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Issue when using xsendfile with galaxy release_16.07

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Issue when using xsendfile with galaxy release_16.07

FredBGA

Hello

 

I’m trying the latest Galaxy (git status gives me : # On branch release_16.07)

 

I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)

apache_xsendfile = True

 

HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv)  is broken on the interface.

 

When I want to preview a txt file :

Not Found

The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server.

 

And apache says :

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:

 

But it looks like this is not really a problem related to access.

Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works.

 

Are you able to reproduce the behavior ?

The same problem occurs on release_16.01.

It’s fine with  the release v15.05 which is my production server right now.

 

Fred

 


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Issue when using xsendfile with galaxy release_16.07

FredBGA

Hello

 

I’m trying the latest Galaxy (git status gives me : # On branch release_16.07)

 

I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)

apache_xsendfile = True

 

HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv)  is broken on the interface.

 

When I want to preview a txt file :

Not Found

The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server.

 

And apache says :

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:

 

But it looks like this is not really a problem related to access.

Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works.

 

Are you able to reproduce the behavior ?

The same problem occurs on release_16.01.

It’s fine with  the release v15.05 which is my production server right now.

 

Fred

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Issue when using xsendfile with galaxy release_16.07

FredBGA

Hello

 

I can still reproduce this issue with release_16.10

 

I’m unable to preview some files (txt, pasted entry) until I have changed their type (ie : to tabular).

 

I’ve switch off the feature but it seems to be better regarding performances so if you could help me to find why it doesn’t work it would be nice.

 

Thank you.

 

Fred

 

De : galaxy-dev [mailto:[hidden email]] De la part de SAPET, Frederic
Envoyé : mercredi 24 août 2016 17:19
À : [hidden email]
Objet : [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

 

Hello

 

I’m trying the latest Galaxy (git status gives me : # On branch release_16.07)

 

I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind a web server proxy, and apply all methods described here : https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)

apache_xsendfile = True

 

HTML, gff3,tabular files are just fine but the preview of some other files (txt, csv)  is broken on the interface.

 

When I want to preview a txt file :

Not Found

The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this server.

 

And apache says :

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file: /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:

 

But it looks like this is not really a problem related to access.

Indeed, from the same file, I switch it from txt to tabular (edit attributes), the preview works.

 

Are you able to reproduce the behavior ?

The same problem occurs on release_16.01.

It’s fine with  the release v15.05 which is my production server right now.

 

Fred

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Issue when using xsendfile with galaxy release_16.07

John Chilton-4
Sorry for the delay in responding - are you sure this is due to a
change in Galaxy and not a configuration difference between your
development and production server?

This line:

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12]
(13)Permission denied: xsendfile: cannot open file:
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer:
http:

Makes it seem like the problem is a Unix permission usage. What are
the permissions for this file?

ls -lsah softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat

It is probably owned by the Galaxy user right? If the user that the
apache server runs as does not match this could definitely explain the
problem. You'll want to make sure that the apache user is the Galaxy
user or more realistically that the apache user belongs to the group
that "owns" those files - perhaps a "galaxy" group. In this second
case - you'll also need to make sure Galaxy files are group readable.

-John



On Tue, Feb 7, 2017 at 11:43 AM, SAPET, Frederic
<[hidden email]> wrote:

> Hello
>
>
>
> I can still reproduce this issue with release_16.10
>
>
>
> I’m unable to preview some files (txt, pasted entry) until I have changed
> their type (ie : to tabular).
>
>
>
> I’ve switch off the feature but it seems to be better regarding performances
> so if you could help me to find why it doesn’t work it would be nice.
>
>
>
> Thank you.
>
>
>
> Fred
>
>
>
> De : galaxy-dev [mailto:[hidden email]] De la
> part de SAPET, Frederic
> Envoyé : mercredi 24 août 2016 17:19
> À : [hidden email]
> Objet : [galaxy-dev] Issue when using xsendfile with galaxy release_16.07
>
>
>
> Hello
>
>
>
> I’m trying the latest Galaxy (git status gives me : # On branch
> release_16.07)
>
>
>
> I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind a web
> server proxy, and apply all methods described here :
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
>
> apache_xsendfile = True
>
>
>
> HTML, gff3,tabular files are just fine but the preview of some other files
> (txt, csv)  is broken on the interface.
>
>
>
> When I want to preview a txt file :
>
> Not Found
>
> The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this
> server.
>
>
>
> And apache says :
>
> [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission
> denied: xsendfile: cannot open file:
> /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:
>
>
>
> But it looks like this is not really a problem related to access.
>
> Indeed, from the same file, I switch it from txt to tabular (edit
> attributes), the preview works.
>
>
>
> Are you able to reproduce the behavior ?
>
> The same problem occurs on release_16.01.
>
> It’s fine with  the release v15.05 which is my production server right now.
>
>
>
> Fred
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Issue when using xsendfile with galaxy release_16.07

FredBGA
Hi John

Thank you for this answer.
You're right, it works now. I think that my apache server was started since a while, without the good user (as root).
By the way I don't understand why it was ok for some type of file and not for others.

Thank you.

Fred

-----Message d'origine-----
De : John Chilton [mailto:[hidden email]]
Envoyé : mardi 7 février 2017 18:56
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

Sorry for the delay in responding - are you sure this is due to a change in Galaxy and not a configuration difference between your development and production server?

