openworm / org.geppetto Goto Github PK

• Add button to start the tutorial in the help dialog
• Show a confirmation dialog informing the user they will be abandoning their current simulation if they decide to load the tutorial
• Add button to quit the tutorial at any time

• Setup development environment
• Test current functionality
• Make sure the widget architecture is updated with the latest one specified in Geppetto
• Connect the proof of concept widget to Geppetto

• Improve Simulation file description
• Make look and feel of custom help button consistent with the arrows icon

The folder repository/usr is empty after launching the script, starting the server fails for this reason:

[2012-11-22 17:13:26.293] fs-watcher Hot deploy failed for file 'owsefull.plan'. org.eclipse.virgo.nano.deployer.api.core.DeploymentException: Deployment of plan 'multi-artifact.plan' version '1.0.0' in scope 'null' failed: bundle 'org.openworm.simulationengine.core' in version range '[1.0.0, oo)' not found

• Upgrade version
• Test development branch
• Merge development into master
• Create bundle
• Smoke test bundle
• Write release notes
• Release
• Send release email

At the moment all the console commands are visualised also if these commands are the consequence of UI actions. Make it so that they are visualised only if debug is true.

To reproduce start a simulation twice from the console.
Expected result: A message showing "The simulation is already started".
Actual result: Geppetto becomes slower.

• Review changes across all bundles
• Test with all samples and test backend
• Extensive testing of all features
• Make sure all qunit tests pass

Note: this is targeted for release 0.1.2 so it should have higher priorities than the rest

Y-axis on the chart widget is not set to autoscale.
Currently the top value of the hhcell.electrical.hhpop[0].spiking plot is not visible.

Originally filed by @msasinski

Transferred here from the main OpenWorm board in this issue

During the resolution of #8 @tarelli @gidili and I realised that large SPH scenes result in a communications bottleneck. We decided that simulation information sent from server to client needs to be compressed in some way. I'll start the ball rolling with some ideas of how to do this:

1. Binary not JSON
2. Data compression
3. Select "rendering particles" at configuration stage - only these are sent, the others are used in calculation only.
4. Work out 3D Convex hulls of particles and send only those
5. Only send particles which have moved by a significant distance. The server will need to keep track of what has been displayed on the client.

If variables are added at different times to variable watch the updates sent from the server still need to be consistent, i.e. to belong to the same timestep for all variables regardless of when they were added.

• Solver doesn't update list of new variables sent to simulation, only creates them once and reuses that same list to send the updates even after new ones have been added.
• JLems also doesn't update list of new variables sent to simulation after adding second addwatchvariable command
• Fix
• Test with testbackend, neuronal and sph
• Write qunit test

When I run locally (i.e point browser to http://localhost:8080/org.geppetto.frontend/) the simulation PCISPH Big Liquid/Elastic scene runs fine. When I run remotely it crashes after a few simulation steps.

The error I see on the server is:

java.lang.OutOfMemoryError: Java heap space
Dumping heap to /home/mike/Downloads/geppetto/serviceability/heap_dump.hprof

A Geppetto widget with the ability of creating/modifying NeuroML files

After pressing the start button, the simulated cube moves toward the bottom of the screen and disappears from the view.

Originally filed by @msasinski

Transferred here from the main OpenWorm board in this issue

There are still some Geppetto issues hanging in the OpenWorm repo, as well as some wiki pages, move them over to org.geppetto or subrepo.

• Move issues
• Copy wiki pages over
• Update wiki links
• Delete old wiki pages

User must click the Pause button first. It's not possible to stop the simulation without this additional step.

Originally filed by @msasinski

Transferred here from the main OpenWorm board in this issue

• Control position
  • Control rotation
  • Control zoom
  • Hook up buttons on the left with these commands

[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[ERROR] FATAL ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Error building POM (may not be this project's POM).

