v1 of protocol checker

components/Inventory.tsx

@@ -66,6 +66,8 @@ const TABLE_COLUMNS: { label: string; key: keyof ChemicalInventory }[] = [
   { label: "Multiple CAS (comma delimited)", key: "multipleCAS" },
 ];
 
+type ImportColumnMapping = keyof ChemicalInventory | "__skip__";
+
 // ── helpers ────────────────────────────────────────────────────────────────
 
 function daysUntil(dateStr: string) {
@@ -144,7 +146,7 @@ export function Inventory() {
   const [importStep, setImportStep] = useState<"upload" | "map" | "result">("upload");
   const [importHeaders, setImportHeaders] = useState<string[]>([]);
   const [importRows, setImportRows] = useState<string[][]>([]);
-  const [columnMapping, setColumnMapping] = useState<Record<string, keyof ChemicalInventory | "__skip__">>({});
+  const [columnMapping, setColumnMapping] = useState<Record<string, ImportColumnMapping>>({});
   const [importResult, setImportResult] = useState<{ imported: number; errors: string[] } | null>(null);
   const [isImporting, setIsImporting] = useState(false);
   const [importError, setImportError] = useState("");
@@ -339,7 +341,7 @@ export function Inventory() {
     return s.toLowerCase().replace(/[^a-z0-9]/g, "");
   }
 
-  function fuzzyMatchColumn(header: string): keyof ChemicalInventory | "__skip__" {
+  function fuzzyMatchColumn(header: string): ImportColumnMapping {
     const norm = normalizeHeader(header);
     if (!norm) return "__skip__";
     for (const col of TABLE_COLUMNS) {
@@ -349,7 +351,7 @@ export function Inventory() {
       const colNorm = normalizeHeader(col.label);
       if (colNorm.startsWith(norm) || norm.startsWith(colNorm)) return col.key;
     }
-    let bestKey: keyof ChemicalInventory | "__skip__" = "__skip__";
+    let bestKey: ImportColumnMapping = "__skip__";
     let bestScore = 0.55;
     for (const col of TABLE_COLUMNS) {
       const colNorm = normalizeHeader(col.label);
@@ -430,7 +432,7 @@ export function Inventory() {
       console.log("[import] headers:", headers, "data rows:", dataRows.length);
       setImportHeaders(headers);
       setImportRows(dataRows);
-      const mapping: Record<string, keyof ChemicalInventory | ""> = {};
+      const mapping: Record<string, ImportColumnMapping> = {};
       for (const h of headers) mapping[h] = fuzzyMatchColumn(h);
       setColumnMapping(mapping);
       console.log("[import] advancing to map step");
@@ -662,7 +664,7 @@ export function Inventory() {
                         <td className="px-3 py-2">
                           <Select
                             value={columnMapping[header] ?? ""}
-                            onValueChange={v => setColumnMapping(m => ({ ...m, [header]: v as keyof ChemicalInventory | "__skip__" }))}
+                            onValueChange={v => setColumnMapping(m => ({ ...m, [header]: v as ImportColumnMapping }))}
                           >
                             <SelectTrigger className="h-7 text-xs w-48">
                               <SelectValue placeholder="— skip —" />

components/ProtocolChecker.tsx

@@ -1,4 +1,4 @@
-import { useState } from "react";
+import { ChangeEvent, DragEvent, KeyboardEvent, useRef, useState } from "react";
 import { protocolsApi } from "../lib/api";
 import { Card } from "./ui/card";
 import { Button } from "./ui/button";
@@ -29,9 +29,13 @@ interface ChatMessage {
 }
 
 export function ProtocolChecker() {
+  const fileInputRef = useRef<HTMLInputElement>(null);
   const [protocol, setProtocol] = useState("");
+  const [selectedFileName, setSelectedFileName] = useState("");
   const [isAnalyzing, setIsAnalyzing] = useState(false);
   const [analyzed, setAnalyzed] = useState(false);
+  const [analysisError, setAnalysisError] = useState("");
+  const [issues, setIssues] = useState<SafetyIssue[]>([]);
   const [chatMessages, setChatMessages] = useState<ChatMessage[]>([
     {
       id: "1",
@@ -42,56 +46,71 @@ export function ProtocolChecker() {
   const [currentMessage, setCurrentMessage] = useState("");
   const [isSending, setIsSending] = useState(false);
 
