hca-schema-validator 0.2.0__py3-none-any.whl

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Files changed (55) hide show
  1. hca_schema_validator/__init__.py +11 -0
  2. hca_schema_validator/_vendored/__init__.py +18 -0
  3. hca_schema_validator/_vendored/cellxgene_schema/LICENSE +20 -0
  4. hca_schema_validator/_vendored/cellxgene_schema/__init__.py +1 -0
  5. hca_schema_validator/_vendored/cellxgene_schema/atac_seq.py +675 -0
  6. hca_schema_validator/_vendored/cellxgene_schema/cli.py +206 -0
  7. hca_schema_validator/_vendored/cellxgene_schema/env.py +9 -0
  8. hca_schema_validator/_vendored/cellxgene_schema/gencode.py +163 -0
  9. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/.gitignore +3 -0
  10. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/drosophila_melanogaster_diff.txt +42 -0
  11. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/gene_info.md +29 -0
  12. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/gene_info.yml +51 -0
  13. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_caenorhabditis_elegans.csv.gz +0 -0
  14. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_callithrix_jacchus.csv.gz +0 -0
  15. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_danio_rerio.csv.gz +0 -0
  16. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_drosophila_melanogaster.csv.gz +0 -0
  17. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_ercc.csv.gz +0 -0
  18. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_gorilla_gorilla.csv.gz +0 -0
  19. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_homo_sapiens.csv.gz +0 -0
  20. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_macaca_fascicularis.csv.gz +0 -0
  21. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_macaca_mulatta.csv.gz +0 -0
  22. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_microcebus_murinus.csv.gz +0 -0
  23. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_mus_musculus.csv.gz +0 -0
  24. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_oryctolagus_cuniculus.csv.gz +0 -0
  25. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_pan_troglodytes.csv.gz +0 -0
  26. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_rattus_norvegicus.csv.gz +0 -0
  27. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_sars_cov_2.csv.gz +0 -0
  28. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/genes_sus_scrofa.csv.gz +0 -0
  29. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/homo_sapiens_diff.txt +1237 -0
  30. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/mus_musculus_diff.txt +549 -0
  31. hca_schema_validator/_vendored/cellxgene_schema/gencode_files/rattus_norvegicus_diff.txt +7306 -0
  32. hca_schema_validator/_vendored/cellxgene_schema/map_species.py +40 -0
  33. hca_schema_validator/_vendored/cellxgene_schema/matrix_utils.py +134 -0
  34. hca_schema_validator/_vendored/cellxgene_schema/migrate.py +145 -0
  35. hca_schema_validator/_vendored/cellxgene_schema/migrate_files/automigrate_terms.json +2 -0
  36. hca_schema_validator/_vendored/cellxgene_schema/migrate_files/donor_updates.json +2 -0
  37. hca_schema_validator/_vendored/cellxgene_schema/migrate_files/non_csr_list.txt +54 -0
  38. hca_schema_validator/_vendored/cellxgene_schema/migrate_files/private_non_csr.json +1 -0
  39. hca_schema_validator/_vendored/cellxgene_schema/migrate_files/title_donor_updates.json +2 -0
  40. hca_schema_validator/_vendored/cellxgene_schema/ontology_files/.gitignore +1 -0
  41. hca_schema_validator/_vendored/cellxgene_schema/ontology_parser.py +3 -0
  42. hca_schema_validator/_vendored/cellxgene_schema/remove_labels.py +74 -0
  43. hca_schema_validator/_vendored/cellxgene_schema/schema.py +21 -0
  44. hca_schema_validator/_vendored/cellxgene_schema/schema_definitions/schema_definition.yaml +841 -0
  45. hca_schema_validator/_vendored/cellxgene_schema/utils.py +242 -0
  46. hca_schema_validator/_vendored/cellxgene_schema/validate.py +2389 -0
  47. hca_schema_validator/_vendored/cellxgene_schema/validation_internals/__init__.py +0 -0
  48. hca_schema_validator/_vendored/cellxgene_schema/validation_internals/check_duplicates.py +87 -0
  49. hca_schema_validator/_vendored/cellxgene_schema/write_labels.py +403 -0
  50. hca_schema_validator/schema_definitions/hca_schema_definition.yaml +839 -0
  51. hca_schema_validator/validator.py +47 -0
  52. hca_schema_validator-0.2.0.dist-info/METADATA +116 -0
  53. hca_schema_validator-0.2.0.dist-info/RECORD +55 -0
  54. hca_schema_validator-0.2.0.dist-info/WHEEL +4 -0
  55. hca_schema_validator-0.2.0.dist-info/licenses/NOTICE +15 -0
@@ -0,0 +1,11 @@
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+ """HCA Schema Validator - HCA-specific extensions for cellxgene schema validation."""
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+
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+ # Define constants first (before importing validator to avoid circular import)
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+ __version__ = "0.2.0"
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+ __schema_version__ = "1.0.0" # HCA schema version (independent from CELLxGENE)
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+ __schema_reference_url__ = "https://data.humancellatlas.org/metadata" # Static URL, no version in path
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+
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+ # Import after constants are defined
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+ from .validator import HCAValidator
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+
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+ __all__ = ["HCAValidator"]
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+ """
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+ Vendored dependencies for hca-schema-validator.
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+
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+ This directory contains vendored copies of third-party code that has been
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+ modified for HCA-specific use.
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+
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+ Vendored packages:
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+ - cellxgene_schema: Modified version of cellxgene-schema
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+ Original: https://github.com/chanzuckerberg/single-cell-curation
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+ Copyright (c) 2020-Present Chan Zuckerberg Initiative
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+ License: MIT (see cellxgene_schema/LICENSE)
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+
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+ This code has been vendored and modified to support HCA-specific validation
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+ requirements. All modifications are also licensed under MIT.
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+
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+ The vendored code is maintained as part of this package and does not require
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+ external updates.
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+ """
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2020-Present Chan Zuckerberg Initiative
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy of
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+ this software and associated documentation files (the "Software"), to deal in
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+ the Software without restriction, including without limitation the rights to
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+ use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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+ the Software, and to permit persons to whom the Software is furnished to do so,
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+ subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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+ FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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+ COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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+ IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -0,0 +1 @@
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+ __schema_version__ = "7.0.0"