.cz.toml
.gitignore
.pre-commit-config.yaml
.pypirc
CHANGELOG.md
LICENSE
README.md
poetry.lock
pyproject.toml
requirements.txt
.vscode/settings.json
docs/README.md
docs/book/01_installation.md
docs/book/02_usage.md
docs/book/03_project_structure.md
docs/book/04_data_modelling.md
docs/drawio/connection-information-diagram-Cermangicola-color.png
docs/drawio/connection-information-diagram-Cermangicola.drawio
docs/manuscript/README.md
docs/manuscript/example-data/bipolaris-gophy.tsv
docs/manuscript/example-data/phaeosphaeriaceae.tsv
docs/manuscript/intermediary-files/reference_data.json
docs/manuscript/supplementary-material/ceratosystis-mangicola-connection.ods
docs/manuscript/supplementary-material/gcon-input-gophy.xlsx
docs/manuscript/supplementary-material/gophy-2023-05-06.tsv
docs/manuscript/supplementary-material/gophy-2023-05-06.xlsx
docs/manuscript/supplementary-material/gcon-output/finished-collect-metadata.lock
docs/manuscript/supplementary-material/gcon-output/out.json
docs/manuscript/supplementary-material/gcon-output/out.tsv
docs/manuscript/supplementary-material/gcon-output/reference_data.json
docs/manuscript/tables/metadata-classifiers.ods
docs/manuscript/tables/score-computation.ods
docs/preamble/ACKNOWLEDGEMENTS.md
docs/preamble/CODE_OF_CONDUCT.md
docs/preamble/CONTRIBUTING.md
docs/preamble/CREDITS.md
src/gcon/__main__.py
src/gcon/__version__.py
src/gcon/settings.py
src/gcon/adapters/__init__.py
src/gcon/adapters/pickledb/__init__.py
src/gcon/adapters/pickledb/repositories/__init__.py
src/gcon/adapters/pickledb/repositories/connector.py
src/gcon/adapters/pickledb/repositories/node_fetching.py
src/gcon/adapters/pickledb/repositories/node_registration.py
src/gcon/core/__init__.py
src/gcon/core/domain/__init__.py
src/gcon/core/domain/dtos/__init__.py
src/gcon/core/domain/dtos/connection.py
src/gcon/core/domain/dtos/metadata.py
src/gcon/core/domain/dtos/node.py
src/gcon/core/domain/dtos/score.py
src/gcon/core/domain/dtos/reference_data/__init__.py
src/gcon/core/domain/dtos/reference_data/schemas.py
src/gcon/core/domain/dtos/tests/__init__.py
src/gcon/core/domain/dtos/tests/test_metadata.py
src/gcon/core/domain/dtos/tests/test_reference_data.py
src/gcon/core/domain/dtos/tests/test_schemas.py
src/gcon/core/domain/entities/__init__.py
src/gcon/core/domain/entities/node_fetching.py
src/gcon/core/domain/entities/node_registration.py
src/gcon/core/use_cases/README.md
src/gcon/core/use_cases/__init__.py
src/gcon/core/use_cases/build_metadata_match_scores/__init__.py
src/gcon/core/use_cases/build_metadata_match_scores/_calculate_connection_match_score.py
src/gcon/core/use_cases/build_metadata_match_scores/_calculate_connection_observed_score.py
src/gcon/core/use_cases/collect_metadata/__init__.py
src/gcon/core/use_cases/collect_metadata/_chunks_accessions.py
src/gcon/core/use_cases/collect_metadata/_collect_single_gene_metadata.py
src/gcon/core/use_cases/collect_metadata/_collect_unique_identifiers.py
src/gcon/core/use_cases/collect_metadata/_place_qualifiers.py
src/gcon/core/use_cases/load_and_validate_source_table/__init__.py
src/gcon/core/use_cases/load_and_validate_source_table/_dtos.py
src/gcon/core/use_cases/load_and_validate_source_table/_validate_genes_fields.py
src/gcon/core/use_cases/load_and_validate_source_table/_validate_optional_fields.py
src/gcon/core/use_cases/load_and_validate_source_table/_validate_required_fields.py
src/gcon/core/use_cases/persist_metadata_on_gc_server/__init__.py
src/gcon/core/use_cases/tests/__init__.py
src/gcon/core/use_cases/tests/test_build_metadata_match_scores.py
src/gcon/core/use_cases/tests/test_collect_metadata.py
src/gcon/core/use_cases/tests/test_load_and_validate_source_table.py
src/gcon/ports/__init__.py
src/gcon/ports/cli/__init__.py
src/gcon/ports/cli/main.py
src/gene_connector_cli.egg-info/PKG-INFO
src/gene_connector_cli.egg-info/SOURCES.txt
src/gene_connector_cli.egg-info/dependency_links.txt
src/gene_connector_cli.egg-info/entry_points.txt
src/gene_connector_cli.egg-info/requires.txt
src/gene_connector_cli.egg-info/top_level.txt
src/tests/mock/bipolaris-invalid.tsv
src/tests/mock/bipolaris-valid.tsv
src/tests/mock/ceratocystis-valid.tsv
src/tests/mock/reference_data.json