sssom 0.0.0__tar.gz

sssom-0.0.0/LICENSE

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+
+The MIT License (MIT)
+
+Copyright (c) 2023 Author 1
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+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.

sssom-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sssom
+Version: 0.0.0
+Summary: Operations on SSSOM mapping tables
+License-Expression: MIT
+License-File: LICENSE
+Author: Chris Mungall
+Author-email: cjmungall@lbl.gov
+Maintainer: Nicolas Matentzoglu
+Maintainer-email: nicolas.matentzoglu@gmail.com
+Requires-Python: >=3.10,<4.0.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: docs
+Provides-Extra: networkx
+Provides-Extra: pansql
+Provides-Extra: rdflib-endpoint
+Provides-Extra: scipy
+Requires-Dist: click (>=8.1.6)
+Requires-Dist: curies (>=0.10.23)
+Requires-Dist: deprecation (>=2.1.0)
+Requires-Dist: fastapi ; extra == "rdflib-endpoint"
+Requires-Dist: httpx ; extra == "rdflib-endpoint"
+Requires-Dist: linkml (>=1.10.0)
+Requires-Dist: linkml-runtime (>=1.10.0)
+Requires-Dist: mkdocs-click (>=0.8.1) ; extra == "docs"
+Requires-Dist: mkdocs-material (>=9.5.0) ; extra == "docs"
+Requires-Dist: mkdocstrings[python] (>=0.24.0) ; extra == "docs"
+Requires-Dist: networkx (>=3.1) ; extra == "networkx"
+Requires-Dist: packaging (>=20.0)
+Requires-Dist: pandas (>=2.0.0)
+Requires-Dist: pansql (>=0.0.1) ; extra == "pansql"
+Requires-Dist: pyyaml (>=6.0.1)
+Requires-Dist: rdflib (>=7.1.3)
+Requires-Dist: rdflib-endpoint ; extra == "rdflib-endpoint"
+Requires-Dist: scipy ; extra == "scipy"
+Requires-Dist: sparqlwrapper (>=2.0.0)
+Requires-Dist: sssom-schema (==1.1.0a4)
+Requires-Dist: uvicorn ; extra == "rdflib-endpoint"
+Requires-Dist: validators (>=0.20.0)
+Description-Content-Type: text/markdown
+
+# Python Utilities for SSSOM
+
+<p align="center">
+    <a href="https://github.com/mapping-commons/sssom-py/actions/workflows/qc.yml">
+        <img alt="Tests" src="https://github.com/mapping-commons/sssom-py/actions/workflows/qc.yml/badge.svg" />
+    </a>
+    <a href="https://pypi.org/project/sssom">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/sssom" />
+    </a>
+    <a href="https://pypi.org/project/sssom">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/sssom" />
+    </a>
+    <a href="https://github.com/mapping-commons/sssom-py/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/sssom" />
+    </a>
+    <a href="https://github.com/psf/black">
+        <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
+    </a>
+    <a href="https://doi.org/10.5281/zenodo.14296666"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14296666.svg" alt="DOI"></a>
+</p>
+
+<img src="https://github.com/tis-lab/closed-illustrations/raw/master/logos/sssom-logos/sssom_logo_black_banner.png" />
+
+A Python library and command line interface (CLI) for working with
+[SSSOM (Simple Standard for Sharing Ontology Mappings)](https://github.com/mapping-commons/sssom).
+
+## Getting Started
+
+A SSSOM TSV can be parsed with
+
+```python
+import sssom
+
+# other SSSOM files can be found on https://mapping-commons.github.io
+url = "https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_eye_impc.sssom.tsv"
+
+# TSV can be parsed into a mapping set dataframe object,
+# which includes a pandas DataFrame, a curies.Converter,
+# and metadata
+msdf = sssom.parse_tsv(url)
+
+# SSSOM comes with several "write" functions
+sssom.write_tsv(msdf, "test.tsv")
+sssom.write_json(msdf, "test.json")
+sssom.write_owl(msdf, "test.owl")
+sssom.write_rdf(msdf, "test.ttl")
+```
+
+> [!WARNING]  
