0.3.0

.dockerignore

@@ -35,4 +35,11 @@ generate_files/*
 generate_files_0/*
 generated_file/*
 generated_files/*
-user_config_openai.key
+user_config_openai.key
+test_uploader.*
+test_display_gxy.py
+outputs_dir/*
+outputs_smolagents_nicegui/*
+!examples.json
+__pycache__
+.*key

.gitignore

@@ -22,4 +22,9 @@ groq_api_key.txt
 *.pdf
 generate_md_report.py
 *.md
-outputs/*
+outputs/*
+outputs_dir/
+user_config_*
+*.pkl
+test*.py
+test*.xml

Dockerfile

@@ -30,11 +30,9 @@ COPY . .
 RUN pip install --no-cache-dir --upgrade pip
 
 # Install Python dependencies from requirements.txt
-RUN pip install --no-cache-dir -r requirements.txt
+RUN pip install --no-cache-dir -r requirements_nicegui_dspy.txt
 
-# Expose Streamlit’s port
-EXPOSE 8501
-ENV STREAMLIT_SERVER_PORT=8501
+EXPOSE 9090
 
 # Adjust permissions if needed
 RUN chmod -R 777 /ChatAnalysis

pages/1_Bookmarks.py

@@ -1,7 +1,8 @@
 # pages/1_Bookmarks.py
 import streamlit as st
 import os
-from PIL import Image # If displaying images from paths
+from PIL import Image
+import json
 
 
 st.set_page_config(
@@ -69,13 +70,18 @@
 
 st.title("🔖 Bookmark Manager")
 
-# Ensure necessary session state variables are accessible
-# These should have been set by Chat_Bot.py when it first ran.
-output_dir = st.session_state.get("generate_file_path", "outputs_smolagents") # Default if not found
+def load_chat_history():
+    if os.path.exists("bookmarks.json"):
+        with open("bookmarks.json", "r") as f:
+            file_contents = f.read().strip()
+            if file_contents:
+                history = json.loads(file_contents)
+                st.session_state["bookmarks"] = history.get("bookmarks", [])
+            else:
+                st.session_state["bookmarks"] = []
 
-if "bookmarks" not in st.session_state:
-    st.session_state["bookmarks"] = [] # Initialize if somehow not present
 
+load_chat_history()
 bookmarks = st.session_state.get("bookmarks", [])
 
 if not bookmarks:
@@ -93,36 +99,33 @@
         file_paths = b_data.get("files", [])
 
         with st.expander(f"Bookmark {i + 1}: {question[:60]}"):
-            st.markdown(f"**❓ Question:**\n```\n{question}\n```")
-            st.markdown(f"**💡 Answer:**\n{answer}") # Assuming answer is markdown-compatible
+            st.markdown(f"**❓ Question:**\n{question}\n")
+            st.markdown(f"**💡 Answer:**\n{answer}")
 
-            if plot_paths:
+            if plot_paths and not (len(plot_paths) == 1 and plot_paths[0] == ""):
                 st.markdown("**📊 Saved Plots:**")
                 for plot_path_in_bookmark in plot_paths:
-                    # Construct full path if paths are stored relative or just basenames
-                    # Assuming paths in bookmark_data are already correct relative to execution
-                    # or are absolute. If relative to output_dir, prepend it.
-                    # For simplicity, let's assume plot_path_in_bookmark is usable as is
-                    # or is a full path. If it's just a basename:
-                    # actual_plot_path = os.path.join(output_dir, os.path.basename(plot_path_in_bookmark))
-                    actual_plot_path = plot_path_in_bookmark # Use this if paths are stored fully qualified or correctly relative
-
-                    if os.path.exists(actual_plot_path):
+                    actual_plot_path = plot_path_in_bookmark
+                    if actual_plot_path == "":
+                        continue
+
+                    if actual_plot_path and os.path.exists(actual_plot_path):
                         try:
                             image = Image.open(actual_plot_path)
                             st.image(image, caption=os.path.basename(actual_plot_path))
                         except Exception as e:
                             st.error(f"Could not load plot {os.path.basename(actual_plot_path)}: {e}")
                     else:
-                        st.warning(f"Plot not found: {actual_plot_path}")
+                        pass
 
