4
- pymetadata/console.py,sha256=lzM55vluLbC43W0ypMMo-wvuAPMXI-qDeLPlTr-L2ZE,331
5
- pymetadata/log.py,sha256=kXJtaRn2y3Ue5vsbztnbwfWcJbetwlA3mPigNw73KKY,663
6
- pymetadata/omex.py,sha256=_FoZtg0LMHfEpi_lTWuLU44y7OQtLSE_UgZF63aXljI,29867
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- pymetadata/omex_v2.py,sha256=2YQIuS7PcBPckbLePgryDhsOJ1kn304fW5b6JSxPfJc,583
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- pymetadata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
9
- pymetadata/unichem.py,sha256=2pySq3Bdx1VvkgY9wqdK_Z34qhfT6DMHuelvczsqH-M,6761
10
- pymetadata/core/__init__.py,sha256=VWZCD9TgSGldzdtXoarvp_2oUHKXQkC1T-VUSvMLwNA,28
11
- pymetadata/core/annotation.py,sha256=OFiasz7onv6dVcI4uxrM5Z0yidmLzs6AY9z9L6YOsS4,13694
12
- pymetadata/core/creator.py,sha256=cA33q6Q0UJdulGFVdntwf5jBx8GvpPcK__ItNfRPNMw,1306
13
- pymetadata/core/synonym.py,sha256=G_hZFAsqbNJnw1xBWEKXO88Q_1OjtfbZwUc8P9sgg-E,154
14
- pymetadata/core/xref.py,sha256=S1g063rdhWogM3w0Bd1OddFQ4hbqy-ekRtV3Yz8js6o,1593
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- pymetadata/examples/__init__.py,sha256=LHY-XmQoiBxoHQW9mQN1_fUYnpfkALuRsdxDXU9sIeU,31
16
- pymetadata/examples/omex_example.py,sha256=qOflDvgbelUSGQrogvuQQUXUFXF3OouCpIPjtE_ipGw,1417
17
- pymetadata/identifiers/__init__.py,sha256=6Jd-w9Izl_wpWKV8IMBv7rW0Aq067V2czu00LNfPTL8,34
18
- pymetadata/identifiers/miriam.py,sha256=pa7lB1_C2cKRUuojFPvxAQ6yDI_ZQNjGEoYMb1395pY,982
19
- pymetadata/identifiers/registry.py,sha256=9JarVbnWkZH21pOCWnz-1a8i_2DX2W4gTlE4A5W_jUY,13761
20
- pymetadata/metadata/__init__.py,sha256=7O7rPwJwW9_uHuvIs6IvQZiQz4MngZSV9Nu7SYL9eA8,102
21
- pymetadata/metadata/eco.py,sha256=wsF-nRuXdI5Fm8T1e8wWYFtBPgzQ9ap2zIkH3nXjab4,662767
22
- pymetadata/metadata/kisao.py,sha256=2tr2Vlc4iwU11vhydIUeY4fGZ8NDKcGc7j1KiezNNPc,88999
23
- pymetadata/metadata/sbo.py,sha256=rJEtdhOP5YUY1i8-6drWsglDmayFEpWVA2h2t3fjLCo,141756
24
- pymetadata/ontologies/__init__.py,sha256=vIpTqwqrhOAOYfnavWBQL149dNMAPv-OE5IyloYQCrQ,18
25
- pymetadata/ontologies/ols.py,sha256=lFejdl20dnKQDrN40AmwGljo1XbEN5g4YJQyHhxoxAk,6818
26
- pymetadata/ontologies/ontology.py,sha256=kigqnhSSUlqJqrFLpawHniBPFyPYxVeo2RJij9gYevo,9141
27
- pymetadata/resources/chebi_webservice_wsdl.xml,sha256=0AEgcZ48bk4L6l3jO5-6BIVwfTr4yXnRZCtXue5NyHo,23846
28
- pymetadata/resources/identifiers_registry.json,sha256=e9_RdHEC8gR-3Q8AnZkv8GvHoa-CRg0AZq1-2Wg5bT0,2072587
29
- pymetadata/resources/templates/ontology_enum.pytemplate,sha256=fK7SBTVfRzVk-z_6wiZ_9MDbTNSlEpGGellRoliGqac,1674
30
- pymetadata-0.4.0.dist-info/LICENSE,sha256=2n6rt7r999OuXp8iOqW9we7ORaxWncIbOwN1ILRGR2g,7651
31
- pymetadata-0.4.0.dist-info/METADATA,sha256=EoZVVFD6tnC6gL0LfCKMOFoVFCutHbpKli85_87xpgs,6778
32
- pymetadata-0.4.0.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
33
- pymetadata-0.4.0.dist-info/top_level.txt,sha256=6X2ZP7y4yuvIEbAghdb6NuNxw9mykRIdV9hdgVIibpY,11
34
- pymetadata-0.4.0.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
35
- pymetadata-0.4.0.dist-info/RECORD,,