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Refactored the library_dataset_dataset_association methods in the library_admin and library controllers, renamed the library_dataset controller to be library_common and moved several common methods to it, and some other code cleanup.

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This commit is contained in:
Greg Von Kuster
2009-09-30 05:16:17 -04:00
parent 91df9752f6
commit baa64fc6a7
43 changed files with 1456 additions and 1635 deletions
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lib/galaxy/web/controllers/library.py
+540 -715
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lib/galaxy/web/controllers/library_admin.py
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lib/galaxy/web/controllers/library_common.py
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import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
from galaxy.web.base.controller import *
from galaxy import util, jobs
from galaxy.datatypes import sniff
from galaxy.security import RBACAgent
from galaxy.util.json import to_json_string
from galaxy.tools.actions import upload_common
from galaxy.web.controllers.forms import get_all_forms
from galaxy.model.orm import *
log = logging.getLogger( __name__ )
class LibraryCommon( BaseController ):
@web.json
def library_item_updates( self, trans, ids=None, states=None ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
# Create new HTML for any that have changed
rval = {}
if ids is not None and states is not None:
ids = map( int, ids.split( "," ) )
states = states.split( "," )
for id, state in zip( ids, states ):
data = self.app.model.LibraryDatasetDatasetAssociation.get( id )
if data.state != state:
job_ldda = data
while job_ldda.copied_from_library_dataset_dataset_association:
job_ldda = job_ldda.copied_from_library_dataset_dataset_association
force_history_refresh = False
rval[id] = {
"state": data.state,
"html": unicode( trans.fill_template( "library/library_item_info.mako", ldda=data ), 'utf-8' )
#"force_history_refresh": force_history_refresh
}
return rval
def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ):
# Set up the traditional tool state/params
tool_id = 'upload1'
tool = trans.app.toolbox.tools_by_id[ tool_id ]
state = tool.new_state( trans )
errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd, changed_dependencies={} )
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append( input )
# Library-specific params
params = util.Params( kwd ) # is this filetoolparam safe?
library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
server_dir = util.restore_text( params.get( 'server_dir', '' ) )
if replace_dataset not in [ None, 'None' ]:
replace_id = replace_dataset.id
else:
replace_id = None
upload_option = params.get( 'upload_option', 'upload_file' )
err_redirect = False
if upload_option == 'upload_directory':
if server_dir in [ None, 'None', '' ]:
err_redirect = True
if controller == 'library_admin':
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
full_dir = os.path.join( import_dir, server_dir )
else:
import_dir = trans.app.config.user_library_import_dir
import_dir_desc = 'user_library_import_dir'
if server_dir == trans.user.email:
full_dir = os.path.join( import_dir, server_dir )
else:
full_dir = os.path.join( import_dir, trans.user.email, server_dir )
if import_dir:
msg = 'Select a directory'
else:
msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
# Proceed with (mostly) regular upload processing
precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller )
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads( tool_params )
uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch )
elif upload_option == 'upload_directory':
uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg )
upload_common.cleanup_unused_precreated_datasets( precreated_datasets )
if upload_option == 'upload_file' and not uploaded_datasets:
msg = 'Select a file, enter a URL or enter text'
err_redirect = True
if err_redirect:
trans.response.send_redirect( web.url_for( controller=controller,
action='upload_library_dataset',
library_id=library_id,
folder_id=folder_id,
replace_id=replace_id,
upload_option=upload_option,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
json_file_path = upload_common.create_paramfile( uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ):
files = []
try:
for entry in os.listdir( full_dir ):
# Only import regular files
if os.path.isfile( os.path.join( full_dir, entry ) ):
files.append( entry )
except Exception, e:
msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) )
err_redirect = True
return None
if not files:
msg = "The directory '%s' contains no valid files" % full_dir
err_redirect = True
return None
uploaded_datasets = []
for file in files:
library_bunch.replace_dataset = None
uploaded_dataset = util.bunch.Bunch()
uploaded_dataset.path = os.path.join( full_dir, file )
if not os.path.isfile( uploaded_dataset.path ):
continue
uploaded_dataset.type = 'server_dir'
uploaded_dataset.name = file
uploaded_dataset.ext = None
uploaded_dataset.file_type = params.file_type
uploaded_dataset.dbkey = params.dbkey
uploaded_dataset.space_to_tab = params.space_to_tab
uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch )
uploaded_datasets.append( uploaded_dataset )
return uploaded_datasets
@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
# if a new template is being added to a library or folder.
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
if obj_id:
library_item = trans.app.model.FormDefinition.get( int( obj_id ) )
library_item_desc = 'information template'
response_id = obj_id
elif folder_id:
library_item = trans.app.model.LibraryFolder.get( int( folder_id ) )
library_item_desc = 'folder'
response_id = folder_id
elif ldda_id:
library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) )
library_item_desc = 'library dataset'
response_id = ldda_id
else:
library_item = trans.app.model.Library.get( int( library_id ) )
library_item_desc = 'library'
response_id = library_id
forms = get_all_forms( trans,
filter=dict( deleted=False ),
form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE )
if not forms:
msg = "There are no forms on which to base the template, so create a form and "
msg += "try again to add the information template to the %s." % library_item_desc
trans.response.send_redirect( web.url_for( controller='forms',
action='new',
new=True,
msg=msg,
messagetype='done' ) )
if params.get( 'add_info_template_button', False ):
form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) )
#fields = list( copy.deepcopy( form.fields ) )
form_values = trans.app.model.FormValues( form, [] )
form_values.flush()
if folder_id:
assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values )
elif ldda_id:
assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values )
else:
assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values )
assoc.flush()
msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc )
trans.response.send_redirect( web.url_for( controller=cntrller,
action=response_action,
obj_id=response_id,
msg=msg,
message_type='done' ) )
# TODO: handle this better
if cntrller == 'library_admin':
tmplt = '/admin/library/select_info_template.mako'
else:
tmplt = '/ibrary/select_info_template.mako'
return trans.fill_template( tmplt,
library_item_name=library_item.name,
library_item_desc=library_item_desc,
library_id=library_id,
folder_id=folder_id,
ldda_id=ldda_id,
forms=forms,
msg=msg,
messagetype=messagetype )
@web.expose
def edit_template_info( self, trans, cntrller, library_id, response_action, num_widgets, library_item_id=None, library_item_type=None, **kwd ):
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
folder_id = None
if library_item_type == 'library':
library_item = trans.app.model.Library.get( library_item_id )
elif library_item_type == 'library_dataset':
library_item = trans.app.model.LibraryDataset.get( library_item_id )
elif library_item_type == 'folder':
library_item = trans.app.model.LibraryFolder.get( library_item_id )
elif library_item_type == 'library_dataset_dataset_association':
library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id )
# This response_action method requires a folder_id
folder_id = library_item.library_dataset.folder.id
else:
msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_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' ) )
# Save updated template field contents
field_contents = []
for index in range( int( num_widgets ) ):
field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) )
if field_contents:
# Since information templates are inherited, the template fields can be displayed on the information
# page for a folder or library dataset when it has no info_association object. If the user has added
# field contents on an inherited template via a parent's info_association, we'll need to create a new
# form_values and info_association for the current object. The value for the returned inherited variable
# is not applicable at this level.
info_association, inherited = library_item.get_info_association( restrict=True )
if info_association:
template = info_association.template
info = info_association.info
form_values = trans.app.model.FormValues.get( info.id )
# Update existing content only if it has changed
if form_values.content != field_contents:
form_values.content = field_contents
form_values.flush()
else:
# Inherit the next available info_association so we can get the template
info_association, inherited = library_item.get_info_association()
template = info_association.template
# Create a new FormValues object
form_values = trans.app.model.FormValues( template, field_contents )
form_values.flush()
# Create a new info_association between the current library item and form_values
if library_item_type == 'folder':
info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values )
info_association.flush()
elif library_item_type == 'library_dataset_dataset_association':
info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values )
info_association.flush()
msg = 'The information has been updated.'
return trans.response.send_redirect( web.url_for( controller=cntrller,
action=response_action,
library_id=library_id,
folder_id=folder_id,
obj_id=library_item.id,
msg=util.sanitize_text( msg ),
messagetype='done' ) )
# ---- Utility methods -------------------------------------------------------
def active_folders( trans, folder ):
# Much faster way of retrieving all active sub-folders within a given folder than the
# performance of the mapper. This query also eagerloads the permissions on each folder.
return trans.sa_session.query( trans.app.model.LibraryFolder ) \
.filter_by( parent=folder, deleted=False ) \
.options( eagerload_all( "actions" ) ) \
.order_by( trans.app.model.LibraryFolder.table.c.name ) \
.all()
def activatable_folders( trans, folder ):
return trans.sa_session.query( trans.app.model.LibraryFolder ) \
.filter_by( parent=folder, purged=False ) \
.options( eagerload_all( "actions" ) ) \
.order_by( trans.app.model.LibraryFolder.table.c.name ) \
.all()
def active_folders_and_lddas( trans, folder ):
folders = active_folders( trans, folder )
# This query is much faster than the folder.active_library_datasets property
lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
.filter_by( deleted=False ) \
.join( "library_dataset" ) \
.filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
.order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
.all()
return folders, lddas
def activatable_folders_and_lddas( trans, folder ):
folders = activatable_folders( trans, folder )
# This query is much faster than the folder.activatable_library_datasets property
lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
.join( "library_dataset" ) \
.filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
.join( "dataset" ) \
.filter( trans.app.model.Dataset.table.c.deleted==False ) \
.order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
.all()
return folders, lddas
lib/galaxy/web/controllers/library_dataset.py
-129
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@@ -1,129 +0,0 @@
import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
from galaxy.web.base.controller import *
from galaxy import util, jobs
from galaxy.datatypes import sniff
from galaxy.security import RBACAgent
from galaxy.util.json import to_json_string
from galaxy.tools.actions import upload_common
log = logging.getLogger( __name__ )
class UploadLibraryDataset( BaseController ):
@web.json
def library_item_updates( self, trans, ids=None, states=None ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
# Create new HTML for any that have changed
rval = {}
if ids is not None and states is not None:
ids = map( int, ids.split( "," ) )
states = states.split( "," )
for id, state in zip( ids, states ):
data = self.app.model.LibraryDatasetDatasetAssociation.get( id )
if data.state != state:
job_ldda = data
while job_ldda.copied_from_library_dataset_dataset_association:
job_ldda = job_ldda.copied_from_library_dataset_dataset_association
force_history_refresh = False
rval[id] = {
"state": data.state,
"html": unicode( trans.fill_template( "library/library_item_info.mako", ldda=data ), 'utf-8' )
#"force_history_refresh": force_history_refresh
}
return rval
def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ):
# Set up the traditional tool state/params
tool_id = 'upload1'
tool = trans.app.toolbox.tools_by_id[ tool_id ]
state = tool.new_state( trans )
errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd, changed_dependencies={} )
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.iteritems():
if input.type == "upload_dataset":
dataset_upload_inputs.append( input )
# Library-specific params
params = util.Params( kwd ) # is this filetoolparam safe?