-  const mockIssues: SafetyIssue[] = [
+  const loadProtocolFile = async (file: File) => {
-    {
+    setAnalyzed(false);
-      type: "critical",
+    setAnalysisError("");
-      category: "PPE Requirements",
+    setIssues([]);
-      message: "No mention of glove type for handling concentrated acids. Nitrile gloves are required for HCl handling.",
+
-      source: "OSHA 29 CFR 1910.132",
+    if (file.size > 10 * 1024 * 1024) {
-      sourceUrl: "https://www.osha.gov/laws-regs/regulations/standardnumber/1910/1910.132"
+      setAnalysisError("File must be 10MB or smaller.");
-    },
+      return;
-    {
-      type: "warning",
-      category: "Ventilation",
-      message: "Protocol should specify use of fume hood when working with volatile organic compounds.",
-      source: "OSHA Laboratory Standard 29 CFR 1910.1450",
-      sourceUrl: "https://www.osha.gov/laws-regs/regulations/standardnumber/1910/1910.1450"
-    },
-    {
-      type: "suggestion",
-      category: "Waste Disposal",
-      message: "Consider adding specific waste disposal instructions for halogenated solvents per EPA regulations.",
-      source: "EPA RCRA Guidelines",
-      sourceUrl: "https://www.epa.gov/rcra"
-    },
-    {
-      type: "warning",
-      category: "Emergency Procedures",
-      message: "Include location of nearest eyewash station and emergency shower as required by ANSI Z358.1.",
-      source: "ANSI Z358.1-2014",
-      sourceUrl: "https://www.ansi.org"
-    },
-    {
-      type: "suggestion",
-      category: "Chemical Storage",
-      message: "Specify incompatible chemicals that should not be stored together per NFPA guidelines.",
-      source: "NFPA 45: Fire Protection for Laboratories",
-      sourceUrl: "https://www.nfpa.org"
     }
-  ];
+
+    const extension = file.name.split(".").pop()?.toLowerCase();
+    if (extension !== "txt") {
+      setAnalysisError("For now, upload a TXT file or paste protocol text. PDF, DOC, and DOCX text extraction is not wired yet.");
+      return;
+    }
+
+    try {
+      const text = await file.text();
+      if (!text.trim()) {
+        setAnalysisError("That file does not contain any readable protocol text.");
+        return;
+      }
+      setProtocol(text);
+      setSelectedFileName(file.name);
+    } catch {
+      setAnalysisError("Could not read that file. Try saving it as a plain TXT file and upload again.");
+    }
+  };
+
+  const handleFileChange = async (event: ChangeEvent<HTMLInputElement>) => {
+    const file = event.target.files?.[0];
+    if (file) await loadProtocolFile(file);
+    event.target.value = "";
+  };
+
+  const handleUploadKeyDown = (event: KeyboardEvent<HTMLDivElement>) => {
+    if (event.key === "Enter" || event.key === " ") {
+      event.preventDefault();
+      fileInputRef.current?.click();
+    }
+  };
+
+  const handleDrop = async (event: DragEvent<HTMLDivElement>) => {
+    event.preventDefault();
+    const file = event.dataTransfer.files?.[0];
+    if (file) await loadProtocolFile(file);
+  };
 
   const handleAnalyze = async () => {
     if (!protocol.trim()) return;
     setIsAnalyzing(true);
+    setAnalyzed(false);
+    setAnalysisError("");
+    setIssues([]);
     try {
       const saved = await protocolsApi.createFromText(
-        `Protocol ${new Date().toLocaleDateString()}`,
+        selectedFileName || `Protocol ${new Date().toLocaleDateString()}`,
         protocol
       );
-      await protocolsApi.saveAnalysis(saved.id, mockIssues);
+      const analyzedProtocol = await protocolsApi.analyze(saved.id);
+      setIssues(analyzedProtocol.analysis_results || []);
       setAnalyzed(true);
     } catch (err) {
       console.error("Failed to save protocol:", err);
+      setAnalysisError(err instanceof Error ? err.message : "Failed to analyze protocol");
     } finally {
       setIsAnalyzing(false);
     }
@@ -162,9 +181,9 @@ export function ProtocolChecker() {
     }
   };
 
