Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

[Peter Cock]

See: https://trello.com/c/YBK8ZPFb/

Hopefully one of the Galaxy team can take a look.

Peter

On Wed, Oct 21, 2015 at 3:48 PM, Marco Ocana  wrote:
> Thanks for you help Peter.
> I have reported the problem using the built in Galaxy reporting tool from
> one of my failed jobs.
> I also created a Trello bug submission.
>
> Regards,
>
> Marco
>
> On Wed, Oct 21, 2015 at 10:15 AM, Peter Cock 
> wrote:
>>
>> Thanks Marco,
>>
>> OK, that seems to still be part of the Galaxy core:
>>
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/tools/genomespace/genomespace_importer.xml
>>
>> I think you need to file a bug with the main GitHub repository (or
>> Trello).
>>
>> Looking at genomespace_importer.xml I don't see how the hidden URL
>> parameter is used, but I would still guess it just needs a  tag
>> to to allow the percent sign for any URL-encoded characters to be passed.
>>
>> Peter
>>
>> On Wed, Oct 21, 2015 at 3:01 PM, Marco Ocana 
>> wrote:
>> > Hi Peter,
>> >
>> > I am getting the metadata for the tool from:
>> >
>> > https://usegalaxy.org/api/tools/genomespace_importer
>> >
>> > Thanks
>> >
>> > Marco
>> >
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[galaxy-dev] issue with install_tool_shed_repositories.py

[Steve.Mcmahon]

Hi,

We are doing a puppet configuration for our Galaxy service and this includes 
installing tools with the "install_tool_shed_repositories.py" script.  It seems 
that when we specify a revision for a tool which is not the latest we get an 
error

e.g.

/usr/bin/python 
/OSM/galaxy/tools/galaxy-dev-03/galaxy-dist/scripts/api/install_tool_shed_repositories.py
 --api x -l http://localhost --url http://toolshed.g2.bx.psu.edu/ 
-o devteam --name fasta_nucleotide_changer --tool-deps --repository-deps -r 
2f868bfbe9de --panel-section-id NGS_QC
HTTP Error 500: Internal Server Error
{"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}

Has anyone seen this?  Shall I create an issue in Trello for it?

Our work around is to use the latest revision.  We'd probably like to not have 
to do that, however.

Cheers.
Steve McMahon
Solution Architect and Senior System Administrator | Scientific Computing
Information Management and Technology
CSIRO
T +61 2 6214 2968 Alt +61 4 0077 9318
steve.mcma...@csiro.au | www.csiro.au
1 Wilf Crane Crescent, Yarralumla ACT 2600

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Re: [galaxy-dev] Tools that make datasets

[Peter van Heusden]

These names have meaning in CollectedDatasetMatch:

designation means designation if that exists else name
name means name
dbkey means dbkey
ext means ext
visible means visible


On 21 October 2015 at 08:44, Steve Cassidy  wrote:

> Thanks, yes that works, though I'm not really sure what the difference is
> between __name__ and __designation__. They both seem to have the same
> effect in my example.
>
> Thanks for your help.
>
> Steve
>
>
> On 21 October 2015 at 16:49, Peter van Heusden  wrote:
>
>> Since you're using a directory, you can use one of the built in patterns:
>>
>> DEFAULT_EXTRA_FILENAME_PATTERN = 
>> r"primary_DATASET_ID_(?P[^_]+)_(?P[^_]+)_(?P[^_]+)(_(?P[^_]+))?"
>>
>> NAMED_PATTERNS = {
>> "__default__": DEFAULT_EXTRA_FILENAME_PATTERN,
>> "__name__": r"(?P.*)",
>> "__designation__": r"(?P.*)",
>> "__name_and_ext__": r"(?P.*)\.(?P[^\.]+)?",
>> "__designation_and_ext__": r"(?P.*)\.(?P[^\._]+)?",
>> }
>>
>> In terms of docs, I don't know what the future is - the Galaxy wiki or 
>> http://galaxy.readthedocs.org/en/master/
>>
>>
>> On 21 October 2015 at 04:26, Steve Cassidy 
>> wrote:
>>
>>> Ah, thankyou, yes, I can now get results by using patterns to match the
>>> output.  I used your example but prepend 'simple' to the filename and then
>>> searches for that with:
>>>
>>> 
>>> this solves the problem for the sample script but not generally since in
>>> general I can't predict the filenames that will be generated - this is a
>>> tool for downloading data from a repository which could be text, audio or
>>> video data.
>>>
>>> If I don't use the 'simple' prefix and omit the file extension I still
>>> get my data but I also get three other files which are temporary scripts
>>> generated by galaxy and placed in the working directory.  So, back to
>>> trying to put things in a subdirectory. It turns out that the issue I was
>>> having was as you pointed out earlier, the directory attribute to
>>> discover_datasets doesn't allow variables, so I need to write to a fixed
>>> directory name:
>>>
>>> 
>>> This now works!
>>>
>>> I had thought that I'd need to use a unique directory name but since
>>> galaxy runs each job in a separate directory, this isn't required.  My real
>>> tool now works too after following the same pattern.
>>>
>>> Thanks for your help.  I'll see if I can write this up in a blog post.
>>>
>>> Steve
>>>
>>>
>>>
>>> On 21 October 2015 at 00:06, Peter van Heusden  wrote:
>>>
 I poked around at your tool XML and the code a bit and the problem is
 directory="$job_name". Galaxy expects to collect files from the job's
 working directory - basically the current working directory the job runs
 in. The directory= argument doesn't have variables expanded as far as I can
 tell. In any event it is used in walk_over_extra_files() that is in
 lib/galaxy/tools/parameters/output_collect.py - if you look there you see
 that it is simply appended to the job's working directory.

 So if you use:

 

 (note the  and  - this is effectively the regexp
 r"(?P.*)\.txt" with the < and > escaped out)

 And alter the code so that it just writes files to the current
 directory, then you'll pick up the files one.txt, two,txt and three.txt.

 Peter

 On 20 October 2015 at 12:28, Steve Cassidy 
 wrote:

> Sorry, it was just an example of a tool that works - the file that it
> writes out is put into that directory, so I assume that's where my files
> should end up too.
>
> Steve
>
> On 20 October 2015 at 21:12, Peter van Heusden 
> wrote:
>
>> Sorry, I don't understand - what does the Upload File tool have to do
>> with this?
>>
>> On 20 October 2015 at 11:49, Steve Cassidy 
>> wrote:
>>
>>> Yes, I'm sure that's where the problem lies. Writing out to the
>>> current directory doesn't work.  The files get written to
>>> 'job_working_directory/000/1/' but if I run the Upload File tool the 
>>> result
>>> is placed in 'files/000/'.  I think I need to work out where to write 
>>> the
>>> files, I found some references to $__new_file_path__ but that doesn't 
>>> seem
>>> to help.
>>>
>>> Steve
>>>
>>>
>>>
>>> On 20 October 2015 at 19:57, Peter van Heusden 
>>> wrote:
>>>
 I suspect that the problem might be in the 
 then. I'm not an export on this, but "__name_and_ext__" turns into the
 regexp r"(?P.*)\.(?P[^\.]+)?" in
 lib/galaxy/tools/parameters/output_collect.py, and is used by the
 DatasetCollector (line 358). This looks like it should match the 
 filenames
 you're creating, but I'm not 100% sure how that code works. One thing I
 

[galaxy-dev] external authentication - empty REMOTE_USER

[Floreline TOUCHARD]

Hi,

I've got an issue with my external authentication configuration. I use
Apache and the mod_perl

modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS
accounts.

I have the authentication form  when I try to access galaxy web page.
But after a successful authentication it seems that the REMOTE_USER
variable is not passed to my galaxy instance. I'm connected under "@
example.org" regardless of the authentication account. That's why I think
the REMOTE_USER passed to Galaxy is not 'null' but empty.

I tested the value of the variable with the following php script:

 $key_value) {
print $key_name . " = " . $key_value . "";

}

?>

I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.

I don't understand where my problem lies.



