(Beginner Question) How to set up intelliJ to develop Plugin?

[Erkan Karabulut]

Hello everyone,

I am new at this. I need to develop a plugin because of my internship. I started with the following topics. 

http://wiki.cytoscape.org/Cytoscape_Plugin_Tutorial#Example_Plugins_.28these_do_not_yet_include_the_plugin.props_file.29

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/IntelliJ

At the second one, i tryed to set up intelliJto develop my plugin. But there is no cytoscaper.jar file in cytoscape folder,which is mentioned at the second topic or i could not find it. How can i solve my problem?

[Srikanth Bezawada]

Hi Erkan,

Once you are familiar with Cytoscape software
- Go through app store and find the apps that are open source(Apps are plugins for Cytoscape3+) 
- Open the open source project in your IDE and start making simple changes to the code
- Build the new jar and test it by deploying in Cytoscape

Refactoring an existing project is a good idea to get started with Cytoscape apps.

Thanks,

Srikanth.

On Mon, Jul 3, 2017 at 1:04 PM, Erkan Karabulut <cwsui...@gmail.com> wrote:

Hello everyone,

I am new at this. I need to develop a plugin because of my internship. I started with the following topics. 

http://wiki.cytoscape.org/Cytoscape_Plugin_Tutorial#Example_Plugins_.28these_do_not_yet_include_the_plugin.props_file.29

http://wiki.cytoscape.org/SettingUpEclipseForPluginDevelopment#Running_the_plugin

At the second one, i tryed to set up eclipse to develop my plugin. But there is no cytoscaper.jar file in cytoscape folder,which is mentioned at the second topic or i could not find it. How can i solve my problem?

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[Erkan Karabulut]

Thank you for your respond Srikanth. I will look at these apps definitely. Can you help me to set up IntelliJ for Cytoscape? There is no information at releated page with this.

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/IntelliJ

3 Temmuz 2017 Pazartesi 22:30:24 UTC+3 tarihinde Srikanth yazdı:

Hi Erkan,

Once you are familiar with Cytoscape software
- Go through app store and find the apps that are open source(Apps are plugins for Cytoscape3+) 
- Open the open source project in your IDE and start making simple changes to the code
- Build the new jar and test it by deploying in Cytoscape

Refactoring an existing project is a good idea to get started with Cytoscape apps.

Thanks,

Srikanth.

On Mon, Jul 3, 2017 at 1:04 PM, Erkan Karabulut <cwsui...@gmail.com> wrote:

Hello everyone,

I am new at this. I need to develop a plugin because of my internship. I started with the following topics. 

http://wiki.cytoscape.org/Cytoscape_Plugin_Tutorial#Example_Plugins_.28these_do_not_yet_include_the_plugin.props_file.29

http://wiki.cytoscape.org/SettingUpEclipseForPluginDevelopment#Running_the_plugin

At the second one, i tryed to set up eclipse to develop my plugin. But there is no cytoscaper.jar file in cytoscape folder,which is mentioned at the second topic or i could not find it. How can i solve my problem?

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[Srikanth Bezawada]

Hi Erkan,

I use netbeans but it should be the same for other IDE's.

- Once you have a repo of a Cytoscape app, open it in the IDE using File -> Open Project.   
- Whenever you make the changes needed, click on the build option within IDE to get the jar(available in the target folder) 

Thanks,

Srikanth.

On Tue, Jul 4, 2017 at 4:56 PM, Erkan Karabulut <cwsui...@gmail.com> wrote:

Thank you for your respond Srikanth. I will look at these apps definitely. Can you help me to set up IntelliJ for Cytoscape? There is no information at releated page with this.

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/IntelliJ

3 Temmuz 2017 Pazartesi 22:30:24 UTC+3 tarihinde Srikanth yazdı:

Hi Erkan,

Once you are familiar with Cytoscape software
- Go through app store and find the apps that are open source(Apps are plugins for Cytoscape3+) 
- Open the open source project in your IDE and start making simple changes to the code
- Build the new jar and test it by deploying in Cytoscape

Refactoring an existing project is a good idea to get started with Cytoscape apps.

Thanks,

Srikanth.

On Mon, Jul 3, 2017 at 1:04 PM, Erkan Karabulut <cwsui...@gmail.com> wrote:

Hello everyone,

I am new at this. I need to develop a plugin because of my internship. I started with the following topics. 

http://wiki.cytoscape.org/Cytoscape_Plugin_Tutorial#Example_Plugins_.28these_do_not_yet_include_the_plugin.props_file.29

http://wiki.cytoscape.org/SettingUpEclipseForPluginDevelopment#Running_the_plugin

At the second one, i tryed to set up eclipse to develop my plugin. But there is no cytoscaper.jar file in cytoscape folder,which is mentioned at the second topic or i could not find it. How can i solve my problem?

