add seed registry, tag vocabulary (measure/seed/program), and Zotero library cleanup
- Tag.measure(), Tag.seed(), Tag.program() factory methods - dev/scripts/register_seeds.py: declarative registry mapping 34 seed files to source URLs, titles, and tags with bidirectional Zotero sync - Zotero library standardization: authors on 2451/2504 items, CFR titles from eCFR API (630 sections with headings, 15 cross-title corrections), 1070 URL-as-title items resolved to real page titles - openpyxl + pdfplumber dev deps for seed file inspection
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dev/scripts/register_seeds.py
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dev/scripts/register_seeds.py
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"""Register dev/seeds/ files in bib.sqlite and Zotero.
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Each seed file gets a parent ``download`` item (with source URL) in
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bib.sqlite, an attachment linking the file, and the ``seed:true`` tag.
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Items are also pushed to Zotero so the seed tag appears there too.
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Usage::
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uv run python dev/scripts/register_seeds.py # register all
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uv run python dev/scripts/register_seeds.py --dry-run # preview only
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uv run python dev/scripts/register_seeds.py --pull # Zotero → dev/seeds/
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"""
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from __future__ import annotations
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import argparse
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import random
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import shutil
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import sqlite3
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import string
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import subprocess
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from dataclasses import dataclass, field
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from datetime import datetime, timezone
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from pathlib import Path
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SEEDS_DIR = Path("dev/seeds")
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BIB_DB = "data/bib.sqlite"
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ZOTERO_DB = "zotero/data/zotero.sqlite"
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ZOTERO_STORAGE = Path("zotero/data/storage")
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# Zotero schema constants (match add_carrier_to_zotero.py / sync.py)
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ZOTERO_TYPE_WEBPAGE = 40
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ZOTERO_TYPE_ATTACHMENT = 3
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ZOTERO_FIELD_TITLE = 1
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ZOTERO_FIELD_URL = 10
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ZOTERO_FIELD_DATE = 6
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ZOTERO_FIELD_ACCESS_DATE = 11
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ZOTERO_FIELD_WEBSITE_TYPE = 42
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ZOTERO_FIELD_WEBSITE_TITLE = 123
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SEED_TAG = "seed:true"
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@dataclass
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class SeedSpec:
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"""Maps a seed file to its provenance metadata."""
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path: str
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url: str
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title: str
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tags: list[str] = field(default_factory=list)
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# ── Registry ─────────────────────────────────────────────────────
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SEED_REGISTRY: tuple[SeedSpec, ...] = (
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# --- CCLF ---
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SeedSpec(
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path="cclf-information-packet.pdf",
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url="https://www.cms.gov/files/document/cclf-information-packet.pdf",
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title="CCLF Information Packet",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="cclf_ip_v41.pdf",
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url="https://www.cms.gov/files/document/cclf-file-data-elements.pdf",
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title="CCLF Information Packet v41",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="CCLF Uses and Limitations v4.pdf",
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url="https://www.cms.gov/files/document/uses-and-limitations-cclfs.pdf",
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title="CCLF Uses and Limitations v4",
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tags=["module:aco", "source:cms-website"],
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),
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# --- CCW ---
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SeedSpec(
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path="codebook-ffs-claims.pdf",
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url="https://www2.ccwdata.org/documents/10280/19022436/codebook-ffs-claims.pdf",
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title="CCW Codebook — FFS Claims",
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tags=["module:ccw", "source:cms-website"],
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),
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SeedSpec(
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path="record-layout-ffs-claims.xlsx",
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url="https://www2.ccwdata.org/documents/10280/19022436/record-layout-ffs-claims.xlsx",
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title="CCW Record Layout — FFS Claims",
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tags=["module:ccw", "source:cms-website"],
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),
