@pikaa-ai/pikaa 0.3.1 → 0.3.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cli.js +1169 -601
- package/dist/index.js +525 -204
- package/package.json +5 -3
- package/skills/adaptyv/references/api-endpoints.md +0 -690
- package/skills/aeon/references/anomaly_detection.md +0 -154
- package/skills/aeon/references/classification.md +0 -144
- package/skills/aeon/references/clustering.md +0 -123
- package/skills/aeon/references/datasets_benchmarking.md +0 -392
- package/skills/aeon/references/distances.md +0 -256
- package/skills/aeon/references/forecasting.md +0 -109
- package/skills/aeon/references/networks.md +0 -289
- package/skills/aeon/references/regression.md +0 -118
- package/skills/aeon/references/segmentation.md +0 -163
- package/skills/aeon/references/similarity_search.md +0 -187
- package/skills/aeon/references/transformations.md +0 -246
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
- package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
- package/skills/analytical-method-validation/references/framework-selection.md +0 -87
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
- package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
- package/skills/analytical-method-validation/references/source-ledger.md +0 -125
- package/skills/analytical-method-validation/references/statistics.md +0 -209
- package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
- package/skills/analytical-method-validation/scripts/_common.py +0 -955
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
- package/skills/analytical-method-validation/scripts/check_response.py +0 -243
- package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
- package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
- package/skills/anndata/references/best_practices.md +0 -532
- package/skills/anndata/references/concatenation.md +0 -399
- package/skills/anndata/references/data_structure.md +0 -314
- package/skills/anndata/references/io_operations.md +0 -466
- package/skills/anndata/references/manipulation.md +0 -516
- package/skills/arbor/references/arbor-upstream.md +0 -91
- package/skills/arbor/references/executor-brief.md +0 -68
- package/skills/arbor/references/htr-methodology.md +0 -177
- package/skills/arbor/references/report-template.md +0 -39
- package/skills/arbor/scripts/tree.py +0 -564
- package/skills/arboreto/references/algorithms.md +0 -152
- package/skills/arboreto/references/basic_inference.md +0 -181
- package/skills/arboreto/references/distributed_computing.md +0 -242
- package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
- package/skills/astropy/references/coordinates.md +0 -280
- package/skills/astropy/references/cosmology.md +0 -309
- package/skills/astropy/references/fits.md +0 -398
- package/skills/astropy/references/tables.md +0 -495
- package/skills/astropy/references/time.md +0 -412
- package/skills/astropy/references/units.md +0 -178
- package/skills/astropy/references/wcs_and_other_modules.md +0 -377
- package/skills/autoskill/config.yaml +0 -53
- package/skills/autoskill/references/https-proxy.md +0 -62
- package/skills/autoskill/references/screenpipe-config.yaml +0 -61
- package/skills/autoskill/scripts/autoskill.py +0 -35
- package/skills/autoskill/scripts/backends.py +0 -116
- package/skills/autoskill/scripts/cluster.py +0 -54
- package/skills/autoskill/scripts/doctor.py +0 -108
- package/skills/autoskill/scripts/fetch_window.py +0 -33
- package/skills/autoskill/scripts/match_skills.py +0 -46
- package/skills/autoskill/scripts/promote.py +0 -58
- package/skills/autoskill/scripts/redact.py +0 -40
- package/skills/autoskill/scripts/run.py +0 -194
- package/skills/autoskill/scripts/synthesize.py +0 -72
- package/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/skills/benchling-integration/references/authentication.md +0 -390
- package/skills/benchling-integration/references/core_capabilities.md +0 -355
- package/skills/benchling-integration/references/eventbridge.md +0 -255
- package/skills/benchling-integration/references/sdk_reference.md +0 -772
- package/skills/bids/references/beps.yml +0 -637
- package/skills/bids/references/bids_schema.json +0 -21015
- package/skills/bids/references/bids_specification.md +0 -165
- package/skills/bids/references/conversion_tools.md +0 -475
- package/skills/bids/references/core_workflows.md +0 -552
- package/skills/bids/references/metadata_fields.md +0 -365
- package/skills/bids/scripts/update_schema.py +0 -89
- package/skills/biopython/references/advanced.md +0 -580
- package/skills/biopython/references/alignment.md +0 -377
- package/skills/biopython/references/blast.md +0 -463
- package/skills/biopython/references/databases.md +0 -492
- package/skills/biopython/references/phylogenetics.md +0 -566
- package/skills/biopython/references/sequence_io.md +0 -289
- package/skills/biopython/references/structure.md +0 -564
- package/skills/bioservices/references/identifier_mapping.md +0 -685
- package/skills/bioservices/references/services_reference.md +0 -638
- package/skills/bioservices/references/workflow_patterns.md +0 -813
- package/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
- package/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
- package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
- package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
- package/skills/cellxgene-census/references/census_schema.md +0 -218
- package/skills/cellxgene-census/references/common_patterns.md +0 -368
- package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
- package/skills/cirq/references/building.md +0 -307
- package/skills/cirq/references/experiments.md +0 -572
- package/skills/cirq/references/hardware.md +0 -527
- package/skills/cirq/references/noise.md +0 -514
- package/skills/cirq/references/simulation.md +0 -353
- package/skills/cirq/references/transformation.md +0 -416
- package/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/skills/citation-management/assets/citation_checklist.md +0 -386
- package/skills/citation-management/references/best_practices.md +0 -91
- package/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/skills/citation-management/references/citation_validation.md +0 -835
- package/skills/citation-management/references/core_workflow.md +0 -569
- package/skills/citation-management/references/example_workflows.md +0 -126
- package/skills/citation-management/references/google_scholar_search.md +0 -732
- package/skills/citation-management/references/metadata_extraction.md +0 -870
- package/skills/citation-management/references/pubmed_search.md +0 -839
- package/skills/citation-management/references/script_reference.md +0 -250
- package/skills/citation-management/references/search_strategies.md +0 -110
- package/skills/citation-management/scripts/_common.py +0 -331
- package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
- package/skills/citation-management/scripts/extract_metadata.py +0 -690
- package/skills/citation-management/scripts/format_bibtex.py +0 -356
- package/skills/citation-management/scripts/search_google_scholar.py +0 -268
- package/skills/citation-management/scripts/search_openalex.py +0 -297
- package/skills/citation-management/scripts/search_pubmed.py +0 -419
- package/skills/citation-management/scripts/validate_citations.py +0 -688
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
- package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
- package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
- package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
- package/skills/clinical-decision-support/references/security_validation.md +0 -60
- package/skills/clinical-decision-support/references/sources.md +0 -119
- package/skills/clinical-decision-support/references/study_reporting.md +0 -134
- package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
- package/skills/clinical-decision-support/scripts/_common.py +0 -223
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
- package/skills/clinical-reports/assets/case_report_template.json +0 -43
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
- package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
- package/skills/clinical-reports/assets/lab_report_template.json +0 -36
- package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
- package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
- package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
- package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
- package/skills/clinical-reports/assets/research_summary_template.json +0 -36
- package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
- package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
- package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
- package/skills/clinical-reports/references/data_presentation.md +0 -92
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
- package/skills/clinical-reports/references/medical_terminology.md +0 -84
- package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
- package/skills/clinical-reports/references/professional_review.md +0 -78
- package/skills/clinical-reports/references/report_type_routing.md +0 -57
- package/skills/clinical-reports/references/safety_reporting.md +0 -109
- package/skills/clinical-reports/references/sources.md +0 -75
- package/skills/clinical-reports/scripts/_common.py +0 -263
- package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
- package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
- package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
- package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
- package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
- package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
- package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
- package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
- package/skills/cobrapy/references/api_quick_reference.md +0 -665
- package/skills/cobrapy/references/workflows.md +0 -600
- package/skills/consciousness-council/references/advanced-configurations.md +0 -96
- package/skills/dask/references/arrays.md +0 -495
- package/skills/dask/references/bags.md +0 -468
- package/skills/dask/references/best-practices.md +0 -277
- package/skills/dask/references/dataframes.md +0 -370
- package/skills/dask/references/futures.md +0 -541
- package/skills/dask/references/schedulers.md +0 -517
- package/skills/database-lookup/references/addgene.md +0 -38
- package/skills/database-lookup/references/alphafold.md +0 -52
- package/skills/database-lookup/references/alphavantage.md +0 -261
- package/skills/database-lookup/references/bea.md +0 -409
- package/skills/database-lookup/references/bindingdb.md +0 -85
- package/skills/database-lookup/references/biogrid.md +0 -110
- package/skills/database-lookup/references/bls.md +0 -235
- package/skills/database-lookup/references/brenda.md +0 -71
- package/skills/database-lookup/references/cbioportal.md +0 -206
- package/skills/database-lookup/references/census.md +0 -251
- package/skills/database-lookup/references/chebi.md +0 -103
- package/skills/database-lookup/references/chembl.md +0 -80
- package/skills/database-lookup/references/clinicaltrials.md +0 -86
- package/skills/database-lookup/references/clinpgx.md +0 -64
- package/skills/database-lookup/references/clinvar.md +0 -91
- package/skills/database-lookup/references/cod.md +0 -121
- package/skills/database-lookup/references/cosmic.md +0 -59
- package/skills/database-lookup/references/dailymed.md +0 -65
- package/skills/database-lookup/references/database_selection_guide.md +0 -166
- package/skills/database-lookup/references/datacommons.md +0 -237
- package/skills/database-lookup/references/dbsnp.md +0 -143
- package/skills/database-lookup/references/disgenet.md +0 -52
- package/skills/database-lookup/references/drugbank.md +0 -54
- package/skills/database-lookup/references/ecb.md +0 -191
- package/skills/database-lookup/references/emdb.md +0 -37
- package/skills/database-lookup/references/ena.md +0 -372
- package/skills/database-lookup/references/encode.md +0 -47
- package/skills/database-lookup/references/ensembl.md +0 -539
- package/skills/database-lookup/references/epa.md +0 -232
- package/skills/database-lookup/references/eurostat.md +0 -237
- package/skills/database-lookup/references/fda.md +0 -64
- package/skills/database-lookup/references/federal-reserve.md +0 -216
- package/skills/database-lookup/references/fred.md +0 -297
- package/skills/database-lookup/references/gene-ontology.md +0 -147
- package/skills/database-lookup/references/geo.md +0 -130
- package/skills/database-lookup/references/gnomad.md +0 -93
- package/skills/database-lookup/references/gtex.md +0 -136
- package/skills/database-lookup/references/gwas-catalog.md +0 -46
- package/skills/database-lookup/references/hca.md +0 -35
- package/skills/database-lookup/references/hpo.md +0 -48
- package/skills/database-lookup/references/human-protein-atlas.md +0 -57
- package/skills/database-lookup/references/interpro.md +0 -120
- package/skills/database-lookup/references/jaspar.md +0 -50
- package/skills/database-lookup/references/kegg.md +0 -78
- package/skills/database-lookup/references/lincs-l1000.md +0 -68
- package/skills/database-lookup/references/materials-project.md +0 -123
- package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
- package/skills/database-lookup/references/monarch.md +0 -46
- package/skills/database-lookup/references/mousemine.md +0 -40
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
- package/skills/database-lookup/references/nasa.md +0 -121
- package/skills/database-lookup/references/ncbi-gene.md +0 -64
- package/skills/database-lookup/references/ncbi-protein.md +0 -104
- package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
- package/skills/database-lookup/references/nist.md +0 -105
- package/skills/database-lookup/references/noaa.md +0 -199
- package/skills/database-lookup/references/omim.md +0 -114
- package/skills/database-lookup/references/opentargets.md +0 -459
- package/skills/database-lookup/references/openweathermap.md +0 -255
- package/skills/database-lookup/references/pdb.md +0 -121
- package/skills/database-lookup/references/pride.md +0 -74
- package/skills/database-lookup/references/pubchem.md +0 -145
- package/skills/database-lookup/references/quickgo.md +0 -45
- package/skills/database-lookup/references/reactome.md +0 -140
- package/skills/database-lookup/references/retrieval-contract.md +0 -123
- package/skills/database-lookup/references/rummageo.md +0 -32
- package/skills/database-lookup/references/sdss.md +0 -130
- package/skills/database-lookup/references/sec-edgar.md +0 -315
- package/skills/database-lookup/references/simbad.md +0 -405
- package/skills/database-lookup/references/sra.md +0 -149
- package/skills/database-lookup/references/string.md +0 -283
- package/skills/database-lookup/references/tcga-gdc.md +0 -58
- package/skills/database-lookup/references/treasury.md +0 -215
- package/skills/database-lookup/references/ucsc-genome.md +0 -135
- package/skills/database-lookup/references/uniprot.md +0 -283
- package/skills/database-lookup/references/usgs.md +0 -260
- package/skills/database-lookup/references/uspto.md +0 -130
- package/skills/database-lookup/references/who.md +0 -283
- package/skills/database-lookup/references/worldbank.md +0 -239
- package/skills/database-lookup/references/zinc.md +0 -202
- package/skills/datamol/references/conformers_module.md +0 -131
- package/skills/datamol/references/core_api.md +0 -136
- package/skills/datamol/references/core_workflows.md +0 -451
- package/skills/datamol/references/descriptors_viz.md +0 -195
- package/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/skills/datamol/references/io_module.md +0 -112
- package/skills/datamol/references/reactions_data.md +0 -218
- package/skills/datamol/references/workflow_patterns.md +0 -104
- package/skills/deepchem/references/api_reference.md +0 -305
- package/skills/deepchem/references/core_capabilities.md +0 -276
- package/skills/deepchem/references/typical_workflows.md +0 -109
- package/skills/deepchem/references/workflows.md +0 -491
- package/skills/deepchem/scripts/graph_neural_network.py +0 -350
- package/skills/deepchem/scripts/predict_solubility.py +0 -223
- package/skills/deepchem/scripts/transfer_learning.py +0 -443
- package/skills/deepspot-m/references/api.md +0 -186
- package/skills/deepspot-m/references/whole_slide.md +0 -174
- package/skills/deeptools/assets/quick_reference.md +0 -65
- package/skills/deeptools/references/core_workflows.md +0 -134
- package/skills/deeptools/references/effective_genome_sizes.md +0 -118
- package/skills/deeptools/references/normalization_methods.md +0 -424
- package/skills/deeptools/references/tools_reference.md +0 -569
- package/skills/deeptools/references/workflows.md +0 -476
- package/skills/deeptools/scripts/validate_files.py +0 -195
- package/skills/deeptools/scripts/workflow_generator.py +0 -520
- package/skills/depmap/references/dependency_analysis.md +0 -178
- package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
- package/skills/diffdock/assets/batch_template.csv +0 -4
- package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
- package/skills/diffdock/references/confidence_and_limitations.md +0 -182
- package/skills/diffdock/references/parameters_reference.md +0 -173
- package/skills/diffdock/references/workflows_examples.md +0 -401
- package/skills/diffdock/scripts/analyze_results.py +0 -346
- package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
- package/skills/diffdock/scripts/setup_check.py +0 -283
- package/skills/dnanexus-integration/references/app-development.md +0 -371
- package/skills/dnanexus-integration/references/authentication.md +0 -226
- package/skills/dnanexus-integration/references/configuration.md +0 -444
- package/skills/dnanexus-integration/references/data-operations.md +0 -474
- package/skills/dnanexus-integration/references/job-execution.md +0 -482
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
- package/skills/dnanexus-integration/references/python-sdk.md +0 -548
- package/skills/dnanexus-integration/references/sources.md +0 -168
- package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
- package/skills/docx/LICENSE.txt +0 -30
- package/skills/docx/scripts/__init__.py +0 -1
- package/skills/docx/scripts/accept_changes.py +0 -135
- package/skills/docx/scripts/comment.py +0 -368
- package/skills/docx/scripts/merge_runs.py +0 -310
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- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/xlsx/scripts/office/soffice.py +0 -232
- package/skills/xlsx/scripts/office/validate.py +0 -173
- package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
- package/skills/xlsx/scripts/office/validators/base.py +0 -875
- package/skills/xlsx/scripts/office/validators/docx.py +0 -466
- package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
- package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
- package/skills/xlsx/scripts/recalc.py +0 -308
- package/skills/zarr-python/references/api_reference.md +0 -162
- package/skills/zarr-python/references/chunking_and_compression.md +0 -138
- package/skills/zarr-python/references/integration.md +0 -147
- package/skills/zarr-python/references/performance_and_patterns.md +0 -198
- package/skills/zarr-python/references/storage_backends.md +0 -91
- package/skills/zarr-python/references/v3_migration.md +0 -127
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#!/usr/bin/env python3
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"""Bounded, dependency-free helpers for local scholar-evaluation records."""
