Hello Ira,

I believe proprietary datatype sniffers included in tool shed repositories are 
loading as expected - at least I cannot reproduce the behavior you are seeing.  
The datatypes_conf.xml file included in the latest revision of the gmap 
repository on the main Galaxy tool shed looks like this:

<?xml version="1.0"?>
<datatypes>
    <datatype_files>
        <datatype_file name="gmap.py"/>
    </datatype_files>
    <registration>
        <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" 
display_in_upload="False"/>
        <datatype extension="gmapsnpindex" 
type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/>
        <datatype extension="iit" 
type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/>
        <datatype extension="splicesites.iit" 
type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" 
display_in_upload="True"/>
        <datatype extension="introns.iit" 
type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/>
        <datatype extension="snps.iit" 
type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/>
        <datatype extension="gmap_annotation" 
type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/>
        <datatype extension="gmap_splicesites" 
type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/>
        <datatype extension="gmap_introns" 
type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/>
        <datatype extension="gmap_snps" 
type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/>
    </registration>
    <sniffers>
        <sniffer type="galaxy.datatypes.gmap:IntervalAnnotation"/>
        <sniffer type="galaxy.datatypes.gmap:SpliceSiteAnnotation"/>
        <sniffer type="galaxy.datatypes.gmap:IntronAnnotation"/>
        <sniffer type="galaxy.datatypes.gmap:SNPAnnotation"/>
    </sniffers>
</datatypes>

Here is the snippet of my paster log when I install the gmap tool shed 
repository - notice that the tools, datatypes and sniffers are all loaded.  I'm 
installing it from a local tool shed, but I downloaded the latest version from 
the main Galaxy tool shed and uploaded it with no changes to my local tool shed 
for testing.

galaxy.web.controllers.admin_toolshed DEBUG 2012-02-06 10:50:33,686 Loading new 
tool panel section: gmap
galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Installing repository 'gmap'
galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Cloning 
http://t...@gvk.bx.psu.edu:9009/repos/test/gmap
destination directory: gmap
requesting all changes
adding changesets
adding manifests
adding file changes
added 1 changesets with 10 changes to 10 files
updating to branch default
10 files updated, 0 files merged, 0 files removed, 0 files unresolved
galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,062 Updating cloned repository 
to revision "dbcccd1e4dfd"
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
docutils WARNING 2012-02-06 10:50:34,388 <string>:10: (WARNING/2) Explicit 
markup ends without a blank line; unexpected unindent.

galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,437 Adding new row (or updating 
an existing row) for repository 'gmap' in the tool_shed_repository table.
docutils WARNING 2012-02-06 10:50:34,533 <string>:10: (WARNING/2) Explicit 
markup ends without a blank line; unexpected unindent.

docutils WARNING 2012-02-06 10:50:34,657 <string>:10: (WARNING/2) Explicit 
markup ends without a blank line; unexpected unindent.

galaxy.tools DEBUG 2012-02-06 10:50:34,718 Reloading section: gmap
galaxy.tools DEBUG 2012-02-06 10:50:34,769 Loaded tool id: 
gvk.bx.psu.edu:9009/repos/test/gmap/gmap/2.0.1, version: 2.0.1.
galaxy.tools DEBUG 2012-02-06 10:50:34,813 Loaded tool id: 
gvk.bx.psu.edu:9009/repos/test/gmap/gmap_build/2.0.0, version: 2.0.0.
docutils WARNING 2012-02-06 10:50:34,846 <string>:10: (WARNING/2) Explicit 
markup ends without a blank line; unexpected unindent.

galaxy.tools DEBUG 2012-02-06 10:50:34,877 Loaded tool id: 
gvk.bx.psu.edu:9009/repos/test/gmap/gsnap/2.0.1, version: 2.0.1.
galaxy.tools DEBUG 2012-02-06 10:50:34,911 Loaded tool id: 
gvk.bx.psu.edu:9009/repos/test/gmap/gmap_iit_store/2.0.0, version: 2.0.0.
galaxy.tools DEBUG 2012-02-06 10:50:34,962 Loaded tool id: 
gvk.bx.psu.edu:9009/repos/test/gmap/gmap_snpindex/2.0.0, version: 2.0.0.
galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,147 Loading datatypes from 
/Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gmap/dbcccd1e4dfd/gmap/gmap-93911bac43da/tool-data/datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,159 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:IntervalAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,160 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:SpliceSiteAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:IntronAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:SNPAnnotation




