[galaxy-commits] commit/galaxy-central: greg: Change the name of the current InstallManager to the more appropriate ToolMigrationManager since it handles only tool migrations. This allows for the InstallManager to be used for more general Tool Shed install processes.

6 May 2014

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/09f80fcdfd85/
Changeset:   09f80fcdfd85
User:        greg
Date:        2014-05-06 16:34:28
Summary:     Change the name of the current InstallManager to the more appropriate ToolMigrationManager since it handles only tool migrations.  This allows for the InstallManager to be used for more general Tool Shed install processes.
Affected #:  11 files
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/galaxy/webapps/galaxy/controllers/admin.py

--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -821,7 +821,7 @@
                     tool_dependencies_dict = {}
                     repository_name = elem.get( 'name' )
                     changeset_revision = elem.get( 'changeset_revision' )
-                    url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \
+                    url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s' % \
                         ( tool_shed_url, repository_name, changeset_revision )
                     text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
                     if text:
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 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
@@ -457,7 +457,7 @@
                                                                                     tool_shed_repository=tool_shed_repository,
                                                                                     tool_dependencies_config=tool_dependencies_config,
                                                                                     tool_dependencies=tool_dependencies,
-                                                                                    from_install_manager=False )
+                                                                                    from_tool_migration_manager=False )
         for installed_tool_dependency in installed_tool_dependencies:
             if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR:
                 text = util.unicodify( installed_tool_dependency.error_message )
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -1,643 +1,8 @@
-"""
-Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml).
-All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed.
-"""
-import json
+import logging
 import os
-import shutil
-import tempfile
-import threading
-import logging
-from galaxy import util
-from galaxy.tools import ToolSection
-import tool_shed.util.shed_util_common as suc
-from tool_shed.util import common_install_util
-from tool_shed.util import common_util
-from tool_shed.util import datatype_util
-from tool_shed.util import hg_util
-from tool_shed.util import metadata_util
-from tool_shed.util import tool_dependency_util
-from tool_shed.util import tool_util
-from tool_shed.util import xml_util
-from galaxy.util.odict import odict
log = logging.getLogger( __name__ )
class InstallManager( object ):
-
-    def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ):
-        """
-        Check tool settings in tool_shed_install_config and install all repositories that are not already installed.  The tool
-        panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml.
-        """
-        self.app = app
-        self.toolbox = self.app.toolbox
-        self.migrated_tools_config = migrated_tools_config
-        # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message.
-        if install_dependencies and app.config.tool_dependency_dir is None:
-            message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini '
-            message += 'file.  Set this location value to the path where you want tool dependencies installed and rerun the migration script.'
-            raise Exception( message )
-        # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml).
-        self.proprietary_tool_confs = self.non_shed_tool_panel_configs
-        self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number )
-        # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
-        tree, error_message = xml_util.parse_xml( migrated_tools_config )
-        if tree is None:
-            print error_message
-        else:
-            root = tree.getroot()
-            self.tool_path = root.get( 'tool_path' )
-            print "Repositories will be installed into configured tool_path location ", str( self.tool_path )
-            # Parse tool_shed_install_config to check each of the tools.
-            self.tool_shed_install_config = tool_shed_install_config
-            tree, error_message = xml_util.parse_xml( tool_shed_install_config )
-            if tree is None:
-                print error_message
-            else:
-                root = tree.getroot()
-                defined_tool_shed_url = root.get( 'name' )
-                self.tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, defined_tool_shed_url )
-                self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url )
-                self.repository_owner = common_util.REPOSITORY_OWNER
-                index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
-                # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
-                # tool_conf.xml.  If no tools associated with the migration stage are defined, no repositories will be installed on disk.
-                # The default behavior is that the tool shed is down.
-                tool_shed_accessible = False
-                tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app )
-                if tool_panel_configs:
-                    # The missing_tool_configs_dict contents are something like:
-                    # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
-                    tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app,
-                                                                                                           tool_panel_configs,
-                                                                                                           latest_migration_script_number )
-                else:
-                    # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
-                    # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
-                    # the database.
-                    tool_shed_accessible = True
-                    missing_tool_configs_dict = odict()
-                if tool_shed_accessible:
-                    if len( self.proprietary_tool_confs ) == 1:
-                        plural = ''
-                        file_names = self.proprietary_tool_confs[ 0 ]
-                    else:
-                        plural = 's'
-                        file_names = ', '.join( self.proprietary_tool_confs )
-                    if missing_tool_configs_dict:
-                        for proprietary_tool_conf in self.proprietary_tool_confs:
-                            # Create a backup of the tool configuration in the un-migrated state.
-                            shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) )
-                        for repository_elem in root:
-                            # Make sure we have a valid repository tag.
-                            if self.__is_valid_repository_tag( repository_elem ):
-                                # Get all repository dependencies for the repository defined by the current repository_elem.  Repository dependency
-                                # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
-                                # dependency that contains a tool.  The repository dependency can only contain items that are not loaded into the Galaxy
-                                # tool panel (e.g., tool dependency definitions, custom datatypes, etc).  This restriction must be followed down the
-                                # entire dependency hierarchy.
-                                name = repository_elem.get( 'name' )
-                                changeset_revision = repository_elem.get( 'changeset_revision' )
-                                tool_shed_accessible, repository_dependencies_dict = \
-                                    common_util.get_repository_dependencies( app,
-                                                                             self.tool_shed_url,
-                                                                             name,
-                                                                             self.repository_owner,
-                                                                             changeset_revision )
-                                # Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database.
-                                created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name,
-                                                                                                                     changeset_revision,
-                                                                                                                     repository_dependencies_dict )
-                                # Order the repositories for proper installation.  This process is similar to the process used when installing tool
-                                # shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/
-                                # repository_util), but does not handle managing tool panel sections and other components since repository dependency
-                                # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
-                                # dependency that contains a tool.
-                                ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories,
-                                                                                                           repository_dependencies_dict )
-
-                                for tool_shed_repository in ordered_tool_shed_repositories:
-                                    is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository )
-                                    self.install_repository( repository_elem,
-                                                             tool_shed_repository,
-                                                             install_dependencies,
-                                                             is_repository_dependency=is_repository_dependency )
-                    else:
-                        message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number )
-                        message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names )
-                        print message
-                else:
-                    message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number )
-                    message += "Try again later.\n"
-                    print message
-
-    def create_or_update_tool_shed_repository_record( self, name, owner, changeset_revision, description=None ):
-
-        # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
-        relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision )
-        clone_dir = os.path.join( self.tool_path, relative_clone_dir )
-        if not self.__iscloned( clone_dir ):
-            repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name )
-            relative_install_dir = os.path.join( relative_clone_dir, name )
-            install_dir = os.path.join( clone_dir, name )
-            ctx_rev = suc.get_ctx_rev( self.app, self.tool_shed_url, name, owner, changeset_revision )
-            tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
-                                                                              name=name,
-                                                                              description=description,
-                                                                              installed_changeset_revision=changeset_revision,
-                                                                              ctx_rev=ctx_rev,
-                                                                              repository_clone_url=repository_clone_url,
-                                                                              metadata_dict={},
-                                                                              status=self.app.install_model.ToolShedRepository.installation_status.NEW,
-                                                                              current_changeset_revision=None,
-                                                                              owner=self.repository_owner,
-                                                                              dist_to_shed=True )
-            return tool_shed_repository
-        return None
-
-    def create_or_update_tool_shed_repository_records( self, name, changeset_revision, repository_dependencies_dict ):
-        """
-        Make sure the repository defined by name and changeset_revision and all of its repository dependencies have
-        associated tool_shed_repository table rows in the Galaxy database.
