Fix Spring bean wiring: make Neo4j-dependent beans conditional for indexing profile

The indexing profile disables Neo4j (codeiq.neo4j.enabled=false) but Spring
still tried to wire beans that depend on GraphStore/GraphRepository, causing
startup failures for index, enrich, stats, and other non-serve commands.

Changes:
- Add @ConditionalOnBean(GraphStore.class) to QueryService, GraphHealthIndicator
- Add @Profile("serving") to GraphController, FlowController
- Make GraphStore/FlowEngine/QueryService dependencies Optional in CLI commands
  (QueryCommand, GraphCommand, FindCommand, FlowCommand, BundleCommand) so they
  gracefully degrade when Neo4j is unavailable
- Keep backward-compatible package-private constructors for test compatibility

All 1,227 tests pass.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: aksOps

src/main/java/io/github/randomcodespace/iq/api/FlowController.java

@@ -2,6 +2,7 @@
 
 import io.github.randomcodespace.iq.flow.FlowEngine;
 import io.github.randomcodespace.iq.flow.FlowModels.FlowDiagram;
+import org.springframework.context.annotation.Profile;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -21,6 +22,7 @@
  */
 @RestController
 @RequestMapping("/api/flow")
+@Profile("serving")
 public class FlowController {
 
     private final FlowEngine flowEngine;

src/main/java/io/github/randomcodespace/iq/api/GraphController.java

@@ -12,6 +12,7 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.context.annotation.Profile;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
@@ -33,6 +34,7 @@
  */
 @RestController
 @RequestMapping("/api")
+@Profile("serving")
 public class GraphController {
 
     private final QueryService queryService;

src/main/java/io/github/randomcodespace/iq/cli/BundleCommand.java

@@ -7,6 +7,7 @@
 import io.github.randomcodespace.iq.config.CodeIqConfig;
 import io.github.randomcodespace.iq.flow.FlowEngine;
 import io.github.randomcodespace.iq.graph.GraphStore;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
@@ -19,6 +20,7 @@
 import java.time.Instant;
 import java.util.LinkedHashMap;
 import java.util.Map;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 import java.util.stream.Stream;
 import java.util.zip.ZipEntry;
@@ -46,8 +48,18 @@ public class BundleCommand implements Callable<Integer> {
     private final GraphStore graphStore;
     private final FlowEngine flowEngine;
 
+    @Autowired
     public BundleCommand(CodeIqConfig config, Analyzer analyzer,
-                         GraphStore graphStore, FlowEngine flowEngine) {
+                         Optional<GraphStore> graphStore, Optional<FlowEngine> flowEngine) {
+        this.config = config;
+        this.analyzer = analyzer;
+        this.graphStore = graphStore.orElse(null);
+        this.flowEngine = flowEngine.orElse(null);
+    }
+
+    /** Convenience constructor for tests. */
+    BundleCommand(CodeIqConfig config, Analyzer analyzer,
+                  GraphStore graphStore, FlowEngine flowEngine) {
         this.config = config;
         this.analyzer = analyzer;
         this.graphStore = graphStore;
@@ -88,12 +100,16 @@ public Integer call() {
                 nodeCount = analysisResult.nodeCount();
                 edgeCount = analysisResult.edgeCount();
                 filesAnalyzed = analysisResult.totalFiles();
-            } else {
+            } else if (graphStore != null) {
                 nodeCount = graphStore.count();
                 edgeCount = graphStore.findAll().stream()
                         .mapToLong(n -> n.getEdges().size())
                         .sum();
                 filesAnalyzed = 0;
+            } else {
+                nodeCount = 0;
+                edgeCount = 0;
+                filesAnalyzed = 0;
             }
 
             // 1. Write manifest.json (matching Python format)
@@ -119,13 +135,15 @@ public Integer call() {
             }
 
             // 3. Generate interactive flow HTML
-            try {
-                String flowHtml = flowEngine.renderInteractive(projectName);
-                zos.putNextEntry(new ZipEntry("flow.html"));
-                zos.write(flowHtml.getBytes(StandardCharsets.UTF_8));
-                zos.closeEntry();
-            } catch (Exception e) {
-                CliOutput.warn("Could not generate flow.html: " + e.getMessage());
+            if (flowEngine != null) {
+                try {
+                    String flowHtml = flowEngine.renderInteractive(projectName);
+                    zos.putNextEntry(new ZipEntry("flow.html"));
+                    zos.write(flowHtml.getBytes(StandardCharsets.UTF_8));
+                    zos.closeEntry();
+                } catch (Exception e) {
+                    CliOutput.warn("Could not generate flow.html: " + e.getMessage());
+                }
             }
 
             // 4. Bundle source files

src/main/java/io/github/randomcodespace/iq/cli/FindCommand.java

@@ -3,13 +3,15 @@
 import io.github.randomcodespace.iq.graph.GraphStore;
 import io.github.randomcodespace.iq.model.CodeNode;
 import io.github.randomcodespace.iq.model.NodeKind;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
 
 import java.nio.file.Path;
 import java.util.List;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 
 /**
@@ -35,12 +37,22 @@ public class FindCommand implements Callable<Integer> {
 
     private final GraphStore graphStore;
 