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# --- ACO REACH ---
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SeedSpec(
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path="ACO_REACH_bulk_upload_participants 5-19 (1).xlsx",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Bulk Upload Participants Template",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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SeedSpec(
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path="ACO_REACH_Calendar_updated_02032026.xlsx",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Calendar (Updated 2026-02-03)",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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SeedSpec(
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path="ACOREACH_DataReportingImplementationGuide_v1.3_updated_508.pdf",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Data Reporting Implementation Guide v1.3",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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SeedSpec(
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path="ACOREACHM.FNCL.ER.IP.4.01.01_Clean.pdf",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Financial — Expenditure Report IP",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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SeedSpec(
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path="ACOReachQualityStrategyPaperPY2023_03-18-2024.pdf",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Quality Strategy Paper PY2023",
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tags=[
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"module:aco",
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"program:reach",
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"year:2023",
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"source:cms-website",
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],
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),
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SeedSpec(
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path="ACOR_Q3 QQR_CoverNotice_Final.docx",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Q3 QQR Cover Notice",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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SeedSpec(
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path="PY2023 ACO REACH Reporting and Data Sharing Overview_v20232203.pdf",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="PY2023 ACO REACH Reporting and Data Sharing Overview",
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tags=[
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"module:aco",
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"program:reach",
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"year:2023",
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"source:cms-website",
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],
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),
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SeedSpec(
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path="Copy of Mock Data File - Beneficiary Alignment Report (1).xlsx",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ACO REACH Mock Beneficiary Alignment Report",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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# --- Quality Measures ---
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SeedSpec(
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path="PY2025 Quarter2 MedicareCQM Data Dictionary.xlsx",
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url="https://www.cms.gov/medicare/quality/initiatives/shared-savings-program/quality-measures",
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title="PY2025 Q2 Medicare CQM Data Dictionary",
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tags=[
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"module:aco",
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"program:mssp",
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"year:2025",
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"source:cms-website",
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],
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),
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SeedSpec(
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path="DataInquiryTemplate_202512_508.xlsx",
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url="https://www.cms.gov/medicare/quality/initiatives/shared-savings-program/quality-measures",
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title="Data Inquiry Template (2025-12)",
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tags=["module:aco", "program:mssp", "year:2025", "source:cms-website"],
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),
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SeedSpec(
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path="Static Report Crosswalk.xlsx",
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url="https://www.cms.gov/medicare/quality/initiatives/shared-savings-program/quality-measures",
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title="Static Report Crosswalk",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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# --- SSP / County ---
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SeedSpec(
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path="County-level Aggregate Expenditure and Risk Score Data on Assignable Beneficiaries.zip",
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url="https://data.cms.gov/medicare-shared-savings-program/county-level-aggregate-expenditure-and-risk-score",
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title="SSP County-Level Aggregate Expenditure — Assignable Beneficiaries PUF",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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SeedSpec(
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path="County_Level_Aggregate_Expenditure_and_Risk_Score_Data_on_Assigned_Beneficiaries_PUF_for_2014-2020.zip",
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url="https://data.cms.gov/medicare-shared-savings-program/county-level-aggregate-expenditure-and-risk-score",
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title="SSP County-Level Aggregate Expenditure — Assigned Beneficiaries PUF 2014-2020",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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SeedSpec(
