Possible bug on "Create a collection of paired datasets"

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Possible bug on "Create a collection of paired datasets"

Ata Roudgar

Hi,

I am a computer cluster admin and I am trying to install
galaxy on our cluster. I used galaxy-release_15.05 and
because we need to serve Galaxy at a sub directory, e.g.
irida-galaxy I modified the options prefix and cookie_path
in the galaxy configuration file as follow:

prefix = /irida-galaxy
filter-with = proxy-prefix
cookie_path = /irida-galaxy

We use apache as an interface with the Following
configuration:

<Proxy http://localhost:9010>
     Order deny,allow
     Allow from all
</Proxy>

RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R]
RewriteRule ^/irida-galaxy/static/style/(.*)
/home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/irida-galaxy/static/scripts/(.*)
/home/irida/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/irida-galaxy/static/(.*)
/home/irida/galaxy-dist/static/$1 [L]
#RewriteRule ^/irida-galaxy/favicon.ico
/home/irida/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/irida-galaxy/robots.txt
/home/irida/galaxy-dist/static/robots.txt [L]
RewriteRule ^/irida-galaxy(.*) <a href="http://localhost:9010$1">http://localhost:9010$1 [P]


Everything works fairly good. Now I want to create a Dataset
Pairs. first I uploads some fastaq files, e.g.,

a_1.fastaq
a_2.fastaq
b_1.fastaq
b_2.fastaq
c_1.fastaq
c_2.fastaq

then I choose: "Build List of Dataset Pairs" (See Fig-1
attached)

There is a window appears on my screen with the
title: Create a collection of paired datasets. Now I am
able to choose a name and save the paired collection.
However, once I click on "Create list" buttons I receive a
error message on top of the windows:

"An error occurred While creating this collection: Not found

See Fig-2 attached. To be able to search the cause of error
I turn on the "Browser Consul" on my web browser and notice
that the error is related to the following web form post:


https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/dataset_collections


Which makes sense because such address do not exist. The
address should be

https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c25989/contents/dataset_collections

So the prefix (irida-galaxy) is missing before
/api/histories...../dataset_collection

Is it a bug or am I missing something?

Please note that such error does not appear when I do not
use prefix in my galaxy configration.

Thanks for your time,
Cheers,
Ata


----
Ata Roudgar
Research Computing
WestGrid Site
IT Services
Simon Fraser University
Burnaby, British Columbia
Canada  V5A 1S6

phone: 778 782-8860
fax:   778 782-4242
___________________________________________________________
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/

Fig-2.jpg (216K) Download Attachment
Fig-1.jpg (215K) Download Attachment
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Re: Possible bug on "Create a collection of paired datasets"

Carl Eberhard
Hi, Ata Roudgar

It is indeed a bug. Thank you very much for the excellent and *helpful* report!

We now have a fix for this on the release_15.05 branch of the github repository:

It should fix the issue but please let us know if it doesn't. Sorry for the trouble.


On Fri, Jul 3, 2015 at 3:46 PM, Ata Roudgar <[hidden email]> wrote:

Hi,

I am a computer cluster admin and I am trying to install galaxy on our cluster. I used galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g. irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file as follow:

prefix = /irida-galaxy
filter-with = proxy-prefix
cookie_path = /irida-galaxy

We use apache as an interface with the Following configuration:

<Proxy http://localhost:9010>
    Order deny,allow
    Allow from all
</Proxy>

RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R]
RewriteRule ^/irida-galaxy/static/style/(.*) /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/irida-galaxy/static/scripts/(.*) /home/irida/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L]
#RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L]
RewriteRule ^/irida-galaxy(.*) http://localhost:9010$1 [P]


Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some fastaq files, e.g.,

a_1.fastaq
a_2.fastaq
b_1.fastaq
b_2.fastaq
c_1.fastaq
c_2.fastaq

then I choose: "Build List of Dataset Pairs" (See Fig-1 attached)

There is a window appears on my screen with the title: Create a collection of paired datasets. Now I am able to choose a name and save the paired collection. However, once I click on "Create list" buttons I receive a error message on top of the windows:

"An error occurred While creating this collection: Not found

See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul" on my web browser and notice that the error is related to the following web form post:


https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/dataset_collections


Which makes sense because such address do not exist. The address should be

https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c25989/contents/dataset_collections

So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection

Is it a bug or am I missing something?

Please note that such error does not appear when I do not use prefix in my galaxy configration.

Thanks for your time,
Cheers,
Ata


----
Ata Roudgar
Research Computing
WestGrid Site
IT Services
Simon Fraser University
Burnaby, British Columbia
Canada  V5A 1S6

phone: <a href="tel:778%20782-8860" value="+17787828860" target="_blank">778 782-8860
fax:   <a href="tel:778%20782-4242" value="+17787824242" target="_blank">778 782-4242
___________________________________________________________
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: Possible bug on "Create a collection of paired datasets"

Ata Roudgar

Hi Carl,

Yes, the problem is fixed. Thank you very much. Just in
case, I see that galaxy-release-15.05 is now free of this
bug but galaxy-release-15.07 has this bug again.

