feat: promote production-mvp to main — drives, scan history, files modularization - #55

Merged

patchmemory merged 406 commits into

mainfrom

Aug 18, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 27, 2026

fix(settings): repair broken API endpoint calls post-migration

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87ef013
fix(settings): resolve remaining 404s in chat behavior settings

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fb20cc0
fix(settings): resolve global syntax error from smart quotes

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1b79eea
feat(database): add source, modified, validation_output fields to scripts table

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740d962
feat(analyses): bootstrap endpoint, validation, restore, and registry UI

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feat(links): bootstrap endpoint, validation, restore, and registry UI

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d7aa8c6
feat(scripts): add GET endpoint for validation result display

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a040f94
feat(settings): create shared validation modal partial

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2ad44f4
feat(analyses): wire validation modal with click handlers

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6d92585
feat(links): wire validation modal with click handlers

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58fd7e6
feat(labels): registry table with push status and sync detection

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5d6933b
fix(files): correct Neo4j connection status display

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25e0082
feat(files): implement live vs snapshot view model

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9269e38
feat(files): unified activity panel with snapshot index

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4198034
feat(files): checkbox file selection mode with indeterminate states

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3fde7a9
feat(files): snapshot configuration modal and refresh/reconfigure flow

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ad45ac0
fix(files): correct activity panel wiring and modal display issues

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329b19e
fix(files): resolve live servers and snapshot mode redundancy

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e215988
fix(files): resolve servers 500 error and snapshot mode empty state

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ec4b2c7
fix(files): resolve servers 500 error with defensive extension access

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8eabe39
fix(files): correct ProviderRegistry iteration in api_servers

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6c769c3
fix(files): maintain tree selection highlighting across modes

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58b05cd
feat(interpreter): implement declared node write pipeline at commit time

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2dccd2f
feat(interpreter): add Bruker SkyScan microCT log interpreter

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636202d

Commits on Feb 28, 2026

feat(schema): integrate SciDK schema layer with sanitization pipeline

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ec0eeff
chore(dev): update submodule to include schema layer contracts

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5f1a38f
feat(schema): implement Label schema push to Neo4j

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192991e
fix(validation): skip Python checks for Cypher link scripts

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c71443e
fix(ui): consolidate Links group and add Examples category

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3628309
feat(links): show wizard links in Settings → Links registry

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a6b233e
fix(scripts): clean database and prevent root-level utility scripts from loading

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e72821f
fix(links): preserve group toggle state when clicking to expand/collapse

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2eb9020
fix(links): preserve group toggle state and standardize wizard display

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987b083
feat(links): unify UI and show properties in results

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dd31ba9
fix(links): correct HTML structure - wizard now renders in right panel

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cbaeef0
fix(links): fix discovered relationships - dedupe, save, and details

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4969c15
feat(links): add discovered relationship import with stub nodes

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fd4b6f0
fix(links): serialize Neo4j objects and optimize instances query

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1d1bc18
fix(links): discovered import wizard validation and scalar query fixes

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a56ed95
fix(links): improve discovered relationship import wizard UX

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5014e65
fix(links): display UID consistently and hide irrelevant buttons in discovered import

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5ed1d4b
feat(links): add status field to link_definitions table

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900a09e
feat(links): redesign Links page with Active/Pending/Available tabs

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d306851
fix(links): fix four bugs in Links page and import functionality

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1bdfa0d
fix(links): add ORDER BY and detailed logging to discovered import pagination

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6214c43
fix(links): add missing logger import in link_service

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48dd6de
fix(links): split preview count queries to avoid Neo4j aggregation limits

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7848d8a
debug(links): add database source logging to preview functions

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474ca96
fix(links): preserve source database context in Available tab

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4c0ce11
fix(links): use exact node counts in preview_discovered_import

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e36c379
feat(links): add progress tracking and auto-adopt for discovered imports

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6b21a68
fix(links): show correct total in import progress (X / 526,291)

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4d4936f
feat(links): add tqdm-style ETA to import progress

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eab80cf
fix(links): prevent state bleed between wizard panel sessions

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9c0447e
fix(links): fix Pending link loading and add job progress recovery

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8585f65
fix(links): call correct function updateDiscoveredImportDisplay

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1be07d1
perf(links): increase batch size from 100 to 5000 for imports

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bcf9b85
fix(links): ensure discovered import rel is set for display

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1c6e609
fix(links): remove source_filters/target_filters from INSERT

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1f7a10f
debug(links): add detailed logging to import progress tracking

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eb10c1e
fix(links): hide wizard buttons when loading discovered import links

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ecdc5d9
fix(links): improve discovered import UX with cancel, delete, and keyset pagination
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283b27f
fix(links): add Cancel button to resumed import progress
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78f6148
fix(links): align Pending tab count with render filter

