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v2.0.4 - DOI-determinative dedup + uncertain-pair review moved to Smart Merge step
- Smart Merge: records with different normalized DOIs are never the same publication. Enforced in the matching negative rule, in the borderline listing (list_borderline), and at the apply step (decide_borderline), so such pairs are never auto-merged nor shown for manual review — even for legacy/pre-fix borderline queues. - Uncertain ("borderline") pair review moved from the Filter step to the Smart Merge step as a Yes/No gate: warn that some pairs need manual review, review on demand, then "save & complete" the merge; or complete directly. - Rewrote all Python module docstrings in English; removed academic citations from file headers. - Removed dead, never-rendered merge-page components and their now-unused imports; added Smart Merge DOI tests (doi_conflict + Stage-4 guard).
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‎apps/api/jobs/runner.py‎

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"""Basit, tek-kullanıcılı job runner.
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"""Simple, single-user job runner.
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- Tek aktif iş + sıralı kuyruk (self-hosted için yeterli)
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- Bellekte log + progress; opsiyonel olarak proje klasörüne persist
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- SSE üzerinden canlı stream
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Runs background jobs as asyncio tasks with in-memory state, log, and progress
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tracking, streamed live to clients over SSE. Provides per-project exclusivity to
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prevent overlapping heavy jobs and a dedicated thread pool for cancellable
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CPU-bound work so the rest of the app stays responsive.
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"""
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from __future__ import annotations

‎apps/api/main.py‎

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"""BibexPy v2 — FastAPI uygulama girişi.
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"""BibexPy FastAPI application entry point.
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Geliştirme:
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cd apps/api && python -m uvicorn main:app --reload --port 8001
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cd apps/web && npm run dev # ayrı terminal
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Backend tüm router'ları `/api/` prefix altında mount eder; bu, ileride
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frontend ile aynı host'tan serve edilse bile URL çakışmasını önler.
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`_frontend_root()` — opsiyonel statik UI mount (varsa). Geliştirmede
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genelde frontend ayrı çalıştığı için `None` döner ve devre dışı kalır.
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Builds the FastAPI app, configures CORS, and mounts all API routers under
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the ``/api`` prefix. Optionally serves the static frontend export when one
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is present, otherwise runs in API-only mode.
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"""
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from __future__ import annotations

‎apps/api/routers/audit.py‎

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"""Audit log endpoint'leri."""
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"""API endpoints for project audit logs.
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Provides routes to list, summarize, append, and clear audit entries for a
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project, plus a Markdown report export. Entries are scoped to the project's
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currently active analysis.
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"""
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from __future__ import annotations
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‎apps/api/routers/downloads.py‎

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"""Üretilen dosyalar için genel indirme endpoint'i."""
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"""Generic file download endpoint for generated project artifacts.
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Serves files from an allow-listed set of project subfolders (raw, processed,
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merged, exports, snapshots), validating the project and folder and guarding
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against path traversal before returning the file.
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"""
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from pathlib import Path
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‎apps/api/routers/export_folder.py‎

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"""Belirli bir lokal klasöre kopyalama — self-hosted için.
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"""API routes for copying project export files to a local folder.
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Self-hosted tek kullanıcı senaryosunda backend ve kullanıcı aynı makinededir;
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backend'in yazma yetkisi olan herhangi bir klasöre çıktıyı bırakabilir.
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Intended for self-hosted single-user deployments where the backend and user
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share the same machine. Provides endpoints to copy selected export files into
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any backend-writable target folder and to suggest common output locations.
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"""
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import shutil

‎apps/api/routers/prepare.py‎

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"""Veri hazırlama orkestratörü.
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"""Data preparation orchestration endpoints.
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Tek butonla ham CSV/TXT'leri otomatik XLSX'e çevirir.
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Kullanıcı dönüşüm seçimleri yapmasına gerek kalmaz.
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Exposes API routes that automatically convert raw uploaded CSV/TXT
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files into merged XLSX outputs, report preparation status (including
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staleness), reset preparation, and delete individual processed files.
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"""
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from pathlib import Path

‎apps/api/routers/quality.py‎

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"""Veri kalitesi & grafik endpoint'leri.
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"""Data quality and chart API endpoints.
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UI bu endpoint'leri:
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- Dashboard panelinde alan-bazlı doluluk yüzdelerini göstermek için
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- Records sayfası üstündeki chart'lar için kullanır.
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Exposes per-field fill-rate statistics and a weighted health score for a
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project's merged dataset, an exportable overview table (CSV/XLSX), and
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aggregated chart data (year, journal, document type, language, citation
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distributions) consumed by the dashboard and records pages.
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from __future__ import annotations

‎apps/api/routers/records.py‎

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"""Kayıt seviyesinde işlemler — toplu silme, seçilenleri zenginleştirme.
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"""API router for record-level operations on a project's merged dataset.
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Her destrüktif işlem önce snapshot alır ve audit log'a yazılır.
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Provides endpoints to bulk-delete records, edit a single record, and list or
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restore dataset snapshots. Every destructive operation takes a snapshot first
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and writes an entry to the audit log.
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"""
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‎apps/api/routers/report.py‎

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"""Rapor endpoint'leri — ham günlük (MD/TXT/PDF) + LLM metodoloji raporu (MD/TXT/PDF).
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"""Report endpoints for the operation log and the methodology report.
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Export adımından sonraki son adım. İki çıktı türü:
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• Ham operasyon günlüğü — sürecin birebir kaydı.
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• Metodoloji raporu — günlüğün LLM ile İngilizce makale metnine dönüştürülmüş hali.
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Serves two output types in Markdown, plain text, and PDF formats:
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- Raw operation log: a faithful record of the processing pipeline.
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- Methodology report: an English narrative generated from the log via an LLM.
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‎apps/api/routers/settings.py‎

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"""Ayarlar endpoint — .env dosyasını UI üzerinden oku/yaz.
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"""Settings endpoints for reading and writing the .env file from the UI.
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Yalnız self-hosted senaryo için tasarlandı. Backend ve frontend aynı makinedeyse
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kullanıcı API key ve email gibi alanları UI'dan girebilir.
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Exposes a FastAPI router that lists editable configuration fields (storage path,
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enrichment API keys, LLM provider/model), validates filesystem paths, and persists
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updates back to the .env file. Intended for self-hosted setups where the backend
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and frontend run on the same machine.
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"""
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