-        """
-        created_tool_shed_repositories = []
-        description = repository_dependencies_dict.get( 'description', None )
-        tool_shed_repository = self.create_or_update_tool_shed_repository_record( name,
-                                                                                  self.repository_owner,
-                                                                                  changeset_revision,
-                                                                                  description=description )
-        if tool_shed_repository:
-            created_tool_shed_repositories.append( tool_shed_repository )
-        for rd_key, rd_tups in repository_dependencies_dict.items():
-            if rd_key in [ 'root_key', 'description' ]:
-                continue
-            for rd_tup in rd_tups:
-                parsed_rd_tup = common_util.parse_repository_dependency_tuple( rd_tup )
-                rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = parsed_rd_tup[ 0:4 ]
-                # TODO: Make sure the repository description is applied to the new repository record during installation.
-                tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name,
-                                                                                          rd_owner,
-                                                                                          rd_changeset_revision,
-                                                                                          description=None )
-                if tool_shed_repository:
-                    created_tool_shed_repositories.append( tool_shed_repository )
-        return created_tool_shed_repositories
-
-    def filter_and_persist_proprietary_tool_panel_configs( self, tool_configs_to_filter ):
-        """Eliminate all entries in all non-shed-related tool panel configs for all tool config file names in the received tool_configs_to_filter."""
-        for proprietary_tool_conf in self.proprietary_tool_confs:
-            persist_required = False
-            tree, error_message = xml_util.parse_xml( proprietary_tool_conf )
-            if tree:
-                root = tree.getroot()
-                for elem in root:
-                    if elem.tag == 'tool':
-                        # Tools outside of sections.
-                        file_path = elem.get( 'file', None )
-                        if file_path:
-                            if file_path in tool_configs_to_filter:
-                                root.remove( elem )
-                                persist_required = True
-                    elif elem.tag == 'section':
-                        # Tools contained in a section.
-                        for section_elem in elem:
-                            if section_elem.tag == 'tool':
-                                file_path = section_elem.get( 'file', None )
-                                if file_path:
-                                    if file_path in tool_configs_to_filter:
-                                        elem.remove( section_elem )
-                                        persist_required = True
-            if persist_required:
-                fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-fapptpc"  )
-                tmp_filename = fh.name
-                fh.close()
-                fh = open( tmp_filename, 'wb' )
-                tree.write( tmp_filename, encoding='utf-8', xml_declaration=True )
-                fh.close()
-                shutil.move( tmp_filename, os.path.abspath( proprietary_tool_conf ) )
-                os.chmod( proprietary_tool_conf, 0644 )
-
-    def get_containing_tool_sections( self, tool_config ):
-        """
-        If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the
-        tool is displayed.  If the tool is displayed outside of any sections, None is appended to the list.
-        """
-        tool_sections = []
-        is_displayed = False
-        for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems:
-            if proprietary_tool_panel_elem.tag == 'tool':
-                # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
-                proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' )
-                if tool_config == proprietary_tool_config:
-                    # The tool is loaded outside of any sections.
-                    tool_sections.append( None )
-                    if not is_displayed:
-                        is_displayed = True
-            if proprietary_tool_panel_elem.tag == 'section':
-                # The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">.
-                for section_elem in proprietary_tool_panel_elem:
-                    if section_elem.tag == 'tool':
-                        # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
-                        proprietary_tool_config = section_elem.get( 'file' )
-                        if tool_config == proprietary_tool_config:
-                            # The tool is loaded inside of the section_elem.
-                            tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
-                            if not is_displayed:
-                                is_displayed = True
-        return is_displayed, tool_sections
-
-    def get_guid( self, repository_clone_url, relative_install_dir, tool_config ):
-        if self.shed_config_dict.get( 'tool_path' ):
-            relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir )
-        tool_config_filename = suc.strip_path( tool_config )
-        for root, dirs, files in os.walk( relative_install_dir ):
-            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-                if '.hg' in dirs:
-                    dirs.remove( '.hg' )
-                for name in files:
-                    filename = suc.strip_path( name )
-                    if filename == tool_config_filename:
-                        full_path = str( os.path.abspath( os.path.join( root, name ) ) )
-                        tool = self.toolbox.load_tool( full_path )
-                        return suc.generate_tool_guid( repository_clone_url, tool )
-        # Not quite sure what should happen here, throw an exception or what?
-        return None
-
-    def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ):
-        """
-        Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received
-        list of tsr_ids and whose associated repository must be installed prior to the repository associated with the tsr_id key.
-        """
-        # Initialize the dictionary.
-        prior_install_required_dict = {}
-        tsr_ids = [ tool_shed_repository.id for tool_shed_repository in tool_shed_repositories ]
-        for tsr_id in tsr_ids:
-            prior_install_required_dict[ tsr_id ] = []
-        # Inspect the repository dependencies about to be installed and populate the dictionary.
-        for rd_key, rd_tups in repository_dependencies_dict.items():
-            if rd_key in [ 'root_key', 'description' ]:
-                continue
-            for rd_tup in rd_tups:
-                prior_install_ids = []
-                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
-                    common_util.parse_repository_dependency_tuple( rd_tup )
-                if util.asbool( prior_installation_required ):
-                    for tsr in tool_shed_repositories:
-                        if tsr.name == name and tsr.owner == owner and tsr.changeset_revision == changeset_revision:
-                            prior_install_ids.append( tsr.id )
-                        prior_install_required_dict[ tsr.id ] = prior_install_ids
-        return prior_install_required_dict
-
-    def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ):
-        """
-        Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
-        either ToolSection elements or Tool elements.  These will be used to generate new entries in the migrated_tools_conf.xml
-        file for the installed tools.
-        """
-        tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
-        # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
-        migrated_tool_configs = []
-        tree, error_message = xml_util.parse_xml( tools_xml_file_path )
-        if tree is None:
-            return []
-        root = tree.getroot()
-        for elem in root:
-            if elem.tag == 'repository':
-                for tool_elem in elem:
-                    migrated_tool_configs.append( tool_elem.get( 'file' ) )
-        # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
-        tool_panel_elems = []
-        for proprietary_tool_conf in self.proprietary_tool_confs:
-            tree, error_message = xml_util.parse_xml( proprietary_tool_conf )
-            if tree is None:
-                return []
-            root = tree.getroot()
-            for elem in root:
-                if elem.tag == 'tool':
-                    # Tools outside of sections.
-                    file_path = elem.get( 'file', None )
-                    if file_path:
-                        if file_path in migrated_tool_configs:
-                            if elem not in tool_panel_elems:
-                                tool_panel_elems.append( elem )
-                elif elem.tag == 'section':
-                    # Tools contained in a section.
-                    for section_elem in elem:
-                        if section_elem.tag == 'tool':
-                            file_path = section_elem.get( 'file', None )
-                            if file_path:
-                                if file_path in migrated_tool_configs:
-                                    # Append the section, not the tool.
-                                    if elem not in tool_panel_elems:
-                                        tool_panel_elems.append( elem )
-        return tool_panel_elems
-
-    def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem,
-                                    install_dependencies, is_repository_dependency=False ):
-        """
-        Generate the metadata for the installed tool shed repository, among other things.  If the installed tool_shed_repository
-        contains tools that are loaded into the Galaxy tool panel, this method will automatically eliminate all entries for each
-        of the tools defined in the received repository_elem from all non-shed-related tool panel configuration files since the
-        entries are automatically added to the reserved migrated_tools_conf.xml file as part of the migration process.
-        """
-        tool_configs_to_filter = []
-        tool_panel_dict_for_display = odict()
-        if self.tool_path:
-            repo_install_dir = os.path.join( self.tool_path, relative_install_dir )
-        else:
-            repo_install_dir = relative_install_dir
-        if not is_repository_dependency:
-            for tool_elem in repository_elem:
-                # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" />
-                tool_config = tool_elem.get( 'file' )
-                guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config )
-                # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems.
-                is_displayed, tool_sections = self.get_containing_tool_sections( tool_config )
-                if is_displayed:
-                    tool_panel_dict_for_tool_config = \
-                        tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
-                    # The tool-panel_dict has the following structure.
-                    # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>,
-                    #                   name : <TooSection name>}]}
-                    for k, v in tool_panel_dict_for_tool_config.items():
-                        tool_panel_dict_for_display[ k ] = v
-                        for tool_panel_dict in v:
-                            # Keep track of tool config file names associated with entries that have been made to the
-                            # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs.
