diff --git a/netpyne_ui/netpyne_geppetto.py b/netpyne_ui/netpyne_geppetto.py index 8922e3c6..9230d406 100644 --- a/netpyne_ui/netpyne_geppetto.py +++ b/netpyne_ui/netpyne_geppetto.py @@ -330,7 +330,9 @@ def simulateNetPyNEModelInGeppetto(self, args): use_prev_inst = args.get('usePrevInst', False) sim_id = args.get('simId', 0) try: - self.validate_netParams() + # Note this has been commented for CNS 24 since some models were failing + # there is a discussion about making this non blocker, to follow up with Salva and Padraig + # self.validate_netParams() experiment = experiments.get_current() if experiment: @@ -805,7 +807,9 @@ def deleteModel(self, modelParams): return utils.getJSONReply() def instantiateNetPyNEModel(self): - self.validate_netParams() + # Note this has been commented for CNS 24 since some models were failing + # there is a discussion about making this non blocker, to follow up with Salva and Padraig + # self.validate_netParams() with redirect_stdout(sys.__stdout__): saveData = sim.allSimData if hasattr(sim, 'allSimData') and 'spkt' in sim.allSimData.keys() and len( sim.allSimData['spkt']) > 0 else False diff --git a/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js b/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js index 587f3b00..5ae414df 100644 --- a/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js +++ b/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js @@ -32,6 +32,10 @@ export default class NetPyNEConnectivityRule extends React.Component { }; } + UNSAFE_componentWillReceiveProps (nextProps) { + this.setState({ currentName: nextProps.name }); + } + handleRenameChange = (event) => { const storedValue = this.props.name; const newValue = Utils.nameValidation(event.target.value); @@ -60,19 +64,7 @@ export default class NetPyNEConnectivityRule extends React.Component { } }; - triggerUpdate (updateMethod) { - // common strategy when triggering processing of a value change, delay it, every time there is a change we reset - // eslint-disable-next-line eqeqeq - if (this.updateTimer !== undefined) { - clearTimeout(this.updateTimer); - } - this.updateTimer = setTimeout(updateMethod, 1000); - } - - select = (index, sectionId) => this.setState({ - selectedIndex: index, - sectionId, - }); + handleChange = (event, index, values) => this.setState({ values }); getBottomNavigationAction (index, sectionId, label, icon, id) { return ( @@ -86,6 +78,20 @@ export default class NetPyNEConnectivityRule extends React.Component { ); } + select = (index, sectionId) => this.setState({ + selectedIndex: index, + sectionId, + }); + + triggerUpdate (updateMethod) { + // common strategy when triggering processing of a value change, delay it, every time there is a change we reset + // eslint-disable-next-line eqeqeq + if (this.updateTimer !== undefined) { + clearTimeout(this.updateTimer); + } + this.updateTimer = setTimeout(updateMethod, 1000); + } + postProcessMenuItems (pythonData, selected) { return pythonData.map((name) => ( @@ -445,6 +447,4 @@ export default class NetPyNEConnectivityRule extends React.Component { ); } - - handleChange = (event, index, values) => this.setState({ values }); } diff --git a/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js b/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js index d1b3b5ca..9c215c4c 100644 --- a/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js +++ b/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js @@ -103,8 +103,9 @@ export default class NetPyNEConnectivityRules extends Component { } componentDidUpdate (prevProps, prevState) { - if (this.props.commands !== prevProps.commands) + if (this.props.commands !