Osb2

.gitignore

@@ -24,4 +24,5 @@ utilities/x86_64
 .idea
 *.iml
 x86_64
-.jupyter-config
+.jupyter-config
+venv

netpyne_ui/__init__.py

@@ -1,6 +1,7 @@
 import logging
+
 from jupyter_geppetto.webapi import RouteManager
 
 from netpyne_ui import api
 
-RouteManager.add_controller(api.NetPyNEController)
+RouteManager.add_controller(api.NetPyNEController)

netpyne_ui/api.py

@@ -8,7 +8,7 @@
 from tempfile import TemporaryDirectory
 from jupyter_geppetto.webapi import get, post
 from notebook.base.handlers import IPythonHandler
-from netpyne_ui.constants import NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME, ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
+from netpyne_ui.constants import ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
 
 def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS):
     return '.' in filename and \
@@ -18,15 +18,16 @@ def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS):
 def send_files(handler, file_path, filename):
     with open(file_path, "rb") as f:
         handler.set_header('Content-Type', 'application/force-download')
-        handler.set_header('Content-Disposition', f"attachment; filename={filename}")
+        handler.set_header('Content-Disposition',
+                           f"attachment; filename={filename}")
 
         try:
             while True:
                 _buffer = f.read(4096)
                 if _buffer:
                     handler.write(_buffer)
                 else:
-                    return 
+                    return
         except:
             handler.set_status(500, f"Error sending files")
 
@@ -35,36 +36,40 @@ def get_file_paths(handler):
     file_paths = False
     if 'uri' in handler.request.arguments:
         file_paths = []
-        tmp_file_paths = [path.decode('utf-8') for path in handler.request.arguments['uri']]
+        tmp_file_paths = [path.decode('utf-8')
+                          for path in handler.request.arguments['uri']]
         for path in tmp_file_paths:
             if os.path.exists(path):
                 file_paths.append(path)
-    
+
     return file_paths
 
+
 class NetPyNEController:  # pytest: no cover
 
     @post('/uploads')
     def uploads(handler: IPythonHandler):
         files = handler.request.files
         files_saved = 0
-        
+
         if len(files) == 0 or 'file' not in files:
-            handler.set_status(400, f"Can't find 'file' or filename is empty. Files received {len(files)}")
+            handler.set_status(
+                400, f"Can't find 'file' or filename is empty. Files received {len(files)}")
         else:
 
             for f in files['file']:
                 if not allowed_file(f.filename):
-                    logging.warn(f"Can't store file {f.filename}. Extension not allowed")
+                    logging.warn(
+                        f"Can't store file {f.filename}. Extension not allowed")
                     continue
 
-                ## Save to file
+                # Save to file
                 filename = f.filename
                 file_path = os.path.join(UPLOAD_FOLDER_PATH, filename)
-                
+
                 with open(file_path, 'wb') as zf:
                     zf.write(f['body'])
-                
+
                 files_saved += 1
 
                 if filename.endswith('.zip'):
@@ -78,34 +83,70 @@ def uploads(handler: IPythonHandler):
                 elif filename.endswith('.gz'):
                     with gzip.open(file_path, "rb") as gz, open(file_path.replace('.gz', ''), 'wb') as ff:
                         shutil.copyfileobj(gz, ff)
-
-            handler.set_status(200, f"Number of files saved: {files_saved}. Number of files sent: {len(files['file'])}")
+
+            handler.set_status(
+                200, f"Number of files saved: {files_saved}. Number of files sent: {len(files['file'])}")
 
         handler.finish()
-    
+
     @get('/downloads')
     def downloads(handler: IPythonHandler):
 
         file_paths = get_file_paths(handler)
-        
+
         if file_paths:
-            
+
             if len(file_paths) == 0:
                 handler.set_status(400, f"Files not found.")
                 handler.finish()
                 return
 
             if len(file_paths) == 1:
-                send_files(handler, file_paths[0], file_paths[0].split('/')[-1])
-
-            else :
+                send_files(handler, file_paths[0],
+                           file_paths[0].split('/')[-1])
+
+            else:
                 with TemporaryDirectory() as dir_path:
                     tar_gz_file_name = f'{str(uuid.uuid4())}.tar.gz'
                     tar_gz_file_path = os.path.join(dir_path, tar_gz_file_name)
                     with tarfile.open(tar_gz_file_path, mode='w:gz') as tar:
                         for file_path in file_paths:
-                            tar.add(file_path, os.path.join('download', file_path.split('/')[-1]))
+                            tar.add(file_path, os.path.join(
+                                'download', file_path.split('/')[-1]))
 