-                            if tool_config not in tool_configs_to_filter:
-                                tool_configs_to_filter.append( tool_config )
-                else:
-                    print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
-                    % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
-            if tool_configs_to_filter:
-                lock = threading.Lock()
-                lock.acquire( True )
-                try:
-                    self.filter_and_persist_proprietary_tool_panel_configs( tool_configs_to_filter )
-                except Exception, e:
-                    log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) )
-                finally:
-                    lock.release()
-        metadata_dict, invalid_file_tups = \
-            metadata_util.generate_metadata_for_changeset_revision( app=self.app,
-                                                                    repository=tool_shed_repository,
-                                                                    changeset_revision=tool_shed_repository.changeset_revision,
-                                                                    repository_clone_url=repository_clone_url,
-                                                                    shed_config_dict = self.shed_config_dict,
-                                                                    relative_install_dir=relative_install_dir,
-                                                                    repository_files_dir=None,
-                                                                    resetting_all_metadata_on_repository=False,
-                                                                    updating_installed_repository=False,
-                                                                    persist=True )
-        tool_shed_repository.metadata = metadata_dict
-        self.app.install_model.context.add( tool_shed_repository )
-        self.app.install_model.context.flush()
-        has_tool_dependencies = self.__has_tool_dependencies( metadata_dict )
-        if has_tool_dependencies:
-            # All tool_dependency objects must be created before the tools are processed even if no
-            # tool dependencies will be installed.
-            tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app,
-                                                                                     tool_shed_repository,
-                                                                                     relative_install_dir,
-                                                                                     set_status=True )
-        else:
-            tool_dependencies = None
-        if 'tools' in metadata_dict:
-            sample_files = metadata_dict.get( 'sample_files', [] )
-            sample_files = [ str( s ) for s in sample_files ]
-            tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
-            tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path )
-            sample_files_copied = [ s for s in tool_index_sample_files ]
-            repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict )
-            if repository_tools_tups:
-                # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups )
-                # Handle missing index files for tool parameters that are dynamically generated select lists.
-                repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app,
-                                                                                                  self.tool_path,
-                                                                                                  sample_files,
-                                                                                                  repository_tools_tups,
-                                                                                                  sample_files_copied )
-                # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance.
-                tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied )
-                if not is_repository_dependency:
-                    tool_util.add_to_tool_panel( self.app,
-                                                 tool_shed_repository.name,
-                                                 repository_clone_url,
-                                                 tool_shed_repository.installed_changeset_revision,
-                                                 repository_tools_tups,
-                                                 self.repository_owner,
-                                                 self.migrated_tools_config,
-                                                 tool_panel_dict=tool_panel_dict_for_display,
-                                                 new_install=True )
-        if install_dependencies and tool_dependencies and has_tool_dependencies:
-            # Install tool dependencies.
-            suc.update_tool_shed_repository_status( self.app,
-                                                    tool_shed_repository,
-                                                    self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
-            # Get the tool_dependencies.xml file from disk.
-            tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
-            installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app,
-                                                                                        tool_shed_repository=tool_shed_repository,
-                                                                                        tool_dependencies_config=tool_dependencies_config,
-                                                                                        tool_dependencies=tool_dependencies,
-                                                                                        from_install_manager=True )
-            for installed_tool_dependency in installed_tool_dependencies:
-                if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
-                    print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':'
-                    print installed_tool_dependency.error_message, '\n\n'
-        if 'datatypes' in metadata_dict:
-            tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
-            if not tool_shed_repository.includes_datatypes:
-                tool_shed_repository.includes_datatypes = True
-            self.app.install_model.context.add( tool_shed_repository )
-            self.app.install_model.context.flush()
-            work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" )
-            datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir )
-            # Load proprietary data types required by tools.  The value of override is not important here since the Galaxy server will be started
-            # after this installation completes.
-            converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir
-            if converter_path or display_path:
-                # Create a dictionary of tool shed repository related information.
-                repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url,
-                                                                                                  name=tool_shed_repository.name,
-                                                                                                  owner=self.repository_owner,
-                                                                                                  installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                                                                  tool_dicts=metadata_dict.get( 'tools', [] ),
-                                                                                                  converter_path=converter_path,
-                                                                                                  display_path=display_path )
-            if converter_path:
-                # Load proprietary datatype converters
-                self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict )
-            if display_path:
-                # Load proprietary datatype display applications
-                self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
-            suc.remove_dir( work_dir )
-
-    def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):
-        """Install a single repository, loading contained tools into the tool panel."""
-        # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
-        relative_clone_dir = os.path.join( tool_shed_repository.tool_shed,
-                                           'repos',
-                                           tool_shed_repository.owner,
-                                           tool_shed_repository.name,
-                                           tool_shed_repository.installed_changeset_revision )
-        clone_dir = os.path.join( self.tool_path, relative_clone_dir )
-        cloned_ok = self.__iscloned( clone_dir )
-        is_installed = False
-        # Any of the following states should count as installed in this context.
-        if tool_shed_repository.status in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
-                                            self.app.install_model.ToolShedRepository.installation_status.ERROR,
-                                            self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
-                                            self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
-            is_installed = True
-        if cloned_ok and is_installed:
-            print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir
-        else:
-            repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name )
-            relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
-            install_dir = os.path.join( clone_dir, tool_shed_repository.name )
-            ctx_rev = suc.get_ctx_rev( self.app,
-                                       self.tool_shed_url,
-                                       tool_shed_repository.name,
-                                       tool_shed_repository.owner,
-                                       tool_shed_repository.installed_changeset_revision )
-            if not cloned_ok:
-                suc.update_tool_shed_repository_status( self.app,
-                                                        tool_shed_repository,
-                                                        self.app.install_model.ToolShedRepository.installation_status.CLONING )
-                cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
-            if cloned_ok and not is_installed:
-                self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
-                                                 repository_clone_url=repository_clone_url,
-                                                 relative_install_dir=relative_install_dir,
-                                                 repository_elem=repository_elem,
-                                                 install_dependencies=install_dependencies,
-                                                 is_repository_dependency=is_repository_dependency )
-                self.app.install_model.context.refresh( tool_shed_repository )
-                metadata_dict = tool_shed_repository.metadata
-                if 'tools' in metadata_dict:
-                    suc.update_tool_shed_repository_status( self.app,
-                                                            tool_shed_repository,
-                                                            self.app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
-                    # Get the tool_versions from the tool shed for each tool in the installed change set.
-                    url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
-                        ( self.tool_shed_url, tool_shed_repository.name, self.repository_owner, tool_shed_repository.installed_changeset_revision )
-                    text = common_util.tool_shed_get( self.app, self.tool_shed_url, url )
-                    if text:
-                        tool_version_dicts = json.loads( text )
-                        tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository )
-                    else:
-                        # Set the tool versions since they seem to be missing for this repository in the tool shed.
-                        # CRITICAL NOTE: These default settings may not properly handle all parent/child associations.
-                        for tool_dict in metadata_dict[ 'tools' ]:
-                            flush_needed = False
-                            tool_id = tool_dict[ 'guid' ]
-                            old_tool_id = tool_dict[ 'id' ]
-                            tool_version = tool_dict[ 'version' ]
-                            tool_version_using_old_id = tool_util.get_tool_version( self.app, old_tool_id )
-                            tool_version_using_guid = tool_util.get_tool_version( self.app, tool_id )
-                            if not tool_version_using_old_id:
-                                tool_version_using_old_id = self.app.install_model.ToolVersion( tool_id=old_tool_id,
-                                                                                        tool_shed_repository=tool_shed_repository )
-                                self.app.install_model.context.add( tool_version_using_old_id )
-                                self.app.install_model.context.flush()
-                            if not tool_version_using_guid:
-                                tool_version_using_guid = self.app.install_model.ToolVersion( tool_id=tool_id,
-                                                                                      tool_shed_repository=tool_shed_repository )
-                                self.app.install_model.context.add( tool_version_using_guid )
-                                self.app.install_model.context.flush()
-                            # Associate the two versions as parent / child.
