changing figure names to be the user-defined names to support "supplemental" type figures

frontend/src/components/AppArtifacts.vue

@@ -81,9 +81,13 @@ const acceptFiles = async (files: any[]) => {
         if (uploadedFileName.value === "") {
           uploadedFileName.value = file.filename;
         }
-
+        const name = uploadedFileName.value.trim() || file.filename
         try {
-          const response = await uploadArtifact(props.session, file.filename, uploadContent, file.mimetype)
+            const response = await uploadArtifact(
+              props.session,
+              name,
+              uploadContent,
+              file.mimetype)
 
           console.log("File uploaded successfully:", response);
 
@@ -94,7 +98,7 @@ const acceptFiles = async (files: any[]) => {
 
           // add it to the list of artifacts
           artifacts.value.push({
-            filename: `Figure ${desc.figure_number}`,
+            filename: name,
             title: desc.title,
             description: desc.description,
             mimetype: file.mimetype,

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/assembler/agent.py

@@ -29,6 +29,14 @@ def manuscript_assembler(callback_context: CallbackContext) -> Optional[types.Co
 
             # then remove the instruction key from the state
             callback_context.state[instructions_key] = ""
+
+    # ---------- Append Supplementary Figures section, if any ----------
+    if "supplementary_figures" in current_state and current_state["supplementary_figures"].strip():
+        manuscript_content += (
+            "\n# Supplementary Figures\n\n"
+            f"{current_state['supplementary_figures']}"
+        )
+    # ------------------------------------------------------------------
 
     return types.Content(
         parts=[types.Part(text=manuscript_content)],

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/coordinator/custom_agent.py

@@ -75,9 +75,16 @@ async def _run_async_impl(
             # simulate an event that there was a transfer of agent
             yield self.get_transfer_to_agent_event(ctx, agent)
 
-            # remove "display_name" since adk does not support it
-            if last_user_input.inline_data is not None:
-                last_user_input.inline_data.display_name = None
+            # --- if the user gave a filename, inject it as a text part ---
+            if last_user_input.inline_data and last_user_input.inline_data.display_name:
+                from google.genai.types import Part
+                file_name = last_user_input.inline_data.display_name
+                # just inject the “Filename:” hint so the LLM sees it
+                ctx.user_content.parts.insert(
+                    0,
+                    Part(text=f"Filename: {file_name}")
+                )
+             # ------------------------------------------------------------------
 
             # call agent
             async for event in agent.run_async(ctx):

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/discussion/prompt.py

@@ -73,6 +73,10 @@
 deal with these weaknesses. The fifth paragraph may then culminate in a
 description of how the paper moves the field forward. Step by step, the reader
 thus learns to put the paper’s conclusions into the right context.
+
+* When referring to data presented in supplementary figures (i.e., those figures with 
+the words Supp., Supplemental, S, etc.), cite them with the format the user used, 
+for example “Figure S1” is Figure S1, "Supplemental Figure 1" is Suplemental Figure 1, etc.
 ```
 
 # Output

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/figure/agent.py

@@ -38,10 +38,21 @@ def process_figure_response(
     # get current state
     state = callback_context.state
 
-    # get agent description about figure
-    figure_desc = llm_response.content.parts[0].text
-    figure_desc_obj = SingleFigureDescription.model_validate_json(figure_desc)
-
+    # parse the LLM’s JSON into our Pydantic model
+    raw = llm_response.content.parts[0].text
+    figure_desc_obj = SingleFigureDescription.model_validate_json(raw)
+
+    # locate the uploaded‐file part anywhere in user_content.parts
+    incoming = None
+    for part in callback_context._invocation_context.user_content.parts:
+        if getattr(part, "inline_data", None) is not None:
+            incoming = part.inline_data
+            break
+
+    # if the user gave a filename, stash it and override figure title
+    if incoming and getattr(incoming, "display_name", None):
+        callback_context.state["current_display_name"] = incoming.display_name
+        figure_desc_obj.title = incoming.display_name
     # compute figure number
     current_figure_id = 1
     if FIGURES_KEY in state:
@@ -75,16 +86,20 @@ def update_figure_state(
 
     current_figure = state[CURRENT_FIGURE_KEY]
     current_figure_obj = SingleFigureDescription.model_validate(current_figure)
+    # load or initialize the figures dict, then store it back on state
+    current_figure_state = state.get(FIGURES_KEY, {})
+    state[FIGURES_KEY] = current_figure_state
 
-    if FIGURES_KEY not in state:
-        state[FIGURES_KEY] = {}
-
-    current_figure_state = state[FIGURES_KEY]
-    current_figure_state[current_figure_obj.figure_number] = {
-        k: v for k, v in current_figure_obj.model_dump().items() if k != "figure_number"
+    entry = {
+        k: v
+        for k, v in current_figure_obj.model_dump().items()
+        if k != "figure_number"
     }
-
-    state[FIGURES_KEY] = current_figure_state
+    # preserve any user‑provided filename exactly
+    display_label = state.get("current_display_name", None)
+    if display_label is not None:
+        entry["display_name"] = display_label
+    current_figure_state[current_figure_obj.figure_number] = entry
 
     state[CURRENT_FIGURE_KEY] = ""
 

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/figure/prompt.py

@@ -1,4 +1,4 @@
-"""Prompt for the abstract_agent"""
+"""Prompt for the figure agent"""
 
 import json
 
@@ -13,6 +13,9 @@
 * Analyze the figure in the context of a scientific paper.
 * Generate an in-depth description of the figure. If you need to add formatting to
 the description, use Markdown.
+*  If the figure’s name (title or file name) contains “Supp.“, “supp.“, “Supplemental“,
+“supplemental“, “Supplementary“, "S", or any clear variant indicating it is a supplementary figure, 
+then set "figure_type": "supplemental"; otherwise leave it as "main".
 * Generate a short title for the figure. If you need to add formatting to the title,
 use Markdown.
 * Respond ONLY with a JSON object matching this schema:

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/introduction/prompt.py

@@ -85,6 +85,10 @@
 the following ways: it does not need to present the context (which has just been
 given), it is somewhat more specific about the results, and it only briefly
 previews the conclusion of the paper, if at all.
+
+* When referring to data presented in supplementary figures (i.e., those figures with 
+the words Supp., Supplemental, S, etc.), cite them with the format the user used, 
+for example “Figure S1” is Figure S1, "Supplemental Figure 1" is Suplemental Figure 1, etc.
 ```
 
