Import dataset from table- not working

[Konika Chawla]

HI

I am trying to follow the tutorial

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:ExpressionAnalysisGenMAPP-CS#Import_your_data

but on clicking the select file button after choosing the 'importdataset from table ' in dropdown box, nothing happens.

I got only the beta version for download from http://www.genmapp.org/beta/genmappcs/download.html  for unix.

Do we have another version?

Thanks

Konika

[Kristina Hanspers]

Hi Konika,

I can't reproduce this problem, and you are the first to report it. Do
you get any messages in Help>Error Console?

The only thing I can recommend is to reinstall the program.

Regards,

Kristina

On Mar 23, 3:30 am, Konika Chawla <komus...@gmail.com> wrote:
> HI

> I am trying to follow the tutorialhttp://opentutorials.cgl.ucsf.edu/index.php/Tutorial:ExpressionAnalys...

> but on clicking the select file button after choosing the 'importdataset
> from table ' in dropdown box, nothing happens.

> I got only the beta version for download fromhttp://www.genmapp.org/beta/genmappcs/download.html for unix.

[Arka Pattanayak]

I had the same problem.
The following (as suggested by Alex Pico) worked:

"I don’t recommend using web service connections anyways, so I’d focus
on getting the local installation to work. Your screenshot shows the
proper steps to attaching the Hs derby file. You’re saying that after
clicking “Open” in the final dialog that the database is not shown
under Sources of ID mapping>Databases? If that’s the case, then
something is terribly wrong and when things go terribly wrong in
GenMAPP-CS (or Cytoscape), there is one solution: delete
your .genmappcs directory found in your User directory. Then restart
GenMAPP-CS and try those steps again.

- Alex"

- Arka P

On Mar 23, 6:30 am, Konika Chawla <komus...@gmail.com> wrote:
> HI

> I am trying to follow the tutorialhttp://opentutorials.cgl.ucsf.edu/index.php/Tutorial:ExpressionAnalys...

> but on clicking the select file button after choosing the 'importdataset
> from table ' in dropdown box, nothing happens.

> I got only the beta version for download fromhttp://www.genmapp.org/beta/genmappcs/download.html for unix.

[Ed Siefker]

I can confirm this problem. There don't appear to be
any relevant messages in the Error Console or
on STDOUT. There are errors on startup, but
not when I try to import a dataset. I'll attach
it to this message just in case it's helpful.

I am using GenMAPP-CS_0_2-beta_unix.sh
on Debian Sid i686.

I can't figure out how to attach files with this
google groups stuff, so I've uuencoded it.
Sorry.





On Mar 23, 3:21 pm, Kristina Hanspers <khansp...@gladstone.ucsf.edu>
wrote:

[Ed Siefker]

I made a video demonstrating this behavior. 
I removed everything GenMapp installs, installed
it from scratch and 'load dataset from file' still
refuses to do anything at all.

You can see this bug for yourself if you download
the video found here: http://temp-share.com/show/2gFHKrnx8

[Chunming]

Hi,
I met the same problem when I tried to import a .bridge file into
"Sources of ID mapping" follow the tutorial by nothing happened after
I selected the file.
I reinstall the Genmapp-cs but it still don't work.

[Alexander Pico]

Just to clarify, "reinstalling" GenMAPP-CS is different from deleting your
.genmappcs directory. The later is the recommended fix.

1. Go to your user directory.
2. Locate .genmappcs (it's a hidden folder so you might need to use command
line)
3. Delete it.
4. Restart GenMAPP-CS (no need to reinstall)

- Alex

[Ed Siefker]

It's been a year and a half, and this problem still exists.  I can reproduce it on both Debian Sid and RHEL6.
This is from an entirely clean install.  "import dataset from table" still does not work.  Can someone please
help me with this? 

I've posted a video showing the error on youtube:  http://www.youtube.com/watch?v=7Bm-qmkYa94
As you can see, GenMAPP simply does nothing when I select "import dataset" from the dropdown.
The error console shows nothing that appears relevant.  Still, i've zipped the error log and attached
it to this message. 

I have absolutely no clue how to get this to work.  Any advice would be greatly appreciated. 

[Kristina Hanspers]

Hi Ed,

Did you try what Alex suggested previously: delete your .genmappcs directory found in your User directory. Then restart GenMAPP-CS and try those steps again. 

Let me know if that works.

Kristina

[Alexander Pico]

Otherwise, we'll have to chalk this one up to unique OS+Java issue. Java applications are less and less "platform independent" these days. Unfortunately, GenMAPP-CS development is complete and no longer funded, so we won't be able to pursue a fix to this (if there is one).

I can recommend Cytoscape and PathVisio as alternative free and open source tools in network biology.

 - Alex

----------------------------------------
Alexander Pico, PhD
NRNB Executive Director
Bioinformatics Assoc. Director
Gladstone Institutes

http://nrnb.org

http://gladstoneinstitutes.org
----------------------------------------

--
You received this message because you are subscribed to the Google Groups "GenMAPP" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genmapp+u...@googlegroups.com.
To post to this group, send email to gen...@googlegroups.com.
Visit this group at http://groups.google.com/group/genmapp.
For more options, visit https://groups.google.com/groups/opt_out.

[Ed Siefker]

Yes, if you watch the video, those lines are clearly visible in the console before I install:

ebs15242@biox:~$ rm -rf /usr/local/GenMAPP-CS_v0.2beta/
ebs15242@biox:~$ rm -rf ~/.genmappcs/
ebs15242@biox:~$ rm -rf GenMAPP-CS-Data/
ebs15242@biox:~$ wget http://www.genmapp.org/beta/genmappcs/download/GenMAPP-CS_0_2-beta_unix.sh

[Alexander Pico]

Great video. This wass the first time we received a youtube bug report. It's really helpful! Here's a video reply:

http://youtu.be/ds39XMBgiTE

I suspect an OS+Java-specific error is occurring. You'll have to launch the application from the .sh file (rather than the executable) from command line to get error messages to display in the console.

 - Alex