Update app.py

app.py

@@ -75,6 +75,7 @@ def retry(max_attempts=3, delay=1):
 # LAB JOURNAL
 # ─────────────────────────────────────────────
 JOURNAL_FILE = "./lab_journal.csv"
+# Уніфікована система кодування (як у Learning Playground)
 JOURNAL_CATEGORIES = [
     # Real Data Tools (S2-A)
     "S2-A·R1a",  # Gray Zones Explorer
@@ -82,7 +83,7 @@ JOURNAL_CATEGORIES = [
     "S2-A·R1c",  # Real Variant Lookup
     "S2-A·R1d",  # Literature Gap Finder
     "S2-A·R1e",  # Druggable Orphans
-    "S2-A·R1f",  # Research Assistant
+    "S2-A·R1f",  # Research Assistant (Chatbot)
     # Learning Sandbox (S2-B)
     "S2-B·R1a",  # miRNA Explorer
     "S2-B·R1b",  # siRNA Targets
@@ -117,12 +118,22 @@ def journal_read(category: str = "All") -> str:
         if df.empty:
             return f"No entries for category: {category}"
         # Format for better readability
-        df_display = df[["timestamp", "category", "action", "result_summary"]].tail(20)
+        df_display = df[["timestamp", "category", "action", "result_summary"]].tail(50)
         return df_display.to_markdown(index=False)
     except Exception as e:
         print(f"Journal read error: {e}")
         return "Error reading journal."
 
+def clear_journal():
+    """Delete the journal file."""
+    try:
+        if os.path.exists(JOURNAL_FILE):
+            os.remove(JOURNAL_FILE)
+        return "Journal cleared."
+    except Exception as e:
+        print(f"Clear journal error: {e}")
+        return "Error clearing journal."
+
 # ─────────────────────────────────────────────
 # CONSTANTS
 # ─────────────────────────────────────────────
@@ -258,6 +269,7 @@ def ot_query(gql: str, variables: dict = None) -> dict:
     except Exception as e:
         print(f"OT query error: {e}")
         return {"error": str(e)}
+
 # ─────────────────────────────────────────────
 # TAB A1 — GRAY ZONES EXPLORER
 # ─────────────────────────────────────────────
@@ -280,7 +292,6 @@ def a1_run(cancer_type: str):
 
     fig, ax = plt.subplots(figsize=(6, 8), facecolor="white")
     valid = df[cancer_type].fillna(0).values.reshape(-1, 1)
-    # Виправлено deprecated get_cmap
     cmap = plt.colormaps.get_cmap("YlOrRd")
     cmap.set_bad("white")
     masked = np.ma.masked_where(df[cancer_type].isna().values.reshape(-1, 1), valid)
@@ -313,7 +324,7 @@ def a1_run(cancer_type: str):
         )
 
     gaps_md = "\n\n---\n\n".join(gap_cards) if gap_cards else "No data available."
-    journal_log("A1-GrayZones", f"cancer={cancer_type}", f"gaps={[p for p,_ in sorted_procs[:5]]}")
+    journal_log("S2-A·R1a", f"cancer={cancer_type}", f"gaps={[p for p,_ in sorted_procs[:5]]}")
     source_note = f"*Source: PubMed E-utilities | Date: {today}*"
     return img, gaps_md + "\n\n" + source_note
 
@@ -447,9 +458,9 @@ def a2_run(cancer_type: str):
         f"and replace `_load_depmap_sample()` in `app.py`."
     )
     if not result_df.empty:
-        journal_log("A2-TargetFinder", f"cancer={cancer_type}", f"top_gap={result_df.iloc[0]['Gene']}")
+        journal_log("S2-A·R1b", f"cancer={cancer_type}", f"top_gap={result_df.iloc[0]['Gene']}")
     else:
-        journal_log("A2-TargetFinder", f"cancer={cancer_type}", "no targets found")
+        journal_log("S2-A·R1b", f"cancer={cancer_type}", "no targets found")
     return result_df, note
 
