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MapMan Bugs

HELP!! I can't use it!

HELP!! I can't use it!
Answer
9/12/06 5:01 AM
>emoticon

Hello everybody.
After I download mapman and had a file MapManInst.exe in the hard disk, I run it and got another executive file ImageAnnotator.exe. I think this is the right one, right?
But the problem was when I run this file, it always said:
"It seems to me that this is your first go.
Say YES to install the newest pathways and mappings from the MapManStore!"
If I choose cancle, it would quit.
If I choose yes, it would connet for a while, and then failed, just told me:
"Error installing!:
Error checking for update:java.net.ConnectException: Connection timed out: connect"
And quit too!!

Is there anybody know what happened? Please told me!

Re: HELP!! I can't use it!
Answer
9/12/06 8:43 AM as a reply to Dear bigbigice.
Hi,

were you connected to the intenet when installing the pathways?

Cheers,
Björn

Re: HELP!! I can't use it!
Answer
9/12/06 2:31 PM as a reply to Dear bigbigice.
yes!
I always connected to the internet, I am sure.
Have you ever met the same problem?

Re: HELP!! I can't use it!
Answer
9/13/06 6:56 AM as a reply to Dear bigbigice.
maybe you have a problem with your firewall or virus detection.
The program needs an internet connection to download the most up to date pathways, mappings and sample data sets.
You would need to allow the program to make an internet connection to a web server.

To get the program running without the downloads you would need to have a basic configuration file within your documents and settings\<username> directory if you are on a windows system.

It must be named '.ImageAnnotator.xml ' be aware of the starting dot!!

Its content as followed:

<?xml version="1.0" encoding="ISO-8859-1"?>

<ImageAnnotatorConfiguration>
</ImageAnnotatorConfiguration>



Having that file would allow you to start MapMan without any pathways and mappings installed, you could than try to manually download the pathways through the menu.


It would be nice to know on what operating system you are trying to get it working. Concerning the firewall and or virus protection problem you might consult your administrator.

Re: HELP!! I can't use it!
Answer
9/13/06 7:31 PM as a reply to Dear bigbigice.
Hi! Axel,
Thanx very much for your kind reply and suggestion but it's a pity it also didn't work. Poor me!
Could you plx introduce some other software for the pathways analysis? Especially for plants except Arabidopsis.
I have a cDNA library in hand but I don't know how to cluster the gene in an efficient way.
Thanx again!

Re: HELP!! I can't use it!
Answer
9/14/06 8:01 AM as a reply to Dear bigbigice.
A little more information about what went wrong and what you were able to achieve might fix the problem. Especially the operating system!!.

I would rather guess that the problem is with some firewall issues.
You would need to allow the MapMan software to make the internet connection.

If you would rather not want to do that we could set up the necessary files (pathways and mappings) on the website for manual download.
That was already on our schedule for the next time.

Re: HELP!! I can't use it!
Answer
9/14/06 9:49 AM as a reply to Dear bigbigice.
Well, you are really responsible!
MY operation system is window XP home edition, and I have a Norton Symantec antivirus in the system. I also have a firewall from XP but I closed it every time when I run the Mapman. And I allow it to connect to interne, but the situation was just as I described before, it prompted that:
"Error installing!:
Error checking for update:java.net.ConnectException: Connection timed out: connect" ???
I doubted that it’s the java’s problem, although I downloaded the 17.4M one which includes Java VM. So I downloaded some advanced java program from Sun's Java web site. But it’s in vain.
I really don’t know what happened! I downloaded another software called Genmapp, which could be used. But I still need Mapman for it’s more helpful to me.
Best regards,
Thanks a lot!

Re: HELP!! I can't use it!
Answer
9/14/06 9:53 AM as a reply to Dear bigbigice.
Well~ Dear Axel,
Do you think you can send necessary files to my mailbox?
;) emoticon

Re: HELP!! I can't use it!
Answer
9/14/06 9:59 AM as a reply to Dear bigbigice.
Give me half a day and we will have the current files upon the web so you will not have the problems with filled up mailboxes and others can go there as well.
I f I understood you correct, you managed to get mapman runnig with the small .ImageAnnotator.xml I suggested ?!
So you have the chance to get the pathways and mappings in there manually.

