Re: [galaxy-dev] History refresh in multi-thread mode and concurrent access

[Carl Eberhard]

Hi, Christophe

Just a note: I'm taking a look at this and seeing if I can reproduce the
problem. Thanks for being patient.

Carl


On Tue, Sep 6, 2016 at 11:18 AM, Christophe Caron 
wrote:

> Hi
>
> we run a Galaxy instance (16.04) in multi-thread mode ( 8 x web handler /
> 2 jobs handler) to manage scalability, with Apache in frontend, and a
> cluster (SGE like).
>
> We test the load of our infrastructure by running several workflows in
> simultaneous :
>   50 workflow with 35 steps (light cpu consuming for each steps)
>
> All jobs are successfull but some steps remain in grey (it seems jobs are
> really ended because the next streps runs), before to appear in green (no
> yellow).
>
> If we force the refresh history (refresh button on the interface), jobs
> appear in green.
>
> When we run only one (or 2:)) workflow, each workflow follow the chain :
>   grey, yellow, green.
>
> Maybe, there is some mechanisms to optimize between web handler/apache and
> clients to avoid this and to get the right color status ?
>
> Any clue ?
>
> Thanks
>
>
> --
> Christophe Caron
> INRA
>
>
>
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Re: [galaxy-dev] tabular file displayed without tabs

[Carl Eberhard]

Strange. Alright, a few questions then:

* Is this the only file that this happens to? Do other outputs from this
tool produce the same sort of error?
* Do you see any javascript errors in the console when attempting the
viewing? (how to here: http://webmasters.stackexchange.com/a/77337)

On Fri, May 27, 2016 at 12:42 PM, Ryan G <ngsbioinformat...@gmail.com>
wrote:

> The format is listed as tabular when I view details.
>
> In fact, in the preview window in the History Pane, it recognizes there
> are columns and that the data is in fact tabular, but when displaying, this
> isn't the case.
>
>
>
> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <carlfeberh...@gmail.com>
> wrote:
>
>> Ok - if it's not zebra striped and it's word wrapping, then it's somehow
>> not displaying as tabular - you're correct.
>>
>> If you click on the 'View details' button of that dataset (the 'i' with
>> the circle around it shown when the dataset is expanded in the right hand
>> side of the 'Analyze Data' page), what does it list the 'Format' as?
>> 'tabular'? (This is also listed as 'Format' in the expanded view itself).
>>
>> On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformat...@gmail.com>
>> wrote:
>>
>>> Odd because I have another tabular file that is displayed with every
>>> other line highlighted and there is not word-wrapping on the file.  However
>>> the file that has the type tabular and displayed as text is word-wrapped
>>> with no lines highlighted.  I suspect its not actually recognized as
>>> tabular or is being overridden where.
>>>
>>>
>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <carlfeberh...@gmail.com
>>> > wrote:
>>>
>>>> Hi, Ryan
>>>>
>>>> Galaxy displays tabular data in the browser using a  tag. It
>>>> *sounds like* the behavior you see (columns losing space between one
>>>> another when narrowing the window and getting more space as you expand the
>>>> window) would reflect that.
>>>>
>>>> Carl
>>>>
>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformat...@gmail.com>
>>>> wrote:
>>>>
>>>>> The file is an output from a tool and in the tool's xml, its format is
>>>>> tabular.
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>>>>> bjoern.gruen...@gmail.com> wrote:
>>>>>
>>>>>> Hi Ryan,
>>>>>>
>>>>>> is it recognised as 'tabular'?
>>>>>>
>>>>>> Ciao,
>>>>>> Bjoern
>>>>>>
>>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G:
>>>>>> > Hi - I have a tools that generates a tab-delimited text file as
>>>>>> output.
>>>>>> > when I click the eye icon to view the data, all the fields are
>>>>>> compressed
>>>>>> > as if there were no tabs.  If I expand the history view, the little
>>>>>> preview
>>>>>> > window shows the contents as tabbed.  I've verified that the spaces
>>>>>> are
>>>>>> > indeed '\t' tab characters.  Why would Galaxy not display this file
>>>>>> as a
>>>>>> > tab-delimited file?
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > ___
>>>>>> > 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"
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>>>>> and other Galaxy lists, please use the interface at:
>>>>>   https://lists.galaxyproject.org/
>>>>>
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>>>>>
>>>>
>>>>
>>>
>>
>
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

most_recently_used *was* broken - thanks for finding that. A pull request
going back to the 16.01 release is here:
https://github.com/galaxyproject/galaxy/pull/2407

A planning issue for a session API is here:
https://github.com/galaxyproject/galaxy/issues/2404

On Tue, May 24, 2016 at 4:16 PM, Carl Eberhard <carlfeberh...@gmail.com>
wrote:

> Yeah - I understand what you're trying to do now and you're right. In an
> effort to make the API stateless I think we've introduced a gap in
> functionality for a good, practical use case.
>
> I've been wanting to replace the history/current_history* endpoints for a
> while now with a session API (that would include a 'current' history) so
> I'll bump that up in priority.
>
> The most_recently_used may be broken - I'll check that now. Note, though,
> that changing the current history doesn't change the update time for a
> given history. You have to alter/change it for the time to change - then it
> will become the 'most recently used'. It's confusing and doesn't really
> match user expectations. I'll see what I can do about that and possibly
> make it an alias to the above API when/if that makes it to a release. In
> any event, again, I'll double check that it's at least doing that.
>
> I'll also take a look and see if there's some other option for something
> like this if most_recently_used won't fit the use case.
>
>
>
> On Tue, May 24, 2016 at 2:16 AM, Suderman Keith <suder...@cs.vassar.edu>
> wrote:
>
>>
>> On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberh...@gmail.com>
>> wrote:
>>
>> There's a way to get the current history data through a non-api url:
>> /history/current_history_json
>>
>>
>> That works, but to get the current history for a user I need to set the
>> galaxysession cookie. So it is not really a good solution unless I can find
>> an api to determine the session cookie for the user.  I’ve also noticed
>> that /api/histories/most_recently_used is not returning the most recently
>> used history!  A bug maybe?
>>
>> Keith
>>
>>
>> ...but, I don't believe those are accessible through any of the bio/blend
>> libraries.
>>
>> Failing the above, is there some way to get the history ID from the UI?
>>
>>
>> You can click the information button ('i' with a circle around it) for
>> any dataset in a history. The encoded history API id will be listed under:
>> history api id.
>>
>> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith <suder...@cs.vassar.edu>
>> wrote:
>>
>>> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2],
>>> but I don’t see any way to obtain the “current” history as selected by the
>>> user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it
>>> seems that simply selecting a history as the current history in the UI does
>>> not make it the “most recently used” (MRU) history; I guess the user has to
>>> actually _do_ something with before it becomes the MRU history.  Am I
>>> missing something?
>>>
>>> Failing the above, is there some way to get the history ID from the UI?
>>>
>>> Thanks,
>>> Keith
>>>
>>> REFERENCES
>>>
>>> 1.http://jmchilton.github.io/blend4j/apidocs/
>>> 2.
>>> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>>>
>>> --
>>> Research Associate
>>> Department of Computer Science
>>> Vassar College
>>> Poughkeepsie, NY
>>>
>>>
>>> ___
>>> 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/
>>>
>>
>>
>> --
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>>
>>
>
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Re: [galaxy-dev] tabular file displayed without tabs

[Carl Eberhard]

Ok - if it's not zebra striped and it's word wrapping, then it's somehow
not displaying as tabular - you're correct.

If you click on the 'View details' button of that dataset (the 'i' with the
circle around it shown when the dataset is expanded in the right hand side
of the 'Analyze Data' page), what does it list the 'Format' as? 'tabular'?
(This is also listed as 'Format' in the expanded view itself).

