ivis-at-bilkent / chise.js Goto Github PK

From @ugurdogrusoz on July 15, 2016 11:55

Following are problems/issues with the viewer code base (unstable branch to be transferred to the master):

• Delete Selected {Simple,Smart} should be available (both in the menu and the toolbar) in the viewer as well.
• Alignment should be available (both in the menu and the toolbar) in the viewer as well.
• Remove Help > How to Use (we can put the User's Guide somewhere in GitHub repository)
• Help > About:
  o 1.0 -> 2.0
  o add MSKCC as well (see http://www.cs.bilkent.edu.tr/~ivis/SBGNViz.js/ for the format)
  o email, repo web page stays the same (not as in http://www.cs.bilkent.edu.tr/~ivis/SBGNViz.js/)

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#156

We need to implement validation checks upon Save (or when the user decides to do such a check).

We should also decide on

• under what menu to make this operation available
• with what format any warnings/errors should be presented to the user

We should discuss whether or not we use libSBGN (http://www.sbgn.org/LibSBGN) for this purpose on server side (not currently available in JavaScript).

In case we support multiple notation (i.e. PD and AF), we should be careful.

We should support grids, guidelines for alignment, and snapping as discussed and designed. Full functionality is to be first supported in the related extension.

From @ugurdogrusoz on June 16, 2016 11:39

Once #137 is done, we can add a "Select All Objects of This Type" functionality to the context menus of nodes and edges.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#138

From @ugurdogrusoz on July 14, 2016 11:11

Currently each node has a label (e.g. gene symbol) and some info boxes (units of information and state variables). In addition, tags defined in PD notation can be used to annotate map objects. However, a more general support for labels (labels associated with nodes, edges or the map itself) would be useful. The labels should be either text or an image!

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#152

Can we display a spinner for loading maps with File > Load as well?

The attached file cannot be loaded (throws an exception). It loads fine with the viewer SBGNViz 1.0 though (http://www.cs.bilkent.edu.tr/~ivis/SBGNViz.js/)!
iNOSPD_SBGN-ED.sbgn.txt

From @ugurdogrusoz on June 17, 2016 7:59

We need to find a way to create an arbitrary number of info boxes that can be controlled (created, edited, and moved) by the user

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#144

We should be able to use arrows for moving nodes (single or multiple selection). I suppose this should go to the related extension. Perhaps the speed of the move could be adjusted as follows:

• Ctrl arrow: move minimally (one pixel at a time)
• Just arrow: move reasonably (a few pixels at a time, 3?)
• Shift arrow: move faster (10 pixes at a time?)

From @ugurdogrusoz on July 15, 2016 7:33

We should not display node tooltips (full node labels)

• when the full label is already being displayed (won't be true for complexes or for nodes with at least one info box)
• when the node is being dragged (basically only when mouse over)

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#153

From @ugurdogrusoz on October 14, 2015 16:16

This model imported from Reactome wont load! Can we find out why not? I changed the file extension so github issue tracker can attach it.
391160.sbgn.txt

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#72

When the user creates a new map using File > New, we should confirm whether or not the user wants to save the current map first (Do you want to save any change(s) to the map? Save, Don't Save, Cancel).

From @teheavy on June 24, 2016 17:4

Hi there,

I'm recently incorprating a pathway module in a webapp, and I found this error:
cytoscape.min.js?_=1466786018527:23 Uncaught TypeError: Cannot read property 'strValue' of undefined

I don't know if it is from cytoscape.js or sbgnviz.js.

Thanks!
Fred

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#147

Moving nodes connected to a process as a process moves (moving a process in its entirety) might be useful. This could be implemented in two different ways:

• use the a extension?
• when the user clicks and holds (or double clicks) on a process, select its immediate neighbors so they can be moved together as a group.
  In any case, we should make sure this doesn't break the animation that takes place during layout, expand, etc.

From @cannin on July 15, 2016 15:15

The alignment markers do not disappear if they are visible, and the user pans around the screen by clicking and dragging around the screen.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#157

When we try to collapse an edge, having bend points, we were getting an error. Currently we are removing bend-points of edges before a node is being collapsed to avoid this bug.

Also, adding bend points to meta edges is problematic.

Can we map the "Delete" key as a shortcut for "Delete Selected Simple"?

In undo-redo extension these shortcuts can be listen optionally. Currently in ChiSE we set this option as false and listening these shortcuts in application level. We should listen them by using extension functionality.

From @ugurdogrusoz on June 16, 2016 11:36

Let's add context menus (not too shiny as cxtmenu extension but something simpler) for nodes, edges, and background. These menus should have functionality that might be commonly used per node, per edge or per map. BioGene dialog that opens up on right-click should go to the context menu of nodes of type macromolecule. Expand/collapse can go to compound nodes.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#137

Let's talk about details first.

From @ugurdogrusoz on July 15, 2016 9:15

We should think about how we can help the user to quickly successively create nodes of the same type. If no better solutions seems feasible, we can just keep the current addition mode upon creation rather than going back to the default selection mode.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#154

Please create a wiki page at https://github.com/iVis-at-Bilkent/chise.js/wiki/Obtaining-A-Working-Copy for this.

In all dialogs, we should change Save to Apply and NOT close the window upon clicking this button. The dialog should be closed only when X is clicked. This applies to all dialogs, including

• File > Properties
• View > Grid
• Layout > Layout Properties
  In the grid dialog, we have the following problems:
• For both Grid Size and Guideline Tolerance, we can enter invalid values that change the previous valid values, which is incorrect behavior.

