details: http://www.bx.psu.edu/hg/galaxy/rev/30cd8d9f8ac9 changeset: 3296:30cd8d9f8ac9 user: Greg Von Kuster greg@bx.psu.edu date: Thu Jan 28 11:06:38 2010 -0500 description: Remove unneeded legacy "export_url" code from the set_peek methods in binary data types - fixes uploading binary files to a library. Also fix main's tool_conf again.
diffstat:
lib/galaxy/datatypes/binary.py | 4 ---- tool_conf.xml.main | 6 +++--- 2 files changed, 3 insertions(+), 7 deletions(-)
diffs (56 lines):
diff -r 3669500f699c -r 30cd8d9f8ac9 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py Thu Jan 28 10:51:38 2010 -0500 +++ b/lib/galaxy/datatypes/binary.py Thu Jan 28 11:06:38 2010 -0500 @@ -35,7 +35,6 @@
def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: - export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'ab1','name':'ab1 sequence','info':'Sequence file','dbkey':dataset.dbkey} ) dataset.peek = "Binary ab1 sequence file" dataset.blurb = data.nice_size( dataset.get_size() ) else: @@ -121,7 +120,6 @@ return False def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: - export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'bam','name':'bam alignments','info':'Alignments file','dbkey':dataset.dbkey} ) dataset.peek = "Binary bam alignments file" dataset.blurb = data.nice_size( dataset.get_size() ) else: @@ -163,7 +161,6 @@
def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: - export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'scf','name':'scf sequence','info':'Sequence file','dbkey':dataset.dbkey}) dataset.peek = "Binary scf sequence file" dataset.blurb = data.nice_size( dataset.get_size() ) else: @@ -193,7 +190,6 @@ return False def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: - export_url = "/history_add_to?" + urlencode( {'history_id':dataset.history_id,'ext':'sff','name':'sff file','info':'sff file','dbkey':dataset.dbkey} ) dataset.peek = "Binary sff file" dataset.blurb = data.nice_size( dataset.get_size() ) else: diff -r 3669500f699c -r 30cd8d9f8ac9 tool_conf.xml.main --- a/tool_conf.xml.main Thu Jan 28 10:51:38 2010 -0500 +++ b/tool_conf.xml.main Thu Jan 28 11:06:38 2010 -0500 @@ -279,14 +279,14 @@ <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> <section name="NGS: Mapping" id="ngs_mapping"> - <label text="Illumina" /> + <label text="Illumina" id="illumina"/> <tool file="sr_mapping/bowtie_wrapper.xml" /> <tool file="sr_mapping/bwa_wrapper.xml" /> - <label text="Roche-454" /> + <label text="Roche-454" id="roche_454"/> <tool file="sr_mapping/lastz_wrapper.xml" /> <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> - <label text="AB-SOLiD" /> + <label text="AB-SOLiD" id="ab_solid"/> <tool file="sr_mapping/bowtie_color_wrapper.xml" /> </section> <section name="NGS: SAM Tools" id="samtools">