 
@@ -575,7 +586,7 @@ def a3_run(hgvs: str):
         )
 
     result_parts.append(f"\n*Source: ClinVar E-utilities + gnomAD GraphQL | Date: {today}*")
-    journal_log("A3-VariantLookup", f"hgvs={hgvs}", result_parts[0][:100] if result_parts else "no results")
+    journal_log("S2-A·R1c", f"hgvs={hgvs}", result_parts[0][:100] if result_parts else "no results")
     return "\n\n".join(result_parts)
 
 
@@ -641,7 +652,7 @@ def a4_run(cancer_type: str, keyword: str):
 
     summary = "\n\n".join(gap_text)
     summary += f"\n\n*Source: PubMed E-utilities | Date: {today}*"
-    journal_log("A4-LitGap", f"cancer={cancer_type}, kw={keyword}", summary[:100])
+    journal_log("S2-A·R1d", f"cancer={cancer_type}, kw={keyword}", summary[:100])
     return img, summary
 
 
@@ -738,8 +749,10 @@ def a5_run(cancer_type: str):
         f"*Source: OpenTargets GraphQL + ClinicalTrials.gov v2 | Date: {today}*\n\n"
         f"*Orphan = no approved drug (OpenTargets knownDrugs.count = 0)*"
     )
-    journal_log("A5-DruggableOrphans", f"cancer={cancer_type}", f"orphans={len(df)}")
+    journal_log("S2-A·R1e", f"cancer={cancer_type}", f"orphans={len(df)}")
     return df, note
+
+
 # ─────────────────────────────────────────────
 # GROUP B — LEARNING SANDBOX
 # ─────────────────────────────────────────────
@@ -819,7 +832,7 @@ def b1_run(gene: str):
         "Expression log2FC": changes,
     })
     context = f"\n\n**Cancer Context:** {db['cancer_context']}"
-    journal_log("B1-miRNA", f"gene={gene}", f"top_miRNA={mirnas[0]}")
+    journal_log("S2-B·R1a", f"gene={gene}", f"top_miRNA={mirnas[0]}")
     return img, df.to_markdown(index=False) + context
 
 
@@ -881,7 +894,7 @@ def b2_run(cancer: str):
         "Off-target Risk": off_risk,
         "Delivery Challenge": delivery,
     })
-    journal_log("B2-siRNA", f"cancer={cancer}", f"top={targets[0]}")
+    journal_log("S2-B·R1b", f"cancer={cancer}", f"top={targets[0]}")
     return img, df.to_markdown(index=False)
 
 
@@ -937,7 +950,7 @@ def b3_run(peg_mol_pct: float, ionizable_pct: float, helper_pct: float,
         + ("High ApoE → enhanced brain/liver targeting via LDLR pathway." if apoe_pct > 25
            else "Low ApoE → reduced receptor-mediated uptake.")
     )
-    journal_log("B3-LNPCorona", f"PEG={peg_mol_pct}%,size={particle_size_nm}nm", f"ApoE={apoe_pct:.1f}%")
+    journal_log("S2-B·R1c", f"PEG={peg_mol_pct}%,size={particle_size_nm}nm", f"ApoE={apoe_pct:.1f}%")
     return img, interpretation
 
 
@@ -981,7 +994,7 @@ def b4_run(time_points: int, kon_albumin: float, kon_apoe: float,
         "The Vroman effect describes sequential protein displacement: "
         "abundant proteins (albumin) adsorb first, then are displaced by higher-affinity proteins (ApoE, fibrinogen)."
     )
-    journal_log("B4-FlowCorona", f"kon_alb={kon_albumin},kon_apoe={kon_apoe}", note[:80])
+    journal_log("S2-B·R1d", f"kon_alb={kon_albumin},kon_apoe={kon_apoe}", note[:80])
     return img, note
 