                     send_files(handler, tar_gz_file_path, tar_gz_file_name)
-        
+
         handler.finish()
+
+
+def create_notebook(filename):
+    import nbformat as nbf
+    from nbformat.v4.nbbase import new_notebook
+    from nbformat import sign
+    import codecs
+
+    directory = os.path.dirname(filename)
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+    nb0 = new_notebook(cells=[nbf.v4.new_markdown_cell("""# Welcome to the NetPyNE-ui!
+
+    """),
+                              nbf.v4.new_code_cell(
+                                  'netpyne_geppetto.netParams'),
+                              nbf.v4.new_code_cell(
+                                  'netpyne_geppetto.simConfig')
+                              ], metadata={"kernelspec": {
+                                  "display_name": "Python 3",
+                                  "language": "python",
+                                  "name": "python3"
+                              }})
+
+    f = codecs.open(filename, encoding='utf-8', mode='w')
+
+    nbf.write(nb0, filename)
+    f.close()
+
+
+# TODO move to jupyter geppetto, using notebook dir path
+if os.path.exists('workspace') and not os.path.exists('workspace/notebook.ipynb'):
+    create_notebook('workspace/notebook.ipynb')

netpyne_ui/constants.py

@@ -3,7 +3,7 @@
 UPLOAD_FOLDER_NAME = 'uploads'
 NETPYNE_WORKDIR = 'workspace'
 
-ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc"]
+ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc", "json"]
 HERE = os.path.dirname(os.path.abspath(__file__))
 ROOT = os.path.dirname(HERE)
 UPLOAD_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME)

netpyne_ui/netpyne_geppetto.py

@@ -9,14 +9,14 @@
 import subprocess
 import logging
 import re
+import base64
 
 from netpyne import specs, sim, analysis
 from netpyne.specs.utils import validateFunction
 from netpyne.conversion.neuronPyHoc import mechVarList
 from netpyne.metadata import metadata
 from netpyne_ui.netpyne_model_interpreter import NetPyNEModelInterpreter
 from pygeppetto.model.model_serializer import GeppettoModelSerializer
-import matplotlib.pyplot as plt
 from pygeppetto import ui
 import numpy as np
 import neuron
@@ -231,6 +231,12 @@ def importModel(self, modelParameters):
                 # Import Model attributes
                 self.netParams = getattr(net_params_module_name, str(modelParameters["netParamsVariable"]))
 
+                if isinstance(self.netParams, dict):
+                  self.netParams = specs.NetParams(self.netParams)
+
+                if isinstance(self.simConfig, dict):
+                  self.simConfig = specs.SimConfig(self.simConfig)
+
                 for key, value in self.netParams.cellParams.items():
                     if hasattr(value, 'todict'):
                         self.netParams.cellParams[key] = value.todict()
@@ -329,12 +335,9 @@ def deleteModel(self, modelParams):
             return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())
 
         try:
-            # This function fails is some keys don't exists
-            # sim.clearAll()
-            # TODO: as part of #264 we should remove the method and use clearAll intstead
-            self.clearSim()
+            sim.clearAll()
         except:
-            pass
+            logging.exception("Failed to clear simulation")
 
         return utils.getJSONReply()
 
@@ -432,7 +435,7 @@ def getPlot(self, plotName, LFPflavour, theme='gui'):
                     # This arg brings dark theme. But some plots are broken by it
                     args['theme'] = theme
 
-                    if plotName in ("iplotConn", "iplot2Dnet") and sim.net.allCells:
+                    if plotName in ("iplotConn", "iplot2Dnet") and hasattr(sim, 'net') and sim.net.allCells:
                         # To prevent unresponsive kernel, we don't show conns if they become too many
                         num_conn = sum([len(cell.conns) for cell in sim.net.allCells if cell.conns])
                         if num_conn > NUM_CONN_LIMIT:
@@ -597,42 +600,51 @@ def header(title, spacer='-'):
             params = ['popParams', 'cellParams', 'synMechParams']
             params += ['connParams', 'stimSourceParams', 'stimTargetParams']
 
-            fname = args['fileName'] if args['fileName'][-3:] == '.py' else args['fileName'] + '.py'
+            fname = args['fileName']
+            if not fname:
+                # default option
+                fname = 'output.py'
+
+            if not fname[-3:] == '.py':
+                fname = f"{fname}.py"
 
