From 497ff6e05dfa834ac9966e8607abec68301e8bc8 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 30 Jul 2008 17:15:40 -0400 Subject: [PATCH] Rolling back Dan's most recent commits, we'll be setting up a branch for this. --- lib/galaxy/datatypes/images.py | 4 +- lib/galaxy/model/__init__.py | 573 +++++-------------------- lib/galaxy/model/mapping.py | 170 -------- lib/galaxy/tools/__init__.py | 4 +- lib/galaxy/tools/actions/__init__.py | 16 +- lib/galaxy/tools/actions/upload.py | 4 +- lib/galaxy/tools/parameters/basic.py | 24 +- lib/galaxy/web/controllers/async.py | 2 +- lib/galaxy/web/controllers/dataset.py | 47 +- lib/galaxy/web/controllers/root.py | 256 ++++------- lib/galaxy/web/controllers/user.py | 34 -- lib/galaxy/web/framework/__init__.py | 5 +- templates/dataset/edit_attributes.mako | 35 +- templates/history/options.mako | 1 - templates/root/history_common.mako | 4 +- templates/user/index.mako | 3 - 16 files changed, 234 insertions(+), 948 deletions(-) diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index 7c58d38f632..90d44ab47f4 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -110,7 +110,7 @@ class Gmaj( data.Data ): "nobutton": "false", "urlpause" :"100", "debug": "false", - "posturl": "history_add_to?%s" % urlencode( { 'history_id': dataset.history_id, 'ext': 'maf', 'name': 'GMAJ Output on data %s' % dataset.hid, 'info': 'Added by GMAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id } ) + "posturl": "history_add_to?%s" % urlencode( { 'history_id': dataset.history_id, 'ext': 'maf', 'name': 'GMAJ Output on data %s' % dataset.hid, 'info': 'Added by GMAJ', 'dbkey': dataset.dbkey } ) } class_name = "edu.psu.bx.gmaj.MajApplet.class" archive = "/static/gmaj/gmaj.jar" @@ -180,7 +180,7 @@ class Laj( data.Text ): "alignfile1": "display?id=%s" % dataset.id, "buttonlabel": "Launch LAJ", "title": "LAJ in Galaxy", - "posturl": "history_add_to?%s" % urlencode( { 'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id } ), + "posturl": "history_add_to?%s" % urlencode( { 'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey } ), "noseq": "true" } class_name = "edu.psu.cse.bio.laj.LajApplet.class" diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 1e3fe2783c4..e852869328f 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -27,99 +27,19 @@ def set_datatypes_registry( d_registry ): datatypes_registry = d_registry class User( object ): - def __init__( self, email=None, password=None, groups = [], roles = [], default_groups = [], default_roles = [] ): + def __init__( self, email=None, password=None ): self.email = email self.password = password self.external = False # Relationships self.histories = [] - if not groups: - groups.append( GalaxyGroup.get( GalaxyGroup.public_id ) ) - default_groups.append( groups[-1] ) - default_groups.append( self.create_private_group() ) - group_id_added = [] - for group in groups: - if group.id not in group_id_added: - group.add_user( self ) - group_id_added.append( group.id ) - group_id_added = [] - for group in default_groups: - if group.id not in group_id_added: - user_group_assoc = DefaultUserGroupAssociation( self, group ) - user_group_assoc.flush() - group_id_added.append( group.id ) - role_id_added = [] - for role in roles: - if role.id not in role_id_added: - role.add_user( self ) - role_id_added.append( role.id ) - role_id_added = [] - for role in default_roles: - if role.id not in role_id_added: - role_group_assoc = DefaultUserRoleAssociation( self, role ) - role_group_assoc.flush() - role_id_added.append( role.id ) def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" self.password = sha.new( cleartext ).hexdigest() def check_password( self, cleartext ): """Check if 'cleartext' matches 'self.password' when hashed.""" return self.password == sha.new( cleartext ).hexdigest() - def create_private_group( self ): - #create private group - group = GalaxyGroup( self.email, priority = 10 ) - group.flush() - #create private dataset access role - role = AccessRole( "%s dataset access" % self.email, list( Dataset.access_actions.__dict__.values() ), priority = 1 ) - role.flush() - #add role to group - group.add_role( role ) - #create roles for user modification of role - user_role = AccessRole( "%s role modification" % self.email, list( AccessRole.access_actions.__dict__.values() ) ) - user_role.flush() - #add role to user - user_role.add_user( self ) - #add role to role - role.add_role( user_role ) - - #create roles for user modification of group - group_role = AccessRole( "%s group modification" % self.email, list( GalaxyGroup.access_actions.