-                            tool_version_association = tool_util.get_tool_version_association( self.app,
-                                                                                               tool_version_using_old_id,
-                                                                                               tool_version_using_guid )
-                            if not tool_version_association:
-                                tool_version_association = self.app.install_model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
-                                                                                                  parent_id=tool_version_using_old_id.id )
-                                self.app.install_model.context.add( tool_version_association )
-                                self.app.install_model.context.flush()
-                suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
-            else:
-                print 'Error attempting to clone repository %s: %s' % ( str( tool_shed_repository.name ), str( error_message ) )
-                suc.update_tool_shed_repository_status( self.app,
-                                                        tool_shed_repository,
-                                                        self.app.install_model.ToolShedRepository.installation_status.ERROR,
-                                                        error_message=error_message )
-
-    @property
-    def non_shed_tool_panel_configs( self ):
-        return common_util.get_non_shed_tool_panel_configs( self.app )
-
-    def order_repositories_for_installation( self, tool_shed_repositories, repository_dependencies_dict ):
-        """
-        Some repositories may have repository dependencies that are required to be installed before the dependent
-        repository.  This method will inspect the list of repositories about to be installed and make sure to order
-        them appropriately.  For each repository about to be installed, if required repositories are not contained
-        in the list of repositories about to be installed, then they are not considered.  Repository dependency
-        definitions that contain circular dependencies should not result in an infinite loop, but obviously prior
-        installation will not be handled for one or more of the repositories that require prior installation.  This
-        process is similar to the process used when installing tool shed repositories (i.e., the
-        order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not
-        handle managing tool panel sections and other components since repository dependency definitions contained
-        in tool shed repositories with migrated tools must never define a relationship to a repository dependency
-        that contains a tool.
-        """
-        ordered_tool_shed_repositories = []
-        ordered_tsr_ids = []
-        processed_tsr_ids = []
-        prior_install_required_dict = self.get_prior_install_required_dict( tool_shed_repositories, repository_dependencies_dict )
-        tsr_ids = [ tool_shed_repository.id for tool_shed_repository in tool_shed_repositories ]
-        while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ):
-            tsr_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_install_required_dict, processed_tsr_ids )
-            processed_tsr_ids.append( tsr_id )
-            # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists.
-            if tsr_id not in ordered_tsr_ids:
-                prior_install_required_ids = prior_install_required_dict[ tsr_id ]
-                for prior_install_required_id in prior_install_required_ids:
-                    if prior_install_required_id not in ordered_tsr_ids:
-                        # Install the associated repository dependency first.
-                        ordered_tsr_ids.append( prior_install_required_id )
-                ordered_tsr_ids.append( tsr_id )
-        for ordered_tsr_id in ordered_tsr_ids:
-            for tool_shed_repository in tool_shed_repositories:
-                if tool_shed_repository.id == ordered_tsr_id:
-                    ordered_tool_shed_repositories.append( tool_shed_repository )
-                    break
-        return ordered_tool_shed_repositories
-
-    def __has_tool_dependencies( self, metadata_dict ):
-        '''Determine if the provided metadata_dict specifies tool dependencies.'''
-        # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case
-        # the metadata is out of date.
-        if 'tool_dependencies' in metadata_dict or 'orphan_tool_dependencies' in metadata_dict:
-            return True
-        return False
-
-    def __iscloned( self, clone_dir ):
-        full_path = os.path.abspath( clone_dir )
-        if os.path.exists( full_path ):
-            for root, dirs, files in os.walk( full_path ):
-                if '.hg' in dirs:
-                    # Assume that the repository has been installed if we find a .hg directory.
-                    return True
-        return False
-
-    def __is_repository_dependency( self, name, changeset_revision, tool_shed_repository ):
-        '''Determine if the provided tool shed repository is a repository dependency.'''
-        if str( tool_shed_repository.name ) != str( name ) or \
-                str( tool_shed_repository.owner ) != str( self.repository_owner ) or \
-                str( tool_shed_repository.changeset_revision ) != str( changeset_revision ):
-            return True
-        return False
-
-    def __is_valid_repository_tag( self, elem ):
-        # <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" />
-        if elem.tag != 'repository':
-            return False
-        if not elem.get( 'name' ):
-            return False
-        if not elem.get( 'changeset_revision' ):
-            return False
-        return True
+    pass
\ No newline at end of file
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/galaxy_install/migrate/common.py
--- a/lib/tool_shed/galaxy_install/migrate/common.py
+++ b/lib/tool_shed/galaxy_install/migrate/common.py
@@ -46,17 +46,19 @@
# Get the latest tool migration script number to send to the Install manager.
         latest_migration_script_number = int( tools_migration_config.split( '_' )[ 0 ] )
-        # The value of migrated_tools_config is migrated_tools_conf.xml, and is reserved for containing only those tools that have been
-        # eliminated from the distribution and moved to the tool shed.  A side-effect of instantiating the InstallManager is the automatic
+        # The value of migrated_tools_config is migrated_tools_conf.xml, and is reserved for
+        # containing only those tools that have been eliminated from the distribution and moved
+        # to the tool shed.  A side-effect of instantiating the ToolMigrationlManager is the automatic
         # installation of all appropriate tool shed repositories.
-        self.install_manager = install_manager.InstallManager( app=self,
-                                                               latest_migration_script_number=latest_migration_script_number,
-                                                               tool_shed_install_config=os.path.join( self.config.root,
-                                                                                                      'scripts',
-                                                                                                      'migrate_tools',
-                                                                                                      tools_migration_config ),
-                                                               migrated_tools_config=self.config.migrated_tools_config,
-                                                               install_dependencies=install_dependencies )
+        self.tool_migration_manager = \
+            tool_migration_manager.ToolMigrationManager( app=self,
+                                                         latest_migration_script_number=latest_migration_script_number,
+                                                         tool_shed_install_config=os.path.join( self.config.root,
+                                                                                                'scripts',
+                                                                                                'migrate_tools',
+                                                                                                tools_migration_config ),
+                                                         migrated_tools_config=self.config.migrated_tools_config,
+                                                         install_dependencies=install_dependencies )
@property
     def sa_session( self ):
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -625,7 +625,7 @@
                                                                                         tool_shed_repository=tool_shed_repository,
                                                                                         tool_dependencies_config=tool_dependencies_config,
                                                                                         tool_dependencies=tool_shed_repository.tool_dependencies,
-                                                                                        from_install_manager=False )
+                                                                                        from_tool_migration_manager=False )
             suc.remove_dir( work_dir )
         suc.update_tool_shed_repository_status( trans.app,
                                                 tool_shed_repository,
@@ -881,7 +881,7 @@
                                                                                         tool_shed_repository=repository,
                                                                                         tool_dependencies_config=tool_dependencies_config,
                                                                                         tool_dependencies=repository.tool_dependencies,
-                                                                                        from_install_manager=False )
+                                                                                        from_tool_migration_manager=False )
             for installed_tool_dependency in installed_tool_dependencies:
                 if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]:
                     repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message )
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -175,7 +175,7 @@
     return text
-def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository, from_install_manager=False ):
+def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository, from_tool_migration_manager=False ):
     """
     Inspect the repository defined by a complex repository dependency definition and take certain steps to enable installation
     of the received package name and version to proceed.  The received elem is the <repository> tag set which defines the complex
@@ -224,7 +224,7 @@
             # framework which installs repositories in 2 stages, those of type tool_dependency_definition
             # followed by those containing valid tools and tool functional test components.  Neither of these
             # scenarios apply when the install manager is running.
-            if from_install_manager:
+            if from_tool_migration_manager:
                 can_install_tool_dependency = True
             else:
                 # Notice that we'll throw away the following tool_dependency if it can be installed.
@@ -306,7 +306,7 @@
     tool_dependency = tool_dependency_util.mark_tool_dependency_installed( app, tool_dependency )
     return tool_dependency
-def install_package( app, elem, tool_shed_repository, tool_dependencies=None, from_install_manager=False ):
+def install_package( app, elem, tool_shed_repository, tool_dependencies=None, from_tool_migration_manager=False ):
     """
     Install a tool dependency package defined by the XML element elem.  The value of tool_dependencies is
     a partial or full list of ToolDependency records associated with the tool_shed_repository.