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path="County-Level_FFS_Data_for_Shared_Savings_Program_Benchmark_PUF_Methodology-508.pdf",
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url="https://data.cms.gov/medicare-shared-savings-program/county-level-aggregate-expenditure-and-risk-score",
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title="County-Level FFS Data for SSP Benchmark PUF Methodology",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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SeedSpec(
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path="County_Lvl_FFS_Data_SSP_Benchmark_PUF_Data_Dictionary.pdf",
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url="https://data.cms.gov/medicare-shared-savings-program/county-level-aggregate-expenditure-and-risk-score",
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title="County-Level FFS Data SSP Benchmark PUF Data Dictionary",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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SeedSpec(
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path="Data Dictionary_ Medicare Shared Savings Program County-Level Aggregate Expenditure and Risk Score Data on Assignable Beneficiaries PUF - County_Lvl_FFS_Data_SSP_Benchmark_PUF_Data_Dictionary.pdf",
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url="https://data.cms.gov/medicare-shared-savings-program/county-level-aggregate-expenditure-and-risk-score",
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title="SSP County-Level PUF Data Dictionary — Assignable Beneficiaries",
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tags=["module:aco", "program:mssp", "source:cms-website"],
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),
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# --- BCDA ---
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SeedSpec(
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path="BCDA_Data_Dictionary.xlsx",
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url="https://bcda.cms.gov/assets/downloads/BCDA_Data_Dictionary.xlsx",
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title="BCDA Data Dictionary",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="BCDA_Partially_Adjudicated_Data_Dictionary.xlsx",
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url="https://bcda.cms.gov/assets/data/BCDA_Partially_Adjudicated_Data_Dictionary.xlsx",
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title="BCDA Partially Adjudicated Data Dictionary",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="unmapped-fields-between-cclf-and-bcda.xlsx",
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url="https://bcda.cms.gov/assets/downloads/unmapped-fields-between-cclf-and-bcda.xlsx",
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title="Unmapped Fields Between CCLF and BCDA",
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tags=["module:aco", "source:cms-website"],
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),
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# --- BCDA v2 (directory) ---
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SeedSpec(
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path="bcda_v2",
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url="https://bcda.cms.gov/api/v2",
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title="BCDA API v2 Response Samples",
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tags=["module:aco", "source:cms-website"],
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),
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# --- BCDA NDJSON samples ---
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SeedSpec(
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path="Coverage.ndjson",
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url="https://bcda.cms.gov/assets/data/Coverage.ndjson",
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title="BCDA Sample — Coverage NDJSON",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="ExplanationOfBenefit.ndjson",
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url="https://bcda.cms.gov/assets/data/ExplanationOfBenefit.ndjson",
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title="BCDA Sample — ExplanationOfBenefit NDJSON",
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tags=["module:aco", "source:cms-website"],
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),
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SeedSpec(
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path="Patient.ndjson",
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url="https://bcda.cms.gov/assets/data/Patient.ndjson",
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title="BCDA Sample — Patient NDJSON",
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tags=["module:aco", "source:cms-website"],
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),
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# --- ALR/ASR ---
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SeedSpec(
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path="ALRASRGuide.pdf",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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title="ALR/ASR Guide",
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tags=["module:aco", "program:reach", "source:cms-website"],
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),
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# --- PY2023 (directory) ---
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SeedSpec(
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path="PY2023",
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url="https://innovation.cms.gov/innovation-models/aco-reach",
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|
title="PY2023 ACO REACH Mock Data and Templates",
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|
tags=[
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|
"module:aco",
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|
"program:reach",
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|
"year:2023",
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|
"source:cms-website",
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|
],
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|
),
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|
SeedSpec(
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|
path="PY2023 Templates.zip",
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|