+> The export formats (json, rdf) of sssom-py are not yet finalised! Expect changes in future releases.
+
+## Documentation
+
+See [documentation](https://mapping-commons.github.io/sssom-py/index.html#)
+
+### Deploy documentation
+
+```console
+$ make sphinx
+$ make deploy-docs
+```
+
+## Schema
+
+See the [schema/](schema) folder for source schema in YAML, plus
+derivations to JSON-Schema, ShEx, etc. 
+
+## Testing
+
+`tox` is similar to `make`, but specific for Python software projects. Its
+configuration is stored in [`tox.ini`](tox.ini) in different "environments"
+whose headers look like `[testenv:...]`. All tests can be run with:
+
+```console
+$ pip install tox
+$ tox
+```
+
+A specific environment can be run using the `-e` flag, such as `tox -e lint` to run
+the linting environment.
+
+## Outstanding Contributors
+
+Outstanding contributors are groups and institutions that have helped with organising the SSSOM
+Python package's development, providing funding, advice and infrastructure. We are very grateful
+for all your contribution - the project would not exist without you!
+
+### Harvard Medical School
+
+<img width="250" src="https://hms.harvard.edu/themes/harvardmedical/logo.svg" alt="Harvard Medical School Logo" />
+
+The [INDRA Lab](https://indralab.github.io), a part of the
+[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
+and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu), is interested in
+natural language processing and large-scale knowledge assembly. Their work on SSSOM is funded by the
+DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
+
+https://indralab.github.io
+
+## Citation
+
+SSSOM itself can be cited with:
+
+```bibtex
+@article{10.1093/database/baac035,
+    author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and Graybeal, John and Gray, Alasdair and Gyori, Benjamin M and Haendel, Melissa and Harmse, Henriette and Harris, Nomi L and Harrow, Ian and Hegde, Harshad B and Hoyt, Amelia L and Hoyt, Charles T and Jiao, Dazhi and Jiménez-Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and Koehler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A and McMurry, Julie A and Moxon, Sierra and Munoz-Torres, Monica C and Osumi-Sutherland, David and Overton, James A and Peters, Bjoern and Putman, Tim and Queralt-Rosinach, Núria and Shefchek, Kent and Solbrig, Harold and Thessen, Anne and Tudorache, Tania and Vasilevsky, Nicole and Wagner, Alex H and Mungall, Christopher J},
+    title = {A Simple Standard for Sharing Ontological Mappings (SSSOM)},
+    journal = {Database},
+    volume = {2022},
+    pages = {baac035},
+    year = {2022},
+    month = {05},
+    issn = {1758-0463},
+    doi = {10.1093/database/baac035},
+    url = {https://doi.org/10.1093/database/baac035},
+    eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
+}
+```
+
+To cite the SSSOM-py software package specifically, use:
+
+```bibtex
+@software{sssom-py,
+  author       = {Harshad Hegde and
+                  Nico Matentzoglu and
+                  Charles Tapley Hoyt and
+                  Chris Mungall and
+                  Joe Flack and
+                  Benjamin M. Gyori and
+                  Damien Goutte-Gattat and
+                  Glass and
+                  Syphax Bouazzouni},
+  title        = {mapping-commons/sssom-py: v0.4.15 release (minor
+                   fixes)
+                  },
+  month        = dec,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v0.4.15},
+  doi          = {10.5281/zenodo.14296666},
+  url          = {https://doi.org/10.5281/zenodo.14296666},
+}
+```
+ 
+

