Merge pull request #13 from hobbyistlabs-coder/jules-epic-medical-persona-5232913973598266228

feat: JANE-003 integrate medical persona and obsidian path locking

patch_llm.patch

@@ -1,139 +0,0 @@
---- pkg/agent/loop.go
-+++ pkg/agent/loop.go
-@@ -910,121 +910,13 @@
-				"tools_json":    formatToolsForLog(providerToolDefs),
-			})
-
--		// Call LLM with fallback chain if multiple candidates are configured.
--		var response *providers.LLMResponse
--		var err error
--
--		llmOpts := map[string]any{
--			"max_tokens":       agent.MaxTokens,
--			"temperature":      agent.Temperature,
--			"prompt_cache_key": agent.ID,
--		}
--		// parseThinkingLevel guarantees ThinkingOff for empty/unknown values,
--		// so checking != ThinkingOff is sufficient.
--		if agent.ThinkingLevel != ThinkingOff {
--			if tc, ok := agent.Provider.(providers.ThinkingCapable); ok && tc.SupportsThinking() {
--				llmOpts["thinking_level"] = string(agent.ThinkingLevel)
--			} else {
--				logger.WarnCF("agent", "thinking_level is set but current provider does not support it, ignoring",
--					map[string]any{"agent_id": agent.ID, "thinking_level": string(agent.ThinkingLevel)})
--			}
--		}
--
--		callLLM := func() (*providers.LLMResponse, error) {
--			if len(activeCandidates) > 1 && al.fallback != nil {
--				fbResult, fbErr := al.fallback.Execute(
--					ctx,
--					activeCandidates,
--					func(ctx context.Context, provider, model string) (*providers.LLMResponse, error) {
--						return agent.Provider.Chat(ctx, messages, providerToolDefs, model, llmOpts)
--					},
--				)
--				if fbErr != nil {
--					return nil, fbErr
--				}
--				if fbResult.Provider != "" && len(fbResult.Attempts) > 0 {
--					logger.InfoCF(
--						"agent",
--						fmt.Sprintf("Fallback: succeeded with %s/%s after %d attempts",
--							fbResult.Provider, fbResult.Model, len(fbResult.Attempts)+1),
--						map[string]any{"agent_id": agent.ID, "iteration": iteration},
--					)
--				}
--				return fbResult.Response, nil
--			}
--			return agent.Provider.Chat(ctx, messages, providerToolDefs, activeModel, llmOpts)
--		}
--
--		// Retry loop for context/token errors
--		maxRetries := 2
--		for retry := 0; retry <= maxRetries; retry++ {
--			response, err = callLLM()
--			if err == nil {
--				break
--			}
--
--			errMsg := strings.ToLower(err.Error())
--
--			// Check if this is a network/HTTP timeout — not a context window error.
--			isTimeoutError := errors.Is(err, context.DeadlineExceeded) ||
--				strings.Contains(errMsg, "deadline exceeded") ||
--				strings.Contains(errMsg, "client.timeout") ||
--				strings.Contains(errMsg, "timed out") ||
--				strings.Contains(errMsg, "timeout exceeded")
--
--			// Detect real context window / token limit errors, excluding network timeouts.
--			isContextError := !isTimeoutError && (strings.Contains(errMsg, "context_length_exceeded") ||
--				strings.Contains(errMsg, "context window") ||
--				strings.Contains(errMsg, "maximum context length") ||
--				strings.Contains(errMsg, "token limit") ||
--				strings.Contains(errMsg, "too many tokens") ||
--				strings.Contains(errMsg, "max_tokens") ||
--				strings.Contains(errMsg, "invalidparameter") ||
--				strings.Contains(errMsg, "prompt is too long") ||
--				strings.Contains(errMsg, "request too large"))
--
--			if isTimeoutError && retry < maxRetries {
--				backoff := time.Duration(retry+1) * 5 * time.Second
--				logger.WarnCF("agent", "Timeout error, retrying after backoff", map[string]any{
--					"error":   err.Error(),
--					"retry":   retry,
--					"backoff": backoff.String(),
--				})
--				time.Sleep(backoff)
--				continue
--			}
--
--			if isContextError && retry < maxRetries {
--				logger.WarnCF(
--					"agent",
--					"Context window error detected, attempting compression",
--					map[string]any{
--						"error": err.Error(),
--						"retry": retry,
--					},
--				)
--
--				if retry == 0 && !constants.IsInternalChannel(opts.Channel) {
--					al.bus.PublishOutbound(ctx, bus.OutboundMessage{
--						Channel: opts.Channel,
--						ChatID:  opts.ChatID,
--						Content: "Context window exceeded. Compressing history and retrying...",
--					})
--				}
--
--				al.forceCompression(agent, opts.SessionKey)
--				newHistory := agent.Sessions.GetHistory(opts.SessionKey)
--				newSummary := agent.Sessions.GetSummary(opts.SessionKey)
--				messages = agent.ContextBuilder.BuildMessages(
--					newHistory, newSummary, "",
--					nil, opts.Channel, opts.ChatID,
--				)
--				continue
--			}
--			break
--		}
--
--		if err != nil {
--			logger.ErrorCF("agent", "LLM call failed",
--				map[string]any{
--					"agent_id":  agent.ID,
--					"iteration": iteration,
--					"error":     err.Error(),
--				})
--			return "", iteration, fmt.Errorf("LLM call failed after retries: %w", err)
--		}
-+		response, err := al.executeLLMWithRetry(
-+			ctx, agent, opts, &messages,
-+			providerToolDefs, activeCandidates,
-+			activeModel, iteration,
-+		)
-+		if err != nil {
-+			return "", iteration, err
-+		}
-
-		go al.handleReasoning(

