def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ):
"""Generate the metadata for the installed tool shed repository, among other things."""
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
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 = shed_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
for k, v in tool_panel_dict_for_tool_config.items():
tool_panel_dict_for_display[ k ] = v
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 [] ) )
metadata_dict, invalid_file_tups = suc.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.sa_session.add( tool_shed_repository )
self.app.sa_session.flush()
if 'tool_dependencies' in metadata_dict:
# All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed.
tool_dependencies = shed_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 = shed_util.get_tool_index_sample_files( sample_files )
shed_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 = shed_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 = shed_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.
shed_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied )
if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict:
# Install tool dependencies.
shed_util.update_tool_shed_repository_status( self.app,
tool_shed_repository,
self.app.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 = shed_util.handle_tool_dependencies( app=self.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies )
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == self.app.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'
shed_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 'datatypes' in metadata_dict:
tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
if not tool_shed_repository.includes_datatypes:
tool_shed_repository.includes_datatypes = True
self.app.sa_session.add( tool_shed_repository )
self.app.sa_session.flush()
work_dir = tempfile.mkdtemp()
datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', 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 = shed_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 = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed,
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 )
try:
shutil.rmtree( work_dir )
except:
pass
def handle_repository_contents(self, tool_shed_repository,
repository_clone_url, relative_install_dir,
repository_elem, install_dependencies):
"""Generate the metadata for the installed tool shed repository, among other things."""
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
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 = shed_util.generate_tool_panel_dict_for_tool_config(
guid, tool_config, tool_sections=tool_sections)
for k, v in tool_panel_dict_for_tool_config.items():
tool_panel_dict_for_display[k] = v
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 [] ) )
metadata_dict, invalid_file_tups = suc.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.sa_session.add(tool_shed_repository)
self.app.sa_session.flush()
if 'tool_dependencies' in metadata_dict:
# All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed.
tool_dependencies = shed_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 = shed_util.get_tool_index_sample_files(
sample_files)
shed_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 = shed_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 = shed_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.
shed_util.copy_sample_files(
self.app,
sample_files,
tool_path=self.tool_path,
sample_files_copied=sample_files_copied)
if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict:
# Install tool dependencies.
shed_util.update_tool_shed_repository_status(
self.app, tool_shed_repository,
self.app.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 = shed_util.handle_tool_dependencies(
app=self.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies)
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == self.app.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'
shed_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 'datatypes' in metadata_dict:
tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
if not tool_shed_repository.includes_datatypes:
tool_shed_repository.includes_datatypes = True
self.app.sa_session.add(tool_shed_repository)
self.app.sa_session.flush()
work_dir = tempfile.mkdtemp()
datatypes_config = suc.get_config_from_disk(
'datatypes_conf.xml', 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 = shed_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 = shed_util.create_repository_dict_for_proprietary_datatypes(
tool_shed=self.tool_shed,
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)
try:
shutil.rmtree(work_dir)
except:
pass
def upload(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
commit_message = util.restore_text(
params.get('commit_message', 'Uploaded'))
category_ids = util.listify(params.get('category_id', ''))
categories = suc.get_categories(trans)
repository_id = params.get('repository_id', '')
repository = suc.get_repository_in_tool_shed(trans, repository_id)
repo_dir = repository.repo_path(trans.app)
repo = hg.repository(suc.get_configured_ui(), repo_dir)
uncompress_file = util.string_as_bool(
params.get('uncompress_file', 'true'))
remove_repo_files_not_in_tar = util.string_as_bool(
params.get('remove_repo_files_not_in_tar', 'true'))
uploaded_file = None
upload_point = self.__get_upload_point(repository, **kwd)
tip = repository.tip(trans.app)
file_data = params.get('file_data', '')
url = params.get('url', '')
# Part of the upload process is sending email notification to those that have registered to
# receive them. One scenario occurs when the first change set is produced for the repository.
# See the suc.handle_email_alerts() method for the definition of the scenarios.
new_repo_alert = repository.is_new(trans.app)
uploaded_directory = None
if params.get('upload_button', False):
if file_data == '' and url == '':
message = 'No files were entered on the upload form.'
status = 'error'
uploaded_file = None
elif url and url.startswith('hg'):
# Use mercurial clone to fetch repository, contents will then be copied over.
uploaded_directory = tempfile.mkdtemp()
repo_url = 'http%s' % url[len('hg'):]
repo_url = repo_url.encode('ascii', 'replace')
commands.clone(suc.get_configured_ui(), repo_url,
uploaded_directory)
elif url:
valid_url = True
try:
stream = urllib.urlopen(url)
except Exception, e:
valid_url = False
message = 'Error uploading file via http: %s' % str(e)
status = 'error'
uploaded_file = None
if valid_url:
fd, uploaded_file_name = tempfile.mkstemp()
uploaded_file = open(uploaded_file_name, 'wb')
while 1:
chunk = stream.read(CHUNK_SIZE)
if not chunk:
break
uploaded_file.write(chunk)
uploaded_file.flush()
uploaded_file_filename = url.split('/')[-1]
isempty = os.path.getsize(
os.path.abspath(uploaded_file_name)) == 0
elif file_data not in ('', None):
uploaded_file = file_data.file
uploaded_file_name = uploaded_file.name
uploaded_file_filename = os.path.split(file_data.filename)[-1]
isempty = os.path.getsize(
os.path.abspath(uploaded_file_name)) == 0
if uploaded_file or uploaded_directory:
ok = True
isgzip = False
isbz2 = False
if uploaded_file:
if uncompress_file:
isgzip = checkers.is_gzip(uploaded_file_name)
if not isgzip:
isbz2 = checkers.is_bz2(uploaded_file_name)
if isempty:
tar = None
istar = False
else:
# Determine what we have - a single file or an archive
try:
if (isgzip or isbz2) and uncompress_file:
# Open for reading with transparent compression.
tar = tarfile.open(uploaded_file_name, 'r:*')
else:
tar = tarfile.open(uploaded_file_name)
istar = True
except tarfile.ReadError, e:
tar = None
istar = False
else:
# Uploaded directory
istar = False
if istar:
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
elif uploaded_directory:
ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
else:
if (isgzip or isbz2) and uncompress_file:
uploaded_file_filename = self.uncompress(
repository, uploaded_file_name,
uploaded_file_filename, isgzip, isbz2)
if upload_point is not None:
full_path = os.path.abspath(
os.path.join(repo_dir, upload_point,
uploaded_file_filename))
else:
full_path = os.path.abspath(
os.path.join(repo_dir, uploaded_file_filename))
# Move the uploaded file to the load_point within the repository hierarchy.
shutil.move(uploaded_file_name, full_path)
# See if any admin users have chosen to receive email alerts when a repository is
# updated. If so, check every uploaded file to ensure content is appropriate.
check_contents = suc.check_file_contents(trans)
if check_contents and os.path.isfile(full_path):
content_alert_str = self.__check_file_content(
full_path)
else:
content_alert_str = ''
commands.add(repo.ui, repo, full_path)
# Convert from unicode to prevent "TypeError: array item must be char"
full_path = full_path.encode('ascii', 'replace')
commands.commit(repo.ui,
repo,
full_path,
user=trans.user.username,
message=commit_message)
if full_path.endswith('tool_data_table_conf.xml.sample'):
# Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
# to the in-memory trans.app.tool_data_tables dictionary.
error, error_message = suc.handle_sample_tool_data_table_conf_file(
trans.app, full_path)
if error:
message = '%s<br/>%s' % (message, error_message)
# See if the content of the change set was valid.
admin_only = len(repository.downloadable_revisions) != 1
suc.handle_email_alerts(
trans,
repository,
content_alert_str=content_alert_str,
new_repo_alert=new_repo_alert,
admin_only=admin_only)
if ok:
# Update the repository files for browsing.
suc.update_repository(repo)
# Get the new repository tip.
if tip == repository.tip(trans.app):
message = 'No changes to repository. '
status = 'warning'
else:
if (isgzip or isbz2) and uncompress_file:
uncompress_str = ' uncompressed and '
else:
uncompress_str = ' '
if uploaded_directory:
source_type = "repository"
source = url
else:
source_type = "file"
source = uploaded_file_filename
message = "The %s '%s' has been successfully%suploaded to the repository. " % (
source_type, source, uncompress_str)
if istar and (undesirable_dirs_removed
or undesirable_files_removed):
items_removed = undesirable_dirs_removed + undesirable_files_removed
message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive. " % items_removed
if istar and remove_repo_files_not_in_tar and files_to_remove:
if upload_point is not None:
message += " %d files were removed from the repository relative to the selected upload point '%s'. " % (
len(files_to_remove), upload_point)
else:
message += " %d files were removed from the repository root. " % len(
files_to_remove)
kwd['message'] = message
suc.set_repository_metadata_due_to_new_tip(
trans,
repository,
content_alert_str=content_alert_str,
**kwd)
# Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
# or some other problem.
if suc.get_config_from_disk('tool_dependencies.xml',
repo_dir):
if repository.metadata_revisions:
# A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload.
metadata_dict = repository.metadata_revisions[
0].metadata
else:
metadata_dict = {}
if suc.has_orphan_tool_dependencies_in_tool_shed(
metadata_dict):
message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", '
message += 'so one or more of the defined tool dependencies are considered orphans within this repository.'
status = 'warning'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
suc.reset_tool_data_tables(trans.app)
trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repository',
id=repository_id,
commit_message='Deleted selected files',
message=message,
status=status))
else:
status = 'error'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
suc.reset_tool_data_tables(trans.app)
def upload( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
commit_message = util.restore_text( params.get( 'commit_message', 'Uploaded' ) )
category_ids = util.listify( params.get( 'category_id', '' ) )
categories = suc.get_categories( trans )
repository_id = params.get( 'repository_id', '' )
repository = suc.get_repository_in_tool_shed( trans, repository_id )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) )
remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) )
uploaded_file = None
upload_point = self.__get_upload_point( repository, **kwd )
tip = repository.tip( trans.app )
file_data = params.get( 'file_data', '' )
url = params.get( 'url', '' )
# Part of the upload process is sending email notification to those that have registered to
# receive them. One scenario occurs when the first change set is produced for the repository.
# See the suc.handle_email_alerts() method for the definition of the scenarios.
new_repo_alert = repository.is_new( trans.app )
uploaded_directory = None
if params.get( 'upload_button', False ):
if file_data == '' and url == '':
message = 'No files were entered on the upload form.'
