Merge branch 'feature/meta_migration' into feature/403-remove-console-flood

Author: enicolasgomez

netpyne_ui/experiments.py

@@ -154,7 +154,7 @@ def get_model_specification(name: str, trial: str) -> dict:
     """
     path = get_trial_output_path(name, trial, fallback=True)
     if path is None or not os.path.exists(path):
-        raise ExperimentsError(f"Trial file {path} not found")
+        raise ExperimentsError(f"Condition file {path} not found")
 
     with open(path, "r") as f:
         trial_output = json.load(f)
@@ -273,7 +273,7 @@ def onerror(func, path, exc_info):
 
 
 def _create_base_model_trial() -> model.Trial:
-    return model.Trial(name="Trial 1", id=BASE_TRIAL_ID)
+    return model.Trial(name="Condition 1", id=BASE_TRIAL_ID)
 
 
 def _create_trials(experiment: model.Experiment) -> List[model.Trial]:
@@ -315,7 +315,7 @@ def _create_trials(experiment: model.Experiment) -> List[model.Trial]:
 
         filename = combinations["filenames"][combIdx][1:]
         indices = combinations["indices"][combIdx]
-        name = f"Trial {combIdx + 1}"
+        name = f"Condition {combIdx + 1}"
 
         trials.append(
             model.Trial(name=name, params=params, indices=indices, id=filename)

netpyne_ui/netpyne_geppetto.py

@@ -138,7 +138,7 @@ def viewExperimentResult(self, payload: dict):
 
         file = experiments.get_trial_output_path(name, trial)
         if file is None or not os.path.exists(file):
-            return utils.getJSONError(f"Couldn't find output file of trial. Please take a look at the simulation log.", "")
+            return utils.getJSONError(f"Couldn't find output file of condition. Please take a look at the simulation log.", "")
 
         if self.doIhaveInstOrSimData()['haveInstance']:
             sim.clearAll()
@@ -184,7 +184,7 @@ def instantiateNetPyNEModelInGeppetto(self, args):
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
 
                 return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
-        except Exception:
+        except Exception as e:
             message = "Error while instantiating the NetPyNE model"
             logging.exception(message)
             return utils.getJSONError(message, sys.exc_info())

tests/backend/netypne_model_importer_test.py

@@ -36,6 +36,7 @@ def setUpClass(cls):
             logging.error("Error loading mechanisms", exc_info=True)
 
     def test_dict_import_1(self):
+        assert 0
         print("------------------------------------")
         print("Dictionary transform importModel:")
         print("------------------------------------")
@@ -60,6 +61,40 @@ def test_dict_import_1(self):
         netpyne = NetPyNEGeppetto()
         netpyne.importModel(netpyne_info)
 
+    def test_netpyne_exported_model_1(self):
+      print("------------------------------------")
+      print("Netpyne exported model sim run")
+      print("------------------------------------")
+
+      params = {}
+
+      HERE = os.path.dirname(os.path.realpath(__file__))
+      ROOT = os.path.dirname(HERE)
+
+      params["areModFieldsRequired"] = False
+      params["compileMod"] = False
+      params["exploreOnlyDirs"] = False
+      params["explorerDialogOpen"] = False
+      params["explorerParameter"] = ""
+      params["freezeInstance"] = True
+      params["freezeSimulation"] = True
+      params["jsonModelFolder"] = ROOT + "/workspace/HHCellNetwork.txt_data.json"
+      params["jsonPath"] = ""
+      params["loadNet"] = True
+      params["loadNetParams"] = True
+      params["loadSimCfg"] = True
+      params["loadSimData"] = True
+      params["modFolder"] = ""
+      params["modPath"] = ""
+      params["tab"] = "simulate"
+
+      netpyne = NetPyNEGeppetto()
+
+      netpyne.loadModel(params)
+      netpyne.instantiateNetPyNEModel()
+
+      return False
+
 if __name__ == '__main__':
     try:
         unittest.main()

webapp/Main.js

@@ -19,9 +19,8 @@ Sentry.init({
     new CaptureConsole({
       levels: ['error']
     })
-    , new Integrations.BrowserTracing()
   ],
-  tracesSampleRate: 1.0,
+  tracesSampleRate: 1.0
 });
 
 initGeppetto();

webapp/components/experiments/ExperimentEdit.js

@@ -25,9 +25,11 @@ import Utils from '../../Utils';
 import ParameterMenu from './ParameterMenu';
 import useStyles from './ExperimentEditStyle';
 import * as ExperimentHelper from './ExperimentHelper';
+import DialogBox from '../general/DialogBox';
 
 const RANGE_VALUE = 0;
 const SUPPORTED_TYPES = [REAL_TYPE.INT, REAL_TYPE.FLOAT, REAL_TYPE.STR, REAL_TYPE.BOOL];
+const MAX_TRIALS = 100;
 
 const {
   RANGE,
@@ -189,11 +191,14 @@ const ExperimentEdit = (props) => {
   const [experimentName, setExperimentName] = useState('');
   const [experimentNameError, setExperimentNameError] = useState('');
   const [selectionParams, setSelectionParams] = useState([]);
+  const [trialNumberErrorDialogOpen, setTrialNumberErrorDialogOpen] = useState({ condition: false, number: 1 });
 
