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MedRecPro

MedRecPro is a pharmaceutical structured product label (SPL) management platform built with ASP.NET Core. It provides secure access to FDA drug label data through a RESTful API, an AI-powered chat interface, a Model Context Protocol (MCP) server for integration with AI assistants like Claude, and an interactive adverse-event risk dashboard built on a multi-stage table-standardization and risk-statistics pipeline.

Specifications

Technology Stack

  • Runtime: ASP.NET Core (.NET 8.0 LTS)
  • Database: Azure SQL Server (Serverless free tier) with Dapper + Entity Framework Core
  • Authentication: Cookie-based auth with Google and Microsoft OAuth providers; JWT bearer tokens for API access; McpBearer JWT scheme for MCP server integration (claims normalized to standard JWT short names: sub, name, email)
  • AI Integration: Claude API for natural language query interpretation and synthesis
  • MCP Protocol: Model Context Protocol server with OAuth 2.1 (PKCE S256) for Claude.ai connector integration
  • Hosting: Azure App Service (Windows, IIS) with Cloudflare CDN/WAF/DNS
  • Secrets: Azure Key Vault
  • API Documentation: Swagger/OpenAPI
  • Error Contracts: Centralized ASP.NET Core IExceptionHandler with sanitized RFC 7807 ProblemDetails responses and request trace correlation
  • Testing: MSTest, WebApplicationFactory<Program>, kept-open SQLite test databases, reviewed Debug/Release OpenAPI snapshots, and real-host HTTP contracts
  • Verification: PowerShell gate runner plus GitHub Actions for fast architecture checks, Debug/Release contracts, and the full regression suite
  • SPL Rendering: RazorLight templates for SPL XML-to-HTML generation

Solution Architecture

The solution's three web projects are deployed to a single Azure App Service using IIS virtual applications (the console, library, React SPA source, prototypes, and test projects are not deployed as separate apps):

                        Cloudflare (CDN/WAF/DNS)
                                |
                                v
    Azure App Service: "MedRecPro" (Windows, IIS)
   +--------------------------------------------------------+
   |                                                        |
   |  /                site\wwwroot       MedRecProStatic   |
   |  /adverse-events  (MedRecProStatic, React island)      |
   |  /api             site\wwwroot\api   MedRecPro API     |
   |  /mcp             site\wwwroot\mcp   MedRecProMCP      |
   |                                                        |
   +--------------------------------------------------------+
                        |
                        v
               Azure Key Vault
              (medrecprovault)
Virtual Path Project Purpose
/ MedRecProStatic Static site, marketing pages, AI chat UI, OAuth/MCP discovery metadata, adverse-event dashboard host
/adverse-events MedRecProReact (hosted by MedRecProStatic) Adverse-event risk dashboard React island
/api MedRecPro REST API: SPL upload/progress boundary, label CRUD, authentication, AI interpret/synthesize, adverse-event dashboard data
/mcp MedRecProMCP MCP server: OAuth 2.1 gateway for Claude.ai integration
(CLI) MedRecProConsole Standalone bulk import utility over the shared import library (SPL labels, FDA Orange Book, and table standardization)
(library) MedRecProImportClass Shared class library: entity models, parsing services, table-standardization pipeline, and EF Core context for SPL and Orange Book import
(SPA source) MedRecProReact React + Vite source for the adverse-event dashboard; builds into MedRecProStatic's web root
(prototypes) MedRecProPrototypes Standalone HTML/JS prototypes (e.g. the AE dashboard) that seed production UI work
(test) MedRecProTest MSTest unit, relational, real-host integration, architecture, and Debug/Release contract coverage

Build and Solution Boundary

MedRecPro.sln is the focused API/import/test solution. It intentionally contains MedRecPro, MedRecProImportClass, and MedRecProTest; the test project references MedRecProConsole, so the CLI stays in the regular regression build without making the solution responsible for every deployed app. MedRecProStatic and MedRecProMCP are separately deployed IIS virtual applications and should be built or published explicitly when their code changes:

dotnet build .\MedRecPro.sln --no-restore -p:UseAppHost=false
dotnet build .\MedRecProStatic\MedRecProStatic.csproj --no-restore -p:UseAppHost=false
dotnet build .\MedRecProMCP\MedRecProMCP.csproj --no-restore -p:UseAppHost=false

If a local apphost executable is locked by a running process, keep output inside the workspace and disable apphost generation for the verification pass, for example dotnet build .\MedRecPro.sln --no-restore -p:UseAppHost=false -p:BaseOutputPath=.\MedRecPro\.codex-build\. The API project excludes bin/** and .codex-build/** from default item globbing so copied RazorLight templates from generated output cannot re-enter compilation when BaseOutputPath is redirected.

How the Projects Relate

MedRecProStatic is the user-facing front end. Its AI chat interface (/Home/Chat) communicates with the API using a request-interpret-execute-synthesize pattern: user queries are sent to the API's AI endpoints, which use Claude to map natural language to API calls. The static site also serves OAuth/MCP discovery metadata (/.well-known/*) at the domain root on behalf of the MCP server, because the MCP SDK resolves discovery URLs relative to the domain root rather than the /mcp path.

MedRecPro (API) is the core backend. It handles label data CRUD, user authentication, AI query interpretation via Claude, database views for navigation, SPL document rendering via RazorLight templates, and the HTTP/progress boundary for SPL ZIP uploads. The public Label surface remains one 51-operation /api/Label route family, but its implementation is split across small feature controllers and injected query/operation services. The former DtoLabelAccess implementation is now owned by those services; one forwarding-only static facade remains for external .NET compatibility. The actual SPL ZIP traversal, XML parsing, duplicate checks, and parser orchestration live in MedRecProImportClass; the API keeps thin compatibility adapters and maps import-library result DTOs back into the web import-progress models.

MedRecProMCP is an OAuth 2.1 gateway that exposes MedRecPro API capabilities as MCP tools. When Claude.ai connects, it authenticates users through Google/Microsoft OAuth, resolves upstream identity provider identities to numeric database user IDs (auto-provisioning new users if needed), then forwards authenticated MCP JWTs to the MedRecPro API. It uses JWT tokens, PKCE (S256), Dynamic Client Registration (RFC 7591), and a shared PKSecret for encrypted user ID exchange with the API.

