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Fixed my previous fix for copying history items to a library, which really didn't fix anything.  Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool.  Renamed the test files for the tools to have the Galaxy supported file extension.

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This commit is contained in:
Greg Von Kuster
2010-01-14 09:44:58 -05:00
parent de4c2cc755
commit 927cfe685c
5 changed files with 16 additions and 14 deletions
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lib/galaxy/web/controllers/library_common.py
+1 -1
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@@ -911,7 +911,7 @@ class LibraryCommon( BaseController ):
dataset_names = []
created_ldda_ids = ''
for hda_id in hda_ids:
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) )
if hda:
ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
templates/library/common/common.mako
+1 -1
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@@ -308,7 +308,7 @@
%endif
%for hda in history.active_datasets:
<div class="form-row">
<input name="hda_ids" value="${hda.id}" type="checkbox"/>${hda.hid}: ${hda.name}
<input name="hda_ids" value="${trans.security.encode_id( hda.id )}" type="checkbox"/>${hda.hid}: ${hda.name}
</div>
%endfor
<div class="form-row">
tools/filters/lav_to_bed.xml
+2 -2
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@@ -9,10 +9,10 @@
<data name="bed_file2" format="bed"/>
</outputs>
<tests>
<!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
<test>
<param name="lav_file" value="2.lav" ftype="lav" />
<output name="bed_file2" file="lav_to_bed_out2.bed" />
<output name="bed_file2" file="lav_to_bed_out_1.bed" />
<output name="bed_file2" file="lav_to_bed_out_2.bed" />
</test>
</tests>
<help>
tools/metag_tools/split_paired_reads.xml
+3 -2
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@@ -12,8 +12,9 @@
</outputs>
<tests>
<test>
<param name="input" value="split_paired_reads_test1.fastq" ftype="fastqsanger"/>
<output name="output1" file="split_paired_reads_test1.out1" ftype="fastqsanger"/>
<param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
<output name="output1" file="split_paired_reads_out_1.fastqsanger" ftype="fastqsanger"/>
<output name="output2" file="split_paired_reads_out_2.fastqsanger" ftype="fastqsanger"/>
</test>
</tests>
<help>
tools/next_gen_conversion/solid2fastq.xml
+9 -8
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@@ -42,26 +42,27 @@
</outputs>
<tests>
<test>
<param name="input1" value="fr.csf" ftype="csfasta"/>
<param name="input2" value="fr.qual" ftype="qualsolid" />
<output name="out_file1" file="f.fastq"/>
<param name="input1" value="fr.csfasta" ftype="csfasta"/>
<param name="input2" value="fr.qualsolid" ftype="qualsolid" />
<param name="paired" value="no"/>
<param name="qual" value="0" />
<param name="trim_first_base" value="No" />
<param name="trim_name" value="No" />
<param name="double_encode" value="No"/>
<output name="out_file1" file="solid2fastq_out_1.fastq"/>
</test>
<test>
<param name="input1" value="fr.csf" ftype="csfasta"/>
<param name="input2" value="fr.qual" ftype="qualsolid" />
<param name="input3" value="rr.csf" ftype="csfasta"/>
<param name="input4" value="rr.qual" ftype="qualsolid" />
<output name="out_file1" file="fr_file1.fastq"/>
<param name="input1" value="fr.csfasta" ftype="csfasta"/>
<param name="input2" value="fr.qualsolid" ftype="qualsolid" />
<param name="input3" value="rr.csfasta" ftype="csfasta"/>
<param name="input4" value="rr.qualsolid" ftype="qualsolid" />
<param name="paired" value="yes"/>
<param name="qual" value="0" />
<param name="trim_first_base" value="No" />
<param name="trim_name" value="Yes" />
<param name="double_encode" value="No"/>
<output name="out_file1" file="solid2fastq_out_2.fastq"/>
<output name="out_file2" file="solid2fastq_out_3.fastq"/>
</test>
</tests>
<help>