@@ -325,7 +325,7 @@
                                                                                          package_name,
                                                                                          package_version,
                                                                                          tool_shed_repository,
-                                                                                         from_install_manager=from_install_manager )
+                                                                                         from_tool_migration_manager=from_tool_migration_manager )
                 for rd_tool_dependency in rd_tool_dependencies:
                     if rd_tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR:
                         # We'll log the error here, but continue installing packages since some may not require this dependency.
@@ -348,7 +348,7 @@
                     # framework which installs repositories in 2 stages, those of type tool_dependency_definition
                     # followed by those containing valid tools and tool functional test components.  Neither of these
                     # scenarios apply when the install manager is running.
-                    if from_install_manager:
+                    if from_tool_migration_manager:
                         can_install_tool_dependency = True
                     else:
                         # Notice that we'll throw away the following tool_dependency if it can be installed.
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/galaxy_install/tool_migration_manager.py
--- /dev/null
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -0,0 +1,643 @@
+"""
+Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml).
+All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed.
+"""
+import json
+import os
+import shutil
+import tempfile
+import threading
+import logging
+from galaxy import util
+from galaxy.tools import ToolSection
+import tool_shed.util.shed_util_common as suc
+from tool_shed.util import common_install_util
+from tool_shed.util import common_util
+from tool_shed.util import datatype_util
+from tool_shed.util import hg_util
+from tool_shed.util import metadata_util
+from tool_shed.util import tool_dependency_util
+from tool_shed.util import tool_util
+from tool_shed.util import xml_util
+from galaxy.util.odict import odict
+
+log = logging.getLogger( __name__ )
+
+
+class ToolMigrationlManager( object ):
+
+    def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ):
+        """
+        Check tool settings in tool_shed_install_config and install all repositories that are not already installed.  The tool
+        panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml.
+        """
+        self.app = app
+        self.toolbox = self.app.toolbox
+        self.migrated_tools_config = migrated_tools_config
+        # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message.
+        if install_dependencies and app.config.tool_dependency_dir is None:
+            message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini '
+            message += 'file.  Set this location value to the path where you want tool dependencies installed and rerun the migration script.'
+            raise Exception( message )
+        # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml).
+        self.proprietary_tool_confs = self.non_shed_tool_panel_configs
+        self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number )
+        # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
+        tree, error_message = xml_util.parse_xml( migrated_tools_config )
+        if tree is None:
+            print error_message
+        else:
+            root = tree.getroot()
+            self.tool_path = root.get( 'tool_path' )
+            print "Repositories will be installed into configured tool_path location ", str( self.tool_path )
+            # Parse tool_shed_install_config to check each of the tools.
+            self.tool_shed_install_config = tool_shed_install_config
+            tree, error_message = xml_util.parse_xml( tool_shed_install_config )
+            if tree is None:
+                print error_message
+            else:
+                root = tree.getroot()
+                defined_tool_shed_url = root.get( 'name' )
+                self.tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, defined_tool_shed_url )
+                self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url )
+                self.repository_owner = common_util.REPOSITORY_OWNER
+                index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
+                # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
+                # tool_conf.xml.  If no tools associated with the migration stage are defined, no repositories will be installed on disk.
+                # The default behavior is that the tool shed is down.
+                tool_shed_accessible = False
+                tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app )
+                if tool_panel_configs:
+                    # The missing_tool_configs_dict contents are something like:
+                    # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]}
+                    tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app,
+                                                                                                           tool_panel_configs,
+                                                                                                           latest_migration_script_number )
+                else:
+                    # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but
+                    # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in
+                    # the database.
+                    tool_shed_accessible = True
+                    missing_tool_configs_dict = odict()
+                if tool_shed_accessible:
+                    if len( self.proprietary_tool_confs ) == 1:
+                        plural = ''
+                        file_names = self.proprietary_tool_confs[ 0 ]
+                    else:
+                        plural = 's'
+                        file_names = ', '.join( self.proprietary_tool_confs )
+                    if missing_tool_configs_dict:
+                        for proprietary_tool_conf in self.proprietary_tool_confs:
+                            # Create a backup of the tool configuration in the un-migrated state.
+                            shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) )
+                        for repository_elem in root:
+                            # Make sure we have a valid repository tag.
+                            if self.__is_valid_repository_tag( repository_elem ):
+                                # Get all repository dependencies for the repository defined by the current repository_elem.  Repository dependency
+                                # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
+                                # dependency that contains a tool.  The repository dependency can only contain items that are not loaded into the Galaxy
+                                # tool panel (e.g., tool dependency definitions, custom datatypes, etc).  This restriction must be followed down the
+                                # entire dependency hierarchy.
+                                name = repository_elem.get( 'name' )
+                                changeset_revision = repository_elem.get( 'changeset_revision' )
+                                tool_shed_accessible, repository_dependencies_dict = \
+                                    common_util.get_repository_dependencies( app,
+                                                                             self.tool_shed_url,
+                                                                             name,
+                                                                             self.repository_owner,
+                                                                             changeset_revision )
+                                # Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database.
+                                created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name,
+                                                                                                                     changeset_revision,
+                                                                                                                     repository_dependencies_dict )
+                                # Order the repositories for proper installation.  This process is similar to the process used when installing tool
+                                # shed repositories (i.e., the order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/
+                                # repository_util), but does not handle managing tool panel sections and other components since repository dependency
+                                # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository
+                                # dependency that contains a tool.
+                                ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories,
+                                                                                                           repository_dependencies_dict )
+
+                                for tool_shed_repository in ordered_tool_shed_repositories:
+                                    is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository )
+                                    self.install_repository( repository_elem,
+                                                             tool_shed_repository,
+                                                             install_dependencies,
+                                                             is_repository_dependency=is_repository_dependency )
+                    else:
+                        message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number )
+                        message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names )
+                        print message
+                else:
+                    message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number )
+                    message += "Try again later.\n"
+                    print message
+
+    def create_or_update_tool_shed_repository_record( self, name, owner, changeset_revision, description=None ):
+
+        # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
+        relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision )
+        clone_dir = os.path.join( self.tool_path, relative_clone_dir )
+        if not self.__iscloned( clone_dir ):
+            repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name )
+            relative_install_dir = os.path.join( relative_clone_dir, name )
+            install_dir = os.path.join( clone_dir, name )
+            ctx_rev = suc.get_ctx_rev( self.app, self.tool_shed_url, name, owner, changeset_revision )
+            tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
+                                                                              name=name,
+                                                                              description=description,
+                                                                              installed_changeset_revision=changeset_revision,
+                                                                              ctx_rev=ctx_rev,
+                                                                              repository_clone_url=repository_clone_url,
+                                                                              metadata_dict={},
+                                                                              status=self.app.install_model.ToolShedRepository.installation_status.NEW,
+                                                                              current_changeset_revision=None,
+                                                                              owner=self.repository_owner,
+                                                                              dist_to_shed=True )
+            return tool_shed_repository
+        return None
+
+    def create_or_update_tool_shed_repository_records( self, name, changeset_revision, repository_dependencies_dict ):
+        """
+        Make sure the repository defined by name and changeset_revision and all of its repository dependencies have
+        associated tool_shed_repository table rows in the Galaxy database.