If I stop and restart my Galaxy server after I've installed the gmap 
repository, everything loads correctly as well:

galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,713 Loading datatypes from 
../shed_tools/gvk.bx.psu.edu/repos/test/gmap/dbcccd1e4dfd/gmap/gmap-93911bac43da/tool-data/datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,715 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:IntervalAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,715 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:SpliceSiteAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,716 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:IntronAnnotation
galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,716 Loaded sniffer for 
datatype: galaxy.datatypes.gmap:SNPAnnotation


Have you made any changes to your local Galaxy instance that may have resulted 
in proprietary datatypes / sniffers not being loaded correctly?  What version 
of the Galaxy distribution are you running?  You should be at 6672:e38a9eb21336 
from the central repository for the latest tool shed code.  However, 
proprietary datatype support has not been touched in some time.


On Feb 5, 2012, at 7:04 PM, Ira Cooke wrote:

> Hi, 
> 
> We're developing a suite of galaxy tools for doing proteomics.  As part of 
> that we're developing a display application ( 
> https://bitbucket.org/Andrew_Brock/proteomics-visualise )  for viewing pepXML 
> and protXML files and we rely very heavily on custom datatypes.  We've got 
> this working in a fork of galaxy-dist ( 
> https://bitbucket.org/iracooke/galaxy-proteomics ) but would love to be able 
> to get rid of this fork and integrate all our customisations into a shed 
> tool. 
> 
> I initially tried following the instructions here 
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Including_proprietary_data_types_that_use_class_modules_contained_in_your_repository
>  and was able to successfully get my custom datatypes to load.  Unfortunately 
> though I could not get my sniffers to work.  I think there are two reasons 
> for this; 
> 
> The first problem is that it looks like the sniffers are never loaded.  I get 
> errors like this when the tool is loaded;
> 
> galaxy.datatypes.registry DEBUG 2012-02-06 10:26:51,317 Loading datatypes 
> from 
> /Users/iracooke/Sources/shed_tools_galaxy_central/toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/93911bac43da/gmap/tool-data/datatypes_conf.xml
> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,318 Error appending 
> sniffer for datatype galaxy.datatypes.gmap:IntervalAnnotation to sniff_order: 
> No module named gmap
> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending 
> sniffer for datatype galaxy.datatypes.gmap:SpliceSiteAnnotation to 
> sniff_order: No module named gmap
> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending 
> sniffer for datatype galaxy.datatypes.gmap:IntronAnnotation to sniff_order: 
> No module named gmap
> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending 
> sniffer for datatype galaxy.datatypes.gmap:SNPAnnotation to sniff_order: No 
> module named gmap
> 
> These errors aren't just restricted to my tool ... as you can see from the 
> above they also occur in the gmap example installed from the main galaxy 
> toolshed.  
> 
> I tried hacking the code in registration.py to get this to work ... it looks 
> like the section where sniffers are loaded does not use the 
> "imported_modules" variable.  I was able to get this error message to go 
> away, but I still don't get proper sniffer behaviour (eg when I click "Auto 
> detect" when editing a dataset the dataset is set to a generic type).  
> 
> Another issue is that I would like the sniffers loaded from my shed_tool to 
> be used by the "Upload" tool .. but if I look at the source for upload.py and 
> upload.xml I see 
> 
> -- Upload.xml
>  <command interpreter="python">
>       upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
> 
> --Upload.py
> def __main__():
> 
> ....
> 
>     registry = Registry()
>     registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] )
> 
> which looks like the upload tool is not configured to use the custom 
> datatypes available in shed tools.
> 
> 
> Would it be possible to make the following changes;
> 
> (a) Add custom sniffers to the sniff order when shed tools are loaded.   
> Importantly since custom datatypes are usually quite specific I would suggest 
> that these are loaded at the top of the sniff order?  Or alternatively if a 
> sniffer is for a datatype that descends from a superclass it should have 
> priority over the parent class (since by definition it is more specific). 
> 
> (b) Change the upload tool so that it respects custom sniffers in shed tools. 
> 
> I guess that our case is a bit unusual in that we are trying to co-opt galaxy 
> ( a genomics tool) to do proteomics ... so I understand that these changes 
> might not be a priority.  Nevertheless, if this could be done it would be 
> fantastic for us as we could abandon our fork and have all our functionality 
> included in a shed tool. 
> 
> 
> Regards
> Ira
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