Organism resource improvements #701
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- Update composer.json and composer.lock for PHP dependencies - Update package.json and package-lock.json for NPM dependencies - Update postcss.config.js and vite.config.js for build configuration - Update filament-shield config for v4 compatibility
- Update AppServiceProvider for Filament v4 compatibility - Update DashboardPanelProvider with new v4 configuration
- Migrate all Dashboard resources to use Schema instead of Form - Update all resource pages (List, Edit, Create, View) for v4 API - Update relation managers with new Table and Schema APIs - Update dashboard widgets and pages - Replace Filament\Forms\Components with Filament\Schemas\Components - Update Actions imports from Filament\Actions namespace
- Update UserResource to use Schema instead of Form - Update LicenseResource to use Schema instead of Form - Update all related pages and relation managers - Migrate to new v4 API structure
- Fix OrganismsTable make() method signature to match parent Field class - Fix Citation model Section import to use Filament\Schemas\Components\Section - Ensure compatibility with Filament v4 component API
- Add new Filament v4 JavaScript components and modules - Add new Filament v4 CSS styles and fonts - Update existing Filament assets (forms, tables, widgets, notifications) - Add new action, schema, and table column components - Update filament-spatie-backup styles - Update spotlight plugin assets
- Update all Livewire blade views for v4 compatibility - Update resources CSS files (app.css, dashboard theme) - Update Filament dashboard widget views - Ensure views work with new Filament v4 components
- Make Database Details section more user-friendly with labels, placeholders, and helper text - Change 'url' to 'URL' with proper capitalization - Add clickable icon to URL field for easy external link access - Update Metadata section (remove DOI from identifier placeholder) - Enhance Display Image section with file type restrictions and size limits - Add infolist for view page with clickable URL that opens in new tab - Update Entries relation manager: change 'Reference id' to 'Reference ID' - Convert Entries relation manager action buttons to icon buttons - Update Molecules relation manager to display structure images instead of SMILES text - Make molecule identifier clickable, opening compound page in new tab - Improve overall form validation and user guidance
- Add pxlrbt/filament-spotlight-pro dependency - Add Spotlight Pro repository to composer.json - Replace free spotlight with pro version - Install rinvex/countries for geographic data
- Import Spotlight Pro CSS in dashboard and control-panel themes - Add Spotlight Pro views to Tailwind content paths - Register SpotlightPlugin with Pages, Resources, Commands providers - Create custom themes for both panels - Update vite config to build both panel themes - Publish Spotlight Pro assets and views - Disable global search in dashboard panel
- Create search button component for both panels - Position button to the right of logo in topbar - Add elegant design with search icon and ⌘K shortcut indicator - Include hover states and dark mode support - Use gray color scheme for professional look
- Publish panel switch views for customization - Add proper dark mode colors to panel switch button - Fix icon text colors in dark mode - Add hover states for better UX
- Qualify geo_location_id with table name in WHERE clause - Replace whereRaw with proper where() method - Remove Total Organisms stat (complex query causing issues) - Keep only Total Molecules stat for clarity
- Hide 'New geo location' button in header - Configure row click to open view page instead of edit - Keep edit icon button available in row actions
- Create MoleculesRelationManager with structure images - Display COCONUT ID, name, and IUPAC name in merged column - Show 2D structure images from ChemInf API - Add status badges - Link COCONUT IDs to public compound details page - Make relation manager read-only (no edit/delete actions)
- Add country, country_code, county fields - Add flag field for country flag emojis - Add latitude/longitude as separate decimal columns (better than comma-separated) - Add boundary as JSON for polygon coordinates - Add indexes on country_code and lat/long for performance - Include complete rollback in down() method
…ntegration ### Model Updates - Add fillable fields for all new geographic columns - Add casts for boundary (array), latitude, longitude (decimal) - Fix molecules relationship to use correct pivot table ### Form Enhancements - Create 3 collapsible sections: Basic Info, Geographic Details, Coordinates - Integrate rinvex/countries package for smart country selection - Auto-fill country name and flag emoji on country selection - Add placeholders and helper text for all fields - Full-width form layout with Grid components - Add description field for additional location notes - Validate latitude (-90 to 90) and longitude (-180 to 180) ### Table Improvements - Add flag column with emoji display (default 🌍) - Show country code as sortable badge - Display county and country as description below location name - Add coordinates column with map pin icon (toggleable) - Show molecules count as success badge - Improve date formatting (readable + relative time) - Add default sort by name - Set proper column widths and alignments
- Rename 'inactive entries' to 'inactive' for organisms with molecule_count <= 0 - Add 'unmapped' preset view for organisms without a rank assigned - Fix query grouping for proper OR condition handling
- Fix isObsolete comparison from string 'false' to boolean false - Fix family rank incorrectly labeled as 'genus' in updateOrganismModel - Auto-generate slug if not exists when updating organism
- Add molecule_count column to organisms table (sortable) - Show IRI as description below organism name - Fix isObsolete boolean comparison in OLS lookup - Clean up unused code
- Add taxonomy search modal with results from multiple sources - Search NCBI Taxonomy (OLS) with exact and similar matches - Search Global Names Finder (GNF) including unverified names - Normalize organism name case before searching - Add Google and Google Scholar hint action links - Allow user to select from search results and apply to form - Fix isObsolete boolean comparison
- Update card layout with table structure for reliable rendering - Show organism name in bold italic (scientific name style) - Display molecule count and IRI link - Add always-visible Edit button with inline styles - Fix array key error for single-word organism names - Fix urldecode on column name string - Improve empty state with search icon
- Add getMaxContentWidth() returning 'full' for better form layout
- Enable ViewOrganism page route - Add ViewAction button to table row actions - Set recordUrl to navigate to view page on row click
- Handle concatenated names (e.g., 'Micheliachampaca' -> 'Michelia') - Handle names without CamelCase using first 8 chars as genus - Add similarity ranking for better result ordering - Sort by similarity rank then by molecule count
- Add merge button to similar organisms table - Implement Filament modal for merge confirmation - Show FROM/INTO organisms and transfer counts in modal - Transfer molecules and sample locations to target organism - Handle duplicate relations gracefully - Update molecule counts after merge - Redirect to target organism after successful merge
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