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from __future__ import annotations
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import json
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import math
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import re
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from dataclasses import dataclass
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from datetime import date
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from pathlib import Path
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from typing import Any, Iterable
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SCHEMA_VERSION = "2.0"
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NOTICE = (
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"DESCRIPTIVE DEVELOPMENTAL ASSESSMENT ONLY — NOT A DECISION "
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"RECOMMENDATION — QUALIFIED HUMAN REVIEW REQUIRED"
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)
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PROHIBITED_USES = {
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"admissions",
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"awards",
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"discipline",
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"funding",
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"hiring",
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"promotion",
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"tenure",
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"other_high_impact_personnel_decision",
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}
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ALLOWED_PURPOSE = "developmental_review_of_scholarly_work"
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ALLOWED_UNIT = "scholarly_work"
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ALLOWED_CLASSIFICATIONS = {
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"synthetic",
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"public_scholarly_work",
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"deidentified_low_stakes",
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}
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RATING_STATUSES = {"rated", "missing", "not_applicable"}
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MAX_INPUT_BYTES = 2 * 1024 * 1024
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MAX_OUTPUT_BYTES = 2 * 1024 * 1024
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MAX_TEXT_CHARS = 4_000
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MAX_LIST_ITEMS = 1_000
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MAX_OBJECT_FIELDS = 100
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MAX_DEPTH = 20
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MAX_TOTAL_NODES = 25_000
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MAX_CRITERIA = 50
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MAX_EVALUATIONS = 50
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MAX_CSV_ROWS = 20_000
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IDENTIFIER_RE = re.compile(r"^[A-Za-z][A-Za-z0-9._:-]{1,95}$")
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PRIVATE_FIELD_KEYS = {
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"applicant_name",
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"application_text",
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"candidate_name",
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"cv_text",
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"date_of_birth",
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"dob",
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"document_text",
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"email",
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"full_name",
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"home_address",
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"person_name",
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"phone",
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"private_application",
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"raw_application",
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"resume_text",
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"social_security_number",
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"ssn",
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}
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PROXY_TERMS = (
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"journal impact factor",
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"impact factor",
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"h-index",
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"h index",
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"citation count",
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"altmetric",
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"conference ranking",
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"journal ranking",
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"institution prestige",
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"journal prestige",
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"venue prestige",
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"university ranking",
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)
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class ValidationError(ValueError):
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"""A deterministic input failure that never includes a supplied value."""
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def __init__(self, code: str, path: str = "$") -> None:
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super().__init__(code)
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self.code = code
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self.path = path
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@dataclass(frozen=True)
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class Issue:
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"""A minimized validation issue."""
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code: str
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path: str
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level: str = "error"
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def as_dict(self) -> dict[str, str]:
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return {"code": self.code, "path": self.path, "level": self.level}
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def _pairs_no_duplicates(pairs: list[tuple[str, Any]]) -> dict[str, Any]:
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result: dict[str, Any] = {}
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for key, value in pairs:
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if key in result:
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raise ValidationError("JSON_DUPLICATE_KEY")
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result[key] = value
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return result
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def _check_local_file(path: Path, suffix: str) -> None:
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if path.suffix.lower() != suffix:
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raise ValidationError("INPUT_SUFFIX_NOT_ALLOWED")
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if not path.exists():
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raise ValidationError("INPUT_NOT_FOUND")
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if path.is_symlink():
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raise ValidationError("INPUT_SYMLINK_NOT_ALLOWED")
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if not path.is_file():
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raise ValidationError("INPUT_NOT_REGULAR_FILE")
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if path.stat().st_size > MAX_INPUT_BYTES:
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raise ValidationError("INPUT_TOO_LARGE")
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def _scan_structure(value: Any, path: str = "$") -> None:
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nodes = 0
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stack: list[tuple[Any, str, int]] = [(value, path, 0)]
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while stack:
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current, current_path, depth = stack.pop()
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nodes += 1
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if nodes > MAX_TOTAL_NODES:
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raise ValidationError("STRUCTURE_TOO_LARGE", current_path)
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if depth > MAX_DEPTH:
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raise ValidationError("STRUCTURE_TOO_DEEP", current_path)
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if isinstance(current, dict):
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if len(current) > MAX_OBJECT_FIELDS:
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raise ValidationError("OBJECT_TOO_LARGE", current_path)
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for key, child in current.items():
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if not isinstance(key, str):
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raise ValidationError("OBJECT_KEY_NOT_TEXT", current_path)
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normalized = key.strip().lower()
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if normalized in PRIVATE_FIELD_KEYS:
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raise ValidationError("PRIVATE_FIELD_NOT_ALLOWED", f"{current_path}.{key}")
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stack.append((child, f"{current_path}.{key}", depth + 1))
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elif isinstance(current, list):
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if len(current) > MAX_LIST_ITEMS:
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raise ValidationError("LIST_TOO_LARGE", current_path)
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for index, child in enumerate(current):
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stack.append((child, f"{current_path}[{index}]", depth + 1))
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elif isinstance(current, str) and len(current) > MAX_TEXT_CHARS:
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raise ValidationError("TEXT_TOO_LONG", current_path)
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elif current is not None and not isinstance(
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current, (str, int, float, bool)
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):
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raise ValidationError("VALUE_TYPE_NOT_ALLOWED", current_path)
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if isinstance(current, float) and not math.isfinite(current):
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raise ValidationError("NUMBER_NOT_FINITE", current_path)
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def read_json(path: Path | str) -> Any:
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"""Read bounded JSON with duplicate-key and private-field rejection."""
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local_path = Path(path)
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_check_local_file(local_path, ".json")
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try:
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data = json.loads(
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local_path.read_text(encoding="utf-8"),
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object_pairs_hook=_pairs_no_duplicates,
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)
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except UnicodeDecodeError as error:
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raise ValidationError("INPUT_NOT_UTF8") from error
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except json.JSONDecodeError as error:
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raise ValidationError("JSON_INVALID") from error
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_scan_structure(data)
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return data
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def read_csv_text(path: Path | str) -> str:
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"""Read a bounded UTF-8 CSV file after local-path checks."""
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local_path = Path(path)
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_check_local_file(local_path, ".csv")
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try:
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return local_path.read_text(encoding="utf-8-sig")
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except UnicodeDecodeError as error:
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raise ValidationError("INPUT_NOT_UTF8") from error
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def write_json(
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value: dict[str, Any], output: Path | None, *, force: bool = False
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) -> None:
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"""Write deterministic JSON locally or print it to standard output."""