This line:

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file:
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer:
http:

Makes it seem like the problem is a Unix permission usage. What are the permissions for this file?

ls -lsah softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat

It is probably owned by the Galaxy user right? If the user that the apache server runs as does not match this could definitely explain the problem. You'll want to make sure that the apache user is the Galaxy user or more realistically that the apache user belongs to the group that "owns" those files - perhaps a "galaxy" group. In this second case - you'll also need to make sure Galaxy files are group readable.

-John



On Tue, Feb 7, 2017 at 11:43 AM, SAPET, Frederic <[hidden email]> wrote:

> Hello
>
>
>
> I can still reproduce this issue with release_16.10
>
>
>
> I’m unable to preview some files (txt, pasted entry) until I have
> changed their type (ie : to tabular).
>
>
>
> I’ve switch off the feature but it seems to be better regarding
> performances so if you could help me to find why it doesn’t work it would be nice.
>
>
>
> Thank you.
>
>
>
> Fred
>
>
>
> De : galaxy-dev [mailto:[hidden email]] De
> la part de SAPET, Frederic Envoyé : mercredi 24 août 2016 17:19 À :
> [hidden email]
> Objet : [galaxy-dev] Issue when using xsendfile with galaxy
> release_16.07
>
>
>
> Hello
>
>
>
> I’m trying the latest Galaxy (git status gives me : # On branch
> release_16.07)
>
>
>
> I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind
> a web server proxy, and apply all methods described here :
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
>
> apache_xsendfile = True
>
>
>
> HTML, gff3,tabular files are just fine but the preview of some other
> files (txt, csv)  is broken on the interface.
>
>
>
> When I want to preview a txt file :
>
> Not Found
>
> The requested URL /datasets/fd1df6a9052810d5/display/ was not found on
> this server.
>
>
>
> And apache says :
>
> [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12]
> (13)Permission
> denied: xsendfile: cannot open file:
> /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:
>
>
>
> But it looks like this is not really a problem related to access.
>
> Indeed, from the same file, I switch it from txt to tabular (edit
> attributes), the preview works.
>
>
>
> Are you able to reproduce the behavior ?
>
> The same problem occurs on release_16.01.
>
> It’s fine with  the release v15.05 which is my production server right now.
>
>
>
> Fred
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Issue when using xsendfile with galaxy release_16.07

FredBGA
In reply to this post by John Chilton-4
Hi,

I forgot to set again apache_xsendfile = True for my last tests,
So it appears that the "real" solution was to deactivate the SELinux mode.

I hope it will help somebody if they run into the same problem.

Fred

-----Message d'origine-----
De : SAPET, Frederic
Envoyé : mercredi 8 février 2017 14:59
À : 'John Chilton' <[hidden email]>
Cc : [hidden email]
Objet : RE: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

Hi John

Thank you for this answer.
You're right, it works now. I think that my apache server was started since a while, without the good user (as root).
By the way I don't understand why it was ok for some type of file and not for others.

Thank you.

Fred

-----Message d'origine-----
De : John Chilton [mailto:[hidden email]] Envoyé : mardi 7 février 2017 18:56 À : SAPET, Frederic <[hidden email]> Cc : [hidden email]
Objet : Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

Sorry for the delay in responding - are you sure this is due to a change in Galaxy and not a configuration difference between your development and production server?

This line:

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission denied: xsendfile: cannot open file:
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer:
http:

Makes it seem like the problem is a Unix permission usage. What are the permissions for this file?

ls -lsah softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat

It is probably owned by the Galaxy user right? If the user that the apache server runs as does not match this could definitely explain the problem. You'll want to make sure that the apache user is the Galaxy user or more realistically that the apache user belongs to the group that "owns" those files - perhaps a "galaxy" group. In this second case - you'll also need to make sure Galaxy files are group readable.

-John



On Tue, Feb 7, 2017 at 11:43 AM, SAPET, Frederic <[hidden email]> wrote:

> Hello
>
>
>
> I can still reproduce this issue with release_16.10
>
>
>
> I’m unable to preview some files (txt, pasted entry) until I have
> changed their type (ie : to tabular).
>
>
>
> I’ve switch off the feature but it seems to be better regarding
> performances so if you could help me to find why it doesn’t work it would be nice.
>
>
>
> Thank you.
>
>
>
> Fred
>
>
>
> De : galaxy-dev [mailto:[hidden email]] De
> la part de SAPET, Frederic Envoyé : mercredi 24 août 2016 17:19 À :
> [hidden email]
> Objet : [galaxy-dev] Issue when using xsendfile with galaxy
> release_16.07
>
>
>
> Hello
>
>
>
> I’m trying the latest Galaxy (git status gives me : # On branch
> release_16.07)
>
>
>
> I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind
> a web server proxy, and apply all methods described here :
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
>
> apache_xsendfile = True
>
>
>
> HTML, gff3,tabular files are just fine but the preview of some other
> files (txt, csv)  is broken on the interface.
>
>
>
> When I want to preview a txt file :
>
> Not Found
>
> The requested URL /datasets/fd1df6a9052810d5/display/ was not found on
> this server.
>
>
>
> And apache says :
>
> [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12]
> (13)Permission
> denied: xsendfile: cannot open file:
> /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:
>
>
>
> But it looks like this is not really a problem related to access.
>
> Indeed, from the same file, I switch it from txt to tabular (edit
> attributes), the preview works.
>
>
>
> Are you able to reproduce the behavior ?
>
> The same problem occurs on release_16.01.
>
> It’s fine with  the release v15.05 which is my production server right now.
>
>
>
> Fred
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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