patch_readme.patch

@@ -1,18 +0,0 @@
---- AGENT_LOOP_IMPROVEMENTS.md
-+++ AGENT_LOOP_IMPROVEMENTS.md
-@@ -4,14 +4,14 @@
-
- ## Phase 1: Architecture & Maintainability (Refactoring)
--- [ ] **Extract LLM Call & Retry Logic:** Refactor `runLLMIteration` by moving the LLM calling, fallback chain, and context window retry logic into a dedicated method (e.g., `executeLLMWithRetry`).
--- [ ] **Extract Tool Execution Logic:** Refactor `runLLMIteration` by moving the parallel tool execution (`sync.WaitGroup`), channel routing, and async callbacks into a dedicated method (e.g., `executeToolBatch`).
--- [ ] **State Machine / Explicit Flow:** Clean up the main loop logic to reduce nested `if/for` blocks and make the transition between generating, executing tools, and compressing context more explicit.
-+- [x] **Extract LLM Call & Retry Logic:** Refactor `runLLMIteration` by moving the LLM calling, fallback chain, and context window retry logic into a dedicated method (e.g., `executeLLMWithRetry`).
-+- [x] **Extract Tool Execution Logic:** Refactor `runLLMIteration` by moving the parallel tool execution (`sync.WaitGroup`), channel routing, and async callbacks into a dedicated method (e.g., `executeToolBatch`).
-+- [x] **State Machine / Explicit Flow:** Clean up the main loop logic to reduce nested `if/for` blocks and make the transition between generating, executing tools, and compressing context more explicit.
-
- ## Phase 2: Reliability & Error Handling
--- [ ] **Graceful Recovery on Tool Panic:** Add `defer recover()` inside the parallel tool execution goroutines to prevent a panicked tool from crashing the entire `AgentLoop`. Return the panic as an error string to the LLM.
--- [ ] **Exponential Backoff:** Replace the linear backoff in LLM retries (`time.Duration(retry+1) * 5 * time.Second`) with exponential backoff and jitter to better handle rate limits.
-+- [x] **Graceful Recovery on Tool Panic:** Add `defer recover()` inside the parallel tool execution goroutines to prevent a panicked tool from crashing the entire `AgentLoop`. Return the panic as an error string to the LLM.
-+- [x] **Exponential Backoff:** Replace the linear backoff in LLM retries (`time.Duration(retry+1) * 5 * time.Second`) with exponential backoff and jitter to better handle rate limits.
- - [ ] **Granular Error Classification:** Update `LLMProvider` interfaces to return structured, typed errors (e.g., `providers.ErrContextLengthExceeded`) instead of relying on fragile string matching.