Project ID: unknown

Reason: Could not find the model file '/tmp/tmp97KXFV/org.openworm.simulationengine.core'. for project unknown

[INFO] ------------------------------------------------------------------------
[INFO] Trace
org.apache.maven.reactor.MavenExecutionException: Could not find the model file '/tmp/tmp97KXFV/org.openworm.simulationengine.core'. for project unknown
at org.apache.maven.DefaultMaven.getProjects(DefaultMaven.java:404)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:272)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)
at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
Caused by: org.apache.maven.project.ProjectBuildingException: Could not find the model file '/tmp/tmp97KXFV/org.openworm.simulationengine.core'. for project unknown
at org.apache.maven.project.DefaultMavenProjectBuilder.readModel(DefaultMavenProjectBuilder.java:1575)
at org.apache.maven.project.DefaultMavenProjectBuilder.buildFromSourceFileInternal(DefaultMavenProjectBuilder.java:506)
at org.apache.maven.project.DefaultMavenProjectBuilder.build(DefaultMavenProjectBuilder.java:200)
at org.apache.maven.DefaultMaven.getProject(DefaultMaven.java:604)
at org.apache.maven.DefaultMaven.collectProjects(DefaultMaven.java:487)
at org.apache.maven.DefaultMaven.collectProjects(DefaultMaven.java:560)
at org.apache.maven.DefaultMaven.getProjects(DefaultMaven.java:391)
... 12 more
Caused by: java.io.FileNotFoundException: /tmp/tmp97KXFV/org.openworm.simulationengine.core (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:137)
at hidden.org.codehaus.plexus.util.xml.XmlReader.(XmlReader.java:124)
at hidden.org.codehaus.plexus.util.xml.XmlStreamReader.(XmlStreamReader.java:67)
at hidden.org.codehaus.plexus.util.ReaderFactory.newXmlReader(ReaderFactory.java:118)
at org.apache.maven.project.DefaultMavenProjectBuilder.readModel(DefaultMavenProjectBuilder.java:1570)
... 18 more
[INFO] ------------------------------------------------------------------------
[INFO] Total time: < 1 second
[INFO] Finished at: Thu Nov 22 16:04:37 UTC 2012
[INFO] Final Memory: 2M/111M
[INFO] ------------------------------------------------------------------------

Some strange box with a list of console commands hides navigation buttons.

Originally filed by @msasinski

Transferred here from the main OpenWorm board in this issue

Matteos-MacBook-Pro:~ matteocantarelli$ python build_server_package.py
Traceback (most recent call last):
File "build_server_package.py", line 10, in
from fabric.api import *
ImportError: No module named fabric.api

Units are now surfacing to jLEMS so it is possible to link them with Geppetto to visualise units for the different states.

Refactor out Widget Controller functionality. as suggested before; "There is some functionality in e.g. the plot controller pertaining to the creation of a plot instance, management of a list of instances, removal... Those look common to all widgets, those should inherit from an abstract WidgetController".

We are currently using a plugin to create our console in Geppetto, http://josscrowcroft.github.io/javascript-sandbox-console/ .

This is working fine in Chrome and all other webkit browser, but is not styling the scrollbars for the console in Firefox and they become visible as seen in the picture.

Ideally the vertical scrollbar would be transparent, and the horizontal one should be invisible.

Due a bug reported in the Mozilla site https://bugzilla.mozilla.org/show_bug.cgi?id=77790, we can't style scrollbars in Firefox. A possibility to solve this will be to use jquery scroll pane

Gives the following error

<HD0002E> Hot deploy failed for file 'owsefull.plan'. org.eclipse.virgo.nano.deployer.api.core.DeploymentException: Deployment of plan 'multi-artifact.plan'    version '1.0.0' in scope 'null' failed: bundle 'org.openworm.simulationengine.core' in version range '[1.0.0, oo)' not found

• Add one sample which has two entities (for instance two purkinje cells) and specifies their position
• Implement code to read the position of an entity off the simulation file
• Add a more complex sample which has a simple hierarchy of nested entities

• Add a Simulator which can be used to read a recording and create a Geppetto state tree
• Write unit tests to check the created state tree from recorded simulation
• Integrate with the rest of Geppetto
• Create Geppetto sample scene with recording
• Test with frontend

• Add support for visualizing a LEMS/NeuroML network
• Test with C.elegans NML
• Test with C302

• Convert simulation tutorial in rst and add to docs.geppetto.org (use markedup XML not images)
• Put back link to tutorial in Simulation dialog
• Make sure the widget tutorial is up to date
• Update default template for custom simulation

The current plot widget uses Flot which proven itself CPU intensive and not really designed for handling real time updates. NVD3 is based on D3.js.
NVD3
Realtime example
Tutorial for creating a Geppetto widget

Let's create this widget in parallel to the current one. I would call it plot2d. The plan is to remove the current one once this one will be working.

Depending on the color of the mesh lighting up causes the mesh to change color first then to go white and the to go back to the original color as opposed of simply going from the original color to white.

This is about creating a Sibernetics Geppetto configuration file from the worm model in sibernetics.

• Get Configuration in text format From Sibernetic
• Update configuration generator if needed
• Generate a worm.xml according to Geppetto SPH Schema for the worm

• Take the latest of development of every bundle
• Add testMembranesSceneWithLiquid to use cube_with_membranes_cube_water_inside
• Try running samples from the GUI and see if they behave as they used to (no explosions)
• Fix testMembranesSceneWithLiquid
• Run all unit tests and report here what is passing and what is failing

It would be great to use Geppetto for basic data analysis / descriptive statistics, without having to embed trivialities (such as calculating an average) in the model description itself. In other words, at the moment it is possible to simulate a model and produce timeseries ([ti, xi] pairs) to be plotted, but what if we would like to calculate/plot functions of x (examples: calculate mean(x) or plot a histogram of cos(x)). Having an (numpy/matlab/R/scilab/...) arraylike data structure, with builtin support for arraywise base mathematical functions and indexing would be fantastic -- and eliminate the need of firing scipy/matlab/etc just to perform trivial exploratory tasks.

Random wishlist -- given an array x with simulation results

    plot(abs(x[-1000:end])) //intuitive indexing, get the last 1000 points
    histogram((x-mean(x))/10)//basic statistics and operations involving arrays/scalars

• Review popup tutorial
• Review GitHub maven repository
• Bring in latest changes from development (should include the popup tutorial)
• Create pull request to merge everything to development
• Remove data toggle from help button
• Make sure the create a widget tutorial is up to date
• Loading a new simulation should also clean the Popup widgets (should we make the code generic so that any widget gets automatically cleaned?)
• Popover should always be in front of everything (if you load a simulation which has widgets they will be behind them)
• Fix javascript errors due to popup widgets getting notified of updated but not having the update method
• Move popovers for the selection a simulation sample below the dropdown instead of its right
• Move popovers for the navigation control to the right of the controls instead of below
• Share popover doesn't move when clicking the share button (the console one does)
• Make the zzz are you still there timer longer (1min?) It shows afters 5 min, and then one minute after that it disconnects. No code has changed since it was created.
• Is there a gap on the welcome dialog on the right? No gap found, there's a border around the whole dialog
• Geppetto is ready message not appearing anymore?
• The popover for the console sometimes is displaced and it appears where the zoom buttons are
• For some steps of the tutorial like start it asks the user to press continue while the event on the start button could be detected to go to the next step

Track this bug and when it's fixed check if we still need to change the flag on virgo.
https://bugs.eclipse.org/bugs/show_bug.cgi?id=354730

• Design NeuroML/LEMS network support

• Review simulation format
• Write a tutorial that goes through how to create a custom simulation file explaining its structure and the different fields
• Add question mark button to the load simulation dialog which links to the tutorial
• Update custom tab in the Load simulation dialog if needed

• [ x] Use mod_deflate for compression of resources, look at this page Pending issue 42
• [x ] Take note of what changes to virgo/tomcat are necessary Pending issue 42
• Make sure that for all vendor libraries we use minified ones

A simple widget to display the value of a single variable or parameter would be a useful addition to Geppetto.

• Add as a wiki page and link it from the README of org.geppetto

We have identified Avast anti-virus makes Geppetto unusable. Pending issue 43

• By default only the entities/aspects + ... + last node is displayed if the user doesn't specify any alias (e.g. entity1.entity2.aspectA...v)
• Hovering over the label will reveal the full instance path for the given state

No reproduction steps still, not sure if it's a problem of some specific configuration or an internal state of Geppetto, let's add here any occurrence of the problem with some details.

Using the test scenes developed in #48

• Allow for each of the entities to be selected on the frontend
• Clicking on an entity results in a command being sent to console Simulation.selectEntity("entityParent.entityChild") where entityParent.entityChild is the instance path of the entity we clicked on
• Selected entities have a different color
• After the first sample is working design meeting to go in depth into how to deal with nested entities

This Stackoverflow post explains how to achieve this.