MedRecProReact is the source for the adverse-event risk dashboard — a React + Vite single-page "island". Its Vite build emits a deterministic bundle directly into MedRecProStatic/wwwroot/ae-dashboard, which MedRecProStatic serves at /adverse-events. The dashboard reads only from the API's /api/AdverseEvent surface (AdverseEventController), which in turn queries the materialized AE risk tables produced by the table-standardization pipeline (Stage 5). Current dashboard focuses cover product-level risk, pharmacologic-class SOC correlation, and MedDRA-system-scoped class correlation. See the MedRecProReact README for the dashboard, and the MedRecProImportClass README for the risk-statistics contract.

Backend Boundaries and Compatibility Safeguards

Area Current design
Startup Program.cs is an ordered composition shell. Capability-focused extensions under MedRecPro/Configuration own data access, platform services, authentication, MVC, Swagger, middleware, rendering, import, and background-service registration.
Feature routing ApiControllerBase retains the compile-time Debug/Release prefix split. FeatureControllerNameConvention applies each split controller's FeatureControllerNameAttribute value, so implementation class names never leak into routes.
Controller ownership The original LabelController and LabelSearchController are empty compatibility shells. Search, document, section, markdown, import, comparison, and metadata operations live in feature controllers with no more than eight actions each.
Label data access Scoped feature services own EF Core query and document-graph behavior. DtoLabelAccess.Compatibility.cs preserves the 57 public names/58 overloads as forwarding-only adapters; first-party runtime callers use DI services.
Queued work Import progress crosses an explicit IImportOperationStatusStore boundary. Comparison jobs use a singleton coordinator that snapshots inputs, creates a fresh scope per job, and links cancellation to application shutdown instead of the originating request.
Encryption DatabaseSecurityOptions is bound centrally and IPrimaryKeyCipher is the injected encryption boundary for migrated Label, authentication, AI, authorization-filter, Claude-search, and Orange Book paths. Architecture tests freeze the explicitly deferred legacy-reader inventory.
Errors and logs MedRecProExceptionHandler owns unexpected HTTP failures in every environment, returning sanitized ProblemDetails and logging the same trace ID. Production logging uses structured templates, filtered/redacted in-memory administration records, and safe typed log DTOs; see logging conventions.
Verification A deterministic real host replaces both SQL contexts with SQLite, removes reviewed unsafe workers, and supplies test authentication/configuration. Debug and separately compiled Release suites protect all 51 Label routes, OpenAPI, headers, files, validation, authorization, and error bodies; see verification gates.

Repository File Structure

The tree below is intentionally curated around deployable projects and the current architecture/verification boundaries. Every named path was checked against the live repository on 2026-07-14.

./
  README.md
  MedRecPro.sln                     # Focused API/import/test solution
  .github/
    workflows/
      medrecpro-verification.yml    # Fast + Debug/Release contract + full CI gates
  scripts/
    Invoke-MedRecProVerification.ps1

  MedRecPro/                        # ASP.NET Core Web API
    Program.cs                      # Ordered composition and middleware shell
    MedRecPro.csproj                # Excludes bin/** and .codex-build/** from source discovery
    Configuration/
      DatabaseSecurityOptions.cs
      MedRecProApplicationServiceExtensions.cs
      MedRecProAuthenticationExtensions.cs
      MedRecProMiddlewareExtensions.cs
      MedRecProMvcExtensions.cs
      MedRecProStartupDiagnosticsExtensions.cs
      MedRecProSwaggerExtensions.cs
    Controllers/
      ApiControllerBase.cs          # Debug api/[controller] vs Release [controller]
      LabelController.cs            # Empty compatibility shell
      LabelSearchController.cs      # Empty compatibility shell
      LabelApplicationController.cs
      LabelClassificationController.cs
      LabelComparisonController.cs
      LabelDocumentController.cs
      LabelImportController.cs
      LabelIngredientController.cs
      LabelMarkdownController.cs
      LabelMetadataController.cs
      LabelProductIdentifierController.cs
      LabelProductSearchController.cs
      LabelSectionController.cs
      LabelSectionNavigationController.cs
      FeatureControllerNameAttribute.cs
      SwaggerGroupAttribute.cs
      AdverseEventController.cs
      AiController.cs
      AuthController.cs
      OrangeBookController.cs
      SettingsController.cs
      UsersController.cs
    Service/
      AeDashboardServices.cs        # Injected AE dashboard use-case services and policies
      AppCacheService.cs            # IAppCache and user-context seams
      PrimaryKeyCipher.cs           # IPrimaryKeyCipher encryption boundary
      ClaudeSkillNameMapper.cs
      SplImportService.cs           # Web compatibility adapter over the import library
      SplParsingService.cs          # Legacy parser adapter over the import library
      Common/
        ActivityLogDispatcher.cs    # Channel dispatcher + scoped hosted consumer
      Label/
        ComparisonJobCoordinator.cs
        CompleteLabelService.cs
        LabelAiSearchService.cs
        LabelQueryServiceContracts.cs
        LabelQueryServices.cs
        LabelSectionCrudService.cs
        LabelXmlDocumentService.cs
        Common/
          LabelQueryCachePolicy.cs
          LegacyDtoLabelCacheKeyBuilder.cs
        Implementation/
          LabelQueryDataAccess.cs
          LabelQueryDataAccess-BatchLoaders.cs
          LabelQueryDataAccess-Document.cs
          LabelQueryDataAccess-Views.cs
          LabelQueryLegacyCompatibility.cs
    DataAccess/
      DtoLabelAccess.Compatibility.cs   # Forwarding-only 57-name/58-overload facade
      DtoLabelAccess-AeDashboard.cs     # AeDashboardDataAccess query implementation
      AeDashboardFavoriteAccess.cs
      AeDashboardDerivation.cs
      AeCorrelationPipelineModels.cs
      RepositoryDataAccess.cs
      UserDataAccess.cs
    Features/
      AeDashboard/
        Mapping/
          AeDashboardDtoMapper.cs
        Models/
          AeDashboardDto.cs
        Persistence/
          AeDashboardModelConfigurations.cs
      Label/
        Mapping/
          LabelDocumentAssembler.cs
    Exceptions/
      AuthorizationExceptions.cs
      MedRecProExceptionHandler.cs
      RequestCorrelation.cs
    Filters/
      ActivityLogActionFilter.cs
      RequireActorAttributeFilter.cs
      RequireUserRoleAttributeFilter.cs
    Mappers/
      ImportResultMapper.cs
    Models/
      ImportStatus.cs               # Web/import operation-status boundary
    Middleware/
      TarpitMiddleware.cs
    Skills/
      skills.md                     # Capability contracts
      selectors.md                  # Skill routing rules
      interfaces/                   # API and response mappings
    Views/
      SplTemplates/                 # RazorLight SPL templates
      Stylesheets/
    SQL/                            # Schema, views, indexes, import/export, AE materialization
    docs/
      logging-conventions.md
      verification-gates.md