url="https://innovation.cms.gov/innovation-models/aco-reach",
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|
title="PY2023 ACO REACH Templates (ZIP)",
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|
tags=[
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|
"module:aco",
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|
"program:reach",
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|
"year:2023",
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|
"source:cms-website",
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|
],
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|
),
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|
# --- Grafana (directory) ---
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SeedSpec(
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|
path="grafana",
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|
url="",
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|
title="Grafana Dashboard Configs",
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|
tags=["source:internal"],
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|
),
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|
# --- Weekly Claims Reduction ---
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|
SeedSpec(
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|
path="Weekly Claims Reduction File Data Dictionary - CMMI-ICD-Appendix-D.docx",
|
||||||
|
url="https://innovation.cms.gov/innovation-models/aco-reach",
|
||||||
|
title="Weekly Claims Reduction File Data Dictionary (Appendix D)",
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||||||
|
tags=["module:aco", "program:reach", "source:cms-website"],
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||||||
|
),
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|
# --- Other ---
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|
SeedSpec(
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|
path="Dremio-Apache-Polaris-The-Definitive-Guide.pdf",
|
||||||
|
url="https://www.dremio.com/resources/guides/apache-polaris/",
|
||||||
|
title="Dremio — Apache Polaris: The Definitive Guide",
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||||||
|
tags=["source:vendor"],
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||||||
|
),
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||||||
|
)
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||||||
|
|
||||||
|
|
||||||
|
# ── Helpers ───────────────────────────────────────────────────────
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|
|
||||||
|
|
||||||
|
def _zotero_key() -> str:
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|
chars = string.ascii_uppercase + string.digits
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return "".join(random.choices(chars, k=8)) # noqa: S311
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||||||
|
|
||||||
|
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||||||
|
def _now_iso() -> str:
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||||||
|
return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
|
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|
|
||||||
|
|
||||||
|
def _ensure_value(con: sqlite3.Connection, value: str) -> int:
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||||||
|
row = con.execute(
|
||||||
|
"SELECT valueID FROM itemDataValues WHERE value = ?", (value,)
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||||||
|
).fetchone()
|
||||||
|
if row:
|
||||||
|
return row[0]
|
||||||
|
cur = con.execute(
|
||||||
|
"INSERT INTO itemDataValues (value) VALUES (?)", (value,)
|
||||||
|
)
|
||||||
|
return cur.lastrowid
|
||||||
|
|
||||||
|
|
||||||
|
def _ensure_tag(con: sqlite3.Connection, name: str) -> int:
|
||||||
|
row = con.execute(
|
||||||
|
"SELECT tagID FROM tags WHERE name = ?", (name,)
|
||||||
|
).fetchone()
|
||||||
|
if row:
|
||||||
|
return row[0]
|
||||||
|
cur = con.execute("INSERT INTO tags (name) VALUES (?)", (name,))
|
||||||
|
return cur.lastrowid
|
||||||
|
|
||||||
|
|
||||||
|
def _set_zotero_field(
|
||||||
|
con: sqlite3.Connection, item_id: int, field_id: int, value: str
|
||||||
|
) -> None:
|
||||||
|
if not value:
|
||||||
|
return
|
||||||
|
value_id = _ensure_value(con, value)
|
||||||
|
con.execute(
|
||||||
|
"INSERT OR REPLACE INTO itemData (itemID, fieldID, valueID) "
|
||||||
|
"VALUES (?, ?, ?)",
|
||||||
|
(item_id, field_id, value_id),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def _content_type(path: Path) -> str:
|
||||||
|
ext = path.suffix.lower()
|
||||||
|
types = {
|
||||||
|
".pdf": "application/pdf",
|
||||||
|
".xlsx": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
|
||||||
|
".docx": "application/vnd.openxmlformats-officedocument.wordprocessingml.document",
|
||||||
|
".zip": "application/zip",
|
||||||
|
".ndjson": "application/x-ndjson",
|
||||||
|
".csv": "text/csv",
|
||||||
|
".txt": "text/plain",
|
||||||
|
".json": "application/json",
|
||||||
|
".ini": "text/plain",
|
||||||
|
}
|
||||||
|
return types.get(ext, "application/octet-stream")
|
||||||
|
|
||||||
|
|
||||||
|
# ── Phase A: tag existing Zotero attachments ──────────────────────
|
||||||
|
|
||||||
|
|
||||||
|
def tag_existing_zotero(
|
||||||
|
con: sqlite3.Connection, spec: SeedSpec, *, dry_run: bool = False
|
||||||
|
) -> bool:
|
||||||
|
"""Find a Zotero attachment by filename and tag its parent."""
|
||||||
|
filename = Path(spec.path).name
|
||||||
|
row = con.execute(
|
||||||
|
"""SELECT ia.parentItemID
|
||||||
|
FROM itemAttachments ia
|
||||||
|
WHERE ia.path LIKE ?
|
||||||
|
LIMIT 1""",
|
||||||
|
(f"%{filename}",),
|
||||||
|
).fetchone()
|
||||||
|
if not row or not row[0]:
|
||||||
|
return False
|
||||||
|
|
||||||
|
parent_id = row[0]
|
||||||
|
if dry_run:
|
||||||
|
print(f" [exists] Zotero parent itemID={parent_id}")
|
||||||
|
return True
|
||||||
|
|
||||||
|
# Add seed tag + any extra tags
|
||||||
|
all_tags = [SEED_TAG] + spec.tags
|
||||||
|
for tag_name in all_tags:
|
||||||
|
tag_id = _ensure_tag(con, tag_name)
|
||||||
|
con.execute(
|
||||||
|
"INSERT OR IGNORE INTO itemTags (itemID, tagID, type) "
|
||||||
|
"VALUES (?, ?, 0)",
|
||||||
|
(parent_id, tag_id),
|
||||||
|
)
|
||||||
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
# ── Phase B: create missing Zotero items ──────────────────────────
|
||||||
|
|
||||||
|
|
||||||
|
def register_in_zotero(
|
||||||
|
con: sqlite3.Connection, spec: SeedSpec, *, dry_run: bool = False
|
||||||
|
) -> None:
|
||||||
|
"""Create a Zotero webpage item + file attachment for a seed."""