library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
server_dir = util.restore_text( params.get( 'server_dir', '' ) )
if replace_dataset not in [ None, 'None' ]:
replace_id = replace_dataset.id
else:
replace_id = None
upload_option = params.get( 'upload_option', 'upload_file' )
err_redirect = False
if upload_option == 'upload_directory':
if server_dir in [ None, 'None', '' ]:
err_redirect = True
if controller == 'library_admin':
import_dir = trans.app.config.library_import_dir
import_dir_desc = 'library_import_dir'
full_dir = os.path.join( import_dir, server_dir )
else:
import_dir = trans.app.config.user_library_import_dir
import_dir_desc = 'user_library_import_dir'
if server_dir == trans.user.email:
full_dir = os.path.join( import_dir, server_dir )
else:
full_dir = os.path.join( import_dir, trans.user.email, server_dir )
if import_dir:
msg = 'Select a directory'
else:
msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
# Proceed with (mostly) regular upload processing
precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller )
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads( tool_params )
uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch )
elif upload_option == 'upload_directory':
uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg )
upload_common.cleanup_unused_precreated_datasets( precreated_datasets )
if upload_option == 'upload_file' and not uploaded_datasets:
msg = 'Select a file, enter a URL or enter text'
err_redirect = True
if err_redirect:
trans.response.send_redirect( web.url_for( controller=controller,
action='library_dataset_dataset_association',
library_id=library_id,
folder_id=folder_id,
replace_id=replace_id,
upload_option=upload_option,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
json_file_path = upload_common.create_paramfile( uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ):
files = []
try:
for entry in os.listdir( full_dir ):
# Only import regular files
if os.path.isfile( os.path.join( full_dir, entry ) ):
files.append( entry )
except Exception, e:
msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) )
err_redirect = True
return None
if not files:
msg = "The directory '%s' contains no valid files" % full_dir
err_redirect = True
return None
uploaded_datasets = []
for file in files:
library_bunch.replace_dataset = None
uploaded_dataset = util.bunch.Bunch()
uploaded_dataset.path = os.path.join( full_dir, file )
if not os.path.isfile( uploaded_dataset.path ):
continue
uploaded_dataset.type = 'server_dir'
uploaded_dataset.name = file
uploaded_dataset.ext = None
uploaded_dataset.file_type = params.file_type
uploaded_dataset.dbkey = params.dbkey
uploaded_dataset.space_to_tab = params.space_to_tab
uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch )
uploaded_datasets.append( uploaded_dataset )
return uploaded_datasets
templates/admin/center.mako
+1 -1
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@@ -37,7 +37,7 @@
users (a library item is one of: a data library, a library folder, a library dataset).
<p/>
<ul>
<li><strong>add library item</strong> - Role members can add library items to this library or folder</li>
<li><strong>add library item</strong> - Role members can add library items to this data library or folder</li>
<li><strong>modify library item</strong> - Role members can modify this library item</li>
<li><strong>manage library permissions</strong> - Role members can manage permissions applied to this library item</li>
</ul>
templates/admin/library/browse_libraries.mako
+1 -1
View File
@@ -42,7 +42,7 @@
<tbody>
%for library in libraries:
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
<td><a href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, deleted=deleted, show_deleted=show_deleted )}">${library.name}</a></td>
<td><a href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library.id, deleted=deleted, show_deleted=show_deleted )}">${library.name}</a></td>
<td><i>${library.description}</i></td>
</tr>
%endfor
templates/admin/library/browse_library.mako
+19 -21
View File
@@ -4,7 +4,7 @@
<%
from time import strftime
from galaxy import util
from galaxy.web.controllers.library import active_folders_and_lddas, activatable_folders_and_lddas
from galaxy.web.controllers.library_common import active_folders_and_lddas, activatable_folders_and_lddas
%>
<%def name="stylesheets()">
@@ -128,18 +128,16 @@
<input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
%endif
<span class="libraryItemDeleted-${ldda.deleted}">
<a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a>
<a href="${h.url_for( controller='library_admin', action='ldda_display_info', library_id=library.id, folder_id=folder.id, obj_id=ldda.id, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a>
</span>
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
%if not library.deleted and not folder.deleted and not library_dataset.deleted:
<div popupmenu="dataset-${ldda.id}-popup">
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='ldda_edit_info', library_id=library.id, folder_id=folder.id, obj_id=ldda.id )}">Edit this dataset's information</a>
<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="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', 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>
@@ -186,18 +184,18 @@
%endif
%if not folder.deleted:
<div popupmenu="folder-${folder.id}-popup">
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, obj_id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', information=True, obj_id=folder.id, library_id=library_id )}">Edit this folder's information</a>
## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition
##%if folder.info_association:
## <% form_id = folder.info_association[0].template.id %>
## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this folder's information template</a>
##%else:
%if not folder.info_association:
<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, folder_id=folder.id, add=True )}">Add an information template to this folder</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library_admin', library_id=library.id, response_action='folder', folder_id=folder.id )}">Add an information template to this folder</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', permissions=True, obj_id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
<a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a>
</div>
%elif not deleted and folder.deleted and not folder.purged:
@@ -246,10 +244,10 @@
<ul class="manage-table-actions">
%if not deleted:
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a>
</li>
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a>
</li>
%endif
</ul>
@@ -274,21 +272,21 @@
<a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="library-${library.id}-popup">
%if not deleted:
<a class="action-button" href="${h.url_for( controller='library_admin', action='library', id=library.id, information=True )}">Edit this data library's information</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library', obj_id=library.id, information=True )}">Edit this data library's information</a>
## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition
##%if library.info_association:
## <% form_id = library.info_association[0].template.id %>
## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this data library's information template</a>
##%else:
%if not library.info_association:
<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library_admin', library_id=library.id, response_action='browse_library' )}">Add an information template to this data library</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_admin', action='library', id=library.id, permissions=True )}">Edit this data library's permissions</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library', obj_id=library.id, permissions=True )}">Edit this data library's permissions</a>
<a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this data library and its contents</a>
%if show_deleted:
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted data library items</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library.id, show_deleted=False )}">Hide deleted data library items</a>
%else:
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted data library items</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library.id, show_deleted=True )}">Show deleted data library items</a>
%endif
%elif not library.purged:
<a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this data library</a>
@@ -310,7 +308,7 @@
<p>
<b>Perform action on selected datasets:</b>
<select name="action" id="action_on_datasets_select">
<option value="edit">Edit selected datasets' permissions</option>
<option value="manage_permissions">Edit selected datasets' permissions</option>
<option value="delete">Delete selected datasets</option>
</select>
<input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/>
templates/admin/library/common.mako
+2 -2
View File
@@ -1,5 +1,5 @@
<%def name="render_template_info( library_item, library_id, widgets, editable=True )">
<%def name="render_template_info( library_item, library_id, response_action, widgets, editable=True )">
<%
library_item_type = 'unknown type'
library_item_desc = ''
@@ -22,7 +22,7 @@
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
<div class="toolFormBody">
%if editable:
<form name="edit_info" action="${h.url_for( controller='library_admin', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post">
<form name="edit_info" action="${h.url_for( controller='library_common', action='edit_template_info', cntrller='library_admin', library_id=library_id, response_action=response_action, num_widgets=len( widgets ) )}" method="post">
<input type="hidden" name="library_item_id" value="${library_item.id}"/>
<input type="hidden" name="library_item_type" value="${library_item_type}"/>
%for i, field in enumerate( widgets ):
templates/admin/library/folder_info.mako
+3 -3
View File
@@ -5,7 +5,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -16,7 +16,7 @@
<div class="toolForm">
<div class="toolFormTitle">Edit folder name and description</div>
<div class="toolFormBody">
<form name="folder" action="${h.url_for( controller='library_admin', action='folder', information=True, id=folder.id, library_id=library_id )}" method="post" >
<form name="folder" action="${h.url_for( controller='library_admin', action='folder', information=True, obj_id=folder.id, library_id=library_id )}" method="post" >
<div class="form-row">
<label>Name:</label>
<input type="text" name="name" value="${folder.name}" size="40"/>
@@ -35,5 +35,5 @@
</div>
%if widgets:
${render_template_info( folder, library_id, widgets )}
${render_template_info( folder, library_id, 'folder', widgets )}
%endif
templates/admin/library/folder_permissions.mako
+2 -2
View File
@@ -5,7 +5,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -17,4 +17,4 @@
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
%>
${render_permission_form( folder, folder.name, h.url_for( controller='library_admin', action='folder', id=folder.id, library_id=library_id, permissions=True ), roles )}
${render_permission_form( folder, folder.name, h.url_for( controller='library_admin', action='folder', obj_id=folder.id, library_id=library_id, permissions=True ), roles )}
templates/admin/library/ldda_edit_info.mako
+11 -11
View File
@@ -12,7 +12,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -20,9 +20,9 @@
${render_msg( msg, messagetype )}
%endif
<%def name="datatype( ldda, datatypes )">
<%def name="datatype( ldda, file_formats )">
<select name="datatype">
%for ext in datatypes:
%for ext in file_formats:
%if ldda.ext == ext:
<option value="${ext}" selected="yes">${ext}</option>
%else:
@@ -35,8 +35,8 @@
<div class="toolForm">
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
<div class="toolFormBody">
<form name="edit_attributes" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<input type="hidden" name="id" value="${ldda.id}"/>
<form name="edit_attributes" action="${h.url_for( controller='library_admin', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<input type="hidden" name="obj_id" value="${ldda.id}"/>
<br/>
<div class="form-row">
<label>Name:</label>
@@ -73,9 +73,9 @@
<input type="submit" name="save" value="Save"/>
</div>
</form>
<form name="auto_detect" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<form name="auto_detect" action="${h.url_for( controller='library_admin', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<div class="form-row">
<input type="hidden" name="id" value="${ldda.id}"/>
<input type="hidden" name="obj_id" value="${ldda.id}"/>
<input type="submit" name="detect" value="Auto-detect"/>
<div class="toolParamHelp" style="clear: both;">
This will inspect the dataset and attempt to correct the above column values if they are not accurate.