-    public FindCommand(GraphStore graphStore) {
+    @Autowired
+    public FindCommand(Optional<GraphStore> graphStore) {
+        this.graphStore = graphStore.orElse(null);
+    }
+
+    /** Convenience constructor for tests. */
+    FindCommand(GraphStore graphStore) {
         this.graphStore = graphStore;
     }
 
     @Override
     public Integer call() {
+        if (graphStore == null) {
+            CliOutput.error("Find queries require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            return 1;
+        }
         NodeKind kind = resolveKind(what);
         if (kind == null) {
             CliOutput.error("Unknown find target: " + what);

src/main/java/io/github/randomcodespace/iq/cli/FlowCommand.java

@@ -2,6 +2,7 @@
 
 import io.github.randomcodespace.iq.flow.FlowEngine;
 import io.github.randomcodespace.iq.flow.FlowModels.FlowDiagram;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
@@ -11,6 +12,7 @@
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 
 /**
@@ -38,12 +40,22 @@ public class FlowCommand implements Callable<Integer> {
 
     private final FlowEngine flowEngine;
 
-    public FlowCommand(FlowEngine flowEngine) {
+    @Autowired
+    public FlowCommand(Optional<FlowEngine> flowEngine) {
+        this.flowEngine = flowEngine.orElse(null);
+    }
+
+    /** Convenience constructor for tests. */
+    FlowCommand(FlowEngine flowEngine) {
         this.flowEngine = flowEngine;
     }
 
     @Override
     public Integer call() {
+        if (flowEngine == null) {
+            CliOutput.error("Flow diagrams require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            return 1;
+        }
         try {
             String content;
 

src/main/java/io/github/randomcodespace/iq/cli/GraphCommand.java

@@ -2,6 +2,7 @@
 
 import io.github.randomcodespace.iq.graph.GraphStore;
 import io.github.randomcodespace.iq.model.CodeNode;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
@@ -16,6 +17,7 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 import java.util.stream.Collectors;
 
@@ -50,12 +52,22 @@ public class GraphCommand implements Callable<Integer> {
 
     private final GraphStore graphStore;
 
-    public GraphCommand(GraphStore graphStore) {
+    @Autowired
+    public GraphCommand(Optional<GraphStore> graphStore) {
+        this.graphStore = graphStore.orElse(null);
+    }
+
+    /** Convenience constructor for tests. */
+    GraphCommand(GraphStore graphStore) {
         this.graphStore = graphStore;
     }
 
     @Override
     public Integer call() {
+        if (graphStore == null) {
+            CliOutput.error("Graph export requires Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            return 1;
+        }
         List<CodeNode> nodes;
         if (focus != null && !focus.isBlank()) {
             nodes = graphStore.findEgoGraph(focus, hops);

src/main/java/io/github/randomcodespace/iq/cli/QueryCommand.java

@@ -1,6 +1,7 @@
 package io.github.randomcodespace.iq.cli;
 
 import io.github.randomcodespace.iq.query.QueryService;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
@@ -9,6 +10,7 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.concurrent.Callable;
 
 /**
@@ -48,12 +50,22 @@ public class QueryCommand implements Callable<Integer> {
 
     private final QueryService queryService;
 
-    public QueryCommand(QueryService queryService) {
+    @Autowired
+    public QueryCommand(Optional<QueryService> queryService) {
+        this.queryService = queryService.orElse(null);
+    }
+
+    /** Convenience constructor for tests. */
+    QueryCommand(QueryService queryService) {
         this.queryService = queryService;
     }
 
     @Override
     public Integer call() {
+        if (queryService == null) {
+            CliOutput.error("Graph queries require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            return 1;
+        }
         if (consumersOf != null) {
             return printResult("Consumers of " + consumersOf, queryService.consumersOf(consumersOf));
         }

src/main/java/io/github/randomcodespace/iq/health/GraphHealthIndicator.java

@@ -1,6 +1,7 @@
 package io.github.randomcodespace.iq.health;
 
 import io.github.randomcodespace.iq.graph.GraphStore;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnBean;
 import org.springframework.boot.health.contributor.Health;
 import org.springframework.boot.health.contributor.HealthIndicator;
 import org.springframework.stereotype.Component;
@@ -10,6 +11,7 @@
  * has been populated with nodes.
  */
 @Component
+@ConditionalOnBean(GraphStore.class)
 public class GraphHealthIndicator implements HealthIndicator {
 
     private final GraphStore graphStore;

src/main/java/io/github/randomcodespace/iq/query/QueryService.java

@@ -4,6 +4,7 @@
 import io.github.randomcodespace.iq.graph.GraphStore;
 import io.github.randomcodespace.iq.model.CodeEdge;
 import io.github.randomcodespace.iq.model.CodeNode;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnBean;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
@@ -18,6 +19,7 @@
  * All methods return simple Map/List structures for JSON serialization.
  */
 @Service
+@ConditionalOnBean(GraphStore.class)
 public class QueryService {
 
     private final GraphStore graphStore;