1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/832bbb3fa9fb/
Changeset: 832bbb3fa9fb
User: dan
Date: 2014-07-24 22:46:24
Summary: Fix for parsing tool <input> attributes when it contains no parameters.
Affected #: 1 file
diff -r 6f7d70f72da237e0d8d37a20b14a4eab1828803d -r 832bbb3fa9fb62d53f2be23cf880755fa2001f46 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1391,7 +1391,7 @@
# Load parameters (optional)
input_elem = root.find("inputs")
enctypes = set()
- if input_elem:
+ if input_elem is not None:
# Handle properties of the input form
self.check_values = string_as_bool( input_elem.get("check_values", self.check_values ) )
self.nginx_upload = string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) )
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/6f7d70f72da2/
Changeset: 6f7d70f72da2
User: jmchilton
Date: 2014-07-24 22:30:51
Summary: Bugfix in test tool demoing two collection params.
Bit problematic functional tests passed despite this bug.
Affected #: 1 file
diff -r b2700f28372549a17f5ca03af60e86964665c3ff -r 6f7d70f72da237e0d8d37a20b14a4eab1828803d test/functional/tools/collection_two_paired.xml
--- a/test/functional/tools/collection_two_paired.xml
+++ b/test/functional/tools/collection_two_paired.xml
@@ -20,8 +20,8 @@
<param name="f2" type="data_collection" collection_type="paired" /></when><when value="list">
- <param name="f1" type="data_collection" collection_type="paired" />
- <param name="f2" type="data_collection" collection_type="paired" />
+ <param name="f1" type="data_collection" collection_type="list" />
+ <param name="f2" type="data_collection" collection_type="list" /></when></conditional></inputs>
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/6fbe4d95a8dc/
Changeset: 6fbe4d95a8dc
User: greg
Date: 2014-07-23 22:31:59
Summary: Fix missing import in the Tool Shed's ToolValidator.
Affected #: 1 file
diff -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 -r 6fbe4d95a8dc64bd222dbf1170bdadcc5321e855 lib/tool_shed/tools/tool_validator.py
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -12,6 +12,7 @@
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_util
+from tool_shed.util import xml_util
log = logging.getLogger( __name__ )
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/e45ed2368920/
Changeset: e45ed2368920
User: greg
Date: 2014-07-23 22:19:39
Summary: Fix for exporting repositories that contain package recipes that define additional packages needed only for compiling the dependent package.
Affected #: 3 files
diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1262,7 +1262,11 @@
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
metadata = repository_metadata.metadata
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
+ # Initialize the repository dependency RelationBuilder.
rb = relation_builder.RelationBuilder( trans.app, repository, repository_metadata, toolshed_base_url )
+ # Work-around to ensure repositories that contain packages needed only for compiling
+ # a dependent package are included in the capsule.
+ rb.set_filter_dependencies_needed_for_compiling( False )
# Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
if repository_dependencies:
diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/tool_shed/capsule/capsule_manager.py
--- a/lib/tool_shed/capsule/capsule_manager.py
+++ b/lib/tool_shed/capsule/capsule_manager.py
@@ -245,9 +245,13 @@
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
self.repository_id,
self.changeset_revision )
- # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
+ # Get a dictionary of all repositories upon which the contents of the current
+ # repository_metadata record depend.
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
rb = RelationBuilder( self.app, repository, repository_metadata, toolshed_base_url )
+ # Work-around to ensure repositories that contain packages needed only for compiling
+ # a dependent package are included in the capsule.
+ rb.set_filter_dependencies_needed_for_compiling( False )
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
repo = hg_util.get_repo_for_repository( self.app,
repository=self.repository,
diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/tool_shed/dependencies/repository/relation_builder.py
--- a/lib/tool_shed/dependencies/repository/relation_builder.py
+++ b/lib/tool_shed/dependencies/repository/relation_builder.py
@@ -23,6 +23,11 @@
self.handled_key_rd_dicts = []
self.key_rd_dicts_to_be_processed = []
self.tool_shed_url = tool_shed_url
+ # This is a temporary work-around for handling repository dependencies that are needed
+ # only if compiling a dependent package. This value should be True unless exporting
+ # a repository capsule, in which case the set_filter_dependencies_needed_for_compiling()
+ # function is called.
+ self.filter_dependencies_needed_for_compiling = True
def can_add_to_key_rd_dicts( self, key_rd_dict, key_rd_dicts ):
"""Handle the case where an update to the changeset revision was done."""
@@ -389,9 +394,12 @@
current_repository_key_rd_dicts = \
self.get_updated_changeset_revisions_for_repository_dependencies( current_repository_key_rd_dicts )
for key_rd_dict in current_repository_key_rd_dicts:
- # Filter out repository dependencies that are required only if compiling the dependent
- # repository's tool dependency.
- key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict )
+ if self.filter_dependencies_needed_for_compiling:
+ # Filter out repository dependencies that are required only if compiling the dependent
+ # repository's tool dependency.
+ # TODO: this temporary work-around should be removed when the underlying framework
+ # support for handling only_if_compiling_contained_td-flagged repositories is completed.
+ key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict )
if key_rd_dict:
is_circular = False
in_handled_key_rd_dicts = self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts )
@@ -483,6 +491,9 @@
clean_key_rd_dicts.append( new_key_rd_dict )
return clean_key_rd_dicts
+ def set_filter_dependencies_needed_for_compiling( self, value ):
+ self.filter_dependencies_needed_for_compiling = asbool( value )
+
def update_circular_repository_dependencies( self, repository_key, repository_dependency, repository_dependencies ):
repository_dependency_as_key = self.get_repository_dependency_as_key( repository_dependency )
repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP )
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/b08a47eb8c3c/
Changeset: b08a47eb8c3c
User: greg
Date: 2014-07-23 19:40:23
Summary: Strip repository names when creating in the Tool Shed.
Affected #: 1 file
diff -r 598a4ec015f66237d41ed2176c673fd52b744f15 -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1062,7 +1062,7 @@
action='browse_repositories',
message=message,
status=status ) )
- name = kwd.get( 'name', '' )
+ name = kwd.get( 'name', '' ).strip()
description = kwd.get( 'description', '' )
long_description = kwd.get( 'long_description', '' )
category_ids = util.listify( kwd.get( 'category_id', '' ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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