Re: Can't export svg format file

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Re: Can't export svg format file

Scott Cain
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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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Fwd: Can't export svg format file

Sean Chen

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
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: Can't export svg format file

Scott Cain
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Can't export svg format file

Sean Chen
Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Can't export svg format file

Scott Cain
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
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Re: Can't export svg format file

Sean Chen
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
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: Can't export svg format file

Scott Cain
Hi Xiao,

I am at somewhat of a loss.  I've looked through the GBrowse code and verified that the track delimiter is supposed to be %5E, which is "^", but you have %1E (the \x1e in your URL), which is a control ^.  Do you have any "outside" javascript in the GBrowse page that might be doing this translation for you (to "help")?

One other thing just occurred to me: do you have something other than English set as your browser's preferred language?  If so, please try setting English as the preferred language and try GBrowse again.  I'm wondering if there is a bad interaction between GBrowse's internationalization code and the SVG link generation code.  Actually, before you change your language preferences, go to 


and try making an SVG image there (where I know it works).  If it doesn't work there, it might be the language settings.  If it does work, that is less likely.

Good luck,
Scott


On Wed, May 17, 2017 at 4:20 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Can't export svg format file

Sean Chen
Hi Scott,

It works there, so it might be something wrong with the SVG link generation process. Do you know any way to update or repair the GBrowse safely? Because we don't have a backup for the GBrowse here. Thanks!

Xiao


2017-05-18 10:46 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I am at somewhat of a loss.  I've looked through the GBrowse code and verified that the track delimiter is supposed to be %5E, which is "^", but you have %1E (the \x1e in your URL), which is a control ^.  Do you have any "outside" javascript in the GBrowse page that might be doing this translation for you (to "help")?

One other thing just occurred to me: do you have something other than English set as your browser's preferred language?  If so, please try setting English as the preferred language and try GBrowse again.  I'm wondering if there is a bad interaction between GBrowse's internationalization code and the SVG link generation code.  Actually, before you change your language preferences, go to 


and try making an SVG image there (where I know it works).  If it doesn't work there, it might be the language settings.  If it does work, that is less likely.

Good luck,
Scott


On Wed, May 17, 2017 at 4:20 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Can't export svg format file

Scott Cain
Hi Xiao,

Certainly, reinstalling GBrowse is possible.  What method did you use to install it in the first place?  Chances are you can just do it again, possibly adding a "force" option, and it will just overwrite the existing files.  I rather doubt that will help, but it can't hurt to try.

I imagine there is an outside force working on your GBrowse instance though--javascript or an apache module or the like, but that might be hard to sort out.

Scott


On Thu, May 18, 2017 at 12:36 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

It works there, so it might be something wrong with the SVG link generation process. Do you know any way to update or repair the GBrowse safely? Because we don't have a backup for the GBrowse here. Thanks!

Xiao


2017-05-18 10:46 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I am at somewhat of a loss.  I've looked through the GBrowse code and verified that the track delimiter is supposed to be %5E, which is "^", but you have %1E (the \x1e in your URL), which is a control ^.  Do you have any "outside" javascript in the GBrowse page that might be doing this translation for you (to "help")?

One other thing just occurred to me: do you have something other than English set as your browser's preferred language?  If so, please try setting English as the preferred language and try GBrowse again.  I'm wondering if there is a bad interaction between GBrowse's internationalization code and the SVG link generation code.  Actually, before you change your language preferences, go to 


and try making an SVG image there (where I know it works).  If it doesn't work there, it might be the language settings.  If it does work, that is less likely.

Good luck,
Scott


On Wed, May 17, 2017 at 4:20 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
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Re: Can't export svg format file

Sean Chen
Hi Scott, 

I find that the url can be successfully resolved if I replace the "\x1e" with "%1e" in it. But do you know what would cause this translation problem?

