[Bioperl-l] Need some bioperl-run tests

[Chris Fields]

All,

I have been updating bioperl-run tests in subversion to use  
Bio::Root::Test.  I need devs and anyone interested to check out the  
latest bioperl-run and run tests checking for failures.  I'll start  
tracking errors.

I have also noticed that Pise.t and AnalysisFactory_soap.t tests are  
failing.  I have updated the tests so they run to completion, but (if  
possible) I need some indication whether these web services are still  
available and should be incldued in a BioPerl-run 1.6 release.

-c

cjfields:run cjfields$ perl -MSOAP::Lite -M5.010 -e 'say  
$SOAP::Lite::VERSION'
0.710.08
cjfields:run cjfields$ perl -v

This is perl, v5.10.0 built for darwin-2level
Copyright 1987-2007, Larry Wall
...
cjfields:run cjfields$ ./Build test --test-files t/ 
AnalysisFactory_soap.t --test-files t/Pise.t --verbose
t/AnalysisFactory_soap......
1..12
ok 1 - use Bio::Tools::Run::AnalysisFactory;
ok 2 - The object isa Bio::Tools::Run::AnalysisFactory
ok 3 - The object isa Bio::Tools::Run::AnalysisFactory
ok 4 - Non existant access method threw an error
ok 5 - use SOAP::Lite;
ok 6 - The object isa ARRAY
ok 7 - available_categories returned category with protein
ok 8 - The object isa ARRAY
ok 9 - available_analyses returned category with seqret
ok 10 - The object isa ARRAY
ok 11 - available_analyses("edit") returned something
not ok 12

#   Failed test at t/AnalysisFactory_soap.t line 51.
# create_analysis failed :proxy: transport protocol not specified
# Looks like you failed 1 test of 12.
  Dubious, test returned 1 (wstat 256, 0x100)
  Failed 1/12 subtests
t/Pise......................
1..15
ok 1 - use Bio::Tools::Run::tRNAscanSE;
ok 2 - use Bio::Root::IO;
ok 3 - use Bio::Seq;
ok 4 - use XML::Parser::PerlSAX;
Subroutine stdout redefined at /Users/cjfields/bioperl/run/Bio/Tools/ 
Run/PiseJob.pm line 609.
Subroutine stderr redefined at /Users/cjfields/bioperl/run/Bio/Tools/ 
Run/PiseJob.pm line 644.
ok 5 - use Bio::Tools::Run::AnalysisFactory::Pise;
ok 6 - use Bio::Tools::Genscan;
ok 7 - use Bio::SeqIO;
ok 8 - The object isa Bio::Tools::Run::AnalysisFactory::Pise
ok 9 - The object isa Bio::Tools::Run::PiseApplication::golden
ok 10 - The object isa Bio::Tools::Run::PiseJob
not ok 11 - No error
# Error: Bio::Tools::Run::PiseJob _submit: Moved Permanently

#   Failed test 'No error'
#   at t/Pise.t line 69.
ok 12 # SKIP Job Error
ok 13 # SKIP Job Error
ok 14 # SKIP Job Error
ok 15 # SKIP Job Error
# Looks like you failed 1 test of 15.
  Dubious, test returned 1 (wstat 256, 0x100)
  Failed 1/15 subtests
	(less 4 skipped subtests: 10 okay)

Test Summary Report
-------------------
t/AnalysisFactory_soap.t (Wstat: 256 Tests: 12 Failed: 1)
   Failed test:  12
   Non-zero exit status: 1
t/Pise.t                (Wstat: 256 Tests: 15 Failed: 1)
   Failed test:  11
   Non-zero exit status: 1
Files=2, Tests=27, 16 wallclock secs ( 0.02 usr  0.01 sys +  1.00  
cusr  0.17 csys =  1.20 CPU)
Result: FAIL
Failed 2/2 test programs. 2/27 subtests failed.