On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:

> Odd because I have another tabular file that is displayed with every other
> line highlighted and there is not word-wrapping on the file.  However the
> file that has the type tabular and displayed as text is word-wrapped with
> no lines highlighted.  I suspect its not actually recognized as tabular or
> is being overridden where.
>
>
> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <carlfeberh...@gmail.com>
> wrote:
>
>> Hi, Ryan
>>
>> Galaxy displays tabular data in the browser using a  tag. It
>> *sounds like* the behavior you see (columns losing space between one
>> another when narrowing the window and getting more space as you expand the
>> window) would reflect that.
>>
>> Carl
>>
>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformat...@gmail.com>
>> wrote:
>>
>>> The file is an output from a tool and in the tool's xml, its format is
>>> tabular.
>>>
>>>
>>>
>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>>> bjoern.gruen...@gmail.com> wrote:
>>>
>>>> Hi Ryan,
>>>>
>>>> is it recognised as 'tabular'?
>>>>
>>>> Ciao,
>>>> Bjoern
>>>>
>>>> Am 27.10.2015 um 04:42 schrieb Ryan G:
>>>> > Hi - I have a tools that generates a tab-delimited text file as
>>>> output.
>>>> > when I click the eye icon to view the data, all the fields are
>>>> compressed
>>>> > as if there were no tabs.  If I expand the history view, the little
>>>> preview
>>>> > window shows the contents as tabbed.  I've verified that the spaces
>>>> are
>>>> > indeed '\t' tab characters.  Why would Galaxy not display this file
>>>> as a
>>>> > tab-delimited file?
>>>> >
>>>> >
>>>> >
>>>> > ___
>>>> > 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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>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

There's a way to get the current history data through a non-api url:
/history/current_history_json

...but, I don't believe those are accessible through any of the bio/blend
libraries.

Failing the above, is there some way to get the history ID from the UI?


You can click the information button ('i' with a circle around it) for any
dataset in a history. The encoded history API id will be listed under:
history api id.

On Sat, May 21, 2016 at 7:03 PM, Suderman Keith 
wrote:

> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2],
> but I don’t see any way to obtain the “current” history as selected by the
> user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it
> seems that simply selecting a history as the current history in the UI does
> not make it the “most recently used” (MRU) history; I guess the user has to
> actually _do_ something with before it becomes the MRU history.  Am I
> missing something?
>
> Failing the above, is there some way to get the history ID from the UI?
>
> Thanks,
> Keith
>
> REFERENCES
>
> 1.http://jmchilton.github.io/blend4j/apidocs/
> 2.
> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

[Carl Eberhard]

https://github.com/galaxyproject/galaxy/pull/1972

Thanks for letting us know about this. Let me know if you spot any problems
with that fix.

On Tue, Mar 22, 2016 at 8:32 AM, Carl Eberhard <carlfeberh...@gmail.com>
wrote:

> Hey, Hans
>
> Looks like a problem with the way we're loading the color-picker library
> Farbtastic. I'll take a look, try to get a fix out, and update here today.
>
> Carl
>
> On Mon, Mar 21, 2016 at 9:01 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>> Hi all
>>
>> Since we upgraded our Galaxy installation from 15.05 to 15.10 (plus the
>> recent security fix, changeset: 17161:3f95c21b1a85), the "Edit settings"
>> button in Trackster is no longer working. The window, which normally allows
>> you to select the colors, etc. doesn't show up anymore.
>>
>> This happens with different browsers on mac and linux. On the console I
>> get: "TypeError: a.browser is undefined"
>>
>> Has anyone else seen this problem? Or is there even already a fix
>> available?
>>
>>
>> Thank you very much for your help
>> Hans-Rudolf
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>>
>>
>> Hans-Rudolf Hotz, PhD
>> Bioinformatics Support
>>
>> Friedrich Miescher Institute for Biomedical Research
>> Maulbeerstrasse 66
>> 4058 Basel/Switzerland
>> ___
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>> and other Galaxy lists, please use the interface at:
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>>
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>>  http://galaxyproject.org/search/mailinglists/
>
>
>
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Re: [galaxy-dev] Login reguried causing nested main page loading

[Carl Eberhard]

Hi, Christian and Ryan

Which versions of Galaxy are you using when this happens?

Thanks,
Carl


On Mon, Jan 11, 2016 at 9:03 AM, Ryan G  wrote:

> I've seen this as well.  I find that restarting galaxy fixes the problem
> but I'd love to know the underlying cause.
>
> Please excuse any typos -- Sent from my iPhone
>
> On Jan 11, 2016, at 5:08 AM, Christian Brenninkmeijer <
> christian.brenninkmei...@manchester.ac.uk> wrote:
>
> Hi All,
>
> I tried to turn on login required in config.ini
>
> But now if you are not logged in it loads the main page where normally the
> welcome.html would go.
> Which then recursively loads other main pages.
>
> Which file am I missing?
>
> Thanks
> Christian
> University of Manchester
>
> ___
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>
>
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Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

[Carl Eberhard]

Give this a try:

*registry.MDA_zip*
And if that doesn't work:

*MDA_zip*
Finally, try this (which won't return true for subclasses of MDA_zip):
*MDA_zip*

(Sorry - initially sent this to Bob only)


On Mon, Dec 14, 2015 at 4:14 PM, <rbrown1...@comcast.net> wrote:

> Thank you Carl for the excellent write-up.  It could serve as a
> visualization plugin tutorial.
>
> However, I am still not able to get the visualization icon to appear, see
> the attachment 2.
>
> I feel if I get the icon to show it will all come together.
>
> A couple questions followed by file dumps and startup info
>
> *1. my   /api/datatypes/mapping dump   it shows registry instead of binary*
>
> *near the top*
>
> "galaxy.datatypes.genetics.RexpBase": {"galaxy.datatypes.images.Html":
> true, "galaxy.datatypes.data.Data": true, "galaxy.datatypes.data.Text":
> true, "galaxy.datatypes.genetics.RexpBase": true}, "galaxy.datatypes.
> *registry*.MDA_zip": {"galaxy.datatypes.*registry*.Binary": true,
> "galaxy.datatypes.data.Data": true, "galaxy.datatypes.binary.Binary": true,
> "galaxy.datatypes.*registry*.MDA_zip": true},
>
> *near the bottom in lower case*
>
> "galaxy.datatypes.registry.Text", "mda_zip":
> "galaxy.datatypes.registry.MDA_zip", "chips":
> "galaxy.datatypes.registry.Text", "gg":
> "galaxy.datatypes.genetics.GenomeGraphs", "syco":
> "galaxy.datatypes.registry.Text",
>
>
>
> 2. I also added a snapshot of the visualization/tool/ sub-directories.
> It shows my extension because I have a format=type in the tool.xml output
> file defition but shows  file type 'binary' at the bottom of the file
> history.   Is this correct, or should it be my extension type there?
>
> Comment -- It appears the only link between the file extension and the
> visualization plugin is via the test line in the /conf/toolxml file.  Is
> that correct?
>
>
>
>
> *My xml in my visualize directory /tool/config/tool.xml (formatting is
> messed up here) attachment 1*
>
> 
>
> 
>
> 
>
>   
>
>  
>
>
> HistoryDatasetAssociation
>
>  result_type="datatype">binary.MDA_zip
>
>   param_attr="id">dataset_id
>
> 
>
>   
>
>   
>
>var_name_in_template="hda" required="true">dataset_id
>
>   
>
>entry_point_type="mako">MDAheatmap.mako
>
> 
>
>
>
> *My templates/tool.mako file (hello world)*
>
> 
>
> 
>
>
>
>  
>
>  A Small Hello
>
>  
>
>
>
> 
>
>Hi
>
>This is very minimal "hello world" HTML document.
>
> 
>
> 
>
> *startup info seems successful*
>
> galaxy.web.base.pluginframework INFO 2015-12-14 13:20:09,631
> VisualizationsRegistry, loaded plugin: MDAheatmap
>
> x.x.10.42 - - [14/Dec/2015:14:11:50 -0400] "PUT
> /api/histories/a799d38679e985db/contents/datasets/fb85969571388350
> HTTP/1.1" 200 - "http://xx.xx.10.4:8082/; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.80
> Safari/537.36"
>
> *no skipping error and no other apparent errors   in startup*
>
>
>
> *here is my Datatypes.conf.xml 2 additions*
>
> mimetype="application/octet-stream" display_in_upload="true"
> subclass="False">
>
> *and sniffer*
>
>
>
>
>
> *my binary.py addition*
>
> class MDA_zip( Binary ):
>
>"""Class describing an MDA Heatmap binary zip file"""
>
>file_ext = "MDA_zip"
>
>def set_peek( self, dataset, is_multi_byte=False ):
>
>if not dataset.dataset.purged:
>
>dataset.peek = "Binary MDA_zip sequence file"
>
>dataset.blurb = nice_size( dataset.get_size() )
>
>else:
>
>dataset.peek = 'file MDA_zip does not exist'
>
>dataset.blurb = 'file MDA_zip purged from disk'
>
>def display_peek( self, dataset ):
>
>try:
>
>return dataset.peek
>
>    except:
>
>return "Binary MDA_zip heatmap file (%s)" % ( nice_size(
> dataset.get_size() ) )
>
>
>
> Binary.register_sniffable_binary_format("MDA_zi