sssom-0.0.0/README.md

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+# Python Utilities for SSSOM
+
+<p align="center">
+    <a href="https://github.com/mapping-commons/sssom-py/actions/workflows/qc.yml">
+        <img alt="Tests" src="https://github.com/mapping-commons/sssom-py/actions/workflows/qc.yml/badge.svg" />
+    </a>
+    <a href="https://pypi.org/project/sssom">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/sssom" />
+    </a>
+    <a href="https://pypi.org/project/sssom">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/sssom" />
+    </a>
+    <a href="https://github.com/mapping-commons/sssom-py/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/sssom" />
+    </a>
+    <a href="https://github.com/psf/black">
+        <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
+    </a>
+    <a href="https://doi.org/10.5281/zenodo.14296666"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14296666.svg" alt="DOI"></a>
+</p>
+
+<img src="https://github.com/tis-lab/closed-illustrations/raw/master/logos/sssom-logos/sssom_logo_black_banner.png" />
+
+A Python library and command line interface (CLI) for working with
+[SSSOM (Simple Standard for Sharing Ontology Mappings)](https://github.com/mapping-commons/sssom).
+
+## Getting Started
+
+A SSSOM TSV can be parsed with
+
+```python
+import sssom
+
+# other SSSOM files can be found on https://mapping-commons.github.io
+url = "https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_eye_impc.sssom.tsv"
+
+# TSV can be parsed into a mapping set dataframe object,
+# which includes a pandas DataFrame, a curies.Converter,
+# and metadata
+msdf = sssom.parse_tsv(url)
+
+# SSSOM comes with several "write" functions
+sssom.write_tsv(msdf, "test.tsv")
+sssom.write_json(msdf, "test.json")
+sssom.write_owl(msdf, "test.owl")
+sssom.write_rdf(msdf, "test.ttl")
+```
+
+> [!WARNING]  
+> The export formats (json, rdf) of sssom-py are not yet finalised! Expect changes in future releases.
+
+## Documentation
+
+See [documentation](https://mapping-commons.github.io/sssom-py/index.html#)
+
+### Deploy documentation
+
+```console
+$ make sphinx
+$ make deploy-docs
+```
+
+## Schema
+
+See the [schema/](schema) folder for source schema in YAML, plus
+derivations to JSON-Schema, ShEx, etc. 
+
+## Testing
+
+`tox` is similar to `make`, but specific for Python software projects. Its
+configuration is stored in [`tox.ini`](tox.ini) in different "environments"
+whose headers look like `[testenv:...]`. All tests can be run with:
+
+```console
+$ pip install tox
+$ tox
+```
+
+A specific environment can be run using the `-e` flag, such as `tox -e lint` to run
+the linting environment.
+
+## Outstanding Contributors
+
+Outstanding contributors are groups and institutions that have helped with organising the SSSOM
+Python package's development, providing funding, advice and infrastructure. We are very grateful
+for all your contribution - the project would not exist without you!
+
+### Harvard Medical School
+
+<img width="250" src="https://hms.harvard.edu/themes/harvardmedical/logo.svg" alt="Harvard Medical School Logo" />
+
+The [INDRA Lab](https://indralab.github.io), a part of the
+[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
+and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu), is interested in
+natural language processing and large-scale knowledge assembly. Their work on SSSOM is funded by the
+DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
+
+https://indralab.github.io
+
+## Citation
+
+SSSOM itself can be cited with:
+
+```bibtex
+@article{10.1093/database/baac035,
+    author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and Graybeal, John and Gray, Alasdair and Gyori, Benjamin M and Haendel, Melissa and Harmse, Henriette and Harris, Nomi L and Harrow, Ian and Hegde, Harshad B and Hoyt, Amelia L and Hoyt, Charles T and Jiao, Dazhi and Jiménez-Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and Koehler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A and McMurry, Julie A and Moxon, Sierra and Munoz-Torres, Monica C and Osumi-Sutherland, David and Overton, James A and Peters, Bjoern and Putman, Tim and Queralt-Rosinach, Núria and Shefchek, Kent and Solbrig, Harold and Thessen, Anne and Tudorache, Tania and Vasilevsky, Nicole and Wagner, Alex H and Mungall, Christopher J},
+    title = {A Simple Standard for Sharing Ontological Mappings (SSSOM)},
+    journal = {Database},
+    volume = {2022},
+    pages = {baac035},
+    year = {2022},
+    month = {05},
+    issn = {1758-0463},
+    doi = {10.1093/database/baac035},
+    url = {https://doi.org/10.1093/database/baac035},
+    eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
+}
+```
+
+To cite the SSSOM-py software package specifically, use:
+
+```bibtex
+@software{sssom-py,
+  author       = {Harshad Hegde and
+                  Nico Matentzoglu and
+                  Charles Tapley Hoyt and
+                  Chris Mungall and
+                  Joe Flack and
+                  Benjamin M. Gyori and
+                  Damien Goutte-Gattat and
+                  Glass and
+                  Syphax Bouazzouni},
+  title        = {mapping-commons/sssom-py: v0.4.15 release (minor
+                   fixes)
+                  },
+  month        = dec,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v0.4.15},
+  doi          = {10.5281/zenodo.14296666},
+  url          = {https://doi.org/10.5281/zenodo.14296666},
+}
+```
+ 