+        """
+        created_tool_shed_repositories = []
+        description = repository_dependencies_dict.get( 'description', None )
+        tool_shed_repository = self.create_or_update_tool_shed_repository_record( name,
+                                                                                  self.repository_owner,
+                                                                                  changeset_revision,
+                                                                                  description=description )
+        if tool_shed_repository:
+            created_tool_shed_repositories.append( tool_shed_repository )
+        for rd_key, rd_tups in repository_dependencies_dict.items():
+            if rd_key in [ 'root_key', 'description' ]:
+                continue
+            for rd_tup in rd_tups:
+                parsed_rd_tup = common_util.parse_repository_dependency_tuple( rd_tup )
+                rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = parsed_rd_tup[ 0:4 ]
+                # TODO: Make sure the repository description is applied to the new repository record during installation.
+                tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name,
+                                                                                          rd_owner,
+                                                                                          rd_changeset_revision,
+                                                                                          description=None )
+                if tool_shed_repository:
+                    created_tool_shed_repositories.append( tool_shed_repository )
+        return created_tool_shed_repositories
+
+    def filter_and_persist_proprietary_tool_panel_configs( self, tool_configs_to_filter ):
+        """Eliminate all entries in all non-shed-related tool panel configs for all tool config file names in the received tool_configs_to_filter."""
+        for proprietary_tool_conf in self.proprietary_tool_confs:
+            persist_required = False
+            tree, error_message = xml_util.parse_xml( proprietary_tool_conf )
+            if tree:
+                root = tree.getroot()
+                for elem in root:
+                    if elem.tag == 'tool':
+                        # Tools outside of sections.
+                        file_path = elem.get( 'file', None )
+                        if file_path:
+                            if file_path in tool_configs_to_filter:
+                                root.remove( elem )
+                                persist_required = True
+                    elif elem.tag == 'section':
+                        # Tools contained in a section.
+                        for section_elem in elem:
+                            if section_elem.tag == 'tool':
+                                file_path = section_elem.get( 'file', None )
+                                if file_path:
+                                    if file_path in tool_configs_to_filter:
+                                        elem.remove( section_elem )
+                                        persist_required = True
+            if persist_required:
+                fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-fapptpc"  )
+                tmp_filename = fh.name
+                fh.close()
+                fh = open( tmp_filename, 'wb' )
+                tree.write( tmp_filename, encoding='utf-8', xml_declaration=True )
+                fh.close()
+                shutil.move( tmp_filename, os.path.abspath( proprietary_tool_conf ) )
+                os.chmod( proprietary_tool_conf, 0644 )
+
+    def get_containing_tool_sections( self, tool_config ):
+        """
+        If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the
+        tool is displayed.  If the tool is displayed outside of any sections, None is appended to the list.
+        """
+        tool_sections = []
+        is_displayed = False
+        for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems:
+            if proprietary_tool_panel_elem.tag == 'tool':
+                # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
+                proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' )
+                if tool_config == proprietary_tool_config:
+                    # The tool is loaded outside of any sections.
+                    tool_sections.append( None )
+                    if not is_displayed:
+                        is_displayed = True
+            if proprietary_tool_panel_elem.tag == 'section':
+                # The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">.
+                for section_elem in proprietary_tool_panel_elem:
+                    if section_elem.tag == 'tool':
+                        # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
+                        proprietary_tool_config = section_elem.get( 'file' )
+                        if tool_config == proprietary_tool_config:
+                            # The tool is loaded inside of the section_elem.
+                            tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
+                            if not is_displayed:
+                                is_displayed = True
+        return is_displayed, tool_sections
+
+    def get_guid( self, repository_clone_url, relative_install_dir, tool_config ):
+        if self.shed_config_dict.get( 'tool_path' ):
+            relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir )
+        tool_config_filename = suc.strip_path( tool_config )
+        for root, dirs, files in os.walk( relative_install_dir ):
+            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+                if '.hg' in dirs:
+                    dirs.remove( '.hg' )
+                for name in files:
+                    filename = suc.strip_path( name )
+                    if filename == tool_config_filename:
+                        full_path = str( os.path.abspath( os.path.join( root, name ) ) )
+                        tool = self.toolbox.load_tool( full_path )
+                        return suc.generate_tool_guid( repository_clone_url, tool )
+        # Not quite sure what should happen here, throw an exception or what?
+        return None
+
+    def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ):
+        """
+        Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received
+        list of tsr_ids and whose associated repository must be installed prior to the repository associated with the tsr_id key.
+        """
+        # Initialize the dictionary.
+        prior_install_required_dict = {}
+        tsr_ids = [ tool_shed_repository.id for tool_shed_repository in tool_shed_repositories ]
+        for tsr_id in tsr_ids:
+            prior_install_required_dict[ tsr_id ] = []
+        # Inspect the repository dependencies about to be installed and populate the dictionary.
+        for rd_key, rd_tups in repository_dependencies_dict.items():
+            if rd_key in [ 'root_key', 'description' ]:
+                continue
+            for rd_tup in rd_tups:
+                prior_install_ids = []
+                tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+                    common_util.parse_repository_dependency_tuple( rd_tup )
+                if util.asbool( prior_installation_required ):
+                    for tsr in tool_shed_repositories:
+                        if tsr.name == name and tsr.owner == owner and tsr.changeset_revision == changeset_revision:
+                            prior_install_ids.append( tsr.id )
+                        prior_install_required_dict[ tsr.id ] = prior_install_ids
+        return prior_install_required_dict
+
+    def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ):
+        """
+        Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
+        either ToolSection elements or Tool elements.  These will be used to generate new entries in the migrated_tools_conf.xml
+        file for the installed tools.
+        """
+        tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
+        # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
+        migrated_tool_configs = []
+        tree, error_message = xml_util.parse_xml( tools_xml_file_path )
+        if tree is None:
+            return []
+        root = tree.getroot()
+        for elem in root:
+            if elem.tag == 'repository':
+                for tool_elem in elem:
+                    migrated_tool_configs.append( tool_elem.get( 'file' ) )
+        # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
+        tool_panel_elems = []
+        for proprietary_tool_conf in self.proprietary_tool_confs:
+            tree, error_message = xml_util.parse_xml( proprietary_tool_conf )
+            if tree is None:
+                return []
+            root = tree.getroot()
+            for elem in root:
+                if elem.tag == 'tool':
+                    # Tools outside of sections.
+                    file_path = elem.get( 'file', None )
+                    if file_path:
+                        if file_path in migrated_tool_configs:
+                            if elem not in tool_panel_elems:
+                                tool_panel_elems.append( elem )
+                elif elem.tag == 'section':
+                    # Tools contained in a section.
+                    for section_elem in elem:
+                        if section_elem.tag == 'tool':
+                            file_path = section_elem.get( 'file', None )
+                            if file_path:
+                                if file_path in migrated_tool_configs:
+                                    # Append the section, not the tool.
+                                    if elem not in tool_panel_elems:
+                                        tool_panel_elems.append( elem )
+        return tool_panel_elems
+
+    def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem,
+                                    install_dependencies, is_repository_dependency=False ):
+        """
+        Generate the metadata for the installed tool shed repository, among other things.  If the installed tool_shed_repository
+        contains tools that are loaded into the Galaxy tool panel, this method will automatically eliminate all entries for each
+        of the tools defined in the received repository_elem from all non-shed-related tool panel configuration files since the
+        entries are automatically added to the reserved migrated_tools_conf.xml file as part of the migration process.
+        """
+        tool_configs_to_filter = []
+        tool_panel_dict_for_display = odict()
+        if self.tool_path:
+            repo_install_dir = os.path.join( self.tool_path, relative_install_dir )
+        else:
+            repo_install_dir = relative_install_dir
+        if not is_repository_dependency:
+            for tool_elem in repository_elem:
+                # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" />
+                tool_config = tool_elem.get( 'file' )
+                guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config )
+                # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems.
+                is_displayed, tool_sections = self.get_containing_tool_sections( tool_config )
+                if is_displayed:
+                    tool_panel_dict_for_tool_config = \
+                        tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
+                    # The tool-panel_dict has the following structure.
+                    # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>,
+                    #                   name : <TooSection name>}]}
+                    for k, v in tool_panel_dict_for_tool_config.items():
+                        tool_panel_dict_for_display[ k ] = v
+                        for tool_panel_dict in v:
+                            # Keep track of tool config file names associated with entries that have been made to the
+                            # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs.
