vital-ai vital-cytoscape issues

vital-ai / vital-cytoscape

vital endpoint plugin for cytoscape

http://vital.ai

Apache License 2.0

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issues

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Bump pax logging version to clear log4shell vulnerability

#31 AlexanderPico closed 2 years ago
4
canceling an expansion should kill the underlying query (vitalservice issue)

#30 hadfield opened 8 years ago
0
selecting zero edges in edge filter tree breaks future queries (with edges selected) (same may be true for nodes)

#29 hadfield opened 8 years ago
0
canceling an expansion never cancels

#28 hadfield closed 8 years ago
1
with a connection to prime, use ontology nodes/edges for path expansion filtering from prime

#27 hadfield opened 8 years ago
0
cytoscape: (only the case of a single node) expanding a single node to put results (that are not already in the graph) in a circular pattern around the source node. (i.e. layout of new nodes/edges)

#26 hadfield opened 8 years ago
0
cytoscape plugin error: $VITAL_HOME: /Users/hadfield/Local/vitalhome Checking vital singleton... fileinstall-/Users/hadfield/CytoscapeConfiguration/3/apps/installed ERROR [ai.vital.vitalsigns.VitalSigns] - Cannot change log level, it may be run in osgi container with a log4j v2 library No signature of method: org.apache.log4j.Logger.setLevel() is applicable for argument types: (org.apache.log4j.Level) values: [WARN]

#25 hadfield opened 8 years ago
0
cytoscape plugin to have contextual menu to open a link of an objects URI which would direct to aspen-dw and bring up a webview of the object (essentially a "details" screen with all properties/values listed, which also allows editing of the object).

#24 hadfield opened 8 years ago
0
full stacktrace of cytoscape exception

#23 hadfield opened 8 years ago
2
layout after a query to only consider new nodes

#22 hadfield opened 8 years ago
0
listen to cache flush events and reload objects as needed, triggering an update in the visualization (for example, the node may change color).

#21 hadfield opened 8 years ago
0
Contextual Menu item Vital AI --> Add --> Node (when no object is selected) to add a new Vital Node object with a generated URI. (item is local, not saved to server)

#20 hadfield opened 8 years ago
0
Contextual Menu Item Vital AI --> Add --> Edge (only available when exactly two nodes are selected). Adds a new Vital Edge object to the graph connecting the two nodes, generating a new URI. (item is local, not saved to server)

#19 hadfield opened 8 years ago
0
use visual style to differentiate between nodes/edges saved in the service vs ones that are not. different color? (unlink would then change the color of unlinked nodes/edges)

#18 hadfield opened 8 years ago
0
Paths to have drop-down parameter for "Direction" with values "Both", "Outgoing", "Incoming". The "Expand Nodes" method and the "Find Paths" method use this parameter. (Default is "Both")

#17 hadfield opened 8 years ago
0
Save/Refresh/Delete/Unlink) functionality added into data table (able to save/refresh/delete/unlink nodes/edges from data table)

#16 hadfield opened 8 years ago
0
contextual menu item for Refresh (gets server-side version, which may be newer)

#15 hadfield opened 8 years ago
0
contextual menu item for "Find Paths". two or more nodes need to be selected. Uses Depth Parameter for finding depth 1 or depth 2 paths (and Direction parameter for edge direction). For each pair of selected nodes (M x N pairs), find connecting paths (of maximum depth according to depth parameter). (depth 1 is direct connection from A to B. depth 2 is A to X to B.)

#14 hadfield opened 8 years ago
0
in side panel "Connection" tab, segment selected (via a drop-down), which chooses where new items will be stored. existing items will be stored in their current segment upon a modification (an update).

#13 hadfield opened 8 years ago
0
contextual menu item for save

#12 hadfield opened 8 years ago
0
contextual menu item for Delete

#11 hadfield opened 8 years ago
0
contextual menu function to save selected graph objects to service

#10 hadfield opened 8 years ago
0
contextual menu item for unlink

#9 hadfield opened 8 years ago
0
data table -- can we add new buttons along the top? these would be for the "vital" cases like adding a new column associated with a vital property

#8 hadfield opened 8 years ago
0
display all available properties (including core ones) in the node or edge table? any downside?

#7 hadfield opened 8 years ago
0
add "Query" as top level tab (between Paths and DataScripts) providing: segment selector (same as Paths), radio button to select a builder-file or a text area for a builder query (like on DataScripts), text area for builder query, button for "Query". Results to appear in a pop-up in a table, with selecting a row showing the details of the row. a button to add all results to a graph (selected from drop-down), or adding the selection (multiple rows) to the graph. results displayed paged with next/previous buttons.

#6 hadfield opened 8 years ago
0
data table (table below the graph visualization) will be used to edit info. verify it works as expected -- i.e. adding columns to add a new property, etc. adding a new property (column) to include type-ahead to choose from properties that exist in ontology (might not be possible to modify column pop-up). display these columns in a separate color so you can see which columns match up to ontology properties.

#5 hadfield opened 8 years ago
0
deleting the value of a cell in the data table removes that property for the object

#4 hadfield opened 8 years ago
0
query filters for node & edge type support for local (non-prime) endpoints

#3 hadfield opened 8 years ago
0
segment lists refresh, test for changed list when tab changes or every N seconds

#2 hadfield opened 8 years ago
0
connect query filters for edge and node types

#1 hadfield opened 8 years ago
0