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rendered = json.dumps(value, indent=2, sort_keys=True, ensure_ascii=False) + "\n"
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if len(rendered.encode("utf-8")) > MAX_OUTPUT_BYTES:
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raise ValidationError("OUTPUT_TOO_LARGE")
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if output is None:
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print(rendered, end="")
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return
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if output.suffix.lower() != ".json":
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raise ValidationError("OUTPUT_SUFFIX_NOT_ALLOWED")
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if output.is_symlink():
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raise ValidationError("OUTPUT_SYMLINK_NOT_ALLOWED")
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if output.exists() and not force:
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raise ValidationError("OUTPUT_EXISTS")
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if not output.parent.exists() or not output.parent.is_dir():
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raise ValidationError("OUTPUT_PARENT_NOT_FOUND")
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output.write_text(rendered, encoding="utf-8")
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def failure_report(error: ValidationError) -> dict[str, Any]:
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return {
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"schema_version": SCHEMA_VERSION,
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"status": "error",
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"issues": [Issue(error.code, error.path).as_dict()],
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}
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def is_number(value: Any) -> bool:
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return isinstance(value, (int, float)) and not isinstance(value, bool)
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def is_identifier(value: Any) -> bool:
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return isinstance(value, str) and bool(IDENTIFIER_RE.fullmatch(value))
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def is_nonempty_text(value: Any, maximum: int = MAX_TEXT_CHARS) -> bool:
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return isinstance(value, str) and bool(value.strip()) and len(value) <= maximum
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def is_reference(value: Any) -> bool:
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if not is_nonempty_text(value, 500):
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return False
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lowered = value.strip().lower()
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return not (
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lowered.startswith(("http://", "https://", "file://"))
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or "\n" in value
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or "\r" in value
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)
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def is_date(value: Any) -> bool:
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if not isinstance(value, str):
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return False
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try:
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date.fromisoformat(value)
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except ValueError:
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return False
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return len(value) == 10
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def exact_keys(
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value: Any,
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expected: Iterable[str],
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path: str,
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issues: list[Issue],
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) -> bool:
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if not isinstance(value, dict):
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issues.append(Issue("SCHEMA_OBJECT_REQUIRED", path))
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return False
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expected_set = set(expected)
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actual_set = set(value)
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for missing in sorted(expected_set - actual_set):
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issues.append(Issue("SCHEMA_REQUIRED_FIELD", f"{path}.{missing}"))
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for unknown in sorted(actual_set - expected_set):
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issues.append(Issue("SCHEMA_UNKNOWN_FIELD", f"{path}.{unknown}"))
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return not (expected_set - actual_set)
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def validate_identifier(
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value: Any, path: str, issues: list[Issue], code: str = "IDENTIFIER_INVALID"
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) -> None:
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if not is_identifier(value):
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issues.append(Issue(code, path))
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def validate_reference(
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value: Any, path: str, issues: list[Issue], *, allow_empty: bool = False
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) -> None:
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if allow_empty and value == "":
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return
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if not is_reference(value):
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issues.append(Issue("LOCAL_REFERENCE_INVALID", path))
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def validate_text(
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value: Any, path: str, issues: list[Issue], *, allow_empty: bool = False
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) -> None:
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if allow_empty and value == "":
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return
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if not is_nonempty_text(value):
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issues.append(Issue("TEXT_INVALID", path))
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def validate_bool(value: Any, path: str, issues: list[Issue]) -> None:
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if not isinstance(value, bool):
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issues.append(Issue("BOOLEAN_REQUIRED", path))
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def validate_text_list(
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value: Any,
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path: str,
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issues: list[Issue],
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*,
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minimum: int = 0,
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maximum: int = 100,
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references: bool = False,
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311
|
-
) -> None:
|
|
312
|
-
if not isinstance(value, list):
|
|
313
|
-
issues.append(Issue("LIST_REQUIRED", path))
|
|
314
|
-
return
|
|
315
|
-
if not minimum <= len(value) <= maximum:
|
|
316
|
-
issues.append(Issue("LIST_LENGTH_INVALID", path))
|
|
317
|
-
for index, item in enumerate(value):
|
|
318
|
-
if references:
|
|
319
|
-
validate_reference(item, f"{path}[{index}]", issues)
|
|
320
|
-
else:
|
|
321
|
-
validate_text(item, f"{path}[{index}]", issues)
|
|
322
|
-
|
|
323
|
-
|
|
324
|
-
def _validate_scale(scale: Any, issues: list[Issue]) -> tuple[float, float, float]:
|
|
325
|
-
path = "$.scale"
|
|
326
|
-
expected = {"minimum", "maximum", "step", "anchors"}
|
|
327
|
-
if not exact_keys(scale, expected, path, issues):
|
|
328
|
-
return 0.0, 0.0, 1.0
|
|
329
|
-
minimum = scale.get("minimum")
|
|
330
|
-
maximum = scale.get("maximum")
|
|
331
|
-
step = scale.get("step")
|
|
332
|
-
if not is_number(minimum) or not is_number(maximum) or not is_number(step):
|
|
333
|
-
issues.append(Issue("SCALE_NUMBER_REQUIRED", path))
|
|
334
|
-
return 0.0, 0.0, 1.0
|
|
335
|
-
minimum_f = float(minimum)
|
|
336
|
-
maximum_f = float(maximum)
|
|
337
|
-
step_f = float(step)
|
|
338
|
-
if minimum_f < 0 or maximum_f <= minimum_f or maximum_f - minimum_f > 10:
|
|
339
|
-
issues.append(Issue("SCALE_BOUNDS_INVALID", path))
|
|
340
|
-
if step_f <= 0 or step_f > maximum_f - minimum_f:
|
|
341
|
-
issues.append(Issue("SCALE_STEP_INVALID", f"{path}.step"))
|
|
342
|
-
anchors = scale.get("anchors")
|
|
343
|
-
if not isinstance(anchors, list) or not 2 <= len(anchors) <= 21:
|
|
344
|
-
issues.append(Issue("SCALE_ANCHORS_INVALID", f"{path}.anchors"))
|
|
345
|
-
return minimum_f, maximum_f, step_f
|
|
346
|
-
anchor_scores: list[float] = []
|
|
347
|
-
for index, anchor in enumerate(anchors):
|
|
348
|
-
anchor_path = f"{path}.anchors[{index}]"
|
|
349
|
-
if not exact_keys(anchor, {"score", "label", "description"}, anchor_path, issues):
|
|
350
|
-
continue
|
|
351
|
-
score = anchor.get("score")
|
|
352
|
-
if not is_number(score):
|
|
353
|
-
issues.append(Issue("ANCHOR_SCORE_INVALID", f"{anchor_path}.score"))
|
|
354
|
-
else:
|
|
355
|
-
anchor_scores.append(float(score))
|
|
356
|
-
validate_text(anchor.get("label"), f"{anchor_path}.label", issues)
|
|
357
|
-
validate_text(anchor.get("description"), f"{anchor_path}.description", issues)
|
|
358
|
-
if anchor_scores:
|
|
359
|
-
if len(anchor_scores) != len(set(anchor_scores)):
|
|
360
|
-
issues.append(Issue("ANCHOR_SCORE_DUPLICATE", f"{path}.anchors"))
|
|
361
|
-
if min(anchor_scores) != minimum_f or max(anchor_scores) != maximum_f:
|
|
362
|
-
issues.append(Issue("ANCHOR_BOUNDS_MISSING", f"{path}.anchors"))
|
|
363
|
-
return minimum_f, maximum_f, step_f
|
|
364
|
-
|
|
365
|
-
|
|
366
|
-
def _validate_proxy_absence(value: Any, path: str, issues: list[Issue]) -> None:
|
|
367
|
-
strings: list[str] = []
|
|
368
|
-
stack = [value]
|
|
369
|
-
while stack:
|
|
370
|
-
current = stack.pop()
|
|
371
|
-
if isinstance(current, str):
|
|
372
|
-
strings.append(current.lower())
|
|
373
|
-
elif isinstance(current, list):
|
|
374
|
-
stack.extend(current)
|
|
375
|
-
elif isinstance(current, dict):
|
|
376
|
-
stack.extend(current.values())
|
|
377
|
-
combined = "\n".join(strings)
|
|
378
|
-
if any(term in combined for term in PROXY_TERMS):
|
|
379
|
-
issues.append(Issue("PROXY_METRIC_CRITERION_PROHIBITED", path))
|
|
380
|
-
|
|
381
|
-
|
|
382
|
-
def validate_rubric(rubric: Any) -> list[Issue]:
|
|
383
|
-
"""Validate the strict local rubric schema."""