   // Existing Experiment.
   const [experiment, setExperiment] = useState(null);
   const experiments = useSelector((state) => state.experiments.experiments);
 
+  let numberOfTrials = 1;
+
   const validateParameter = (param) => {
     let updatedParam = param;
     if (param.type === LIST) {
@@ -339,7 +344,19 @@ const ExperimentEdit = (props) => {
       params,
     };
 
-    if (editState) {
+    numberOfTrials = 1;
+
+    params.forEach((param) => {
+      if (param.type === LIST) {
+        numberOfTrials *= param.values.length;
+      } else if (param.type === RANGE) {
+        numberOfTrials *= Math.ceil((param.max - param.min) / param.step);
+      }
+    });
+
+    if (numberOfTrials > MAX_TRIALS) {
+      setTrialNumberErrorDialogOpen({ condition: true, number: numberOfTrials });
+    } else if (editState) {
       ExperimentsApi.editExperiment(experiment?.name, newExperimentDetails)
         .then(() => {
           setView(EXPERIMENT_VIEWS.list);
@@ -467,34 +484,35 @@ const ExperimentEdit = (props) => {
   };
 
   return (
-    <GridLayout className={classes.root}>
-      <Box className="editExperimentContainer">
-        <Box my={3} className="editExperimentBack">
-          <ArrowBackIcon onClick={() => setView(EXPERIMENT_VIEWS.list)} />
-          <Typography variant="body2">{!editState ? 'New Experiment' : 'Edit Experiment'}</Typography>
-        </Box>
-        <Box mb={2} className="editExperimentHead">
-          <form noValidate autoComplete="off">
-            <TextField
-              id="experiment-name"
-              label="Experiment Name"
-              variant="filled"
-              value={experimentName}
-              onChange={(e) => setExperimentNameInfo(e.target.value)}
-              error={experimentNameError !== ''}
-              helperText={experimentNameError}
-            />
-          </form>
-          <Box mt={3}>
-            <Divider />
+    <>
+      <GridLayout className={classes.root}>
+        <Box className="editExperimentContainer">
+          <Box my={3} className="editExperimentBack">
+            <ArrowBackIcon onClick={() => setView(EXPERIMENT_VIEWS.list)} />
+            <Typography variant="body2">{!editState ? 'New Experiment' : 'Edit Experiment'}</Typography>
           </Box>
-        </Box>
-        <Box className="editExperimentContent">
-          <Box mb={1} className="editExperimentDefault">
-            <Box mb={2} className="editExperimentBreadcrumb">
-              <Typography variant="body2">Parameters</Typography>
+          <Box mb={2} className="editExperimentHead">
+            <form noValidate autoComplete="off">
+              <TextField
+                id="experiment-name"
+                label="Experiment Name"
+                variant="filled"
+                value={experimentName}
+                onChange={(e) => setExperimentNameInfo(e.target.value)}
+                error={experimentNameError !== ''}
+                helperText={experimentNameError}
+              />
+            </form>
+            <Box mt={3}>
+              <Divider />
             </Box>
-            {groupParameters.length > 0 && (
+          </Box>
+          <Box className="editExperimentContent">
+            <Box mb={1} className="editExperimentDefault">
+              <Box mb={2} className="editExperimentBreadcrumb">
+                <Typography variant="body2">Parameters</Typography>
+              </Box>
+              {groupParameters.length > 0 && (
               <Box mb={2} className="editExperimentGroup">
                 <Box mb={2} className="editExperimentBreadcrumb">
                   <Typography variant="body2">Grouped Parameters</Typography>
@@ -512,43 +530,53 @@ const ExperimentEdit = (props) => {
                   </Box>
                 )}
               </Box>
-            )}
-            {selectionParams.length > 0 && (
+              )}
+              {selectionParams.length > 0 && (
               <Box className="editExperimentRow">
                 {parameters.map((parameter, index) => (
                   ParameterRow(parameter, index, handleParamSelection, handleChange,
                     handleRangeInput, handleInputValues, addToGroup, removeFromGroup,
                     removeParameter, selectionParams, classes)
                 ))}
               </Box>
-            )}
+              )}
+            </Box>
+          </Box>
+          <Box>
+            <Link to="true" color="primary" onClick={addParameter}>
+              <AddIcon />
+              Add parameter
+            </Link>
           </Box>
         </Box>
-        <Box>
-          <Link to="true" color="primary" onClick={addParameter}>
-            <AddIcon />
-            Add parameter
-          </Link>
-        </Box>
-      </Box>
-      <Box
-        className="scrollbar scrollchild"
-        mt={1}
-        display="flex"
-        flexWrap="wrap"
-      >
-        <Box className="editExperimentFooter">
-          <Box display="flex">
-            <Button color="secondary" onClick={() => setView(EXPERIMENT_VIEWS.list)}>
-              Cancel
-            </Button>
-            <Button variant="contained" color="primary" onClick={submit}>
-              {editState ? 'Save' : 'Create'}
-            </Button>
+        <Box
+          className="scrollbar scrollchild"
+          mt={1}
+          display="flex"
+          flexWrap="wrap"
+        >
+          <Box className="editExperimentFooter">
+            <Box display="flex">
+              <Button color="secondary" onClick={() => setView(EXPERIMENT_VIEWS.list)}>
+                Cancel
+              </Button>
+              <Button variant="contained" color="primary" onClick={submit}>
+                {editState ? 'Save' : 'Create'}
+              </Button>
+            </Box>
           </Box>
         </Box>
-      </Box>
-    </GridLayout>
+      </GridLayout>
+      <DialogBox
+        open={trialNumberErrorDialogOpen.condition}
+        onDialogResponse={() => setTrialNumberErrorDialogOpen({ condition: false, number: 1 })}
+        textForDialog={{
+          heading: 'Error - Number of conditions is too large',
+          content: `Please change your exploration parameters to
+          reduce the number of experimental conditions to less than 100. Last number of conditions: ${trialNumberErrorDialogOpen.number}`,
+        }}
+      />
+    </>
   );
 };
 