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

[Carl Eberhard]

Hi, Bob

There are a number of ways to visualize data in Galaxy, so let's settle on
some terminology first for the three major ways:
* *display applications*: these are definitions of external websites that
can fetch galaxy datasets and display them in their visualization
applications. Examples are the UCSC genome browser, GBrowse, and IGV.
* *tools*: although the tool framework generally produces 'raw' data like
tabular or binary files, it can also produce the html (and js even) that
can display data for visualization. An example would be 'Boxplot of quality
statistics'.
* *visualization plugins*: these are python/mako/js files that are meant to
be more interactive visualizations in order to explore data

It sounds to me like you'd like to use the visualization plugin system, so:
* since they're for external code or websites, *let's take display
applications off the table entirely*.
* since they can be a viable alternative to the plugin system, so *I'd keep
tools as another option but keep our focus on the plugin system*

It also sounds like you have two elements you'd like to incorporate:
* a *datatype*
* a *plugin* to display datasets of that datatype

*The datatype*
I'm more familiar with the plugin part of this process, but for the
datatype it sounds like you want to subclass the binary datatype and add it
to your galaxy installation. I'd start here (I imagine you've already seen
it, tho):
* https://wiki.galaxyproject.org/Admin/Datatypes
* https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes

Note: to see if your datatype was loaded successfully, with your server
running - you can go to: /api/datatypes/mapping. You should be able to see
your datatype listed at the first level of the json map, generally
beginning with 'galaxy.datatypes.' and the python module name you added it
to (like a python import namespace): e.g. galaxy.datatypes.binary.H5 or
galaxy.datatypes.binary.mydatatype

To simplify:
1. Add a definition to your datatypes_conf file
2. Add a sniffer for your datatype
3. Add a subclass/class for your datatype

*The plugin*
For the plugin, I also imagine you've seen this, but it's a (hopefully)
good place to start:
https://wiki.galaxyproject.org/VisualizationsRegistry

*The filesystem layout*
Here's a simplified process for creating an outline for a visualization
plugin project:
1. in the filesystem, start at */config/plugins/visualizations*
2. *think of an id for your plugin*. This can be any (filesystem
permissible) file name and is only used as an id by the registry - the
users never see it. It should be unique from any other plugins in that
directory. (e.g. myplugin)
3. *create a main directory using your id*. (e.g. /config/plugins/visualizations/myplugin)
4. inside that directory, *create three more directories: config,
templates, static*. This is where the plugin configuration, the mako
templates, and any (optional) javascript or static files are kept
respectively.
5. *the configuration file should use the same id* you used above for the
directory: e.g. config/myplugin.xml. Most people copy and rename a simple
config file like the one in
config/plugins/visualizations/scatterplot/config/scatterplot.xml. We'll
change the datatype it applies to later, but there's more at:
https://wiki.galaxyproject.org/VisualizationsRegistry#The_visualization_configuration_file
and https://wiki.galaxyproject.org/VisualizationsRegistry/Configuration
6. *a mako template file should go into the templates directory*: e.g.
templates/myplugin.mako. This template file is the entry point for your
visualization and is loaded first. You don't have to do any major coding
here and can instead just launch javascript to render the visualization.
https://wiki.galaxyproject.org/VisualizationsRegistry#Creating_the_code_and_markup_for_your_visualization

At this point, your config/plugins/visualizations/myplugin directory should
look like one of the two trees displayed here:
https://wiki.galaxyproject.org/VisualizationsRegistry#Configuring_your_visualization_plugin_in_the_.60visualization_plugins_directory.60

*The configuration*
Now, we'll configure the plugin by editing the
config/plugins/visualizations/myplugin/config/myplugin.xml file. Let's
assume you've copied the scatterplot config file (
https://github.com/galaxyproject/galaxy/blob/dev/config/plugins/visualizations/scatterplot/config/scatterplot.xml
):

1. change the name displayed to what you'd like users to see in the dataset
visualizations dropdown menu:
l

2. change the configuration for your visualization to test for your
datatype. For example, if you have mydatatype, change:


HistoryDatasetAssociation

*binary.MyDatatype*
dataset_id



The above is basically saying, if an object is a) a
HistoryDatasetAssociation (a dataset in a history) and b) it's a subclass
or instance of binary.MyDatatype, then put a link:
* in the dataset visualization dropdown menu
* that will start my visualization
* pass the encoded id of the 

Re: [galaxy-dev] Need urgent help: ItemOwnershipException: History is not owned by user

[Carl Eberhard]

I'm stumped:

   - I'm not sure how that url ("
   
http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c184a9/contents;)
   could have been formed
   - Calling that link from a local galaxy results in 'No route for' when
   the error is an api authentication 403

Maybe it's possible that an authentication error is confounding/combining
with a client error?

Zuzanna, can you:

   - tell us what version of Galaxy you're using?
   - open a javascript console on the history/view_multiple page and see
   what it says 'galaxy_conf.root' equals?