|
||||||
|
if not spec.url:
|
||||||
|
if dry_run:
|
||||||
|
print(" [skip-zotero] no URL")
|
||||||
|
return
|
||||||
|
|
||||||
|
if dry_run:
|
||||||
|
print(" [create] new Zotero webpage item")
|
||||||
|
return
|
||||||
|
|
||||||
|
now = _now_iso()
|
||||||
|
next_id = con.execute(
|
||||||
|
"SELECT COALESCE(MAX(itemID), 0) + 1 FROM items"
|
||||||
|
).fetchone()[0]
|
||||||
|
parent_key = _zotero_key()
|
||||||
|
|
||||||
|
# Create parent webpage item
|
||||||
|
con.execute(
|
||||||
|
"""INSERT INTO items
|
||||||
|
(itemID, itemTypeID, dateAdded, dateModified,
|
||||||
|
key, version, synced, libraryID)
|
||||||
|
VALUES (?, ?, ?, ?, ?, 0, 0, 1)""",
|
||||||
|
(next_id, ZOTERO_TYPE_WEBPAGE, now, now, parent_key),
|
||||||
|
)
|
||||||
|
|
||||||
|
_set_zotero_field(con, next_id, ZOTERO_FIELD_TITLE, spec.title)
|
||||||
|
_set_zotero_field(con, next_id, ZOTERO_FIELD_URL, spec.url)
|
||||||
|
_set_zotero_field(con, next_id, ZOTERO_FIELD_DATE, now[:10])
|
||||||
|
_set_zotero_field(con, next_id, ZOTERO_FIELD_ACCESS_DATE, now)
|
||||||
|
_set_zotero_field(
|
||||||
|
con, next_id, ZOTERO_FIELD_WEBSITE_TYPE, "Government Data Portal"
|
||||||
|
)
|
||||||
|
_set_zotero_field(
|
||||||
|
con,
|
||||||
|
next_id,
|
||||||
|
ZOTERO_FIELD_WEBSITE_TITLE,
|
||||||
|
"Centers for Medicare & Medicaid Services",
|
||||||
|
)
|
||||||
|
|
||||||
|
# Tags
|
||||||
|
all_tags = [SEED_TAG] + spec.tags
|
||||||
|
for tag_name in all_tags:
|
||||||
|
tag_id = _ensure_tag(con, tag_name)
|
||||||
|
con.execute(
|
||||||
|
"INSERT OR IGNORE INTO itemTags (itemID, tagID, type) "
|
||||||
|
"VALUES (?, ?, 0)",
|
||||||
|
(next_id, tag_id),
|
||||||
|
)
|
||||||
|
|
||||||
|
# Attach file (skip directories)
|
||||||
|
seed_path = SEEDS_DIR / spec.path
|
||||||
|
if seed_path.is_file():
|
||||||
|
att_id = con.execute(
|
||||||
|
"SELECT COALESCE(MAX(itemID), 0) + 1 FROM items"
|
||||||
|
).fetchone()[0]
|
||||||
|
att_key = _zotero_key()
|
||||||
|
|
||||||
|
# Copy to Zotero storage
|
||||||
|
storage_dir = ZOTERO_STORAGE / att_key
|
||||||
|
subprocess.run(
|
||||||
|
["sudo", "mkdir", "-p", str(storage_dir)], check=True
|
||||||
|
)
|
||||||
|
dest = storage_dir / seed_path.name
|
||||||
|
subprocess.run(
|
||||||
|
["sudo", "cp", str(seed_path), str(dest)], check=True
|
||||||
|
)
|
||||||
|
subprocess.run(
|
||||||
|
["sudo", "chown", "-R", "100999:100999", str(storage_dir)],
|
||||||
|
check=True,
|
||||||
|
)
|
||||||
|
|
||||||
|
con.execute(
|
||||||
|
"""INSERT INTO items
|
||||||
|
(itemID, itemTypeID, dateAdded, dateModified,
|
||||||
|
key, version, synced, libraryID)
|
||||||
|
VALUES (?, ?, ?, ?, ?, 0, 0, 1)""",
|
||||||
|
(att_id, ZOTERO_TYPE_ATTACHMENT, now, now, att_key),
|
||||||
|
)
|
||||||
|
con.execute(
|
||||||
|
"""INSERT INTO itemAttachments
|
||||||
|
(itemID, parentItemID, linkMode, contentType, path)
|
||||||
|
VALUES (?, ?, 0, ?, ?)""",
|
||||||
|
(
|
||||||
|
att_id,
|
||||||
|
next_id,
|
||||||
|
_content_type(seed_path),
|
||||||
|
f"storage:{seed_path.name}",
|
||||||
|
),
|
||||||
|
)
|
||||||
|
title_val = _ensure_value(con, seed_path.name)
|
||||||
|
con.execute(
|
||||||
|
"INSERT INTO itemData (itemID, fieldID, valueID) "
|
||||||
|
"VALUES (?, ?, ?)",
|
||||||
|
(att_id, ZOTERO_FIELD_TITLE, title_val),
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
# ── Phase C: register in bib.sqlite ──────────────────────────────
|
||||||
|
|
||||||
|
|
||||||
|
def register_in_bib(spec: SeedSpec, *, dry_run: bool = False) -> str:
|
||||||
|
"""Create a bib item for a seed. Returns the item key."""