== prevProps.commands) { this.forceUpdate(); + } // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable const newConnectivityRuleName = this.hasSelectedConnectivityRuleBeenRenamed( prevState, diff --git a/webapp/components/definition/populations/NetPyNEPopulation.js b/webapp/components/definition/populations/NetPyNEPopulation.js index a163db61..4e3cb6c5 100644 --- a/webapp/components/definition/populations/NetPyNEPopulation.js +++ b/webapp/components/definition/populations/NetPyNEPopulation.js @@ -1,7 +1,8 @@ import React, { useState } from 'react'; import TextField from '@material-ui/core/TextField'; -import { BottomNavigation, BottomNavigationAction, Grid, Switch, Typography } from '@material-ui/core'; -import FontIcon from '@material-ui/core/Icon'; +import { + BottomNavigation, BottomNavigationAction, Grid, Switch, Typography, +} from '@material-ui/core'; import Box from '@material-ui/core/Box'; import Dialog from '@material-ui/core/Dialog/Dialog'; import Button from '@material-ui/core/Button'; @@ -14,7 +15,6 @@ import DialogContent from '@material-ui/core/DialogContent'; import DialogContentText from '@material-ui/core/DialogContentText'; import DialogTitle from '@material-ui/core/DialogTitle'; - import { withStyles } from '@material-ui/core/styles'; import { Dimensions, @@ -47,7 +47,7 @@ const newPulseObject = { }; class NetPyNEPopulation extends React.Component { - constructor(props) { + constructor (props) { super(props); this.state = { currentName: props.name, @@ -56,29 +56,30 @@ class NetPyNEPopulation extends React.Component { errorMessage: undefined, errorDetails: undefined, startParam: 'start', - model: undefined + model: undefined, }; - this.updateModel() + this.resetError = this.resetError.bind(this); + this.updateModel(); } updateModel = async (componentName) => { - const name = componentName ? componentName : this.props.name; - const command = `utils.convertToJS(netpyne_geppetto.netParams.popParams['${name}'])` - const response = await execPythonMessage(command) - this.setState({ model: response }) + const name = componentName || this.props.name; + const command = `utils.convertToJS(netpyne_geppetto.netParams.popParams['${name}'])`; + const response = await execPythonMessage(command); + this.setState({ model: response }); } - UNSAFE_componentWillReceiveProps(nextProps) { + UNSAFE_componentWillReceiveProps (nextProps) { this.setState({ currentName: nextProps.name, selectedIndex: 0, sectionId: 'General', }); - this.updateModel(nextProps.name) + this.updateModel(nextProps.name); } - shouldComponentUpdate(nextProps, nextState) { + shouldComponentUpdate (nextProps, nextState) { return ( this.state.model == undefined || this.state.currentName != nextState.currentName @@ -101,7 +102,7 @@ class NetPyNEPopulation extends React.Component { id="generalPopTab" key="General" label="General" - icon={} + icon={} onClick={() => select(0, 'General')} />, ); @@ -110,7 +111,7 @@ class NetPyNEPopulation extends React.Component { id="spatialDistPopTab" key="SpatialDistribution" label="Spatial Distribution" - icon={} + icon={} onClick={() => select(1, 'SpatialDistribution')} />, ); @@ -122,7 +123,7 @@ class NetPyNEPopulation extends React.Component { } + icon={} onClick={() => select(2, this.state.cellModel)} />, ); @@ -131,7 +132,7 @@ class NetPyNEPopulation extends React.Component { } + icon={} onClick={() => select(4, 'Stimulation')} />, ); @@ -160,7 +161,6 @@ class NetPyNEPopulation extends React.Component { newValue, (response, newValue) => { this.renaming = false; - this.props.updateCards(); }, ); this.renaming = true; @@ -168,7 +168,7 @@ class NetPyNEPopulation extends React.Component { } }; - triggerUpdate(updateMethod) { + triggerUpdate (updateMethod) { // common strategy when triggering processing of a value change, delay it, every time there is a change we reset if (this.updateTimer != undefined) { clearTimeout(this.updateTimer); @@ -176,7 +176,7 @@ class NetPyNEPopulation extends React.Component { this.updateTimer = setTimeout(updateMethod, 1000); } - postProcessMenuItems(pythonData, selected) { + postProcessMenuItems (pythonData, selected) { return pythonData.map((name) => ( { - this.updateModel() + this.updateModel(); } changeCellPattern = (newValue) => { if (!newValue) { - execPythonMessage(`del netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']`) - } - else { + execPythonMessage(`del netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']`); + } else { execPythonMessage(`netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] = {} -netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']['type'] = '${newValue}'`) +netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']['type'] = '${newValue}'`); } - this.updateModel() + this.updateModel(); } handleStartMaxChange = (newValue) => { - const maxIsSet = !(!newValue || newValue === '') + const maxIsSet = !(!newValue || newValue === ''); if (maxIsSet) { const command = ` pattern = netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] -pattern['start'], pattern['startMin'] = -1, pattern.get('start', '')` - execPythonMessage(command) +pattern['start'], pattern['startMin'] = -1, pattern.get('start', '')`; + execPythonMessage(command); } else { const command = ` pattern = netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] pattern['start'] = pattern['startMin'] -del pattern['startMin']` - execPythonMessage(command) +del pattern['startMin']`; + execPythonMessage(command); } this.setState({ - startParam: maxIsSet ? "startMin" : "start" - }) + startParam: maxIsSet ? 'startMin' : 'start', + }); } - rhythmicLayout = () => { - return <> - - Start - + rhythmicLayout = () => ( + <> + + + Start + + - } + ) - evokedLayout = () => { - return <> + evokedLayout = () => ( + <> - } + ) - poissonLayout = () => { - return <> + poissonLayout = () => ( + <> - } + ) - gaussLayout = () => { - return <> + gaussLayout = () => ( + <> - } + ) changeStimulationPatternLayout = (pattern) => { const patternKey = `${pattern}Layout`; if (!(patternKey in this)) { - return <> + return <>; } - return this[patternKey]() + return this[patternKey](); } addAnotherPulse = () => { const command = ` pulse = {'start': 0, 'end': 0, 'rate': 0, 'noise': 0} netpyne_geppetto.netParams.popParams['${this.props.name}'].setdefault('pulses', []).append(pulse) -pulse` +pulse`; execPythonMessage(command).then((_) => { - this.updateModel() - }) + this.updateModel(); + }); }; removePulse = (index) => { const command = ` -netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index})` +netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index})`; execPythonMessage(command).then((_) => { - this.updateModel() - }) + this.updateModel(); + }); } displayPulses = () => { if (!this.state.model || !this.state.model.pulses) { - return <> + return <>; } return this.state.model.pulses.map((pulse, index) => ( - + this.removePulse(index)}> @@ -469,91 +472,102 @@ netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index */} - )) + + )); } cellStimulationLayout = () => { if (!this.state.model) { - return <> + return <>; } - if (!["VecStim", "NetStim"].includes(this.state.model.cellModel)) { - return <> + if (!