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fa659b4
fix(links): include status field in list_all_links() normalized output

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3bfe696
feat(links): add unified refresh with Active verification, Available rescan, and auto-promotion
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4b6d733
fix(links): remove Primary from Available tab and deduplicate by triple pattern

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11d0db5
fix(links): show tab-specific total in "Showing X of Y" display

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d3796dc
feat(links): add sync status and "Sync Now" button to Active import links

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a22be3a
fix(links): query primary database directly for accurate sync status display

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ada47ff
feat(links): add paginated "View & Download" index panel to all tabs

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bc2f82a
fix(links): clean up Active link UI and show index for all Active links

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9940d6f
fix(links): render sync status and index for Active links

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a085c5a
fix(links): handle missing UID properties in Active link index

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9b1f4b8
fix(links): show relationship index for Active links without match_config

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c698496

Commits on Mar 1, 2026

docs(links): clarify match_config fallback for wizard-defined links

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55d7c8e
fix(links): two bugs in Active import link UI

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2c72ea9
refactor(links): extract JavaScript into separate module files

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7ad5616
refactor(links): clean read-only view for Active links with editable UID selectors

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ba84f66
feat(links): add relationship property enrichment for Active import links

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e6533e1
fix(links): resolve cross-module scope issues in JavaScript modules
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ea68c29
fix(links): preserve triple badge and restore UID auto-selection in Active links

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3e7eb37
feat(links): add property selection to Enrich Relationships section

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7c7988f
fix: update stale test assertions for JS modularization and builtin count
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92b3779
test: add coverage for relationship enrichment endpoint
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2d0868f
fix(links): correct import path for get_settings_by_prefix in _try_apoc_import
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02a68b5
feat(security): add Security Overview page to Settings

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6477bf8
fix(security): make Users link navigate correctly via onclick
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3681a68

Commits on Mar 2, 2026

feat(interpreters): add Bio-Formats integration layer

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5d8873c
feat(interpreters): register Bio-Formats interpreters

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0ca9b2f
test(interpreters): add Bio-Formats integration tests

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c5f6741
docs(bioformats): add comprehensive setup guide

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ad787bc
docs(interpreters): add comprehensive imaging interpreter template

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6c33809
docs(contracts): update interpreter contract to class-based standard

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c7354c3
feat(interpreters): add Bruker MicroCT composite dataset interpreter

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4a64440
feat(chat): Sprint 1 — ChatSEEK patterns + intent routing + query library
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2096a0b
fix(tests): resolve 4 pre-existing test failures + 2 env issues
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b9bae53
Merge origin/main into production-mvp
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dda2803
fix(intent_classifier): remove stray quote in regex pattern
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Merge branch 'main' of github.com:patchmemory/scidk into production-mvp
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03799a3
fix: enable VPN access and fix DriveInfo API error

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80c3329
fix: enable first-time admin user setup without authentication

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8e86c4b
fix: add reverse proxy subpath support for /scidk deployment

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0b485ff

Commits on Mar 3, 2026

fix: fix login/logout redirects for subpath deployments

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3b37ce0
fix(auth): add SCIDK_BASE to login.html for subpath deployment
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061ffc0
fix(templates): fix remaining SCIDK_BASE misses in login and settings
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c441c29
fix(frontend): SCIDK_BASE for static JS files and remaining template fixes
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feat(ui): add knowledge graph favicon
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fix(config): load .env automatically via python-dotenv
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fix(deps): add python-dotenv to requirements.txt
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0208b17
fix(frontend): complete SCIDK_BASE audit - fix all remaining hardcoded API paths for subpath deployment

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2997a62
fix(frontend): fix URL variable patterns missed by SCIDK_BASE audit
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8219284
fix(links): auto-refresh relationship index when UID property changes

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772c349
fix(links): restore triple display visibility when switching from Active to Available links

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900cbc0
fix(links): fix Refresh button and relationship index for Active links

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8d9c978
fix(neo4j): connect profile system to app startup + encrypt passwords

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5beb3ec
Revert "fix(neo4j): connect profile system to app startup + encrypt passwords"
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85b31af
fix(links): add Save button to Available links and filter Read-Only from Active

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ea718b3
ci(e2e): resolve issues with map api link refactoring
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8bbd041

Commits on Mar 9, 2026

feat: Schema Intelligence Layer (Phases 1-3, 6)

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bd175eb
feat: Concept Graph infrastructure

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feat: Concept Graph service layer and pipeline wiring

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feat: Chat AI infrastructure (ReAct loop, summarization, cypher utils)

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feat: Chat service context retrieval

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feat: Chat UI streaming and ReAct step visualization

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ac4b07a
config: add concept graph, chat history, and schema intelligence env vars