Cheers,
Ata


On Wednesday 2015-07-15 07:54, Carl Eberhard wrote:

>Date: Wed, 15 Jul 2015 07:54:05
>From: Carl Eberhard <[hidden email]>
>To: Ata Roudgar <[hidden email]>
>Cc: Galaxy Dev List <[hidden email]>,
>    Martin Siegert <[hidden email]>, Matthew Laird <[hidden email]>,
>    Franklin Bristow <[hidden email]>
>Subject: Re: [galaxy-dev] Possible bug on
>    "Create a collection of paired datasets"
>
>Hi, Ata Roudgar
>It is indeed a bug. Thank you very much for the excellent and *helpful* report!
>
>We now have a fix for this on the release_15.05 branch of the github repository:
>https://github.com/galaxyproject/galaxy/commit/13a40b3ef206f8662a49dfd06fbbc05b026f8c64
>
>It should fix the issue but please let us know if it doesn't. Sorry for the trouble.
>
>
>On Fri, Jul 3, 2015 at 3:46 PM, Ata Roudgar <[hidden email]> wrote:
>
>      Hi,
>
>      I am a computer cluster admin and I am trying to install galaxy on our cluster. I used
>      galaxy-release_15.05 and because we need to serve Galaxy at a sub directory, e.g.
>      irida-galaxy I modified the options prefix and cookie_path in the galaxy configuration file
>      as follow:
>
>      prefix = /irida-galaxy
>      filter-with = proxy-prefix
>      cookie_path = /irida-galaxy
>
>      We use apache as an interface with the Following configuration:
>
>      <Proxy http://localhost:9010>
>          Order deny,allow
>          Allow from all
>      </Proxy>
>
>      RewriteRule ^/irida-galaxy$ /irida-galaxy/ [R]
>      RewriteRule ^/irida-galaxy/static/style/(.*)
>      /home/irida/galaxy-dist/static/june_2007_style/blue/$1 [L]
>      RewriteRule ^/irida-galaxy/static/scripts/(.*)
>      /home/irida/galaxy-dist/static/scripts/packed/$1 [L]
>      RewriteRule ^/irida-galaxy/static/(.*) /home/irida/galaxy-dist/static/$1 [L]
>      #RewriteRule ^/irida-galaxy/favicon.ico /home/irida/galaxy-dist/static/favicon.ico [L]
>      RewriteRule ^/irida-galaxy/robots.txt /home/irida/galaxy-dist/static/robots.txt [L]
>      RewriteRule ^/irida-galaxy(.*) <a href="http://localhost:9010$1">http://localhost:9010$1 [P]
>
>
>      Everything works fairly good. Now I want to create a Dataset Pairs. first I uploads some
>      fastaq files, e.g.,
>
>      a_1.fastaq
>      a_2.fastaq
>      b_1.fastaq
>      b_2.fastaq
>      c_1.fastaq
>      c_2.fastaq
>
>      then I choose: "Build List of Dataset Pairs" (See Fig-1 attached)
>
>      There is a window appears on my screen with the title: Create a collection of paired
>      datasets. Now I am able to choose a name and save the paired collection. However, once I
>      click on "Create list" buttons I receive a error message on top of the windows:
>
>      "An error occurred While creating this collection: Not found
>
>      See Fig-2 attached. To be able to search the cause of error I turn on the "Browser Consul"
>      on my web browser and notice that the error is related to the following web form post:
>
>
>      https://newrobson.westgrid.ca:8444/api/histories/4936629215c25989/contents/dataset_collections
>
>
>      Which makes sense because such address do not exist. The address should be
>
>https://newrobson.westgrid.ca:8444/irida-galaxy/api/histories/4936629215c25989/contents/dataset_collec
>      tions
>
>      So the prefix (irida-galaxy) is missing before /api/histories...../dataset_collection
>
>      Is it a bug or am I missing something?
>
>      Please note that such error does not appear when I do not use prefix in my galaxy
>      configration.
>
>      Thanks for your time,
>      Cheers,
>      Ata
>
>
>      ----
>      Ata Roudgar
>      Research Computing
>      WestGrid Site
>      IT Services
>      Simon Fraser University
>      Burnaby, British Columbia
>      Canada  V5A 1S6
>
>      phone: 778 782-8860
>      fax:   778 782-4242
>      ___________________________________________________________
>      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/
>
>
>
>
----
Ata Roudgar
Research Computing
WestGrid Site
IT Services
Simon Fraser University
Burnaby, British Columbia
Canada  V5A 1S6

phone: 778 782-8860
fax:   778 782-4242
___________________________________________________________
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/