Re: HELP!! I can't use it!
Answer
9/14/06 10:13 AM as a reply to Dear bigbigice.
It would be nice if you could help as tracking down the problem.
You could try to query the following url from your web browser:

http://gabi.rzpd.de/database/java-bin/MappingDownloader?Mode=ListPathways

It will retrieve a gzipped file containing an xml list of all available mappings.

It is one of the urls which are used internally by the program to communicate with the MapManStore server.

many it's so far ;-)

Re: HELP!! I can't use it!
Answer
9/14/06 10:14 AM as a reply to Dear bigbigice.
Oh, no. Sorry, I forgot it!
I can't find the .ImageAnnotator.xml at all. It's ImageAnnotator.exe instead. :emoticon
So I don't have chance to get it? :-[
Half a day? OK! Thanks for your hard work!

Re: HELP!! I can't use it!
Answer
9/14/06 10:22 AM as a reply to Dear bigbigice.
The .ImageAnnotator.xml resides within your
C:/documents and settings/<username>

folder AFTER the first successfull start. So we just fake it:

So you create the .ImageAnnotator.xml file using a text editor with the following content there.

<?xml version="1.0" encoding="ISO-8859-1"?>

<ImageAnnotatorConfiguration>
<pathway_list name="Pathways:"></pathway_list>
<mapping_list></mapping_list>
</ImageAnnotatorConfiguration>


p.s.: update the xml structure

Re: HELP!! I can't use it!
Answer
9/14/06 10:40 AM as a reply to Dear bigbigice.
I also thought of it.
But I don't know how to make a xml file. Which program I can use to make it?
When I open other xml file, it's show in IE.

Re: HELP!! I can't use it!
Answer
9/14/06 10:44 AM as a reply to Dear bigbigice.
I will send it to you as email. we might put it on the website as well.

Re: HELP!! I can't use it!
Answer
9/14/06 10:54 AM as a reply to Dear bigbigice.
vielen Dank !
My mail address is email <removed for privacy, no need to get spammed>

Re: HELP!! I can't use it!
Answer
9/14/06 3:41 PM as a reply to Dear bigbigice.
It needs another half day for the pathways and mappings to be downloadable from our website,
sorry

Re: HELP!! I can't use it!
Answer
9/14/06 3:58 PM as a reply to Dear bigbigice.
That's all right.emoticon emoticon

Re: HELP!! I can't use it!
Answer
9/15/06 7:20 AM as a reply to Dear bigbigice.
here is the download url:

http://gabi.rzpd.de/database/java-bin/MappingDownloader

hopefully you can access that. It's the same that the MapMan application uses internally to retrieve the pathways and mappings.

Re: HELP!! I can't use it!
Answer
9/15/06 8:41 AM as a reply to Dear bigbigice.
Thanks for your hard work!
It's really a big job.
I have downloaded them already.
But I think maybe some compressed files including them would be more easier.

Now I will try to use them.
emoticon
emoticon

Re: HELP!! I can't use it!
Answer
9/15/06 9:06 AM as a reply to Dear bigbigice.
We would need to keep an archive up to date or to create it on the fly.As usually those files can be accessed by the MapMan software directly I will hope it works.

Maybe in your case, your network firewall (within your local network or the great on e :-( ) stopps the request. But as I just read that sends connection reset requests (hmm, I'am not really wanting to go into that detail).

We might need to work on letting the request from MapMan show up as some firefox browser. But that is only guesswork.
The list of available mappings and pathways is created dynamically from our central storage, so you will find updates and new pathways there as well.

hopefully it was worse the trouble to get it installed :-)

RE: HELP!! I can't use it!
Answer
5/30/24 2:03 PM as a reply to Dear bigbigice.
Hello! If you could record a video of your screen, it would be much clearer what your problem is. You can find out how to record a clip on your PC and do it.
Then perhaps I can help you, because most likely I have encountered a similar problem.