1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ded3aac16a24/
changeset: ded3aac16a24
user: natefoo
date: 2011-12-06 17:41:32
summary: Missing template changes from the last commit.
affected #: 1 file
diff -r 3c9f7bfc1bcf2be295c61857b836eb44b7dc8982 -r ded3aac16a24060d04c34da015958a1aee94610b templates/show_params.mako
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -50,6 +50,8 @@
<tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr><tr><td>Format:</td><td>${hda.ext}</td></tr><tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr>
+ <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr>
+ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr></table><br /><table class="tabletip">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/87268f2b439d/
changeset: 87268f2b439d
user: dannon
date: 2011-12-06 15:15:43
summary: Fix bad merge.
affected #: 1 file
diff -r 8993f7342095d3fac1feb3458ecee909ba678e11 -r 87268f2b439d844df43ce0065ec01e130c8b1a09 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -353,7 +353,7 @@
dataset.metadata.columns = 12
dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
- def merge( split_files, output_file):
+ def merge( split_files, output_file):
"""
Multiple SAM files may each have headers. Since the headers should all be the same, remove
the headers from files 1-n, keeping them in the first file only
https://bitbucket.org/galaxy/galaxy-central/changeset/c28e9ef4036a/
changeset: c28e9ef4036a
user: dannon
date: 2011-12-06 15:15:57
summary: Merge.
affected #: 1 file
diff -r 87268f2b439d844df43ce0065ec01e130c8b1a09 -r c28e9ef4036aca6a897db2aa93517577b0afddda test/functional/test_library_templates.py
--- a/test/functional/test_library_templates.py
+++ b/test/functional/test_library_templates.py
@@ -403,7 +403,7 @@
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
- strings_displayed=[ ldda.name, admin_user.email ] )
+ strings_displayed=[ ldda.name, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library3.id ),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9eb66dabc6ee/
changeset: 9eb66dabc6ee
user: greg
date: 2011-12-06 14:56:21
summary: Fix for data library functional test.
affected #: 1 file
diff -r 8993f7342095d3fac1feb3458ecee909ba678e11 -r 9eb66dabc6ee75a924632dc8140daab470a86f9d test/functional/test_library_templates.py
--- a/test/functional/test_library_templates.py
+++ b/test/functional/test_library_templates.py
@@ -403,7 +403,7 @@
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
- strings_displayed=[ ldda.name, admin_user.email ] )
+ strings_displayed=[ ldda.name, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library3.id ),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/af58b5faffec/
changeset: af58b5faffec
user: John Duddy
date: 2011-11-29 00:37:37
summary: Add merge method to SAM datatype so BWA can do split/merge
affected #: 1 file
diff -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 -r af58b5faffec3b6715850e6d50b7bef69a5bbef5 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -352,6 +352,22 @@
dataset.metadata.comment_lines = comment_lines
dataset.metadata.columns = 12
dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
+355,369d354
+ def merge( split_files, output_file):
+ """
+ Multiple SAM files may each have headers. Since the headers should all be the same, remove
+ the headers from files 1-n, keeping them in the first file only
+ """
+ cmd = 'mv %s %s' % ( split_files[0], output_file )
+ result = os.system(cmd)
+ if result != 0:
+ raise Exception('Result %s from %s' % (result, cmd))
+ if len(split_files) > 1:
+ cmd = 'egrep -v "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file )
+ result = os.system(cmd)
+ if result != 0:
+ raise Exception('Result %s from %s' % (result, cmd))
+ merge = staticmethod(merge)
class Pileup( Tabular ):
"""Tab delimited data in pileup (6- or 10-column) format"""
https://bitbucket.org/galaxy/galaxy-central/changeset/8993f7342095/
changeset: 8993f7342095
user: dannon
date: 2011-12-06 14:43:32
summary: Pull in jdlogicman's SAM merge.
affected #: 1 file
diff -r 43326a266e8eb5818c695c235df82a025a3b6893 -r 8993f7342095d3fac1feb3458ecee909ba678e11 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -353,6 +353,22 @@
dataset.metadata.columns = 12
dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
+ def merge( split_files, output_file):
+ """
+ Multiple SAM files may each have headers. Since the headers should all be the same, remove
+ the headers from files 1-n, keeping them in the first file only
+ """
+ cmd = 'mv %s %s' % ( split_files[0], output_file )
+ result = os.system(cmd)
+ if result != 0:
+ raise Exception('Result %s from %s' % (result, cmd))
+ if len(split_files) > 1:
+ cmd = 'egrep -v "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file )
+ result = os.system(cmd)
+ if result != 0:
+ raise Exception('Result %s from %s' % (result, cmd))
+ merge = staticmethod(merge)
+
class Pileup( Tabular ):
"""Tab delimited data in pileup (6- or 10-column) format"""
file_ext = "pileup"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/6ce661b68417/
changeset: 6ce661b68417
user: dannon
date: 2011-12-06 14:01:06
summary: Small patch to sanitizer to remove javascript content from sanitized anchors.
affected #: 1 file
diff -r 35fee32991ce5463d79ce278cb3a9c1155e8982f -r 6ce661b68417f81727c0f23aa8fb5d2769a8c502 lib/galaxy/util/sanitize_html.py
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -373,7 +373,9 @@
clean_attrs = []
for key, value in self.normalize_attrs(attrs):
- if key in acceptable_attributes:
+ if key=="href" and value.startswith("javascript"):
+ pass
+ elif key in acceptable_attributes:
key=keymap.get(key,key)
clean_attrs.append((key,value))
elif key=='style':
@@ -436,4 +438,4 @@
p.feed(htmlSource)
data = p.output()
data = data.strip().replace('\r\n', '\n')
- return data
\ No newline at end of file
+ return data
https://bitbucket.org/galaxy/galaxy-central/changeset/43326a266e8e/
changeset: 43326a266e8e
user: dannon
date: 2011-12-06 14:08:16
summary: Small tweak on patch, strip first to prevent whitespace loophole.
affected #: 1 file
diff -r 6ce661b68417f81727c0f23aa8fb5d2769a8c502 -r 43326a266e8eb5818c695c235df82a025a3b6893 lib/galaxy/util/sanitize_html.py
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -373,7 +373,7 @@
clean_attrs = []
for key, value in self.normalize_attrs(attrs):
- if key=="href" and value.startswith("javascript"):
+ if key=="href" and value.strip().startswith("javascript"):
pass
elif key in acceptable_attributes:
key=keymap.get(key,key)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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