-            if file_paths:
+            if file_paths and not (len(file_paths) == 1 and file_paths[0] == ""):
                 st.markdown("**📄 Saved Files:**")
                 for file_path_in_bookmark in file_paths:
-                    # actual_file_path = os.path.join(output_dir, os.path.basename(file_path_in_bookmark))
-                    actual_file_path = file_path_in_bookmark # Similar assumption as plots
+                    actual_file_path = file_path_in_bookmark
+                    if actual_file_path == "":
+                        continue
 
-                    if os.path.exists(actual_file_path):
+                    if actual_file_path and os.path.exists(actual_file_path):
                         try:
                             with open(actual_file_path, "rb") as f_download:
                                 st.download_button(
@@ -134,16 +137,4 @@
                         except Exception as e:
                             st.error(f"Could not prepare file {os.path.basename(actual_file_path)} for download: {e}")
                     else:
-                        st.warning(f"File not found: {actual_file_path}")
-
-            # Add delete/rerun functionality if desired (would need to modify st.session_state.bookmarks and save)
-            # e.g., if st.button("Delete Bookmark", key=f"delete_bm_{i}"):
-            #   st.session_state.bookmarks.pop(i)
-            #   # Need a way to trigger save_chat_history() from StreamlitApp if it's responsible,
-            #   # or manage bookmark saving directly via session state + json persistence here.
-            #   # For now, keep it simple.
-            #   st.experimental_rerun()
-
-# If you have common sidebar elements (like API config) that should appear on all pages,
-# you might need to duplicate that logic here or move it to a shared utility function.
-# For now, the Bookmarks page is simple and doesn't re-declare the LLM config sidebar.
+                        pass

tools/chat_analysis.xml

@@ -1,15 +1,15 @@
-<tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.2.2">
+<tool id="interactive_tool_chat_analysis" tool_type="interactive" name="Chat with your data" version="0.3.0">
     <icon src="datachat.png" />
     <description>Use natural language to work with and analyze your data</description>
     <requirements>
         <container type="docker">
-            quay.io/goeckslab/chatanalysis:release
+            quay.io/goeckslab/chatanalysis:0.3.0
         </container>
     </requirements>
     <entry_points>
         <entry_point name="Chat with $input_dataset.element_identifier" requires_domain="True">
             <port>
-                8501
+                9090
             </port>
             <url>
                 /
@@ -21,23 +21,22 @@
         #import re
         echo "Starting Streamlit" &&
         echo "working dir now: `pwd`" &&
-        mkdir -p generated_files &&
+        mkdir -p outputs_dir &&
         #set $sanitized_input_dataset = re.sub('[^\w\-_\.]', '_', $input_dataset.element_identifier.strip())
         ln -sf '$input_dataset' "./${sanitized_input_dataset}";
         echo "sanitized input dataset: $sanitized_input_dataset" &&
         echo "input dataset: $input_dataset" &&
         echo "$input_dataset.ext" &&
         ln -sf $__tool_directory__/.env /ChatAnalysis/.env &&
-        streamlit run /ChatAnalysis/Chat.py
-            "$__user_email__"
-            "$openai_api_key_file"
-            "$groq_api_key_file"
-            "$chat_history"
-            "./generated_files"
-            "$input_dataset"
-            "$input_dataset.ext"
-            --browser.gatherUsageStats false &&
-        echo "Streamlit finished" &&
+        python /ChatAnalysis/chat_dspy.py
+            --user_id "$__user_email__"
+            --openai_key_file "$openai_api_key_file"
+            --groq_key_file "$groq_api_key_file"
+            --chat_history "$chat_history"
+            --outputs_dir "./outputs_dir"
+            --input_file "$input_dataset"
+            --input_type "$input_dataset.ext" &&
+        echo "finished" &&
         echo "working dir now: '.' "
 
         ]]>