Hi Anne,

We're aware that many tests require certain local data to be set up beforehand. 
 As such, these tests can't really be run at a local site.  As part of 
relocating our tools to the tool shed, we hope to fix this issue.

Thanks,
--nate

On Feb 20, 2012, at 1:25 PM, Anne Pajon wrote:

> Hello,
> 
> I am trying to have all functional tests on our production server 
> (galaxy-dist 6621:26920e20157f) run successfully but I do still have failures 
> that I do not know how to solve. 
> 
> Theses failures are related to unexpected differences probably due to 
> versions of software that have been upgraded recently.
> 
> ( Extract genomic DNA 1 ) > Test-1
> ( Extract genomic DNA 1 ) > Test-2
> ( Extract genomic DNA 1 ) > Test-3
> ( Extract genomic DNA 1 ) > Test-4
> ( Extract genomic DNA 1 ) > Test-5
> ( GeneBed_Maf_Fasta2 ) > Test-1
> ( Interval2Maf1 ) > Test-1
> ( Interval2Maf1 ) > Test-3
> ( Interval_Maf_Merged_Fasta2 ) > Test-1
> ( Interval_Maf_Merged_Fasta2 ) > Test-2
> ( LinearRegression1 ) > Test-1
> ( XY_Plot_1 ) > Test-1
> ( cca1 ) > Test-1
> ( histogram_rpy ) > Test-1
> ( kpca1 ) > Test-1
> ( pca1 ) > Test-1
> ( pca1 ) > Test-2
> ( pca1 ) > Test-3
> ( plot_for_lda_output1 ) > Test-1
> ( qual_stats_boxplot ) > Test-1
>    AssertionError: History item 2 different than expected, difference (using 
> diff)
> 
> ( gops_join_1 ) > Test-4
>   TwillAssertionError: code is 500 != 200
> 
> I do also have failures due to missing data but I am struggling to find out 
> where to download them.
> 
> ( gd_select_snps ) > Test-1
>   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
> blurb: error
>   'bighorn' does not appear in location file 
> '/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc'
> 
> ( Annotation_Profiler_0 ) > Test-1
> ( Annotation_Profiler_0 ) > Test-2
>   AssertionError: Configuration error: Table directory is missing 
> (/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18)
> 
> ( Interval2Maf_pairwise1 ) > Test-1
>   AssertionError: Attempting to set field 'mafType' to value 
> '['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find 
> value/label "PAIRWISE_hg17_fr1" in list control
> 
> ( maf_stats1 ) > Test-1
> ( maf_stats1 ) > Test-2
>   AssertionError: Attempting to set field 'maf_source_type|mafType' to value 
> '['8_WAY_MULTIZ_hg17']' in form 'tool_form' threw exception: cannot find 
> value/label "8_WAY_MULTIZ_hg17" in list control
> 
> ( phastOdds_for_intervals ) > Test-1
>   AssertionError: Attempting to set field 'score_file' to value 
> '['/galaxy/data/phastOdds_precomputed/encode_SEP-2005_\
> tba.v2_phastOdds']' in form 'tool_form' threw exception: cannot find 
> value/label "/galaxy/data/phas..2_phastOdds" in li\
> st control
> 
> ( aggregate_scores_in_intervals2 ) > Test-1
> ( aggregate_scores_in_intervals2 ) > Test-2
>   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
> blurb: error
> 
> ( gencode_partition1 ) > Test-1
>   Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
>   Error loading partitioning dataset.
> 
> ( lda_analy1 ) > Test-1
>   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
> blurb: error
> 
> The last failure is related to genome diversity and the fact that it calls 
> python2.5. I've changed it to python for testing but the test still fails.
> 
> ( gd_extract_flanking_dna ) > Test-1
> ( gd_extract_primers ) > Test-1
> ( gd_select_restriction_enzymes ) > Test-1
>   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
> blurb: error
>   python2.5: command not found
>> if changed to python: ERROR: 'NoneType' object has no attribute 'rfind'
> 
> 
> Is there a way to fix these failures? Any help would be very much 
> appreciated. 
> Thanks,
> Anne.
> 
> --
> Anne Pajon, Ph.D.
> Cancer Research UK - Cambridge Research Institute
> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> anne.pa...@cancer.org.uk | +44 (0)1223 404 334
> 
> 
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