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9c4f270
chore: add gunicorn restart script and ignore log file

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test: add chat, intent routing, Neo4j, and streaming test suite

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e632798

Commits on Mar 10, 2026

feat: schema intelligence export/import and label profile API

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feat: schema intelligence REST API endpoints (Phase 4+5)

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feat: Chat Intelligence section in Labels page (Phase 4)

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feat: Schema Intelligence settings section (Phase 5)

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feat: Concept Graph Phase 2 — add traversal_log to SSE done events

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feat: Concept Graph Phase 2 — reasoning block in chat UI

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fix: expose toggleReasoning as global function for onclick handler

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feat: concept graph editor UI + fix summarize + fix edge warnings
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033805d
fix: add Schema Intelligence and Concept Graph to settings sidebar navigation
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abc1cc1
feat: enhance Chat History page with Neo4j chat graph info
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2cd47c4
fix: use raw message for intent classification, not conversation context
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feat: Schema Intelligence editable UI in Labels page (Phase 4B-D)

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a05ec19
feat: add Neo4j full-text indexes on string properties

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feat: MCP server scaffold (5 core tools, stdio transport)

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feat: Concept Graph Phase 3 — decay, MCP tools, export/import

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fix: set last_updated in feedback loop for weight decay

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feat: Connections page consolidation + Schema Map
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ec026fc
refactor: native SUMMARIZE streaming + Cytoscape graph_utils
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c27ad24
fix: wait for SciDKGraph to load before initializing graphs
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0972be9
fix: defer Cytoscape init until container is visible in DOM
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64fc765
fix: graph_utils.js stylesheet and element data issues
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fix: correct edge field names in queryResultsToElements and schemaToElements
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debug: add extensive logging to queryResultsToElements
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49079db
fix: handle node ID 0 correctly in _extractId
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debug: comprehensive edge/node ID logging
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40f6b90
fix: deduplicate edges by ID in queryResultsToElements
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f45a6eb
cleanup: remove debug logging from queryResultsToElements
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5624a51
debug: add graph rendering diagnostics to chat.html
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4a12723
fix: use SciDKGraph.init in renderGraph instead of manual cytoscape init
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fe67aae
debug: add try/catch to expose actual errors in SciDKGraph.init and renderGraph
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b3de067
fix: preserve Cytoscape ID fields when merging properties
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chore: Clean up debug logging from Cytoscape refactor

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a39adae

Commits on Mar 13, 2026

Commits on Jun 25, 2026

fix(neo4j): fall back to env vars when SQLite has no config (J1)

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3aefcfc
fix(chat): define module logger and correct concept-graph imports (J3, J4)

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fix(plugins): encrypt plugin credentials with Fernet (J9)

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docs: refresh guides and add CONTRIBUTING; sync security docs with code

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Commits on Jun 26, 2026

Commits on Jun 30, 2026

feat(datasets): wire Dataset node creation into background scan worker

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feat(auth): add API token (Bearer) auth + harden admin decorator bootstrap

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docs: add rclone setup guide

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Commits on Jul 20, 2026

feat: Maps canvas mode Push 1 — toggle, node search, add-to-canvas

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feat: Maps canvas Push 2 — edge drawing, provisional layer, session persistence

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feat: Maps canvas Push 3 — commit flow, Cypher/Python export, snapshot diff, ellipsis

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feat: Maps canvas Push 4 — correct exports + RO-Crate

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Commits on Jul 21, 2026

feat: Maps canvas Push 5 — keystrokes, batch edges, undo/redo, sidebar instance mode

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feat: Maps canvas Push 6 — selection inspector panel

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ffeae2a

Commits on Aug 3, 2026

fix: create Schema Intelligence tables on startup (Cycle 1, Task A)

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8c46264
fix: attribute properties to their own label, not every label (Cycle 1, Task B)

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fix: one scheduler per deployment, not one per worker (Cycle 1, Task C)

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feat: schedule flush_rankings() every 6 hours (Cycle 1, Task D / J7)

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6626b15

Commits on Aug 4, 2026

fix: match MCP write keywords as tokens, not substrings (Cycle 2, Task A)

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7fb00e8
fix: guard the label before it reaches MCP Cypher (Cycle 2, Task B)

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2548f13
fix: attribute audit rows to g.scidk_user, not 'system' (Cycle 2, Task D / J10)

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fix: require authentication for canvas export routes (Cycle 2, Task E)

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feat: route MCP get_label_profile through schema intelligence (Cycle 2, Task C / J6)

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e774af1
feat: implement the DataSourcePlugin contract for SharePoint (Cycle 3, Task A)

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38a7b7e
refactor: strip all ETL logic from the SharePoint plugin (Cycle 3, Task B)

