Hello Ira,

Very sorry for the back-and-forth on this.  The behavior you encountered was accurate - the environment in which I was testing was not pristine.  I have committed a fix for this issue in revision b4ba8b20d78d, which is now available from our central repo.  

I started looking at changing things so that proprietary sniffers are loaded before the sniffers defined in the Galaxy distribution, and determined that this will be a bit non-trivial.  Problems arise due to potential conflicts between a proprietary datatype that has the same extension as a datatype defined in the Galaxy distribution.  The approach I've taken to deal with this is that datatypes in the Galaxy distribution get loaded first, and then any conflicting proprietary datatypes will be ignored.  Loading proprietary datatypes first will not allow for this rule.  

I'll gladly listen to advice from the community on this, but in the meantime, proprietary datatypes and sniffers are loaded after those in the distribution.

Thanks for your patience and help on this issue.

Greg

On Feb 6, 2012, at 11:37 PM, Ira Cooke wrote:

Hi Greg, 

As far as I know there is nothing in my local setup that affects this.  As I test I did the following; 

Checked out a clean copy of galaxy-central 
Edited my universe_wsgi.ini as follows;
- Changed the port to 8300
- Added an admin user
- Uncommented this line
tool_config_file = tool_conf.xml,shed_tool_conf.xml

Edited shed_tool_conf.xml to point to ../shed_tools_galaxy_central (which is an empty directory)

Started up galaxy 
./run.sh --reload

I then went straight to admin -> "Search and browse tool sheds" and selected the main galaxy toolshed. 
I then selected the gmap tool and told it to install.  My paster log is at the bottom of this mail.

My system is Mac OSX 10.7.2 and I'm running python 2.7.1

I then went to the relevant bit of code and inserted some print statements.  I found that; 

On line 191 in registry.py there is;

module = __import__( datatype_module )

and the value of datatype_module is galaxy.datatypes.gmap

this line seems to be causing the exception ... I'm not a python programmer so I don't really know how module importing works ... could this be related to the version of python I'm running?  
alternatively should the "imported_modules" variable be used here .. since wouldn't galaxy.datatypes.gmap suggest that the module needs to be located inside the main galaxy lib rather than in the shed_tools.

Strange that I'm the only one who gets these errors?  Any ideas what it could be?

Ira


-- paster log --

destination directory: gmap
requesting all changes
adding changesets
adding manifests
adding file changes
added 11 changesets with 32 changes to 17 files
updating to branch default
resolving manifests
getting README
getting gmap.xml
getting gmap_build.xml
getting gsnap.xml
getting iit_store.xml
getting lib/galaxy/datatypes/gmap.py
getting snpindex.xml
getting tool-data/datatypes_conf.xml
getting tool-data/gmap_indices.loc.sample
9 files updated, 0 files merged, 0 files removed, 0 files unresolved
galaxy.util.shed_util DEBUG 2012-02-07 14:25:35,100 Updating cloned repository to revision "93911bac43da"
resolving manifests
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
docutils WARNING 2012-02-07 14:25:35,512 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.

galaxy.util.shed_util DEBUG 2012-02-07 14:25:35,589 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table.
docutils WARNING 2012-02-07 14:25:35,701 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.

docutils WARNING 2012-02-07 14:25:35,863 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.

galaxy.tools DEBUG 2012-02-07 14:25:35,932 Reloading section: gmap
galaxy.tools DEBUG 2012-02-07 14:25:35,997 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap/2.0.1, version: 2.0.1.
galaxy.tools DEBUG 2012-02-07 14:25:36,026 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_build/2.0.0, version: 2.0.0.
docutils WARNING 2012-02-07 14:25:36,077 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent.

galaxy.tools DEBUG 2012-02-07 14:25:36,103 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gsnap/2.0.1, version: 2.0.1.
galaxy.tools DEBUG 2012-02-07 14:25:36,268 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_iit_store/2.0.0, version: 2.0.0.
galaxy.tools DEBUG 2012-02-07 14:25:36,316 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_snpindex/2.0.0, version: 2.0.0.
galaxy.datatypes.registry DEBUG 2012-02-07 14:25:38,608 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 2012-02-07 14:25:38,609 Error appending sniffer for datatype galaxy.datatypes.gmap:IntervalAnnotation to sniff_order: No module named gmap
galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,609 Error appending sniffer for datatype galaxy.datatypes.gmap:SpliceSiteAnnotation to sniff_order: No module named gmap
galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,610 Error appending sniffer for datatype galaxy.datatypes.gmap:IntronAnnotation to sniff_order: No module named gmap
galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,610 Error appending sniffer for datatype galaxy.datatypes.gmap:SNPAnnotation to sniff_order: No module named gmap




On 07/02/2012, at 3:05 AM, Greg Von Kuster wrote:

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://test@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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