Here is my galaxy.conf file :

Listen 2208




RewriteEngine on
DocumentRoot "/path/to/static"


   

Options +Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all


AuthType Basic
AuthName "Authentifiez vous"
PerlAuthenHandler Apache2::AuthenNIS
PerlAuthzHandler Apache2::AuthzNIS
PerlSetVar AllowAlternateAuth no
require valid-user


   


RewriteEngine on
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
RequestHeader set REMOTE_USER %{RU}e



   RewriteRule ^/galaxy$ /galaxy/ [R]
   RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
[L]
   RewriteRule ^/static/scripts/(.*)
/softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1

[L]
   RewriteRule ^/static/(.*) /path/to/static/$1 [L]
   RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
   RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
   RewriteRule ^(.*) http://localhost:2209$1 [P]





Thanks in advance !

F.T
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Ryan G]

I just recently submitted a patch that will display all the environment 
variables being passed to Galaxy in pastor.log.  That should help you determine 
if the variables are set and to what. 


Please excuse any typos -- Sent from my iPhone

> On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD 
>  wrote:
> 
> Hi,
> 
> I've got an issue with my external authentication configuration. I use Apache 
> and the mod_perl
> 
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS 
> accounts.
> 
> I have the authentication form  when I try to access galaxy web page. 
> But after a successful authentication it seems that the REMOTE_USER variable 
> is not passed to my galaxy instance. I'm connected under "@example.org" 
> regardless of the authentication account. That's why I think the REMOTE_USER 
> passed to Galaxy is not 'null' but empty.
> 
> I tested the value of the variable with the following php script:
> 
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
> 
> }
> 
> ?>
> 
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
> 
> I don't understand where my problem lies.
> 
>  
> 
> Here is my galaxy.conf file :
> 
> Listen 2208
> 
> 
> 
> 
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
> 
>
> 
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
> 
> 
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
> 
> 
>
> 
> 
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
> 
> 
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*) 
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
> 
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
> 
> 
> 
> 
> 
> Thanks in advance !
> 
> F.T
> 
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
> 
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Re: [galaxy-dev] Tools that make datasets

[Steve Cassidy]

A brief writeup of my experiences:

http://web.science.mq.edu.au/~cassidy/wordpress/2015/10/21/galaxy-tool-generating-datasets/

Steve

On 21 October 2015 at 18:27, Peter van Heusden  wrote:

> These names have meaning in CollectedDatasetMatch:
>
> designation means designation if that exists else name
> name means name
> dbkey means dbkey
> ext means ext
> visible means visible
>
>
> On 21 October 2015 at 08:44, Steve Cassidy 
> wrote:
>
>> Thanks, yes that works, though I'm not really sure what the difference is
>> between __name__ and __designation__. They both seem to have the same
>> effect in my example.
>>
>> Thanks for your help.
>>
>> Steve
>>
>>
>> On 21 October 2015 at 16:49, Peter van Heusden  wrote:
>>
>>> Since you're using a directory, you can use one of the built in patterns:
>>>
>>> DEFAULT_EXTRA_FILENAME_PATTERN = 
>>> r"primary_DATASET_ID_(?P[^_]+)_(?P[^_]+)_(?P[^_]+)(_(?P[^_]+))?"
>>>
>>> NAMED_PATTERNS = {
>>> "__default__": DEFAULT_EXTRA_FILENAME_PATTERN,
>>> "__name__": r"(?P.*)",
>>> "__designation__": r"(?P.*)",
>>> "__name_and_ext__": r"(?P.*)\.(?P[^\.]+)?",
>>> "__designation_and_ext__": r"(?P.*)\.(?P[^\._]+)?",
>>> }
>>>
>>> In terms of docs, I don't know what the future is - the Galaxy wiki or 
>>> http://galaxy.readthedocs.org/en/master/
>>>
>>>
>>> On 21 October 2015 at 04:26, Steve Cassidy 
>>> wrote:
>>>
 Ah, thankyou, yes, I can now get results by using patterns to match the
 output.  I used your example but prepend 'simple' to the filename and then
 searches for that with:

 
 this solves the problem for the sample script but not generally since
 in general I can't predict the filenames that will be generated - this is a
 tool for downloading data from a repository which could be text, audio or
 video data.

