import pkg_resources
pkg_resources.require( "twill==0.9" )
import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil
from itertools import *
import twill
import twill.commands as tc
from twill.other_packages._mechanize_dist import ClientForm
pkg_resources.require( "elementtree" )
from elementtree import ElementTree
from galaxy.web import security
from galaxy.web.framework.helpers import iff
buffer = StringIO.StringIO()
#Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose?
twill.set_output(buffer)
tc.config('use_tidy', 0)
# Dial ClientCookie logging down (very noisy)
logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING )
log = logging.getLogger( __name__ )
class TwillTestCase( unittest.TestCase ):
def setUp( self ):
# Security helper
self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' )
self.history_id = os.environ.get( 'GALAXY_TEST_HISTORY_ID', None )
self.host = os.environ.get( 'GALAXY_TEST_HOST' )
self.port = os.environ.get( 'GALAXY_TEST_PORT' )
self.url = "http://%s:%s" % ( self.host, self.port )
self.file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR' )
self.home()
#self.set_history()
# Functions associated with files
def files_diff( self, file1, file2, attributes=None ):
"""Checks the contents of 2 files for differences"""
def get_lines_diff( diff ):
count = 0
for line in diff:
if ( line.startswith( '+' ) and not line.startswith( '+++' ) ) or ( line.startswith( '-' ) and not line.startswith( '---' ) ):
count += 1
return count
if not filecmp.cmp( file1, file2 ):
files_differ = False
local_file = open( file1, 'U' ).readlines()
history_data = open( file2, 'U' ).readlines()
if attributes is None:
attributes = {}
if attributes.get( 'sort', False ):
history_data.sort()
##Why even bother with the check loop below, why not just use the diff output? This seems wasteful.
if len( local_file ) == len( history_data ):
for i in range( len( history_data ) ):
if local_file[i].rstrip( '\r\n' ) != history_data[i].rstrip( '\r\n' ):
files_differ = True
break
else:
files_differ = True
if files_differ:
allowed_diff_count = int(attributes.get( 'lines_diff', 0 ))
diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) )
diff_lines = get_lines_diff( diff )
log.debug('## files diff on %s and %s lines_diff=%d, found diff = %d' % (file1,file2,allowed_diff_count,diff_lines))
if diff_lines > allowed_diff_count:
diff_slice = diff[0:40]
#FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff
#due to unknown desired behavior when used in conjunction with a non-zero lines_diff
#PDF forgiveness can probably be handled better by not special casing by __extension__ here
#and instead using lines_diff or a regular expression matching
#or by creating and using a specialized pdf comparison function
if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ):
# PDF files contain creation dates, modification dates, ids and descriptions that change with each
# new file, so we need to handle these differences. As long as the rest of the PDF file does
# not differ we're ok.
valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator' ]
valid_diff = False
for line in diff_slice:
# Make sure to lower case strings before checking.
line = line.lower()
# Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n'
if ( line.startswith( '+' ) or line.startswith( '-' ) ) and line.find( 'local_file' ) < 0 and line.find( 'history_data' ) < 0:
for vdf in valid_diff_strs:
if line.find( vdf ) < 0:
valid_diff = False
else:
valid_diff = True
# Stop checking as soon as we know we have a valid difference
break
if not valid_diff:
# Print out diff_slice so we can see what failed
print "###### diff_slice ######"
raise AssertionError( "".join( diff_slice ) )
else:
for line in diff_slice:
for char in line:
if ord( char ) > 128:
raise AssertionError( "Binary data detected, not displaying diff" )
raise AssertionError( "".join( diff_slice ) )
def files_re_match( self, file1, file2, attributes=None ):
"""Checks the contents of 2 files for differences using re.match"""
local_file = open( file1, 'U' ).readlines() #regex file
history_data = open( file2, 'U' ).readlines()
assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)' % ( len( local_file ), len( history_data ) )
if attributes is None:
attributes = {}
if attributes.get( 'sort', False ):
history_data.sort()
lines_diff = int(attributes.get( 'lines_diff', 0 ))
line_diff_count = 0
diffs = []
for i in range( len( history_data ) ):
if not re.match( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ):
line_diff_count += 1
diffs.append( 'Regular Expression: %s\nData file : %s' % ( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ) )
if line_diff_count > lines_diff:
raise AssertionError, "Regular expression did not match data file (allowed variants=%i):\n%s" % ( lines_diff, "".join( diffs ) )