Thanks,
Xiao


2017-05-18 16:34 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Certainly, reinstalling GBrowse is possible.  What method did you use to install it in the first place?  Chances are you can just do it again, possibly adding a "force" option, and it will just overwrite the existing files.  I rather doubt that will help, but it can't hurt to try.

I imagine there is an outside force working on your GBrowse instance though--javascript or an apache module or the like, but that might be hard to sort out.

Scott


On Thu, May 18, 2017 at 12:36 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

It works there, so it might be something wrong with the SVG link generation process. Do you know any way to update or repair the GBrowse safely? Because we don't have a backup for the GBrowse here. Thanks!

Xiao


2017-05-18 10:46 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I am at somewhat of a loss.  I've looked through the GBrowse code and verified that the track delimiter is supposed to be %5E, which is "^", but you have %1E (the \x1e in your URL), which is a control ^.  Do you have any "outside" javascript in the GBrowse page that might be doing this translation for you (to "help")?

One other thing just occurred to me: do you have something other than English set as your browser's preferred language?  If so, please try setting English as the preferred language and try GBrowse again.  I'm wondering if there is a bad interaction between GBrowse's internationalization code and the SVG link generation code.  Actually, before you change your language preferences, go to 


and try making an SVG image there (where I know it works).  If it doesn't work there, it might be the language settings.  If it does work, that is less likely.

Good luck,
Scott


On Wed, May 17, 2017 at 4:20 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: Can't export svg format file

Sean Chen
In another word, can you tell me where the string below is generated? I guess that's where the problem is.

'<a href="http://172.20.26.72/gb2/gbrowse_img/tetmac2014/?name=scf_8254776:369425..379425;l=DNA\x1epredictedgenes\x1emRNA\x1e77803_77804_ATAC_MAC_merged_50_100\x1e77803_77804_ATAC_MAC_merged_120_200\x1eCoverageXyplot11-2\x1e56946_K4me3_2_SDS\x1e56948_K27me3_2_SDS\x1eChIP_SampleA_1\x1e6mA_Qv20\x1echenxiao_CU428;width=1600;id=40e03658eb8531e61ebcd45408337abc;format=PDF;keystyle=between;grid=0;h_feat=ttherm_00495900@yellow">http://172.20.26.72/gb2/gbrowse_img/tetmac2014/?name=scf_8254776:369425..379425;l=DNA\x1epredictedgenes\x1emRNA\x1e77803_77804_ATAC_MAC_merged_50_100\x1e77803_77804_ATAC_MAC_merged_120_200\x1eCoverageXyplot11-2\x1e56946_K4me3_2_SDS\x1e56948_K27me3_2_SDS\x1eChIP_SampleA_1\x1e6mA_Qv20\x1echenxiao_CU428;width=1600;id=40e03658eb8531e61ebcd45408337abc;format=PDF;keystyle=between;grid=0;h_feat=ttherm_00495900@yellow' 


2017-06-05 15:01 GMT-04:00 Sean Chen <[hidden email]>:
Hi Scott, 

I find that the url can be successfully resolved if I replace the "\x1e" with "%1e" in it. But do you know what would cause this translation problem?

Thanks,
Xiao


2017-05-18 16:34 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Certainly, reinstalling GBrowse is possible.  What method did you use to install it in the first place?  Chances are you can just do it again, possibly adding a "force" option, and it will just overwrite the existing files.  I rather doubt that will help, but it can't hurt to try.

I imagine there is an outside force working on your GBrowse instance though--javascript or an apache module or the like, but that might be hard to sort out.

Scott


On Thu, May 18, 2017 at 12:36 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

It works there, so it might be something wrong with the SVG link generation process. Do you know any way to update or repair the GBrowse safely? Because we don't have a backup for the GBrowse here. Thanks!

Xiao


2017-05-18 10:46 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I am at somewhat of a loss.  I've looked through the GBrowse code and verified that the track delimiter is supposed to be %5E, which is "^", but you have %1E (the \x1e in your URL), which is a control ^.  Do you have any "outside" javascript in the GBrowse page that might be doing this translation for you (to "help")?