On Mon, Sep 21, 2015 at 10:39 AM, Zuzanna K. Filutowska <
plat...@man.poznan.pl> wrote:

> Dnia 2015-09-21, pon o godzinie 15:14 +0200, Hans-Rudolf Hotz pisze:
>
> I have created a new test user, and here is the output, when trying to
> import and show imported histories (/history/view_multiple)
> {
>   "agent": "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:40.0)
> Gecko/20100101 Firefox/40.0",
>   "url":
> "
> http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c184a9/contents
> ",
>   "data": "",
>   "options": {
> "data": {},
> "silent": true,
> "parse": true,
> "emulateHTTP": false,
> "emulateJSON": false
>   },
>   "xhr": {
> "readyState": 4,
> "responseText": "{\"err_msg\": \"API authentication required for
> this request\", \"err_code\": 403001}",
> "responseJSON": {
>   "err_msg": "API authentication required for this request",
>   "err_code": 403001
> },
> "status": 403,
> "statusText": "Forbidden",
> "responseHeaders": {
>   "Date": "Mon, 21 Sep 2015 14:37:59 GMT\r",
>   "Server": "PasteWSGIServer/0.5 Python/2.7.10\r",
>   "X-Frame-Options": "SAMEORIGIN\r",
>   "Content-Type": "text/html; charset=UTF-8\r",
>   "Vary": "Accept-Encoding\r",
>   "Content-Encoding": "gzip\r",
>   "Connection": "close\r",
>   "Transfer-Encoding": "chunked\r"
> }
>   },
>   "source": [],
>   "user": {
> "username": "plgjdoe",
> "quota_percent": null,
> "total_disk_usage": 20139875,
> "nice_total_disk_usage": "19.2 MB",
> "email": "plgj...@galaxy.man.poznan.pl",
> "is_admin": false,
> "tags_used": [],
> "model_class": "User",
> "id": "3cc0effd29705aa3"
>   }
> }
> --
>
> Pozdrawiam,
>
> --
> Zuzanna K. Filutowska, HPC Systems Administrator
> Poznan Supercomputing and Networking Center
> Institute of Bioorganic Chemistry Polish Academy of Sciences
> Seize the day boys! Make your lifes extraordinary! --John Keating
>
> ___
> 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/

Re: [galaxy-dev] Get dataset/API ids for a dataset

[Carl Eberhard]

Each python ORM object for a dataset has both create_time and update_time.

If I understand correctly and there's one job that's producing the bam
files and json file you can use 'hda.creating_job.output_datasets' (in
python and where 'hda' is the ORM object for the json file) to get all the
datasets produced by the job that produced the json file (including that
file itself).

Hope that helps.

On Thu, Aug 27, 2015 at 1:14 PM, Asma Riyaz asmariya...@gmail.com wrote:

 Hi Carl,

 Thank you for your help, I was able to access all the dataset ids in
 history with the pointers you gave, but I am not finding an immediate way
 to deduce which original file is from which id. I think if I can get the
 timestamp of the datasets I can use this and the dataset type metadata.
 Would there be a way (with h or trans objects or something else) to
 grab the timestamp?

 Another side question: is there an id that remains common to multiple
 outputs produced from one tool?

 Thank you,
 -Asma

 On Wed, Aug 26, 2015 at 10:07 AM, Carl Eberhard carlfeberh...@gmail.com
 wrote:

 Hi, Asma

 Sorry for the confusion. You may want to have a look here:
 http://docs.makotemplates.org/en/latest/index.html

 Mako is a python templating language. No tag is required to run python in
 it (when the server is building the page). Simply use the brackets:
 %
 # executes python code while the page is built
 # here we can access the database since this is server side code
 %
 Make sure you use '% %' and not '%! %' so that everything is loaded
 properly.

 Once you have the dataset ids or urls in an array you can 'print' their
 JSON into a script tag for use with javascript when the page is loaded onto
 the client browser using the mako expression syntax:
 script type=text/javascript
 var datasetIds = ${ h.dumps( dataset_ids ) };
 /script

 'h' is for helpers which are objects that Galaxy puts into all the mako
 templates and have utility functions. 'dumps' is part of the json library
 and is 'dump'ing a JSON 's'tring into the template. Notice there are no
 quotes around the JSON. Mako will print the server side dataset_ids as
 javascript-usable JSON so they can be used by the page on the client side
 to build your urls.

 Essentially you have to use the JSON to communicate between the python
 and javascript. You cannot use python or python objects (like
 trans.history) from javascript code directly though.

 'trans' should definitely be available and defined. igv.mako is being
 loaded as part of the visualization framework, correct?

 If this fails to help, let me know and we can work directly with the code
 if you'd like.

 On Tue, Aug 25, 2015 at 1:48 PM, Asma Riyaz asmariya...@gmail.com
 wrote:

 In addition to my previous attempts, here is another I have tried:

 *in igv.mako:*

 %!
   users_current_history = trans.history
   dataset_ids = [ trans.security.encode_id( d.id ) for d in
 users_current_history.datasets ]
 %
 %def name=getDataset_ids()
%
  return dataset_ids
%
 /%def
script
  var dataset_ids = '${getDataset_ids()}';
  console.log(dataset_ids);
/script

 But this fails again and error appears in galaxy as 'name trans not
 defined'.

 -Asma

 On Tue, Aug 25, 2015 at 1:12 PM, Asma Riyaz asmariya...@gmail.com
 wrote:

 Hello,

 I have tried to access user's current history in the script tags in
 mako template:

 script
 var users_current_history = '${trans.history}';
 console.log( users_current_history.datasets );
 for (var dataset in users_current_history.datasets) {
 console.log( dataset );
 }
 /script

 The first console.log shows that 'users_current_history.datasets' is
 undefined.

 According this piece of code from Carl, accessing dataset ids should be
 done in python within a mako template tag
 %
  users_current_history = trans.history
   dataset_ids = [ trans.security.encode_id( d.id ) for d in
  users_current_history.datasets ]
 %

 but all the examples I have seen so far have some html tag associated
 with such code. How can I avoid using these tags and still use python 
 alone?

 -Asma



 On Fri, Aug 21, 2015 at 11:41 AM, Carl Eberhard 
 carlfeberh...@gmail.com wrote:

 As far as I know, it's best to write tool wrappers as if they were
 meant to be called outside of Galaxy. In other words, it would not be best
 to try and get Galaxy dataset ids within the tool code.

 If we zoom out on the problem and take a higher view, is the JSON file
 primary used to launch the visualization or does it have another use as
 well?

 Can/is the JSON passed to IGV directly in javascript? or does it need
 to be read from the file separately by IGV and independent from the
 visualization mako and its associated javascript?

 If the JSON data is only for the visualization, doesn't need to be
 100% correct in the file, and can be passed within javascript, you can
 alter the JSON data directly in the visualization mako/js by decorating
 with the bam ids before

Re: [galaxy-dev] Get dataset/API ids for a dataset

[Carl Eberhard]

Hi, Asma

Sorry for the confusion. You may want to have a look here:
http://docs.makotemplates.org/en/latest/index.html

Mako is a python templating language. No tag is required to run python in
it (when the server is building the page). Simply use the brackets:
%
# executes python code while the page is built
# here we can access the database since this is server side code
%
Make sure you use '% %' and not '%! %' so that everything is loaded
properly.

Once you have the dataset ids or urls in an array you can 'print' their
JSON into a script tag for use with javascript when the page is loaded onto
the client browser using the mako expression syntax:
script type=text/javascript
var datasetIds = ${ h.dumps( dataset_ids ) };
/script

'h' is for helpers which are objects that Galaxy puts into all the mako
templates and have utility functions. 'dumps' is part of the json library
and is 'dump'ing a JSON 's'tring into the template. Notice there are no
quotes around the JSON. Mako will print the server side dataset_ids as
javascript-usable JSON so they can be used by the page on the client side
to build your urls.

Essentially you have to use the JSON to communicate between the python and
javascript. You cannot use python or python objects (like trans.history)
from javascript code directly though.

'trans' should definitely be available and defined. igv.mako is being
loaded as part of the visualization framework, correct?

If this fails to help, let me know and we can work directly with the code
if you'd like.

On Tue, Aug 25, 2015 at 1:48 PM, Asma Riyaz asmariya...@gmail.com wrote:

 In addition to my previous attempts, here is another I have tried:

 *in igv.mako:*

 %!
   users_current_history = trans.history
   dataset_ids = [ trans.security.encode_id( d.id ) for d in
 users_current_history.datasets ]
 %
 %def name=getDataset_ids()
%
  return dataset_ids
%
 /%def
script
  var dataset_ids = '${getDataset_ids()}';
  console.log(dataset_ids);
/script

 But this fails again and error appears in galaxy as 'name trans not
 defined'.