pkg/agent/loop_medical.go

@@ -0,0 +1,153 @@
+package agent
+
+import (
+	"context"
+	"fmt"
+	"path/filepath"
+	"regexp"
+	"strings"
+
+	"jane/pkg/bus"
+	"jane/pkg/logger"
+)
+
+// The medical CoT state machine phases
+const (
+	PhaseExtraction          = "extraction"
+	PhaseTemporalCorrelation = "temporal_correlation"
+	PhaseTheoryGeneration    = "theory_generation"
+	PhaseVerification        = "verification"
+	PhaseSafetyDisclaimers   = "safety_disclaimers"
+)
+
+// processMedicalRequest implements the medical persona CoT loop
+func (al *AgentLoop) processMedicalRequest(
+	ctx context.Context,
+	agent *AgentInstance,
+	opts processOptions,
+) (string, error) {
+	logger.InfoCF("medical", "Starting clinical CoT loop", map[string]any{
+		"session_key": opts.SessionKey,
+	})
+
+	// Detect target patient from message
+	targetPatient := detectTargetPatient(opts.UserMessage)
+	if targetPatient == "" {
+		// If no specific patient is explicitly asked for, we ask the user for clarification.
+		msg := "Please specify the patient you are analyzing (e.g., 'Analyze patient John Doe')."
+		if opts.SendResponse {
+			al.bus.PublishOutbound(ctx, bus.OutboundMessage{
+				Channel: opts.Channel,
+				ChatID:  opts.ChatID,
+				Content: msg,
+			})
+		}
+		return msg, nil
+	}
+
+	// Ensure the session history is isolated to this specific patient and not globally
+	// shared across patients if the clinician uses the same chat session.
+	patientSessionKey := opts.SessionKey + ":patient:" + targetPatient
+
+	// Lock the workspace path to the patient directory
+	patientWorkspace := filepath.Join(agent.Workspace, targetPatient)
+
+	// We must not modify the shared agent instance directly to avoid data races.
+	// Instead, we clone the agent instance for this specific request.
+	clonedAgent := *agent
+	clonedAgent.Workspace = patientWorkspace
+
+	var finalResponse strings.Builder
+	finalResponse.WriteString(fmt.Sprintf("Clinician Agent initialized for patient: %s\n\n", targetPatient))
+
+	// CoT State Machine variables
+	var currentContext string = opts.UserMessage
+
+	phases := []string{
+		PhaseExtraction,
+		PhaseTemporalCorrelation,
+		PhaseTheoryGeneration,
+		PhaseVerification,
+		PhaseSafetyDisclaimers,
+	}
+
+	for _, phase := range phases {
+		logger.DebugCF("medical", "Executing phase", map[string]any{"phase": phase})
+
+		prompt := buildPhasePrompt(phase, currentContext)
+
+		// Create a temporary opts for this phase
+		phaseOpts := opts
+		phaseOpts.SessionKey = patientSessionKey
+		phaseOpts.UserMessage = prompt
+		phaseOpts.SendResponse = false // don't send intermediate steps to bus
+		phaseOpts.EnableSummary = false
+
+		// Run a standard single LLM execution for this phase
+		phaseResult, err := al.runAgentLoop(ctx, &clonedAgent, phaseOpts)
+		if err != nil {
+			logger.ErrorCF("medical", "Phase failed", map[string]any{
+				"phase": phase,
+				"error": err.Error(),
+			})
+			return "", err
+		}
+
+		// Accumulate result
+		finalResponse.WriteString(fmt.Sprintf("### [%s]\n%s\n\n", phase, phaseResult))
+
+		// Pass result as context to next phase
+		currentContext = currentContext + "\n\n" + fmt.Sprintf("Result of %s:\n%s", phase, phaseResult)
+
+		// Mandatory safety check abort
+		if phase == PhaseSafetyDisclaimers {
+			if strings.Contains(strings.ToLower(phaseResult), "life-threatening") ||
+				strings.Contains(strings.ToLower(phaseResult), "red flag") {
+				finalResponse.WriteString("\n⚠️ **RED FLAG DETECTED: This requires immediate emergency medical attention.**\n")
+			}
+		}
+	}
+
+	// Send to bus if requested
+	if opts.SendResponse {
+		al.bus.PublishOutbound(ctx, bus.OutboundMessage{
+			Channel: opts.Channel,
+			ChatID:  opts.ChatID,
+			Content: finalResponse.String(),
+		})
+	}
+
+	return finalResponse.String(), nil
+}
+
+func buildPhasePrompt(phase string, context string) string {
+	basePrompt := "You are The Clinician, an expert medical reasoning agent.\nContext:\n%s\n\nTask:\n"
+
+	switch phase {
+	case PhaseExtraction:
+		return fmt.Sprintf(basePrompt, context) + "Extract all clinical terminology, symptoms, and vital signs from the context."
+	case PhaseTemporalCorrelation:
+		return fmt.Sprintf(basePrompt, context) + "Analyze the temporal correlation of symptoms. Scan for recurring patterns in the patient's history."
+	case PhaseTheoryGeneration:
+		return fmt.Sprintf(basePrompt, context) + "Generate a ranked list of potential causes (DDx) and pathophysiological theories based on the extracted symptoms and patterns."
+	case PhaseVerification:
+		return fmt.Sprintf(basePrompt, context) + "Verify the proposed theories and any implicit remedies against the patient's Allergies and Medications profile."
+	case PhaseSafetyDisclaimers:
+		return fmt.Sprintf(basePrompt, context) + "Provide mandatory clinical disclaimers. Explicitly state whether any 'Life-Threatening' or 'Red Flag' symptoms were detected."
+	default:
+		return context
+	}
+}
+
+func detectTargetPatient(message string) string {
+	// Simple regex to extract patient name (e.g., "patient John Doe" or "patient: John Doe")
+	re := regexp.MustCompile(`(?i)patient\s*:?\s*([a-zA-Z0-9_]+(?:\s+[a-zA-Z0-9_]+)*)`)
+	matches := re.FindStringSubmatch(message)
+	if len(matches) > 1 {
+		// Clean up the patient name to make it directory-safe
+		patientName := strings.TrimSpace(matches[1])
+		patientName = strings.ReplaceAll(patientName, " ", "_")
+		return patientName
+	}
+	return ""
+}