['VecStim', 'NetStim'].includes(this.state.model.cellModel)) { + return <>; } - return <> - - - - - - - - + + + + - Spiking Pulse - - - {this.displayPulses()} + + + + + Spiking Pulse + + + {this.displayPulses()} + - - - - - - - - + + + + + + - {/* + {/* */} - - - + - - - {this.changeStimulationPatternLayout(this.state.model?.spikePattern?.type)} + postProcessItems={this.postProcessMenuItems} + postHandleChange={this.changeCellPattern} + /> + + {this.changeStimulationPatternLayout(this.state.model?.spikePattern?.type)} - + + ); } - render() { + resetError () { + const { updateCards } = this.props; + this.setState({ + errorMessage: undefined, + errorDetails: undefined, + }, updateCards()); + } + render () { const { classes } = this.props; const dialogPop = this.state.errorMessage != undefined ? ( @@ -570,10 +584,7 @@ netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index @@ -694,7 +705,7 @@ netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index >View Configurations in stim. source */} - + { - if ((typeof response === 'object') && (response.density)) { - this.setState({ type: response.density.type, density: response.density }); // splitting so it fires update - } - }); + componentDidMount () { + this.refreshComponent(); + } + + UNSAFE_componentWillReceiveProps (nextProps) { + this.setState({ currentName: nextProps.name, type: nextProps.model.density }); } componentDidUpdate (prevProps, prevState) { if (JSON.stringify(prevProps.model) != JSON.stringify(this.props.model)) this.refreshComponent(); } - componentDidMount () { - this.refreshComponent(); + getDialogPop () { + return this.state.errorMessage !== undefined ? ( + + + {this.state.errorMessage} + + + + {this.state.errorDetails} + + + + + + + ) : undefined; } handleRenameChange = (event) => { @@ -67,7 +96,7 @@ export default class NetPyNESubCellsConnectivityRule extends React.Component { newValue, event.target.value, this, - 'ConnectionRule', + 'SubConnectionRule', ); if (triggerCondition) { @@ -86,19 +115,14 @@ export default class NetPyNESubCellsConnectivityRule extends React.Component { } }; - triggerUpdate (updateMethod) { - // common strategy when triggering processing of a value change, delay it, every time there is a change we reset - // eslint-disable-next-line eqeqeq - if (this.updateTimer !== undefined) { - clearTimeout(this.updateTimer); - } - this.updateTimer = setTimeout(updateMethod, 1000); - } + handleChange = (event, index, values) => this.setState({ values }); - select = (index, sectionId) => this.setState({ - selectedIndex: index, - sectionId, - }); + handleDensity (value) { + this.setState({ type: value }); + Utils.execPythonMessage( + `netpyne_geppetto.netParams.subConnParams['${this.props.name}']['density'] = { 'type': '${value}' }`, + ); + } getBottomNavigationAction (index, sectionId, label, icon, id) { return ( @@ -112,6 +136,15 @@ export default class NetPyNESubCellsConnectivityRule extends React.Component { ); } + triggerUpdate (updateMethod) { + // common strategy when triggering processing of a value change, delay it, every time there is a change we reset + // eslint-disable-next-line eqeqeq + if (this.updateTimer !== undefined) { + clearTimeout(this.updateTimer); + } + this.updateTimer = setTimeout(updateMethod, 1000); + } + postProcessMenuItems (pythonData, selected) { return pythonData.map((name) => ( - - {this.state.errorMessage} - - - - {this.state.errorDetails} - - - - - - - ) : undefined; - - if (this.state.sectionId === 'General') { - var content = ( - - - - - - - pythonData.map((name) => ( - - {name} - - ))} - /> - - - - - - - - - - - {densityExtras} - - {dialogPop} - - ); - } else if (this.state.sectionId === 'Pre Conditions') { - var content = ( - - - - - - - - - - + + + - + pythonData.map((name) => ( + + {name} + + ))} /> + - + - - ); - } else if (this.state.sectionId === 'Post Conditions') { - var content = ( - - - - - - - - - - + + + + - + ); + } + + getPreConditionsTab () { + return ( + + + + + + + + + + + + + + + + ); + } - + + - - ); + + + + + + + + + + + + + ); + } + + select (index, sectionId) { + if (sectionId === 'General') { + this.content = this.getGeneralTab(); + } else if (sectionId === 'Pre Conditions') { + this.content = this.getPreConditionsTab(); + } else if (sectionId === 'Post Conditions') { + this.content = this.getPostConditionsTab(); } - // Generate