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test: unit test the SharePoint transform library (Cycle 3, Task C)

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test: narrow the SharePoint tests to the plugin contract (Cycle 3, Task D)

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feat: the Pipeline ETL backend — mapping engine, runner, persistence (Cycle 3B)

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ee949f7
refactor: key canvas sessions by (user_id, context_id) and normalize the user key

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feat: persistent jobstore so pipeline schedules take effect without a restart (Task F)

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feat: Pipeline sources page, connection step, runs and scheduling (Cycle 3B A, B, F)

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test: make the Pipeline HTTP tests independent of any real Neo4j

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feat: Arrows.app schema format for a Pipeline source (Cycle 3B Task C)

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feat: schema routes for a Pipeline source (Cycle 3B Task C)

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feat: schema-space elements on the shared canvas (Cycle 3B Task C)

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feat: the schema canvas, scoped to a Pipeline source (Cycle 3B Task C)

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feat: Step 2 of the add flow — the three schema entry points (Cycle 3B Task C)

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0241870
fix: three things a browser found in the schema canvas

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fix: keep schema labels out of the Maps styling sidebar

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feat: Step 3 of the add flow — column mapping (Cycle 3B Task D)

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feat: the FAIR check — what a run would write (Cycle 3B Task E)

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feat: one Connections page for every graph backend (Cycle 4 Task A)

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docs: say which security controls exist and which are aspirational (Cycle 5 Task C)

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feat: one tool registry, three consumers (Cycle 6 Task A)

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1ecb633
test: pin the canvas RO-Crate export before refactoring it (Cycle 7 Task A)

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feat: one module that knows how the graph maps to an RO-Crate (Cycle 7 Task A)

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feat: build an RO-Crate from a Files page selection (Cycle 7 Task B)

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feat: draft an NIH DMS plan from the live graph (Cycle 7 Task C)

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fb31895
refactor: move weight decay onto the scheduler seam Cycle 1 built (Cycle 8 Task A)

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feat: carry the registry's tool category into the graph and back out (Cycle 8 Task B)

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feat: a seeding entry point that does not need a running server (Cycle 8 Task C)

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dcb003f
feat: export/import controls on the Connections Concept Graph card (Cycle 8 Task C)

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974b15f
refactor: fold the nav down to six researcher-facing pages

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1a13d69

Commits on Aug 5, 2026

refactor: call them Resources, not Pipelines

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478aa73

Commits on Aug 7, 2026

feat: a typed interpreter contract and a registry that dispatches on it

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091d752
Revert "feat: a typed interpreter contract and a registry that dispatches on it"

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3a8c47e
fix: stop discarding interpreter-declared nodes before they reach the graph

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22470d9
fix: make the service-layer scan path persist interpretation too

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2cc1818
fix: align scanner interpreter ids with the registry, and stop over-reporting coverage

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8a067a7
fix: actually create INTERPRETED_AS edges on both commit paths

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4c7ee8b
fix: give the Interpretation node a payload and an edge to its File

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adc3493
feat: carry interpreted_as onto the File node so the graph can be queried on it

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5ad1f05
refactor: one copy of the format-recognition tables

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1bda5a2
fix: route matched directory patterns to interpreted_as

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3f67396
fix: use composite File index and batch existence check in enrichment dispatcher

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c0bf68d
perf: index files for extension-only and path lookups (v26)

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de044b1
docs: note the imaging extra needed for whole-slide interpretation

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4734e17
fix: move the files indexes out of migrations and into init_db

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b95fe91
fix: add now() as a Jinja2 global for plugins template
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32f079c

Commits on Aug 10, 2026

Add schema-aware Filter Builder — service, routes, JS component

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76b1e63
Add Folder Attribution — service, routes, panel (anchor_label generalized)

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3554e87
Generalize attribution: anchors, targets, graph-emergent relationships

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84b0e27

Commits on Aug 11, 2026

Attribution: anchor property filter, stale-anchor fix, vendored Tom Select

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e413927
Attribution: FilterBuilder target section, backend property filters

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57c3f33

Commits on Aug 18, 2026

Files page: split the monolith into a shell plus per-drawer modules

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6713ae7
Drives, scan history, interpret status, and Collection -> Dataset

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e4c4eb7
Walk the filesystem with os.scandir instead of rglob

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7f8b9fc
Persist background tasks, and estimate a scan total up front

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db36369
docs: roadmap, the drives/history/collection diagnostic, FilterBuilder spike

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38ca6bb
chore: resolve merge conflicts, keep production-mvp as source of truth
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0b457bc
chore: bump dev submodule to latest
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b03c303
Declare python-dotenv in pyproject, not just requirements.txt

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5af5bf7
Stop CI failing on tests that need services CI does not have

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2057c17