__dict__.values() ) ) - group_role.flush() - #add role to group - group.add_access_role( group_role ) - #associate role and user - group_role.add_user( self ) - - #add user to group - group.add_user( self ) - group.flush() - return group - def add_group( self, group ): - return group.add_user( self ) - def has_group( self, check_group ): - return bool( UserGroupAssociation.get_by( group_id = check_group.id, user_id = self.id ) ) - def has_role( self, check_role ): - return bool( UserRoleAssociation.get_by( role_id = check_role.id, user_id = self.id ) ) - def set_default_access( self, groups = None, roles = None, history = False, dataset = False ): - if groups is not None: - for assoc in self.default_groups: #this is the association not the actual group - assoc.delete() - assoc.flush() - for group in groups: - assoc = DefaultUserGroupAssociation( self, group ) - assoc.flush() - if roles is not None: - for assoc in self.default_roles: #this is the association not the actual group - assoc.delete() - assoc.flush() - for role in roles: - assoc = DefaultUserRoleAssociation( self, role ) - assoc.flush() - if history: - for history in self.histories: - history.set_default_access( groups = groups, roles = roles, dataset = dataset ) - class Job( object ): """ A job represents a request to run a tool given input datasets, tool @@ -181,337 +101,10 @@ class JobToOutputDatasetAssociation( object ): self.name = name self.dataset = dataset -class AccessRole( object ): - dataset_actions = Bunch( VIEW = 'dataset_view', #viewing/downloading - USE = 'dataset_use', #use in jobs - ADD_ROLE = 'dataset_add_role', #dataset can be added to roles - REMOVE_ROLE = 'dataset_remove_role', #dataset can be removed from roles - ADD_GROUP = 'dataset_add_group', #dataset can be added to groups - REMOVE_GROUP = 'dataset_remove_group' ) #dataset can be removed from groups - role_actions = Bunch( ADD_DATASET = 'role_add_dataset', #add role to dataset - REMOVE_DATASET = 'role_remove_dataset', #remove role from dataset - DELETE = 'role_delete', #delete a role - MODIFY = 'role_modify', #change a role's actions, - ADD_GROUP = 'role_add_group', #add role to a group - REMOVE_GROUP = 'role_remove_group' ) #remove role from a group - group_actions = Bunch( ADD_DATASET = 'group_add_dataset', #add group to dataset - REMOVE_DATASET = 'group_remove_dataset', #remove dataset from group - DELETE = 'group_delete', #delete a group - ADD_ROLE = 'group_add_role', #add role to group - REMOVE_ROLE = 'group_remove_role', #remove role from group - ADD_USER = 'group_add_user' ) #add users to group - - access_actions = role_actions - - def __init__( self, name, actions, priority = 0 ): - self.name = name - if not isinstance( actions, list ): - actions = [ actions ] - self.actions = actions - self.priority = priority - def add_user( self, user ): - assoc = UserRoleAssociation( user, self ) - assoc.flush() - return assoc - def add_group( self, group ): - assoc = GroupRoleAssociation( group, self ) - assoc.flush() - return assoc - def add_role( self, role ): - assoc = RoleRoleAssociation( role, self ) - assoc.flush() - return assoc - def add_dataset( self, dataset ): - assoc = RoleDatasetAssociation( self, dataset ) - assoc.flush() - return assoc - -class GalaxyGroup( object ): - public_id = None - access_actions = AccessRole.group_actions - def __init__( self, name, priority = 0 ): - self.name = name - self.priority = priority - def add_user( self, user ): - assoc = UserGroupAssociation( user, self ) - assoc.flush() - return assoc - def add_role( self, role ): - return role.add_group( self ) - def add_access_role( self, role ): - assoc = GroupRoleAccessAssociation( self, role ) - assoc.flush() - return assoc - def add_dataset( self, dataset ): - assoc = GroupDatasetAssociation( self, dataset ) - assoc.flush() - return assoc - -class UserGroupAssociation( object ): - def __init__( self, user, group ): - self.user = user - self.group = group - -class RoleRoleAssociation( object ): - def __init__( self, role, target_role ): - self.role = role - self.target_role = target_role - -class GroupRoleAccessAssociation( object ): - def __init__( self, group, role ): - self.group = group - self.role = role - -class GroupRoleAssociation( object ): - def __init__( self, group, role ): - self.group = group - self.role = role - -class UserRoleAssociation( object ): - def __init__( self, user, role ): - self.user = user - self.role = role - -class GroupDatasetAssociation( object ): - def __init__( self, group, dataset ): - if isinstance( group, GroupDatasetAssociation ) or isinstance( group, DefaultUserGroupAssociation ) or isinstance( group, DefaultHistoryGroupAssociation ): - group = group.group - self.group = group - - if isinstance( dataset, HistoryDatasetAssociation ): - dataset = dataset.dataset - self.dataset = dataset - -class RoleDatasetAssociation( object ): - def __init__( self, role, dataset ): - if isinstance( role, RoleDatasetAssociation ) or isinstance( role, DefaultUserRoleAssociation ) or isinstance( role, DefaultHistoryRoleAssociation ): - role = role.role - self.role = role - - if isinstance( dataset, HistoryDatasetAssociation ): - dataset = dataset.dataset - self.dataset = dataset - -class DefaultUserRoleAssociation( object ): - def __init__( self, user, role ): - if isinstance( role, RoleDatasetAssociation ) or isinstance( role, DefaultUserRoleAssociation ) or isinstance( role, DefaultHistoryRoleAssociation ): - role = role.role - self.user = user - self.role = role - -class DefaultUserGroupAssociation( object ): - def __init__( self, user, group ): - if isinstance( group, GroupDatasetAssociation ) or isinstance( group, DefaultUserGroupAssociation ) or isinstance( group, DefaultHistoryGroupAssociation ): - group = group.group - self.user = user - self.group = group - -class DefaultHistoryRoleAssociation( object ): - def __init__( self, history, role ): - if isinstance( role, RoleDatasetAssociation ) or isinstance( role, DefaultUserRoleAssociation ) or isinstance( role, DefaultHistoryRoleAssociation ): - role = role.role - self.history = history - self.role = role - -class DefaultHistoryGroupAssociation( object ): - def __init__( self, history, group ): - if isinstance( group, GroupDatasetAssociation ) or isinstance( group, DefaultUserGroupAssociation ) or isinstance( group, DefaultHistoryGroupAssociation ): - group = group.group - self.history = history - self.group = group - -class Dataset( object ): - states = Bunch( NEW = 'new', - QUEUED = 'queued', - RUNNING = 'running', - OK = 'ok', - EMPTY = 'empty', - ERROR = 'error', - DISCARDED = 'discarded' ) - access_actions = AccessRole.dataset_actions - file_path = "/tmp/" - engine = None - def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, access_groups=[], access_roles=[] ): - self.id = id - self.state = state - self.deleted = False - self.purged = False - self.purgable = purgable - self.external_filename = external_filename - self._extra_files_path = extra_files_path - self.file_size = file_size - if access_groups or access_roles: - #self.flush() - for group in access_groups: - group.add_dataset( self ) - group.flush() - for role in access_roles: - role.add_dataset( self ) - role.flush() - def get_file_name( self ): - if not self.external_filename: - assert self.id is not None, "ID must be set before filename used (commit the object)" - # First try filename directly under file_path - filename = os.path.join( self.file_path, "dataset_%d.dat" % self.id ) - # Only use that filename if it already exists (backward compatibility), - # otherwise construct hashed path - if not os.path.exists( filename ): - dir = os.path.join( self.file_path, *directory_hash_id( self.id ) ) - # Create directory if it does not exist - try: - os.makedirs( dir ) - except OSError, e: - # File Exists is okay, otherwise reraise - if e.errno != errno.EEXIST: - raise - # Return filename inside hashed directory - return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) - else: - filename = self.external_filename - # Make filename absolute - return os.path.abspath( filename ) - - def set_file_name ( self, filename ): - if not filename: - self.external_filename = None - else: - self.external_filename = filename - - file_name = property( get_file_name, set_file_name ) - - @property - def extra_files_path( self ): - if self._extra_files_path: - path = self._extra_files_path - else: - path = os.path.join( self.file_path, "dataset_%d_files" % self.id ) - #only use path directly under self.file_path if it exists - if not os.path.exists( path ): - path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) - # Make path absolute - return os.path.abspath( path ) - - def get_size( self ): - """Returns the size of the data on disk""" - if self.file_size: - return self.file_size - else: - try: - return os.path.getsize( self.file_name ) - except OSError: - return 0 - def set_size( self ): - """Returns the size of the data on disk""" - try: - self.file_size = os.path.getsize( self.file_name ) - except OSError: - self.file_size = 0 - def has_data( self ): - """Detects whether there is any data""" - return self.get_size() > 0 - def mark_deleted( self, include_children=True ): - self.deleted = True - def allow_action( self, user, action ): - """Returns true when user has permission to perform an action""" - - #if dataset is in public group, we always return true for viewing and using - #this may need to change when the ability to alter groups and roles is allowed - if action in [ self.access_actions.USE, self.access_actions.VIEW ] and GroupDatasetAssociation.get_by( group_id = GalaxyGroup.public_id, dataset_id = self.id ): - return True - elif user is not None: - #loop through permissions and if allowed return true: - #check roles associated directly with dataset first - for role_dataset_assoc in self.roles: - if action in role_dataset_assoc.role.actions and user.has_role( role_dataset_assoc.role ): - return True - #check roles associated with dataset through groups - for group_dataset_assoc in self.groups: - if user.has_group( group_dataset_assoc.group ): - for group_role_assoc in group_dataset_assoc.group.roles: - if action in group_role_assoc.role.actions: - return True - return False #no user and dataset not in public group, or user