149 covariance analysis tools

src/main/java/edu/jhuapl/trinity/AppAsyncManager.java

@@ -10,6 +10,10 @@
 import edu.jhuapl.trinity.data.messages.xai.FeatureCollection;
 import edu.jhuapl.trinity.data.messages.xai.FeatureVector;
 import edu.jhuapl.trinity.javafx.components.MatrixOverlay;
+import edu.jhuapl.trinity.javafx.components.hyperdrive.JsonExtractionProfile;
+import edu.jhuapl.trinity.javafx.components.hyperdrive.JsonSchemaMappingPane;
+import edu.jhuapl.trinity.javafx.components.hyperdrive.TopicDiscoveryEngine;
+import edu.jhuapl.trinity.javafx.components.hyperdrive.TopicDiscoveryReviewPane;
 import edu.jhuapl.trinity.javafx.components.panes.AnalysisLogPane;
 import edu.jhuapl.trinity.javafx.components.panes.CocoViewerPane;
 import edu.jhuapl.trinity.javafx.components.panes.FeatureVectorManagerPane;
@@ -43,6 +47,7 @@
 import edu.jhuapl.trinity.javafx.events.FeatureVectorEvent;
 import edu.jhuapl.trinity.javafx.events.GaussianMixtureEvent;
 import edu.jhuapl.trinity.javafx.events.HitEvent;
+import edu.jhuapl.trinity.javafx.events.HyperdriveEvent;
 import edu.jhuapl.trinity.javafx.events.ManifoldEvent;
 import edu.jhuapl.trinity.javafx.events.MissionTimerXEvent;
 import edu.jhuapl.trinity.javafx.events.RestEvent;
@@ -143,6 +148,8 @@ public class AppAsyncManager extends Task<Void> {
     PixelSelectionPane pixelSelectionPane;
     ImageInspectorPane imageInspectorPane;
     HyperdrivePane hyperdrivePane;
+    JsonSchemaMappingPane jsonSchemaMappingPane;
+    TopicDiscoveryReviewPane topicDiscoveryReviewPane;
     MatrixOverlay matrixOverlay;
     RetroWavePane retroWavePane = null;
 
@@ -775,6 +782,45 @@ protected Void call() throws Exception {
                 projectorPane.scanAndAnimate();
             }
         });
+        // Hyperdrive editor overlays are independent LitPathPanes on the shared desktop.
+        // Hyperdrive and each overlay communicate only through HyperdriveEvent.
+        scene.addEventHandler(HyperdriveEvent.OPEN_JSON_SCHEMA_MAPPING, event -> {
+            JsonExtractionProfile profile = event.object1 instanceof JsonExtractionProfile p ? p.copy() : null;
+            if (jsonSchemaMappingPane != null && desktopPane.getChildren().contains(jsonSchemaMappingPane)) {
+                jsonSchemaMappingPane.toFront();
+                jsonSchemaMappingPane.show();
+                return;
+            }
+            jsonSchemaMappingPane = new JsonSchemaMappingPane(scene, desktopPane, profile);
+            desktopPane.getChildren().add(jsonSchemaMappingPane);
+            jsonSchemaMappingPane.setLayoutX(Math.max(20, (desktopPane.getWidth() - 1120) / 2));
+            jsonSchemaMappingPane.setLayoutY(Math.max(20, (desktopPane.getHeight() - 710) / 2));
+            jsonSchemaMappingPane.toFront();
+            jsonSchemaMappingPane.slideInPane();
+        });
+        scene.addEventHandler(HyperdriveEvent.OPEN_TOPIC_REVIEW, event -> {
+            if (!(event.object1 instanceof java.util.List<?> list)
+                || !list.stream().allMatch(TopicDiscoveryEngine.Topic.class::isInstance)) return;
+            java.util.List<TopicDiscoveryEngine.Topic> topics = new java.util.ArrayList<>();
+            for (Object candidate : list) topics.add((TopicDiscoveryEngine.Topic) candidate);
+            if (topicDiscoveryReviewPane != null && desktopPane.getChildren().contains(topicDiscoveryReviewPane)) {
+                topicDiscoveryReviewPane.toFront();
+                topicDiscoveryReviewPane.show();
+                return;
+            }
+            topicDiscoveryReviewPane = new TopicDiscoveryReviewPane(scene, desktopPane, topics);
+            desktopPane.getChildren().add(topicDiscoveryReviewPane);
+            topicDiscoveryReviewPane.setLayoutX(Math.max(20, (desktopPane.getWidth() - 1000) / 2));
+            topicDiscoveryReviewPane.setLayoutY(Math.max(20, (desktopPane.getHeight() - 690) / 2));
+            topicDiscoveryReviewPane.toFront();
+            topicDiscoveryReviewPane.slideInPane();
+        });
+        scene.addEventHandler(HyperdriveEvent.CLOSE_TOPIC_REVIEW, event -> {
+            if (topicDiscoveryReviewPane != null) {
+                topicDiscoveryReviewPane.close();
+                topicDiscoveryReviewPane = null;
+            }
+        });
         scene.addEventHandler(ApplicationEvent.SHOW_HYPERDRIVE_PANE, e -> {
             if (!desktopPane.getChildren().contains(hyperdrivePane)) {
                 desktopPane.getChildren().add(hyperdrivePane);

src/main/java/edu/jhuapl/trinity/data/messages/llm/ChatCompletionsOutput.java

@@ -56,11 +56,14 @@ public class ChatCompletionsOutput extends MessageData {
     //</editor-fold>
 
