details: http://www.bx.psu.edu/hg/galaxy/rev/8938319bf173 changeset: 3550:8938319bf173 user: fubar: ross Lazarus at gmail period com date: Mon Mar 22 12:32:14 2010 -0400 description: Assume plink is on the executing node path for converters Add a non-specific exception catcher to archive creation code in library_common
diffstat:
lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml | 2 +- lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml | 2 +- lib/galaxy/datatypes/genetics.py | 5 ++++- lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/library_common.py | 5 +++++ 5 files changed, 12 insertions(+), 4 deletions(-)
diffs (66 lines):
diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml --- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml Mon Mar 22 12:32:14 2010 -0400 @@ -3,7 +3,7 @@ <!-- Used on the metadata edit page. --> <command interpreter="python"> lped_to_pbed_converter.py '$input1.extra_files_path/$input1.metadata.base_name' - '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' + '$output1' '$output1.files_path' 'plink' </command> <inputs> <param format="lped" name="input1" type="data" label="Choose linkage pedigree file"/> diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml --- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml Mon Mar 22 12:32:14 2010 -0400 @@ -3,7 +3,7 @@ <!-- Used on the metadata edit page. --> <command interpreter="python"> pbed_to_lped_converter.py '$input1.extra_files_path/$input1.metadata.base_name' - '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' + '$output1' '$output1.files_path' 'plink' </command> <inputs> <param format="pbed" name="input1" type="data" label="Choose compressed Plink binary format genotype file"/> diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Mar 22 12:32:14 2010 -0400 @@ -114,7 +114,10 @@ npeek = 5 out = ['<table cellspacing="0" cellpadding="3">'] f = open(dataset.file_name,'r') - d = [f.next() for x in range(npeek)] + d = f.readlines()[:5] + if len(d) == 0: + out = "Cannot find anything to parse in %s" % dataset.name + return out hasheader = 0 try: test = ['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Mon Mar 22 12:32:14 2010 -0400 @@ -332,7 +332,7 @@ trans.response.set_content_type( mime ) return open( file_path ) else: - return "Could not find '%s' on the extra files path." % filename + return "Could not find '%s' on the extra files path %s." % (filename,file_path)
mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Mar 22 12:32:14 2010 -0400 @@ -1334,6 +1334,11 @@ log.exception( "Unable to create archive for download" ) msg = "Unable to create archive for download, please report this error" messagetype = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0]) + msg = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + messagetype = 'error' if not error: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) seen = []