Menu + this.setState({ + selectedIndex: index, + sectionId, + }, () => { + this.props.updateCards(); + }); + } + + refreshComponent () { + // get initial values + Utils.evalPythonMessage(`netpyne_geppetto.netParams.subConnParams["${ + this.props.name + }"]`) + .then((response) => { + if ((typeof response === 'object') && (response.density)) { + this.setState({ type: response.density.type, density: response.density }); // splitting so it fires update + } + }); + } + + render () { let index = 0; const bottomNavigationItems = []; bottomNavigationItems.push( @@ -532,10 +560,8 @@ export default class NetPyNESubCellsConnectivityRule extends React.Component { {bottomNavigationItems} - {content} + {this.content} ); } - - handleChange = (event, index, values) => this.setState({ values }); } diff --git a/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js index b828eced..239f354c 100644 --- a/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js +++ b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js @@ -8,7 +8,7 @@ import Utils from '../../../Utils'; import NetPyNEHome from '../../general/NetPyNEHome'; import NetPyNEAddNew from '../../general/NetPyNEAddNew'; -import NetPyNEConnectivityRule from './NetPyNESubcellsConnectivityRule'; +import NetPyNESubcellsConnectivityRule from './NetPyNESubcellsConnectivityRule'; import RulePath from '../../general/RulePath'; import Accordion from '../../general/ExpansionPanel'; @@ -254,11 +254,12 @@ export default class NetPyNESubCellsConnectivityRules extends Component { .indexOf(this.state.selectedConnectivityRule) > -1 ) { selectedConnectivityRule = ( - ); } diff --git a/webapp/components/general/NetPyNECoordsRange.js b/webapp/components/general/NetPyNECoordsRange.js index 0d35b5f9..65571187 100644 --- a/webapp/components/general/NetPyNECoordsRange.js +++ b/webapp/components/general/NetPyNECoordsRange.js @@ -127,7 +127,7 @@ export default class NetPyNECoordsRange extends Component { this.setState({ rangeType}) } - //preConds: pop, cellType, cellModel, x, y, z, xnorm, ynorm, znorm + // preConds: pop, cellType, cellModel, x, y, z, xnorm, ynorm, znorm handleCoordParamChange(index, newValue) { const { model, @@ -135,6 +135,9 @@ export default class NetPyNECoordsRange extends Component { name, } = this.props; + if (Object.is(newValue, NaN)) { + newValue = 0; + } if (newValue === '' || (/^\d+$/.test(newValue))) { if (this.state.rangeType && this.state.rangeType.length > 0) diff --git a/webapp/components/index.js b/webapp/components/index.js index 30528ed5..c907c469 100644 --- a/webapp/components/index.js +++ b/webapp/components/index.js @@ -10,15 +10,25 @@ import { newWidget, maximiseWidget, } from '@metacell/geppetto-meta-client/common/actions'; +import { WidgetStatus } from '@metacell/geppetto-meta-client/common/layout/model'; import { TOPBAR_CONSTANTS } from '../constants'; import PythonControlledCapability from './general/PythonControlledCapability'; import { openBackendErrorDialog, closeBackendErrorDialog } from '../redux/actions/errors'; import { updateCards, editModel, simulateNetwork, createNetwork, closeDialog, createAndSimulateNetwork, showNetwork, pythonCall, deleteNetParamsObj, resetModel, - setDefaultWidgets, changeInstanceColor, openConfirmationDialog, closeConfirmationDialog, selectInstances, + setDefaultWidgets, openConfirmationDialog, closeConfirmationDialog, selectInstances, } from '../redux/actions/general'; -import { runControlledStep, startTutorial, stopTutorial, addDiscoveredStep, runControlledStepByElementId, incrementTutorialStep, validateTutorialStep, checkBubbleRender } from '../redux/actions/tutorials'; +import { + runControlledStep, + startTutorial, + stopTutorial, + addDiscoveredStep, + runControlledStepByElementId, + incrementTutorialStep, + validateTutorialStep, + checkBubbleRender, +} from '../redux/actions/tutorials'; import { updateConsole } from '../redux/actions/console'; import { cloneExperiment, @@ -26,7 +36,7 @@ import { openLaunchDialog, removeExperiment, addExperiment, - editExperiment + editExperiment, } from '../redux/actions/experiments'; import { @@ -72,12 +82,9 @@ import _ExperimentEdit from './experiments/ExperimentEdit'; import _ExperimentManager from './experiments/ExperimentManager'; import _LaunchDialog from './topbar/dialogs/LaunchDialog'; import _NetPyNEPythonConsole from './general/NetPyNEPythonConsole'; -import _PlotViewer from './general/PlotViewer'; import _TutorialObserver from './general/TutorialObserver'; import _ExperimentControlPanel from './general/ExperimentControlPanel'; import _Rxd from './rxd/Wrapper'; -import { WidgetStatus } from '@metacell/geppetto-meta-client/common/layout/model'; -import Textbox from './general/Textbox'; const updateCardsDispatch = (dispatch) => ({ updateCards: () => dispatch(updateCards) }); @@ -123,8 +130,16 @@ export const NetPyNEConnectivityRules = connect( ), ); -export const NetPyNESubcellsConnectivityRules = PythonControlledCapability.createPythonControlledComponent( - _NetPyNESubcellsConnectivityRules +export const NetPyNESubcellsConnectivityRules = connect( + (state, ownProps) => ({ + ...ownProps, + commands: state.console.commands, + }), + updateCardsDispatch, +)( + PythonControlledCapability.createPythonControlledComponent( + _NetPyNESubcellsConnectivityRules, + ), ); export const NetPyNEPlots = PythonControlledCapability.createPythonControlledComponent( @@ -222,7 +237,7 @@ export const ExperimentEdit = connect( ...ownProps, updates: state.general.updates, widgets: state.widgets, - visible: state.widgets?.experimentManager?.status != WidgetStatus.HIDDEN + visible: state.widgets?.experimentManager?.status != WidgetStatus.HIDDEN, }), (dispatch) => ({ editExperiment: (name, details) => dispatch(editExperiment(name, details)), @@ -387,10 +402,10 @@ export const ErrorDialog = connect( export const NetPyNEPythonConsole = connect( (state) => ({ extensionLoaded: state.client.jupyter_geppetto_extension.loaded, - notebookVisible: state.widgets?.python?.status != WidgetStatus.MINIMIZED + notebookVisible: state.widgets?.python?.status != WidgetStatus.MINIMIZED, }), (dispatch) => ({ - updateConsole: (commands) => dispatch(updateConsole(commands)) + updateConsole: (commands) => dispatch(updateConsole(commands)), }), )(_NetPyNEPythonConsole); @@ -503,18 +518,17 @@ export const TutorialObserver = connect( lastCheckRender: state.tutorial.lastCheckRender, }), (dispatch) => ({ - startTutorialStep: () => { dispatch(startTutorial()) }, - runControlledStep: () => { dispatch(runControlledStep()) }, - stopTutorialStep: () => { dispatch(stopTutorial()) }, - validateTutorialStep: (e) => { dispatch(validateTutorialStep(e)) }, - addDiscoveredStep: (nodeIdList) => { dispatch(addDiscoveredStep(nodeIdList)) }, - runControlledStepByElementId: (e) => { dispatch(runControlledStepByElementId(e))}, + startTutorialStep: () => { dispatch(startTutorial()); }, + runControlledStep: () => { dispatch(runControlledStep()); }, + stopTutorialStep: () => { dispatch(stopTutorial()); }, + validateTutorialStep: (e) => { dispatch(validateTutorialStep(e)); }, + addDiscoveredStep: (nodeIdList) => { dispatch(addDiscoveredStep(nodeIdList)); }, + runControlledStepByElementId: (e) => { dispatch(runControlledStepByElementId(e)); }, incrementTutorialStep: (e) => { dispatch(incrementTutorialStep()); }, - checkBubbleRender: (e) => { dispatch(checkBubbleRender(e))} + checkBubbleRender: (e) => { dispatch(checkBubbleRender(e)); }, }), )(_TutorialObserver); - // ---------------------------------------------------------------------------------------- // // DEFAULTS