status = 'error'
uploaded_file = None
elif url and url.startswith( 'hg' ):
# Use mercurial clone to fetch repository, contents will then be copied over.
uploaded_directory = tempfile.mkdtemp()
repo_url = 'http%s' % url[ len( 'hg' ): ]
repo_url = repo_url.encode( 'ascii', 'replace' )
commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory )
elif url:
valid_url = True
try:
stream = urllib.urlopen( url )
except Exception, e:
valid_url = False
message = 'Error uploading file via http: %s' % str( e )
status = 'error'
uploaded_file = None
if valid_url:
fd, uploaded_file_name = tempfile.mkstemp()
uploaded_file = open( uploaded_file_name, 'wb' )
while 1:
chunk = stream.read( CHUNK_SIZE )
if not chunk:
break
uploaded_file.write( chunk )
uploaded_file.flush()
uploaded_file_filename = url.split( '/' )[ -1 ]
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
elif file_data not in ( '', None ):
uploaded_file = file_data.file
uploaded_file_name = uploaded_file.name
uploaded_file_filename = os.path.split( file_data.filename )[ -1 ]
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
if uploaded_file or uploaded_directory:
ok = True
isgzip = False
isbz2 = False
if uploaded_file:
if uncompress_file:
isgzip = checkers.is_gzip( uploaded_file_name )
if not isgzip:
isbz2 = checkers.is_bz2( uploaded_file_name )
if isempty:
tar = None
istar = False
else:
# Determine what we have - a single file or an archive
try:
if ( isgzip or isbz2 ) and uncompress_file:
# Open for reading with transparent compression.
tar = tarfile.open( uploaded_file_name, 'r:*' )
else:
tar = tarfile.open( uploaded_file_name )
istar = True
except tarfile.ReadError, e:
tar = None
istar = False
else:
# Uploaded directory
istar = False
if istar:
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
elif uploaded_directory:
ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
else:
if ( isgzip or isbz2 ) and uncompress_file:
uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 )
if upload_point is not None:
full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
else:
full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
# Move the uploaded file to the load_point within the repository hierarchy.
shutil.move( uploaded_file_name, full_path )
# See if any admin users have chosen to receive email alerts when a repository is
# updated. If so, check every uploaded file to ensure content is appropriate.
check_contents = suc.check_file_contents( trans )
if check_contents and os.path.isfile( full_path ):
content_alert_str = self.__check_file_content( full_path )
else:
content_alert_str = ''
commands.add( repo.ui, repo, full_path )
# Convert from unicode to prevent "TypeError: array item must be char"
full_path = full_path.encode( 'ascii', 'replace' )
commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
# Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
# to the in-memory trans.app.tool_data_tables dictionary.
error, error_message = suc.handle_sample_tool_data_table_conf_file( trans.app, full_path )
if error:
message = '%s<br/>%s' % ( message, error_message )
# See if the content of the change set was valid.
admin_only = len( repository.downloadable_revisions ) != 1
suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
if ok:
# Update the repository files for browsing.
suc.update_repository( repo )
# Get the new repository tip.
if tip == repository.tip( trans.app ):
message = 'No changes to repository. '
status = 'warning'
else:
if ( isgzip or isbz2 ) and uncompress_file:
uncompress_str = ' uncompressed and '
else:
uncompress_str = ' '
if uploaded_directory:
source_type = "repository"
source = url
else:
source_type = "file"
source = uploaded_file_filename
message = "The %s '%s' has been successfully%suploaded to the repository. " % ( source_type, source, uncompress_str )
if istar and ( undesirable_dirs_removed or undesirable_files_removed ):
items_removed = undesirable_dirs_removed + undesirable_files_removed
message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive. " % items_removed
if istar and remove_repo_files_not_in_tar and files_to_remove:
if upload_point is not None:
message += " %d files were removed from the repository relative to the selected upload point '%s'. " % ( len( files_to_remove ), upload_point )
else:
message += " %d files were removed from the repository root. " % len( files_to_remove )
kwd[ 'message' ] = message
suc.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd )
# Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
# or some other problem.
if suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir ):
if repository.metadata_revisions:
# A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload.
metadata_dict = repository.metadata_revisions[0].metadata
else:
metadata_dict = {}
if suc.has_orphan_tool_dependencies_in_tool_shed( metadata_dict ):
message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", '
message += 'so one or more of the defined tool dependencies are considered orphans within this repository.'
status = 'warning'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
suc.reset_tool_data_tables( trans.app )
trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repository',
id=repository_id,
commit_message='Deleted selected files',
message=message,
status=status ) )
else:
status = 'error'
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
suc.reset_tool_data_tables( trans.app )