lacks permission - def guess_derived_groups_roles( self, other_datasets = [] ): - """Returns a list of output roles and groups based upon itself and provided datasets""" - if not other_datasets: - return [ data_group_assoc.group for data_group_assoc in self.groups ], [ data_role_assoc.role for data_role_assoc in self.roles ] - access_roles = None - priority_access_role = None - access_groups = None - priority_access_group = None - for dataset in [ self ] + other_datasets: - #determine access roles and groups for output datasets - #roles and groups for output dataset is the intersection across all inputs - #if we end up with no intersection between inputs, then we rely on priorities - if isinstance( dataset, HistoryDatasetAssociation ): - dataset = dataset.dataset - roles = [ data_role_assoc.role for data_role_assoc in dataset.roles ] - for role in roles: - if priority_access_role is None or priority_access_role.priority < role.priority: - priority_access_role = role - groups = [ data_group_assoc.group for data_group_assoc in dataset.groups ] - for group in groups: - if priority_access_group is None or priority_access_group.priority < group.priority: - priority_access_group = group - if access_roles is None: - access_roles = set( roles ) - access_groups = set( groups ) - else: - access_roles.intersection_update( set( roles ) ) - access_groups.intersection_update( set( groups ) ) - - #complete lists for output dataset access - if access_roles: - access_roles = list( access_roles ) - else: - access_roles = [] - if access_groups: - access_groups = list( access_groups) - else: - access_groups = [] - #if we have no roles or groups left after intersection, - #take the highest priority group or role - if not access_roles and not access_groups: - if priority_access_role and priority_access_group: - if priority_access_group.priority == priority_access_role.priority: - access_groups = [ priority_access_group ] - access_roles = [ priority_access_role ] - elif priority_access_group.priority > priority_access_role.priority: - access_groups = [ priority_access_group ] - else: - access_roles = [ priority_access_role ] - elif priority_access_role: - access_roles = [ priority_access_role ] - elif priority_access_group: - access_groups = [ priority_access_group ] - - return access_groups, access_roles - def add_group( self, group ): - return group.add_dataset( self ) - def add_role( self, role ): - return role.add_dataset( self ) - - def has_group( self, group ): - return bool( GroupDatasetAssociation.get_by( group_id = group.id, dataset_id = self.id ) ) - def has_role( self, role ): - return bool( RoleDatasetAssociation.get_by( role_id = role.id, dataset_id = self.id ) ) - - # FIXME: sqlalchemy will replace this - def _delete(self): - """Remove the file that corresponds to this data""" - try: - os.remove(self.data.file_name) - except OSError, e: - log.critical('%s delete error %s' % (self.__class__.__name__, e)) - - - class HistoryDatasetAssociation( object ): - states = Dataset.states - access_actions = Dataset.access_actions def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset = False, access_groups = [], access_roles = [] ): + parent_id=None, validation_errors=None, visible=True, create_dataset = False ): self.name = name or "Unnamed dataset" self.id = id self.hid = hid @@ -527,7 +120,7 @@ class HistoryDatasetAssociation( object ): # Relationships self.history = history if not dataset and create_dataset: - dataset = Dataset( access_groups = access_groups, access_roles = access_roles ) + dataset = Dataset() dataset.flush() self.dataset = dataset self.parent_id = parent_id @@ -537,6 +130,10 @@ class HistoryDatasetAssociation( object ): def ext( self ): return self.extension + @property + def states( self ): + return self.dataset.states + def get_dataset_state( self ): return self.dataset.state def set_dataset_state ( self, state ): @@ -654,8 +251,7 @@ class HistoryDatasetAssociation( object ): def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry) - def copy( self, copy_children = False, parent_id = None, target_user = None ): - if target_user is None: target_user = self.user + def copy( self, copy_children = False, parent_id = None ): des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id ) des.flush() if copy_children: @@ -677,12 +273,10 @@ class HistoryDatasetAssociation( object ): for child in self.children: child.mark_deleted() - def allow_action( self, user, action ): - return self.dataset.allow_action( user, action ) class History( object ): - def __init__( self, id=None, name=None, user=None, default_roles = [], default_groups = [] ): + def __init__( self, id=None, name=None, user=None ): self.id = id self.name = name or "Unnamed history" self.deleted = False @@ -693,18 +287,6 @@ class History( object ): self.datasets = [] self.galaxy_sessions = [] - if not default_roles: - if user: - default_roles = user.default_roles - if not default_groups: - if user: - default_groups = user.default_groups - else: - default_groups = [ GalaxyGroup.get( GalaxyGroup.public_id ) ] - - - self.set_default_access( roles = default_roles, groups = default_groups ) - def _next_hid( self ): # TODO: override this with something in the database that ensures # better integrity @@ -743,55 +325,18 @@ class History( object ): self.genome_build = genome_build self.datasets.append( dataset ) - def copy( self, target_user = None ): - if not target_user: - target_user = self.user - des = History( user = target_user ) + def copy(self): + des = History() des.flush() des.name = self.name + des.user_id = self.user_id for data in self.datasets: - new_data = data.copy( copy_children = True, target_user = target_user ) + new_data = data.copy( copy_children = True ) des.add_dataset( new_data ) new_data.flush() des.hid_counter = self.hid_counter des.flush() return des - - def set_default_access( self, groups = None, roles = None, dataset = False ): - if groups is not None: - for assoc in self.default_groups: #this is the association not the actual group - assoc.delete() - assoc.flush() - for group in groups: - assoc = DefaultHistoryGroupAssociation( self, group ) - assoc.flush() - if roles is not None: - for assoc in self.default_roles: #this is the association not the actual group - assoc.delete() - assoc.flush() - for role in roles: - assoc = DefaultHistoryRoleAssociation( self, role ) - assoc.flush() - if dataset: - for data in self.datasets: - for hda in data.dataset.history_associations: - if self.user and hda.history not in self.user.histories: - break - else: - if groups is not None: - for assoc in data.dataset.groups: #this is the association not the actual group - assoc.delete() - assoc.flush() - for group in groups: - group.add_dataset( data ) - if roles is not None: - for assoc in data.dataset.roles: #this is the association not the actual group - assoc.delete() - assoc.flush() - for role in roles: - role.add_dataset( data ) - - # class Query( object ): # def __init__( self, name=None, state=None, tool_parameters=None, history=None ): @@ -802,6 +347,98 @@ class History( object ): # self.history = history # self.datasets = [] +class Dataset( object ): + states = Bunch( NEW = 'new', + QUEUED = 'queued', + RUNNING = 'running', + OK = 'ok', + EMPTY = 'empty', + ERROR = 'error', + DISCARDED = 'discarded' ) + file_path = "/tmp/" + engine = None + def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ): + self.id = id + self.state = state + self.deleted = False + self.purged = False + self.purgable = purgable + self.external_filename = external_filename + self._extra_files_path = extra_files_path + self.file_size = file_size + + def get_file_name( self ): + if not self.external_filename: + assert self.id is not None, "ID must be set before filename used (commit the object)" + # First try filename directly under file_path + filename = os.path.join( self.file_path, "dataset_%d.dat" % self.id ) + # Only use that filename if it already exists (backward compatibility), + # otherwise construct hashed path + if not os.path.exists( filename ): + dir = os.path.join( self.file_path, *directory_hash_id( self.id ) ) + # Create directory if it does not exist + try: + os.makedirs( dir ) + except OSError, e: + # File Exists is okay, otherwise reraise + if e.errno != errno.EEXIST: + raise + # Return filename inside hashed directory + return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) + else: + filename = self.external_filename + # Make filename absolute + return os.path.abspath( filename ) + + def set_file_name ( self, filename ): + if not filename: + self.external_filename = None + else: + self.external_filename = filename + + file_name = property( get_file_name, set_file_name ) + + @property + def extra_files_path( self ): + if self._extra_files_path: + path = self._extra_files_path + else: + path = os.path.join( self.file_path, "dataset_%d_files" % self.id ) + #only use path directly under self.file_path if it exists + if not os.path.exists( path ): + path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) + # Make path absolute + return os.path.abspath( path ) + + def get_size( self ): + """Returns the size of the data on disk""" + if self.file_size: + return self.file_size + else: + try: + return os.path.getsize( self.file_name ) + except OSError: + return 0 + def set_size( self ): + """Returns the size of the data on disk""" + try: + self.file_size = os.path.getsize( self.file_name ) + except OSError: + self.file_size = 0 + def has_data( self ): + """Detects whether there is any data""" + return self.get_size() > 0 + def mark_deleted( self, include_children=True ): + self.deleted = True + + # FIXME: sqlalchemy will replace this + def _delete(self): + """Remove the file that corresponds to this data""" + try: + os.remove(self.data.file_name) + except OSError, e: + log.critical('%s delete error %s' % (self.__class__.__name__, e)) + class Old_Dataset( Dataset ): pass diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index e98747fea0c..dd9df386629 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -113,99 +113,6 @@ ValidationError.table = Table( "validation_error", metadata, Column( "err_type", TrimmedString( 64 ) ), Column( "attributes", TEXT ) ) -GalaxyGroup.table = Table( "galaxy_group", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "name", TEXT ), - Column( "priority", Integer ) ) - -UserGroupAssociation.table = Table( "user_group_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -AccessRole.table = Table( "access_role", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "name", TEXT ), - Column( "actions", JSONType(), default=[] ), - Column( "priority", Integer ) ) - -UserRoleAssociation.table = Table( "user_role_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -GroupRoleAssociation.table = Table( "group_role_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -GroupDatasetAssociation.table = Table( "group_dataset_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -RoleDatasetAssociation.table = Table( "role_dataset_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -RoleRoleAssociation.table = Table( "role_role_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "target_role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -GroupRoleAccessAssociation.table = Table( "group_role_access_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - - -DefaultUserRoleAssociation.table = Table( "default_user_role_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -DefaultUserGroupAssociation.table = Table( "default_user_group_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -DefaultHistoryRoleAssociation.table = Table( "default_history_role_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "role_id", Integer, ForeignKey( "access_role.id" ), index=True ), - Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - -DefaultHistoryGroupAssociation.table = Table( "default_history_group_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), - Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ) ) - Job.table = Table( "job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -386,56 +293,6 @@ assign_mapper( context, User, User.table, collection_class=ordering_list( 'order_index' ) ) ) ) -assign_mapper( context, GalaxyGroup, GalaxyGroup.table, - properties=dict( users=relation( UserGroupAssociation ), - datasets=relation( GroupDatasetAssociation ) ) ) - -assign_mapper( context, UserGroupAssociation, UserGroupAssociation.table, - properties=dict( user=relation( User, backref = "groups" ), - group=relation( GalaxyGroup, backref = "users" ) ) ) - -assign_mapper( context, UserRoleAssociation, UserRoleAssociation.table, - properties=dict( role=relation( AccessRole, backref = "users" ), - user=relation( User, backref = "roles" ) ) ) - -assign_mapper( context, GroupRoleAssociation, GroupRoleAssociation.table, - properties=dict( role=relation( AccessRole, backref = "groups" ), - group=relation( GalaxyGroup, backref = "roles" ) ) ) - -assign_mapper( context, AccessRole, AccessRole.table ) - -assign_mapper( context, GroupDatasetAssociation, GroupDatasetAssociation.table, - properties=dict( dataset=relation( Dataset, backref = "groups" ), - group=relation( GalaxyGroup, backref = "datasets" ) ) ) - -assign_mapper( context, RoleDatasetAssociation, RoleDatasetAssociation.table, - properties=dict( dataset=relation( Dataset, backref = "roles" ), - role=relation( AccessRole ) ) ) - -assign_mapper( context, RoleRoleAssociation, RoleRoleAssociation.table, - properties=dict( role=relation( AccessRole, primaryjoin=( ( RoleRoleAssociation.table.c.role_id == AccessRole.table.c.id ) ) ), - target_role=relation( AccessRole, primaryjoin=( RoleRoleAssociation.table.c.target_role_id == AccessRole.table.c.id ), backref="roles" ) ) ) - -assign_mapper( context, GroupRoleAccessAssociation, GroupRoleAccessAssociation.table, - properties=dict( role=relation( AccessRole, backref="access_groups" ), - group=relation( GalaxyGroup, backref="access_roles" ) ) ) - -assign_mapper( context, DefaultUserRoleAssociation, DefaultUserRoleAssociation.table, - properties=dict( user=relation( User, backref = "default_roles" ), - role=relation( AccessRole ) ) ) - -assign_mapper( context, DefaultUserGroupAssociation, DefaultUserGroupAssociation.table, - properties=dict( user=relation( User, backref = "default_groups" ), - group=relation( GalaxyGroup ) ) ) - -assign_mapper( context, DefaultHistoryRoleAssociation, DefaultHistoryRoleAssociation.table, - properties=dict( history=relation( History, backref = "default_roles" ), - role=relation( AccessRole ) ) ) - -assign_mapper( context, DefaultHistoryGroupAssociation, DefaultHistoryGroupAssociation.table, - properties=dict( history=relation( History, backref = "default_groups" ), - group=relation( GalaxyGroup ) ) ) - assign_mapper( context, JobToInputDatasetAssociation, JobToInputDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation ) ) ) @@ -549,33 +406,6 @@ def init( file_path, url, engine_options={}, create_tables=False ): result.flush = lambda *args, **kwargs: context.current.flush( *args, **kwargs ) result.context = context result.create_tables = create_tables - #set up default table entries here, currently only exist for access controls - if result.AccessRole.count() == 0: - log.warning( "There were no access roles located, setting up default (public) access roles." ) - #create public group - public_group = result.GalaxyGroup( 'public' ) - public_group.flush() - #create public_all role - public_role = result.AccessRole( 'public', [ result.Dataset.access_actions.USE, result.Dataset.access_actions.VIEW, result.GalaxyGroup.access_actions.ADD_DATASET, result.GalaxyGroup.access_actions.REMOVE_DATASET ] ) - public_role.flush() - public_group.add_role( public_role ) - - #store public group id - GalaxyGroup.public_id = public_group.id #we use the id instead of the object, because of alchemy sessions - #add all datasets to public group - for dataset in result.Dataset.select(): - public_group.add_dataset( dataset ) - - #loop through all current users and associate with the public group - #and create and associate with user's own group - for user in result.User.select(): - public_group.add_user( user ) - private_group = user.create_private_group() - user.set_default_access( groups = [ public_group, private_group ], roles = [], history = True, dataset = True ) - else: - #retrieve from database and store public group id, assume first created group is public - GalaxyGroup.public_id = result.GalaxyGroup.select( order_by = asc( result.GalaxyGroup.table.c.create_time ) )[0].id #we use the id instead of the object, because of alchemy sessions - log.debug( "Public Group identified as id = %s." % ( GalaxyGroup.public_id ) ) return result def get_suite(): diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index e021cc8d2a9..9a7f9a26781 100644 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1084,7 +1084,7 @@ class Tool: if visible == "visible": visible = True else: visible = False ext = fields.pop(0).lower() - child_dataset = self.app.model.HistoryDatasetAssociation( extension=ext, parent_id=outdata.id, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True, access_groups=outdata.dataset.groups, access_roles=outdata.dataset.roles ) + child_dataset = self.app.model.HistoryDatasetAssociation( extension=ext, parent_id=outdata.id, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True ) # Move data from temp location to dataset location shutil.move( filename, child_dataset.file_name ) child_dataset.flush() @@ -1120,7 +1120,7 @@ class Tool: else: visible = False ext = fields.pop(0).lower() # Create new primary dataset - primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True, access_groups=outdata.dataset.groups, access_roles=outdata.dataset.roles ) + primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True ) primary_data.flush() # Move data from temp location to dataset location shutil.move( filename, primary_data.file_name ) diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 058caf07203..f2bb0cd8185 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -43,8 +43,6 @@ class DefaultToolAction( object ): assoc.flush() data = new_data break - if data and not data.allow_action( trans.user, data.access_actions.USE ): - raise "User does not have permission to use a dataset (%s) provided for input." % data.id return data if isinstance( input, DataToolParameter ): if isinstance( value, list ): @@ -81,16 +79,6 @@ class DefaultToolAction( object ): data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) if data.dbkey not in [None, '?']: input_dbkey = data.dbkey - - #determine output dataset access list - existing_datasets = [ inp for inp in inp_data.values() if inp ] - if existing_datasets: - output_access_groups, output_access_roles = existing_datasets[0].dataset.guess_derived_groups_roles( existing_datasets[1:] ) - else: - #no valid inputs, we will use history defaults - output_access_roles = [ role.role for role in trans.history.default_roles ] - output_access_groups = [ group.group for group in trans.history.default_groups ] - # Build name for output datasets based on tool name and input names if len( input_names ) == 1: on_text = input_names[0] @@ -129,7 +117,7 @@ class DefaultToolAction( object ): ext = output.format if ext == "input": ext = input_ext - data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True, access_groups=output_access_groups, access_roles=output_access_roles ) + data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True ) # Commit the dataset immediately so it gets database assigned unique id data.flush() # Create an empty file immediately @@ -195,8 +183,6 @@ class DefaultToolAction( object ): job.add_parameter( name, value ) for name, dataset in inp_data.iteritems(): if dataset: - if not dataset.allow_action( trans.user, dataset.access_actions.USE ): - raise "User does not have permission to use a dataset (%s) provided for input." % data.id job.add_input_dataset( name, dataset ) else: job.add_input_dataset( name, None ) diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py index 5c68786b6b1..b3904436a63 100644 --- a/lib/galaxy/tools/actions/upload.py +++ b/lib/galaxy/tools/actions/upload.py @@ -65,7 +65,7 @@ class UploadToolAction( object ): return dict( output=data_list[0] ) def upload_empty(self, trans, err_code, err_msg): - data = trans.app.model.HistoryDatasetAssociation( create_dataset = True, access_groups = [ group.group for group in trans.history.default_groups ], access_roles = [ role.role for role in trans.history.default_roles ] ) + data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) data.name = err_code data.extension = "txt" data.dbkey = "?" @@ -158,7 +158,7 @@ class UploadToolAction( object ): if info is None: info = 'uploaded %s file' %data_type - data = trans.app.model.HistoryDatasetAssociation( history = trans.history, extension = ext, create_dataset = True, access_groups = [ group.group for group in trans.history.default_groups ], access_roles = [ role.role for role in trans.history.default_roles ] ) + data = trans.app.model.HistoryDatasetAssociation( history = trans.history, extension = ext, create_dataset = True ) data.name = file_name data.dbkey = dbkey data.info = info diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 212a691d6aa..b10b51bdb5e 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -979,25 +979,19 @@ class DataToolParameter( ToolParameter ): displayed as radio buttons and multiple selects as a set of checkboxes >>> # Mock up a history (not connected to database) - >>> from galaxy.model import History, HistoryDatasetAssociation, User, AccessRole, GalaxyGroup, GroupRoleAssociation + >>> from galaxy.model import History, HistoryDatasetAssociation >>> from galaxy.util.bunch import Bunch >>> hist = History() >>> hist.flush() - >>> role = AccessRole( 'test', list( AccessRole.dataset_actions.__dict__.values() ) ) - >>> role.flush() - >>> group = GalaxyGroup( 'test' ) - >>> group.flush() - >>> GalaxyGroup.public_id = group.id - >>> GroupRoleAssociation( group, role ).flush() - >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='txt', create_dataset=True, access_groups=[ group ] ) ) - >>> hist.add_dataset( HistoryDatasetAssociation( id=2, extension='bed', create_dataset=True, access_groups=[ group ] ) ) - >>> hist.add_dataset( HistoryDatasetAssociation( id=3, extension='fasta', create_dataset=True, access_groups=[ group ] ) ) - >>> hist.add_dataset( HistoryDatasetAssociation( id=4, extension='png', create_dataset=True, access_groups=[ group ] ) ) - >>> hist.add_dataset( HistoryDatasetAssociation( id=5, extension='interval', create_dataset=True, access_groups=[ group ] ) ) + >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='txt', create_dataset=True ) ) + >>> hist.add_dataset( HistoryDatasetAssociation( id=2, extension='bed', create_dataset=True ) ) + >>> hist.add_dataset( HistoryDatasetAssociation( id=3, extension='fasta', create_dataset=True ) ) + >>> hist.add_dataset( HistoryDatasetAssociation( id=4, extension='png', create_dataset=True ) ) + >>> hist.add_dataset( HistoryDatasetAssociation( id=5, extension='interval', create_dataset=True ) ) >>> p = DataToolParameter( None, XML( '' ) ) >>> print p.name blah - >>> print p.get_html( trans=Bunch( history=hist, user=None ) ) + >>> print p.get_html( trans=Bunch( history=hist ) ) -
- - <% checked = "" %> - %if not data.dataset.has_group( trans.app.model.GalaxyGroup.get( trans.app.model.GalaxyGroup.public_id ) ): - <% checked = " checked" %> - %endif -
- -
-
-
- This will prevent other users from viewing or utilizing this dataset, even if you share your history with them. -
-
-
-
- -
- - - -%endif diff --git a/templates/history/options.mako b/templates/history/options.mako index 1bb2794a32b..4faa967742d 100644 --- a/templates/history/options.mako +++ b/templates/history/options.mako @@ -18,7 +18,6 @@ %endif %if app.config.enable_beta_features:
  • Construct workflow from the current history
    • -
  • Change default permissions for the current history
    • %endif
  • Share current history %endif diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako index d7093121868..877705614ed 100644 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -32,9 +32,7 @@ ## Body for history items, extra info and actions, data "peek"
    - %if not data.allow_action( trans.user, data.access_actions.VIEW ): -
    You do not have permision to view this dataset.
    - %elif data_state == "queued": + %if data_state == "queued":
    Job is waiting to run
    %elif data_state == "running":
    Job is currently running
    diff --git a/templates/user/index.mako b/templates/user/index.mako index 64d23dd2410..2b11262cece 100644 --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -8,9 +8,6 @@ %else: