Discussion:
[Gmod-gbrowse] Can't export svg format file
Scott Cain
2017-05-15 17:23:26 UTC
Permalink
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2.125:64727..
74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE100Tolsample37241DCL1K
O10;width=800;id=40e03658eb8531e61ebcd45408337abc;format=GD::SVG;keystyle=
request, referer: http://172.20.26.72/gb2/gbrowse/mic/
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
Sean Chen
2017-05-15 20:08:46 UTC
Permalink
---------- Forwarded message ----------
From: Sean Chen <***@gmail.com>
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
To: Scott Cain <***@scottcain.net>


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
Post by 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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
Email: ***@gmail.com
--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China
Email: ***@gmail.com
Scott Cain
2017-05-15 20:31:52 UTC
Permalink
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
Sean Chen
2017-05-15 21:01:11 UTC
Permalink
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.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
Email: ***@gmail.com
Scott Cain
2017-05-17 15:00:35 UTC
Permalink
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 <***@gmail.com> 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.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
<(216)%20392-3087>
Ontario Institute for Cancer Research
--
Xiao Chen
Laboratory of Protozoology
Institute of Evolution & Marine Biodiversity
Ocean University of China
Qingdao 266003
China
Email: ***@gmail.com
Sean Chen
2017-05-17 20:20:05 UTC
Permalink
Hi Scott,

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

Thanks!

Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Email: ***@gmail.com
Scott Cain
2017-05-18 14:46:47 UTC
Permalink
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

http://staging.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/#

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
Post by Sean Chen
Hi Scott,
Yes, except exporting SVG, it works normally and can successfully create
PNG files.
Thanks!
Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Sean Chen
2017-05-18 16:36:52 UTC
Permalink
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
Post by 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
http://staging.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/#
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
Post by Sean Chen
Hi Scott,
Yes, except exporting SVG, it works normally and can successfully create
PNG files.
Thanks!
Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Email: ***@gmail.com
Scott Cain
2017-05-18 20:34:48 UTC
Permalink
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
Post by 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
Post by 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
http://staging.wormbase.org/tools/genome/gbrowse/c_elegans_PRJNA13758/#
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
Post by Sean Chen
Hi Scott,
Yes, except exporting SVG, it works normally and can successfully create
PNG files.
Thanks!
Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
http://172.20.26.72/gb2/gbrowse/mic/
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Sean Chen
2017-06-05 19:01:35 UTC
Permalink
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
Post by 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
Post by 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
Post by 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
http://staging.wormbase.org/tools/genome/gbrowse/c_elegans
_PRJNA13758/#
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
Post by Sean Chen
Hi Scott,
Yes, except exporting SVG, it works normally and can successfully
create PNG files.
Thanks!
Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598] [client
10.21.209.31:53434] AH02430: Response header 'Location' value of '
http://172.20.26.72/gb2/gbrowse_img/mic/?name=Supercontig_2
.125:64727..74727;l=CovPE100Tolsample37239EZLKO10\x1eCovPE10
0Tolsample37241DCL1KO10;width=800;id=40e03658eb8531e61ebcd45
408337abc;format=GD::SVG;keystyle=between;grid=1;h_feat=ies1
http://172.20.26.72/gb2/gbrowse/mic/
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 <(216)%20392-3087>
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Email: ***@gmail.com
Sean Chen
2017-06-05 19:07:20 UTC
Permalink
In another word, can you tell me where the string below is generated? I
guess that's where the problem is.

'
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=***@yellow
'
Post by 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
Post by 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
Post by 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
Post by 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
http://staging.wormbase.org/tools/genome/gbrowse/c_elegans
_PRJNA13758/#
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
Post by Sean Chen
Hi Scott,
Yes, except exporting SVG, it works normally and can successfully
create PNG files.
Thanks!
Xiao
Post by 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
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
*Internal Server Error*
The server encountered an internal error or misconfiguration and was
unable to complete your request.
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
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
Post by Sean Chen
---------- Forwarded message ----------
Date: 2017-05-15 13:38 GMT-04:00
Subject: Re: Can't export svg format file
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_s
pecific_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_s
pecific_C10_RNA_Seq_Tol_mapped_reads_including_multiple_mapping
label = 0 # Labels on wiggle tracks are redu
autoscale = local
Thanks!
Xiao
Post by 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
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
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
[Fri May 12 15:08:00.170967 2017] [http:error] [pid 26598]
[client 10.21.209.31:53434] AH02430: Response header 'Location'
value of 'http://172.20.26.72/gb2/gbrow
se_img/mic/?name=Supercontig_2.125:64727..74727;l=CovPE100To
lsample37239EZLKO10\x1eCovPE100Tolsample37241DCL1KO10;width=
800;id=40e03658eb8531e61ebcd45408337abc;format=GD::SVG;keyst
http://172.20.26.72/gb2/gbrowse/mic/
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 <(216)%20392-3087>
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
<(216)%20392-3087>
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
<(216)%20392-3087>
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
Email: ***@gmail.com
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