|
|
384
|
-
|
|
385
|
-
issues: list[Issue] = []
|
|
386
|
-
top_keys = {
|
|
387
|
-
"schema_version",
|
|
388
|
-
"rubric_id",
|
|
389
|
-
"title",
|
|
390
|
-
"intended_use",
|
|
391
|
-
"construct",
|
|
392
|
-
"provenance",
|
|
393
|
-
"scale",
|
|
394
|
-
"criteria",
|
|
395
|
-
"rater_protocol",
|
|
396
|
-
"governance",
|
|
397
|
-
}
|
|
398
|
-
if not exact_keys(rubric, top_keys, "$", issues):
|
|
399
|
-
return issues
|
|
400
|
-
if rubric.get("schema_version") != SCHEMA_VERSION:
|
|
401
|
-
issues.append(Issue("SCHEMA_VERSION_UNSUPPORTED", "$.schema_version"))
|
|
402
|
-
validate_identifier(rubric.get("rubric_id"), "$.rubric_id", issues)
|
|
403
|
-
validate_text(rubric.get("title"), "$.title", issues)
|
|
404
|
-
|
|
405
|
-
intended = rubric.get("intended_use")
|
|
406
|
-
if exact_keys(
|
|
407
|
-
intended,
|
|
408
|
-
{"purpose", "unit_of_assessment", "allowed_contexts", "prohibited_uses"},
|
|
409
|
-
"$.intended_use",
|
|
410
|
-
issues,
|
|
411
|
-
):
|
|
412
|
-
if intended.get("purpose") != ALLOWED_PURPOSE:
|
|
413
|
-
issues.append(Issue("PURPOSE_NOT_ALLOWED", "$.intended_use.purpose"))
|
|
414
|
-
if intended.get("unit_of_assessment") != ALLOWED_UNIT:
|
|
415
|
-
issues.append(
|
|
416
|
-
Issue("UNIT_OF_ASSESSMENT_NOT_ALLOWED", "$.intended_use.unit_of_assessment")
|
|
417
|
-
)
|
|
418
|
-
validate_text_list(
|
|
419
|
-
intended.get("allowed_contexts"),
|
|
420
|
-
"$.intended_use.allowed_contexts",
|
|
421
|
-
issues,
|
|
422
|
-
minimum=1,
|
|
423
|
-
maximum=20,
|
|
424
|
-
)
|
|
425
|
-
prohibited = intended.get("prohibited_uses")
|
|
426
|
-
validate_text_list(
|
|
427
|
-
prohibited,
|
|
428
|
-
"$.intended_use.prohibited_uses",
|
|
429
|
-
issues,
|
|
430
|
-
minimum=len(PROHIBITED_USES),
|
|
431
|
-
maximum=30,
|
|
432
|
-
)
|
|
433
|
-
prohibited_set = (
|
|
434
|
-
set(prohibited)
|
|
435
|
-
if isinstance(prohibited, list)
|
|
436
|
-
and all(isinstance(item, str) for item in prohibited)
|
|
437
|
-
else set()
|
|
438
|
-
)
|
|
439
|
-
if isinstance(prohibited, list) and not PROHIBITED_USES.issubset(
|
|
440
|
-
prohibited_set
|
|
441
|
-
):
|
|
442
|
-
issues.append(
|
|
443
|
-
Issue("PROHIBITED_USES_INCOMPLETE", "$.intended_use.prohibited_uses")
|
|
444
|
-
)
|
|
445
|
-
|
|
446
|
-
construct = rubric.get("construct")
|
|
447
|
-
if exact_keys(
|
|
448
|
-
construct,
|
|
449
|
-
{"label", "definition", "boundaries", "limitations"},
|
|
450
|
-
"$.construct",
|
|
451
|
-
issues,
|
|
452
|
-
):
|
|
453
|
-
validate_text(construct.get("label"), "$.construct.label", issues)
|
|
454
|
-
validate_text(construct.get("definition"), "$.construct.definition", issues)
|
|
455
|
-
validate_text_list(
|
|
456
|
-
construct.get("boundaries"),
|
|
457
|
-
"$.construct.boundaries",
|
|
458
|
-
issues,
|
|
459
|
-
minimum=1,
|
|
460
|
-
maximum=20,
|
|
461
|
-
)
|
|
462
|
-
validate_text_list(
|
|
463
|
-
construct.get("limitations"),
|
|
464
|
-
"$.construct.limitations",
|
|
465
|
-
issues,
|
|
466
|
-
minimum=1,
|
|
467
|
-
maximum=20,
|
|
468
|
-
)
|
|
469
|
-
|
|
470
|
-
provenance = rubric.get("provenance")
|
|
471
|
-
if exact_keys(
|
|
472
|
-
provenance,
|
|
473
|
-
{
|
|
474
|
-
"rubric_version",
|
|
475
|
-
"owner_role",
|
|
476
|
-
"source_ids",
|
|
477
|
-
"content_validity_status",
|
|
478
|
-
"content_validity_evidence_ref",
|
|
479
|
-
"last_reviewed_date",
|
|
480
|
-
},
|
|
481
|
-
"$.provenance",
|
|
482
|
-
issues,
|
|
483
|
-
):
|
|
484
|
-
validate_text(provenance.get("rubric_version"), "$.provenance.rubric_version", issues)
|
|
485
|
-
validate_text(provenance.get("owner_role"), "$.provenance.owner_role", issues)
|
|
486
|
-
validate_text_list(
|
|
487
|
-
provenance.get("source_ids"),
|
|
488
|
-
"$.provenance.source_ids",
|
|
489
|
-
issues,
|
|
490
|
-
minimum=1,
|
|
491
|
-
maximum=50,
|
|
492
|
-
references=True,
|
|
493
|
-
)
|
|
494
|
-
validity_status = provenance.get("content_validity_status")
|
|
495
|
-
if validity_status not in {"not_established", "pilot_evidence", "documented"}:
|
|
496
|
-
issues.append(
|
|
497
|
-
Issue(
|
|
498
|
-
"CONTENT_VALIDITY_STATUS_INVALID",
|
|
499
|
-
"$.provenance.content_validity_status",
|
|
500
|
-
)
|
|
501
|
-
)
|
|
502
|
-
validate_reference(
|
|
503
|
-
provenance.get("content_validity_evidence_ref"),
|
|
504
|
-
"$.provenance.content_validity_evidence_ref",
|
|
505
|
-
issues,
|
|
506
|
-
allow_empty=validity_status == "not_established",
|
|
507
|
-
)
|
|
508
|
-
if validity_status != "documented":
|
|
509
|
-
issues.append(
|
|
510
|
-
Issue(
|
|
511
|
-
"CONTENT_VALIDITY_NOT_DOCUMENTED",
|
|
512
|
-
"$.provenance.content_validity_status",
|
|
513
|
-
"warning",
|
|
514
|
-
)
|
|
515
|
-
)
|
|
516
|
-
if not is_date(provenance.get("last_reviewed_date")):
|
|
517
|
-
issues.append(Issue("DATE_INVALID", "$.provenance.last_reviewed_date"))
|
|
518
|
-
|
|
519
|
-
scale_object = rubric.get("scale")
|
|
520
|
-
minimum, maximum, step = _validate_scale(scale_object, issues)
|
|
521
|
-
raw_scale_anchors = (
|
|
522
|
-
scale_object.get("anchors") if isinstance(scale_object, dict) else []
|
|
523
|
-
)
|
|
524
|
-
if not isinstance(raw_scale_anchors, list):
|
|
525
|
-
raw_scale_anchors = []
|
|
526
|
-
scale_anchor_scores = {
|
|
527
|
-
float(anchor["score"])
|
|
528
|
-
for anchor in raw_scale_anchors
|
|
529
|
-
if isinstance(anchor, dict) and is_number(anchor.get("score"))
|
|
530
|
-
}
|
|
531
|
-
|
|
532
|
-
criteria = rubric.get("criteria")
|
|
533
|
-
criterion_ids: set[str] = set()
|
|
534
|
-
total_weight = 0.0
|
|
535
|
-
if not isinstance(criteria, list) or not 1 <= len(criteria) <= MAX_CRITERIA:
|
|
536
|
-
issues.append(Issue("CRITERIA_INVALID", "$.criteria"))
|
|
537
|
-
else:
|
|
538
|
-
for index, criterion in enumerate(criteria):
|
|
539
|
-
path = f"$.criteria[{index}]"
|
|
540
|
-
if not exact_keys(
|
|
541
|
-
criterion,
|
|
542
|
-
{
|
|
543
|
-
"criterion_id",
|
|
544
|
-
"label",
|
|
545
|
-
"construct_component",
|
|
546
|
-
"weight",
|
|
547
|
-
"required",
|
|
548
|
-
"anchors",
|
|
549
|
-
"evidence_requirements",
|
|
550
|
-
"limitations",
|
|
551
|
-
},
|
|
552
|
-
path,
|
|
553
|
-
issues,
|
|
554
|
-
):
|
|
555
|
-
continue
|
|
556
|
-
criterion_id = criterion.get("criterion_id")
|
|
557
|
-
validate_identifier(criterion_id, f"{path}.criterion_id", issues)
|
|
558
|
-
if isinstance(criterion_id, str):
|
|
559
|
-
if criterion_id in criterion_ids:
|
|
560
|
-
issues.append(Issue("CRITERION_ID_DUPLICATE", f"{path}.criterion_id"))
|
|
561
|
-
criterion_ids.add(criterion_id)
|
|
562
|
-
validate_text(criterion.get("label"), f"{path}.label", issues)
|
|
563
|
-
validate_text(
|
|
564
|
-
criterion.get("construct_component"),
|
|
565
|
-
f"{path}.construct_component",
