Re: [galaxy-dev] functional test failures
Hi Nate, Thanks for your answer. I am looking forward at the relocation of the tools to the tool shed then. Cheers, Anne. On 26 Mar 2012, at 14:49, Nate Coraor wrote: 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 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other
Re: [galaxy-dev] functional test failures
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 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/ ___ Please keep all replies on the list by
[galaxy-dev] functional test failures
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 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/