+            # TODO: use methods offered by netpyne to create this script!
             with open(fname, 'w') as script:
-                script.write('from netpyne import specs, sim\n')
-                script.write(header('documentation'))
-                script.write("''' Script generated with NetPyNE-UI. Please visit:\n")
-                script.write("    - https://www.netpyne.org\n    - https://github.com/MetaCell/NetPyNE-UI\n'''\n")
-                script.write(header('script', spacer='='))
-                script.write('netParams = specs.NetParams()\n')
-                script.write('simConfig = specs.SimConfig()\n')
-                script.write(header('single value attributes'))
+                script.write("from netpyne import specs, sim\n")
+                script.write(header("documentation"))
+                script.write("Script generated with NetPyNE-UI. Please visit:\n")
+                script.write("    - https://www.netpyne.org\n    - https://github.com/MetaCell/NetPyNE-UI\n\n")
+                script.write(header("script", spacer="="))
+                script.write("netParams = specs.NetParams()\n")
+                script.write("simConfig = specs.SimConfig()\n")
+                script.write(header("single value attributes"))
                 for attr, value in list(self.netParams.__dict__.items()):
                     if attr not in params:
                         if value != getattr(specs.NetParams(), attr):
-                            script.write('netParams.' + attr + ' = ')
-                            script.write(convert2bool(json.dumps(value, indent=4)) + '\n')
+                            script.write("netParams." + attr + " = ")
+                            script.write(convert2bool(json.dumps(value, indent=4)) + "\n")
 
-                script.write(header('network attributes'))
+                script.write(header("network attributes"))
                 for param in params:
                     for key, value in list(getattr(self.netParams, param).items()):
-                        script.write("netParams." + param + "['" + key + "'] = ")
-                        script.write(convert2bool(json.dumps(value, indent=4)) + '\n')
+                        script.write("netParams." + param + "[" + key + "] = ")
+                        script.write(convert2bool(json.dumps(value, indent=4)) + "\n")
 
-                script.write(header('network configuration'))
+                script.write(header("network configuration"))
                 for attr, value in list(self.simConfig.__dict__.items()):
                     if value != getattr(specs.SimConfig(), attr):
-                        script.write('simConfig.' + attr + ' = ')
-                        script.write(convert2bool(json.dumps(value, indent=4)) + '\n')
+                        script.write("simConfig." + attr + " = ")
+                        script.write(convert2bool(json.dumps(value, indent=4)) + "\n")
 
-                script.write(header('create simulate analyze  network'))
-                script.write('# sim.createSimulateAnalyze(netParams=netParams, simConfig=simConfig)\n')
+                script.write(header("create simulate analyze  network"))
+                script.write("# sim.createSimulateAnalyze(netParams=netParams, simConfig=simConfig)\n")
 
-                script.write(header('end script', spacer='='))
+                script.write(header("end script", spacer="="))
 
             with open(fname) as f:
-                return f.read()
+                file_b64 = base64.b64encode(bytes(f.read(), 'utf-8')).decode()
+                export_info = {"fileContent": file_b64, "fileName": fname}
+                return export_info
 
         except:
             return utils.getJSONError("Error while importing the NetPyNE model", sys.exc_info())
@@ -740,50 +752,6 @@ def propagate_syn_mech_rename(self, new, old):
                                 else:
                                     self.netParams.stimTargetParams[label]['synMech'] = new
 
-    def clearSim(self):
-        # clean up
-        sim.pc.barrier()
-        sim.pc.gid_clear()  # clear previous gid settings
-
-        # clean cells and simData in all nodes
-        sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.cells])
-        if 'stims' in list(sim.simData.keys()):
-            sim.clearObj([stim for stim in sim.simData['stims']])
-
-        for key in list(sim.simData.keys()): del sim.simData[key]
-
-        if hasattr(sim, 'net'):
-            for c in sim.net.cells: del c
-            for p in sim.net.pops: del p
-            if hasattr(sim.net, 'params'):
-                del sim.net.params
-
-        # clean cells and simData gathered in master node
-        if sim.rank == 0:
-            if hasattr(sim.net, 'allCells'):
-                sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.allCells])
-            if hasattr(sim, 'allSimData'):
-                if 'stims' in list(sim.allSimData.keys()):
-                    sim.clearObj([stim for stim in sim.allSimData['stims']])
-                for key in list(sim.allSimData.keys()): del sim.allSimData[key]
-                del sim.allSimData
-
-            import matplotlib
-            matplotlib.pyplot.clf()
-            matplotlib.pyplot.close('all')
-
-        if hasattr(sim, 'net'):
-            if hasattr(sim.net, 'allCells'):
-                for c in sim.net.allCells: del c
-                del sim.net.allCells
-            if hasattr(sim.net, 'allPops'):
-                for p in sim.net.allPops: del p
-
-            del sim.net
-
-        import gc;
-        gc.collect()
-
     def create_celltype_from_template(self, label="CellType", conds={}, cell_template_name="Blank"):
         try:
             with redirect_stdout(sys.__stdout__):