Add vbi components for inversion

docker/Dockerfile-hpc

@@ -4,11 +4,9 @@ ARG ENV_BIN=/opt/conda/envs/tvb-run/bin
 ARG PIP=$ENV_BIN/pip
 
 USER root
-RUN cd tvb-root; \
-    cd tvb_bin; \
-    $PIP install -e .
-
-RUN $PIP install tvb-library==2.6
+WORKDIR /tvb-root/tvb_bin
+RUN "$PIP" install -e . && \
+    "$PIP" install tvb-library==2.6
 # RUN $PIP install tvb-ext-xircuits
 
 WORKDIR /home
@@ -17,9 +15,9 @@ ARG LAST_SHA=LATEST
 
 ARG JUPYTER=$ENV_BIN/jupyter
 
-RUN cd tvb-ext-xircuits; \
-    git pull; \
-    $PIP install -e .
+WORKDIR /home/tvb-ext-xircuits
+RUN git pull; \
+    "$PIP" install -e .
 
 #    $JUPYTER labextension develop . --overwrite; \
 #    $JUPYTER server extension enable xircuits

package.json

@@ -1,6 +1,6 @@
 {
   "name": "tvb-ext-xircuits",
-  "version": "2.1.3",
+  "version": "3.0.0",
   "description": "Jupyterlab extension for building TVB workflows in a visual and interactive manner",
   "keywords": [
     "jupyter",

pyproject.toml

@@ -50,6 +50,8 @@ dependencies = [
     "importlib_resources",
     "asgiref",
     "dill",
+    "joblib",
+    "json5"
 ]
 dynamic = ["version", "description", "authors", "urls", "keywords"]
 
@@ -66,6 +68,9 @@ full = [
     "tvb-gdist",
     "tvb-framework",
     "tvb-widgets>=1.0",
+    "vbi[inference]",
+    "torch",
+    "sbi"
 ]
 
 [tool.hatch.version]

schema/settings.json

@@ -1,6 +1,6 @@
 {
-  "title": "Base Directory Setting",
-  "description": "Setting to define the base directory.",
+  "title": "tvb-ext-xircuits",
+  "description": "tvb-ext-xircuits extension settings.",
   "type": "object",
   "properties": {
     "baseDirectoryWeb": {

src/commands/NodeActionCommands.tsx

@@ -89,13 +89,15 @@ export function addNodeActionCommands(
                 })
                 return;
             }
-
+            let xircuits_filename = tracker.currentWidget.context.path;
+            xircuits_filename = xircuits_filename.split('/').pop().replace('.xircuits', '');
             const dataToSend = {
                 'component': node.name,
                 'component_id': node.options.id,
                 'component_inputs': gatherNodeInPortValues(node),
                 'path':  node.extras.path,
-                'xircuits_id': node.parent.parent.options.id
+                'xircuits_id': node.parent.parent.options.id,
+                'xircuits_filename': xircuits_filename
             };
 
             const response = await requestAPI<any>('components/', {

src/components/XircuitsBodyWidget.tsx

@@ -693,17 +693,15 @@ export const BodyWidget: FC<BodyWidgetProps> = ({
 		// Run Mode
 		context.ready.then(async () => {
 			const workflow_path = context.path;
-			let model_path = workflow_path.split(".xircuits")[0] + ".py";
+			const model_path = workflow_path.split(".xircuits")[0] + ".py";
 			let code = startRunOutputStr();
 
 			let result;
-
-			// Convert the model_path to be bash aware
-			model_path = `"${model_path}"`;
+
 			if (runType == 'run') {
 				result = await handleLocalRunDialog();
 				if (result.status === 'ok') {
-				code += `%run ${model_path} ${result.args}`;
+				code += `%run "${model_path}" ${result.args}`;
 				commands.execute(commandIDs.executeToOutputPanel, { code });
 				}
 				else if (result.status === 'cancelled') {

src/components/runner/RemoteRun.tsx

@@ -11,23 +11,28 @@ export function buildRemoteRunCommand(path: string, config: { formattedCommand:
           '$XIRCUITS_PATH': path
       };
 
-      let command_str = command + " " + path + " " + config['run_config_name']
-            + " " + config['project']
-            + " " + config['stage_out']
-            + " " + config['filesystem']
-            + " " + config['envName']
-            + " " + config['python']
-            + " " + config['modules']
-            + " " + config['libraries'];
+      let args = [
+          ...command.trim().split(/\s+/),
+          path,
+          config['run_config_name'],
+          config['project'],
+          config['stage_out'],
+          config['filesystem'],
+          config['envName'],
+          config['python'],
+          config['modules'],
+          config['libraries']];
       Object.keys(envVariables).forEach(key => {
-          command_str = command_str.replace(new RegExp(`\\${key}`, 'g'), envVariables[key]);
+          args = args.map(arg =>
+            arg.replace(new RegExp(`\\${key}`, 'g'), envVariables[key])
+          );
       });
 
       let code_str = "\nfrom subprocess import Popen, PIPE\n\n";
-      code_str += `command_str= "${command_str}"\n`;
-      code_str += "p=Popen(command_str, stdout=PIPE, stderr=PIPE, universal_newlines=True, shell=True)\n";
+      code_str += `args= ${JSON.stringify(args)}\n`;
+      code_str += "p=Popen(args, stdout=PIPE, stderr=PIPE, universal_newlines=True, shell=False)\n";
       code_str += "print('Remote Execution Run Mode.\\n')\n";
-      code_str += `print(f'[COMMAND]\\n{command_str}\\n')\n`;
+      code_str += `print(f'[COMMAND]\\n{args}\\n')\n`;
 