@@ -89,11 +89,11 @@
<div class="toolFormTitle">Change data type of ${ldda.name}</div>
<div class="toolFormBody">
%if ldda.datatype.allow_datatype_change:
<form name="change_datatype" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<input type="hidden" name="id" value="${ldda.id}"/>
<form name="change_datatype" action="${h.url_for( controller='library_admin', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<input type="hidden" name="obj_id" value="${ldda.id}"/>
<div class="form-row">
<label>New Type:</label>
${datatype( ldda, datatypes )}
${datatype( ldda, file_formats )}
<div class="toolParamHelp" style="clear: both;">
This will change the datatype of the existing dataset
but <i>not</i> modify its contents. Use this if Galaxy
@@ -114,5 +114,5 @@
</div>
%if widgets:
${render_template_info( ldda, library_id, widgets )}
${render_template_info( ldda, library_id, 'ldda_edit_info', widgets )}
%endif
templates/admin/library/ldda_info.mako
+9 -11
View File
@@ -20,7 +20,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -41,18 +41,16 @@
%if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted:
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="dataset-${ldda.id}-popup">
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id, obj_id=ldda.id )}">Edit this dataset's information</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='ldda_manage_permissions', library_id=library_id, folder_id=ldda.library_dataset.folder.id, obj_id=ldda.id )}">Edit this dataset's permissions</a>
%if current_version:
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
<a class="action-button" href="${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="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', 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.deleted:
<a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Delete this dataset</a>
%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>
%endif
</div>
%endif
@@ -96,7 +94,7 @@
%endif
</div>
%if widgets:
${render_template_info( ldda, library.id, widgets, editable=False )}
${render_template_info( ldda, library.id, 'ldda_display_info', widgets, editable=False )}
%endif
%if current_version:
<% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
@@ -104,7 +102,7 @@
<div class="toolFormTitle">Expired versions of ${ldda.name}</div>
%for expired_ldda in expired_lddas:
<div class="form-row">
<a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a>
<a href="${h.url_for( controller='library_admin', action='ldda_display_info', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, obj_id=expired_ldda.id )}">${expired_ldda.name}</a>
</div>
%endfor
%endif
templates/admin/library/ldda_permissions.mako
+4 -4
View File
@@ -5,17 +5,17 @@
<%
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
lddas = util.listify( ldda )
if len( lddas ) > 1:
name_str = '%d selected datasets' % len( lddas )
else:
ldda = lddas[0]
name_str = ldda.name
%>
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -35,7 +35,7 @@
<a id="ldda-${ldd_assoc.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
</div>
<div popupmenu="ldd_assoc-${ldd_assoc.id}-popup">
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset', id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset', obj_id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a>
</div>
</td>
<td>
@@ -59,4 +59,4 @@
%endif
<% ldda_ids = ",".join( [ str( d.id ) for d in lddas ] ) %>
${render_permission_form( lddas[0], name_str, h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, id=ldda_ids, permissions=True ), roles )}
${render_permission_form( lddas[0], name_str, h.url_for( controller='library_admin', action='ldda_manage_permissions', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, obj_id=ldda_ids ), roles )}
templates/admin/library/library_dataset_info.mako
+3 -3
View File
@@ -11,7 +11,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -23,7 +23,7 @@
<div class="toolFormTitle">Edit attributes of ${library_dataset.name}</div>
<div class="toolFormBody">
<form name="edit_attributes" action="${h.url_for( controller='library_admin', action='library_dataset' )}" method="post">
<input type="hidden" name="id" value="${library_dataset.id}"/>
<input type="hidden" name="obj_id" value="${library_dataset.id}"/>
<div class="form-row">
<label>Name:</label>
<div style="float: left; width: 250px; margin-right: 10px;">
@@ -46,5 +46,5 @@
</div>
%if widgets:
${render_template_info( library_dataset, library.id, widgets )}
${render_template_info( library_dataset, library.id, '', widgets )}
%endif
templates/admin/library/library_dataset_permissions.mako
+2 -2
View File
@@ -11,7 +11,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -23,4 +23,4 @@
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
%>
${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='library_admin', action='library_dataset', id=library_dataset.id, library_id=library_id, permissions=True ), roles )}
${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='library_admin', action='library_dataset', obj_id=library_dataset.id, library_id=library_id, permissions=True ), roles )}
templates/admin/library/library_info.mako
+3 -3
View File
@@ -5,7 +5,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library.id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -16,7 +16,7 @@
<div class="toolForm">
<div class="toolFormTitle">Change library name and description</div>
<div class="toolFormBody">
<form name="library" action="${h.url_for( controller='library_admin', action='library', information=True, id=library.id )}" method="post" >
<form name="library" action="${h.url_for( controller='library_admin', action='library', information=True, obj_id=library.id )}" method="post" >
<div class="form-row">
<label>Name:</label>
<div style="float: left; width: 250px; margin-right: 10px;">
@@ -44,5 +44,5 @@
%>
%if widgets:
${render_template_info( library, library.id, widgets )}
${render_template_info( library, library.id, 'library', widgets )}
%endif
templates/admin/library/library_permissions.mako
+2 -2
View File
@@ -5,7 +5,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library.id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -16,4 +16,4 @@
<%
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
%>
${render_permission_form( library, library.name, h.url_for( conroller='admin', action='library', id=library.id, permissions=True ), roles )}
${render_permission_form( library, library.name, h.url_for( conroller='admin', action='library', obj_id=library.id, permissions=True ), roles )}
templates/admin/library/new_folder.mako
+2 -2
View File
@@ -4,7 +4,7 @@
<br/<br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -15,7 +15,7 @@
<div class="toolForm">
<div class="toolFormTitle">Create a new folder</div>
<div class="toolFormBody">
<form name="folder" action="${h.url_for( controller='library_admin', action='folder', id=folder.id, library_id=library_id )}" method="post" >
<form name="folder" action="${h.url_for( controller='library_admin', action='folder', obj_id=folder.id, library_id=library_id )}" method="post" >
<div class="form-row">
<label>Name:</label>
<div style="float: left; width: 250px; margin-right: 10px;">
templates/admin/library/select_info_template.mako
+5 -2
View File
@@ -4,7 +4,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -14,16 +14,19 @@
<div class="toolForm">
<div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div>
<form name="new_info_template" action="${h.url_for( controller='library_admin', action='info_template', add=True )}" method="post" >
<form name="new_info_template" action="${h.url_for( controller='library_common', action='info_template', cntrller='library_admin' )}" method="post" >
<div class="toolFormBody">
<div class="form-row">
<input type="hidden" name="library_id" value="${library_id}"/>
%if library_dataset_id:
<input type="hidden" name="library_dataset_id" value="${library_dataset_id}"/>
<input type="hidden" name="response_action" value="ldda_edit_info"/>
%elif folder_id:
<input type="hidden" name="folder_id" value="${folder_id}"/>
<input type="hidden" name="response_action" value="folder"/>
%elif ldda_id:
<input type="hidden" name="ldda_id" value="${ldda_id}"/>
<input type="hidden" name="response_action" value="ldda_edit_info"/>
%endif
<label>Template:</label>
<select name="form_id">
templates/admin/library/upload.mako
+5 -6
View File
@@ -1,6 +1,5 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/admin/library/common.mako" import="render_template_info" />
<%namespace file="/library/library_dataset_common.mako" import="render_upload_form" />
<% import os, os.path %>
@@ -15,16 +14,16 @@
<b>Create new data library datasets</b>
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="upload-librarydataset--popup">
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=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="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
%endif
<a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
</div>
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -32,4 +31,4 @@
${render_msg( msg, messagetype )}
%endif
${render_upload_form( 'library_admin', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
${render_upload_form( 'library_admin', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )}
templates/admin/requests/show_request.mako
+1 -1
View File
@@ -102,7 +102,7 @@
<i>None</i>
%else:
%if rd['label'] == 'Data library':
<a href="${h.url_for( controller='library_admin', action='browse_library', id=request.library.id )}">${rd['value']}</a>
<a href="${h.url_for( controller='library_admin', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
%else:
${rd['value']}
%endif
templates/base_panels.mako
+2 -2
View File
@@ -114,9 +114,9 @@
if ( $(this).find("input[name='folder_id']").val() != undefined ) {
var library_id = $(this).find("input[name='library_id']").val();
if ( location.pathname.indexOf( 'library_admin' ) ) {
$("iframe#galaxy_main").attr("src","${h.url_for(controller='library_admin', action='browse_library' )}?id=" + library_id + "&created_ldda_ids=" + async_datasets);
$("iframe#galaxy_main").attr("src","${h.url_for( controller='library_admin', action='browse_library' )}?obj_id=" + library_id + "&created_ldda_ids=" + async_datasets);
} else {
$("iframe#galaxy_main").attr("src","${h.url_for(controller='library', action='browse_library' )}?id=" + library_id + "&created_ldda_ids=" + async_datasets);
$("iframe#galaxy_main").attr("src","${h.url_for( controller='library', action='browse_library' )}?obj_id=" + library_id + "&created_ldda_ids=" + async_datasets);
}
} else {
$("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}");
templates/library/browse_libraries.mako
+1 -1
View File
@@ -22,7 +22,7 @@
<tbody>
%for library, hidden_folder_ids in libraries.items():
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
<td><a href="${h.url_for( controller='library', action='browse_library', id=library.id, hidden_folder_ids=hidden_folder_ids )}">${library.name}</a></td>
