BridgeDb not working in Cytoscape 3.8.0?

Question

BridgeDb not working in Cytoscape 3.8.0?

remizallot opened this issue 5 years ago · 11 comments

Hi,
I would like to report that BridgeDB seems to not work with Cytoscape 3.8.0 on PC.

I just installed the latest version of Cytoscape 3.8.0 on Windows 10.
At the first Cytoscape launch, I installed BridgeDB using the Cytoscape app manager.

In the "Currently installed" tab of Cytoscape, BridgeDb 1.1.0.2 status is "Failed to Start".

Thanks you!

Answer 1 · 2020-04-20T14:18:32.000Z

@AlexanderPico, can you plz have a look at this?

Answer 2 · 2020-08-12T05:50:34.000Z

@remizallot, I am not an expert in Cytoscape (I use it about once a year actively), but understood the BridgeDb functionality is now core part of the Cytoscape and I am not sure if the BridgeDb app gives functionality that the core does not already. This is why I pinged Alex, but he seems to have missed this ping or simply not had time. @mkutmon, do you know if the BridgeDb app should be used with Cytoscape 3.8?

Answer 3 · 2020-08-12T18:42:23.000Z

Here! Sorry for the delay.

Right. My first question would be what are you trying to do? Most BridgeDb functionality is now built-in and the app is not needed at all. The app hasn't been touched in 6 years! I might just remove it from the app store...

Answer 4 · 2020-08-13T10:18:41.000Z

Hello, Alexander, please do not delete the BridgeDB app. Some Cyotscape users (like me) prefer to use older versions (pre 3.6). I have been told that what I have been doing with BridgeDB is Cytoscape can now be done directly in newer versions of Cytoscape. I have not tried it yet. There is information in the Cytoscape user manual about that ( http://manual.cytoscape.org/en/stable/Node_and_Edge_Column_Data.html). I have used BridgeDB in Cytoscape to map specific attributes to specific node IDs. We are speaking about adding attributes for 10 of thousands of nodes at a time, from a tab formatted file that are automatically generated. On that page (https://efi.igb.illinois.edu/training/videos.php), you can hear me in the video "Adding Custom Node Attributes to a SSN" that explains how I use Cytoscape and BridgeDB, on a small scale. I am available and open to answer questions, if needed. Best regards, Remi Zallot Le mer. 12 août 2020 à 19:42, Alexander Pico <notifications@github.com> a écrit :

…

Here! Sorry for the delay. Right. My first question would be what are you trying to do? Most BridgeDb functionality is now built-in and the app is not needed at all. The app hasn't been touched in 6 years! I might just remove it from the app store... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#151 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACSDWAGRGAAIT6M7F37ZS73SALPDFANCNFSM4MMON6ZA> .

Answer 5 · 2020-08-21T22:24:11.000Z

Ok. App is marked "inactive" on the App Store so no one tries to download it in it's current, broken state. We need to find a Java developer interested in updating the old codebase. Might be simple; might be complicated. Hard to know at this stage. If we can upload an updated/working version the app, then we can mark it as "active" again.

The active/inactive state in the App Store does not affect your ability to continue using older verions.

Answer 6 · 2020-08-21T22:27:18.000Z

ping @mkutmon, is this something "we" can pick up? I've never done it, and I would insist on continuous integration and easy release making.

Answer 7 · 2020-09-04T09:02:37.000Z

Hello, it looks like the BridgeDB app is not present in the app store any more. This means that there is no way anymore to map IDs for earlier versions of Cytoscape. Is it possible to reinstate BridgeDB to be active on the App Store? Otherwise, would it be possible me to obtain a copy so that I can manually install it if needed? Thank you Le ven. 21 août 2020 à 23:27, Egon Willighagen <notifications@github.com> a écrit :

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ping @mkutmon <https://github.com/mkutmon>, is this something "we" can pick up? I've never done it, and I would insist on continuous integration and easy release making. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#151 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACSDWADQZKFFDPDVYVNGSPTSB3YFFANCNFSM4MMON6ZA> .

Answer 8 · 2020-11-22T17:18:37.000Z

@Chris-Evelo, is this something Lucas could look at?

Answer 9 · 2020-11-22T21:58:27.000Z

I submitted a fixed version of the app on Sept 10th.
http://apps.cytoscape.org/apps/bridgedb

Answer 10 · 2020-11-23T08:07:37.000Z

Oh, sorry, I missed that!

Answer 11 · 2020-11-23T09:13:21.000Z

About Lucas, he will write usage recipes for all the different implementations of BridgeDb which we will ask you to review. Of course, that might mean that he can stumble on more things that are no longer working.