-  const criticalCount = mockIssues.filter(i => i.type === "critical").length;
+  const criticalCount = issues.filter(i => i.type === "critical").length;
-  const warningCount = mockIssues.filter(i => i.type === "warning").length;
+  const warningCount = issues.filter(i => i.type === "warning").length;
-  const suggestionCount = mockIssues.filter(i => i.type === "suggestion").length;
+  const suggestionCount = issues.filter(i => i.type === "suggestion").length;
 
   return (
     <div className="p-8">
@@ -196,10 +215,29 @@ export function ProtocolChecker() {
                     <p className="text-muted-foreground">Paste your protocol text or upload a file</p>
                   </div>
                   
-                  <div className="border-2 border-dashed border-border rounded-lg p-8 text-center mb-4 hover:border-primary transition-colors cursor-pointer">
+                  <input
+                    ref={fileInputRef}
+                    type="file"
+                    accept=".txt,text/plain"
+                    className="hidden"
+                    onChange={handleFileChange}
+                  />
+
+                  <div
+                    role="button"
+                    tabIndex={0}
+                    className="border-2 border-dashed border-border rounded-lg p-8 text-center mb-4 hover:border-primary transition-colors cursor-pointer"
+                    onClick={() => fileInputRef.current?.click()}
+                    onKeyDown={handleUploadKeyDown}
+                    onDragOver={(event) => event.preventDefault()}
+                    onDrop={handleDrop}
+                  >
                     <Upload className="w-12 h-12 text-muted-foreground mx-auto mb-3" />
                     <p className="text-foreground mb-1">Click to upload or drag and drop</p>
-                    <p className="text-muted-foreground">PDF, DOC, DOCX, TXT (max 10MB)</p>
+                    <p className="text-muted-foreground">TXT files for now (max 10MB)</p>
+                    {selectedFileName && (
+                      <p className="text-primary mt-2">{selectedFileName}</p>
+                    )}
                   </div>
 
                   <div className="relative mb-4">
@@ -241,6 +279,15 @@ Example:
                       </>
                     )}
                   </Button>
+
+                  {analysisError && (
+                    <Alert className="mt-4 border-red-200 bg-red-50">
+                      <AlertTriangle className="h-4 w-4 text-red-600" />
+                      <AlertDescription className="text-red-700">
+                        {analysisError}
+                      </AlertDescription>
+                    </Alert>
+                  )}
                 </Card>
 
                 {/* Results */}
@@ -258,7 +305,12 @@ Example:
                     </div>
 
                     <div className="space-y-4">
-                      {mockIssues.map((issue, idx) => {
+                      {issues.length === 0 && (
+                        <p className="text-muted-foreground">
+                          No safety issues were returned for this protocol.
+                        </p>
+                      )}
+                      {issues.map((issue, idx) => {
                         const colors = getIssueColor(issue.type);
                         return (
                           <div 

components/ui/calendar.tsx

@@ -60,12 +60,10 @@ function Calendar({
         ...classNames,
       }}
       components={{
-        IconLeft: ({ className, ...props }) => (
+        Chevron: ({ className, orientation, ...props }) => {
-          <ChevronLeft className={cn("size-4", className)} {...props} />
+          const Icon = orientation === "left" ? ChevronLeft : ChevronRight;
-        ),
+          return <Icon className={cn("size-4", className)} {...props} />;
-        IconRight: ({ className, ...props }) => (
+        },
-          <ChevronRight className={cn("size-4", className)} {...props} />
-        ),
       }}
       {...props}
     />

lib/api.ts

@@ -1,4 +1,4 @@
-import type { ChemicalInventory, SafetyIssue } from '../shared/types';
+import type { ChemicalInventory, Protocol, SafetyIssue } from '../shared/types';
 
 async function apiFetch(path: string, options: RequestInit = {}): Promise<Response> {
   const res = await fetch(path, {
@@ -64,6 +64,11 @@ export const protocolsApi = {
       body: JSON.stringify({ analysis_results: results }),
     }).then(r => r.json()),
 