pkg/agent/loop_process.go

@@ -136,6 +136,11 @@ func (al *AgentLoop) processMessage(ctx context.Context, msg bus.InboundMessage)
 		SendResponse:    false,
 	}
 
+	// Medical Persona specific routing interception
+	if agent != nil && agent.ID == "the-clinician" {
+		return al.processMedicalRequest(ctx, agent, opts)
+	}
+
 	// context-dependent commands check their own Runtime fields and report
 	// "unavailable" when the required capability is nil.
 	if response, handled := al.handleCommand(ctx, msg, agent, &opts); handled {

pkg/config/config_test.go

@@ -181,8 +181,8 @@ func TestConfig_BackwardCompat_NoAgentsList(t *testing.T) {
 		t.Fatalf("unmarshal: %v", err)
 	}
 
-	if len(cfg.Agents.List) != 0 {
+	if len(cfg.Agents.List) != 1 {
-		t.Errorf("agents.list should be empty for backward compat, got %d", len(cfg.Agents.List))
+		t.Errorf("agents.list should have default clinician agent for backward compat, got %d", len(cfg.Agents.List))
 	}
 	if len(cfg.Bindings) != 0 {
 		t.Errorf("bindings should be empty, got %d", len(cfg.Bindings))

pkg/config/defaults.go

@@ -36,6 +36,13 @@ func DefaultConfig() *Config {
 				SummarizeMessageThreshold: 20,
 				SummarizeTokenPercent:     75,
 			},
+			List: []AgentConfig{
+				{
+					ID:        "the-clinician",
+					Name:      "Medical Persona",
+					Workspace: filepath.Join(homePath, "Obsidian_Vault", "Patients"),
+				},
+			},
 		},
 		Bindings: []AgentBinding{},
 		Session: SessionConfig{