  MedRecProImportClass/             # Shared SPL/Orange Book import and analytics library
    Models/
      Import.cs
      ImportStatus.cs
      OrangeBook.cs
    DataAccess/
      RepositoryDataAccess.cs
      UserDataAccess.cs
    Service/
      SplImportService.cs
      SplParsingService.cs
      SplDataService.cs
      ParsingServices/              # SPL and Orange Book parsers
      ParsingValidators/
      TransformationServices/
        TableStandardizationServiceCollectionExtensions.cs
        ClaudeCorrectionPayloadBuilder.cs
        BaseTableFlattening/
          ColumnStandardizationService.cs
        AdverseEventTableFlattening/
    TableStandards/
      normalization-rules.md
      column-contracts.md
      table-types.md
    Context/
      ApplicationDbContext.cs

  MedRecProConsole/                 # Bulk SPL/Orange Book import CLI
    Program.cs
    Services/
      ImportService.cs
      ImportProgressTracker.cs
      OrangeBookImportService.cs
    Models/
    Helpers/

  MedRecProStatic/                  # Static site, AI chat, and dashboard host
    Program.cs
    Controllers/
      HomeController.cs
      AdverseEventDashboardController.cs
    Views/
      Home/
      AdverseEventDashboard/
      Shared/
    wwwroot/
      ae-dashboard/                 # Committed MedRecProReact build
      js/
        chat/

  MedRecProReact/                   # React + Vite adverse-event dashboard source
    package.json
    vite.config.js
    src/
      App.jsx
      api/
      components/
      hooks/
      lib/
      test/

  MedRecProMCP/                     # OAuth 2.1 MCP gateway
    Program.cs
    Endpoints/
      OAuthEndpoints.cs
      OAuthMetadataEndpoints.cs
    Services/
    Tools/
      DrugLabelTools.cs
      UserTools.cs

  MedRecProPrototypes/              # Standalone UI prototypes

  MedRecProTest/                    # MSTest unit, relational, host, and contract suite
    MedRecProTest.csproj
    TestInfrastructure/
      MedRecProTestConfiguration.cs
      MedRecProWebApplicationFactory.cs
      MedRecProHostFixture.cs
      TestAuthenticationHandler.cs
      TestExceptionThrowingStartupFilter.cs
      CountingDbCommandInterceptor.cs
      ControllerArchitectureTests.cs
      LoggingAndErrorHandlingArchitectureTests.cs
      ReflectionUsageArchitectureTests.cs
      TestProjectDependencyGuardTests.cs
    Contracts/
      LabelOpenApiContractTests.cs
    Integration/
      LabelHttpContractTests.cs
      StartupSmokeTests.cs
    TestData/
      OpenApi/
        label-debug.contract.json
        label-release.contract.json
    ColumnStandardizationServiceTests.cs   # Thin shared-fixture shell
    ColumnStandardizationTestFixture.cs
    ColumnStandardization/
      ColumnStandardizationCleanupTests.cs
      ColumnStandardizationColumnContractTests.cs
      ColumnStandardizationInitializationAndCategoryTests.cs
      ColumnStandardizationPipelineTests.cs
      ColumnStandardizationPkAndDefectRegressionTests.cs
      ColumnStandardizationTreatmentArmRulesPart1Tests.cs
      ColumnStandardizationTreatmentArmRulesPart2Tests.cs
    TableParserTests.cs                    # Thin shared-parser shell
    TableParserTestHelper.cs
    TableParsing/
      TableParserEfficacyAndRouterTests.cs
      TableParserGeneralRegressionTests.cs
      TableParserPkBasicAndCompoundTests.cs
      TableParserPkHeaderRegressionTests.cs
      TableParserPkRoutingTests.cs
      TableParserPkWaveAndHygieneTests.cs
      TableParserSimpleArmAndAeTests.cs
    DtoLabelAccessFacadeArchitectureTests.cs
    DtoLabelAccessSignatureCompatibilityTests.cs
    LabelControllerRouteCompatibilityTests.cs
    MedRecProPublicSurfaceInventoryTests.cs
    ServiceRegistrationTests.cs

API Endpoints Summary

All API endpoints are accessed under /api in production (IIS virtual application). API controllers inherit the #if DEBUG route in ApiControllerBase, preserving the local /api/[controller] prefix and the production app-relative route where IIS supplies and strips /api.

Authentication (/api/Auth)

Method Route Description
GET login/{provider} Start OAuth flow (Google or Microsoft)
GET external-logincallback OAuth callback handler
GET user Get current authenticated user info
POST logout Log out current user
POST token-placeholder Token exchange
GET login Login page
GET loginfailure Login failure handler
GET lockout Account lockout handler
GET accessdenied Access denied handler

Users (/api/Users)

Method Route Description
GET me Get current user profile
GET {encryptedUserId} Get user by encrypted ID
GET byemail Get user by email
POST signup Create new user account
POST authenticate Authenticate user
PUT {encryptedUserId}/profile Update user profile
DELETE {encryptedUserId} Delete user account
PUT admin-update Administrative user update
POST rotate-password Rotate user password
GET user/{encryptedUserId}/activity Get user activity log
GET user/{encryptedUserId}/activity/daterange Get activity within date range
GET endpoint-stats Get endpoint performance statistics
POST resolve-mcp Resolve email to encrypted user ID (McpBearer auth; auto-provisions new users)

Labels (/api/Label)

The compatibility-stable Label route family contains 51 operations covering navigation views, search, CRUD, import, rendering, and AI features. Internally, those actions are distributed across feature controllers; LabelController and LabelSearchController remain empty shells so the public controller name and Swagger/route contracts stay unchanged.

Navigation & Search Views:

Method Route Description
GET product/search Search products
GET product/related Related products
GET product/latest Latest product labels
GET product/latest/details Latest product label details
GET product/indications Product indications search
GET ingredient/search Search by ingredient (active/inactive)
GET ingredient/summaries Ingredient summary list
GET ingredient/active/summaries Active ingredients only
GET ingredient/inactive/summaries Inactive ingredients only
GET ingredient/advanced Advanced ingredient search
GET ingredient/by-application Ingredients by application number
GET ingredient/related Related ingredients
GET labeler/search Search by manufacturer/labeler
GET labeler/summaries Labeler summary list
GET ndc/search Search by NDC code
GET ndc/package/search Search by NDC package code
GET application-number/search Search by application number (NDA/ANDA)
GET application-number/summaries Application number summaries
GET pharmacologic-class/search Search by pharmacologic class
GET pharmacologic-class/hierarchy Pharmacologic class hierarchy
GET pharmacologic-class/summaries Pharmacologic class summaries
GET section/search Search by LOINC section code
GET section/summaries Section summaries
GET document/navigation Document navigation tree
GET document/version-history/{setGuidOrDocumentGuid} Document version history

Label Content & Rendering:

Method Route Description
GET section/content/{documentGuid} Get section content for a document
GET markdown/sections/{documentGuid} Get label sections as markdown
GET markdown/export/{documentGuid} Export full label as markdown
GET markdown/download/{documentGuid} Download label markdown file
GET markdown/display/{documentGuid} Render label as HTML from markdown
GET generate/{documentGuid}/{minify} Generate updated SPL XML
GET original/{documentGuid}/{minify} Get original SPL XML
GET single/{documentGuid} Get single label details
GET complete/{pageNumber?}/{pageSize?} Paginated complete label list

Drug Safety:

Method Route Description
GET drug-safety/dea-schedule DEA schedule classification

AI-Powered Endpoints:

Method Route Description
GET extract-product AI-powered product extraction from text
GET indication/search AI-assisted indication search with label-text validation
GET comparison/analysis/{documentGuid} Get comparison analysis
POST comparison/analysis/{documentGuid} Start AI comparison analysis
GET comparison/progress/{operationId} Check comparison progress

CRUD & Import:

Method Route Description
GET {menuSelection}/{encryptedId} Get single entity by type
GET section/{menuSelection} Get records for a label entity type
POST {menuSelection} Create entity by type
PUT {menuSelection}/{encryptedId} Update entity by type
DELETE {menuSelection}/{encryptedId} Delete entity by type
POST import Bulk SPL ZIP import
GET import/progress/{operationId} Check import progress

Reference:

Method Route Description
GET guide API usage guide
GET inventory/summary Database inventory overview
GET sectionMenu Available section menu items
GET {menuSelection}/documentation Documentation for a data type

AI (/api/Ai)

Method Route Description
GET context Get AI context (auth status, demo mode, data counts)
POST interpret Interpret natural language query into API endpoint specs
POST synthesize Synthesize API results into human-readable response
GET chat Convenience endpoint for simple queries
POST conversations Create new conversation
GET conversations/{conversationId} Get conversation
GET conversations/{conversationId}/history Get conversation history
DELETE conversations/{conversationId} Delete conversation
GET conversations/stats Get conversation statistics
POST retry Retry last AI operation

Settings (/api/Settings)

Method Route Description
GET demomode Check demo mode status
GET info Application info
GET features Feature flags
GET database-limits Database limits
GET metrics/database-cost Azure SQL free tier usage and cost projections
POST clearmanagedcache Clear managed cache
GET logs Activity logs
GET logs/statistics Log statistics
GET logs/categories Log categories
GET logs/by-date Logs filtered by date
GET logs/by-category Logs filtered by category
GET logs/by-user Logs filtered by user
GET logs/users Users with log entries
GET test/app-credential Test Azure credentials
GET test/app-metrics-pipeline Test metrics pipeline

Administrative log endpoints remain Admin-only and return typed, redacted projections. Invalid log filters use validation ProblemDetails; unexpected failures use the global trace-correlated ProblemDetails contract.

Adverse Event Dashboard (/api/AdverseEvent)

Backs the React adverse-event risk dashboard. The whole controller is gated by the FeatureFlags:AeDashboard:Enabled flag (returns 503 when disabled). Reads are anonymous (favorite state is enriched for authenticated users); favorite writes require ApiAccess. Class-picker and MedDRA system-picker responses expose pagination/aggregate totals via the X-Page-Number, X-Page-Size, X-Total-Count, and X-Chartable-Count headers.

Method Route Description
GET products Dashboard product list with KPI/coverage data (paged)
GET products/catalog Slim cached product catalog for the picker
GET products/count Distinct product inventory count
GET products/favorites Authenticated user's favorite products
PUT products/{documentGuid}/favorite Add a favorite (idempotent, 204)
DELETE products/{documentGuid}/favorite Remove a favorite (idempotent, 204)
GET products/{documentGuid}/triage Tiered triage signals for one product
GET products/{documentGuid}/forest Forest-plot payload for one product
GET products/{documentGuid}/quadrant Risk-vs-precision quadrant payload
GET reverse-lookup Products reporting one or more exact AE terms
GET interchange Comparator-aware two-product therapeutic interchange comparison
GET correlation/classes Pharmacologic classes with AE data (class picker)
GET correlation SOC × SOC correlation map for one class
GET correlation/heatmap Sparse SOC × drug RR heatmap for one class
GET correlation/cell Per-drug drill-down for one correlation cell
GET correlation/systems MedDRA System Organ Classes with AE rows (system picker)
GET correlation/systems/map Selected-system pharmacologic-class × pharmacologic-class correlation map
GET correlation/systems/heatmap Selected-system pharmacologic-class × drug RR heatmap
GET correlation/systems/cell Per-term drill-down for one selected-system class-pair cell

MCP Server (/mcp)

The MCP server exposes its own endpoints. See the MedRecProMCP README for full details.