One other thing just occurred to me: do you have something other than English set as your browser's preferred language?  If so, please try setting English as the preferred language and try GBrowse again.  I'm wondering if there is a bad interaction between GBrowse's internationalization code and the SVG link generation code.  Actually, before you change your language preferences, go to 


and try making an SVG image there (where I know it works).  If it doesn't work there, it might be the language settings.  If it does work, that is less likely.

Good luck,
Scott


On Wed, May 17, 2017 at 4:20 PM, Sean Chen <[hidden email]> wrote:
Hi Scott,

Yes, except exporting SVG, it works normally and can successfully create PNG files. 

Thanks!

Xiao


2017-05-17 11:00 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

It seems like the code that is joining the track identifiers when building the URL is using a control-^ instead of a comma, which is what I would expect it to use.  I'm really not sure what to do about that.  GBrowse works ok besides creating SVGs, right?  Creating an png works?  Perhaps there is some bad interaction between the module that is creating the SVG url and the character set.

Scott




On May 15, 2017, at 5:01 PM, Sean Chen <[hidden email]> wrote:

Hi Scott,

When only one track is open, exporting SVG will lead to automatical downloading of a SVG format file. However, if multiple tracks are open, it will lead to a error page like this:

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

I'm pretty sure it's not the conf file's reason, because the conf files worked normally and were not modified before this problem arose. Is there any possibility that some services related to character resolving are not successfully initiated or the character set is not correct?

Thanks,

Xiao


2017-05-15 16:31 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

Can you clarify what happens if you try to make an SVG of one of the tracks and not the other?  I contend if it does work with one but not both that I even more strongly suggest you have a stray control character in you config file that is messing things up for you.  If that is the case, the easiest way to fix it would be to delete the lines with square brackets in your config file and retype them by hand (that is, not by copy and pasting).  If that doesn't fix it, we can try other things (though off the top of my head, I'm not sure what those other things are).

Scott


On Mon, May 15, 2017 at 4:08 PM, Sean Chen <[hidden email]> wrote:

---------- Forwarded message ----------
From: Sean Chen <[hidden email]>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <[hidden email]>


Hi Scott,

Thanks for your reply! I think the conf file is clean and it always worked well before a reboot of our server several days ago. I also doubt about the "\x1e" is what apache cannot identify, cause there won't be a problem when exporting SVG if only one track is left and other tracks are closed, but I don't know how to fix it.

FYI, here is some information of our tracks.

[CovPE100Tolsample37239EZLKO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37239EZLKO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37239_EZLKOC10_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local

[CovPE100Tolsample37241DCL1KO10]
feature        = coverage
glyph          = wiggle_xyplot
database       = PE100Tolsample37241DCL1KO10
height         = 50
fgcolor        = black
bicolor_pivot  = 20
pos_color      = red
neg_color      = red
key            = sample37241_DCL1KO_Tol
category       = 010.RNA-PE100_Run1105_Strand_specific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label          = 0 # Labels on wiggle tracks are redu
autoscale      = local


Thanks!

Xiao


2017-05-15 13:23 GMT-04:00 Scott Cain <[hidden email]>:
Hi Xiao,

I'm cc'ng this to the GBrowse mailing list, since there are lots of people on the list who have a variety of experiences.

The "invalid characters" part makes me wonder what it might be complaining about. The part of the url that has \x1e seems a little weird: I think it translates to control-^ in ascii, which is probably what apache is complaining about.  Can you identify where that is coming from in your config file (perhaps it is a hidden character in the track key (the part in square brackets)).

Good luck!
Scott


On Mon, May 15, 2017 at 10:43 AM, Sean Chen <[hidden email]> wrote:
Hi,

There is a problem blocking me to export the high-resolution picture as SVG format file, and the error info in the error_log of httpd is attached below:

Thanks!

Xiao


--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
------------------------------------------------------------------------
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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



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



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China



--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse