mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Only allow 'uload files' option when replacing a dataset with a new version, more code merging, a few bugs fixes and additional functional tests for libraries.
This commit is contained in:
Greg Von Kuster
@@ -568,64 +568,31 @@ class Library( BaseController ):
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
lddas.append( ldda )
|
||||
if params.get( 'update_roles_button', False ):
|
||||
if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
|
||||
trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
|
||||
permissions = {}
|
||||
for k, v in trans.app.model.Dataset.permitted_actions.items():
|
||||
in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
|
||||
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
|
||||
for ldda in lddas:
|
||||
# Set the DATASET permissions on the Dataset
|
||||
trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
|
||||
ldda.dataset.refresh()
|
||||
permissions = {}
|
||||
for k, v in trans.app.model.Library.permitted_actions.items():
|
||||
in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
|
||||
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
|
||||
for ldda in lddas:
|
||||
# Set the LIBRARY permissions on the LibraryDataset
|
||||
# NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
|
||||
trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
|
||||
ldda.library_dataset.refresh()
|
||||
# Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
|
||||
trans.app.security_agent.set_all_library_permissions( ldda, permissions )
|
||||
ldda.refresh()
|
||||
msg = 'Permissions and roles have been updated on %d datasets' % len( lddas )
|
||||
messagetype = 'done'
|
||||
else:
|
||||
msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
|
||||
messagetype = 'error'
|
||||
return trans.fill_template( "/library/ldda_permissions.mako",
|
||||
ldda=lddas,
|
||||
library_id=library_id,
|
||||
msg=msg,
|
||||
messagetype=messagetype )
|
||||
if params.get( 'update_roles_button', False ):
|
||||
if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
|
||||
trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
|
||||
# Ensure that the permissions across all library items are identical, otherwise we can't update them together.
|
||||
check_list = []
|
||||
permissions = {}
|
||||
for k, v in trans.app.model.Dataset.permitted_actions.items():
|
||||
in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
|
||||
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
|
||||
for ldda in lddas:
|
||||
permissions = []
|
||||
# Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
|
||||
# will always be the same as the permissions on the associated LibraryDataset, so we only need to
|
||||
# check one Library object
|
||||
for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ):
|
||||
if library_permission.action not in permissions:
|
||||
permissions.append( library_permission.action )
|
||||
for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ):
|
||||
if dataset_permission.action not in permissions:
|
||||
permissions.append( dataset_permission.action )
|
||||
permissions.sort()
|
||||
if not check_list:
|
||||
check_list = permissions
|
||||
if permissions != check_list:
|
||||
msg = 'The datasets you selected do not have identical permissions, so they can not be updated together'
|
||||
trans.response.send_redirect( web.url_for( controller='library',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
# Set the DATASET permissions on the Dataset
|
||||
trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
|
||||
ldda.dataset.refresh()
|
||||
permissions = {}
|
||||
for k, v in trans.app.model.Library.permitted_actions.items():
|
||||
in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
|
||||
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
|
||||
for ldda in lddas:
|
||||
# Set the LIBRARY permissions on the LibraryDataset
|
||||
# NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
|
||||
trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
|
||||
ldda.library_dataset.refresh()
|
||||
# Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
|
||||
trans.app.security_agent.set_all_library_permissions( ldda, permissions )
|
||||
ldda.refresh()
|
||||
msg = 'Permissions and roles have been updated on %d datasets' % len( lddas )
|
||||
messagetype = 'done'
|
||||
else:
|
||||
msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
|
||||
messagetype = 'error'
|
||||
@@ -634,6 +601,39 @@ class Library( BaseController ):
|
||||
library_id=library_id,
|
||||
msg=msg,
|
||||
messagetype=messagetype )
|
||||
if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
|
||||
trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
|
||||
# Ensure that the permissions across all library items are identical, otherwise we can't update them together.
|
||||
check_list = []
|
||||
for ldda in lddas:
|
||||
permissions = []
|
||||
# Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
|
||||
# will always be the same as the permissions on the associated LibraryDataset, so we only need to
|
||||
# check one Library object
|
||||
for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ):
|
||||
if library_permission.action not in permissions:
|
||||
permissions.append( library_permission.action )
|
||||
for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ):
|
||||
if dataset_permission.action not in permissions:
|
||||
permissions.append( dataset_permission.action )
|
||||
permissions.sort()
|
||||
if not check_list:
|
||||
check_list = permissions
|
||||
if permissions != check_list:
|
||||
msg = 'The datasets you selected do not have identical permissions, so they can not be updated together'
|
||||
trans.response.send_redirect( web.url_for( controller='library',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
else:
|
||||
msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
|
||||
messagetype = 'error'
|
||||
return trans.fill_template( "/library/ldda_permissions.mako",
|
||||
ldda=lddas,
|
||||
library_id=library_id,
|
||||
msg=msg,
|
||||
messagetype=messagetype )
|
||||
@web.expose
|
||||
def upload_library_dataset( self, trans, library_id, folder_id, **kwd ):
|
||||
params = util.Params( kwd )
|
||||
@@ -652,8 +652,11 @@ class Library( BaseController ):
|
||||
replace_dataset = trans.app.model.LibraryDataset.get( params.get( 'replace_id', None ) )
|
||||
if not last_used_build:
|
||||
last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
|
||||
# Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
|
||||
upload_option = 'upload_file'
|
||||
else:
|
||||
replace_dataset = None
|
||||
upload_option = params.get( 'upload_option', 'upload_file' )
|
||||
user, roles = trans.get_user_and_roles()
|
||||
if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \
|
||||
( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ):
|
||||
@@ -666,15 +669,14 @@ class Library( BaseController ):
|
||||
else:
|
||||
template_id = 'None'
|
||||
widgets = []
|
||||
upload_option = params.get( 'upload_option', 'upload_file' )
|
||||
created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
|
||||
controller='library',
|
||||
library_id=library_id,
|
||||
folder_id=folder_id,
|
||||
template_id=template_id,
|
||||
widgets=widgets,
|
||||
replace_dataset=replace_dataset,
|
||||
**kwd )
|
||||
controller='library',
|
||||
library_id=library_id,
|
||||
folder_id=folder_id,
|
||||
template_id=template_id,
|
||||
widgets=widgets,
|
||||
replace_dataset=replace_dataset,
|
||||
**kwd )
|
||||
if created_outputs:
|
||||
ldda_id_list = [ str( v.id ) for v in created_outputs.values() ]
|
||||
total_added = len( created_outputs.values() )
|
||||
@@ -860,35 +862,6 @@ class Library( BaseController ):
|
||||
msg=msg,
|
||||
messagetype=messagetype )
|
||||
@web.expose
|
||||
def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd):
|
||||
"""Catches the dataset id and displays file contents as directed"""
|
||||
# id must refer to a LibraryDatasetDatasetAssociation object
|
||||
ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
|
||||
if not ldda.dataset:
|
||||
msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
|
||||
return trans.response.send_redirect( web.url_for( controller='library',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=msg,
|
||||
messagetype='error' ) )
|
||||
mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
|
||||
trans.response.set_content_type( mime )
|
||||
fStat = os.stat( ldda.file_name )
|
||||
trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
|
||||
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
|
||||
fname = ldda.name
|
||||
fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
|
||||
trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname )
|
||||
try:
|
||||
return open( ldda.file_name )
|
||||
except:
|
||||
msg = 'This dataset contains no content'
|
||||
return trans.response.send_redirect( web.url_for( controller='library',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=msg,
|
||||
messagetype='error' ) )
|
||||
@web.expose
|
||||
def datasets( self, trans, library_id, ldda_ids='', **kwd ):
|
||||
# This method is used by the select list labeled "Perform action on selected datasets"
|
||||
# on the analysis library browser.
|
||||
|
||||
@@ -673,8 +673,11 @@ class LibraryAdmin( BaseController ):
|
||||
replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) )
|
||||
if not last_used_build:
|
||||
last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
|
||||
# Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
|
||||
upload_option = 'upload_file'
|
||||
else:
|
||||
replace_dataset = None
|
||||
upload_option = params.get( 'upload_option', 'upload_file' )
|
||||
if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ):
|
||||
# See if we have any inherited templates, but do not inherit contents.
|
||||
info_association, inherited = folder.get_info_association( inherited=True )
|
||||
@@ -684,15 +687,14 @@ class LibraryAdmin( BaseController ):
|
||||
else:
|
||||
template_id = 'None'
|
||||
widgets = []
|
||||
upload_option = params.get( 'upload_option', 'upload_file' )
|
||||
created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
|
||||
controller='library_admin',
|
||||
library_id=library_id,
|
||||
folder_id=folder_id,
|
||||
template_id=template_id,
|
||||
widgets=widgets,
|
||||
replace_dataset=replace_dataset,
|
||||
**kwd )
|
||||
controller='library_admin',
|
||||
library_id=library_id,
|
||||
folder_id=folder_id,
|
||||
template_id=template_id,
|
||||
widgets=widgets,
|
||||
replace_dataset=replace_dataset,
|
||||
**kwd )
|
||||
if created_outputs:
|
||||
total_added = len( created_outputs.values() )
|
||||
if replace_dataset:
|
||||
@@ -851,36 +853,6 @@ class LibraryAdmin( BaseController ):
|
||||
messagetype=messagetype )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd):
|
||||
"""Catches the dataset id and displays file contents as directed"""
|
||||
# id must refer to a LibraryDatasetDatasetAssociation object
|
||||
ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
|
||||
if not ldda.dataset:
|
||||
msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
|
||||
return trans.response.send_redirect( web.url_for( controller='library_admin',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
|
||||
trans.response.set_content_type( mime )
|
||||
fStat = os.stat( ldda.file_name )
|
||||
trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
|
||||
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
|
||||
fname = ldda.name
|
||||
fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
|
||||
trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname )
|
||||
try:
|
||||
return open( ldda.file_name )
|
||||
except:
|
||||
msg = 'This dataset contains no content'
|
||||
return trans.response.send_redirect( web.url_for( controller='library_admin',
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def datasets( self, trans, library_id, **kwd ):
|
||||
# This method is used by the select list labeled "Perform action on selected datasets"
|
||||
# on the admin library browser.
|
||||
|
||||
@@ -181,6 +181,35 @@ class LibraryCommon( BaseController ):
|
||||
return None, err_redirect, msg
|
||||
return uploaded_datasets, None, None
|
||||
@web.expose
|
||||
def download_dataset_from_folder( self, trans, cntrller, obj_id, library_id=None, **kwd ):
|
||||
"""Catches the dataset id and displays file contents as directed"""
|
||||
# id must refer to a LibraryDatasetDatasetAssociation object
|
||||
ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
|
||||
if not ldda.dataset:
|
||||
msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
|
||||
return trans.response.send_redirect( web.url_for( controller=cntrller,
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
|
||||
trans.response.set_content_type( mime )
|
||||
fStat = os.stat( ldda.file_name )
|
||||
trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
|
||||
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
|
||||
fname = ldda.name
|
||||
fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
|
||||
trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname )
|
||||
try:
|
||||
return open( ldda.file_name )
|
||||
except:
|
||||
msg = 'This dataset contains no content'
|
||||
return trans.response.send_redirect( web.url_for( controller=cntrller,
|
||||
action='browse_library',
|
||||
obj_id=library_id,
|
||||
msg=util.sanitize_text( msg ),
|
||||
messagetype='error' ) )
|
||||
@web.expose
|
||||
def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ):
|
||||
# Only adding a new templAte to a library or folder is currently allowed. Editing an existing template is
|
||||
# a future enhancement. The response_action param is the name of the method to which this method will redirect
|
||||
|
||||
@@ -137,7 +137,7 @@
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='ldda_manage_permissions', library_id=library.id, folder_id=folder.id, obj_id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', cntrller='library_admin', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a>
|
||||
%endif
|
||||
<a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a>
|
||||
</div>
|
||||
|
||||
@@ -47,7 +47,7 @@
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', cntrller='library_admin', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
%endif
|
||||
%if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.library_dataset.deleted:
|
||||
<a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, folder_id=ldda.library_dataset.folder.id, library_item_id=ldda.library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a>
|
||||
|
||||
@@ -12,17 +12,20 @@
|
||||
%>
|
||||
|
||||
<b>Create new data library datasets</b>
|
||||
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="upload-librarydataset--popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
|
||||
%if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ):
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
|
||||
%endif
|
||||
%if trans.app.config.allow_library_path_paste:
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a>
|
||||
%endif
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
|
||||
</div>
|
||||
%if replace_dataset in [ None, 'None' ]:
|
||||
## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
|
||||
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="upload-librarydataset--popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
|
||||
%if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ):
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
|
||||
%endif
|
||||
%if trans.app.config.allow_library_path_paste:
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a>
|
||||
%endif
|
||||
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
|
||||
</div>
|
||||
%endif
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
|
||||
@@ -178,7 +178,7 @@ class RowCounter( object ):
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller='library', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a>
|
||||
%endif
|
||||
</div>
|
||||
</td>
|
||||
|
||||
@@ -53,7 +53,7 @@
|
||||
%endif
|
||||
%if ldda.has_data:
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library_id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller='library', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -12,14 +12,17 @@
|
||||
%>
|
||||
|
||||
<b>Create new data library datasets</b>
|
||||
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="upload-librarydataset--popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
|
||||
%if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
|
||||
%endif
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
|
||||
</div>
|
||||
%if replace_dataset in [ None, 'None' ]:
|
||||
## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
|
||||
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="upload-librarydataset--popup">
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
|
||||
%if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ):
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
|
||||
%endif
|
||||
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
|
||||
</div>
|
||||
%endif
|
||||
<br/><br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
|
||||
@@ -1144,14 +1144,15 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.fv( "1", "2", description ) # form field 1 is the field named name...
|
||||
tc.submit( "create_library_button" )
|
||||
self.home()
|
||||
def set_library_permissions( self, library_id, library_name, role_id, permissions_in, permissions_out ):
|
||||
def set_library_permissions( self, library_id, library_name, role_ids_str, permissions_in, permissions_out ):
|
||||
# role_ids_str must be a comma-separated string of role ids
|
||||
url = "library_admin/library?obj_id=%s&permissions=True&update_roles_button=Save" % ( library_id )
|
||||
for po in permissions_out:
|
||||
key = '%s_out' % po
|
||||
url ="%s&%s=%s" % ( url, key, str( role_id ) )
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
for pi in permissions_in:
|
||||
key = '%s_in' % pi
|
||||
url ="%s&%s=%s" % ( url, key, str( role_id ) )
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
self.home()
|
||||
self.visit_url( "%s/%s" % ( self.url, url ) )
|
||||
check_str = "Permissions updated for library '%s'" % library_name
|
||||
@@ -1276,17 +1277,16 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.check_page_for_string( check_str )
|
||||
self.library_wait( library_id )
|
||||
self.home()
|
||||
def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_id, permissions_in, permissions_out ):
|
||||
def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_ids_str, permissions_in, permissions_out ):
|
||||
# role_ids_str must be a comma-separated string of role ids
|
||||
url = "library_admin/ldda_manage_permissions?library_id=%s&folder_id=%s&obj_id=%s&update_roles_button=Save" % \
|
||||
( library_id, folder_id, ldda_id )
|
||||
#role_ids = util.listify( role_ids )
|
||||
#for role_id in role_ids:
|
||||
for po in permissions_out:
|
||||
key = '%s_out' % po
|
||||
url ="%s&%s=%s" % ( url, key, str( role_id ) )
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
for pi in permissions_in:
|
||||
key = '%s_in' % pi
|
||||
url ="%s&%s=%s" % ( url, key, str( role_id ) )
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
self.home()
|
||||
self.visit_url( "%s/%s" % ( self.url, url ) )
|
||||
check_str = "Permissions have been updated on 1 datasets"
|
||||
|
||||
@@ -176,6 +176,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
actions_in = [ 'manage permissions' ]
|
||||
permissions_out = [ 'DATASET_ACCESS' ]
|
||||
actions_out = [ 'access' ]
|
||||
global regular_user2_private_role
|
||||
regular_user2_private_role = None
|
||||
for role in regular_user2.all_roles():
|
||||
if role.name == regular_user2.email and role.description == 'Private Role for %s' % regular_user2.email:
|
||||
@@ -849,9 +850,9 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
permissions_in = [ k for k, v in galaxy.model.Dataset.permitted_actions.items() ] + \
|
||||
[ k for k, v in galaxy.model.Library.permitted_actions.items() ]
|
||||
permissions_out = []
|
||||
role_ids = "%s,%s" % ( str( role_one.id ), str( admin_user_private_role.id ) )
|
||||
role_ids_str = '%s,%s' % ( str( role_one.id ), str( admin_user_private_role.id ) )
|
||||
self.set_library_dataset_permissions( str( library_one.id ), str( folder_one.id ), str( ldda_four.id ), ldda_four.name,
|
||||
role_ids, permissions_in, permissions_out )
|
||||
role_ids_str, permissions_in, permissions_out )
|
||||
# admin_user should now be able to see 4.bed from the analysis view's access libraries
|
||||
self.home()
|
||||
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
|
||||
@@ -1309,6 +1310,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
|
||||
def test_170_mark_group_deleted( self ):
|
||||
"""Testing marking a group as deleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.visit_url( '%s/admin/groups' % self.url )
|
||||
self.check_page_for_string( group_two.name )
|
||||
@@ -1323,12 +1325,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name )
|
||||
def test_175_undelete_group( self ):
|
||||
"""Testing undeleting a deleted group"""
|
||||
# Logged in as admin_user
|
||||
self.undelete_group( str( group_two.id ), group_two.name )
|
||||
group_two.refresh()
|
||||
if group_two.deleted:
|
||||
raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name )
|
||||
def test_180_mark_role_deleted( self ):
|
||||
"""Testing marking a role as deleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.visit_url( '%s/admin/roles' % self.url )
|
||||
self.check_page_for_string( role_two.name )
|
||||
@@ -1343,9 +1347,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name )
|
||||
def test_185_undelete_role( self ):
|
||||
"""Testing undeleting a deleted role"""
|
||||
# Logged in as admin_user
|
||||
self.undelete_role( str( role_two.id ), role_two.name )
|
||||
def test_190_mark_dataset_deleted( self ):
|
||||
"""Testing marking a library dataset as deleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.delete_library_item( str( library_one.id ), str( ldda_two.library_dataset.id ), ldda_two.name, library_item_type='library_dataset' )
|
||||
self.home()
|
||||
@@ -1359,12 +1365,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_195_display_deleted_dataset( self ):
|
||||
"""Testing displaying deleted dataset"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.visit_url( "%s/library_admin/browse_library?obj_id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) )
|
||||
self.check_page_for_string( ldda_two.name )
|
||||
self.home()
|
||||
def test_200_hide_deleted_dataset( self ):
|
||||
"""Testing hiding deleted dataset"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.visit_url( "%s/library_admin/browse_library?obj_id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) )
|
||||
try:
|
||||
@@ -1375,6 +1383,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_205_mark_folder_deleted( self ):
|
||||
"""Testing marking a library folder as deleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
|
||||
self.home()
|
||||
@@ -1387,6 +1396,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_210_mark_folder_undeleted( self ):
|
||||
"""Testing marking a library folder as undeleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
|
||||
self.home()
|
||||
@@ -1402,6 +1412,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_215_mark_library_deleted( self ):
|
||||
"""Testing marking a library as deleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
# First mark folder_two as deleted to further test state saving when we undelete the library
|
||||
self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
|
||||
@@ -1412,6 +1423,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_220_mark_library_undeleted( self ):
|
||||
"""Testing marking a library as undeleted"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.undelete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
|
||||
self.home()
|
||||
@@ -1426,6 +1438,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_225_purge_user( self ):
|
||||
"""Testing purging a user account"""
|
||||
# Logged in as admin_user
|
||||
self.mark_user_deleted( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email )
|
||||
regular_user3.refresh()
|
||||
self.purge_user( self.security.encode_id( regular_user3.id ), regular_user3.email )
|
||||
@@ -1458,6 +1471,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email )
|
||||
def test_230_manually_unpurge_user( self ):
|
||||
"""Testing manually un-purging a user account"""
|
||||
# Logged in as admin_user
|
||||
# Reset the user for later test runs. The user's private Role and DefaultUserPermissions for that role
|
||||
# should have been preserved, so all we need to do is reset purged and deleted.
|
||||
# TODO: If we decide to implement the GUI feature for un-purging a user, replace this with a method call
|
||||
@@ -1466,6 +1480,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
regular_user3.flush()
|
||||
def test_235_purge_group( self ):
|
||||
"""Testing purging a group"""
|
||||
# Logged in as admin_user
|
||||
group_id = str( group_two.id )
|
||||
self.mark_group_deleted( group_id, group_two.name )
|
||||
self.purge_group( group_id, group_two.name )
|
||||
@@ -1481,6 +1496,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.undelete_group( group_id, group_two.name )
|
||||
def test_240_purge_role( self ):
|
||||
"""Testing purging a role"""
|
||||
# Logged in as admin_user
|
||||
role_id = str( role_two.id )
|
||||
self.mark_role_deleted( role_id, role_two.name )
|
||||
self.purge_role( role_id, role_two.name )
|
||||
@@ -1506,6 +1522,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id )
|
||||
def test_245_manually_unpurge_role( self ):
|
||||
"""Testing manually un-purging a role"""
|
||||
# Logged in as admin_user
|
||||
# Manually unpurge, then undelete the role for later test runs
|
||||
# TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call
|
||||
role_two.purged = False
|
||||
@@ -1513,6 +1530,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.undelete_role( str( role_two.id ), role_two.name )
|
||||
def test_250_purge_library( self ):
|
||||
"""Testing purging a library"""
|
||||
# Logged in as admin_user
|
||||
self.home()
|
||||
self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
|
||||
self.purge_library( str( library_one.id ), library_one.name )
|
||||
@@ -1549,6 +1567,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
check_folder( library_one.root_folder )
|
||||
def test_255_no_library_template( self ):
|
||||
"""Test library features when library has no template"""
|
||||
# Logged in as admin_user
|
||||
name = "Library Two"
|
||||
description = "This is Library Two"
|
||||
# Create a library, adding no template
|
||||
@@ -1585,6 +1604,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
self.home()
|
||||
def test_260_library_permissions( self ):
|
||||
"""Test library permissions"""
|
||||
# Logged in as admin_user
|
||||
name = "Library Three"
|
||||
description = "This is Library Three"
|
||||
# Create a library, adding no template
|
||||
@@ -1596,12 +1616,30 @@ class TestSecurityAndLibraries( TwillTestCase ):
|
||||
galaxy.model.Library.table.c.description==description,
|
||||
galaxy.model.Library.table.c.deleted==False ) ).first()
|
||||
assert library_three is not None, 'Problem retrieving library named "%s" from the database' % name
|
||||
# TODO: add tests here...
|
||||
self.home()
|
||||
# Set library permissions for regular_user1 and regular_user2. Each of these users will be permitted to
|
||||
# LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items.
|
||||
permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ]
|
||||
permissions_out = []
|
||||
role_ids_str = '%s,%s' % ( str( regular_user1_private_role.id ), str( regular_user2_private_role.id ) )
|
||||
self.set_library_permissions( str( library_three.id ), library_three.name, role_ids_str, permissions_in, permissions_out )
|
||||
self.logout()
|
||||
# Login as regular_user1 and make sure they can see the library
|
||||
self.login( email=regular_user1.email )
|
||||
self.visit_url( '%s/library/browse_libraries' % self.url )
|
||||
self.check_page_for_string( name )
|
||||
self.logout()
|
||||
# Login as regular_user1 and make sure they can see the library
|
||||
self.login( email=regular_user2.email )
|
||||
self.visit_url( '%s/library/browse_libraries' % self.url )
|
||||
self.check_page_for_string( name )
|
||||
# TODO: add more tests here to cover adding, modifying, managing permissions from the Librarys persoective as a regular user
|
||||
self.logout()
|
||||
self.login( email=admin_user.email )
|
||||
self.delete_library_item( str( library_three.id ), str( library_three.id ), library_three.name, library_item_type='library' )
|
||||
self.purge_library( str( library_three.id ), library_three.name )
|
||||
def test_265_reset_data_for_later_test_runs( self ):
|
||||
"""Reseting data to enable later test runs to pass"""
|
||||
# Logged in as admin_user
|
||||
##################
|
||||
# Eliminate all non-private roles
|
||||
##################
|
||||
|
||||
Reference in New Issue
Block a user