1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/950e68808ba6/
Changeset: 950e68808ba6
User: jgoecks
Date: 2014-05-27 23:42:10
Summary: Remove jStorage from Trackster requirements because it is not used.
Affected #: 1 file
diff -r be58520000c71329d6e63830fc5776604c7b8382 -r 950e68808ba693d8eeec87b4be9ce78e4b864456 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -8,7 +8,6 @@
[
// load js libraries
'utils/utils',
- 'libs/jquery/jstorage',
'libs/jquery/jquery.event.drag',
'libs/jquery/jquery.event.hover',
'libs/jquery/jquery.mousewheel',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/26952d141e42/
Changeset: 26952d141e42
Branch: next-stable
User: dannon
Date: 2014-05-27 23:11:01
Summary: Fix dep_value being undefined at use. Someone needs to look at the logic here, this is purely an operational fix preventing a crash -- there's logic that still needs to happen somewhere in the chain here.
Affected #: 1 file
diff -r 7a6ce727849489c03fbf766bc98357af52d4ffb8 -r 26952d141e42bd936eab9465c2761325204f9531 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -894,6 +894,10 @@
# If we got this far, we can actually look at the dependencies
# to see if their values will not be available until runtime.
for dep_name in self.get_dependencies():
+ # This may not be completely correct, but it's possible to go
+ # through the layers indicated below without assigning dep_value,
+ # which is even worse. TODO fix it?
+ dep_value = None
if dep_name in context:
dep_value = context[ dep_name ]
else:
@@ -1063,7 +1067,7 @@
'value': value
})
return d
-
+
def _get_dbkey_names( self, trans=None ):
if not self.tool:
# Hack for unit tests, since we have no tool
@@ -1735,7 +1739,7 @@
field_name = "%s%s" % ( self.name, suffix )
field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
-
+
dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
for history_dataset_collection in history.active_dataset_collections:
https://bitbucket.org/galaxy/galaxy-central/commits/be58520000c7/
Changeset: be58520000c7
User: dannon
Date: 2014-05-27 23:11:13
Summary: merge next-stable.
Affected #: 1 file
diff -r fefcf6f47abe795b392348fbb901ffdf7b5c61ab -r be58520000c71329d6e63830fc5776604c7b8382 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -894,6 +894,10 @@
# If we got this far, we can actually look at the dependencies
# to see if their values will not be available until runtime.
for dep_name in self.get_dependencies():
+ # This may not be completely correct, but it's possible to go
+ # through the layers indicated below without assigning dep_value,
+ # which is even worse. TODO fix it?
+ dep_value = None
if dep_name in context:
dep_value = context[ dep_name ]
else:
@@ -1063,7 +1067,7 @@
'value': value
})
return d
-
+
def _get_dbkey_names( self, trans=None ):
if not self.tool:
# Hack for unit tests, since we have no tool
@@ -1735,7 +1739,7 @@
field_name = "%s%s" % ( self.name, suffix )
field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
-
+
dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
for history_dataset_collection in history.active_dataset_collections:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/bdff5a8cc4b9/
Changeset: bdff5a8cc4b9
Branch: next-stable
User: greg
Date: 2014-05-27 19:32:49
Summary: Improve exception handling for generated Tool Shed URLs.
Affected #: 4 files
diff -r 2cab30fd7436a0e38bb3d60eea5b5fa929f62244 -r bdff5a8cc4b91ec6deff722884bde7357e67e6ef lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -383,6 +383,11 @@
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
+ message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required "
+ message += "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( repository_name, repository_owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/get_tool_dependencies%s' % params )
@@ -403,6 +408,11 @@
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
+ message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
+ message += "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository_name ),
str( repository_owner ),
changeset_revision )
diff -r 2cab30fd7436a0e38bb3d60eea5b5fa929f62244 -r bdff5a8cc4b91ec6deff722884bde7357e67e6ef lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -161,6 +161,11 @@
def create_temporary_tool_dependencies_config( self, app, tool_shed_url, name, owner, changeset_revision ):
"""Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the "
+ message += "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/get_tool_dependencies_config_contents%s' % params )
@@ -175,7 +180,7 @@
fh.close()
return tmp_filename
else:
- message = "Unable to retrieve required tool_dependencies.xml file from the tool shed for revision "
+ message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed for revision "
message += "%s of installed repository %s owned by %s." % ( str( changeset_revision ), str( name ), str( owner ) )
raise Exception( message )
return None
diff -r 2cab30fd7436a0e38bb3d60eea5b5fa929f62244 -r bdff5a8cc4b91ec6deff722884bde7357e67e6ef lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -107,7 +107,7 @@
def generate_clone_url_for_installed_repository( app, repository ):
"""Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
- return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
+ return url_join( tool_shed_url, 'repos', str( repository.owner ), str( repository.name ) )
def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
"""Generate the URL for cloning a repository that is in the tool shed."""
