Merge pull request #10 from zhanghaomiao/feat/config

refactor: Migrate workflow timeline from Google Charts to ECharts and…

Author: zhanghaomiao

app/api/endpoints/workflows.py

@@ -165,7 +165,7 @@ async def get_workflow_log(
     return await service.get_workflow_log(workflow_id)
 
 
-@router.get("/{workflow_id}/configfiles", response_model=dict[str, str])
+@router.get("/{workflow_id}/configfiles", response_model=list[PathContent])
 async def get_configfiles(
     workflow_id: uuid.UUID,
     db: AsyncSession = Depends(get_async_session),

app/core/config.py

@@ -6,7 +6,7 @@
 
 def get_env_files() -> list[str]:
     """Safely get environment files, avoiding permission errors in containers."""
-    files = [".env"]
+    files = []
     try:
         # Check for user-level config
         home_cfg = Path.home() / ".config/flowo/.env"
@@ -16,6 +16,7 @@ def get_env_files() -> list[str]:
     except (PermissionError, RuntimeError):
         # Fallback if home directory is restricted
         pass
+    files.append(".env")
     return files
 
 

app/plugin/client/log_handler.py

@@ -132,7 +132,12 @@ def emit(self, record: LogRecord) -> None:
             schema_data = parser_func(record)
 
             # 2. Send to API
-            self._send_to_api(event_name, schema_data.model_dump(mode="json"))
+            data = schema_data.model_dump(mode="json")
+
+            if event_name == "workflow_started":
+                self.context["configfiles"] = self._get_configfiles()
+
+            self._send_to_api(event_name, data)
         except Exception as e:
             logger.debug(f"Failed to process event {event_name}: {e}")
 
@@ -189,9 +194,27 @@ def flowo_path_valid(self):
             )
             return
 
+    def _get_configfiles(self) -> list[str]:
+        """Extract configfiles from global snakemake workflow object."""
+        try:
+            import snakemake.workflow
+
+            if (
+                hasattr(snakemake.workflow, "workflow")
+                and snakemake.workflow.workflow
+                and hasattr(snakemake.workflow.workflow, "configfiles")
+            ):
+                return [str(f) for f in snakemake.workflow.workflow.configfiles]
+        except Exception as e:
+            logger.debug(f"Failed to access snakemake workflow configfiles: {e}")
+        return []
+
     def close(self) -> None:
         self.file_handler.close()
 
+        if self._client.is_closed:
+            return
+
         workflow_id = self.context.get("current_workflow_id")
         if workflow_id and settings.FLOWO_USER_TOKEN:
             url = (

app/plugin/server/handlers.py

@@ -42,8 +42,7 @@ def handle(
             dryrun=context.get("dryrun", False),
             status=Status.RUNNING,
             started_at=datetime.now(),
-            # maybe we need to get configfiles later
-            # configfiles=context.get("configfiles"),
+            configfiles=context.get("configfiles"),
         )
         session.add(workflow)
         context["current_workflow_id"] = data.workflow_id

app/services/workflow.py

@@ -186,16 +186,18 @@ async def get_configfiles(self, workflow_id: uuid.UUID):
                 status_code=404, detail="configfiles or workflow not found"
             )
 
-        data = {}
+        data = []
         for configfile in workflow.configfiles:
             try:
-                configfile_path = str(configfile).replace(
-                    workflow.flowo_working_path, "/work_dir/"
-                )
-                with open(configfile_path) as f:
-                    data[configfile] = f.read()
+                content = get_file_content(configfile)
+                content.path = configfile
+                data.append(content)
             except Exception as e:
-                data[configfile] = f"Failed to open file: {str(e)}"
+                data.append(
+                    PathContent(
+                        path=configfile, content=f"Error reading file: {str(e)}"
+                    )
+                )
 
         return data
 

docker-compose.dev.yml

@@ -75,7 +75,7 @@ services:
       - caddy_data_dev:/data
       - caddy_config_dev:/config
     ports:
-      - "${PORT:-3101}:80"
+      - "${PORT:-3100}:80"
     depends_on:
       - flowo-backend
       - flowo-frontend