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Fix for displaying the Installation status for tool dependencies installed along with repositories into Galaxy, and fix broken tool shed functional tests.

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This commit is contained in:
Greg Von Kuster
2013-08-06 10:21:37 -04:00
parent cd54689f20
commit ff56ade8b9
3 changed files with 4 additions and 15 deletions
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lib/galaxy/webapps/tool_shed/util/container_util.py
+1 -8
View File
@@ -257,13 +257,12 @@ class Tool( object ):
class ToolDependency( object ):
"""Tool dependency object"""
def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None,
def __init__( self, id=None, name=None, version=None, type=None, readme=None, installation_status=None, repository_id=None,
tool_dependency_id=None, is_orphan=None ):
self.id = id
self.name = name
self.version = version
self.type = type
self.install_dir = install_dir
self.readme = readme
self.installation_status = installation_status
self.repository_id = repository_id
@@ -948,12 +947,10 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
# Insert a header row.
tool_dependency_id += 1
if trans.webapp.name == 'galaxy':
# Include the installation directory.
tool_dependency = ToolDependency( id=tool_dependency_id,
name='Name',
version='Version',
type='Type',
install_dir='Install directory',
readme=None,
installation_status='Installation status',
repository_id=None,
@@ -964,7 +961,6 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
name='Name',
version='Version',
type='Type',
install_dir=None,
readme=None,
installation_status=None,
repository_id=None,
@@ -995,7 +991,6 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
name=name,
version=None,
type=type,
install_dir=None,
readme=None,
installation_status=installation_status,
repository_id=repository_id,
@@ -1013,7 +1008,6 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
name = requirements_dict[ 'name' ]
version = requirements_dict[ 'version' ]
type = requirements_dict[ 'type' ]
install_dir = requirements_dict.get( 'install_dir', None )
repository_id = requirements_dict.get( 'repository_id', None )
td_id = requirements_dict.get( 'tool_dependency_id', None )
if trans.webapp.name == 'galaxy':
@@ -1024,7 +1018,6 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
name=name,
version=version,
type=type,
install_dir=install_dir,
readme=None,
installation_status=installation_status,
repository_id=repository_id,
templates/webapps/tool_shed/repository/common.mako
+1 -5
View File
@@ -888,11 +888,7 @@
<${cell_type}>${tool_dependency.type | h}</${cell_type}>
<${cell_type}>
%if trans.webapp.name == 'galaxy':
%if is_missing:
${tool_dependency.installation_status | h}
%elif tool_dependency.install_dir:
${tool_dependency.install_dir | h}
%endif
${tool_dependency.installation_status | h}
%else:
%if row_is_header:
${tool_dependency.is_orphan | h}
test/tool_shed/functional/test_1170_complex_prior_installation_required.py
+2 -2
View File
@@ -63,7 +63,7 @@ class TestComplexPriorInstallation( ShedTwillTestCase ):
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded matplotlib tool dependency tarball.',
strings_displayed=['orphan'],
strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ],
strings_not_displayed=[] )
def test_0010_create_numpy_repository( self ):
@@ -89,7 +89,7 @@ class TestComplexPriorInstallation( ShedTwillTestCase ):
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded numpy tool dependency tarball.',
strings_displayed=['orphan'],
strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ],
strings_not_displayed=[] )
def test_0015_create_complex_repository_dependency( self ):