Method Route Description
POST /mcp MCP Streamable HTTP transport (JSON-RPC)
GET /mcp/health Health check
GET /mcp/docs HTML documentation page
GET /mcp/.well-known/oauth-protected-resource Protected Resource Metadata (RFC 9728)
GET /mcp/.well-known/oauth-authorization-server Authorization Server Metadata (RFC 8414)
GET /mcp/oauth/authorize OAuth authorization endpoint
POST /mcp/oauth/token Token exchange endpoint
POST /mcp/oauth/register Dynamic Client Registration (RFC 7591)
GET /mcp/oauth/callback/google Google OAuth callback
GET /mcp/oauth/callback/microsoft Microsoft OAuth callback

MedRecProStatic and MCP Relationship

MedRecProStatic serves the OAuth/MCP discovery metadata at the domain root because the MCP SDK resolves /.well-known/* relative to the domain, not the MCP endpoint path. When Claude connects to https://www.medrecpro.com/mcp, the SDK looks for discovery at https://www.medrecpro.com/.well-known/oauth-protected-resource and /.well-known/oauth-authorization-server.

These endpoints are registered directly in MedRecProStatic's Program.cs as static JSON responses. Attempts to redirect from the root site to /mcp/.well-known/* failed because 302 redirects cause the MCP SDK to derive the wrong resource URI, and reverse proxying through Cloudflare triggers Bot Fight Mode (403 errors).

MedRecProStatic also has a critical web.config setting (httpErrors existingResponse="PassThrough") placed outside the <location> element so it is inherited by the MCP and API virtual applications. Without this, IIS replaces 401 responses with HTML error pages, breaking the MCP OAuth challenge flow.

Database Schema and SQL Scripts

Database schema definitions and maintenance scripts are maintained in MedRecPro/SQL/. These are the authoritative source for schema updates, view definitions, and index management.

Script Purpose
MedRecPro.sql Full database schema (tables, constraints, relationships)
MedRecPro_Views.sql View definitions used by navigation and search endpoints
MedRecPro_Indexes.sql Index definitions for query performance
MedRecPro-Deployment.sql Deployment-time schema updates
DbTriggerSetup.sql Database trigger configuration
MedRecPro-Azure-Data-Refresh.ps1 Normal single entry point for a manifest-bound local-to-Azure refresh
MedRecPro-Export-Import.ps1 Supported lower-level primary-domain BCP export/import tool
MedRecPro-AzureStatus.sql Azure SQL status and diagnostics queries
MedRecPro-AzureRebuildIndex.sql Index rebuild for Azure SQL
MedRecPro-AzureDisableIndex.sql Disable indexes during bulk operations
MedRecPro-AzureOnlineQueryEditorRebuildIndex.sql Index rebuild via Azure Query Editor
MedRecPro-AzureNuke.sql Full database reset (destructive)
MedRecPro-TableNames.sql List all table names
MedRecPro-TableTruncate.sql Truncate tables for reimport
MedRecPro-TableMissingIndexes.sql Identify missing indexes
MedRecPro-TableCreate-OrangeBook.sql Orange Book table definitions (7 tables, indexes, extended properties)
MedRecPro-AzureOrangeBookNuke.sql Targeted Orange Book truncation with safety preview mode
MedRecPro-Table-tmp_FlattenedAdverseEventCoverageTable.sql Stage 5 AE source-row coverage / non-RR audit table
MedRecPro-Table-tmp_FlattenedAdverseEventTable.sql Stage 5 RR-ready AE statistics (RR/DNRR/CI + PERSISTED log columns)
MedRecPro-Table-tmp_FlattenedAdverseEventRiskTable.sql Materialization of dbo.vw_AeRisk for the dashboard
MedRecPro-Table-tmp_AeDashboardProductCatalog.sql Materialization of dbo.vw_AeDashboardProductCatalog (picker)
MedRecPro-AdverseEvent-Export-Import.ps1 BCP full-refresh of the AE tables (local SQL Server → Azure SQL, truncate-then-import)

Azure data refresh

For a normal complete local-to-Azure data refresh, start only the unified entry point. It exports and validates the Core, Orange Book, materialized temp, and adverse-event domains before Azure mutation; shows the resolved source/target and inventory; then requires the exact REFRESH server.database.windows.net/MedRecPro confirmation token. It records only non-secret run state under C:\MedRecPro-Migration\Refreshes and attempts index recovery before an incomplete run exits.

.\MedRecPro\SQL\MedRecPro-Azure-Data-Refresh.ps1 `
  -AzureServer "server.database.windows.net" `
  -AzureDatabase "MedRecPro" `
  -AzureUser "migration-user"

A start without an explicit mode first asks for the run mode (validate / export / full refresh; Enter chooses validate-only), and missing Azure connection values are requested interactively with an immediate connection test, so an interactive launch cannot drift into the destructive path by default. Use -ExportOnly to create a validated local snapshot without Azure mutation, -ValidateOnly for source/target preflight, -RefreshExclusionRules only when the normally preserved PharmClassDosageFormExclusion table must be refreshed, and -ResumeRun <run-directory> only for that run's unchanged manifest and data files. -WhatIf previews the stage graph and never acts as destructive authorization. The individual domain workers and nuke/index SQL files remain supported manual/recovery tools; do not combine them with a unified run. When updating database schemas or views, modify the scripts in MedRecPro/SQL/ and run them against the target database. The MedRecPro_Views.sql file is particularly important as the navigation view queries (ingredient search, labeler search, pharmacologic class hierarchy, etc.) are defined there and power many of the API search endpoints. The adverse-event dashboard is backed by the dbo.vw_AeRisk, dbo.vw_AeDrugSummary, and dbo.vw_AeDashboardProductCatalog views (also in MedRecPro_Views.sql), the last two materialized into tmp_ tables by the Stage 5 pipeline so the dashboard reads without runtime statistics.

AI Skills System

The API includes an agentic AI layer that enables natural language interaction with pharmaceutical data. The system follows a request-interpret-execute-synthesize pattern:

  1. User submits a natural language query to POST /api/Ai/interpret
  2. Claude interprets the query and returns API endpoint specifications
  3. The client executes the specified API endpoints
  4. Results are sent to POST /api/Ai/synthesize
  5. Claude produces a human-readable response with suggested follow-ups

AI skills are defined as markdown prompt files in MedRecPro/Skills/. Key skills include:

  • Indication Discovery - Find drugs by indication/use case
  • Equianalgesic Conversion - Opioid dose conversion calculations
  • Product Extraction - AI-powered extraction of product details from text
  • Pharmacologic Class Matching - Map drugs to pharmacologic classifications
  • Label Content - Retrieve and synthesize label sections
  • Data Rescue - Fallback strategies for missing or incomplete data

Adverse Event Risk Dashboard

The platform turns the free-text adverse-event tables buried in SPL labels into comparable risk statistics and exposes them as an interactive dashboard at /adverse-events.

The data flow spans three projects:

  1. MedRecProImportClass / MedRecProConsole — the SPL table-standardization pipeline parses heterogeneous label tables into a uniform analytical schema and, in Stage 5, pre-computes Relative Risk (RR), Dose-Normalized RR (DNRR), and 95% confidence intervals per adverse-event row. Results are materialized into the tmp_FlattenedAdverseEvent* tables. See the MedRecProImportClass README for the full pipeline and the statistical contract.
  2. MedRecPro (API) — AdverseEventController (/api/AdverseEvent) serves dashboard-ready, encrypted-ID payloads from the materialized risk views: per-product triage/forest/quadrant, symptom reverse lookup, comparator-aware two-product therapeutic interchange, pharmacologic-class SOC × SOC correlation maps/heatmaps/cell drill-downs, and MedDRA-system-scoped class × class / class × drug correlation views. The feature is gated by FeatureFlags:AeDashboard:Enabled.
  3. MedRecProReact — a React + Vite single-page island that renders the product, class, and By System dashboard focuses. Its build output is committed into MedRecProStatic/wwwroot/ae-dashboard and served by MedRecProStatic. See the MedRecProReact README.

Because the observation units for correlation views are intentionally narrow — a single drug within a class for SOC × SOC maps, or shared selected-system terms for By System class-pair maps — sample sizes can be small. The dashboard is deliberately honesty-first: below-floor cells are suppressed rather than fabricated, non-renderable system matrices return warnings, the By System focus is single-system by design, and comparator-mixed payloads are explicitly flagged. The displayed figures are bounded by what each label discloses and what the parser can extract — absence of a signal is not evidence of its absence in practice.

FDA Orange Book Integration

The platform imports and cross-references data from the FDA's Approved Drug Products with Therapeutic Equivalence Evaluations (Orange Book), linking FDA approval records to existing SPL label data.

Orange Book Database Schema

Seven normalized tables store Orange Book data, with three junction tables linking to existing SPL entities:

Table Purpose
OrangeBookApplicant Pharmaceutical companies holding FDA approvals
OrangeBookProduct Drug products (natural key: ApplType + ApplNo + ProductNo)
OrangeBookPatent Patent records per product with expiration dates
OrangeBookExclusivity Marketing exclusivity periods (NCE, ODE, RTO, etc.)
OrangeBookProductMarketingCategory Junction: OB Product → SPL MarketingCategory (by application number)
OrangeBookProductIngredientSubstance Junction: OB Product → SPL IngredientSubstance
OrangeBookApplicantOrganization Junction: OB Applicant → SPL Organization

No foreign key constraints are enforced; relationships are managed by the import module. The main nuke script (MedRecPro-AzureNuke.sql) excludes Orange Book tables, which have their own dedicated truncation script.

Orange Book Import Process

The console application (MedRecProConsole) imports Orange Book data from FDA-published ZIP archives containing tilde-delimited text files. The import pipeline:

  1. Extract products.txt from the ZIP archive
  2. Parse tilde-delimited rows (14 columns) into normalized entities
  3. Upsert applicants and products in batches (5,000 rows per batch)
  4. Match applicants to SPL organizations using a two-tier strategy:
    • Tier 1 (Normalized Exact): Strips corporate suffixes (INC, LLC, CORP, LTD, GMBH, etc.), punctuation, and whitespace; case-insensitive exact match
    • Tier 2 (Token Similarity): Two-pass fuzzy matching using Jaccard/containment scoring with a 0.67 threshold; strips pharma noise words on the second pass only when sufficient tokens remain
  5. Match ingredients to SPL IngredientSubstance records (semicolon-delimited ingredient lists parsed and matched individually)
  6. Match products to SPL MarketingCategory records via application number

The import is idempotent (upsert-based), so re-running is safe without crash recovery queues. Real-time multi-phase progress is displayed via Spectre.Console.

Orange Book CLI Usage

Interactive mode:

cd MedRecProConsole
dotnet run
# Select "orange-book" or "ob" from the menu

Unattended mode:

MedRecProConsole.exe --orange-book "path/to/EOBZIP_2026_01.zip" --nuke --auto-quit
Argument Description
--orange-book <path> Path to Orange Book ZIP file
--nuke Truncate all Orange Book tables before import
--connection <name> Database connection name from appsettings.json
--auto-quit Exit after completion
--verbose Enable debug logging

Getting Started

Prerequisites

  • .NET 8.0 SDK (LTS)
  • SQL Server (local) or Azure SQL Database
  • Visual Studio 2022 or VS Code