 -Asma

 On Tue, Aug 25, 2015 at 1:12 PM, Asma Riyaz asmariya...@gmail.com wrote:

 Hello,

 I have tried to access user's current history in the script tags in
 mako template:

 script
 var users_current_history = '${trans.history}';
 console.log( users_current_history.datasets );
 for (var dataset in users_current_history.datasets) {
 console.log( dataset );
 }
 /script

 The first console.log shows that 'users_current_history.datasets' is
 undefined.

 According this piece of code from Carl, accessing dataset ids should be
 done in python within a mako template tag
 %
  users_current_history = trans.history
   dataset_ids = [ trans.security.encode_id( d.id ) for d in
  users_current_history.datasets ]
 %

 but all the examples I have seen so far have some html tag associated
 with such code. How can I avoid using these tags and still use python alone?

 -Asma



 On Fri, Aug 21, 2015 at 11:41 AM, Carl Eberhard carlfeberh...@gmail.com
 wrote:

 As far as I know, it's best to write tool wrappers as if they were meant
 to be called outside of Galaxy. In other words, it would not be best to try
 and get Galaxy dataset ids within the tool code.

 If we zoom out on the problem and take a higher view, is the JSON file
 primary used to launch the visualization or does it have another use as
 well?

 Can/is the JSON passed to IGV directly in javascript? or does it need to
 be read from the file separately by IGV and independent from the
 visualization mako and its associated javascript?

 If the JSON data is only for the visualization, doesn't need to be 100%
 correct in the file, and can be passed within javascript, you can alter the
 JSON data directly in the visualization mako/js by decorating with the bam
 ids before passing it to IGV. In that case, the previous code (or a cleaner
 version of it) will begin to get you there.

 Unfortunately, the previous code should work in the visualization mako
 only. (With the correction:
 from galaxy import model
 instead of
 import model

 The trans is an object describing the current WebTransaction
 (request/response). It allows access to a sqlalchemy (sa) database session:
 trans.sa_session

 On Fri, Aug 21, 2015 at 11:23 AM, Asma Riyaz asmariya...@gmail.com
 wrote:

 Hi Carl,

 The visualization comes into play after a lab implemented tool in
 galaxy is ran; I am not using galaxy's workflow. Is tracing back ids still
 possible in this case with the test case you wrote earlier?

 Also I couldn't figure out what trans refers to in your previous
 message.

 Thank you,
 Asma

 On Thu, Aug 20, 2015 at 3:03 PM, Asma Riyaz asmariya...@gmail.com
 wrote:


 -- Forwarded message --
 From: Carl Eberhard carlfeberh...@gmail.com
 Date: Thu, Aug 20, 2015 at 2:46 PM
 Subject: Re: [galaxy-dev] Get dataset/API ids for a dataset
 To: Asma Riyaz asmariya...@gmail.com
 Cc

Re: [galaxy-dev] Get dataset/API ids for a dataset

[Carl Eberhard]

If I understand correctly, this begins to sound less like something the
visualization level can do and more something that needs to be handled at
your tool level.

Let me repeat back what I understand to be the process:
1. Your pipeline is activated by the user and some initial step in the
pipeline creates the JSON file that will configure your visualization
2. Some indeterminate number of bam files are created
3. The pipeline finishes and at this point the encoded ids of all the bam
files created by the pipeline should be used in urls added to the JSON file
from step 1
4. The user then clicks on one of the outputs (the JSON file?) from the
pipeline to launch the visualization and the JSON file is read

Do I have that right? When you say pipeline does that mean a Galaxy
workflow?

If so, you can access the workflow using the ORM by tracing up from the
dataset that invoked the visualization and then back down to the bam files
that were created in the workflow steps:

%
# get the bam datasets created by the workflow that created 'hda'
# where 'hda' is the dataset the visualization launched from
import model
w = trans.sa_session.query( model.WorkflowInvocationStep )
.filter( WorkflowInvocationStep.job == hda.creating_job
).one().workflow_invocation
ids = [ d.dataset.id for d in s.job.output_datasets if d.dataset.ext ==
'bam' ] for s in w.steps if s.job ]
urls = [ ... ]
%

(The above is really horrible code, but sketches one way you could get the
ids from the visualization mako)

If it's not a workflow and a pipeline being run from within a Galaxy tool
wrapper, then the tool wrapper code should be writing the ids to the JSON
file. Is that the case instead?

On Thu, Aug 20, 2015 at 1:28 PM, Asma Riyaz asmariya...@gmail.com wrote:

 Hi Carl,

 Thank you for your reply. This definitely helps me get started, my
 question being:

 trans.history will get all the dataset ids in users history regardless of
 which run the datasets are associated with. Hence if the user has multiple
 bams loaded in history there will be no way of distinguishing them.

 Here is a rough idea of what I am envisioning my pipeline to do:

 Galaxy pipeline runs - while it is running, dataset ids that are
 generated should be retrieved for each output (in my case bams and JSON
 file) - when main pipeline finishes, ids are updated within the JSON file
 - all the outputs are fed to users history.

 this way there will be no ambiguity as to which bams are being accessed
 for viz. Is this intermediate way of getting dataset ids possible?

 Thank you
 -Asma





 On Wed, Aug 19, 2015 at 4:27 PM, Carl Eberhard carlfeberh...@gmail.com
 wrote:

 Hi, Asma

 If you're looking through datasets via the mako part of your
 visualization, you can use:

 users_current_history = trans.history
 dataset_ids = [ trans.security.encode_id( d.id ) for d in
 users_current_history.datasets ]

 (or similar) to build the ids needed for the urls.

 If you want to get the info via javascript, you can use something like
 the python above and template into a js var:

 var url = /datasets/${ dna_dataset_id }/display?to_ext=bam


 ...or encode and template the history id and use ajax and the api after
 the page is served:

 var historyId = ${ trans.security.encode_id( trans.history.id ) };
 jQuery.ajax( galaxy_config.root + 'api/histories/' + historyId +
 '/contents' )
 .done( function( response ){ /* will contain summary json for each
 dataset including encoded ids for each */ })


 Let me know if that's not what you were looking for or if you find any
 problems with it.

 On Wed, Aug 19, 2015 at 11:01 AM, Asma Riyaz asmariya...@gmail.com
 wrote:

 Hello Galaxy-dev,

 I thank you so much for all the help you have given me.

 I have a question about data set ids in galaxy. As a background, I am
 running my own galaxy instance on a server. A pipeline implemented in
 the lab produces the following files in the history:

 1) 2 BAM files
 2) A JSON file

 My goal is to use this JSON file to pass the path/URL of bam files into
 a custom JS we wrote for visualization purpose.

 This JSON file contains among many other details the paths/URLs to the
 above bam files. I am using JSON filetypes to send data to the JS
 visualization within Galaxy. To do this, I have my own JS which loads a BAM
 file from URL provided into an IGV.js track. IGV.js, which is
 responsible for making the tracks, expects a valid URL which is updated in
 the JSON file in this manner:

 1) Extract the API_key and history id from a loaded BAM file
 2) Edit the JSON file to reflect the BAM file's dataset id to be
 something like this:

 {
   CLL-HL_pilot.r1.fastq: {
 DNA: /datasets/36ddb788a0f14eb3/display?to_ext=bam,
 ...

 This works fine if I know the API Key for bam files. When a pipeline
 executes dataset ids are generated for each output. I want to access and
 include these ids in the JSON file and load the updated JSON file into the
 history with the bams. Is there a way to get the ids

Re: [galaxy-dev] new visualization tool for composite datatype?

[Carl Eberhard]

Yes, you can still use the framework to create interactive python-only
visualizations. The simplest way to do this is form-based interaction.

1. The visualization mako page renders a form that contains the options the
user can choose from
2. The user chooses and submits the form
3. Galaxy will re-render the visualization mako and now, since those
options are passed as parameters, the chosen visualization can be rendered

So you can render the form with your options:
%if not query.get( 'param2', None ):
## initial render of form
form
input name=param2 /
input name=param3 /
input name=param4 /
button type=submitDraw/button
/form
%else:
## second render drawing with param2
...

Note: this will default to a GET based form whose 'action' url will be the
visualization's url. Any html5 form based controls will work: radio
buttons, ranges, etc.

When the user submits the form, each of the params, will now be part of the
query string when the mako renders the second time:
/visualization/show/myvis?param2=somethingparam3=...

You can then use these params to call your python code with the user chosen
options:
arg2 = query.get( 'param2', default )
arg3 = query.get( 'param3', ...

from draw import main
returned = main( arg2, arg3, ... )

svg
${ returned }
/svg
(or something similar)

Other things that may help?:

   - you can use action=post if you want to post data instead of get -
   handy for larger parameters
   - try to not bootstrap/load all your data into the mako file as this
   will be re-fetched everytime the form is re-submitted
   - you can add the arg2, arg3, etc. params to the config file and the
   registry will parse those for you and put them in the template's 'config'
   variable, e.g.: int_param2 = config.param2
   - when using these query/form parameters you can now save/generate urls
   that will auto-start your visualizations since all the configuration
   options are sent in the url


Let me know if I can give more info or that doesn't end up working.


On Wed, Aug 19, 2015 at 9:30 AM, Anne Claire Fouilloux 
a.c.fouill...@geo.uio.no wrote:

 Hi Carl,


 Yes I have a python code to manipulate and draw the data (it creates svg
 files and I wish to add this visualization tool to my galaxy instance:

 Let's say my composite datatype contains 3 files:

 -file1.dat

 -file2.dat

 -file3.dat

 My python code takes 4 arguments (for instance draw.py arg1 arg2 arg3
 arg4).

 arg1: The first argument is a path giving the location of these 3 files.

 arg2, arg3 and arg4 are list of options. These lists are dynamic as they
 depend on the content of these 3 files.

 Once the user has selected some options, I have a draw button and would
 like the python script draw.py to be executed and generate a plot.

 Your answer was very helpful; at least it clarifies a number of things.
 Now I understood I can access to these files using hda.extra_files_path in
 my mako file:

 %

 composite_file_path=hda.extra_files_path + '/' + date + '/'

 %

 Which is helpful to generate my select buttons (for arg2, arg3 and arg4)
 as I fist need to read the content of these files for the generation of
 these buttons.


 I still need to call my python script with the option chosen by the user.
 Is it something I can easily do with galaxy?


 Thanks,


 Anne.



 --
 *From:* Carl Eberhard carlfeberh...@gmail.com
 *Sent:* 18 August 2015 18:59
 *To:* Anne Claire Fouilloux
 *Cc:* galaxy-dev@lists.galaxyproject.org
 *Subject:* Re: [galaxy-dev] new visualization tool for composite datatype?

 Hi, Anne

 Can you be more specific about how you'd like to visualize the files? It
 sounds like you've already got a tool that will build an html file which is
 the classic way to make visualizations with galaxy.

 Now you'd like to make it more interactive? Do you already have javascript
 or python code that will be used to manipulate or draw the data? The
 visualization registry will help you link a user's data to your
 visualization code but will not create the code that does the rendering or
 interaction.

 Aside from that, if you know the structure and filenames of your
 composite's extra files directory, currently you can access those files
 using:
 api/histories/{history_id}/contents/{content_id}/display?filename=some
 file
 The meme type will be guessed based on the extension generally and more
 complex paths can also be specified using the filename parameter.

 So, for example, if I have a FastQC Html composite file with an extra
 files path of:
 database/files/000/dataset_83_files

 And within that directory, fastqc makes an additional subdirectory:
 sample1_fastqc/Icons
 sample1_fastqc/Images
 sample1_fastqc/summary.txt

 I can fetch the summary.txt file (with the 'text/plain' memetype) using:

 api/histories/{history_id}/contents/{content_id}/display?filename=sample1_fastqc/summary.txt

 Let me know if that wasn't the info you were after or I misunderstood the
 question.
 Carl


 On Fri, Aug

Re: [galaxy-dev] new visualization tool for composite datatype?

[Carl Eberhard]

Hi, Anne

Can you be more specific about how you'd like to visualize the files? It
sounds like you've already got a tool that will build an html file which is
the classic way to make visualizations with galaxy.

Now you'd like to make it more interactive? Do you already have javascript
or python code that will be used to manipulate or draw the data? The
visualization registry will help you link a user's data to your
visualization code but will not create the code that does the rendering or
interaction.

Aside from that, if you know the structure and filenames of your
composite's extra files directory, currently you can access those files
using:
api/histories/{history_id}/contents/{content_id}/display?filename=some
file
The meme type will be guessed based on the extension generally and more
complex paths can also be specified using the filename parameter.

So, for example, if I have a FastQC Html composite file with an extra files
path of:
database/files/000/dataset_83_files

And within that directory, fastqc makes an additional subdirectory:
sample1_fastqc/Icons
sample1_fastqc/Images
sample1_fastqc/summary.txt

I can fetch the summary.txt file (with the 'text/plain' memetype) using:
api/histories/{history_id}/contents/{content_id}/display?filename=sample1_fastqc/summary.txt

Let me know if that wasn't the info you were after or I misunderstood the
question.
Carl


On Fri, Aug 14, 2015 at 7:50 AM, Anne Claire Fouilloux 
a.c.fouill...@geo.uio.no wrote:

 Hi,


 I created a new composite datatype (class derived from Html class)
 myDatatype and I sucessfully use it in a new created tool.


 When I click on View data it shows my Html file with a list of binary
 files and everything is Ok.


 Now I would like to Visualize my data. I created a new directory in

 galaxy-dist/config/plugins/visualizations/ following instructions given at

 https://wiki.galaxyproject.org/VisualizationsRegistry and read

 https://wiki.galaxyproject.org/VisualizationsRegistry/Configuration and

 https://wiki.galaxyproject.org/DataProviders


 However, I still don't understand what I should do to be able to access
 files from my composite datatype to be able to visualize myDatatype (I mean
 I need to visualize the files containing in the directory listed by the
 html file).


 Is it possible? Where can I find some information on how to do it?


 Thanks,


 Anne.



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Re: [galaxy-dev] 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:
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 aroud...@sfu.ca 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: 778 782-8860
 fax:   778 782-4242
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Re: [galaxy-dev] User is not allowed to view history

[Carl Eberhard]

 She got that error message when she clicked on settings and tried to view
 saved histories.


It looks like this error when loading '/history/view' was fixed with
release_13.02:
https://github.com/galaxyproject/galaxy/commit/3deac8edfba8e8088de855789a28e7d3a328b9b5

If possible, you could update to git branch release_13.02 and get the fix.
Alternately, you could apply that particular patch above to your current
installation but that may cause more conflicts later if you decide to
update.

saw that their history wasn't loading on the right-hand side.


The above does not help the underlying problem of the user's history
erroring in the 'Analyze Data' page.

If you or the user open the javascript console:
http://webmasters.stackexchange.com/questions/8525/how-to-open-the-javascript-console-in-different-browsers

and attempt to load the history, do you see any javascript errors? Do you
see any errors in the server log when he/she attempts to load the history?