+                            if tool_config not in tool_configs_to_filter:
+                                tool_configs_to_filter.append( tool_config )
+                else:
+                    print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
+                    % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
+            if tool_configs_to_filter:
+                lock = threading.Lock()
+                lock.acquire( True )
+                try:
+                    self.filter_and_persist_proprietary_tool_panel_configs( tool_configs_to_filter )
+                except Exception, e:
+                    log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) )
+                finally:
+                    lock.release()
+        metadata_dict, invalid_file_tups = \
+            metadata_util.generate_metadata_for_changeset_revision( app=self.app,
+                                                                    repository=tool_shed_repository,
+                                                                    changeset_revision=tool_shed_repository.changeset_revision,
+                                                                    repository_clone_url=repository_clone_url,
+                                                                    shed_config_dict = self.shed_config_dict,
+                                                                    relative_install_dir=relative_install_dir,
+                                                                    repository_files_dir=None,
+                                                                    resetting_all_metadata_on_repository=False,
+                                                                    updating_installed_repository=False,
+                                                                    persist=True )
+        tool_shed_repository.metadata = metadata_dict
+        self.app.install_model.context.add( tool_shed_repository )
+        self.app.install_model.context.flush()
+        has_tool_dependencies = self.__has_tool_dependencies( metadata_dict )
+        if has_tool_dependencies:
+            # All tool_dependency objects must be created before the tools are processed even if no
+            # tool dependencies will be installed.
+            tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app,
+                                                                                     tool_shed_repository,
+                                                                                     relative_install_dir,
+                                                                                     set_status=True )
+        else:
+            tool_dependencies = None
+        if 'tools' in metadata_dict:
+            sample_files = metadata_dict.get( 'sample_files', [] )
+            sample_files = [ str( s ) for s in sample_files ]
+            tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
+            tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path )
+            sample_files_copied = [ s for s in tool_index_sample_files ]
+            repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict )
+            if repository_tools_tups:
+                # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+                repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups )
+                # Handle missing index files for tool parameters that are dynamically generated select lists.
+                repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app,
+                                                                                                  self.tool_path,
+                                                                                                  sample_files,
+                                                                                                  repository_tools_tups,
+                                                                                                  sample_files_copied )
+                # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance.
+                tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied )
+                if not is_repository_dependency:
+                    tool_util.add_to_tool_panel( self.app,
+                                                 tool_shed_repository.name,
+                                                 repository_clone_url,
+                                                 tool_shed_repository.installed_changeset_revision,
+                                                 repository_tools_tups,
+                                                 self.repository_owner,
+                                                 self.migrated_tools_config,
+                                                 tool_panel_dict=tool_panel_dict_for_display,
+                                                 new_install=True )
+        if install_dependencies and tool_dependencies and has_tool_dependencies:
+            # Install tool dependencies.
+            suc.update_tool_shed_repository_status( self.app,
+                                                    tool_shed_repository,
+                                                    self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
+            # Get the tool_dependencies.xml file from disk.
+            tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
+            installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app,
+                                                                                        tool_shed_repository=tool_shed_repository,
+                                                                                        tool_dependencies_config=tool_dependencies_config,
+                                                                                        tool_dependencies=tool_dependencies,
+                                                                                        from_tool_migration_manager=True )
+            for installed_tool_dependency in installed_tool_dependencies:
+                if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
+                    print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':'
+                    print installed_tool_dependency.error_message, '\n\n'
+        if 'datatypes' in metadata_dict:
+            tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
+            if not tool_shed_repository.includes_datatypes:
+                tool_shed_repository.includes_datatypes = True
+            self.app.install_model.context.add( tool_shed_repository )
+            self.app.install_model.context.flush()
+            work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" )
+            datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir )
+            # Load proprietary data types required by tools.  The value of override is not important here since the Galaxy server will be started
+            # after this installation completes.
+            converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir
+            if converter_path or display_path:
+                # Create a dictionary of tool shed repository related information.
+                repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url,
+                                                                                                  name=tool_shed_repository.name,
+                                                                                                  owner=self.repository_owner,
+                                                                                                  installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+                                                                                                  tool_dicts=metadata_dict.get( 'tools', [] ),
+                                                                                                  converter_path=converter_path,
+                                                                                                  display_path=display_path )
+            if converter_path:
+                # Load proprietary datatype converters
+                self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict )
+            if display_path:
+                # Load proprietary datatype display applications
+                self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+            suc.remove_dir( work_dir )
+
+    def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):
+        """Install a single repository, loading contained tools into the tool panel."""
+        # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
+        relative_clone_dir = os.path.join( tool_shed_repository.tool_shed,
+                                           'repos',
+                                           tool_shed_repository.owner,
+                                           tool_shed_repository.name,
+                                           tool_shed_repository.installed_changeset_revision )
+        clone_dir = os.path.join( self.tool_path, relative_clone_dir )
+        cloned_ok = self.__iscloned( clone_dir )
+        is_installed = False
+        # Any of the following states should count as installed in this context.
+        if tool_shed_repository.status in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
+                                            self.app.install_model.ToolShedRepository.installation_status.ERROR,
+                                            self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
+                                            self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
+            is_installed = True
+        if cloned_ok and is_installed:
+            print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir
+        else:
+            repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name )
+            relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
+            install_dir = os.path.join( clone_dir, tool_shed_repository.name )
+            ctx_rev = suc.get_ctx_rev( self.app,
+                                       self.tool_shed_url,
+                                       tool_shed_repository.name,
+                                       tool_shed_repository.owner,
+                                       tool_shed_repository.installed_changeset_revision )
+            if not cloned_ok:
+                suc.update_tool_shed_repository_status( self.app,
+                                                        tool_shed_repository,
+                                                        self.app.install_model.ToolShedRepository.installation_status.CLONING )
+                cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
+            if cloned_ok and not is_installed:
+                self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
+                                                 repository_clone_url=repository_clone_url,
+                                                 relative_install_dir=relative_install_dir,
+                                                 repository_elem=repository_elem,
+                                                 install_dependencies=install_dependencies,
+                                                 is_repository_dependency=is_repository_dependency )
+                self.app.install_model.context.refresh( tool_shed_repository )
+                metadata_dict = tool_shed_repository.metadata
+                if 'tools' in metadata_dict:
+                    suc.update_tool_shed_repository_status( self.app,
+                                                            tool_shed_repository,
+                                                            self.app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
+                    # Get the tool_versions from the tool shed for each tool in the installed change set.
+                    url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
+                        ( self.tool_shed_url, tool_shed_repository.name, self.repository_owner, tool_shed_repository.installed_changeset_revision )
+                    text = common_util.tool_shed_get( self.app, self.tool_shed_url, url )
+                    if text:
+                        tool_version_dicts = json.loads( text )
+                        tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository )
+                    else:
+                        # Set the tool versions since they seem to be missing for this repository in the tool shed.
+                        # CRITICAL NOTE: These default settings may not properly handle all parent/child associations.
+                        for tool_dict in metadata_dict[ 'tools' ]:
+                            flush_needed = False
+                            tool_id = tool_dict[ 'guid' ]
+                            old_tool_id = tool_dict[ 'id' ]
+                            tool_version = tool_dict[ 'version' ]
+                            tool_version_using_old_id = tool_util.get_tool_version( self.app, old_tool_id )
+                            tool_version_using_guid = tool_util.get_tool_version( self.app, tool_id )
+                            if not tool_version_using_old_id:
+                                tool_version_using_old_id = self.app.install_model.ToolVersion( tool_id=old_tool_id,
+                                                                                        tool_shed_repository=tool_shed_repository )
+                                self.app.install_model.context.add( tool_version_using_old_id )
+                                self.app.install_model.context.flush()
+                            if not tool_version_using_guid:
+                                tool_version_using_guid = self.app.install_model.ToolVersion( tool_id=tool_id,
+                                                                                      tool_shed_repository=tool_shed_repository )
+                                self.app.install_model.context.add( tool_version_using_guid )
+                                self.app.install_model.context.flush()
+                            # Associate the two versions as parent / child.