From @ugurdogrusoz on June 21, 2016 8:49

Let's add a simple query facility to PC query submenu named "By URI..." (http://www.pathwaycommons.org/pc2/).

Also, "Paths Between" -> "Paths Between..."

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#145

From @teheavy on June 24, 2016 17:9

Hi there,

Another error that I'm not sure what it means:
jquery.fancybox-1.3.4.pack.js Line 18: Uncaught TypeError: Cannot read property 'msie' of undefined

Thanks,
Fred

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#149

From @ugurdogrusoz on June 16, 2016 11:47

Processes should be created to be much smaller by default (about 40 percent of what dimensions are now). In general default node dimensions for new nodes should be similar to those in the samples.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#141

From @ugurdogrusoz on June 17, 2016 7:37

Expose the new cose-bilkent options in Layout Properties

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#142

From @ugurdogrusoz on April 22, 2016 12:33

This high priority feature is to enable users to easily create certain types of processes such as associations and dissociations using templates provided. This is detailed out in Metin's GSoC project proposal.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#118

We can make bend point editing easier / more convenient if following are supported:

• [3] Ability to select a specific bend point (as opposed to or in addition to selecting the whole edge with bend points) and using Delete key to delete that bend point,
• [2] Ability to click anywhere on the edge to introduce and relocate a bendpoint by dragging,
• [1] If a bend point is released (during drag) "near" the line from the previous bend point to the next one (these neighboring bend points could be edge clipping points in case there is no such bend point), the bend point should be deleted.

From @ugurdogrusoz on June 14, 2016 6:37

The new (draft) version of SBGN PD 2.0 uses stadiums for state variables instead of ellipses.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#135

Except for molecular complexes (leave these as is), all nodes should have a white background by default.

When you left-click and drag in the root, it's panning by default (from Cytoscape.js). You need to use Shift or Ctrl for dragging to perform marquee/rectangle selection. Can we swap the two somehow? By default drag should map to selection not drag.

If you load a graph, you lose the grid and the guidelines; they no longer work! The bug might be in the related extension...

Use the new node-resize extension for resizing nodes. I would use the orange that we use for selection for grapples (and gray for bounding box?), and bounding rectangle and a very tight padding (not touching the node). Also we should no longer color the border of nodes in selection color since selection is now signified by grapples!
Let's keep in mind that

• some nodes aren't allowed to be resized, and
• some nodes are only allowed resizing keeping aspect ratio.

When "highlight neighbors" is called after "highlight processes", the processes of the selected element remain highlighted.

When the user makes a change in the inspector and then changes focus to some other window (say click on the canvas) to close the inspector, the change is lost. Can we do something to make sure change is actually saved?

From @ugurdogrusoz on July 14, 2016 11:6

Currently node labels can be small, medium or large only. The users might want to have a better control of node label style.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#151

Change the default for Fit Labels to Nodes from True to False.

• Edges, info box labels, etc. are not "ghosted" (still visible) as expected from this feature.
• Doesn't work on maps other than the default sample diagram.

From @fdurupinar on June 21, 2016 20:46

Targets of logical arcs should be allowed to be logical operators.

From the current sbgn specs:
Origin: Any EPN (Section 2.4) or logical operator (Section 2.10).
Target: Any logical operator (Section 2.10).

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#146

Please change the tool name as follows:

• html page title (SBGNViz.js -> Chisio SBGN Editor)
• upper left tile at menubar (SBGNViz.js -> Chisio SBGN Editor)
• Help > About (SBGNViz.js Editor version 1.0 -> Chisio SBGN Editor version 1.0)
• Help > About (.../iVis-at-Bilkent/sbgnviz-js -> .../iVis-at-Bilkent/chise.js)

From @ugurdogrusoz on December 17, 2015 14:50

Currently we do not support these node types (mainly since we do not like the way they are represented and drawn in SBGN-PD). We should discuss this and think about how they could be supported.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#101

From @ugurdogrusoz on January 7, 2016 16:23

This was fixed in the past (please see this old issue #82 for the problem) but it's back to smaller sizes now.

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#105

When the user drags a node towards the edge of the canvas, can we pan automatically (at a constant slow pace) and let the user drag the node further outward?

From @ugurdogrusoz on May 18, 2016 8:51

We need to update the User's Guide with all the new features (esp. editing features).

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#123

From @ugurdogrusoz on June 12, 2015 14:58

This needs to be improved in paxtools/PC

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#32

Separate the line from the triangle a bit

Some node and edge properties available in SBGNViz are not actually required by SBGN-ML (e.g. node color). We should persist such properties as well in SBGN-ML similar to other SGBN tools (so we can exchange such properties as well).

From @teheavy on June 24, 2016 17:7

Hi there,

Another warning:
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user's experience.
from sbgnml-to-json-converter.js Line 8

Please fix, thanks!
Fred

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#148

From @ugurdogrusoz on June 16, 2016 11:42

We should display node width and height (both integers) in the inspector and allow editing. We should have a checkbox to lock/unlock aspect ratio. Note that this should not be displayed for compound nodes since their geometry is based on their children. We should talk about whether to keep the center or the upper left corner fixed on dimension changes. Make sure this is part of multiple object selection as well (i.e. support changing dimensions of multiple nodes)

Copied from original issue: iVis-at-Bilkent/sbgnviz.js#139

See iVis-at-Bilkent/cytoscape.js-grid-guide#9