def files_re_match_multiline( self, file1, file2, attributes=None ):
"""Checks the contents of 2 files for differences using re.match in multiline mode"""
local_file = open( file1, 'U' ).read() #regex file
if attributes is None:
attributes = {}
if attributes.get( 'sort', False ):
history_data = open( file2, 'U' ).readlines()
history_data.sort()
history_data = ''.join( history_data )
else:
history_data = open( file2, 'U' ).read()
#lines_diff not applicable to multiline matching
assert re.match( local_file, history_data, re.MULTILINE ), "Multiline Regular expression did not match data file"
def get_filename( self, filename ):
full = os.path.join( self.file_dir, filename)
return os.path.abspath(full)
def save_log( *path ):
"""Saves the log to a file"""
filename = os.path.join( *path )
file(filename, 'wt').write(buffer.getvalue())
def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', space_to_tab = False, metadata = None, composite_data = None ):
"""Uploads a file"""
self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url )
try:
self.refresh_form( "file_type", ftype ) #Refresh, to support composite files
tc.fv("1","dbkey", dbkey)
if metadata:
for elem in metadata:
tc.fv( "1", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) )
if composite_data:
for i, composite_file in enumerate( composite_data ):
filename = self.get_filename( composite_file.get( 'value' ) )
tc.formfile( "1", "files_%i|file_data" % i, filename )
tc.fv( "1", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) )
else:
filename = self.get_filename( filename )
tc.formfile( "1", "file_data", filename )
tc.fv( "1", "space_to_tab", space_to_tab )
tc.submit("runtool_btn")
self.home()
except AssertionError, err:
errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename
errmsg += str( err )
raise AssertionError( errmsg )
# Make sure every history item has a valid hid
hids = self.get_hids_in_history()
for hid in hids:
try:
valid_hid = int( hid )
except:
raise AssertionError, "Invalid hid (%s) created when uploading file %s" % ( hid, filename )
# Wait for upload processing to finish (TODO: this should be done in each test case instead)
self.wait()
def upload_url_paste( self, url_paste, ftype='auto', dbkey='unspecified (?)' ):
"""Pasted data in the upload utility"""
self.visit_page( "tool_runner/index?tool_id=upload1" )
try:
tc.fv( "1", "file_type", ftype )
tc.fv( "1", "dbkey", dbkey )
tc.fv( "1", "url_paste", url_paste )
tc.submit( "runtool_btn" )
self.home()
except Exception, e:
errmsg = "Problem executing upload utility using url_paste: %s" % str( e )
raise AssertionError( e )
# Make sure every history item has a valid hid
hids = self.get_hids_in_history()
for hid in hids:
try:
valid_hid = int( hid )
except:
raise AssertionError, "Invalid hid (%s) created when pasting %s" % ( hid, url_paste )
# Wait for upload processing to finish (TODO: this should be done in each test case instead)
self.wait()
# Functions associated with histories
def check_history_for_errors( self ):
"""Raises an exception if there are errors in a history"""
self.home()
self.visit_page( "history" )
page = self.last_page()
if page.find( 'error' ) > -1:
raise AssertionError('Errors in the history for user %s' % self.user )
def check_history_for_string( self, patt, show_deleted=False ):
"""Looks for 'string' in history page"""
self.home()
if show_deleted:
self.visit_page( "history?show_deleted=True" )
else:
self.visit_page( "history" )
for subpatt in patt.split():
tc.find(subpatt)
self.home()
def clear_history( self ):
"""Empties a history of all datasets"""
self.visit_page( "clear_history" )
self.check_history_for_string( 'Your history is empty' )
self.home()
def delete_history( self, id ):
"""Deletes one or more histories"""
history_list = self.get_histories_as_data_list()
self.assertTrue( history_list )
num_deleted = len( id.split( ',' ) )
self.home()
self.visit_page( "history/list?operation=delete&id=%s" % ( id ) )
check_str = 'Deleted %d %s' % ( num_deleted, iff( num_deleted != 1, "histories", "history" ) )
self.check_page_for_string( check_str )
self.home()
def delete_current_history( self, strings_displayed=[] ):
"""Deletes the current history"""
self.home()
self.visit_page( "history/delete_current" )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.home()
def get_histories_as_data_list( self ):
"""Returns the data elements of all histories"""
tree = self.histories_as_xml_tree()
data_list = [ elem for elem in tree.findall("data") ]
return data_list
def get_history_as_data_list( self, show_deleted=False ):
"""Returns the data elements of a history"""
tree = self.history_as_xml_tree( show_deleted=show_deleted )
