From: <Loraine>, Ann <Ann.Loraine@uncc.edu>
Date: Thursday, June 11, 2015 at 12:59 PM
To: "Norris, David" <dcnorris@uncc.edu>, "nicholas.provart@utoronto.ca" <nicholas.provart@utoronto.ca>, "Loraine, Ann" <Ann.Loraine@uncc.edu>
Cc: "Meyer, Mason" <mmeyer20@uncc.edu>, "Blakley, Ivory" <ieclabau@uncc.edu>, Alison Wu <alison.wu@mail.utoronto.ca>, Richard Song <richardmc.song@mail.utoronto.ca>
Subject: Re: IGB metadata file format?

I created a couple of public Dropboxes for testing the annots.xml files.

Instructions for using a Dropbox “Public” folder to share data via IGBQuickLoad: https://wiki.transvar.org/display/igbman/Set+up+a+Quickload+in+Dropbox

Dropbox Quickload with my edits to the annots.xml: https://dl.dropboxusercontent.com/u/15094167/AnnsEditsAIP (works fine with released version of IGB)

Dropbox Quickload with your original annots.xml, minus the reference to a nonexistent local “DTD” file:

https://dl.dropboxusercontent.com/u/15094167/NicksAIP

Also, to get your data sets to appear in folders, add a “slash” character to the title, as with this annots.xml file:

http://www.igbquickload.org/abiotic/A_thaliana_Jun_2009/annots.xml

Also, an image. See attached.

From: <Norris>, David <dcnorris@uncc.edu>
Date: Thursday, June 11, 2015 at 12:45 PM
To: "nicholas.provart@utoronto.ca" <nicholas.provart@utoronto.ca>, "Loraine, Ann" <Ann.Loraine@uncc.edu>
Cc: "Meyer, Mason" <mmeyer20@uncc.edu>, "Blakley, Ivory" <ieclabau@uncc.edu>, Alison Wu <alison.wu@mail.utoronto.ca>, Richard Song <richardmc.song@mail.utoronto.ca>
Subject: RE: IGB metadata file format?

Hi Nick,

I was able to look at your annots.xml, and can tell you why IGB wasn't able to handle it in the form you were using. You were including a local dtd reference in the xml (i.e. <!DOCTYPE files SYSTEM "bamlocator.dtd">), which caused issues with XML validation. I have corrected this on our development branch, and the upcoming release of IGB will be able to handle the inclusion of an unexpected dtd reference. If you would like to work with the preview version of our upcoming IGB release, you can get a copy from http://test.bioviz.org/igb/index.html. Don't hesitate to reach out directly if you have any additional problems.

Best Regards,
David

From: nicholas.provart@gmail.com [nicholas.provart@gmail.com] on behalf of Nicholas Provart [nicholas.provart@utoronto.ca]
Sent: Thursday, June 11, 2015 12:28 PM
To: Loraine, Ann
Cc: Meyer, Mason; Blakley, Ivory; Norris, David; Alison Wu; Richard Song
Subject: Re: IGB metadata file format?

Hi Ann and Mason,

Were you able to take a look at our annots.xml file and can you tell us why we're not seeing those RNA-seq tracks from iPlant?

Thanks!

Nick

From: <Norris>, David <dcnorris@uncc.edu<dcnorris@uncc.edu>>
Date: Thu 5/28/2015 5:58 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu<Ann.Loraine@uncc.edu>>, "Meyer, Mason" <mmeyer20@uncc.edu<mmeyer20@uncc.edu>>
Subject: RE: IGB metadata file format?

I also fixed the name parsing differences. IGB 8.4.0 now tolerates the remote url format and the relative path format which is more typical on our own servers. The original unmodified quickload site now works as expected on IGB 8.4.0.

From: Loraine, Ann
Sent: Thursday, May 28, 2015 5:08 PM
To: Norris, David; Meyer, Mason
Subject: Re: IGB metadata file format?

OK - agreed. Let’s allow the parser to tolerate any and all unused (by QuickLoad) tags. Let’s not alert the user by showing a popup.

Try accessing QL site

https://dl.dropboxusercontent.com/u/15094167/NicksAIP

Using both 8.4 and 8.3.4.

It has data sets from Arabidopsis.

Main problem is that the annots.xml Nick provided references a DTD file:

java.io.FileNotFoundException: /Applications/Integrated Genome Browser 8.3/bamlocator.dtd (No such file or directory) at java.io.FileInputStream.open0(Native Method) ~[na:1.8.0_40] at java.io.FileInputStream.open(FileInputStream.java:195) ~[na:1.8.0_40] at java.io.FileInputStream.<init>(FileInputStream.java:138) ~[na:1.8.0_40]