       if (config.url) {
           code_str += `print('[URL]\\nPlease go to ${config.url} for more details\\n')\n`;

tvbextxircuits/compiler/generator.py

@@ -57,7 +57,7 @@ def generate(self, filelike):
             self._generate_component_imports(),
             self._generate_flows(flow_name),
             self._generate_main(flow_name),
-            self._generate_trailer()
+            self._generate_trailer(flow_name)
         ))
 
         with open(filelike.name, 'w', encoding='utf-8') as f:
@@ -356,20 +356,20 @@ def _build_node_set(self):
                     node_queue.append(port.source)
         return nodes
 
-    def _generate_trailer(self):
+    def _generate_trailer(self, flow_name):
         code = """
 if __name__ == '__main__':
     args, _ = parser.parse_known_args()
     main(args)
     print("\\nFinished Executing")
         """
         body = ast.parse(code).body[0]
-        arg_parsing = self._generate_argument_parsing()
+        arg_parsing = self._generate_argument_parsing(flow_name=flow_name)
         arg_parsing.extend(body.body)
         body.body = arg_parsing
         return [body]
 
-    def _generate_argument_parsing(self):
+    def _generate_argument_parsing(self, flow_name):
         # Unfortunately, we don't have the information anywhere else and updating the file format isn't an option at the moment
         pattern = re.compile(r'^Argument \(.+?\): (.+)$')
 
@@ -381,9 +381,10 @@ def _generate_argument_parsing(self):
             "any": "any"
         }
 
-        code = """
+        code = f"""
 parser = ArgumentParser()
 parser.add_argument('--is_hpc_launch', default=False, type=bool)  
+parser.add_argument('--xircuits_filename', default='{flow_name}', type=str)  
         """
         body = ast.parse(code).body
 

tvbextxircuits/handlers/component_parser.py

@@ -10,7 +10,7 @@
 from .config import get_config
 
 import xai_components
-from xai_components.base_tvb import ComponentWithWidget
+from xai_components.base_tvb import ComponentWithWidget, ComponentWithViewer
 from tvbextxircuits.logger.builder import get_logger
 
 LOGGER = get_logger(__name__)
@@ -102,7 +102,8 @@ def read_orig_code(node: ast.AST, lines):
 
 
 def component_has_widget_assigned(node):
-    if any(base_class.id == ComponentWithWidget.__name__ for base_class in node.bases):
+    if any(base_class.id in {ComponentWithWidget.__name__, ComponentWithViewer.__name__}
+           for base_class in node.bases):
         return True
 
     return False

tvbextxircuits/handlers/components.py

@@ -52,19 +52,20 @@ def post(self):
             component_path = input_data["path"]
             xircuits_id = input_data["xircuits_id"]
             component_inputs = input_data['component_inputs']
+            xircuits_filename = input_data['xircuits_filename']
 
             notebook_path = self._generate_widget_notebook(component, component_id, component_path, xircuits_id,
-                                                           component_inputs)
+                                                           component_inputs, xircuits_filename)
             data = {"widget": notebook_path}
             self.finish(json.dumps(data))
 
         except KeyError:
             data = {"error_msg": "Could not determine the component from POST params!"}
             self.finish(json.dumps(data))
 
-    def _generate_widget_notebook(self, component, component_id, component_path, xircuits_id, component_inputs):
+    def _generate_widget_notebook(self, component, component_id, component_path, xircuits_id, component_inputs, xircuits_filename):
         factory = NotebookFactory()
         notebook = factory.get_notebook_for_component(component, component_id, component_path, component_inputs,
-                                                      xircuits_id)
+                                                      xircuits_id, xircuits_filename)
         path = factory.store(notebook, component, xircuits_id)
         return path

tvbextxircuits/hpc_config/pyunicore_config.py

@@ -167,7 +167,7 @@ def _dev_mode(self, home_storage, client):
         LOGGER.info(f"You are running in dev mode, starting to install {local_package_name} on HPC {self.site}...")
         home_storage.rm(local_package_name)
         home_storage.upload(
-            input_file=f'dist/{local_package_name}',
+            file_name=f'dist/{local_package_name}',
             destination=f'{self.env_dir}/{local_package_name}')
         self.pip_libraries = self.pip_libraries.replace('tvb-ext-xircuits', local_package_name)
         job_description = {
@@ -221,9 +221,10 @@ def submit_job(self, executable, inputs, do_stage_out):
             LOGGER.info(f"Successfully finished the environment setup.")
 
         LOGGER.info("Launching workflow...")
+        xircuits_filename = executable.replace('.py', '')
         job_description = {
             self.EXECUTABLE_KEY: f"{self._module_load_command} && {self._activate_command} && "
-                                 f"python {executable} --is_hpc_launch=True",
+                                 f"python {executable} --is_hpc_launch=True --xircuits_filename='{xircuits_filename}'",
             self.PROJECT_KEY: self.project}
         job_workflow = client.new_job(job_description, inputs=inputs)
         LOGGER.info(f"Job is running at {self.site}."