|
|
566
|
-
issues,
|
|
567
|
-
)
|
|
568
|
-
validate_bool(criterion.get("required"), f"{path}.required", issues)
|
|
569
|
-
weight = criterion.get("weight")
|
|
570
|
-
if not is_number(weight) or not 0 < float(weight) <= 1:
|
|
571
|
-
issues.append(Issue("CRITERION_WEIGHT_INVALID", f"{path}.weight"))
|
|
572
|
-
else:
|
|
573
|
-
total_weight += float(weight)
|
|
574
|
-
validate_text_list(
|
|
575
|
-
criterion.get("evidence_requirements"),
|
|
576
|
-
f"{path}.evidence_requirements",
|
|
577
|
-
issues,
|
|
578
|
-
minimum=1,
|
|
579
|
-
maximum=20,
|
|
580
|
-
)
|
|
581
|
-
validate_text_list(
|
|
582
|
-
criterion.get("limitations"),
|
|
583
|
-
f"{path}.limitations",
|
|
584
|
-
issues,
|
|
585
|
-
minimum=1,
|
|
586
|
-
maximum=20,
|
|
587
|
-
)
|
|
588
|
-
anchors = criterion.get("anchors")
|
|
589
|
-
criterion_anchor_scores: set[float] = set()
|
|
590
|
-
if not isinstance(anchors, list) or not 2 <= len(anchors) <= 21:
|
|
591
|
-
issues.append(Issue("CRITERION_ANCHORS_INVALID", f"{path}.anchors"))
|
|
592
|
-
else:
|
|
593
|
-
for anchor_index, anchor in enumerate(anchors):
|
|
594
|
-
anchor_path = f"{path}.anchors[{anchor_index}]"
|
|
595
|
-
if not exact_keys(
|
|
596
|
-
anchor, {"score", "description"}, anchor_path, issues
|
|
597
|
-
):
|
|
598
|
-
continue
|
|
599
|
-
if not is_number(anchor.get("score")):
|
|
600
|
-
issues.append(
|
|
601
|
-
Issue("ANCHOR_SCORE_INVALID", f"{anchor_path}.score")
|
|
602
|
-
)
|
|
603
|
-
else:
|
|
604
|
-
criterion_anchor_scores.add(float(anchor["score"]))
|
|
605
|
-
validate_text(
|
|
606
|
-
anchor.get("description"),
|
|
607
|
-
f"{anchor_path}.description",
|
|
608
|
-
issues,
|
|
609
|
-
)
|
|
610
|
-
if criterion_anchor_scores != scale_anchor_scores:
|
|
611
|
-
issues.append(Issue("CRITERION_ANCHORS_INCOMPLETE", f"{path}.anchors"))
|
|
612
|
-
_validate_proxy_absence(criterion, path, issues)
|
|
613
|
-
if criteria and not math.isclose(total_weight, 1.0, abs_tol=1e-9):
|
|
614
|
-
issues.append(Issue("CRITERION_WEIGHTS_MUST_SUM_TO_ONE", "$.criteria"))
|
|
615
|
-
|
|
616
|
-
protocol = rubric.get("rater_protocol")
|
|
617
|
-
if exact_keys(
|
|
618
|
-
protocol,
|
|
619
|
-
{
|
|
620
|
-
"minimum_raters",
|
|
621
|
-
"training_required",
|
|
622
|
-
"training_ref",
|
|
623
|
-
"calibration_required",
|
|
624
|
-
"calibration_ref",
|
|
625
|
-
"agreement_method",
|
|
626
|
-
"inter_rater_reliability_status",
|
|
627
|
-
"inter_rater_reliability_ref",
|
|
628
|
-
"drift_monitoring_required",
|
|
629
|
-
"drift_review_ref",
|
|
630
|
-
},
|
|
631
|
-
"$.rater_protocol",
|
|
632
|
-
issues,
|
|
633
|
-
):
|
|
634
|
-
minimum_raters = protocol.get("minimum_raters")
|
|
635
|
-
if (
|
|
636
|
-
not isinstance(minimum_raters, int)
|
|
637
|
-
or isinstance(minimum_raters, bool)
|
|
638
|
-
or not 2 <= minimum_raters <= 50
|
|
639
|
-
):
|
|
640
|
-
issues.append(
|
|
641
|
-
Issue("MINIMUM_RATERS_INVALID", "$.rater_protocol.minimum_raters")
|
|
642
|
-
)
|
|
643
|
-
for field in (
|
|
644
|
-
"training_required",
|
|
645
|
-
"calibration_required",
|
|
646
|
-
"drift_monitoring_required",
|
|
647
|
-
):
|
|
648
|
-
validate_bool(protocol.get(field), f"$.rater_protocol.{field}", issues)
|
|
649
|
-
if protocol.get(field) is not True:
|
|
650
|
-
issues.append(
|
|
651
|
-
Issue("RATER_CONTROL_MUST_BE_REQUIRED", f"$.rater_protocol.{field}")
|
|
652
|
-
)
|
|
653
|
-
for field in ("training_ref", "calibration_ref", "drift_review_ref"):
|
|
654
|
-
validate_reference(protocol.get(field), f"$.rater_protocol.{field}", issues)
|
|
655
|
-
if protocol.get("agreement_method") != (
|
|
656
|
-
"exact_within_step_and_mean_absolute_difference"
|
|
657
|
-
):
|
|
658
|
-
issues.append(
|
|
659
|
-
Issue(
|
|
660
|
-
"AGREEMENT_METHOD_INVALID", "$.rater_protocol.agreement_method"
|
|
661
|
-
)
|
|
662
|
-
)
|
|
663
|
-
reliability_status = protocol.get("inter_rater_reliability_status")
|
|
664
|
-
if reliability_status not in {
|
|
665
|
-
"not_established",
|
|
666
|
-
"pilot_evidence",
|
|
667
|
-
"documented",
|
|
668
|
-
}:
|
|
669
|
-
issues.append(
|
|
670
|
-
Issue(
|
|
671
|
-
"INTER_RATER_RELIABILITY_STATUS_INVALID",
|
|
672
|
-
"$.rater_protocol.inter_rater_reliability_status",
|
|
673
|
-
)
|
|
674
|
-
)
|
|
675
|
-
validate_reference(
|
|
676
|
-
protocol.get("inter_rater_reliability_ref"),
|
|
677
|
-
"$.rater_protocol.inter_rater_reliability_ref",
|
|
678
|
-
issues,
|
|
679
|
-
allow_empty=reliability_status == "not_established",
|
|
680
|
-
)
|
|
681
|
-
if reliability_status != "documented":
|
|
682
|
-
issues.append(
|
|
683
|
-
Issue(
|
|
684
|
-
"INTER_RATER_RELIABILITY_NOT_DOCUMENTED",
|
|
685
|
-
"$.rater_protocol.inter_rater_reliability_status",
|
|
686
|
-
"warning",
|
|
687
|
-
)
|
|
688
|
-
)
|
|
689
|
-
|
|
690
|
-
governance = rubric.get("governance")
|
|
691
|
-
governance_bool_fields = (
|
|
692
|
-
"accountable_committee_required",
|
|
693
|
-
"conflict_disclosure_required",
|
|
694
|
-
"recusal_required",
|
|
695
|
-
"appeal_process_required",
|
|
696
|
-
"accessibility_accommodations_required",
|
|
697
|
-
"data_protection_review_required",
|
|
698
|
-
"subgroup_bias_review_required",
|
|
699
|
-
)
|
|
700
|
-
governance_ref_fields = (
|
|
701
|
-
"committee_owner_role",
|
|
702
|
-
"appeal_process_ref",
|
|
703
|
-
"accessibility_process_ref",
|
|
704
|
-
"data_protection_process_ref",
|
|
705
|
-
"subgroup_review_ref",
|
|
706
|
-
"review_cycle_ref",
|
|
707
|
-
)
|
|
708
|
-
if exact_keys(
|
|
709
|
-
governance,
|
|
710
|
-
set(governance_bool_fields) | set(governance_ref_fields),
|
|
711
|
-
"$.governance",
|
|
712
|
-
issues,
|
|
713
|
-
):
|
|
714
|
-
for field in governance_bool_fields:
|
|
715
|
-
validate_bool(governance.get(field), f"$.governance.{field}", issues)
|
|
716
|
-
if governance.get(field) is not True:
|
|
717
|
-
issues.append(
|
|
718
|
-
Issue("GOVERNANCE_CONTROL_MUST_BE_REQUIRED", f"$.governance.{field}")
|
|
719
|
-
)
|
|
720
|
-
for field in governance_ref_fields:
|
|
721
|
-
validate_reference(governance.get(field), f"$.governance.{field}", issues)
|
|
722
|
-
|
|
723
|
-
if maximum <= minimum or step <= 0:
|
|
724
|
-
issues.append(Issue("SCALE_UNUSABLE", "$.scale"))
|
|
725
|
-
return issues
|
|
726
|
-
|
|
727
|
-
|
|
728
|
-
def scale_values(rubric: dict[str, Any]) -> set[float]:
|
|
729
|
-
return {
|
|
730
|
-
float(anchor["score"])
|
|
731
|
-
for anchor in rubric["scale"]["anchors"]
|
|
732
|
-
if is_number(anchor["score"])
|
|
733
|
-
}
|
|
734
|
-
|
|
735
|
-
|
|
736
|
-
def validate_evaluation(
|
|
737
|
-
evaluation: Any, rubric: dict[str, Any]
|
|
738
|
-
) -> list[Issue]:
|
|
739
|
-
"""Validate one strict scholarly-work evaluation record."""
