1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f70167e188f9/
Changeset: f70167e188f9
User: davebgx
Date: 2014-06-04 21:15:23
Summary: Merge bugfix from stable.
Affected #: 2 files
diff -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -1694,6 +1694,8 @@
def reset_all_metadata_on_installed_repository( trans, id ):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
+ invalid_file_tups = []
+ metadata_dict = {}
repository = suc.get_installed_tool_shed_repository( trans, id )
repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fb68af9a775a/
Changeset: fb68af9a775a
Branch: stable
User: davebgx
Date: 2014-06-04 21:04:33
Summary: Fix resetting all metadata based on issue found by Nicola Soranzo.
Affected #: 1 file
diff -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 -r fb68af9a775a956fcc397b22d16f2119401d926d lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -1712,6 +1712,8 @@
def reset_all_metadata_on_installed_repository( trans, id ):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
+ invalid_file_tups = []
+ metadata_dict = {}
repository = suc.get_installed_tool_shed_repository( trans, id )
repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/18777feed30b/
Changeset: 18777feed30b
Branch: stable
User: dan
Date: 2014-06-04 17:05:36
Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
Affected #: 1 file
diff -r c68aa8a8e769437473bd23586d1b55fc66cc8c47 -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -448,6 +448,8 @@
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' )
+ # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided
+ url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
response = urllib2.urlopen( request ).read()
if response:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3d6b71244ff9/
Changeset: 3d6b71244ff9
User: dan
Date: 2014-06-04 17:05:36
Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
Affected #: 1 file
diff -r 819818c880b543d9ef32aa61a099235c20937dae -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -447,6 +447,8 @@
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' )
+ # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided
+ url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
response = urllib2.urlopen( request ).read()
if response:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/819818c880b5/
Changeset: 819818c880b5
User: greg
Date: 2014-06-04 15:21:18
Summary: Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
Affected #: 1 file
diff -r 0cb88fa06c32e13c8881ed90af02b239aa574313 -r 819818c880b543d9ef32aa61a099235c20937dae lib/tool_shed/scripts/api/common.py
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -197,7 +197,7 @@
print e.read( 1024 )
sys.exit( 1 )
else:
- return 'Error. '+ str( e.read( 1024 ) )
+ return dict( status='error', message=str( e.read( 1024 ) ) )
if not return_formatted:
return r
print 'Response'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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