1. Clone the repository

git clone <repo-url>
cd MedRecPro

2. Configure the API

Create user secrets for the MedRecPro API project:

cd MedRecPro
dotnet user-secrets init
dotnet user-secrets set "Dev:DB:Connection" "Server=localhost;Database=MedRecProDB;User Id=sa;Password=your-password;"
dotnet user-secrets set "Security:DB:PKSecret" "your-encryption-key"
dotnet user-secrets set "Jwt:Key" "your-jwt-signing-key-min-32-chars"
dotnet user-secrets set "Jwt:Issuer" "MedRecPro"
dotnet user-secrets set "Jwt:Audience" "MedRecUsers"
dotnet user-secrets set "Authentication:Google:ClientId" "your-google-client-id"
dotnet user-secrets set "Authentication:Google:ClientSecret" "your-google-client-secret"
dotnet user-secrets set "Authentication:Microsoft:ClientId" "your-microsoft-app-id"
dotnet user-secrets set "Authentication:Microsoft:ClientSecret:Dev" "your-microsoft-secret"
dotnet user-secrets set "Authentication:Microsoft:TenantId" "your-tenant-id"
dotnet user-secrets set "ClaudeApiSettings:ApiKey" "your-claude-api-key"

3. Set up the database

Run the schema script from MedRecPro/SQL/MedRecPro.sql against your SQL Server instance, then apply views and indexes:

# Apply schema, views, and indexes in order
sqlcmd -S localhost -d MedRecProDB -i MedRecPro/SQL/MedRecPro.sql
sqlcmd -S localhost -d MedRecProDB -i MedRecPro/SQL/MedRecPro_Views.sql
sqlcmd -S localhost -d MedRecProDB -i MedRecPro/SQL/MedRecPro_Indexes.sql

Or run EF Core migrations:

cd MedRecPro
dotnet ef database update

4. Run the projects

# Terminal 1: API (port 5093)
cd MedRecPro
dotnet run

# Terminal 2: Static site (port 5001)
cd MedRecProStatic
dotnet run

# Terminal 3: MCP server (port 5233, optional)
cd MedRecProMCP
dotnet run

# Terminal 4: Adverse-event dashboard (Vite dev server, port 50346, optional)
cd MedRecProReact
npm install
npm run dev

The MVC-hosted dashboard at http://localhost:5001/adverse-events is served from the committed Vite bundle; the Vite dev server above is only for iterating on the React source. After changing React source, run npm run build and commit the regenerated MedRecProStatic/wwwroot/ae-dashboard assets (the .NET build does not run Vite).

API diagnostic baseline

Use the Chat page test commands to exercise the browser-facing endpoint diagnostic. In local Debug, run the API at http://localhost:5093 and the static site at http://localhost:5001; when deployed, the diagnostic uses the same-origin /api path.

Command Purpose
/test api all Run the non-destructive baseline locally; deployed sites open an explicit online full-diagnostic panel before any request starts.
/test api all fast Run the nine-request browser-health check across Settings, sign-in, Labels, the AE product picker, Orange Book, and AI context.
/test api safe Run the complete safe anonymous profile; use a private window when the current browser is signed in.
/test api read-auth Run authenticated read coverage without writes.
/test api report Show the redacted summary for the latest API diagnostic.

On a deployed site, /test api smoke and /test api all fast are capped at nine monitored /api requests. /test api all fast uses the authenticated-session preflight plus the minimum Label seed and browser-facing Settings, Label, AE picker, Orange Book, and AI-context reads. It excludes the full-table AE correlation picker, status/administration routes, and AI conversation statistics, which are not browser-health checks. An online full baseline does not start from chat: its panel shows the expected duration and requires an explicit start. Online requests use 34-second inter-request pacing (keeping the ten-per-five-minute endpoint monitor below its threshold) and a 60-second timeout safeguard for the 30-second tarpit cap. The current 137-request baseline is therefore expected to take roughly 1 hour 18 minutes when most requests are monitored. Deployed runs suppress in-memory conversation lifecycle requests and skip deliberate 404 probes unless tarpit-disabled status has been independently attested; query parameters, chat commands, and client request metadata do not disable tarpit protection. The baseline never starts paid-AI, import, logout, or mutation profiles; those profiles remain local-only and blocked until their exact confirmations are entered in the endpoint panel. OAuth provider initiation is verified manually through the normal login flow or Swagger rather than through the browser baseline.

The panel's complete count is the number of scheduled diagnostic records, not the number of API routes. Accounted: 120 is the audited inventory of unique HTTP-method-and-route operations. One operation can have several records, for example a successful read, an invalid-input contract check, and an authorization check; a few records are internal manifest or seed checks. Invoked counts records that issued a request, while Positive contracts counts records that verified an expected successful contract. The current Debug acceptance baseline completed with 154 PASS, 0 FAIL, and 15 intentional SKIP across 169 diagnostic records; it retained all 120 operations in the inventory.

5. Import data

Upload SPL ZIP files through the API import endpoint or use the console importer:

cd MedRecProConsole
dotnet run -- --help

SPL ZIP files can be downloaded from the DailyMed SPL Resources page.

Orange Book ZIP files can be downloaded from the FDA Orange Book Data Files page. See the FDA Orange Book Integration section for import details.

6. Run verification

The repository-level runner provides the same named gates used by CI:

powershell -NoProfile -ExecutionPolicy Bypass -File .\scripts\Invoke-MedRecProVerification.ps1 -Gate Fast
powershell -NoProfile -ExecutionPolicy Bypass -File .\scripts\Invoke-MedRecProVerification.ps1 -Gate DebugContract
powershell -NoProfile -ExecutionPolicy Bypass -File .\scripts\Invoke-MedRecProVerification.ps1 -Gate ReleaseContract
powershell -NoProfile -ExecutionPolicy Bypass -File .\scripts\Invoke-MedRecProVerification.ps1 -Gate Full
powershell -NoProfile -ExecutionPolicy Bypass -File .\scripts\Invoke-MedRecProVerification.ps1 -Gate All
  • Fast runs dependency, reflection, public-surface, and route guards for ordinary changes.
  • DebugContract runs the reviewed 27-case Label contract lane in Debug: the original 24 public-contract/startup cases plus three progress-response contract cases, excluding isolated OpenAPI filter units.
  • ReleaseContract separately compiles the same 27-case contract lane in Release under MedRecPro/.codex-build/test-contract-release.
  • Full builds the solution, runs every MSTest test, performs deterministic-test/source inventories, and checks the diff.
  • All executes every gate in order and is the phase/merge-boundary command used by the MedRecPro Verification workflow.

