How to select nodes using bingo outpu table - cytoscape

I'm making enrichment analysis with Bingo app. When I select category in tabular output and click "select nodes" nothing happens.
Does anyone know how to fix it.
I'm using Ubuntu 20.04.5 LTS with Cytoscape 3.9.1 and java-11-openjdk-amd64 and Bingo 3.0.5.

The nodes are selected in the original network, not in the BiNGO network. Also note that selecting the category doesn't actually enable the selection of nodes within that category. You need to check the box at the far left, then you can use the select nodes button.
-- scooter

Related

Configure Graylog dashboard widget to link to query

I'm using a system that recently upgraded to Graylog3. In Graylog 2 dashboard widgets it was easy to click a button that looked like a "Play" triangle to dive into a query.
In Graylog 3 the widget looks like the image below and none of the options I've clicked on seem to get to the underlying query. If I edit the widget I can see the query and then go recreate it manually, but I just want a "one click" way to get to the underlying data so I can dig into it.
There is play button in graylog widgets from version 3.2.3
https://docs.graylog.org/en/3.2/pages/changelog.html#graylog-3-2-3

Neo4j - web interface database info says "no node labels in database" when my nodes have labels

I imported a graph database into neo4j where the node files had labels assigned in the headers, as the manual instructed. When I use the web interface, the database details tab says there are no labels in my database though. When I run queries involving node labels, everything seems to work. Has anybody else run into this issue?
Try reloading the browser page. The displayed Node labels are not updated dynamically.

Neo4j 2.0.1 graphstyle.grass stylesheet issue

I've somehow managed to import a bad/malformed graphstyle.grass file and now nothing gets displayed in the new (http://< server >:7474/browser/) graph view. In the table view I can see the nodes, so I know the query is hitting (I'm just using 'match n return n limit 25').
So here's where the rub comes.. because the nodes aren't showing up.. I can't click on them to open the properties where I could say 'View Stylesheet' and hit load default or import a fixed stylesheet. I poked around Neo4j files a bit to see if graphstyle.grass was stored within the files but didn't find anything. Any help is greatly appreciated because I ^think^ the nuclear option is reinstalling the server (which isn't a huge deal but trying to avoid that if I can).
Assuming you're on chrome browser. Press F12 to open web developer, tab Resources, Local storage and remove all the stuff from <server>:7474.
Other browser should offer a similar way.

Change Or Delete Label with Cypher in Neo4j

In a Test, I made many types of nodes and relationships with Cypher syntax.
After all, I delete all of unneccessary nodes and their relations.
Actually, there are Types and Labels still there in my Browser
Are there any method to clear Or change name of unneccessary Type, Label with Neo4j and Cypher..??
Best regards
All the information is stored in the browser local storage. So If you are using chrome browser, once you are in localhost:7474/browser. right click your mouse and select "Inspect Element", this will open a chrome developer tool, then go to Resources and under resources, go to "Local Storage", you should see "http: //localhost:7474". select it. and select the key neo4j.grass, you can modify the value, by copying out and copying it back. or you can just delete the whole record (key and value) and close your browser. Open your browser again. start clicking on the labels. you will only see the labels you want. You can repeat this to clean up until neo4j come out with a better way.
if you are using firefox, you can install firebug, and click on the firebug then dom then local storage. then you can do the similar thing
for other browser I am sure that you can figure out ways(google) to clear the local storage
This cypher query deletes all nodes and relationships:
start n=node(*) match n-[r?]-() delete n, r;
You can customize it adding index or asking if it has attributes:
start n=node:users(':') match n-[r?]-() delete n, r;
If you've removed the labels from all nodes you should be able to get a clean result visualization stream by clearing your web browser's cache/cookies. This will not remove them from the info bar on your left, only from the graph vis. frame. Since labels and relationship types are database global constructs, unlike properties, they can exist in the database also after all their instances have been deleted. That may be the intended behavior, but I would expect there to also be a way to remove them completely from the database when 2.0 is released (if there isn't a way already that I've missed). If you want a clean start you can always stop your server, delete your database directory, and restart the server. You may still have to clear your browser or you may see ghost labels from your old database still haunt your visualization stream.
Searching for a removed label, I found that they are still left in data/graph.db/neostore.labeltokenstore.db.names, wh.
Remove nodes you don't want, backup DB, purge DB data dir, stop / start server, reinsert DB, enjoy.
I tried following on both Firefox and Chromium and it didn't work:
removing all nodes of types I no longer used
clearing localStorage neo4j.grass key - it does contain labels, but this doesn't help
clearing whole localStorage (completely)
stopping / killing server and bringing it back after points above
removing files with labels in their names from DB data dir
removing all neo4j cookies (in fact, later, whole browser cache as well)
Since purging DB and reinserting data worked, and since clearing local storage and launching another browser gets you same labels you had, I'm guessing the info is held partially in localStorage AND partially in files in graph.db dir (or however your DB dir is called). Files there are often binary, so I picked redoing whole DB (since it wasn't big anyway) over blind edits or decoding binaries - simply faster.
EDIT:
You may try something I've just spotted:
label > properties > view Stylesheet > click on drop icon (looks like extinguisher). This should drop the grass key.
You may need to have at least one node of given type for that, to open a view where you actually set up node display (colors and other properties) to get to it's stylesheet.

Can I hide selected area/iteration nodes in TFS 2010?

In order to make sure that obsolete versions of the product aren't selected for a work item's iteration, I would like to be able to cloak certain iteration nodes from view, when opening a new work item.
For example, if the current production version of my site is 3.5, and 3.6 and 4.0 are in development, I want to make sure that when a user creates a new work item, versions that are older than 3.5 (e.g. 3.4, 2.7) will not be selectable.
I can conceive of a way to do this creating a custom control, but I'd like to avoid those, as they'd require development of both desktop and web controls, and would have to be deployed to all users.
Any ideas, directions, or just an "it can't be done", would be appreciated.
Thanks,
Assaf.
I am not sure if you can hide it as a selection.
However you can set the security for "Edit work items in this node" to deny and they will not be able to save workitems with the area or iteration selected.
I'm 90% sure it can't be done.
I haven't tried this myself:
Along the line of access control, I believe if you deny "View this node" permission on a user then she will not be able to see this node at all. Be aware that she will probably not be able to see the work items that are under this node, but I guess you are fine with that.
Another thing to note is that this solution might not work with Administrators (because if all Administrators are denied view permission and cannot see the area path then it's lost forever).

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