<td><a href="${h.url_for( controller='library', action='browse_library', obj_id=library.id, hidden_folder_ids=hidden_folder_ids )}">${library.name}</a></td>
<td><i>${library.description}</i></td>
</tr>
%endfor
templates/library/browse_library.mako
+19 -19
View File
@@ -3,7 +3,7 @@
<%namespace file="/library/library_item_info.mako" import="render_library_item_info" />
<%
from galaxy import util
from galaxy.web.controllers.library import active_folders
from galaxy.web.controllers.library_common import active_folders
from time import strftime
user, roles = trans.get_user_and_roles()
%>
@@ -162,23 +162,23 @@ class RowCounter( object ):
%else:
<input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
%endif
<a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a>
<a href="${h.url_for( controller='library', action='ldda_display_info', library_id=library.id, folder_id=folder.id, obj_id=ldda.id )}"><b>${ldda.name[:50]}</b></a>
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="dataset-${ldda.id}-popup">
%if can_modify_library_dataset:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_edit_info', library_id=library.id, folder_id=folder.id, obj_id=ldda.id )}">Edit this dataset's information</a>
%else:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_display_info', library_id=library.id, folder_id=folder.id, obj_id=ldda.id, information=True )}">View this dataset's information</a>
%endif
%if can_manage_library_dataset:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_manage_permissions', library_id=library.id, folder_id=folder.id, obj_id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
%endif
%if can_modify_library_dataset:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
<a class="action-button" href="${h.url_for( controller='library', 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>
%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', id=ldda.id, library_id=library.id )}">Download this dataset</a>
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a>
%endif
</div>
</td>
@@ -237,19 +237,19 @@ class RowCounter( object ):
<a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="folder_img-${folder.id}-popup">
%if can_add:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, obj_id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
%endif
%if can_modify:
<a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, obj_id=folder.id, library_id=library_id )}">Edit this folder's information</a>
%else:
<a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, obj_id=folder.id, library_id=library_id )}">View this folder's information</a>
%endif
%if can_add and forms and not folder.info_association:
<a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this folder</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library', library_id=library.id, response_action='folder', folder_id=folder.id )}">Add an information template to this folder</a>
%endif
%if can_manage:
<a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, obj_id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
%endif
</div>
</div>
@@ -287,22 +287,22 @@ class RowCounter( object ):
<ul class="manage-table-actions">
%if can_add:
<li>
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a>
</li>
<li>
<a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a>
<a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a>
</li>
%endif
%if can_modify:
<li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a></li>
<li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">Edit this data library's information</a></li>
%else:
<li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li>
<li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">View this data library's information</a></li>
%endif
%if can_add and forms and not library.info_association:
<a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library', library_id=library.id, response_action='browse_library' )}">Add an information template to this data library</a>
%endif
%if can_manage:
<li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li>
<li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, obj_id=library.id )}">Edit this data library's permissions</a></li>
%endif
</ul>
templates/library/common.mako
+2 -2
View File
@@ -1,4 +1,4 @@
<%def name="render_template_info( library_item, library_id, widgets, editable=True )">
<%def name="render_template_info( library_item, library_id, response_action, widgets, editable=True )">
<%
library_item_type = 'unknown type'
library_item_desc = ''
@@ -22,7 +22,7 @@
<div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
<div class="toolFormBody">
%if editable and trans.app.security_agent.can_modify_library_item( user, roles, library_item ):
<form name="edit_info" action="${h.url_for( controller='library', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post">
<form name="edit_info" action="${h.url_for( controller='library_common', action='edit_template_info', cntrller='library', library_id=library_id, response_action=response_action, num_widgets=len( widgets ) )}" method="post">
<input type="hidden" name="library_item_id" value="${library_item.id}"/>
<input type="hidden" name="library_item_type" value="${library_item_type}"/>
%for i, field in enumerate( widgets ):
templates/library/folder_info.mako
+3 -3
View File
@@ -7,7 +7,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -19,7 +19,7 @@
<div class="toolFormTitle">Edit folder name and description</div>
<div class="toolFormBody">
%if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
<form name="folder" action="${h.url_for( controller='library', action='folder', rename=True, id=folder.id, library_id=library_id )}" method="post" >
<form name="folder" action="${h.url_for( controller='library', action='folder', rename=True, obj_id=folder.id, library_id=library_id )}" method="post" >
<div class="form-row">
<label>Name:</label>
<input type="text" name="name" value="${folder.name}" size="40"/>
@@ -49,5 +49,5 @@
</div>
</div>
%if widgets:
${render_template_info( folder, library_id, widgets )}
${render_template_info( folder, library_id, 'folder', widgets )}
%endif
templates/library/folder_permissions.mako
+2 -2
View File
@@ -7,7 +7,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -16,5 +16,5 @@
%endif
%if trans.app.security_agent.can_manage_library_item( user, roles, folder ):
${render_permission_form( folder, folder.name, h.url_for( controller='library', action='folder', id=folder.id, library_id=library_id, permissions=True ), trans.user.all_roles() )}
${render_permission_form( folder, folder.name, h.url_for( controller='library', action='folder', obj_id=folder.id, library_id=library_id, permissions=True ), trans.user.all_roles() )}
%endif
templates/library/ldda_edit_info.mako
+9 -9
View File
@@ -14,7 +14,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -22,9 +22,9 @@
${render_msg( msg, messagetype )}
%endif
<%def name="datatype( ldda, datatypes )">
<%def name="datatype( ldda, file_formats )">
<select name="datatype">
%for ext in datatypes:
%for ext in file_formats:
%if ldda.ext == ext:
<option value="${ext}" selected="yes">${ext}</option>
%else:
@@ -38,8 +38,8 @@
<div class="toolForm">
<div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
<div class="toolFormBody">
<form name="edit_attributes" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<input type="hidden" name="id" value="${ldda.id}"/>
<form name="edit_attributes" action="${h.url_for( controller='library', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<input type="hidden" name="obj_id" value="${ldda.id}"/>
<div class="form-row">
<label>Name:</label>
<input type="text" name="name" value="${ldda.name}" size="40"/>
@@ -75,7 +75,7 @@
<input type="submit" name="save" value="Save"/>
</div>
</form>
<form name="auto_detect" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<form name="auto_detect" action="${h.url_for( controller='library', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<div class="form-row">
<input type="hidden" name="id" value="${ldda.id}"/>
<input type="submit" name="detect" value="Auto-detect"/>
@@ -91,11 +91,11 @@
<div class="toolFormTitle">Change data type</div>
<div class="toolFormBody">
%if ldda.datatype.allow_datatype_change:
<form name="change_datatype" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post">
<form name="change_datatype" action="${h.url_for( controller='library', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id )}" method="post">
<input type="hidden" name="id" value="${ldda.id}"/>
<div class="form-row">
<label>New Type:</label>
${datatype( ldda, datatypes )}
${datatype( ldda, file_formats )}
<div class="toolParamHelp" style="clear: both;">
This will change the datatype of the existing dataset
but <i>not</i> modify its contents. Use this if Galaxy
@@ -147,5 +147,5 @@
</div>
%endif
%if widgets:
${render_template_info( ldda, library_id, widgets )}
${render_template_info( ldda, library_id, 'ldda_edit_info', widgets )}
%endif
templates/library/ldda_info.mako
+8 -8
View File
@@ -20,7 +20,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -41,19 +41,19 @@
<a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="dataset-${ldda.id}-popup">
%if trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ):
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_edit_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id, obj_id=ldda.id )}">Edit this dataset's information</a>
%else:
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_display_info', library_id=library_id, folder_id=ldda.library_dataset.folder.id, obj_id=ldda.id )}">View this dataset's information</a>
%endif
%if trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ) and trans.app.security_agent.can_manage_library_item( user, roles, ldda.library_dataset ):
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
<a class="action-button" href="${h.url_for( controller='library', action='ldda_manage_permissions', library_id=library_id, folder_id=ldda.library_dataset.folder.id, obj_id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
%endif
%if current_version and trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ):
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', 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>
<a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
%endif
%if ldda.has_data:
<a class="action-button" href="${h.url_for( controller='library', 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="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a>
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a>
%endif
</div>
</div>
@@ -96,7 +96,7 @@
%endif
</div>
%if widgets:
${render_template_info( ldda, library_id, widgets, editable=False )}
${render_template_info( ldda, library_id, 'ldda_display_info', widgets, editable=False )}
%endif
%if current_version:
<% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %>
@@ -104,7 +104,7 @@
<div class="toolFormTitle">Expired versions of ${ldda.name}</div>
%for expired_ldda in expired_lddas:
<div class="form-row">
<a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a>
<a href="${h.url_for( controller='library', action='ldda_display_info', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, obj_id=expired_ldda.id )}">${expired_ldda.name}</a>
</div>
%endfor
%endif
templates/library/ldda_permissions.mako
+3 -3
View File
@@ -15,7 +15,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -35,7 +35,7 @@
<a id="ldda-${ldd_assoc.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
</div>
<div popupmenu="ldd_assoc-${ldd_assoc.id}-popup">
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset', id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a>
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset', obj_id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a>
</div>
</td>
<td>
@@ -59,4 +59,4 @@
%endif
<% ldda_ids = ",".join( [ str( d.id ) for d in lddas ] ) %>
${render_permission_form( lddas[0], name_str, h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, id=ldda_ids, permissions=True ), roles )}
${render_permission_form( lddas[0], name_str, h.url_for( controller='library', action='ldda_manage_permissions', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, obj_id=ldda_ids ), roles )}
templates/library/library_dataset_common.mako
+2 -2
View File
@@ -17,7 +17,7 @@
%if replace_dataset not in [ None, 'None' ]:
<input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
<div class="form-row">
You are currently selecting a new file to replace '<a href="${h.url_for( controller=controller, action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
You are currently selecting a new file to replace '<a href="${h.url_for( controller=controller, action='ldda_display_info', library_id=library_id, folder_id=folder_id, obj_id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
<div style="clear: both"></div>
</div>
%endif
@@ -194,7 +194,7 @@
%if replace_dataset not in [ None, 'None' ]:
<input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
<div class="form-row">
You are currently selecting a new file to replace '<a href="${h.url_for( controller=controller, action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
You are currently selecting a new file to replace '<a href="${h.url_for( controller=controller, action='ldda_display_info', library_id=library_id, folder_id=folder_id, obj_id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
<div style="clear: both"></div>
</div>
%endif
templates/library/library_dataset_info.mako
+3 -3
View File
@@ -13,7 +13,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -25,7 +25,7 @@
<div class="toolForm">
<div class="toolFormTitle">Edit attributes of ${library_dataset.name}</div>
<div class="toolFormBody">
<form name="edit_attributes" action="${h.url_for( controller='library', action='library_dataset', id=library_dataset.id, library_id=library_id, information=True )}" method="post">
<form name="edit_attributes" action="${h.url_for( controller='library', action='library_dataset', obj_id=library_dataset.id, library_id=library_id, information=True )}" method="post">
<div class="form-row">
<label>Name:</label>
<div style="float: left; width: 250px; margin-right: 10px;">
@@ -64,5 +64,5 @@
%endif
%if widgets:
${render_template_info( library_dataset, library_id, widgets )}
${render_template_info( library_dataset, library_id, '', widgets )}
%endif
templates/library/library_dataset_permissions.mako
+2 -2
View File
@@ -13,7 +13,7 @@
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -25,5 +25,5 @@
<%
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
%>
${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='library', action='library_dataset', id=library_dataset.id, library_id=library_id, permissions=True ), roles )}
${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='library', action='library_dataset', obj_id=library_dataset.id, library_id=library_id, permissions=True ), roles )}
%endif
templates/library/library_info.mako
+3 -3
View File
@@ -7,7 +7,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library.id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -36,7 +36,7 @@
</div>
<div class="form-row">
<div style="float: left; width: 250px; margin-right: 10px;">
<input type="hidden" name="id" value="${library.id}"/>
<input type="hidden" name="obj_id" value="${library.id}"/>
</div>
<div style="clear: both"></div>
</div>
@@ -60,5 +60,5 @@
%endif
%if widgets:
${render_template_info( library, library.id, widgets )}
${render_template_info( library, library.id, 'library', widgets )}
%endif
templates/library/library_permissions.mako
+2 -2
View File
@@ -7,7 +7,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library.id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library.id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -19,5 +19,5 @@
<%
roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
%>
${render_permission_form( library, library.name, h.url_for( controller='library', action='library', id=library.id, permissions=True ), roles )}
${render_permission_form( library, library.name, h.url_for( controller='library', action='library', obj_id=library.id, permissions=True ), roles )}
%endif
templates/library/new_folder.mako
+2 -2
View File
@@ -4,7 +4,7 @@
<br/<br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -15,7 +15,7 @@
<div class="toolForm">
<div class="toolFormTitle">Create a new folder</div>
<div class="toolFormBody">
<form name="folder" action="${h.url_for( controller='library', action='folder', id=folder.id, library_id=library_id )}" method="post" >
<form name="folder" action="${h.url_for( controller='library', action='folder', obj_id=folder.id, library_id=library_id )}" method="post" >
<div class="form-row">
<label>Name:</label>
<div style="float: left; width: 250px; margin-right: 10px;">
templates/library/select_info_template.mako
+5 -2
View File
@@ -4,7 +4,7 @@
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -14,16 +14,19 @@
<div class="toolForm">
<div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div>
<form name="new_info_template" action="${h.url_for( controller='library', action='info_template', add=True )}" method="post" >
<form name="new_info_template" action="${h.url_for( controller='library_common', action='info_template', cntrller='library' )}" method="post" >
<div class="toolFormBody">
<div class="form-row">
<input type="hidden" name="library_id" value="${library_id}"/>
%if library_dataset_id:
<input type="hidden" name="library_dataset_id" value="${library_dataset_id}"/>
<input type="hidden" name="response_action" value="ldda_edit_info"/>
%elif folder_id:
<input type="hidden" name="folder_id" value="${folder_id}"/>
<input type="hidden" name="response_action" value="folder"/>
%elif ldda_id:
<input type="hidden" name="ldda_id" value="${ldda_id}"/>
<input type="hidden" name="response_action" value="ldda_edit_info"/>
%endif
<label>Template:</label>
<select name="form_id">
templates/library/upload.mako
+5 -6
View File
@@ -1,6 +1,5 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/admin/library/common.mako" import="render_template_info" />
<%namespace file="/library/library_dataset_common.mako" import="render_upload_form" />
<% import os, os.path %>
@@ -15,16 +14,16 @@
<b>Create new data library datasets</b>
<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">&#9660;</a>
<div popupmenu="upload-librarydataset--popup">
<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
<a class="action-button" href="${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="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
<a class="action-button" href="${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="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
<a class="action-button" href="${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>
<br/><br/>
<ul class="manage-table-actions">
<li>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', id=library_id )}"><span>Browse this data library</span></a>
<a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a>
</li>
</ul>
@@ -32,4 +31,4 @@
${render_msg( msg, messagetype )}
%endif
${render_upload_form( 'library', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
${render_upload_form( 'library', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )}
templates/mobile/manage_library.mako
+3 -3
View File
@@ -30,7 +30,7 @@
</div>
<div class="form-row">
<div style="float: left; width: 250px; margin-right: 10px;">
<input type="hidden" name="id" value="${library.id}"/>
<input type="hidden" name="obj_id" value="${library.id}"/>
</div>
<div style="clear: both"></div>
</div>
@@ -51,7 +51,7 @@
</div>
</div>
<div class="toolForm">
${render_template_info( library, library.id )}
${render_template_info( library, library.id, 'library' )}
</div>
</div>
%endif
@@ -63,5 +63,5 @@
%endif
%if widgets:
${render_template_info( library, library_id, widgets )}
${render_template_info( library, library_id, 'library', widgets )}
%endif
templates/requests/show_request.mako
+1 -1
View File
@@ -104,7 +104,7 @@
%else:
%if rd['label'] == 'Data library':
%if rd['value']:
<a href="${h.url_for( controller='library', action='browse_library', id=request.library.id )}">${rd['value']}</a>
<a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
%else:
<i>None</i>
%endif
test/base/twilltestcase.py
+26 -26
View File
@@ -1145,7 +1145,7 @@ class TwillTestCase( unittest.TestCase ):
tc.submit( "create_library_button" )
self.home()
def set_library_permissions( self, library_id, library_name, role_id, permissions_in, permissions_out ):
url = "library_admin/library?id=%s&permissions=True&update_roles_button=Save" % ( library_id )
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 ) )
@@ -1160,44 +1160,44 @@ class TwillTestCase( unittest.TestCase ):
def rename_library( self, library_id, old_name, name='Library One Renamed', description='This is Library One Re-described' ):
"""Rename a library"""
self.home()
self.visit_url( "%s/library_admin/library?information=True&id=%s" % ( self.url, library_id ) )
self.visit_url( "%s/library_admin/library?obj_id=%s&information=True" % ( self.url, library_id ) )
self.check_page_for_string( 'Change library name and description' )
# Since twill barfs on the form submisson, we ar forced to simulate it
url = "%s/library_admin/library?information=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \
url = "%s/library_admin/library?obj_id=%s&information=True&rename_library_button=Save&description=%s&name=%s" % \
( self.url, library_id, description.replace( ' ', '+' ), name.replace( ' ', '+' ) )
self.home()
self.visit_url( url )
check_str = "Library '%s' has been renamed to '%s'" % ( old_name, name )
self.check_page_for_string( check_str )
self.home()
def add_library_info_template( self, library_id, library_name, form_id, form_name ):
def add_library_info_template( self, cntrller, library_id, library_name, form_id, form_name ):
"""Add a new info template to a library"""
self.home()
url = "%s/library_admin/info_template?library_id=%s&add=True" % ( self.url, library_id )
url = "%s/library_common/info_template?cntrller=%s&library_id=%s&response_action='browse_library'" % ( self.url, cntrller, library_id )
self.visit_url( url )
self.check_page_for_string ( "Select a form on which to base the template" )
tc.fv( '1', 'library_id', library_id )
tc.submit( 'add_info_template_button' )
self.check_page_for_string = 'An information template based on the form "%s" has been added to this library.' % form_name
self.check_page_for_string = 'An information template based on the form "%s" has been added to this data library.' % form_name
self.home()
def edit_library_info( self, library_id, library_name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents ):
"""Add information to a library using an existing template with 2 elements"""
self.home()
self.visit_url( "%s/library_admin/library?information=True&id=%s" % ( self.url, library_id ) )
self.visit_url( "%s/library_admin/library?obj_id=%s&information=True" % ( self.url, library_id ) )
check_str = 'Other information about library %s' % library_name
self.check_page_for_string( check_str )
tc.fv( '2', ele_1_field_name, ele_1_contents )
tc.fv( '2', ele_2_field_name, ele_2_contents )
tc.submit( 'create_new_info_button' )
self.home()
def edit_library_info_template( self, library_id, id, name, ele_name_1, name_1,
def edit_library_info_template( self, library_id, obj_id, name, ele_name_1, name_1,
ele_desc_1, desc_1, ele_name_2, name_2, ele_desc_2, desc_2 ):
"""Edit an existing library info template"""
self.home()
url = "%s/library_admin/info_template?library_id=%s&id=%s&edit_template=True" % ( self.url, library_id, id )
url = "%s/library_admin/edit_info_template?library_id=%s&obj_id=%s&response_action='browse_library'" % ( self.url, library_id, obj_id )
self.visit_url( url )
self.check_page_for_string ( 'Edit template' )
tc.fv( '1', 'id', id )
tc.fv( '1', 'obj_id', obj_id )
tc.fv( '1', 'set_num_fields', '0' )
tc.fv( '1', 'name', name )
tc.fv( '1', ele_name_1, name_1 )
@@ -1208,12 +1208,12 @@ class TwillTestCase( unittest.TestCase ):
check_str = "Information template '%s' has been updated" % name
self.check_page_for_string( check_str )
self.home()
def add_folder_info_template( self, library_id, library_name, folder_id, folder_name, num_fields='2',
def add_folder_info_template( self, cntrller, library_id, library_name, folder_id, folder_name, num_fields='2',
name='Folder Template 1', ele_name_0='Fu', ele_help_0='', ele_name_1='Bar', ele_help_1='' ):
"""Add a new info template to a folder"""
self.home()
url = "%s/library_admin/info_template?library_id=%s&folder_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % \
( self.url, library_id, folder_id )
url = "%s/library_admin/info_template?cntrller=%s&library_id=%s&response_action='folder'&create_info_template_button=Go" % \
( self.url, cntrller, library_id, folder_id )
self.home()
self.visit_url( url )
check_str = "Create a new information template for folder '%s'" % folder_name
@@ -1231,7 +1231,7 @@ class TwillTestCase( unittest.TestCase ):
def add_folder( self, library_id, folder_id, name='Folder One', description='This is Folder One' ):
"""Create a new folder"""
self.home()
self.visit_url( "%s/library_admin/folder?library_id=%s&id=%s&new=True" % ( self.url, library_id, folder_id ) )
self.visit_url( "%s/library_admin/folder?library_id=%s&obj_id=%s&new=True" % ( self.url, library_id, folder_id ) )
self.check_page_for_string( 'Create a new folder' )
tc.fv( "1", "name", name ) # form field 1 is the field named name...
tc.fv( "1", "description", description ) # form field 2 is the field named description...
@@ -1240,10 +1240,10 @@ class TwillTestCase( unittest.TestCase ):
def rename_folder( self, library_id, folder_id, old_name, name='Folder One Renamed', description='This is Folder One Re-described' ):
"""Rename a Folder"""
self.home()
self.visit_url( "%s/library_admin/folder?library_id=%s&manage=True&id=%s" % ( self.url, library_id, folder_id ) )
self.visit_url( "%s/library_admin/folder?library_id=%s&manage=True&obj_id=%s" % ( self.url, library_id, folder_id ) )
self.check_page_for_string( 'Edit folder name and description' )
# Since twill barfs on the form submisson, we ar forced to simulate it
url = "%s/library_admin/folder?library_id=%s&manage=True&id=%s&rename_folder_button=Save&description=%s&name=%s" % \
url = "%s/library_admin/folder?library_id=%s&manage=True&obj_id=%s&rename_folder_button=Save&description=%s&name=%s" % \
( self.url, library_id, folder_id, description.replace( ' ', '+' ), name.replace( ' ', '+' ) )
self.home()
self.visit_url( url )
@@ -1255,7 +1255,7 @@ class TwillTestCase( unittest.TestCase ):
"""Add a dataset to a folder"""
filename = self.get_filename( filename )
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \
self.visit_url( "%s/library_admin/upload_library_dataset?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \
( self.url, library_id, folder_id, message ) )
self.check_page_for_string( 'Upload files' )
tc.fv( "1", "folder_id", folder_id )
@@ -1277,7 +1277,7 @@ class TwillTestCase( unittest.TestCase ):
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 ):
url = "library_admin/library_dataset_dataset_association?library_id=%s&folder_id=%s&&id=%s&permissions=True&update_roles_button=Save" % \
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:
@@ -1289,7 +1289,7 @@ class TwillTestCase( unittest.TestCase ):
url ="%s&%s=%s" % ( url, key, str( role_id ) )
self.home()
self.visit_url( "%s/%s" % ( self.url, url ) )
check_str = "Permissions updated for dataset '%s'" % ldda_name
check_str = "Permissions have been updated on 1 datasets"
self.check_page_for_string( check_str )
self.home()
def edit_ldda_template_element_info( self, library_id, folder_id, ldda_id, ldda_name, ele_1_field_name,
@@ -1297,7 +1297,7 @@ class TwillTestCase( unittest.TestCase ):
ele_3_field_name='', ele_3_contents='', ele_3_help='' ):
"""Edit library_dataset_dataset_association template element information"""
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, library_id, folder_id, ldda_id ) )
check_str = 'Edit attributes of %s' % ldda_name
self.check_page_for_string( check_str )
@@ -1329,7 +1329,7 @@ class TwillTestCase( unittest.TestCase ):
def edit_ldda_attribute_info( self, library_id, folder_id, ldda_id, ldda_name, new_ldda_name ):
"""Edit library_dataset_dataset_association attribute information"""
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, library_id, folder_id, ldda_id ) )
check_str = 'Edit attributes of %s' % ldda_name
self.check_page_for_string( check_str )
@@ -1345,7 +1345,7 @@ class TwillTestCase( unittest.TestCase ):
"""Upload new version(s) of a dataset"""
self.home()
filename = self.get_filename( filename )
self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \
self.visit_url( "%s/library_admin/upload_library_dataset?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \
( self.url, library_id, folder_id, library_dataset_id, message ) )
self.check_page_for_string( 'Upload files' )
self.check_page_for_string( 'You are currently selecting a new file to replace' )
@@ -1378,7 +1378,7 @@ class TwillTestCase( unittest.TestCase ):
"""Add a directory of datasets to a folder"""
# roles is a list of tuples: [ ( role_id, role_description ) ]
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) )
self.visit_url( "%s/library_admin/upload_library_dataset?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) )
self.check_page_for_string( 'Upload a directory of files' )
tc.fv( "1", "folder_id", folder_id )
tc.fv( "1", "file_type", file_type )
@@ -1400,7 +1400,7 @@ class TwillTestCase( unittest.TestCase ):
"""Add a directory of datasets to a folder"""
# roles is a list of tuples: [ ( role_id, role_description ) ]
self.home()
self.visit_url( "%s/library/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % \
self.visit_url( "%s/library/upload_library_dataset?upload_option=upload_directory&library_id=%s&folder_id=%s" % \
( self.url, library_id, folder_id ) )
self.check_page_for_string( 'Upload a directory of files' )
tc.fv( "1", "folder_id", folder_id )
@@ -1445,7 +1445,7 @@ class TwillTestCase( unittest.TestCase ):
def purge_library( self, library_id, library_name ):
"""Purge a library"""
self.home()
self.visit_url( "%s/library_admin/purge_library?id=%s" % ( self.url, library_id ) )
self.visit_url( "%s/library_admin/purge_library?obj_id=%s" % ( self.url, library_id ) )
check_str = "Library '%s' and all of its contents have been purged" % library_name
self.check_page_for_string( check_str )
self.home()
@@ -1456,7 +1456,7 @@ class TwillTestCase( unittest.TestCase ):
self.home()
while count < maxiter:
count += 1
self.visit_url( "%s/%s/browse_library?id=%s" % ( self.url, controller, library_id ) )
self.visit_url( "%s/%s/browse_library?obj_id=%s" % ( self.url, controller, library_id ) )
page = tc.browser.get_html()
if page.find( '<!-- running: do not change this comment, used by TwillTestCase.library_wait -->' ) > -1:
time.sleep( sleep_amount )
test/functional/test_forms_and_requests.py
+1 -1
View File
@@ -162,7 +162,7 @@ class TestFormsAndRequests( TwillTestCase ):
galaxy.model.LibraryFolder.table.c.name==name ) ).first()
assert folder_one is not None, 'Problem retrieving library folder named "%s" from the database' % name
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( name )
# create address
#self.create_address( user_address1 )
test/functional/test_security_and_libraries.py
+92 -77
View File
@@ -30,7 +30,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
self.check_page_for_string( not_logged_in_security_msg )
self.visit_url( "%s/library_admin/library" % self.url )
self.check_page_for_string( not_logged_in_security_msg )
self.visit_url( "%s/library_admin/folder?id=1&new=True" % self.url )
self.visit_url( "%s/library_admin/folder?obj_id=1&new=True" % self.url )
self.check_page_for_string( not_logged_in_security_msg )
def test_005_login_as_admin_user( self ):
"""Testing logging in as an admin user test@bx.psu.edu - tests initial settings for DefaultUserPermissions and DefaultHistoryPermissions"""
@@ -494,7 +494,8 @@ class TestSecurityAndLibraries( TwillTestCase ):
assert form_one is not None, 'Problem retrieving form named (%s) from the database' % form_name
# Add a new information template to the library
template_name = 'Library Template 1'
self.add_library_info_template( str( library_one.id ),
self.add_library_info_template( 'library_admin',
str( library_one.id ),
library_one.name,
str( form_one.id ),
form_one.name )
@@ -510,14 +511,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
global form_one_field_name
form_one_field_name = 'field_0'
contents = '%s library contents' % form_one_field_label
self.visit_url( '%s/library_admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/library?obj_id=%s&information=True' % ( self.url, str( library_one.id ) ) )
# There are 2 forms on this page and the template is the 2nd form
tc.fv( '2', form_one_field_name, contents )
tc.submit( 'edit_info_button' )
