Hi Peter,

Looks like you are missing the -data_managers flag, try this:

run_functional_tests.sh -data_managers -id data_manager_blast_db

Let us know if you encounter more issues.

Thanks,

Dan


On Apr 11, 2014, at 12:15 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> Hi all,
> 
> I'm currently trying to manually install Dan's example Data Manager
> for the NCBI BLAST databases - but without using the Tool Shed:
> http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb
> 
> To be precise, I'm currently using a slightly modified version which
> we've moved into the Galaxy BLAST+ wrapper repository (thus far,
> only slight changes to folder names have been made from Dan's original):
> https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb
> https://github.com/peterjc/galaxy_blast/commit/21d7cff3e8dca13c4bd0f716a79a9f00c59f0b5c
> 
> My goal is to be able to run the functional tests,
> 
> $ ./run_functional_tests.sh -id data_manager_blast_db
> 
> As with any other manually installed tool, I have added this
> data-manager to my tool_conf.xml.sample file (and for local
> testing via the GUI, the tool_conf.xml file as well):
> 
>    <tool file="ncbi_blastdb/blastdb.xml" />
> 
> Specific to data-managers, I have manually incorporated
> the additions to the central data_manager_conf.xml file
> (this would normally be merged at runtime if installed from
> the ToolShed):
> 
> $ more data_manager_conf.xml
> <?xml version="1.0"?>
> <data_managers>
>    <data_manager tool_file="ncbi_blastdb/blastdb.xml"
> id="data_manager_blast_db">
>        <data_table name="blastdb">
>            <output>
>                <column name="value" />
>                <column name="name" />
>                <column name="path" output_ref="out_file" >
>                    <move type="directory">
>                        <target
> base="${GALAXY_DATA_MANAGER_DATA_PATH}">blastdb/${path}</target>
>                    </move>
> 
> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/blastdb/${path}/${nucleotide_alias_name}</value_translation>
>                    <value_translation
> type="function">abspath</value_translation>
>                </column>
>            </output>
>        </data_table>
>    </data_manager>
> </data_managers>
> 
> Note the tool_file setting points correctly at the relative path
> within the tools
> folder, and the tool does define a test:
> 
> $ more tools/ncbi_blastdb/blastdb.xml
> <tool id="data_manager_blast_db" name="Blast DB" version="0.0.2"
> tool_type="manage_data">
>    <description>Downloader</description>
> ...
>    <tests>
>        <test>
>            <param name="blastdb_name" value="est"/>
>            <param name="advanced_selector" value="basic"/>
>            <output name="out_file" file="est_out.json"/>
>        </test>
>    </tests>
> ...
> 
> $ ./run_functional_tests.sh -list | grep manager
> data_manager_blast_db                            Blast DB
> 
> $ ./run_functional_tests.sh -id data_manager_blast_db
> ...
> galaxy.tools DEBUG 2014-04-11 15:59:00,780 Loaded tool id:
> data_manager_blast_db, version: 0.0.2 into tool panel.
> ...
> galaxy.tools.data_manager.manager DEBUG 2014-04-11 15:59:00,864 Loaded
> Data Manager: data_manager_blast_db
> ...
> Failure: ValueError (No such test TestForTool_data_manager_blast_db) ... ERROR
> 
> ======================================================================
> ERROR: Failure: ValueError (No such test TestForTool_data_manager_blast_db)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/mnt/galaxy/galaxy-central/eggs/nose-0.11.1-py2.6.egg/nose/failure.py",
> line 39, in runTest
>    raise self.exc_class(self.exc_val)
> ValueError: No such test TestForTool_data_manager_blast_db
> 
> ----------------------------------------------------------------------
> 
> I get the same error via TravisCI, e.g.
> https://travis-ci.org/peterjc/galaxy_blast/builds/22782979
> 
> (This suggests using Twill vs the API does not matter)
> 
> Am I missing something simple here?
> 
> Thanks,
> 
> Peter

___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to