mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fixes for handling tool dependencies and missing tool dependencies for installed tool shed repositories and tose being installed.
This commit is contained in:
Greg Von Kuster
@@ -1749,14 +1749,31 @@ def get_tool_panel_config_tool_path_install_dir( app, repository ):
|
||||
relative_install_dir = None
|
||||
shed_config_dict = repository.get_shed_config_dict( app )
|
||||
if not shed_config_dict:
|
||||
#just pick a semi-random shed config
|
||||
# Just pick a semi-random shed config.
|
||||
for shed_config_dict in app.toolbox.shed_tool_confs:
|
||||
if ( repository.dist_to_shed and shed_config_dict['config_filename'] == app.config.migrated_tools_config ) or ( not repository.dist_to_shed and shed_config_dict['config_filename'] != app.config.migrated_tools_config ):
|
||||
if ( repository.dist_to_shed and shed_config_dict[ 'config_filename' ] == app.config.migrated_tools_config ) \
|
||||
or ( not repository.dist_to_shed and shed_config_dict[ 'config_filename' ] != app.config.migrated_tools_config ):
|
||||
break
|
||||
shed_tool_conf = shed_config_dict[ 'config_filename' ]
|
||||
tool_path = shed_config_dict[ 'tool_path' ]
|
||||
relative_install_dir = partial_install_dir
|
||||
return shed_tool_conf, tool_path, relative_install_dir
|
||||
def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ):
|
||||
"""
|
||||
Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the
|
||||
dictionary whose config_filename key has a value matching the received shed_tool_conf.
|
||||
"""
|
||||
for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
|
||||
config_filename = shed_tool_conf_dict[ 'config_filename' ]
|
||||
if config_filename == shed_tool_conf:
|
||||
tool_path = shed_tool_conf_dict[ 'tool_path' ]
|
||||
break
|
||||
else:
|
||||
file_name = strip_path( config_filename )
|
||||
if file_name == shed_tool_conf:
|
||||
tool_path = shed_tool_conf_dict[ 'tool_path' ]
|
||||
break
|
||||
return tool_path
|
||||
def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
sa_session = app.model.context.current
|
||||
|
||||
@@ -898,7 +898,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
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 )
|
||||
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 )
|
||||
valid_tools = metadata.get( 'tools', None )
|
||||
workflows = metadata.get( 'workflows', None )
|
||||
@@ -1126,7 +1126,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
if ( not includes_tools and not includes_repository_dependencies ) or \
|
||||
( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ):
|
||||
install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
|
||||
if includes_tools:
|
||||
if includes_tool_dependencies:
|
||||
install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
|
||||
shed_tool_conf = kwd[ 'shed_tool_conf' ]
|
||||
else:
|
||||
@@ -1134,17 +1134,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
# If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config
|
||||
# setting points.
|
||||
shed_tool_conf = trans.app.config.migrated_tools_config
|
||||
# Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf.
|
||||
for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
|
||||
config_filename = shed_tool_conf_dict[ 'config_filename' ]
|
||||
if config_filename == shed_tool_conf:
|
||||
tool_path = shed_tool_conf_dict[ 'tool_path' ]
|
||||
break
|
||||
else:
|
||||
file_name = suc.strip_path( config_filename )
|
||||
if file_name == shed_tool_conf:
|
||||
tool_path = shed_tool_conf_dict[ 'tool_path' ]
|
||||
break
|
||||
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
|
||||
created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \
|
||||
shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False )
|
||||
if message and len( repo_info_dicts ) == 1:
|
||||
@@ -1232,6 +1222,8 @@ class AdminToolshed( AdminGalaxy ):
|
||||
raw_text = response.read()
|
||||
response.close()
|
||||
readme_files_dict = from_json_string( raw_text )
|
||||
# Since we are installing a new repository, no tool dependencies will be considered "missing". Most of the repository contents
|
||||
# are set to None since we don't yet know what they are.
|
||||
containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
|
||||
toolshed_base_url=tool_shed_url,
|
||||
repository_name=name,
|
||||
@@ -1247,7 +1239,13 @@ class AdminToolshed( AdminGalaxy ):
|
||||
valid_tools=None,
|
||||
workflows=None )
|
||||
else:
|
||||
containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
|
||||
containers_dict = dict( datatypes=None,
|
||||
invalid_tools=None,
|
||||
readme_files_dict=None,
|
||||
repository_dependencies=None,
|
||||
tool_dependencies=None,
|
||||
valid_tools=None,
|
||||
workflows=None )
|
||||
# Handle tool dependencies chack box.
|
||||
if trans.app.config.tool_dependency_dir is None:
|
||||
if includes_tool_dependencies:
|
||||
@@ -1260,6 +1258,17 @@ class AdminToolshed( AdminGalaxy ):
|
||||
install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
|
||||
# Handle repository dependencies check box.
|
||||
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
|
||||
log.debug("PPPPP In prepare_for_install, containers_dict: %s" % str( containers_dict ))
|
||||
"""
|
||||
PPPPP In prepare_for_install,
|
||||
containers_dict:
|
||||
{'repository_dependencies': None,
|
||||
'missing_tool_dependencies': <galaxy.webapps.community.util.container_util.Folder object at 0x108a56f0>,
|
||||
'readme_files': None,
|
||||
'tool_dependencies': None}
|
||||
FAIL
|
||||
|
||||
"""
|
||||
return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
|
||||
encoded_repo_info_dicts=encoded_repo_info_dicts,
|
||||
includes_tools=includes_tools,
|
||||
@@ -1456,6 +1465,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
includes_repository_dependencies = True
|
||||
else:
|
||||
includes_repository_dependencies = False
|
||||
includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies
|
||||
repo_info_dict = suc.create_repo_info_dict( trans=trans,
|
||||
repository_clone_url=repository_clone_url,
|
||||
changeset_revision=tool_shed_repository.installed_changeset_revision,
|
||||
@@ -1527,6 +1537,10 @@ class AdminToolshed( AdminGalaxy ):
|
||||
all_tool_dependencies )
|
||||
valid_tools = metadata.get( 'tools', None )
|
||||
workflows = metadata.get( 'workflows', None )
|
||||
# All tool dependencies will be considered missing since we are reinstalling the repository.
|
||||
for td in tool_dependencies:
|
||||
missing_tool_dependencies.append( td )
|
||||
tool_dependencies = None
|
||||
containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
|
||||
toolshed_base_url=tool_shed_url,
|
||||
repository_name=tool_shed_repository.name,
|
||||
@@ -1538,16 +1552,22 @@ class AdminToolshed( AdminGalaxy ):
|
||||
missing_tool_dependencies=missing_tool_dependencies,
|
||||
readme_files_dict=readme_files_dict,
|
||||
repository_dependencies=repository_dependencies,
|
||||
tool_dependencies=tool_dependencies,
|
||||
tool_dependencies=missing_tool_dependencies,
|
||||
valid_tools=valid_tools,
|
||||
workflows=workflows )
|
||||
else:
|
||||
containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
|
||||
containers_dict = dict( datatypes=None,
|
||||
invalid_tools=None,
|
||||
readme_files_dict=None,
|
||||
repository_dependencies=None,
|
||||
tool_dependencies=None,
|
||||
valid_tools=None,
|
||||
workflows=None )
|
||||
# Handle repository dependencies check box.
|
||||
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
|
||||
# Handle tool dependencies check box.
|
||||
if trans.app.config.tool_dependency_dir is None:
|
||||
if tool_shed_repository.includes_tool_dependencies:
|
||||
if includes_tool_dependencies:
|
||||
message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
|
||||
message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. "
|
||||
status = "warning"
|
||||
|
||||
@@ -509,7 +509,7 @@
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
%if repository_dependencies_root_folder or tool_dependencies_root_folder:
|
||||
%if repository_dependencies_root_folder or tool_dependencies_root_folder or missing_tool_dependencies_root_folder:
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Dependencies of this repository</div>
|
||||
<div class="toolFormBody">
|
||||
|
||||
Reference in New Issue
Block a user