 If I don't use the 'simple' prefix and omit the file extension I still
 get my data but I also get three other files which are temporary scripts
 generated by galaxy and placed in the working directory.  So, back to
 trying to put things in a subdirectory. It turns out that the issue I was
 having was as you pointed out earlier, the directory attribute to
 discover_datasets doesn't allow variables, so I need to write to a fixed
 directory name:

 
 This now works!

 I had thought that I'd need to use a unique directory name but since
 galaxy runs each job in a separate directory, this isn't required.  My real
 tool now works too after following the same pattern.

 Thanks for your help.  I'll see if I can write this up in a blog post.

 Steve



 On 21 October 2015 at 00:06, Peter van Heusden  wrote:

> I poked around at your tool XML and the code a bit and the problem is
> directory="$job_name". Galaxy expects to collect files from the job's
> working directory - basically the current working directory the job runs
> in. The directory= argument doesn't have variables expanded as far as I 
> can
> tell. In any event it is used in walk_over_extra_files() that is in
> lib/galaxy/tools/parameters/output_collect.py - if you look there you see
> that it is simply appended to the job's working directory.
>
> So if you use:
>
> 
>
> (note the  and  - this is effectively the regexp
> r"(?P.*)\.txt" with the < and > escaped out)
>
> And alter the code so that it just writes files to the current
> directory, then you'll pick up the files one.txt, two,txt and three.txt.
>
> Peter
>
> On 20 October 2015 at 12:28, Steve Cassidy 
> wrote:
>
>> Sorry, it was just an example of a tool that works - the file that it
>> writes out is put into that directory, so I assume that's where my files
>> should end up too.
>>
>> Steve
>>
>> On 20 October 2015 at 21:12, Peter van Heusden 
>> wrote:
>>
>>> Sorry, I don't understand - what does the Upload File tool have to
>>> do with this?
>>>
>>> On 20 October 2015 at 11:49, Steve Cassidy 
>>> wrote:
>>>
 Yes, I'm sure that's where the problem lies. Writing out to the
 current directory doesn't work.  The files get written to
 'job_working_directory/000/1/' but if I run the Upload File tool the 
 result
 is placed in 'files/000/'.  I think I need to work out where to write 
 the
 files, I found some references to $__new_file_path__ but that doesn't 
 seem
 to help.

 Steve



 On 20 October 2015 at 19:57, Peter van Heusden 
 wrote:

> I suspect that the problem might be in the 
> then. I'm not an 

Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Floreline TOUCHARD]

Thank you ! Can you tell me which files are to update or download ?
I installed my application on a server that was not open to the outside.
Currently I do not support different versions or updates of my application
with git.
I can download the files to edit and transfer them to the server but not to
update the entire application at the moment.

F. T
Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" 
a écrit :

> Hi,
>
> I've got an issue with my external authentication configuration. I use
> Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
> NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under "@
> example.org" regardless of the authentication account. That's why I think
> the REMOTE_USER passed to Galaxy is not 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
> [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
___
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Eric Rasche]

Hi Floreline,

The files from Ryan's pull request are visible here:
https://github.com/galaxyproject/galaxy/pull/823/files

It's a pretty simple change to enable some extra debugging information that 
might help you discover the cause of your issue.


On 10/21/2015 07:40 AM, Floreline TOUCHARD wrote:
> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my
> application with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
>
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD"
> > a
> écrit :
>
> Hi,
>
> I've got an issue with my external authentication configuration. I
> use Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy
> with NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under
> "@example.org " regardless of the authentication
> account. That's why I think the REMOTE_USER passed to Galaxy is not
> 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>  
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*)
> /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
>
>
> ___
> 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/
>
Ciao,
Eric
-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Ryan G]