|
||||||
|
from bib.item import Item
|
||||||
|
from bib.store import Store
|
||||||
|
|
||||||
|
if dry_run:
|
||||||
|
print(" [bib] would create")
|
||||||
|
return ""
|
||||||
|
|
||||||
|
store = Store(BIB_DB)
|
||||||
|
tags = [SEED_TAG] + spec.tags
|
||||||
|
|
||||||
|
# Check if this exact title already exists with seed tag
|
||||||
|
existing = store.list_items(tag=SEED_TAG, query=spec.title)
|
||||||
|
if existing:
|
||||||
|
print(f" [bib] already exists: {existing[0].key}")
|
||||||
|
store.close()
|
||||||
|
return existing[0].key
|
||||||
|
|
||||||
|
item = Item(
|
||||||
|
item_type="download",
|
||||||
|
title=spec.title,
|
||||||
|
url=spec.url,
|
||||||
|
institution="Centers for Medicare & Medicaid Services",
|
||||||
|
tags=tags,
|
||||||
|
)
|
||||||
|
|
||||||
|
key = store.create(item, tags=None)
|
||||||
|
|
||||||
|
# Attach the file (skip directories)
|
||||||
|
seed_path = SEEDS_DIR / spec.path
|
||||||
|
if seed_path.is_file():
|
||||||
|
store.attach_file(key, seed_path)
|
||||||
|
|
||||||
|
store.close()
|
||||||
|
return key
|
||||||
|
|
||||||
|
|
||||||
|
# ── Pull mode: Zotero → dev/seeds/ ───────────────────────────────
|
||||||
|
|
||||||
|
|
||||||
|
def pull_from_zotero(*, dry_run: bool = False) -> int:
|
||||||
|
"""Copy seed-tagged Zotero attachments missing from dev/seeds/."""
|
||||||
|
con = sqlite3.connect(ZOTERO_DB, timeout=10)
|
||||||
|
rows = con.execute(
|
||||||
|
"""SELECT ia.path, ia.parentItemID
|
||||||
|
FROM itemAttachments ia
|
||||||
|
JOIN items i ON ia.itemID = i.itemID
|
||||||
|
JOIN itemTags it ON ia.parentItemID = it.itemID
|
||||||
|
JOIN tags t ON it.tagID = t.tagID
|
||||||
|
WHERE t.name = ?
|
||||||
|
AND ia.path IS NOT NULL
|
||||||
|
AND ia.linkMode = 0""",
|
||||||
|
(SEED_TAG,),
|
||||||
|
).fetchall()
|
||||||
|
con.close()
|
||||||
|
|
||||||
|
copied = 0
|
||||||
|
for row in rows:
|
||||||
|
zpath = row[0] # "storage:filename"
|
||||||
|
if not zpath.startswith("storage:"):
|
||||||
|
continue
|
||||||
|
filename = zpath[len("storage:"):]
|
||||||
|
|
||||||
|
dest = SEEDS_DIR / filename
|
||||||
|
if dest.exists():
|
||||||
|
continue
|
||||||
|
|
||||||
|
# Find the file in Zotero storage
|
||||||
|
for storage_sub in ZOTERO_STORAGE.iterdir():
|
||||||
|
candidate = storage_sub / filename
|
||||||
|
if candidate.exists():
|
||||||
|
if dry_run:
|
||||||
|
print(f" [pull] {filename}")
|
||||||
|
else:
|
||||||
|
shutil.copy2(candidate, dest)
|
||||||
|
print(f" pulled {filename}")
|
||||||
|
copied += 1
|
||||||
|
break
|
||||||
|
|
||||||
|
return copied
|
||||||
|
|
||||||
|
|
||||||
|
# ── Main ──────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
|
||||||
|
def main() -> None:
|
||||||
|
parser = argparse.ArgumentParser(
|
||||||
|
description="Register dev/seeds/ files in bib & Zotero"
|
||||||
|
)
|
||||||
|
parser.add_argument(
|
||||||
|
"--dry-run",
|
||||||
|
action="store_true",
|
||||||
|
help="Preview without modifying databases",
|
||||||
|
)
|
||||||
|
parser.add_argument(
|
||||||
|
"--pull",
|
||||||
|
action="store_true",
|
||||||
|
help="Pull seed-tagged Zotero attachments into dev/seeds/",
|
||||||
|
)
|
||||||
|
args = parser.parse_args()
|
||||||
|
|
||||||
|
if args.pull:
|
||||||
|
print("Pulling seed-tagged attachments from Zotero...")
|
||||||
|
n = pull_from_zotero(dry_run=args.dry_run)
|
||||||
|
print(f"{'Would copy' if args.dry_run else 'Copied'} {n} files")
|
||||||
|
return
|
||||||
|
|
||||||
|
zotero_db_path = Path(ZOTERO_DB)
|
||||||
|
has_zotero = zotero_db_path.exists()
|
||||||
|
zcon = None
|
||||||
|
if has_zotero:
|
||||||
|
try:
|
||||||
|
zcon = sqlite3.connect(ZOTERO_DB, timeout=10)
|
||||||
|
# Test that we can actually read
|
||||||
|
zcon.execute("SELECT 1 FROM items LIMIT 1")
|
||||||
|
except sqlite3.OperationalError as exc:
|
||||||
|
print(f"Zotero DB locked ({exc}), skipping Zotero phases")
|
||||||
|
zcon = None
|
||||||
|
|
||||||
|
total = len(SEED_REGISTRY)
|
||||||
|
tagged = 0
|
||||||
|
created_z = 0
|
||||||
|
created_b = 0
|
||||||
|
|
||||||
|
for i, spec in enumerate(SEED_REGISTRY, 1):
|
||||||
|
seed_path = SEEDS_DIR / spec.path
|
||||||
|
exists = seed_path.exists()
|
||||||
|
status = "OK" if exists else "MISSING"
|
||||||
|
print(f"[{i}/{total}] {spec.path} [{status}]")
|
||||||
|
|
||||||
|
if not exists:
|
||||||
|
print(" [skip] file not found")
|
||||||
|
continue
|
||||||
|
|
||||||
|
# Phase A+B: Zotero
|
||||||
|
if zcon:
|
||||||
|
found = tag_existing_zotero(zcon, spec, dry_run=args.dry_run)
|
||||||
|
if found:
|
||||||
|
tagged += 1
|
||||||
|
else:
|
||||||
|
register_in_zotero(zcon, spec, dry_run=args.dry_run)
|
||||||
|
created_z += 1
|
||||||
|
|
||||||
|
# Phase C: bib.sqlite
|
||||||
|
register_in_bib(spec, dry_run=args.dry_run)
|
||||||
|
created_b += 1
|
||||||
|
|
||||||
|
if zcon:
|
||||||
|
if not args.dry_run:
|
||||||
|
zcon.commit()
|
||||||
|
zcon.close()
|
||||||
|
|
||||||
|
label = "Would register" if args.dry_run else "Registered"
|
||||||
|
print(f"\n{label}:")
|
||||||
|
print(f" Zotero tagged existing: {tagged}")
|
||||||
|
print(f" Zotero created new: {created_z}")
|
||||||
|
print(f" Bib items upserted: {created_b}")
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
main()
|
||||||
@@ -19,6 +19,8 @@ dev = [
|
|||||||
"coverage>=7.13.4",
|
"coverage>=7.13.4",
|
||||||
"dbt-core==1.10.15",
|
"dbt-core==1.10.15",
|
||||||
"dbt-duckdb>=1.10,<1.11",
|
"dbt-duckdb>=1.10,<1.11",
|
||||||
|
"openpyxl>=3.1.5",
|
||||||
|
"pdfplumber>=0.11.9",
|
||||||
"polars>=1.38.1",
|
"polars>=1.38.1",
|
||||||
"pytest>=9.0.2",
|
"pytest>=9.0.2",
|
||||||
"pytest-cov>=7.0.0",
|
"pytest-cov>=7.0.0",
|
||||||
|
|||||||
@@ -131,6 +131,47 @@ class Tag(BaseModel):
|
|||||||
"""
|
"""
|
||||||
return cls(namespace="sup", value=slug)
|
return cls(namespace="sup", value=slug)
|
||||||
|
|
||||||
|
@classmethod
|
||||||
|
def measure(cls, measure_id: str) -> Tag:
|
||||||
|
"""Tag for a CMS quality measure identifier.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
measure_id : str
|
||||||
|
Short measure code, e.g. ``UAMCC``, ``ACR``, ``HWR``,
|
||||||
|
``MCC``, ``NQF2888``, ``NQF1789``.