 
@@ -1035,10 +1048,8 @@ def b5_run(classification: str):
         f"> ⚠️ SIMULATED — This is a rule-based educational model only. "
         f"Real variant classification requires expert review and full ACMG/AMP criteria evaluation."
     )
-    journal_log("B5-VariantConcepts", f"class={classification}", output[:100])
+    journal_log("S2-B·R1e", f"class={classification}", output[:100])
     return output
-
-
 # ─────────────────────────────────────────────
 # GRADIO UI ASSEMBLY
 # ─────────────────────────────────────────────
@@ -1055,17 +1066,16 @@ body { font-family: 'Inter', sans-serif; }
     background: #f8f9fa; border-left: 4px solid #d73027;
     padding: 10px 14px; margin: 6px 0; border-radius: 4px;
 }
-footer { display: none !important; }
-
 /* Зміна курсора на pointer для всіх інтерактивних елементів */
 .gr-dropdown, .gr-button, .gr-slider, .gr-radio, .gr-checkbox,
-.tab-nav button, .gr-accordion, .gr-textbox, .gr-number, .gr-dataset {
+.tab-nav button, .gr-accordion, .gr-dataset {
     cursor: pointer !important;
 }
 /* Для текстових полів залишаємо звичайний текстовий курсор */
 .gr-textbox input, .gr-textarea textarea {
     cursor: text !important;
 }
+footer { display: none !important; }
 """
 
 
@@ -1080,7 +1090,7 @@ def build_app():
         with gr.Row():
             # ── MAIN CONTENT ──
             with gr.Column(scale=4):
-                with gr.Tabs():
+                with gr.Tabs() as main_tabs:
 
                     # ════════════════════════════════
                     # GROUP A — REAL DATA TOOLS
@@ -1361,9 +1371,33 @@ def build_app():
                                     )
                                 b5_btn.click(b5_run, inputs=[b5_class], outputs=[b5_result])
 
-            # ── SIDEBAR (JOURNAL) ──
+                    # ════════════════════════════════
+                    # JOURNAL — окрема вкладка
+                    # ════════════════════════════════
+                    with gr.Tab("📓 Journal"):
+                        gr.Markdown("## Lab Journal — Full History")
+                        with gr.Row():
+                            journal_filter = gr.Dropdown(
+                                choices=["All"] + JOURNAL_CATEGORIES,
+                                value="All",
+                                label="Filter by category"
+                            )
+                            refresh_btn = gr.Button("🔄 Refresh", size="sm", variant="secondary")
+                            clear_btn = gr.Button("🗑️ Clear Journal", size="sm", variant="stop")
+                        journal_display = gr.Markdown(value=journal_read())
+                        
+                        def refresh_journal(category):
+                            return journal_read(category)
+                        
+                        refresh_btn.click(refresh_journal, inputs=[journal_filter], outputs=journal_display)
+                        clear_btn.click(clear_journal, [], journal_display).then(
+                            refresh_journal, inputs=[journal_filter], outputs=journal_display
+                        )
+                        journal_filter.change(refresh_journal, inputs=[journal_filter], outputs=journal_display)
+
+            # ── SIDEBAR (Quick Note) ──
             with gr.Column(scale=1, min_width=260):
-                gr.Markdown("## 📓 Lab Journal")
+                gr.Markdown("## 📝 Quick Note")
                 note_category = gr.Dropdown(
                     choices=JOURNAL_CATEGORIES,
                     value="Manual",
@@ -1379,33 +1413,18 @@ def build_app():
                     clear_note_btn = gr.Button("🗑️ Clear", size="sm")
                 save_status = gr.Markdown("")
 
-                gr.Markdown("---")
-                gr.Markdown("## 🔍 Full Journal")
-                journal_filter = gr.Dropdown(
-                    choices=["All"] + JOURNAL_CATEGORIES,
-                    value="All",
-                    label="Filter by category"
-                )
-                refresh_btn = gr.Button("🔄 Refresh", size="sm")
-                journal_display = gr.Markdown(value=journal_read())
-
                 def save_note(category, note):
                     if note.strip():
                         journal_log(category, "manual note", note, note)
                         return "✅ Note saved.", ""
                     return "⚠️ Note is empty.", ""
 
-                def refresh_journal(category):
-                    return journal_read(category)
-
                 save_btn.click(
                     save_note,
                     inputs=[note_category, note_input],
                     outputs=[save_status, note_input]
                 )
                 clear_note_btn.click(lambda: ("", ""), outputs=[note_input, save_status])
-                refresh_btn.click(refresh_journal, inputs=[journal_filter], outputs=journal_display)
-                journal_filter.change(refresh_journal, inputs=[journal_filter], outputs=journal_display)
 
         # === Інтеграція з Learning Playground ===
         with gr.Row():