+  analyze: (id: string): Promise<Protocol> =>
+    apiFetch(`/api/protocols/${id}/analyze`, {
+      method: 'POST',
+    }).then(r => r.json()),
+
   remove: (id: string): Promise<void> =>
     apiFetch(`/api/protocols/${id}`, { method: 'DELETE' }).then(() => undefined),
 };

server/.env.example

@@ -0,0 +1,6 @@
+DATABASE_URL=postgresql://labwise:labwise_dev_pw@localhost:5432/labwise_db
+MAILGUN_API_KEY=your_mailgun_api_key_here
+MAILGUN_DOMAIN=your_mailgun_domain_here
+FROM_EMAIL=LabWise <postmaster@your_mailgun_domain_here>
+OPENAI_API_KEY=your_openai_api_key_here
+OPENAI_MODEL=gpt-5-mini

server/src/ai/protocolAnalysis.ts

@@ -0,0 +1,177 @@
+const OPENAI_RESPONSES_URL = 'https://api.openai.com/v1/responses';
+
+type SafetyIssue = {
+  type: 'critical' | 'warning' | 'suggestion';
+  category: string;
+  message: string;
+  source: string;
+  sourceUrl: string;
+};
+
+type ProtocolAnalysis = {
+  issues: SafetyIssue[];
+};
+
+const analysisSchema = {
+  type: 'object',
+  properties: {
+    issues: {
+      type: 'array',
+      description: 'Safety issues found in the protocol. Return an empty array when no issues are found.',
+      items: {
+        type: 'object',
+        properties: {
+          type: {
+            type: 'string',
+            enum: ['critical', 'warning', 'suggestion'],
+            description: 'critical for immediate safety risks, warning for notable compliance or procedural gaps, suggestion for lower-risk improvements.',
+          },
+          category: {
+            type: 'string',
+            description: 'Short label such as PPE Requirements, Ventilation, Waste Disposal, Emergency Procedures, or Chemical Storage.',
+          },
+          message: {
+            type: 'string',
+            description: 'Clear, actionable finding written for lab staff.',
+          },
+          source: {
+            type: 'string',
+            description: 'Short source title, regulation, or guidance name.',
+          },
+          sourceUrl: {
+            type: 'string',
+            description: 'Clickable URL for the source.',
+          },
+        },
+        required: ['type', 'category', 'message', 'source', 'sourceUrl'],
+        additionalProperties: false,
+      },
+    },
+  },
+  required: ['issues'],
+  additionalProperties: false,
+};
+
+function getOutputText(response: any): string {
+  if (typeof response.output_text === 'string') return response.output_text;
+
+  const parts: string[] = [];
+  for (const item of response.output ?? []) {
+    for (const content of item.content ?? []) {
+      if (content.type === 'output_text' && typeof content.text === 'string') {
+        parts.push(content.text);
+      }
+    }
+  }
+  return parts.join('\n');
+}
+
+function normalizeAnalysis(value: unknown): SafetyIssue[] {
+  const parsed = value as Partial<ProtocolAnalysis>;
+  if (!Array.isArray(parsed.issues)) return [];
+
+  return parsed.issues
+    .filter((issue): issue is SafetyIssue =>
+      issue != null &&
+      ['critical', 'warning', 'suggestion'].includes((issue as SafetyIssue).type) &&
+      typeof (issue as SafetyIssue).category === 'string' &&
+      typeof (issue as SafetyIssue).message === 'string' &&
+      typeof (issue as SafetyIssue).source === 'string' &&
+      typeof (issue as SafetyIssue).sourceUrl === 'string'
+    )
+    .map(issue => ({
+      type: issue.type,
+      category: issue.category.trim(),
+      message: issue.message.trim(),
+      source: issue.source.trim(),
+      sourceUrl: issue.sourceUrl.trim(),
+    }))
+    .filter(issue => issue.category && issue.message && issue.source && issue.sourceUrl);
+}
+
+export async function analyzeProtocolWithOpenAI(protocolText: string): Promise<SafetyIssue[]> {
+  const apiKey = process.env.OPENAI_API_KEY;
+  if (!apiKey) {
+    throw new Error('OPENAI_API_KEY is not configured');
+  }
+
+  const model = process.env.OPENAI_MODEL || 'gpt-5-mini';
+  const requestBody: Record<string, unknown> = {
+    model,
+    input: [
+      {
+        role: 'system',
+        content:
+          'You are a laboratory safety reviewer. Analyze protocols for practical safety and compliance gaps. ' +
+          'Return JSON only. Each finding must use one of: critical, warning, suggestion. ' +
+          'Cite authoritative sources such as OSHA, EPA, CDC/NIOSH, NFPA, ANSI, or university EHS guidance. ' +
+          'Do not invent source URLs; use a relevant official source URL for every finding.',
+      },
+      {
+        role: 'user',
+        content:
+          'Analyze this lab protocol. Focus on PPE, chemical compatibility, ventilation, waste disposal, emergency procedures, storage, and missing hazard controls.\n\n' +
+          protocolText,
+      },
+    ],
+    tools: [
+      {
+        type: 'web_search',
+        filters: {
+          allowed_domains: [
+            'www.osha.gov',
+            'www.epa.gov',
+            'www.cdc.gov',
+            'www.nfpa.org',
+            'www.ansi.org',
+            'ehs.princeton.edu',
+            'ehs.stanford.edu',
+            'ehs.ucsf.edu',
+          ],
+        },
+      },
+    ],
+    tool_choice: 'required',
+    text: {
+      format: {
+        type: 'json_schema',
+        name: 'protocol_safety_analysis',
+        strict: true,
+        schema: analysisSchema,
+      },
+    },
+  };
+
+  if (model.startsWith('gpt-5')) {
+    requestBody.reasoning = { effort: 'low' };
+  }
+
+  const response = await fetch(OPENAI_RESPONSES_URL, {
+    method: 'POST',
+    headers: {
+      Authorization: `Bearer ${apiKey}`,
+      'Content-Type': 'application/json',
+    },
+    body: JSON.stringify(requestBody),
+  });
+
+  if (!response.ok) {
+    const errorBody = await response.text().catch(() => '');
+    throw new Error(`OpenAI protocol analysis failed (${response.status}): ${errorBody || response.statusText}`);
+  }
+
+  const data = await response.json();
+  const outputText = getOutputText(data);
+  if (!outputText) {
+    throw new Error('OpenAI returned an empty protocol analysis');
+  }
+
+  let parsed: unknown;
+  try {
+    parsed = JSON.parse(outputText);
+  } catch {
+    throw new Error('OpenAI returned protocol analysis that was not valid JSON');
+  }
+
+  return normalizeAnalysis(parsed);
+}