Here is the pull request:  https://github.com/galaxyproject/galaxy/pull/823

You can see what file was edited

On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my application
> with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <
> floreline.touch...@gmail.com> a écrit :
>
>> Hi,
>>
>> I've got an issue with my external authentication configuration. I use
>> Apache and the mod_perl
>>
>> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
>> NIS accounts.
>>
>> I have the authentication form  when I try to access galaxy web page.
>> But after a successful authentication it seems that the REMOTE_USER
>> variable is not passed to my galaxy instance. I'm connected under "@
>> example.org" regardless of the authentication account. That's why I
>> think the REMOTE_USER passed to Galaxy is not 'null' but empty.
>>
>> I tested the value of the variable with the following php script:
>>
>> > foreach($_SERVER as $key_name => $key_value) {
>> print $key_name . " = " . $key_value . "";
>>
>> }
>>
>> ?>
>>
>> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>>
>> I don't understand where my problem lies.
>>
>>
>>
>> Here is my galaxy.conf file :
>>
>> Listen 2208
>>
>> 
>>
>>
>> RewriteEngine on
>> DocumentRoot "/path/to/static"
>>
>>
>>
>>
>> Options +Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> Allow from all
>>
>>
>> AuthType Basic
>> AuthName "Authentifiez vous"
>> PerlAuthenHandler Apache2::AuthenNIS
>> PerlAuthzHandler Apache2::AuthzNIS
>> PerlSetVar AllowAlternateAuth no
>> require valid-user
>>
>>
>>
>>
>>
>> RewriteEngine on
>> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
>> RequestHeader set REMOTE_USER %{RU}e
>>
>>
>>
>>RewriteRule ^/galaxy$ /galaxy/ [R]
>>RewriteRule ^/static/style/(.*)
>> /path/to/static/june_2007_style/blue/$1 [L]
>>RewriteRule ^/static/scripts/(.*)
>> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>>
>> [L]
>>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>>RewriteRule ^(.*) http://localhost:2209$1 [P]
>>
>>
>> 
>>
>>
>> Thanks in advance !
>>
>> F.T
>>
>
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Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

[Peter Cock]

Hi Marco,

I'd lay money on the the tool parameter sanitization done in Cheetah
intended to avoid any command insertion into the shell command.
This can be configured within the tool definition using the 
tag set:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set

Which genomespace_importer are you working from (URL please)?

Peter

On Wed, Oct 21, 2015 at 3:20 AM, Marco Ocana  wrote:
> Hi,
>
> I am encountering a problem executing the genomespace_importer tool using
> the Galaxy API.
>
> The tool works just fine to copy files in GenomeSpace into Galay a history
> dataset EXCEPT when the GenomeSpace file URL includes a space (" ") of any
> sort.
>
> Below is an example problem request (the GenomeSpace URL is public, so you
> should be able to try it if you like).
>
> Note that the "URL" parameter includes a couple of %20 which are supposed to
> url-encode the space character.
>
>
> POST https://usegalaxy.org/api/tools?key=XX
>
> {
>
>   "history_id": "039421d939e31170",
>
>   "tool_id": "genomespace_importer",
>
>   "inputs": {
>
> "URL":
> "https://dm.genomespace.org/datamanager/file/Home/Public/RecipeData/SequenceData_fa%20fasta%20fastq/RNA-Seq.fastq;,
>
> "gs-token": null
>
>   }
>
> }
>
> The job is accepted by Galaxy but eventually it fails. An HTTP error occurs
> during the execution of the job.
>
> I looked through the logs in GenomeSpace. Turns out that the URL being used
> by Galaxy to do a GET on the file is
>
> https://gsui.genomespace.org/datamanager/v1.0/file/Home/Public/RecipeData/SequenceData_faX20fastaX20fastq/RNA-Seq.fastq
>
> The "percents" are converted to X (I made the Xs bigger for emphasis).
>
> I attempted a couple of other experiments in the tool job submission, using
> actual space characters instead of %20. I also tried using the + instead of
> space.
>
> In both of these attempts, the exact same file path in the URL param was
> used for the GenomeSpace GET, leading to a BAD REQUEST error with the actual
> space character and NOT FOUND error with the + .
>
> So the question is: what kind of decoding is going on in the Galaxy
> genomespace_importer tool and how do I get rid of the Xs?
>
> Thanks
>
> Marco
>
>
>
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