 # Output

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/methods/prompt.py

@@ -100,6 +100,10 @@
 give exact volumes, times, and temperatures. Clarity: avoid jargon; define any
 uncommon abbreviation at first use. Self-contained: every reagent or piece of
 equipment needed to reproduce should be listed here or in a table.
+
+* When referring to data presented in supplementary figures (i.e., those figures with 
+the words Supp., Supplemental, S, etc.), cite them with the format the user used, 
+for example “Figure S1” is Figure S1, "Supplemental Figure 1" is Suplemental Figure 1, etc.
 ```
 
 # Output

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/results/prompt.py

@@ -87,6 +87,11 @@
 statement, and paragraphs farther down in the text rely on the logical
 conclusions of previous paragraphs, much as theorems are built in mathematical
 literature.
+
+* When referring to data presented in supplementary figures (i.e., those figures with 
+the words Supp., Supplemental, S, etc.), cite them with the format the user used, 
+for example “Figure S1” is Figure S1, "Supplemental Figure 1" is Suplemental Figure 1, etc.
+
 ```
 
 # Output

packages/manugen-ai/src/manugen_ai/agents/ai_science_writer/sub_agents/reviewer/agent.py

@@ -25,6 +25,8 @@
 Your job:
 1. Provide a concise bullet-list of any changes needed.
 2. If **no** changes are needed (content is publication-ready), call the tool `exit_loop` instead of returning bullets.
+3. Ensure there are no captions in `{supplementary_figures}` that lack a matching citation
+
 
 Return either:
 - A JSON list of feedback bullets,

packages/manugen-ai/src/manugen_ai/schema.py

@@ -25,14 +25,15 @@ def prepare_instructions(callback_context: CallbackContext) -> Optional[types.Co
             callback_context.state[key1] = ""
 
     # add figures descriptions
-    figure_descriptions = ""
+    callback_context.state[FIGURES_DESCRIPTIONS_KEY] = ""
     if FIGURES_KEY in current_state:
-        current_figure_state = current_state[FIGURES_KEY]
-        for figure_number, figure_data in current_figure_state.items():
-            figure_descriptions += f"Figure {figure_number}: {figure_data['title']}\n{figure_data['description']}\n\n"
-
-    callback_context.state[FIGURES_DESCRIPTIONS_KEY] = figure_descriptions.strip()
-
+        figure_descriptions = ""
+        for num, fig in current_state[FIGURES_KEY].items():
+            label = fig.get("display_name", f"Figure {num}")
+            figure_descriptions += (
+                f"{label}: {fig['title']}\n{fig['description']}\n\n"
+            )
+        callback_context.state[FIGURES_DESCRIPTIONS_KEY] = figure_descriptions.strip()
 
 class ManuscriptStructure(BaseModel):
     title: str = Field(default="")