|
|
740
|
-
|
|
741
|
-
issues: list[Issue] = []
|
|
742
|
-
if not exact_keys(
|
|
743
|
-
evaluation,
|
|
744
|
-
{
|
|
745
|
-
"schema_version",
|
|
746
|
-
"evaluation_id",
|
|
747
|
-
"rubric_id",
|
|
748
|
-
"work_id",
|
|
749
|
-
"data_classification",
|
|
750
|
-
"purpose",
|
|
751
|
-
"ratings",
|
|
752
|
-
},
|
|
753
|
-
"$",
|
|
754
|
-
issues,
|
|
755
|
-
):
|
|
756
|
-
return issues
|
|
757
|
-
if evaluation.get("schema_version") != SCHEMA_VERSION:
|
|
758
|
-
issues.append(Issue("SCHEMA_VERSION_UNSUPPORTED", "$.schema_version"))
|
|
759
|
-
validate_identifier(evaluation.get("evaluation_id"), "$.evaluation_id", issues)
|
|
760
|
-
validate_identifier(evaluation.get("rubric_id"), "$.rubric_id", issues)
|
|
761
|
-
validate_identifier(evaluation.get("work_id"), "$.work_id", issues)
|
|
762
|
-
if evaluation.get("rubric_id") != rubric.get("rubric_id"):
|
|
763
|
-
issues.append(Issue("RUBRIC_ID_MISMATCH", "$.rubric_id"))
|
|
764
|
-
if evaluation.get("data_classification") not in ALLOWED_CLASSIFICATIONS:
|
|
765
|
-
issues.append(Issue("DATA_CLASSIFICATION_NOT_ALLOWED", "$.data_classification"))
|
|
766
|
-
if evaluation.get("purpose") != ALLOWED_PURPOSE:
|
|
767
|
-
issues.append(Issue("PURPOSE_NOT_ALLOWED", "$.purpose"))
|
|
768
|
-
|
|
769
|
-
criteria = {criterion["criterion_id"]: criterion for criterion in rubric["criteria"]}
|
|
770
|
-
accepted_scores = scale_values(rubric)
|
|
771
|
-
maximum_uncertainty = float(rubric["scale"]["maximum"]) - float(
|
|
772
|
-
rubric["scale"]["minimum"]
|
|
773
|
-
)
|
|
774
|
-
ratings = evaluation.get("ratings")
|
|
775
|
-
seen: set[str] = set()
|
|
776
|
-
if not isinstance(ratings, list) or not 1 <= len(ratings) <= MAX_CRITERIA:
|
|
777
|
-
issues.append(Issue("RATINGS_INVALID", "$.ratings"))
|
|
778
|
-
return issues
|
|
779
|
-
for index, rating in enumerate(ratings):
|
|
780
|
-
path = f"$.ratings[{index}]"
|
|
781
|
-
if not exact_keys(
|
|
782
|
-
rating,
|
|
783
|
-
{
|
|
784
|
-
"criterion_id",
|
|
785
|
-
"status",
|
|
786
|
-
"score",
|
|
787
|
-
"uncertainty",
|
|
788
|
-
"evidence_ids",
|
|
789
|
-
"rationale_ref",
|
|
790
|
-
},
|
|
791
|
-
path,
|
|
792
|
-
issues,
|
|
793
|
-
):
|
|
794
|
-
continue
|
|
795
|
-
criterion_id = rating.get("criterion_id")
|
|
796
|
-
validate_identifier(criterion_id, f"{path}.criterion_id", issues)
|
|
797
|
-
if isinstance(criterion_id, str):
|
|
798
|
-
if criterion_id in seen:
|
|
799
|
-
issues.append(Issue("RATING_DUPLICATE", f"{path}.criterion_id"))
|
|
800
|
-
seen.add(criterion_id)
|
|
801
|
-
if criterion_id not in criteria:
|
|
802
|
-
issues.append(Issue("CRITERION_UNKNOWN", f"{path}.criterion_id"))
|
|
803
|
-
status = rating.get("status")
|
|
804
|
-
if status not in RATING_STATUSES:
|
|
805
|
-
issues.append(Issue("RATING_STATUS_INVALID", f"{path}.status"))
|
|
806
|
-
evidence_ids = rating.get("evidence_ids")
|
|
807
|
-
if not isinstance(evidence_ids, list) or len(evidence_ids) > 100:
|
|
808
|
-
issues.append(Issue("EVIDENCE_IDS_INVALID", f"{path}.evidence_ids"))
|
|
809
|
-
evidence_ids = []
|
|
810
|
-
else:
|
|
811
|
-
hashable_evidence_ids = [
|
|
812
|
-
evidence_id
|
|
813
|
-
for evidence_id in evidence_ids
|
|
814
|
-
if isinstance(evidence_id, str)
|
|
815
|
-
]
|
|
816
|
-
if len(hashable_evidence_ids) != len(set(hashable_evidence_ids)):
|
|
817
|
-
issues.append(Issue("EVIDENCE_ID_DUPLICATE", f"{path}.evidence_ids"))
|
|
818
|
-
for evidence_index, evidence_id in enumerate(evidence_ids):
|
|
819
|
-
validate_identifier(
|
|
820
|
-
evidence_id,
|
|
821
|
-
f"{path}.evidence_ids[{evidence_index}]",
|
|
822
|
-
issues,
|
|
823
|
-
"EVIDENCE_ID_INVALID",
|
|
824
|
-
)
|
|
825
|
-
validate_reference(rating.get("rationale_ref"), f"{path}.rationale_ref", issues)
|
|
826
|
-
if status == "rated":
|
|
827
|
-
score = rating.get("score")
|
|
828
|
-
uncertainty = rating.get("uncertainty")
|
|
829
|
-
if not is_number(score) or float(score) not in accepted_scores:
|
|
830
|
-
issues.append(Issue("SCORE_NOT_ON_SCALE", f"{path}.score"))
|
|
831
|
-
if (
|
|
832
|
-
not is_number(uncertainty)
|
|
833
|
-
or not 0 <= float(uncertainty) <= maximum_uncertainty
|
|
834
|
-
):
|
|
835
|
-
issues.append(Issue("UNCERTAINTY_INVALID", f"{path}.uncertainty"))
|
|
836
|
-
if not evidence_ids:
|
|
837
|
-
issues.append(Issue("RATED_EVIDENCE_REQUIRED", f"{path}.evidence_ids"))
|
|
838
|
-
elif status in {"missing", "not_applicable"}:
|
|
839
|
-
if rating.get("score") is not None:
|
|
840
|
-
issues.append(Issue("UNRATED_SCORE_MUST_BE_NULL", f"{path}.score"))
|
|
841
|
-
if rating.get("uncertainty") is not None:
|
|
842
|
-
issues.append(
|
|
843
|
-
Issue("UNRATED_UNCERTAINTY_MUST_BE_NULL", f"{path}.uncertainty")
|
|
844
|
-
)
|
|
845
|
-
if evidence_ids:
|
|
846
|
-
issues.append(
|
|
847
|
-
Issue("UNRATED_EVIDENCE_MUST_BE_EMPTY", f"{path}.evidence_ids")
|
|
848
|
-
)
|
|
849
|
-
missing_criteria = set(criteria) - seen
|
|
850
|
-
for criterion_id in sorted(missing_criteria):
|
|
851
|
-
issues.append(Issue("CRITERION_RATING_REQUIRED", f"$.ratings.{criterion_id}"))
|
|
852
|
-
return issues
|
|
853
|
-
|
|
854
|
-
|
|
855
|
-
def error_issues(issues: Iterable[Issue]) -> list[Issue]:
|
|
856
|
-
return [issue for issue in issues if issue.level == "error"]
|
|
857
|
-
|
|
858
|
-
|
|
859
|
-
def require_valid(issues: Iterable[Issue]) -> None:
|
|
860
|
-
errors = error_issues(issues)
|
|
861
|
-
if errors:
|
|
862
|
-
raise ValidationError(errors[0].code, errors[0].path)
|
|
863
|
-
|
|
864
|
-
|
|
865
|
-
def rounded(value: float | None) -> float | None:
|
|
866
|
-
if value is None:
|
|
867
|
-
return None
|
|
868
|
-
return round(value, 6)
|
|
869
|
-
|
|
870
|
-
|
|
871
|
-
def weights_by_criterion(rubric: dict[str, Any]) -> dict[str, float]:
|
|
872
|
-
return {
|
|
873
|
-
criterion["criterion_id"]: float(criterion["weight"])
|
|
874
|
-
for criterion in rubric["criteria"]
|
|
875
|
-
}
|
|
876
|
-
|
|
877
|
-
|
|
878
|
-
def score_evaluation(
|
|
879
|
-
rubric: dict[str, Any],
|
|
880
|
-
evaluation: dict[str, Any],
|
|
881
|
-
*,
|
|
882
|
-
weights: dict[str, float] | None = None,
|
|
883
|
-
) -> dict[str, Any]:
|
|
884
|
-
"""Calculate bounded descriptive rubric math without a recommendation."""
|
|
885
|
-
|
|
886
|
-
selected_weights = weights or weights_by_criterion(rubric)
|
|
887
|
-
scale_minimum = float(rubric["scale"]["minimum"])
|
|
888
|
-
scale_maximum = float(rubric["scale"]["maximum"])
|
|
889
|
-
rating_by_id = {
|
|
890
|
-
rating["criterion_id"]: rating for rating in evaluation["ratings"]
|
|
891
|
-
}
|
|
892
|
-
criteria_output: list[dict[str, Any]] = []
|
|
893
|
-
weighted_sum = 0.0
|
|
894
|
-
lower_sum = 0.0
|
|
895
|
-
upper_sum = 0.0
|
|
896
|
-
rated_weight = 0.0
|
|
897
|
-
missing_weight = 0.0
|
|
898
|
-
not_applicable_weight = 0.0
|
|
899
|
-
for criterion in rubric["criteria"]:
|
|
900
|
-
criterion_id = criterion["criterion_id"]
|
|
901
|
-
rating = rating_by_id[criterion_id]
|
|
902
|
-
weight = float(selected_weights[criterion_id])
|
|
903
|
-
status = rating["status"]
|
|
904
|
-
item: dict[str, Any] = {
|
|
905
|
-
"criterion_id": criterion_id,
|
|
906
|
-
"status": status,
|
|
907
|
-
"weight": rounded(weight),
|
|
908
|
-
"score": None,
|
|
909
|
-
"uncertainty": None,
|
|
910
|
-
"weighted_contribution": None,
|
|
911
|
-
"lower_contribution": None,
|
|
912
|
-
"upper_contribution": None,
|
|
913
|
-
}
|
|
914
|
-
if status == "rated":
|
|
915
|
-
score = float(rating["score"])
|
|
916
|
-
uncertainty = float(rating["uncertainty"])
|
|
917
|
-
lower = max(scale_minimum, score - uncertainty)
|
|
918
|
-
upper = min(scale_maximum, score + uncertainty)
|
|
919
|
-
contribution = weight * score
|
|
920
|
-
weighted_sum += contribution
|
|
921
|
-
lower_sum += weight * lower
|
|
922
|
-
upper_sum += weight * upper
|
|
923
|
-
rated_weight += weight
|
|
924
|
-
item.update(
|
|
925
|
-
{
|
|
926
|
-
"score": rounded(score),
|
|
927
|
-
"uncertainty": rounded(uncertainty),
|
|
928
|
-
"weighted_contribution": rounded(contribution),
|
|
929
|
-
"lower_contribution": rounded(weight * lower),
|
|
930
|
-
"upper_contribution": rounded(weight * upper),
|
|
931
|
-
}
|
|
932
|
-
)
|
|
933
|
-
elif status == "missing":
|
|
934
|
-
missing_weight += weight
|
|
935
|
-
else:
|
|
936
|
-
not_applicable_weight += weight
|
|
937
|
-
criteria_output.append(item)
|
|
938
|
-
applicable_weight = rated_weight + missing_weight
|
|
939
|
-
normalized = weighted_sum / rated_weight if rated_weight else None
|
|
940
|
-
lower_score = lower_sum / rated_weight if rated_weight else None
|
|
941
|
-
upper_score = upper_sum / rated_weight if rated_weight else None
|
|
942
|
-
coverage = rated_weight / applicable_weight if applicable_weight else None
|
|
943
|
-
warnings: list[str] = []
|
|
944
|
-
if missing_weight > 0:
|
|
945
|
-
warnings.append("MISSING_RATINGS_EXCLUDED_FROM_NORMALIZED_SCORE")
|
|
946
|
-
if not_applicable_weight > 0:
|
|
947
|
-
warnings.append("NOT_APPLICABLE_RATINGS_EXCLUDED")
|
|
948
|
-
if coverage is None or coverage < 1.0:
|
|
949
|
-
warnings.append("INCOMPLETE_APPLICABLE_COVERAGE")
|
|
950
|
-
if normalized is None:
|
|
951
|
-
warnings.append("NO_NORMALIZED_SCORE_AVAILABLE")
|
|
952
|
-
return {
|
|
953
|
-
"schema_version": SCHEMA_VERSION,
|
|
954
|
-
"report_type": "bounded_descriptive_rubric_score",
|
|
955
|
-
"notice": NOTICE,
|
|
956
|
-
"evaluation_id": evaluation["evaluation_id"],
|
|
957
|
-
"work_id": evaluation["work_id"],
|
|
958
|
-
"rubric_id": rubric["rubric_id"],
|
|
959
|
-
"scale": {"minimum": scale_minimum, "maximum": scale_maximum},
|
|
960
|
-
"formula": (
|
|
961
|
-
"normalized_score = sum(score_i * weight_i for rated criteria) "
|
|
962
|
-
"/ sum(weight_i for rated criteria); missing and not_applicable "
|
|
963
|
-
"criteria are reported and excluded"
|
|
964
|
-
),
|
|
965
|
-
"criteria": criteria_output,
|
|
966
|
-
"aggregates": {
|
|
967
|
-
"total_weight": rounded(sum(selected_weights.values())),
|
|
968
|
-
"applicable_weight": rounded(applicable_weight),
|
|
969
|
-
"rated_weight": rounded(rated_weight),
|
|
970
|
-
"missing_weight": rounded(missing_weight),
|
|
971
|
-
"not_applicable_weight": rounded(not_applicable_weight),
|
|
972
|
-
"coverage_of_applicable_weight": rounded(coverage),
|
|
973
|
-
"weighted_sum": rounded(weighted_sum),
|
|
974
|
-
"normalized_score": rounded(normalized),
|
|
975
|
-
"uncertainty_interval": {
|
|
976
|
-
"lower": rounded(lower_score),
|
|
977
|
-
"upper": rounded(upper_score),
|
|
978
|
-
"method": (
|
|
979
|
-
"weighted aggregation of criterion-level bounded uncertainty "
|
|
980
|
-
"intervals; not a confidence interval"
|
|
981
|
-
),
|
|
982
|
-
},
|
|
983
|
-
},
|
|
984
|
-
"warnings": warnings,
|
|
985
|
-
"decision_recommendation_provided": False,
|
|
986
|
-
}
|