On Mon, Jul 13, 2015 at 11:38 AM, Lina L Faller lina.fal...@gmail.com
wrote:

 Hi Carl,

 Thanks for getting back to me!

- The galaxy version is release_2013.01.13.
- The user logged into their galaxy account and saw that their history
wasn't loading on the right-hand side. She got that error message when she
clicked on settings and tried to view saved histories.
- It's not an imported history, she has had the same history since she
first logged in.

 Thanks for any advice you might have!
 Cheers,
 ~Lina

 On Mon, Jul 13, 2015 at 11:24 AM, Carl Eberhard carlfeberh...@gmail.com
 wrote:

 Hi, Lina

 Apologies for the delay. A few questions, please:

- What version is your Galaxy instance running?
- What URL or operation is the user trying when they get that error?
Is it just the 'Analyze Data' page or something else like
'galaxy/history/view?id=id'?
- Is the history imported? Is it accidentally/possibly from a
different user/account?



 On Tue, Jul 7, 2015 at 3:19 PM, Lina L Faller lina.fal...@gmail.com
 wrote:

 Hi all,

 I am new to maintaining the galaxy server at my institute and a user
 emailed me that they get the following error message when trying to view
 their history:

 Either you are not allowed to view this history or the owner of this
 history has not made it accessible.

 Is there a way to modify access privileges of the users' histories?

 Thanks for any advice!
 ~Lina

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Re: [galaxy-dev] filtering html tables in a history item

[Carl Eberhard]

Hi, Mark

This could be done - but not easily. Essentially (if I understand
correctly) you'd want to have a tool that uses a non-conventional control
(the html table and row checkboxes) to allow the user to remove selected
rows.

One of the challenges is: how to create a new (smaller) dataset and still
maintain the chain of reproducibility. You wouldn't want to simply make a
new dataset appear (aka pasted text upload): that wouldn't trace back to
the original table.

I think one of the ways you might do this is:

   1. Create a tool that takes a list of row indices and then removes the
   indicated rows from a selected dataset (this would allow keeping the edits
   in the chain of reproducibility)
   2. Create a simple visualization that renders the original table and
   checkboxes and, when the user is done, calls the tool in (1) via the API
   with the selected row indices.

Like I said - not easy, but that's my idea for it.

Alternately:

   - There may already be a way to select the rows visually using one of
   the more sophisticated tool inputs (someone else will have to speak on that)
   - I believe someone else is working on a table editor - so you may be
   able to wait it out


Carl


On Thu, Jun 4, 2015 at 12:34 PM, Rose Mark USRE mark.r...@syngenta.com
wrote:

  Hello



 Here is what I would like to do.  Any suggestions are appreciated.



 I have a history item that is an html page with an html table.  This table
 has a checkbox on the end of each table row.  I would like it if a user
 could check which rows he would like to keep and then be able to filter out
 all unchecked rows.  I would like for this filtered table to be a
 persistent, new history item.



 Can this be done and how?



 Thanks



 Mark


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 *This message may contain confidential information. If you are not the
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Re: [galaxy-dev] Fwd: History panel error

[Carl Eberhard]

Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization
code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release
(15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05
release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed,
but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after
doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros 
jjalma...@gmail.com wrote:

 Hello Dannon,

 This is the log when a job is executed:

 galaxy.jobs DEBUG 2015-04-24 17:25:27,266 (9568) Working directory for
 job is:
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568
 galaxy.jobs.handler DEBUG 2015-04-24 17:25:27,313 (9568) Dispatching to
 local runner
 galaxy.jobs DEBUG 2015-04-24 17:25:27,600 (9568) Persisting job
 destination (destination id: local)
 galaxy.jobs.handler INFO 2015-04-24 17:25:27,686 (9568) Job dispatched
 galaxy.jobs.runners DEBUG 2015-04-24 17:25:28,465 (9568) command is:
 python
 /steno-internal/projects/galaxy/galaxy-dist/tools/table_gen/generator.py
 /steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat
 1; return_code=$?; python
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/set_metadata_MH6prK.py
 /steno-internal/projects/galaxy/galaxy-dist/database/tmp/tmpw80FFi
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy.json
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_in_HistoryDatasetAssociation_14967_7w0ALE,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_kwds_HistoryDatasetAssociation_14967_uH3ZBP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_out_HistoryDatasetAssociation_14967_5iEavP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_results_HistoryDatasetAssociation_14967_6FT2qV,/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_override_HistoryDatasetAssociation_14967_iOPJoQ;
 sh -c exit $return_code
 galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:28,475 (9568) executing
 job script:
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh
 galaxy.jobs DEBUG 2015-04-24 17:25:28,617 (9568) Persisting job
 destination (destination id: local)
 galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:31,960 execution
 finished:
 /steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh
 galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:32,207 loading metadata
 from file for: HistoryDatasetAssociation 14967
 galaxy.jobs INFO 2015-04-24 17:25:34,775 Collecting job metrics for
 galaxy.model.Job object at 0x7f3154cacad0
 galaxy.jobs DEBUG 2015-04-24 17:25:34,799 job 9568 ended
 galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:34,800 Cleaning up
 external metadata files






 I am not sure at all but I think this is the internal error that I got
 with the history panel problem:

 130.225.125.174 - - [24/Apr/2015:15:22:19 +0200] GET
 /api/histories/32c70b5011288952/contents HTTP/1.1 500 - 
 http://galaxy.bric.dk/history/view_multiple; Mozilla/5.0 (X11; Linux
 x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120
 Safari/537.36
 galaxy.web.framework.decorators ERROR 2015-04-24 15:22:20,033 Uncaught
 exception in exposed API method:
 Traceback (most recent call last):
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py,
 line 251, in decorator
 rval = func( self, trans, *args, **kwargs)
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py,
 line 105, in index
 hda_dict = self.hda_serializer.serialize_to_view( trans, content,
 view=view )
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py,
 line 621, in serialize_to_view
 return self.serialize( trans, item, all_keys )
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py,
 line 453, in serialize
 serialized = super( HDASerializer, self ).serialize( trans, hda, keys )
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py,
 line 566, in serialize
 returned[ key ] = self.serializers[ key ]( trans, item, key )
   File
 /steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py,
 line 403, in 

Re: [galaxy-dev] Visualization in anonymous mode ?

[Carl Eberhard]

Hi Loraine,
I'm glad you solved it.

Understood on the reviewer question. We too would love to get something
reliable, secure, and as-fully-as-possible for both anonymous and
registered users.

Thanks again,
Carl


On Thu, Apr 9, 2015 at 8:44 AM, Loraine Guéguen 
loraine.gueg...@sb-roscoff.fr wrote:

  Hi Carl,

 Sorry for answering so late: I was waiting to see if my solution was
 satisfying. It seems to be ; therefore I don't need the patch (thanks for
 you offer !).
 To enable the phylogeny visualization (with Archaeopteryx), I added an
 html output dataset with links to open each tree created by the tool
 (through javascript). That works.

 Nevertheless, I voted for the trello card, because basic workflow usage
 and visualization would be useful in anonymous mode.

 To answer your question: to my mind, reviewers want to stay anonymous and
 don't want to create an account.

 Thanks,

 Loraine




 Le 08/01/2015 16:50, Carl Eberhard a écrit :

 Hi, Loraine

  It isn't possible currently without modifying the code for your
 installation.

  If you'd like I can provide a patch file that can be applied which will
 allow the visualization button (and the link to phyloviz) to be displayed
 for an anonymous user. This may, however, make it difficult to update at a
 later date and cause problems if the user tries to save or do user-related
 functions in the visualization. Let me know if you'd like that patch.

  I don't have a good answer for your anonymous reviewer problem. If I
 understand correctly, allowing them to be anonymous would be much easier
 for them than logging in?

