[Gmod-ajax] Non-apache web server and failing plugin

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[Gmod-ajax] Non-apache web server and failing plugin

Scott Cain
Hi All,

I've got a strange situation where a plugin that works just fun when being served from apache fails to load when being served from a non-apache web server (it's Amazon's S3 web server, whatever that is).  The JBrowse version is 1.12.1-dev.  The problematic plugin at the moment is the MotifSearch plug in I wrote:


and is working fine at WormBase:


However, when I serve it up from AWS S3, I get an error that looks like this:


dojo.js:1821
Error: scriptError at makeError (dojo.js:106) at HTMLScriptElement.<anonymous> (dojo.js:1656)

Any idea what that's about?

If you'd like to see JBrowse running properly (without the plug) on S3, it's here:


and with the failing plugin (and a much longer error string), it's here:


Finally, I should note that I think there are other plugins that fail in a similar way (like the NeatFeature ones) but I deactivated all the plugins and then turned them on one by one looking for a solution.

Thanks for any suggestions you might have,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                  scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Non-apache web server and failing plugin

Scott Cain
Hi All,

It seems the script I wrote to copy files up to S3 was magically missing the MotifSearch plugin, so now it almost works.  It fails now because it assumes that the sequence files are on the same server as the JBrowse javascript files, which was probably an assumption I made when writing the plugin without thinking about it.*  Unfortunately in this case, that assumption is incorrect and all of the track, sequence and name data are in a separate S3 bucket.  Thanks to Colin for pointing out the obvious :-)

Scott

*there's probably even an appropriate API for fetching sequence data that I wrote around without realizing it and had I used the proper API, I wouldn't have this problem now.

On Thu, Apr 27, 2017 at 10:22 AM, Scott Cain <[hidden email]> wrote:
Hi All,

I've got a strange situation where a plugin that works just fun when being served from apache fails to load when being served from a non-apache web server (it's Amazon's S3 web server, whatever that is).  The JBrowse version is 1.12.1-dev.  The problematic plugin at the moment is the MotifSearch plug in I wrote:


and is working fine at WormBase:


However, when I serve it up from AWS S3, I get an error that looks like this:


dojo.js:1821
Error: scriptError at makeError (dojo.js:106) at HTMLScriptElement.<anonymous> (dojo.js:1656)

Any idea what that's about?

If you'd like to see JBrowse running properly (without the plug) on S3, it's here:


and with the failing plugin (and a much longer error string), it's here:


Finally, I should note that I think there are other plugins that fail in a similar way (like the NeatFeature ones) but I deactivated all the plugins and then turned them on one by one looking for a solution.

Thanks for any suggestions you might have,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                  scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: Non-apache web server and failing plugin

Scott Cain
And, as an aside, it seems that the FeatureSequence plugin makes the same erroneous assumptions: I have it turned on for the "Curated Genes (protein coding)" track on 


and it throws an error similar to what the MotifSearch plugin throws. :-/



On Thu, Apr 27, 2017 at 10:56 AM, Scott Cain <[hidden email]> wrote:
Hi All,

It seems the script I wrote to copy files up to S3 was magically missing the MotifSearch plugin, so now it almost works.  It fails now because it assumes that the sequence files are on the same server as the JBrowse javascript files, which was probably an assumption I made when writing the plugin without thinking about it.*  Unfortunately in this case, that assumption is incorrect and all of the track, sequence and name data are in a separate S3 bucket.  Thanks to Colin for pointing out the obvious :-)

Scott

*there's probably even an appropriate API for fetching sequence data that I wrote around without realizing it and had I used the proper API, I wouldn't have this problem now.

On Thu, Apr 27, 2017 at 10:22 AM, Scott Cain <[hidden email]> wrote:
Hi All,

I've got a strange situation where a plugin that works just fun when being served from apache fails to load when being served from a non-apache web server (it's Amazon's S3 web server, whatever that is).  The JBrowse version is 1.12.1-dev.  The problematic plugin at the moment is the MotifSearch plug in I wrote:


and is working fine at WormBase:


However, when I serve it up from AWS S3, I get an error that looks like this:


dojo.js:1821
Error: scriptError at makeError (dojo.js:106) at HTMLScriptElement.<anonymous> (dojo.js:1656)

Any idea what that's about?

If you'd like to see JBrowse running properly (without the plug) on S3, it's here:


and with the failing plugin (and a much longer error string), it's here:


Finally, I should note that I think there are other plugins that fail in a similar way (like the NeatFeature ones) but I deactivated all the plugins and then turned them on one by one looking for a solution.

Thanks for any suggestions you might have,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                  scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: Non-apache web server and failing plugin

Saari, Travis

Scott,

 

I think this has to do with the server not allowing cross-site XMLHTTPrequests, which I think is usually the default for security reasons. I’m not sure if this can be changed for an S3 server, but it might be worth looking into. I used refSeqStore.getReferenceSequence() to grab the sequence for the FeatureSequence plugin, which to my knowledge is the standard way of doing it; the same method is used in the View Details default dialog if I remember correctly. Hopefully others can chime in to back up/refute/offer suggestions for the issue.