# For some reason, the following check:
# self.check_page_for_string ( 'The information has been updated.' )
# ...throws the following exception - I have not idea why!
# self.check_page_for_string ( 'The information has been updated.' )
# TypeError: 'str' object is not callable
# The work-around is to not make ANY self.check_page_for_string() calls until the next method
def test_080_edit_template_contents_admin_view( self ):
@@ -525,7 +525,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# First make sure the templlate contents from the previous method were correctly saved
contents = '%s library contents' % form_one_field_label
contents_edited = contents + ' edited'
self.visit_url( '%s/library_admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/library?obj_id=%s&information=True' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( contents )
# Edit the contents and then save them
tc.fv( '2', form_one_field_name, contents_edited )
@@ -554,7 +554,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_one is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_one from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "1.bed" )
self.check_page_for_string( message )
self.check_page_for_string( admin_user.email )
@@ -576,14 +576,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
% ( ldda_one.dataset.id, dp.action ) )
# Make sure the library template contents were correctly saved
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) )
self.check_page_for_string( template_contents )
# Make sure other users can access the dataset from the Libraries view
self.logout()
self.login( email=regular_user2.email )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "1.bed" )
self.logout()
self.login( email=admin_user.email )
@@ -600,11 +600,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
galaxy.model.LibraryFolder.table.c.description==description ) ).first()
assert folder_one is not None, 'Problem retrieving library folder named "%s" from the database' % name
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( name )
self.check_page_for_string( description )
self.home()
self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
self.visit_url( '%s/library_admin/folder?obj_id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) )
# Make sure the template was inherited
self.check_page_for_string( form_one_field_name )
# Make sure the template contents were NOT inherited
@@ -632,11 +632,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
galaxy.model.LibraryFolder.table.c.description==description ) ).first()
assert subfolder_one is not None, 'Problem retrieving library folder named "Folder Ones Subfolder" from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( name )
self.check_page_for_string( description )
self.home()
self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) )
self.visit_url( '%s/library_admin/folder?obj_id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) )
# Make sure the template was inherited
self.check_page_for_string( form_one_field_name )
# Make sure the template contents were NOT inherited
@@ -665,11 +665,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
galaxy.model.LibraryFolder.table.c.description==description ) ).first()
assert folder_two is not None, 'Problem retrieving library folder named "%s" from the database' % name
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( name )
self.check_page_for_string( description )
self.home()
self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) )
self.visit_url( '%s/library_admin/folder?obj_id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) )
# Make sure the template was inherited
self.check_page_for_string( form_one_field_name )
# Make sure the template contents were NOT inherited
@@ -701,13 +701,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_two from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "2.bed" )
self.check_page_for_string( message )
self.check_page_for_string( admin_user.email )
# Make sure the library template contents were correctly saved
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) )
self.check_page_for_string( template_contents )
def test_110_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ):
@@ -732,13 +732,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_three is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_three from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "3.bed" )
self.check_page_for_string( message )
self.check_page_for_string( admin_user.email )
# Make sure the library template contents were correctly saved
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_three.id ) ) )
self.check_page_for_string( template_contents )
def test_115_add_dataset_with_private_role_restriction_to_folder( self ):
@@ -775,21 +775,21 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_four is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_four from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "4.bed" )
self.check_page_for_string( message )
self.check_page_for_string( admin_user.email )
self.home()
# Make sure the library template contents were correctly saved
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_four.id ) ) )
self.check_page_for_string( template_contents )
def test_120_accessing_dataset_with_private_role_restriction( self ):
"""Testing accessing a dataset with a private role restriction"""
# admin_user should not be able to see 2.bed from the analysis view's access libraries
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
try:
self.check_page_for_string( folder_one.name )
raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
@@ -807,7 +807,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# since it was associated with regular_user1's private role
self.login( email='test1@bx.psu.edu' )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( folder_one.name )
self.check_page_for_string( '4.bed' )
self.logout()
@@ -854,7 +854,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
role_ids, 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?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( ldda_four.name )
self.home()
def test_130_add_dataset_with_role_associated_with_group_and_users( self ):
@@ -882,28 +882,28 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_five is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_five from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "5.bed" )
self.check_page_for_string( message )
self.check_page_for_string( admin_user.email )
self.home()
# Make sure the library template contents were correctly saved
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_five.id ) ) )
self.check_page_for_string( template_contents )
def test_135_accessing_dataset_with_role_associated_with_group_and_users( self ):
"""Testing accessing a dataset with a role that is associated with a group and users"""
# admin_user should be able to see 5.bed since she is associated with role_two
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( "5.bed" )
self.check_page_for_string( admin_user.email )
self.logout()
# regular_user1 should be able to see 5.bed since she is associated with group_two
self.login( email = 'test1@bx.psu.edu' )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( folder_one.name )
self.check_page_for_string( '5.bed' )
self.check_page_for_string( admin_user.email )
@@ -920,7 +920,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# LIBRARY_MANAGE = Role One
# Role One aassociations: test@bx.psu.edu, test1@bx.psu.edu, test3@bx.psu.edu
self.home()
self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \
self.visit_url( '%s/library/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s' \
% ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_five.id ) ) )
self.check_page_for_string( '5.bed' )
self.check_page_for_string( 'This is the latest version of this library dataset' )
@@ -937,7 +937,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# regular_user2 should not be able to see 5.bed
self.login( email = 'test2@bx.psu.edu' )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
try:
self.check_page_for_string( folder_one.name )
raise AssertionError( '%s can see library folder %s when it contains only datasets restricted by role %s' \
@@ -954,7 +954,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# can access ) since she has Role One, and Role One has all library permissions ( see above ).
self.login( email = 'test3@bx.psu.edu' )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( folder_one.name )
# regular_user3 should not be able to see 5.bed since users must have every role associated
# with the dataset in order to access it, and regular_user3 isnot associated with Role Two
@@ -989,7 +989,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
assert ldda_six is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six from the database'
self.home()
# Make sure the correct template was inherited
self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \
self.visit_url( '%s/library/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s' \
% ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) )
self.check_page_for_string( form_one_field_name )
# Make sure the template contents were NOT inherited
@@ -1005,11 +1005,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
self.edit_ldda_attribute_info( str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ), ldda_six.name, new_ldda_name )
self.home()
ldda_six.refresh()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
self.check_page_for_string( ldda_six.name )
self.home()
# Make sure the template contents were NOT inherited
self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \
self.visit_url( '%s/library/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s' \
% ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) )
self.check_page_for_string( form_one_field_name )
contents = "%s contents for Folder One's Subfolder" % form_one_field_label
@@ -1019,7 +1019,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
except:
pass
def test_150_uploading_new_dataset_version( self ):
"""Testing uploading a new version of a dataset"""
"""Testing uploading a new version of a library dataset"""
message = 'Testing uploading a new version of a dataset'
# The form_one template should be inherited to the library dataset upload form.
template_contents = "%s contents for %s new version of 6.bed" % ( form_one_field_label, folder_one.name )
@@ -1039,7 +1039,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_six_version_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_two from the database'
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) )
self.check_page_for_string( 'This is the latest version of this library dataset' )
# Make sure the correct template was inherited
@@ -1069,21 +1069,19 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( 'ldda.dataset "%s" actions "%s" != ldda.dataset "%s" actions "%s"' \
% ( ldda_six.name, str( ldda_six.dataset.actions ), ldda_six_version_two.name, str( ldda_six_version_two.dataset.actions ) ) )
# Check the previous version
self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_display_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) )
self.check_page_for_string( 'This is an expired version of this library dataset' )
self.home()
# Make sure ldda_six is no longer displayed in the library
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
try:
self.check_page_for_string( ldda_six.name )
raise AssertionError, "Old version of library dataset %s is displayed in library" % ldda_six.name
except:
pass
self.home()
def test_155_uploading_new_dataset_versions( self ):
"""Testing uploading new versions of a dataset using a directory of files"""
message = 'Testing uploading new versions of a dataset using a directory of files'
message = 'Testing uploading a new version of a library dataset'
