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Fix for displaying an installed repository that includes one or more readme files.

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This commit is contained in:
Dave Bouvier
2012-12-19 16:48:09 -05:00
parent 5960802952
commit e39ca0fab4
3 changed files with 15 additions and 10 deletions
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lib/galaxy/util/shed_util_common.py
+6 -3
View File
@@ -57,13 +57,16 @@ def add_installation_directories_to_tool_dependencies( trans, repository_name, r
requirements_dict[ 'install_dir' ] = install_dir
tool_dependencies[ dependency_key ] = requirements_dict
return tool_dependencies
def build_readme_files_dict( metadata ):
def build_readme_files_dict( metadata, tool_path=None ):
"""Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata."""
readme_files_dict = {}
if metadata and 'readme_files' in metadata:
for relative_path_to_readme_file in metadata[ 'readme_files' ]:
readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
if tool_path:
full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) )
else:
full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
try:
f = open( full_path_to_readme_file, 'r' )
text = f.read()
@@ -103,7 +106,7 @@ def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository
containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder
# Readme files container.
if readme_files_dict:
folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict )
folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict )
containers_dict[ 'readme_files' ] = readme_files_root_folder
# Repository dependencies container.
if repository_dependencies:
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+8 -6
View File
@@ -881,7 +881,7 @@ class AdminToolshed( AdminGalaxy ):
datatypes = metadata.get( 'datatypes', None )
invalid_tools = metadata.get( 'invalid_tools', None )
if repository.has_readme_files:
readme_files_dict = suc.build_readme_files_dict( repository.metadata )
readme_files_dict = suc.build_readme_files_dict( repository.metadata, tool_path )
else:
readme_files_dict = None
repository_dependencies = metadata.get( 'repository_dependencies', None )
@@ -1515,17 +1515,19 @@ class AdminToolshed( AdminGalaxy ):
if repository_dependencies:
# We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool
# shed repository metadata.
root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed,
repository.name,
repository.owner,
repository.installed_changeset_revision )
root_key = container_util.generate_repository_dependencies_key_for_repository( tool_shed_repository.tool_shed,
tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision )
rd_tups_for_display = []
rd_tups = repository_dependencies[ 'repository_dependencies' ]
repository_dependencies_dict_for_display[ 'root_key' ] = root_key
repository_dependencies_dict_for_display[ root_key ] = rd_tups
repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ]
all_tool_dependencies = metadata.get( 'tool_dependencies', None )
tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies )
tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans,
tool_shed_repository,
all_tool_dependencies )
valid_tools = metadata.get( 'tools', None )
workflows = metadata.get( 'workflows', None )
containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
templates/webapps/community/repository/common.mako
+1 -1
View File
@@ -388,7 +388,7 @@
<a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a>
</div>
%else:
<a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a>
<a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a>
%endif
%else:
${tool.name | h}