 

Best,

 

 

Travis

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, April 27, 2017 10:39 AM
To: [hidden email]
Subject: Re: [Gmod-ajax] Non-apache web server and failing plugin

 

And, as an aside, it seems that the FeatureSequence plugin makes the same erroneous assumptions: I have it turned on for the "Curated Genes (protein coding)" track on 

 

 

and it throws an error similar to what the MotifSearch plugin throws. :-/

 

 

 

On Thu, Apr 27, 2017 at 10:56 AM, Scott Cain <[hidden email]> wrote:

Hi All,

 

It seems the script I wrote to copy files up to S3 was magically missing the MotifSearch plugin, so now it almost works.  It fails now because it assumes that the sequence files are on the same server as the JBrowse javascript files, which was probably an assumption I made when writing the plugin without thinking about it.*  Unfortunately in this case, that assumption is incorrect and all of the track, sequence and name data are in a separate S3 bucket.  Thanks to Colin for pointing out the obvious :-)

 

Scott

 

*there's probably even an appropriate API for fetching sequence data that I wrote around without realizing it and had I used the proper API, I wouldn't have this problem now.

 

On Thu, Apr 27, 2017 at 10:22 AM, Scott Cain <[hidden email]> wrote:

Hi All,

 

I've got a strange situation where a plugin that works just fun when being served from apache fails to load when being served from a non-apache web server (it's Amazon's S3 web server, whatever that is).  The JBrowse version is 1.12.1-dev.  The problematic plugin at the moment is the MotifSearch plug in I wrote:

 

 

and is working fine at WormBase:

 

 

However, when I serve it up from AWS S3, I get an error that looks like this:

 


dojo.js:1821
Error: scriptError at makeError (dojo.js:106) at HTMLScriptElement.<anonymous> (dojo.js:1656)

 

Any idea what that's about?

 

If you'd like to see JBrowse running properly (without the plug) on S3, it's here:

 

 

and with the failing plugin (and a much longer error string), it's here:

 

 

Finally, I should note that I think there are other plugins that fail in a similar way (like the NeatFeature ones) but I deactivated all the plugins and then turned them on one by one looking for a solution.

 

Thanks for any suggestions you might have,

Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                  scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Check out the vibrant tech community on one of the world's most
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Re: Non-apache web server and failing plugin

Scott Cain
Hi Travis and all,

It turns out that I'm somewhat of an idiot. :-)  When I was setting up JBrowse, I copied all of my track config files from my WormBase config files, and then used a perl one liner to update all of the urlTemplate entries.  Worked great, at least for all of the "regular" tracks.  Not so much with the DNA track: I didn't notice that it wasn't updated, so when I copied all of the files up to S3, it was configured to still look on the "current" server for the DNA residues rather than the data S3 bucket like I was convinced was the case.  Sorry for implying that there was bugginess associated with your and other code associated with sequence!

So, to be clear, I think everything is working fine now with http://agrjbrowsestatic.s3-website-us-east-1.amazonaws.com/

Thanks,
Scott


On Thu, Apr 27, 2017 at 1:33 PM, Saari, Travis <[hidden email]> wrote:

Scott,

 

I think this has to do with the server not allowing cross-site XMLHTTPrequests, which I think is usually the default for security reasons. I’m not sure if this can be changed for an S3 server, but it might be worth looking into. I used refSeqStore.getReferenceSequence() to grab the sequence for the FeatureSequence plugin, which to my knowledge is the standard way of doing it; the same method is used in the View Details default dialog if I remember correctly. Hopefully others can chime in to back up/refute/offer suggestions for the issue.

 

Best,

 

 

Travis

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, April 27, 2017 10:39 AM
To: [hidden email]
Subject: Re: [Gmod-ajax] Non-apache web server and failing plugin

 

And, as an aside, it seems that the FeatureSequence plugin makes the same erroneous assumptions: I have it turned on for the "Curated Genes (protein coding)" track on 

 

 

and it throws an error similar to what the MotifSearch plugin throws. :-/

 

 

 

On Thu, Apr 27, 2017 at 10:56 AM, Scott Cain <[hidden email]> wrote:

Hi All,

 

It seems the script I wrote to copy files up to S3 was magically missing the MotifSearch plugin, so now it almost works.  It fails now because it assumes that the sequence files are on the same server as the JBrowse javascript files, which was probably an assumption I made when writing the plugin without thinking about it.*  Unfortunately in this case, that assumption is incorrect and all of the track, sequence and name data are in a separate S3 bucket.  Thanks to Colin for pointing out the obvious :-)

 

Scott

 

*there's probably even an appropriate API for fetching sequence data that I wrote around without realizing it and had I used the proper API, I wouldn't have this problem now.

 

On Thu, Apr 27, 2017 at 10:22 AM, Scott Cain <[hidden email]> wrote:

Hi All,

 

I've got a strange situation where a plugin that works just fun when being served from apache fails to load when being served from a non-apache web server (it's Amazon's S3 web server, whatever that is).  The JBrowse version is 1.12.1-dev.  The problematic plugin at the moment is the MotifSearch plug in I wrote:

 

 

and is working fine at WormBase:

 

 

However, when I serve it up from AWS S3, I get an error that looks like this:

 


dojo.js:1821
Error: scriptError at makeError (dojo.js:106) at HTMLScriptElement.<anonymous> (dojo.js:1656)

 

Any idea what that's about?

 

If you'd like to see JBrowse running properly (without the plug) on S3, it's here:

 

 

and with the failing plugin (and a much longer error string), it's here:

 

 

Finally, I should note that I think there are other plugins that fail in a similar way (like the NeatFeature ones) but I deactivated all the plugins and then turned them on one by one looking for a solution.

 

Thanks for any suggestions you might have,

Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                  scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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