# The form_one template should be inherited to the library dataset upload form.
template_contents = "%s contents for %s 5th new version of 6.bed" % ( form_one_field_label, folder_one.name )
ldda_six_version_two.refresh()
@@ -1103,7 +1101,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_six_version_five is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_five from the database'
self.home()
self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_edit_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) )
self.check_page_for_string( 'This is the latest version of this library dataset' )
# Make sure the correct template was inherited
@@ -1120,13 +1118,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
tc.submit( 'edit_info_button' )
self.check_page_for_string( 'The information has been updated.' )
self.check_page_for_string( template_contents )
self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_display_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) )
check_str = 'Expired versions of %s' % ldda_six_version_five.name
self.check_page_for_string( check_str )
self.check_page_for_string( ldda_six.name )
self.home()
# Make sure th permissions are the same
# Make sure the permissions are the same
ldda_six.refresh()
if len( ldda_six.actions ) != len( ldda_six_version_five.actions ):
raise AssertionError( 'ldda "%s" actions "%s" != ldda "%s" actions "%s"' \
@@ -1139,11 +1137,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( 'ldda.dataset "%s" actions "%s" != ldda.dataset "%s" actions "%s"' \
% ( ldda_six.name, str( ldda_six.dataset.actions ), ldda_six_version_five.name, str( ldda_six_version_five.dataset.actions ) ) )
# Check the previous version
self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_admin/ldda_display_info?library_id=%s&folder_id=%s&obj_id=%s" % \
( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) )
self.check_page_for_string( 'This is an expired version of this library dataset' )
self.home()
def test_160_upload_directory_of_files_from_admin_view( self ):
def test_155_upload_directory_of_files_from_admin_view( self ):
"""Testing uploading a directory of files to a root folder from the Admin view"""
message = 'This is a test for uploading a directory of files'
template_contents = "%s contents for directory of 3 datasets in %s" % ( form_one_field_label, folder_one.name )
@@ -1156,11 +1154,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
template_field_name1=form_one_field_name,
template_field_contents1=template_contents )
self.home()
self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library_admin/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
self.check_page_for_string( admin_user.email )
self.check_page_for_string( message )
self.home()
def test_165_change_permissions_on_datasets_uploaded_from_library_dir( self ):
def test_160_change_permissions_on_datasets_uploaded_from_library_dir( self ):
"""Testing changing the permissions on datasets uploaded from a directory"""
# It would be nice if twill functioned such that the above test resulted in a
# form with the uploaded datasets selected, but it does not ( they're not checked ),
@@ -1176,7 +1174,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
def build_url( permissions, role ):
# We'll bypass the library_admin/datasets method and directly call the library_admin/dataset method, setting
# access, manage permissions, and edit metadata permissions to role_one
url = '/library_admin/library_dataset_dataset_association?permissions=True&id=%s&library_id=%s&folder_id=%s&update_roles_button=Save' % ( ldda_ids, str( library_one.id ), str( folder_one.id ) )
url = '/library_admin/ldda_manage_permissions?obj_id=%s&library_id=%s&folder_id=%s&update_roles_button=Save' % ( ldda_ids, str( library_one.id ), str( folder_one.id ) )
for p in permissions:
url += '&%s_in=%s' % ( p, str( role.id ) )
return url
@@ -1213,7 +1211,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# access to any of the 3 datasets, so she will not see folder_one on the libraries page
self.login( email='test2@bx.psu.edu' )
self.home()
self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) )
self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) )
try:
self.check_page_for_string( folder_one.name )
raise AssertionError( '%s can access folder %s even though all contained datasets should be restricted from access by her' \
@@ -1268,7 +1266,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
pass
check_edit_page2( latest_3_lddas )
self.home()
def test_170_upload_directory_of_files_from_libraries_view( self ):
def test_165_upload_directory_of_files_from_libraries_view( self ):
"""Testing uploading a directory of files to a root folder from the Data Libraries view"""
# admin_user will not have the option sto upload a directory of files from the
# Libraries view since a sub-directory named the same as their email is not contained
@@ -1287,7 +1285,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
check_str_after_submit=check_str_after_submit,
message=message.replace( '+', ' ' ) )
self.home()
self.visit_page( 'library/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
self.check_page_for_string( regular_user1.email )
self.check_page_for_string( message )
self.logout()
@@ -1302,14 +1300,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
check_str_after_submit=check_str_after_submit,
message=message.replace( '+', ' ' ) )
self.home()
self.visit_page( 'library/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
self.check_page_for_string( regular_user3.email )
self.check_page_for_string( message )
self.home()
self.logout()
self.login( email=admin_user.email )
def test_175_mark_group_deleted( self ):
def test_170_mark_group_deleted( self ):
"""Testing marking a group as deleted"""
self.home()
self.visit_url( '%s/admin/groups' % self.url )
@@ -1323,13 +1321,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( '%s incorrectly lost all members when it was marked as deleted.' % group_two.name )
if not group_two.roles:
raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name )
def test_180_undelete_group( self ):
def test_175_undelete_group( self ):
"""Testing undeleting a deleted group"""
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_185_mark_role_deleted( self ):
def test_180_mark_role_deleted( self ):
"""Testing marking a role as deleted"""
self.home()
self.visit_url( '%s/admin/roles' % self.url )
@@ -1343,15 +1341,15 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( '%s incorrectly lost all user associations when it was marked as deleted.' % role_two.name )
if not role_two.groups:
raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name )
def test_190_undelete_role( self ):
def test_185_undelete_role( self ):
"""Testing undeleting a deleted role"""
self.undelete_role( str( role_two.id ), role_two.name )
def test_195_mark_dataset_deleted( self ):
def test_190_mark_dataset_deleted( self ):
"""Testing marking a library dataset as deleted"""
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()
self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library_admin/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
try:
# 2.bed was only contained in the library in 1 place, so it should no longer display
self.check_page_for_string( ldda_two.name )
@@ -1359,40 +1357,40 @@ class TestSecurityAndLibraries( TwillTestCase ):
except:
pass
self.home()
def test_200_display_deleted_dataset( self ):
def test_195_display_deleted_dataset( self ):
"""Testing displaying deleted dataset"""
self.home()
self.visit_url( "%s/library_admin/browse_library?id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) )
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_205_hide_deleted_dataset( self ):
def test_200_hide_deleted_dataset( self ):
"""Testing hiding deleted dataset"""
self.home()
self.visit_url( "%s/library_admin/browse_library?id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) )
self.visit_url( "%s/library_admin/browse_library?obj_id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) )
try:
self.check_page_for_string( ldda_two.name )
raise AssertionError( "Dataset '%s' is incorrectly displayed in the library after it has been deleted." % ldda_two.name )
except:
pass
self.home()
def test_210_mark_folder_deleted( self ):
def test_205_mark_folder_deleted( self ):
"""Testing marking a library folder as deleted"""
self.home()
self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
self.home()
self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library_admin/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
try:
self.check_page_for_string( folder_two.name )
raise AssertionError( "Folder '%s' is incorrectly displayed in the library after it has been deleted." % folder_two.name )
except:
pass
self.home()
def test_215_mark_folder_undeleted( self ):
def test_210_mark_folder_undeleted( self ):
"""Testing marking a library folder as undeleted"""
self.home()
self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
self.home()
self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library_admin/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
self.check_page_for_string( folder_two.name )
try:
# 2.bed was deleted before the folder was deleted, so state should have been saved. In order
@@ -1402,7 +1400,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
except:
pass
self.home()
def test_220_mark_library_deleted( self ):
def test_215_mark_library_deleted( self ):
"""Testing marking a library as deleted"""
self.home()
# First mark folder_two as deleted to further test state saving when we undelete the library
@@ -1412,12 +1410,12 @@ class TestSecurityAndLibraries( TwillTestCase ):
self.visit_page( 'library_admin/deleted_libraries' )
self.check_page_for_string( library_one.name )
self.home()
def test_225_mark_library_undeleted( self ):
def test_220_mark_library_undeleted( self ):
"""Testing marking a library as undeleted"""
self.home()
self.undelete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
self.home()
self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) )
self.visit_page( 'library_admin/browse_library?obj_id=%s' % ( str( library_one.id ) ) )
self.check_page_for_string( library_one.name )
try:
# folder_two was marked deleted before the library was deleted, so it should not be displayed
@@ -1426,7 +1424,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
except:
pass
self.home()
def test_230_purge_user( self ):
def test_225_purge_user( self ):
"""Testing purging a user account"""
self.mark_user_deleted( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email )
regular_user3.refresh()
@@ -1458,7 +1456,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
role = galaxy.model.Role.get( ura.role_id )
if role.type != 'private':
raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email )
def test_235_manually_unpurge_user( self ):
def test_230_manually_unpurge_user( self ):
"""Testing manually un-purging a user account"""
# 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.
@@ -1466,7 +1464,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
regular_user3.purged = False
regular_user3.deleted = False
regular_user3.flush()
def test_240_purge_group( self ):
def test_235_purge_group( self ):
"""Testing purging a group"""
group_id = str( group_two.id )
self.mark_group_deleted( group_id, group_two.name )
@@ -1481,7 +1479,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id )
# Undelete the group for later test runs
self.undelete_group( group_id, group_two.name )
def test_245_purge_role( self ):
def test_240_purge_role( self ):
"""Testing purging a role"""
role_id = str( role_two.id )
self.mark_role_deleted( role_id, role_two.name )
@@ -1506,14 +1504,14 @@ class TestSecurityAndLibraries( TwillTestCase ):
dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ).all()
if dp:
raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id )
def test_250_manually_unpurge_role( self ):
def test_245_manually_unpurge_role( self ):
"""Testing manually un-purging a role"""
# 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
role_two.flush()
self.undelete_role( str( role_two.id ), role_two.name )
def test_255_purge_library( self ):
def test_250_purge_library( self ):
"""Testing purging a library"""
self.home()
self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
@@ -1549,7 +1547,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \
( str( library_dataset.id ), library_dataset.name ) )
check_folder( library_one.root_folder )
def test_260_no_library_template( self ):
def test_255_no_library_template( self ):
"""Test library features when library has no template"""
name = "Library Two"
description = "This is Library Two"
@@ -1575,7 +1573,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
.order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first()
assert ldda_seven is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_seven from the database'
self.home()
self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_two.id ) ) )
self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_two.id ) ) )
self.check_page_for_string( "7.bed" )
self.check_page_for_string( admin_user.email )
# TODO: add a functional test to cover adding a library dataset via url_paste here...
@@ -1585,6 +1583,23 @@ class TestSecurityAndLibraries( TwillTestCase ):
self.delete_library_item( str( library_two.id ), str( library_two.id ), library_two.name, library_item_type='library' )
self.purge_library( str( library_two.id ), library_two.name )
self.home()
def test_260_library_permissions( self ):
"""Test library permissions"""
name = "Library Three"
description = "This is Library Three"
# Create a library, adding no template
self.create_library( name=name, description=description )
self.visit_page( 'library_admin/browse_libraries' )
self.check_page_for_string( name )
self.check_page_for_string( description )
library_three = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==name,
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()
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"""
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