  In the long run we may be able to make a version of workflows and
 visualizations that can be used by anonymous users (they likely wouldn't be
 fully-featured). This is currently on our list here:
 https://trello.com/c/gja5TtwF. Please feel free to add thoughts,
 suggestions, and your vote for priority.

  Thanks for the information,
 Carl

 On Tue, Jan 6, 2015 at 4:25 AM, Loraine Guéguen 
 loraine.gueg...@sb-roscoff.fr wrote:

  Hi Carl,

 Thanks for your answer.
 I need a tool to visualize a phyloxml file (like phyloviz). No need for
 saving or publishing, only to open the phyloxml file with a visualisator
 through Galaxy. It is not possible ?

 Visualization, and also workflow, in anonymous mode would be useful to us
 in other cases in the future, typically for the reviewers to be able to
 test submitted tools or pipelines.

 Loraine


 Le 05/01/2015 15:54, Carl Eberhard a écrit :

 Hi, Loraine

  At this time there is no way to activate visualizations for anonymous
 users. The logged-in user data is required by most visualizations for some
 features to work (e.g. saving visualizations, publishing, etc.).

  In the future, it might be possible to de-couple these systems and
 provide what your looking for on a case-by-case basis. Which visualization
 would you want to be available? Trackster, Charts, or a local/custom
 visualization?


 On Mon, Dec 22, 2014 at 10:00 AM, Loraine Guéguen 
 loraine.gueg...@sb-roscoff.fr wrote:

 Hi,

 I'd like to use the visualization in anonymous mode, but the visualize
 icon on the dataset is not available in anonymous mode (although it works
 fine when connected).
 Is it possible to activate the dataset visualization in anonymous mode ?

 Thanks,

 Loraine

 --
 Loraine Guéguen

 Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
 Service Informatique et Bioinformatique
 Station Biologique de Roscoff
 FR 2424 CNRS UPMC
 Place Georges Teissier
 CS 90074
 29688 Roscoff cedex
 tel: ++33 (0)2 98 29 56 46 %2B%2B33%20%280%292%2098%2029%2056%2046
 (interne : 415)
 http://abims.sb-roscoff.fr/
 http://www.sb-roscoff.fr/

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 --
 Loraine Guéguen

 Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
 Service Informatique et Bioinformatique
 Station Biologique de Roscoff
 FR 2424 CNRS UPMC
 Place Georges Teissier
 CS 90074
 29688 Roscoff cedex
 tel: ++33 (0)2 98 29 56 46 (interne : 
 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/



 --
 Loraine Guéguen

 Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
 Service Informatique et Bioinformatique
 Station Biologique de Roscoff
 FR 2424 CNRS UPMC
 Place Georges Teissier
 CS 90074
 29688 Roscoff cedex
 tel: ++33 (0)2 98 29 56 46 (interne : 
 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/


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Re: [galaxy-dev] Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

[Carl Eberhard]

In short:


 Question: How can I save a static snapshot...?

You can't yet.

Question: If so, can I then ...recreate the pie chart?

No, not yet.

Overall, these are features that we definitely want and we are working
towards them. Questions remain for me, if I understand your original
questions, about these two features.

Re: saving a visualization to a history:

   - What is the final use of the 'hardcopy' (png or pdf) of the
   visualization? In other words, is it for: publication or exposition,
   summary/overview info, a jumping off point for exploring the data, or
   something else?
   - Isn't this an artifact (a view or byproduct) of the analysis and not
   actually a dataset itself?
   - Do you want a static version or, if possible, easier access to a
   pre-configured interactive visualization?
   - Would a saved visualization (of the type you find under
   'Visualizations-Saved Visualizations' menu) work in a png or pdf's place?

In any event, I think more flexible conversion of visualizations to
hardcopies is doable with some added backend technology like ImageMagick to
render SVG to PNG, etc. If also wrapped in a tool, this would let us add
these to the history.

Re: generating a visualization from a workflow:

   - Would a saved visualization work here as well?


I think the main problem here is translation of what may be a more complex
visualization UI (to control the configuration) to something that can be
more simply rendered in a workflow page (as tool configurations are now).
At least some of the configuration could be handled this way, at any rate -
things like Chart's chart type, and data columns, etc.

There are ways to pass visualization configurations directly over the url,
so this may be easier than I think too.

These are good ideas. Thanks, Peter.


On Tue, Mar 10, 2015 at 7:46 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 On Tue, Mar 10, 2015 at 11:24 AM, Peter Cock p.j.a.c...@googlemail.com
 wrote:
  Hello all,
 
  I'm hoping to construct a workflow which produces a simple tally table
  (using the Count1 tool, Count occurrences of each record, which is
  still shipped with the Galaxy core) and then draws this as a Pie Chart.
 
  1. Using Count1, generate tally table (a simple two column tabular
 file,
  counts and labels as c1 and c2) in the history.
 
  2. Click on the tally table in the history to expand the green box
 
  3. Click on the Visualize icon, pick Charts, click on Pie Chart
 
  4. Click Draw or the Configuration tab.
 
  5. Change donut ratio to zero, show legend to true, and show labels
  output to true.
 
  6. Click Draw or the Add Data tab.
 
  7. Under Select Columns, Labels, pick c2
 
  8. Under Select Columns, Values, keep default c1
 
  9. Click Draw
 
  10. Admire interactive Pie Chart
 
  11. Click Screenshot, offered PNG / SVG / PDF but these are
  only direct downloads (well, PDF is more complicated).
 
  Question: How can I save a static snapshot of the Pie Chart as a
  new history item (other than downloading it locally and then uploading
  it)?
 
  Question: If so, can I then turn this history into a workflow which
  would recreate the pie chart?
 
  As a work around I could write a traditional Galaxy tool which takes
  as input data files(s) and pre-sets the columns and visualisation
  settings, and produces static image(s) as output (e.g. PDF and PNG).
 
  Peter

 I should add that I've tried this on both the latest Galaxy from GitHub
 running locally as my development server, and with the current stable
 release at http://usegalaxy.org

 Also the Screenshot button has a camera icon (makes sense). I'd
 like a Save button (using the disk icon) as well or instead. Meanwhile
 the Draw button (used in steps 4, 6, 9) has a disk icon which seems
 somewhat confusing to me (it doesn't save - it takes you to another
 interactive page within Galaxy).

 Peter
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Re: [galaxy-dev] small issue with the black frame around displayed history item

[Carl Eberhard]

Hi, Hans.

Sorry for the confusion on this.

I've got a card to improve that feature here:
https://trello.com/c/xWdgs01z

I may remove it for visualizations as they're too variable in where/how
they display. Thanks for the info.

Carl

On Tue, Dec 2, 2014 at 11:41 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:

 Hi all

 I am in the process of updating our galaxy servers (from
 latest_2014.08.11 to latest_2014.10.06).

 As announced in the NewsBriefs (https://wiki.galaxyproject.
 org/DevNewsBriefs/2014_10_06), the current/active dataset (the dataset
 being shown/manipulated in the center panel of 'analyze data') is now
 highlighted.

 This is great and will help our users a lot. Thank you very much for this
 new feature!


 Unfortunately, I have encountered a small issue:  when I hover to another
 history item, and click on the 'Visualize' icon. The black frame switches
 to that history item - though nothing changes in the center panel


 As I said not a big problem, just a little bit confusing...shall I make
 Trello card or is there a quick fix possible?


 Regards
 Hans-Rudolf


 --



 Hans-Rudolf Hotz, PhD
 Bioinformatics Support

 Friedrich Miescher Institute for Biomedical Research
 Maulbeerstrasse 66
 4058 Basel/Switzerland
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