webapp/components/experiments/ExperimentView.js

@@ -269,7 +269,7 @@ function EnhancedTableHead (props) {
       id: 'name',
       numeric: false,
       disablePadding: true,
-      label: 'TRIAL NAME',
+      label: 'EXPERIMENTAL CONDITIONS',
     },
     ...paramHeaders,
   ];
@@ -564,7 +564,7 @@ const ExperimentView = (props) => {
                   experimentFinished={experimentFinished}
                 />
                 <TableBody>
-                  {stableSort(filteredRows, getComparator(order, orderBy))
+                  {stableSort(filteredRows, getComparator(order, 'indices'))
                     .slice(page * rowsPerPage, page * rowsPerPage + rowsPerPage)
                     .map((row) => (
                       <TableRow tabIndex={-1} key={row.name}>

webapp/components/general/GeppettoJupyterUtils.js

@@ -10,7 +10,6 @@ const handle_output = function (data) {
       GEPPETTO.trigger(GEPPETTO.Events.Hide_spinner);
       break;
     case 'execute_result':
-      console.log(data.content.data['text/plain'].trim(), true);
       try {
         var response = JSON.parse(data.content.data['text/plain'].replace(/^'(.*)'$/, '$1'));
       } catch (error) {
@@ -27,7 +26,6 @@ const handle_output = function (data) {
 };
 
 const execPythonMessage = function (command, callback = handle_output) {
-  console.log(`Executing Python command: ${command}`, true);
   const { kernel } = IPython.notebook;
   const messageID = kernel.execute(command, { iopub: { output: callback } }, { silent: false, stop_on_error: true, store_history: true });
 

webapp/components/general/PlotViewer.js

@@ -1,5 +1,5 @@
 import React from 'react';
-import HTMLViewer from '../index';
+import HTMLViewer from './HTMLViewer';
 
 const PlotViewer = ({ key, id, method }) => {
   const data = window.plotCache[id];

webapp/components/index.js

@@ -357,10 +357,6 @@ export const SelectCellTemplate = connect(
   }),
 )(_SelectCellTemplate);
 
-export const PlotViewer = connect(
-  null,
-  null,
-)(_PlotViewer);
 // ---------------------------------------------------------------------------------------- //
 
 // DEFAULTS

webapp/components/instantiation/NetPyNEInstantiated.js

@@ -7,7 +7,7 @@ import CameraControls from '@metacell/geppetto-meta-ui/camera-controls/CameraCon
 // import ControlPanel from 'geppetto-client/js/components/interface/controlPanel/controlpanel';
 
 import { NetWorkControlButtons } from 'netpyne/components';
-import { primaryColor, canvasBgDark, canvasBgLight } from '../../theme';
+import { primaryColor, canvasBgDark, canvasBgLight, bgRegular } from '../../theme';
 import { THEMES } from '../../constants';
 
 const CANVAS_LIGHT = 'canvas-toolbar-btns-light';
@@ -222,7 +222,7 @@ class NetPyNEInstantiated extends React.Component {
           cameraOptions={camOptions}
           key="CanvasContainer"
           data={canvasData}
-          backgroundColor="#000000"
+          backgroundColor={bgRegular}
         />
         <div id="controlpanel" style={{ top: 0 }}>
           {/* TODO: refactor the control panel with the list viewer