mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Eliminate a duplicate method from shed_util_common and add missing documentation to several utility methods.
This commit is contained in:
Greg Von Kuster
@@ -184,7 +184,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
params = util.Params( kwd )
|
||||
repository_id = params.get( 'id', None )
|
||||
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
|
||||
@@ -314,7 +314,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
need it so that we can derive the tool shed from which it was installed.
|
||||
"""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( repository_name, repository_owner, changeset_revision ) )
|
||||
@@ -337,7 +337,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
it so that we can derive the tool shed from which it was installed.
|
||||
"""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( repository_name, repository_owner, changeset_revision ) )
|
||||
@@ -359,7 +359,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
uninstalled tool shed repository.
|
||||
"""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( repository_name, repository_owner, changeset_revision ) )
|
||||
@@ -654,7 +654,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
suc.update_tool_shed_repository_status( trans.app,
|
||||
tool_shed_repository,
|
||||
trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
|
||||
@@ -711,7 +711,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
if not repository:
|
||||
return trans.show_error_message( 'Invalid repository specified.' )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]:
|
||||
tool_shed_repository_ids = [ repository_id ]
|
||||
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
|
||||
@@ -1172,7 +1172,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
clone_dir = os.path.join( tool_path, suc.generate_tool_shed_repository_install_dir( repository_clone_url,
|
||||
tool_shed_repository.installed_changeset_revision ) )
|
||||
relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
|
||||
tool_section = None
|
||||
tool_panel_section = kwd.get( 'tool_panel_section', '' )
|
||||
new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
|
||||
@@ -1317,7 +1317,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
|
||||
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
|
||||
metadata = tool_shed_repository.metadata
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
|
||||
tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app )
|
||||
if latest_changeset_revision and latest_ctx_rev:
|
||||
# There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from
|
||||
@@ -1481,7 +1481,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
def reset_repository_metadata( self, trans, id ):
|
||||
"""Reset all metadata on a single installed tool shed repository."""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
|
||||
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
|
||||
if relative_install_dir:
|
||||
@@ -1560,7 +1560,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
metadata for the repository's revision in the Galaxy database.
|
||||
"""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( repository.name, repository.owner, repository.changeset_revision ) )
|
||||
|
||||
@@ -279,7 +279,7 @@ class InstallManager( object ):
|
||||
if self.__isinstalled( clone_dir ):
|
||||
print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir
|
||||
else:
|
||||
tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( self.app, self.tool_shed )
|
||||
repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name )
|
||||
relative_install_dir = os.path.join( relative_clone_dir, name )
|
||||
install_dir = os.path.join( clone_dir, name )
|
||||
@@ -351,16 +351,6 @@ class InstallManager( object ):
|
||||
@property
|
||||
def non_shed_tool_panel_configs( self ):
|
||||
return common_util.get_non_shed_tool_panel_configs( self.app )
|
||||
def __get_url_from_tool_shed( self, tool_shed ):
|
||||
# The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like:
|
||||
# http://toolshed.g2.bx.psu.edu/
|
||||
for shed_name, shed_url in self.app.tool_shed_registry.tool_sheds.items():
|
||||
if shed_url.find( tool_shed ) >= 0:
|
||||
if shed_url.endswith( '/' ):
|
||||
shed_url = shed_url.rstrip( '/' )
|
||||
return shed_url
|
||||
# The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml.
|
||||
return None
|
||||
def __isinstalled( self, clone_dir ):
|
||||
full_path = os.path.abspath( clone_dir )
|
||||
if os.path.exists( full_path ):
|
||||
|
||||
@@ -77,7 +77,7 @@ def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_
|
||||
def get_update_to_changeset_revision_and_ctx_rev( trans, repository ):
|
||||
"""Return the changeset revision hash to which the repository can be updated."""
|
||||
changeset_revision_dict = {}
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( repository.name, repository.owner, repository.installed_changeset_revision ) )
|
||||
try:
|
||||
|
||||
@@ -34,7 +34,7 @@ class UpdateManager( object ):
|
||||
self.sleeper.sleep( self.seconds_to_sleep )
|
||||
log.info( 'Transfer job restarter shutting down...' )
|
||||
def check_for_update( self, repository ):
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( self.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( self.app, repository.tool_shed )
|
||||
url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \
|
||||
( tool_shed_url, repository.name, repository.owner, repository.changeset_revision )
|
||||
try:
|
||||
|
||||
@@ -1432,7 +1432,7 @@ def populate_containers_dict_from_repository_metadata( trans, tool_shed_url, too
|
||||
def reset_all_metadata_on_installed_repository( trans, id ):
|
||||
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
|
||||
repository = suc.get_installed_tool_shed_repository( trans, id )
|
||||
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
|
||||
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
|
||||
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
|
||||
if relative_install_dir:
|
||||
|
||||
@@ -160,7 +160,7 @@ def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ):
|
||||
return False, error_message
|
||||
|
||||
def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ):
|
||||
# Persist the current in-memory list of config_elems to a file named by the value of config_filename.
|
||||
"""Persist the current in-memory list of config_elems to a file named by the value of config_filename."""
|
||||
fd, filename = tempfile.mkstemp()
|
||||
os.write( fd, '<?xml version="1.0"?>\n' )
|
||||
os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) )
|
||||
@@ -242,7 +242,7 @@ def create_or_update_tool_shed_repository( app, name, description, installed_cha
|
||||
|
||||
def generate_clone_url_for_installed_repository( app, repository ):
|
||||
"""Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
|
||||
tool_shed_url = get_url_from_repository_tool_shed( app, repository )
|
||||
tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed )
|
||||
return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
|
||||
|
||||
def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
|
||||
@@ -469,7 +469,7 @@ def get_file_context_from_ctx( ctx, filename ):
|
||||
return None
|
||||
|
||||
def get_installed_tool_shed_repository( trans, id ):
|
||||
"""Get a repository on the Galaxy side from the database via id"""
|
||||
"""Get a tool shed repository record from the Galaxy database defined by the id."""
|
||||
return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
|
||||
|
||||
def get_named_tmpfile_from_ctx( ctx, filename, dir ):
|
||||
@@ -516,6 +516,11 @@ def get_next_downloadable_changeset_revision( repository, repo, after_changeset_
|
||||
return None
|
||||
|
||||
def get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ):
|
||||
"""
|
||||
Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision
|
||||
or installed_changeset_revision. A new tool shed repository record will be created if one is not located.
|
||||
"""
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
repository = get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision )
|
||||
if not repository:
|
||||
tool_shed_url = get_url_from_tool_shed( trans.app, tool_shed )
|
||||
@@ -572,7 +577,7 @@ def get_previous_downloadable_changeset_revision( repository, repo, before_chang
|
||||
previous_changeset_revision = changeset_revision
|
||||
|
||||
def get_repo_info_tuple_contents( repo_info_tuple ):
|
||||
# Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.
|
||||
"""Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced."""
|
||||
if len( repo_info_tuple ) == 6:
|
||||
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
|
||||
repository_dependencies = None
|
||||
@@ -613,6 +618,8 @@ def get_repository_by_name_and_owner( app, name, owner ):
|
||||
return None
|
||||
|
||||
def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ):
|
||||
"""Return a tool shed repository database record that is defined by either the current changeset revision or the installed_changeset_revision."""
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app,
|
||||
tool_shed=tool_shed,
|
||||
name=name,
|
||||
@@ -627,6 +634,7 @@ def get_repository_for_dependency_relationship( app, tool_shed, name, owner, cha
|
||||
return repository
|
||||
|
||||
def get_repository_file_contents( file_path ):
|
||||
"""Return the display-safe contents of a repository file."""
|
||||
if checkers.is_gzip( file_path ):
|
||||
safe_str = to_safe_string( '\ngzip compressed file\n' )
|
||||
elif checkers.is_bz2( file_path ):
|
||||
@@ -646,6 +654,7 @@ def get_repository_file_contents( file_path ):
|
||||
return safe_str
|
||||
|
||||
def get_repository_files( trans, folder_path ):
|
||||
"""Return the file hierarchy of a tool shed repository."""
|
||||
contents = []
|
||||
for item in os.listdir( folder_path ):
|
||||
# Skip .hg directories
|
||||
@@ -684,6 +693,7 @@ def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision
|
||||
return None
|
||||
|
||||
def get_repository_owner( cleaned_repository_url ):
|
||||
"""Gvien a "cleaned" repository clone URL, return the owner of the repository."""
|
||||
items = cleaned_repository_url.split( '/repos/' )
|
||||
repo_path = items[ 1 ]
|
||||
if repo_path.startswith( '/' ):
|
||||
@@ -691,11 +701,13 @@ def get_repository_owner( cleaned_repository_url ):
|
||||
return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
|
||||
|
||||
def get_repository_owner_from_clone_url( repository_clone_url ):
|
||||
"""Given a repository clone URL, return the owner of the repository."""
|
||||
tmp_url = clean_repository_clone_url( repository_clone_url )
|
||||
tool_shed = tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
|
||||
return get_repository_owner( tmp_url )
|
||||
|
||||
def get_repository_tools_tups( app, metadata_dict ):
|
||||
"""Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata."""
|
||||
repository_tools_tups = []
|
||||
index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) )
|
||||
if 'tools' in metadata_dict:
|
||||
@@ -713,6 +725,7 @@ def get_repository_tools_tups( app, metadata_dict ):
|
||||
return repository_tools_tups
|
||||
|
||||
def get_reversed_changelog_changesets( repo ):
|
||||
"""Return a list of changesets in reverse order from that provided by the repository manifest."""
|
||||
reversed_changelog = []
|
||||
for changeset in repo.changelog:
|
||||
reversed_changelog.insert( 0, changeset )
|
||||
@@ -728,6 +741,7 @@ def get_revision_label( trans, repository, changeset_revision ):
|
||||
return "-1:%s" % changeset_revision
|
||||
|
||||
def get_rev_label_from_changeset_revision( repo, changeset_revision ):
|
||||
"""Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash."""
|
||||
ctx = get_changectx_for_changeset( repo, changeset_revision )
|
||||
if ctx:
|
||||
rev = '%04d' % ctx.rev()
|
||||
@@ -748,8 +762,10 @@ def get_shed_tool_conf_dict( app, shed_tool_conf ):
|
||||
return index, shed_tool_conf_dict
|
||||
|
||||
def get_tool_panel_config_tool_path_install_dir( app, repository ):
|
||||
# Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the
|
||||
# repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config.
|
||||
"""
|
||||
Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the repository is installed.
|
||||
This method assumes all repository tools are defined in a single shed-related tool panel config.
|
||||
"""
|
||||
tool_shed = clean_tool_shed_url( repository.tool_shed )
|
||||
partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision )
|
||||
# Get the relative tool installation paths from each of the shed tool configs.
|
||||
@@ -782,11 +798,14 @@ def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ):
|
||||
return None
|
||||
|
||||
def get_tool_shed_repository_by_id( trans, repository_id ):
|
||||
"""Return a tool shed repository database record defined by the id."""
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
return trans.sa_session.query( trans.model.ToolShedRepository ) \
|
||||
.filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \
|
||||
.first()
|
||||
|
||||
def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
|
||||
"""Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and current changeet_revision."""
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
sa_session = app.model.context.current
|
||||
if tool_shed.find( '//' ) > 0:
|
||||
@@ -800,6 +819,7 @@ def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_sh
|
||||
.first()
|
||||
|
||||
def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ):
|
||||
"""Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and installed_changeet_revision."""
|
||||
# This method is used only in Galaxy, not the tool shed.
|
||||
sa_session = app.model.context.current
|
||||
if tool_shed.find( '//' ) > 0:
|
||||
@@ -816,22 +836,11 @@ def get_tool_shed_from_clone_url( repository_clone_url ):
|
||||
tmp_url = clean_repository_clone_url( repository_clone_url )
|
||||
return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
|
||||
|
||||
def get_url_from_repository_tool_shed( app, repository ):
|
||||
"""
|
||||
The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is
|
||||
something like: http://toolshed.g2.bx.psu.edu/.
|
||||
"""
|
||||
for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items():
|
||||
if shed_url.find( repository.tool_shed ) >= 0:
|
||||
if shed_url.endswith( '/' ):
|
||||
shed_url = shed_url.rstrip( '/' )
|
||||
return shed_url
|
||||
# The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml.
|
||||
return None
|
||||
|
||||
def get_url_from_tool_shed( app, tool_shed ):
|
||||
# The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like:
|
||||
# http://toolshed.g2.bx.psu.edu/
|
||||
"""
|
||||
The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like:
|
||||
http://toolshed.g2.bx.psu.edu/
|
||||
"""
|
||||
for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items():
|
||||
if shed_url.find( tool_shed ) >= 0:
|
||||
if shed_url.endswith( '/' ):
|
||||
@@ -856,26 +865,28 @@ def get_user_by_username( app, username ):
|
||||
return None
|
||||
|
||||
def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ):
|
||||
# There are 2 complementary features that enable a tool shed user to receive email notification:
|
||||
# 1. Within User Preferences, they can elect to receive email when the first (or first valid)
|
||||
# change set is produced for a new repository.
|
||||
# 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
|
||||
# which caused them to receive email alerts when updates to the repository occur. This same feature
|
||||
# is available on a per-repository basis on the repository grid within the tool shed.
|
||||
#
|
||||
# There are currently 4 scenarios for sending email notification when a change is made to a repository:
|
||||
# 1. An admin user elects to receive email when the first change set is produced for a new repository
|
||||
# from User Preferences. The change set does not have to include any valid content. This allows for
|
||||
# the capture of inappropriate content being uploaded to new repositories.
|
||||
# 2. A regular user elects to receive email when the first valid change set is produced for a new repository
|
||||
# from User Preferences. This differs from 1 above in that the user will not receive email until a
|
||||
# change set tha tincludes valid content is produced.
|
||||
# 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the
|
||||
# user is an admin user, the email will include information about both HTML and image content that was
|
||||
# included in the change set.
|
||||
# 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the
|
||||
# user is not an admin user, the email will not include any information about both HTML and image content
|
||||
# that was included in the change set.
|
||||
"""
|
||||
There are 2 complementary features that enable a tool shed user to receive email notification:
|
||||
1. Within User Preferences, they can elect to receive email when the first (or first valid)
|
||||
change set is produced for a new repository.
|
||||
2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
|
||||
which caused them to receive email alerts when updates to the repository occur. This same feature
|
||||
is available on a per-repository basis on the repository grid within the tool shed.
|
||||
|
||||
There are currently 4 scenarios for sending email notification when a change is made to a repository:
|
||||
1. An admin user elects to receive email when the first change set is produced for a new repository
|
||||
from User Preferences. The change set does not have to include any valid content. This allows for
|
||||
the capture of inappropriate content being uploaded to new repositories.
|
||||
2. A regular user elects to receive email when the first valid change set is produced for a new repository
|
||||
from User Preferences. This differs from 1 above in that the user will not receive email until a
|
||||
change set tha tincludes valid content is produced.
|
||||
3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the
|
||||
user is an admin user, the email will include information about both HTML and image content that was
|
||||
included in the change set.
|
||||
4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the
|
||||
user is not an admin user, the email will not include any information about both HTML and image content
|
||||
that was included in the change set.
|
||||
"""
|
||||
repo_dir = repository.repo_path( trans.app )
|
||||
repo = hg.repository( get_configured_ui(), repo_dir )
|
||||
sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None )
|
||||
@@ -948,6 +959,7 @@ def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert
|
||||
log.exception( "An error occurred sending a tool shed repository update alert by email." )
|
||||
|
||||
def open_repository_files_folder( trans, folder_path ):
|
||||
"""Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy."""
|
||||
try:
|
||||
files_list = get_repository_files( trans, folder_path )
|
||||
except OSError, e:
|
||||
@@ -957,19 +969,20 @@ def open_repository_files_folder( trans, folder_path ):
|
||||
folder_contents = []
|
||||
for filename in files_list:
|
||||
is_folder = False
|
||||
if filename and filename[-1] == os.sep:
|
||||
if filename and filename[ -1 ] == os.sep:
|
||||
is_folder = True
|
||||
if filename:
|
||||
full_path = os.path.join( folder_path, filename )
|
||||
node = { "title": filename,
|
||||
"isFolder": is_folder,
|
||||
"isLazy": is_folder,
|
||||
"tooltip": full_path,
|
||||
"key": full_path }
|
||||
node = { "title" : filename,
|
||||
"isFolder" : is_folder,
|
||||
"isLazy" : is_folder,
|
||||
"tooltip" : full_path,
|
||||
"key" : full_path }
|
||||
folder_contents.append( node )
|
||||
return folder_contents
|
||||
|
||||
def remove_dir( dir ):
|
||||
"""Attempt to remove a directory from disk."""
|
||||
if os.path.exists( dir ):
|
||||
try:
|
||||
shutil.rmtree( dir )
|
||||
@@ -1029,9 +1042,11 @@ def reversed_lower_upper_bounded_changelog( repo, excluded_lower_bounds_changese
|
||||
return reversed_changelog
|
||||
|
||||
def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ):
|
||||
"""Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision."""
|
||||
return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision )
|
||||
|
||||
def strip_path( fpath ):
|
||||
"""Attempt to strip the path from a file name."""
|
||||
if not fpath:
|
||||
return fpath
|
||||
try:
|
||||
@@ -1072,12 +1087,15 @@ def to_safe_string( text, to_html=True ):
|
||||
return text
|
||||
|
||||
def tool_shed_from_repository_clone_url( repository_clone_url ):
|
||||
"""Given a repository clone URL, return the tool shed that contains the repository."""
|
||||
return clean_repository_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' )
|
||||
|
||||
def tool_shed_is_this_tool_shed( toolshed_base_url ):
|
||||
"""Determine if a tool shed is the current tool shed."""
|
||||
return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
|
||||
|
||||
def translate_string( raw_text, to_html=True ):
|
||||
"""Return a subset of a string (up to MAX_CONTENT_SIZE) translated to a safe string for display in a browser."""
|
||||
if raw_text:
|
||||
if len( raw_text ) <= MAX_CONTENT_SIZE:
|
||||
translated_string = to_safe_string( raw_text, to_html=to_html )
|
||||
@@ -1141,12 +1159,14 @@ def update_repository( repo, ctx_rev=None ):
|
||||
commands.update( get_configured_ui(), repo, rev=ctx_rev )
|
||||
|
||||
def update_tool_shed_repository_status( app, tool_shed_repository, status ):
|
||||
"""Update the status of a tool shed repository in the process of being installed into Galaxy."""
|
||||
sa_session = app.model.context.current
|
||||
tool_shed_repository.status = status
|
||||
sa_session.add( tool_shed_repository )
|
||||
sa_session.flush()
|
||||
|
||||
def url_join( *args ):
|
||||
"""Return a valid URL produced by appending a base URL and a set of request parameters."""
|
||||
parts = []
|
||||
for arg in args:
|
||||
parts.append( arg.strip( '/' ) )
|
||||
|
||||
Reference in New Issue
Block a user