See MedRecPro verification gates for gate boundaries and CI behavior.

Setup Pitfalls and Fixes

IIS Virtual Application Path Stripping

IIS strips the virtual application prefix from requests before forwarding to ASP.NET Core. A request to /api/Label/search arrives at Kestrel as /Label/search. API controllers inherit the conditional route from ApiControllerBase:

#if DEBUG
[Route("api/[controller]")]   // Local: full path
#else
[Route("[controller]")]        // Azure: IIS strips /api prefix
#endif

Split controllers do not declare type-level routes. FeatureControllerNameConvention resolves each annotated controller's [controller] token from FeatureControllerNameAttribute; the current Label feature controllers use "Label", preserving the same 51 Debug and Release operations. SwaggerGroupAttribute independently controls documentation grouping without participating in routing. The same virtual-application consideration applies to MCP routes and Swagger paths.

Cloudflare + Azure App Service Managed Certificates

Azure App Service Managed Certificates do not work with Cloudflare proxy enabled. Use Cloudflare Origin Certificates instead:

  1. Create an Origin Certificate in Cloudflare (SSL/TLS > Origin Server)
  2. Convert to PFX: openssl pkcs12 -export -out origin.pfx -inkey key.pem -in cert.pem
  3. Upload to Azure App Service > Certificates
  4. Bind to custom domains with SNI SSL

OAuth Redirect URI Prefix

Production redirect URIs must include the /api/ prefix:

  • Correct: https://your-domain.com/api/signin-google
  • Wrong: https://your-domain.com/signin-google

Cloudflare Bot Blocking

Cloudflare has multiple independent bot-blocking systems that can interfere with MCP and server-to-server calls:

  • "Block AI Bots" (WAF managed rule) - Must allow Claude-User via AI Crawl Control settings
  • "Bot Fight Mode" - Blocks requests from hosting provider IPs. Cannot be bypassed with WAF rules. Whitelist Azure App Service outbound IPs via IP Access Rules (Security > WAF > Tools)
  • Always set a User-Agent header on outbound HttpClients to avoid bot detection

Azure SQL Serverless Cold Starts

Azure SQL Serverless auto-pauses after inactivity. Resuming takes 30-60 seconds, which can exceed default timeouts. Mitigations:

  • DatabaseKeepAliveService pings the database with SELECT 1 every 14 minutes during business hours (Mon-Fri, 8 AM - 8 PM Eastern) to prevent auto-pause. Each ping cycle includes 3 retry attempts with escalating delays (10s, 30s, 60s) and a 90-second connect timeout to accommodate cold resume. Configured via the DatabaseKeepAlive section in appsettings.json
  • EnableRetryOnFailure() is configured on the EF Core DbContext with 3 retries and a 60-second command timeout to handle transient failures across all application database operations
  • Increase the auto-pause delay during active development

Key Vault Secret Naming

Key Vault uses -- (double dash) as separator; ASP.NET Core configuration uses : (colon). The framework maps between them automatically:

  • Key Vault: Authentication--Google--ClientId
  • Config: Authentication:Google:ClientId

Ensure no extra characters (trailing commas, quotes) in Key Vault secret values.

IIS httpErrors PassThrough

Without <httpErrors existingResponse="PassThrough" /> in the root site's web.config, IIS replaces HTTP 401 responses with HTML error pages. This breaks OAuth challenge flows where the WWW-Authenticate header must reach the client. This setting must be in the root site (MedRecProStatic) because child virtual applications inherit it.

JWT Multi-Issuer/Audience

When both the API and MCP server issue JWT tokens with different issuer/audience values, the JWT Bearer handler must accept both using ValidIssuers and ValidAudiences arrays instead of the singular properties.

Azure SQL Free Tier Monitoring

The API includes built-in monitoring for Azure SQL Database's serverless free tier (100,000 vCore seconds/month). The AzureSqlMetricsService queries Azure Monitor Metrics to track consumption, project monthly costs, and recommend throttling levels. See the GET /api/Settings/metrics/database-cost endpoint.

Security Configuration

Security settings should be stored in user secrets (development) or Azure Key Vault (production):

{
  "Authentication:Google:ClientId": "your-google-client-id.apps.googleusercontent.com",
  "Authentication:Google:ClientSecret": "your-google-client-secret",
  "Authentication:Microsoft:ClientId": "your-microsoft-app-id",
  "Authentication:Microsoft:ClientSecret:Dev": "your-microsoft-secret",
  "Authentication:Microsoft:ClientSecret:Prod": "your-microsoft-secret",
  "Authentication:Microsoft:TenantId": "your-tenant-id",
  "Security:DB:PKSecret": "your-encryption-key",
  "Jwt:Key": "your-jwt-signing-key",
  "Jwt:Issuer": "MedRecPro",
  "Jwt:Audience": "MedRecUsers",
  "Jwt:ExpirationMinutes": 60,
  "ClaudeApiSettings:ApiKey": "your-claude-api-key",
  "Dev:DB:Connection": "your-dev-connection-string",
  "Prod:DB:Connection": "your-prod-connection-string"
}

Changing Security:DB:PKSecret will break all existing encrypted URLs, favorites, and bookmarks.

Production Deployment

See the detailed deployment guides in each project's README:

  • MedRecProMCP README - MCP server setup, OAuth provider config, Cloudflare rules, Claude.ai connector integration, and troubleshooting
  • MedRecProStatic README - Static site deployment, content management, and IIS configuration

Deployment Checklist

  1. Run Invoke-MedRecProVerification.ps1 -Gate All
  2. Publish each project to its virtual application path on Azure App Service
  3. Verify Azure Key Vault secrets are configured
  4. Purge Cloudflare cache after deployment
  5. Test authentication flows (Google and Microsoft OAuth)
  6. Verify Swagger UI loads at /api/swagger/index.html
  7. Verify MCP health check at /mcp/health
  8. Test AI chat at the static site

License

See the LICENSE.txt file for details.

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