     //<editor-fold defaultstate="collapsed" desc="Payload Fields">
+    private String id;
+    private Long created;
     private String object;
     private String model;
     private String prompt;
     private List<ChatCompletionChoice> choices;
     private ChatGenerationParameters generation_parameters;
+    private ChatUsage usage;
 
     //</editor-fold>
     //extra helper fields
@@ -74,6 +77,30 @@ public ChatCompletionsOutput() {
 
     //<editor-fold defaultstate="collapsed" desc="Properties">
 
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public Long getCreated() {
+        return created;
+    }
+
+    public void setCreated(Long created) {
+        this.created = created;
+    }
+
+    public ChatUsage getUsage() {
+        return usage;
+    }
+
+    public void setUsage(ChatUsage usage) {
+        this.usage = usage;
+    }
+
     /**
      * @return the object
      */

src/main/java/edu/jhuapl/trinity/data/messages/llm/ChatGenerationParameters.java

@@ -31,7 +31,7 @@ public class ChatGenerationParameters {
 
     */
     private List<String> bad_words;
-    private String stop;
+    private Stop stop;
     private Integer output_length;
     private Integer top_k;
     private Integer top_p;
@@ -65,14 +65,14 @@ public void setBad_words(List<String> bad_words) {
     /**
      * @return the stop
      */
-    public String getStop() {
+    public Stop getStop() {
         return stop;
     }
 
     /**
      * @param stop the stop to set
      */
-    public void setStop(String stop) {
+    public void setStop(Stop stop) {
         this.stop = stop;
     }
 

src/main/java/edu/jhuapl/trinity/data/messages/llm/ChatUsage.java

@@ -0,0 +1,42 @@
+package edu.jhuapl.trinity.data.messages.llm;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+
+/**
+ * Token counts provided by a chat completion response.
+ */
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class ChatUsage {
+    private Integer completion_tokens;
+    private Integer prompt_tokens;
+    private Integer total_tokens;
+
+    public ChatUsage() {
+    }
+
+    public Integer getCompletion_tokens() {
+        return completion_tokens;
+    }
+
+    public void setCompletion_tokens(Integer completion_tokens) {
+        this.completion_tokens = completion_tokens;
+    }
+
+    public Integer getPrompt_tokens() {
+        return prompt_tokens;
+    }
+
+    public void setPrompt_tokens(Integer prompt_tokens) {
+        this.prompt_tokens = prompt_tokens;
+    }
+
+    public Integer getTotal_tokens() {
+        return total_tokens;
+    }
+
+    public void setTotal_tokens(Integer total_tokens) {
+        this.total_tokens = total_tokens;
+    }
+}

src/main/java/edu/jhuapl/trinity/data/messages/llm/EmbeddingsTextBatchInput.java

@@ -0,0 +1,31 @@
+package edu.jhuapl.trinity.data.messages.llm;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import java.util.List;
+
+/** OpenAI-compatible batch of text inputs (one embedding per input string). */
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class EmbeddingsTextBatchInput {
+    private Object input;
+    private String model;
+    private String encoding_format = "float";
+    private String embedding_type = "all";
+    private int dimensions = 512;
+    private String user = "string";
+
+    public Object getInput() { return input; }
+    public void setInput(List<String> input) { this.input = input; }
+    public void setInput(String input) { this.input = input; }
+    public String getModel() { return model; }
+    public void setModel(String model) { this.model = model; }
+    public String getEncoding_format() { return encoding_format; }
+    public void setEncoding_format(String value) { encoding_format = value; }
+    public String getEmbedding_type() { return embedding_type; }
+    public void setEmbedding_type(String value) { embedding_type = value; }
+    public int getDimensions() { return dimensions; }
+    public void setDimensions(int value) { dimensions = value; }
+    public String getUser() { return user; }
+    public void setUser(String value) { user = value; }
+}

src/main/java/edu/jhuapl/trinity/data/messages/llm/ResponseChatMessage.java

@@ -1,16 +1,30 @@
 package edu.jhuapl.trinity.data.messages.llm;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+
 import java.util.ArrayList;
 import java.util.List;
 
 /**
  * @author Sean Phillips
  */
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class ResponseChatMessage {
     private String role;
     private String content;
+    private String reasoning_content;
     private List<String> tool_calls;
 
+    public String getReasoning_content() {
+        return reasoning_content;
+    }
+
+    public void setReasoning_content(String reasoning_content) {
+        this.reasoning_content = reasoning_content;
+    }
+
     public ResponseChatMessage() {
         tool_calls = new ArrayList<>();
     }

src/main/java/edu/jhuapl/trinity/data/messages/llm/Stop.java

@@ -0,0 +1,36 @@
+package edu.jhuapl.trinity.data.messages.llm;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Stop sequences returned in chat generation parameters.
+ *
+ * The observed response shape is a nested array, such as [[""]],
+ * rather than a JSON object. This value object preserves that shape
+ * with standard Jackson binding annotations.
+ */
+public class Stop {
+    private List<List<String>> sequences;
+
+    public Stop() {
+        this.sequences = new ArrayList<>();
+    }
+
+    @JsonCreator(mode = JsonCreator.Mode.DELEGATING)
+    public Stop(List<List<String>> sequences) {
+        this.sequences = sequences;
+    }
+
+    @JsonValue
+    public List<List<String>> getSequences() {
+        return sequences;
+    }
+
+    public void setSequences(List<List<String>> sequences) {
+        this.sequences = sequences;
+    }
+}