Galaxy SNPEff Display Bug (2nd Independent Report)
Hi Pablo, About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy – we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418 The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable. I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken too…. -John
This was addressed in 6788:e58a87c91bc4. The reason for the initial change that's causing these display issues was to eliminate potential XSS vulnerabilities. There's now a configuration option (sanitize_all_html, which is True by default) for local instances where you can disable the extra html sanitization. -Dannon On Mar 8, 2012, at 10:33 AM, John David Osborne wrote:
Hi Pablo,
About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy – we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418
The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable.
I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken too….
-John
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Very helpful, thank you! I don't see this option in universe_wsgi.ini, but hopefully I will when we update our galaxy. Thanks! -John On 3/8/12 9:53 AM, "Dannon Baker" <dannonbaker@me.com> wrote:
This was addressed in 6788:e58a87c91bc4. The reason for the initial change that's causing these display issues was to eliminate potential XSS vulnerabilities. There's now a configuration option (sanitize_all_html, which is True by default) for local instances where you can disable the extra html sanitization.
-Dannon
On Mar 8, 2012, at 10:33 AM, John David Osborne wrote:
Hi Pablo,
About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418
The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable.
I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken tooŠ.
-John
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello Dannon, Thanks for resolving the issue of snpEff HTML display. It's working well with the new changeset. But the gene file link in the bottom (dataset_*.dat.genes.txt) is still in broken state, says "could not find file". Any update on this? -Raj -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John David Osborne Sent: Thursday, March 08, 2012 9:34 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu; David K Crossman; Pablo; Shantanu@lists.bx..psu.edu Subject: Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report) Very helpful, thank you! I don't see this option in universe_wsgi.ini, but hopefully I will when we update our galaxy. Thanks! -John On 3/8/12 9:53 AM, "Dannon Baker" <dannonbaker@me.com> wrote:
This was addressed in 6788:e58a87c91bc4. The reason for the initial change that's causing these display issues was to eliminate potential XSS vulnerabilities. There's now a configuration option (sanitize_all_html, which is True by default) for local instances where you can disable the extra html sanitization.
-Dannon
On Mar 8, 2012, at 10:33 AM, John David Osborne wrote:
Hi Pablo,
About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418
The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable.
I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken tooŠ.
-John
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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participants (3)
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Dannon Baker -
John David Osborne -
Praveen Raj Somarajan