Daniel Blankenberg 994f2acdea Allow uploading and use of composite files in toolbox tests. Along with setting each component of a composite datatype, metadata attributes (e.g. basename in Rgenetics datatypes) can be set. ...

Example Tool:

<tool id='temp' name='temp test'>
    <description>test</description>
    <command>cat ${i.extra_files_path}/${i.metadata.base_name}.fam &gt; $out_file1</command>
    <inputs>
      <param name="i"  type="data" label="RGenetics genotype data from your current history" format="pbed" />
    </inputs>
   <outputs>
       <data format="text" name="out_file1" />
   </outputs>
<tests>
<test>
 <param name='i' ftype='pbed'>
    <metadata name='base_name' value='rgenetics_CHANGED' />
    <composite_data value='temp/somefile1' />
    <composite_data value='temp/somefile2' />
    <composite_data value='temp/somefile3' />
 </param>
 <output name='out_file1' file='temp/somefile3' />
 </test>
 </tests>
</tool>

2010-03-09 13:54:30 -05:00

..

__init__.py

New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.

2009-10-20 13:08:29 -04:00

test_DNAse_flanked_genes.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

test_forms_and_requests.py

Fixed broken functional tests

2010-03-03 13:51:29 -05:00

test_get_data.py

Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.

2009-12-07 16:04:33 -05:00

test_history_functions.py

Unified sharing model for histories, workflows, and pages; these items can now be private, shared with a set of users, accessible via link for viewing and importing, or published. Specific features added are: (1) added published flag to histories and workflows, added importable flag to pages; (2) added unified sharing interface for setting sharing options; (3) updated grid framework to use new sharing model; (4) updated functional tests to reflect new sharing model; (5) added legacy support for making pretty URLs for items already made importable. Also, new sharing model does not yet allow sharing of multiple items at once, so functional test for this feature has been commented out. Fixes #229; Fixes #182.

2010-01-20 12:26:13 -05:00

test_metadata_editing.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

test_security_and_libraries.py

Re-fix new functional test support for setting check boxes and boolean tool params to false, and fix a broken functional test in the security and libraries suite.

2010-02-19 10:01:33 -05:00

test_toolbox.py

Allow uploading and use of composite files in toolbox tests. Along with setting each component of a composite datatype, metadata attributes (e.g. basename in Rgenetics datatypes) can be set.

2010-03-09 13:54:30 -05:00

test_user_info.py

Passwords are no longer changed ( sanitized ) as part of processing the request. Enhanced functional tests to cover the scenario where passwords include chars that break in sanitization.

2010-03-01 16:07:54 -05:00