server/src/routes/protocols.ts

@@ -5,6 +5,7 @@ import multer from 'multer';
 import path from 'path';
 import fs from 'fs';
 import { fileURLToPath } from 'url';
+import { analyzeProtocolWithOpenAI } from '../ai/protocolAnalysis.js';
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 
@@ -89,6 +90,36 @@ router.patch('/:id/analysis', async (req, res) => {
   }
 });
 
+// POST /api/protocols/:id/analyze
+router.post('/:id/analyze', async (req, res) => {
+  try {
+    const protocol = await pool.query(
+      'SELECT * FROM protocols WHERE id = $1 AND user_id = $2',
+      [req.params.id, req.user!.id]
+    );
+    if (protocol.rows.length === 0) return res.status(404).json({ error: 'Not found' });
+
+    const content = protocol.rows[0].content;
+    if (!content || !content.trim()) {
+      return res.status(400).json({ error: 'Protocol content is required before analysis' });
+    }
+
+    const analysisResults = await analyzeProtocolWithOpenAI(content);
+    const result = await pool.query(
+      `UPDATE protocols SET analysis_results = $1::jsonb, updated_at = NOW()
+       WHERE id = $2 AND user_id = $3 RETURNING *`,
+      [JSON.stringify(analysisResults), req.params.id, req.user!.id]
+    );
+
+    res.json(result.rows[0]);
+  } catch (err) {
+    console.error(err);
+    const message = err instanceof Error ? err.message : 'Protocol analysis failed';
+    const status = message.includes('OPENAI_API_KEY') ? 500 : 502;
+    res.status(status).json({ error: message });
+  }
+});
+
 // DELETE /api/protocols/:id
 router.delete('/:id', async (req, res) => {
   try {