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[Barry Demchak]

Hi, all –

 

For the best and most reliable starting point for building apps, please see this ladder: http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder

 

Please note that some confusion can arise … “plugin” refers to the Cytoscape 2.x products, while “app” refers to the Cytoscape 3.x products. This is important for anyone developing “plugins” because Cytoscape 2.x is now desupported, as Cytoscape 3.x is 4 years old now. No “plugins” are accepted into the Cytoscape app store … we are happy to have apps, though.

Thanks,

Srikanth.

 

 

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/IntelliJ

Thanks,

Srikanth.

 

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

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[Erkan Karabulut]

I solve my problem. Thanks to everyone.

[eldrvar...@gmail.com]

Guys hello!!

I am also new to the development of cytoscape and relatively new in the development of big projects, but we all have to start from somewhere.

I would like your help in the building of cytoscape in the eclipse IDE because unfortunately the app ladder site is down for the count the last 3 weeks.

For starters I want to build an app for cytoscape.

If you could help me I would appreciate it.

[Barry Demchak]

Hi --

Sorry you're having such trouble with the wiki. Where did you find the link you followed? The reason I ask is that we moved the wiki, and if you see an obsolete link, we'd like to update it.

As for the app ladder, it's alive and well here: https://github.com/cytoscape/cytoscape/wiki/Cytoscape-App-Ladder

As for instructions on building Cytoscape, we can certainly supply what we core developers use, but I'm not sure they'll help you much, as you don't need to compile Cytoscape to create an app (see the App Ladder). Nevertheless, here they are (temporarily, until we can move it to the new wiki): http://wikiold.cytoscape.org/Cytoscape_3/CoreDevelopment

Thanks for your interest in Cytoscape ... we're happy to answer more questions, too. Please consider using cytoscape-app-dev@googlegroups.com for your questions.

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--

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: National Resource for Network Biology (NRNB)
: UC San Diego
: Department of Medicine
: Biomedical Research Facility II, Room 3A15
: http://orcid.org/0000-0001-7065-7786
: Land line: (858) 822-4756, Mobile: (858) 452-8700
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[eldrvar...@gmail.com]

On Saturday, March 24, 2018 at 4:37:51 AM UTC+2, Barry Demchak wrote:
> Hi --
>
>
> Sorry you're having such trouble with the wiki. Where did you find the link you followed? The reason I ask is that we moved the wiki, and if you see an obsolete link, we'd like to update it.
>
>
> As for the app ladder, it's alive and well here: https://github.com/cytoscape/cytoscape/wiki/Cytoscape-App-Ladder
>
>
> As for instructions on building Cytoscape, we can certainly supply what we core developers use, but I'm not sure they'll help you much, as you don't need to compile Cytoscape to create an app (see the App Ladder). Nevertheless, here they are (temporarily, until we can move it to the new wiki): http://wikiold.cytoscape.org/Cytoscape_3/CoreDevelopment
>
>

> Thanks for your interest in Cytoscape ... we're happy to answer more questions, too. Please consider using cytoscap...@googlegroups.com for your questions.

>
>
>
>
> On Fri, Mar 23, 2018 at 6:59 PM, <eldrvar...@gmail.com> wrote:
> Guys hello!!
>
>
>
> I am also new to the development of cytoscape and relatively new in the development of big projects, but we all have to start from somewhere.
>
>
>
> I would like your help in the building of cytoscape in the eclipse IDE because unfortunately the app ladder site is down for the count the last 3 weeks.
>
>
>
> For starters I want to build an app for cytoscape.
>
>
>
> If you could help me I would appreciate it.
>
>
>
> --
>
> You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
>

> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
>
> To post to this group, send email to cytoscape...@googlegroups.com.

>
> Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
>
> To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/b7858b04-5372-4880-9e3d-44bcb7c9bcf1%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
>
> --
>
>
>
>
> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
> : Barry Demchak, PhD
> : National Resource for Network Biology (NRNB)
> : UC San Diego
> : Department of Medicine
> : Biomedical Research Facility II, Room 3A15
> : http://orcid.org/0000-0001-7065-7786
> : Land line: (858) 822-4756, Mobile: (858) 452-8700
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The link I found was from the developers documentation, only days before the cytoscape wiki was taken down, and it is this http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder . I asked now because i cant figure out how to continue.

Thanks for the immediate response.