@@ -316,5 +316,6 @@
"""Return a valid URL produced by appending a base URL and a set of request parameters."""
parts = []
for arg in args:
- parts.append( arg.strip( '/' ) )
+ if arg is not None:
+ parts.append( arg.strip( '/' ) )
return '/'.join( parts )
diff -r 2cab30fd7436a0e38bb3d60eea5b5fa929f62244 -r bdff5a8cc4b91ec6deff722884bde7357e67e6ef lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -942,6 +942,11 @@
"""
# This method is used only in Galaxy, not the Tool Shed. We store the port (if one exists) in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
+ if tool_shed is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to retrieve the repository record from the database because one or more of the following "
+ message += "required parameters is None: tool_shed: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app,
tool_shed=tool_shed,
name=name,
@@ -1356,6 +1361,11 @@
the received tool_shed_url / name / owner combination.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to get updated changeset revisions from the Tool Shed because one or more of the following "
+ message += "required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/updated_changeset_revisions%s' % params )
https://bitbucket.org/galaxy/galaxy-central/commits/472fa62aaf72/
Changeset: 472fa62aaf72
User: greg
Date: 2014-05-27 19:33:16
Summary: Merged next-stable
Affected #: 4 files
diff -r 44df8d9c9aa11acf796f88203551a92ac03c559d -r 472fa62aaf72a1b7c8a2520665efdc833d2ab5fc lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -377,6 +377,11 @@
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
+ message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required "
+ message += "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( repository_name, repository_owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/get_tool_dependencies%s' % params )
@@ -397,6 +402,11 @@
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None:
+ message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following "
+ message += "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository_name ),
str( repository_owner ),
changeset_revision )
diff -r 44df8d9c9aa11acf796f88203551a92ac03c559d -r 472fa62aaf72a1b7c8a2520665efdc833d2ab5fc lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -161,6 +161,11 @@
def create_temporary_tool_dependencies_config( self, app, tool_shed_url, name, owner, changeset_revision ):
"""Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed because one or more of the "
+ message += "following required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/get_tool_dependencies_config_contents%s' % params )
@@ -175,7 +180,7 @@
fh.close()
return tmp_filename
else:
- message = "Unable to retrieve required tool_dependencies.xml file from the tool shed for revision "
+ message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed for revision "
message += "%s of installed repository %s owned by %s." % ( str( changeset_revision ), str( name ), str( owner ) )
raise Exception( message )
return None
diff -r 44df8d9c9aa11acf796f88203551a92ac03c559d -r 472fa62aaf72a1b7c8a2520665efdc833d2ab5fc lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -107,7 +107,7 @@
def generate_clone_url_for_installed_repository( app, repository ):
"""Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
- return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
+ return url_join( tool_shed_url, 'repos', str( repository.owner ), str( repository.name ) )
def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
"""Generate the URL for cloning a repository that is in the tool shed."""
@@ -316,5 +316,6 @@
"""Return a valid URL produced by appending a base URL and a set of request parameters."""
parts = []
for arg in args:
- parts.append( arg.strip( '/' ) )
+ if arg is not None:
+ parts.append( arg.strip( '/' ) )
return '/'.join( parts )
diff -r 44df8d9c9aa11acf796f88203551a92ac03c559d -r 472fa62aaf72a1b7c8a2520665efdc833d2ab5fc lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -929,6 +929,11 @@
"""
# This method is used only in Galaxy, not the Tool Shed. We store the port (if one exists) in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
+ if tool_shed is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to retrieve the repository record from the database because one or more of the following "
+ message += "required parameters is None: tool_shed: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app,
tool_shed=tool_shed,
name=name,
@@ -1343,6 +1348,11 @@
the received tool_shed_url / name / owner combination.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
+ message = "Unable to get updated changeset revisions from the Tool Shed because one or more of the following "
+ message += "required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
+ ( str( tool_shed_url ), str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
url = common_util.url_join( tool_shed_url,
'repository/updated_changeset_revisions%s' % params )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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