+                            tool_version_association = tool_util.get_tool_version_association( self.app,
+                                                                                               tool_version_using_old_id,
+                                                                                               tool_version_using_guid )
+                            if not tool_version_association:
+                                tool_version_association = self.app.install_model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
+                                                                                                  parent_id=tool_version_using_old_id.id )
+                                self.app.install_model.context.add( tool_version_association )
+                                self.app.install_model.context.flush()
+                suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
+            else:
+                print 'Error attempting to clone repository %s: %s' % ( str( tool_shed_repository.name ), str( error_message ) )
+                suc.update_tool_shed_repository_status( self.app,
+                                                        tool_shed_repository,
+                                                        self.app.install_model.ToolShedRepository.installation_status.ERROR,
+                                                        error_message=error_message )
+
+    @property
+    def non_shed_tool_panel_configs( self ):
+        return common_util.get_non_shed_tool_panel_configs( self.app )
+
+    def order_repositories_for_installation( self, tool_shed_repositories, repository_dependencies_dict ):
+        """
+        Some repositories may have repository dependencies that are required to be installed before the dependent
+        repository.  This method will inspect the list of repositories about to be installed and make sure to order
+        them appropriately.  For each repository about to be installed, if required repositories are not contained
+        in the list of repositories about to be installed, then they are not considered.  Repository dependency
+        definitions that contain circular dependencies should not result in an infinite loop, but obviously prior
+        installation will not be handled for one or more of the repositories that require prior installation.  This
+        process is similar to the process used when installing tool shed repositories (i.e., the
+        order_components_for_installation() method in ~/lib/tool_shed/galaxy_install/repository_util), but does not
+        handle managing tool panel sections and other components since repository dependency definitions contained
+        in tool shed repositories with migrated tools must never define a relationship to a repository dependency
+        that contains a tool.
+        """
+        ordered_tool_shed_repositories = []
+        ordered_tsr_ids = []
+        processed_tsr_ids = []
+        prior_install_required_dict = self.get_prior_install_required_dict( tool_shed_repositories, repository_dependencies_dict )
+        tsr_ids = [ tool_shed_repository.id for tool_shed_repository in tool_shed_repositories ]
+        while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ):
+            tsr_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_install_required_dict, processed_tsr_ids )
+            processed_tsr_ids.append( tsr_id )
+            # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists.
+            if tsr_id not in ordered_tsr_ids:
+                prior_install_required_ids = prior_install_required_dict[ tsr_id ]
+                for prior_install_required_id in prior_install_required_ids:
+                    if prior_install_required_id not in ordered_tsr_ids:
+                        # Install the associated repository dependency first.
+                        ordered_tsr_ids.append( prior_install_required_id )
+                ordered_tsr_ids.append( tsr_id )
+        for ordered_tsr_id in ordered_tsr_ids:
+            for tool_shed_repository in tool_shed_repositories:
+                if tool_shed_repository.id == ordered_tsr_id:
+                    ordered_tool_shed_repositories.append( tool_shed_repository )
+                    break
+        return ordered_tool_shed_repositories
+
+    def __has_tool_dependencies( self, metadata_dict ):
+        '''Determine if the provided metadata_dict specifies tool dependencies.'''
+        # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case
+        # the metadata is out of date.
+        if 'tool_dependencies' in metadata_dict or 'orphan_tool_dependencies' in metadata_dict:
+            return True
+        return False
+
+    def __iscloned( self, clone_dir ):
+        full_path = os.path.abspath( clone_dir )
+        if os.path.exists( full_path ):
+            for root, dirs, files in os.walk( full_path ):
+                if '.hg' in dirs:
+                    # Assume that the repository has been installed if we find a .hg directory.
+                    return True
+        return False
+
+    def __is_repository_dependency( self, name, changeset_revision, tool_shed_repository ):
+        '''Determine if the provided tool shed repository is a repository dependency.'''
+        if str( tool_shed_repository.name ) != str( name ) or \
+                str( tool_shed_repository.owner ) != str( self.repository_owner ) or \
+                str( tool_shed_repository.changeset_revision ) != str( changeset_revision ):
+            return True
+        return False
+
+    def __is_valid_repository_tag( self, elem ):
+        # <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" />
+        if elem.tag != 'repository':
+            return False
+        if not elem.get( 'name' ):
+            return False
+        if not elem.get( 'changeset_revision' ):
+            return False
+        return True
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -483,7 +483,7 @@
                     all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts
     return all_required_repo_info_dict
-def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_install_manager=False ):
+def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False ):
     """
     Install and build tool dependencies defined in the tool_dependencies_config.  This config's tag sets can currently refer to installation
     methods in Galaxy's tool_dependencies module.  In the future, proprietary fabric scripts contained in the repository will be supported.
@@ -542,7 +542,7 @@
                                                                    elem, 
                                                                    tool_shed_repository, 
                                                                    tool_dependencies=tool_dependencies, 
-                                                                   from_install_manager=from_install_manager )
+                                                                   from_tool_migration_manager=from_tool_migration_manager )
                         except Exception, e:
                             error_message = "Error installing tool dependency package %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) )
                             log.exception( error_message )
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -163,7 +163,7 @@
 def get_tool_dependencies( app, tool_shed_url, repository_name, repository_owner, changeset_revision ):
     tool_dependencies = []
     tool_shed_accessible = True
-    url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \
+    url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
     ( tool_shed_url, repository_name, repository_owner, changeset_revision )
     try:
         text = tool_shed_get( app, tool_shed_url, url )
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 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
@@ -182,7 +182,7 @@
     If a record defined by the received tool shed, repository name and owner does not exist, create
     a new record with the received information.
     """
-    # The received value for dist_to_shed will be True if the InstallManager is installing a repository
+    # The received value for dist_to_shed will be True if the ToolMigrationManager is installing a repository
     # that contains tools or datatypes that used to be in the Galaxy distribution, but have been moved
     # to the main Galaxy tool shed.
     if current_changeset_revision is None:
diff -r 912ba22e939f505a33ef83d3bfbdbe26aa9c6a9f -r 09f80fcdfd85bf1b009b9c831e51fa92a6ff9306 scripts/migrate_tools/migrate_tools.py
--- a/scripts/migrate_tools/migrate_tools.py
+++ b/scripts/migrate_tools/migrate_tools.py
@@ -1,8 +1,8 @@
 """
-This script will start up its own web application which includes an InstallManager (~/lib/galaxy/tool_shed/install_manager.py).
+This script will start up its own web application which includes a ToolMigrationManager (~/lib/galaxy/tool_shed/tool_migration_manager.py).
 For each tool discovered missing, the tool shed repository that contains it will be installed on disk and a new entry will be
 created for it in the migrated_tools_conf.xml file.  These entries will be made so that the tool panel will be displayed the same
-as it was before the tools were eliminated from the Galaxy distribution.  The InstallManager will properly handle entries in 
+as it was before the tools were eliminated from the Galaxy distribution.  The ToolMigrationManager will properly handle entries in 
 migrated_tools_conf.xml for tools outside tool panel sections as well as tools inside tool panel sections, depending upon the
 layout of the local tool_conf.xml file.  Entries will not be created in migrated_tools_conf.xml for tools included in the tool
 shed repository but not defined in tool_conf.xml.
@@ -19,7 +19,7 @@
 from tool_shed.galaxy_install.migrate.common import MigrateToolsApplication
app = MigrateToolsApplication( sys.argv[ 1 ] )
-non_shed_tool_confs = app.install_manager.proprietary_tool_confs
+non_shed_tool_confs = app.tool_migration_manager.proprietary_tool_confs
 if len( non_shed_tool_confs ) == 1:
     plural = ''
     file_names = non_shed_tool_confs[ 0 ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: greg: Change the name of the current InstallManager to the more appropriate ToolMigrationManager since it handles only tool migrations. This allows for the InstallManager to be used for more general Tool Shed install processes.