sssom-0.0.0/pyproject.toml

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+[project]
+name = "sssom"
+version = "0.0.0"
+description = "Operations on SSSOM mapping tables"
+authors = [
+    { name = "Chris Mungall", email = "cjmungall@lbl.gov" },
+    { name = "Nicolas Matentzoglu", email = "nicolas.matentzoglu@gmail.com" },
+    { name = "Harshad Hegde", email = "hhegde@lbl.gov" },
+]
+maintainers = [
+    { name = "Nicolas Matentzoglu", email = "nicolas.matentzoglu@gmail.com" },
+    { name = "Charles Tapley Hoyt", email = "cthoyt@gmail.com" },
+    { name = "Damien Goutte-Gattat", email = "dgouttegattat@incenp.org" },
+]
+license = "MIT"
+license-files = ["LICENSE"]
+readme = "README.md"
+requires-python = ">=3.10,<4.0.0"
+
+dependencies = [
+    "click>=8.1.6",
+    "curies>=0.10.23",
+    "linkml-runtime>=1.10.0",
+    "linkml>=1.10.0",
+    "packaging>=20.0",
+    "pandas>=2.0.0",
+    "sssom-schema==1.1.0a4",
+    "sparqlwrapper>=2.0.0",
+    "validators>=0.20.0",
+    "deprecation>=2.1.0",
+    "pyyaml>=6.0.1",
+    "rdflib>=7.1.3",
+]
+
+# see https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#dependencies-optional-dependencies
+[project.optional-dependencies]
+networkx = [
+    "networkx>=3.1",
+]
+pansql = [
+    "pansql>=0.0.1",
+]
+scipy = [
+    "scipy",
+]
+docs = [
+    "mkdocs-material>=9.5.0",
+    "mkdocstrings[python]>=0.24.0",
+    "mkdocs-click>=0.8.1",
+]
+rdflib-endpoint = [
+    "uvicorn",
+    "fastapi",
+    "rdflib-endpoint",
+    "httpx",  # only used in tests, but this is small
+]
+
+[project.scripts]
+sssom = "sssom.cli:main"
+
+[tool.poetry.group.dev.dependencies]
+pytest = {version = ">=7.1.2"}
+tox = {version = ">=3.25.1"}
+
+[tool.poetry-dynamic-versioning]
+enable = false
+vcs = "git"
+style = "pep440"
+
+[tool.black]
+line-length = 100
+target-version = ["py310", "py311", "py312", "py313"]
+
+[[tool.mypy.overrides]]
+ module = [
+     'sssom.cliquesummary'
+ ]
+ ignore_errors = true
+    
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+line_length = 100
+include_trailing_comma = true
+reverse_relative = true
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"

sssom-0.0.0/src/sssom/__init__.py

@@ -0,0 +1,51 @@
+"""sssom-py package."""
+
+import importlib.metadata
+
+try:
+    __version__ = importlib.metadata.version(__name__)
+except importlib.metadata.PackageNotFoundError:
+    # package is not installed
+    __version__ = "0.0.0"  # pragma: no cover
+
+from sssom_schema import Mapping, MappingSet, slots
+
+from sssom.io import get_metadata_and_prefix_map
+from sssom.sssom_document import MappingSetDocument
+from sssom.util import (
+    MappingSetDataFrame,
+    collapse,
+    compare_dataframes,
+    dataframe_to_ptable,
+    filter_redundant_rows,
+    group_mappings,
+    reconcile_prefix_and_data,
+)
+
+from .constants import generate_mapping_set_id, get_default_metadata
+from .parsers import parse_csv, parse_sssom_table, parse_tsv
+from .writers import write_json, write_owl, write_rdf, write_tsv
+
+__all__ = [
+    "write_json",
+    "write_owl",
+    "write_rdf",
+    "write_tsv",
+    "parse_csv",
+    "generate_mapping_set_id",
+    "get_default_metadata",
+    "parse_sssom_table",
+    "parse_tsv",
+    "Mapping",
+    "MappingSet",
+    "MappingSetDocument",
+    "MappingSetDataFrame",
+    "slots",
+    "get_metadata_and_prefix_map",
+    "collapse",
+    "compare_dataframes",
+    "dataframe_to_ptable",
+    "filter_redundant_rows",
+    "group_mappings",
+    "reconcile_prefix_and_data",
+]