|
||||||
|
|
||||||
|
Examples::
|
||||||
|
|
||||||
|
Tag.measure("UAMCC") # measure:UAMCC
|
||||||
|
Tag.measure("ACR") # measure:ACR
|
||||||
|
Tag.measure("HWR") # measure:HWR
|
||||||
|
"""
|
||||||
|
return cls(namespace="measure", value=measure_id.upper())
|
||||||
|
|
||||||
|
@classmethod
|
||||||
|
def seed(cls) -> Tag:
|
||||||
|
"""Tag marking an item as a dev/seeds/ seed file."""
|
||||||
|
return cls(namespace="seed", value="true")
|
||||||
|
|
||||||
|
@classmethod
|
||||||
|
def program(cls, program_name: str) -> Tag:
|
||||||
|
"""Tag for the CMS payment / quality program context.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
program_name : str
|
||||||
|
Program identifier, e.g. ``reach``, ``mssp``, ``mips``,
|
||||||
|
``vbp``, ``hacrp``.
|
||||||
|
|
||||||
|
Examples::
|
||||||
|
|
||||||
|
Tag.program("reach") # program:reach
|
||||||
|
Tag.program("mssp") # program:mssp
|
||||||
|
Tag.program("mips") # program:mips
|
||||||
|
"""
|
||||||
|
return cls(namespace="program", value=program_name.lower())
|
||||||
|
|
||||||
|
|
||||||
_RULE_KIND = {"Final": "FR", "Proposed": "PR", "Correction": "CR"}
|
_RULE_KIND = {"Final": "FR", "Proposed": "PR", "Correction": "CR"}
|
||||||
|
|
||||||
|
|||||||
150
uv.lock
generated
150
uv.lock
generated
@@ -568,6 +568,15 @@ wheels = [
|
|||||||
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||||||
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "pytest"
|
name = "pytest"
|
||||||
version = "9.0.2"
|
version = "9.0.2"
|
||||||
@@ -1464,6 +1610,8 @@ dev = [
|
|||||||
{ name = "coverage" },
|
{ name = "coverage" },
|
||||||
{ name = "dbt-core" },
|
{ name = "dbt-core" },
|
||||||
{ name = "dbt-duckdb" },
|
{ name = "dbt-duckdb" },
|
||||||
|
{ name = "openpyxl" },
|
||||||
|
{ name = "pdfplumber" },
|
||||||
{ name = "polars" },
|
{ name = "polars" },
|
||||||
{ name = "pytest" },
|
{ name = "pytest" },
|
||||||
{ name = "pytest-cov" },
|
{ name = "pytest-cov" },
|
||||||
@@ -1486,6 +1634,8 @@ dev = [
|
|||||||
{ name = "coverage", specifier = ">=7.13.4" },
|
{ name = "coverage", specifier = ">=7.13.4" },
|
||||||
{ name = "dbt-core", specifier = "==1.10.15" },
|
{ name = "dbt-core", specifier = "==1.10.15" },
|
||||||
{ name = "dbt-duckdb", specifier = ">=1.10,<1.11" },
|
{ name = "dbt-duckdb", specifier = ">=1.10,<1.11" },
|
||||||
|
{ name = "openpyxl", specifier = ">=3.1.5" },
|
||||||
|
{ name = "pdfplumber", specifier = ">=0.11.9" },
|
||||||
{ name = "polars", specifier = ">=1.38.1" },
|
{ name = "polars", specifier = ">=1.38.1" },
|
||||||
{ name = "pytest", specifier = ">=9.0.2" },
|
{ name = "pytest", specifier = ">=9.0.2" },
|
||||||
{ name = "pytest-cov", specifier = ">=7.0.0" },
|
{ name = "pytest-cov", specifier = ">=7.0.0" },
|
||||||
|
|||||||
Reference in New Issue
Block a user