data_list = [ elem for elem in tree.findall("data") ]
return data_list
def history_as_xml_tree( self, show_deleted=False ):
"""Returns a parsed xml object of a history"""
self.home()
self.visit_page( 'history?as_xml=True&show_deleted=%s' % show_deleted )
xml = self.last_page()
tree = ElementTree.fromstring(xml)
return tree
def histories_as_xml_tree( self ):
"""Returns a parsed xml object of all histories"""
self.home()
self.visit_page( 'history/list_as_xml' )
xml = self.last_page()
tree = ElementTree.fromstring(xml)
return tree
def history_options( self, user=False, active_datasets=False, activatable_datasets=False, histories_shared_by_others=False ):
"""Mimics user clicking on history options link"""
self.home()
self.visit_page( "root/history_options" )
if user:
self.check_page_for_string( 'Previously stored histories' )
if active_datasets:
self.check_page_for_string( 'Create a new empty history' )
self.check_page_for_string( 'Construct workflow from current history' )
self.check_page_for_string( 'Clone current history' )
self.check_page_for_string( 'Share current history' )
self.check_page_for_string( 'Change default permissions for current history' )
if histories_shared_by_others:
self.check_page_for_string( 'Histories shared with you by others' )
if activatable_datasets:
self.check_page_for_string( 'Show deleted datasets in current history' )
self.check_page_for_string( 'Rename current history' )
self.check_page_for_string( 'Delete current history' )
self.home()
def new_history( self, name=None ):
"""Creates a new, empty history"""
self.home()
if name:
self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) )
else:
self.visit_url( "%s/history_new" % self.url )
self.check_history_for_string('Your history is empty')
self.home()
def rename_history( self, id, old_name, new_name ):
"""Rename an existing history"""
self.home()
self.visit_page( "history/rename?id=%s&name=%s" %( id, new_name ) )
check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) )
self.check_page_for_string( check_str )
self.home()
def set_history( self ):
"""Sets the history (stores the cookies for this run)"""
if self.history_id:
self.home()
self.visit_page( "history?id=%s" % self.history_id )
else:
self.new_history()
self.home()
def share_current_history( self, email, strings_displayed=[], strings_displayed_after_submit=[],
action='', action_strings_displayed=[], action_strings_displayed_after_submit=[] ):
"""Share the current history with different users"""
self.visit_url( "%s/history/share" % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( 'share', 'email', email )
tc.submit( 'share_button' )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
if action:
# If we have an action, then we are sharing datasets with users that do not have access permissions on them
for check_str in action_strings_displayed:
self.check_page_for_string( check_str )
tc.fv( 'share_restricted', 'action', action )
tc.submit( "share_restricted_button" )
for check_str in action_strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
def share_histories_with_users( self, ids, emails, strings_displayed=[], strings_displayed_after_submit=[],
action=None, action_strings_displayed=[] ):
"""Share one or more histories with one or more different users"""
self.visit_url( "%s/history/list?id=%s&operation=Share" % ( self.url, ids ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( 'share', 'email', emails )
tc.submit( 'share_button' )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
if action:
# If we have an action, then we are sharing datasets with users that do not have access permissions on them
tc.fv( 'share_restricted', 'action', action )
tc.submit( "share_restricted_button" )
for check_str in action_strings_displayed:
self.check_page_for_string( check_str )
self.home()
def unshare_history( self, history_id, user_id, strings_displayed=[] ):
"""Unshare a history that has been shared with another user"""
self.visit_url( "%s/history/list?id=%s&operation=share+or+publish" % ( self.url, history_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.visit_url( "%s/history/sharing?unshare_user=%s&id=%s" % ( self.url, user_id, history_id ) )
self.home()
def switch_history( self, id='', name='' ):
"""Switches to a history in the current list of histories"""
self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) )
if name:
self.check_history_for_string( name )
self.home()
def view_stored_active_histories( self, strings_displayed=[] ):
self.home()
self.visit_page( "history/list" )
self.check_page_for_string( 'Saved Histories' )
self.check_page_for_string( '> begin tool stderr << -----------------------\n"
errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n"
errmsg += "----------------------- >> end tool stderr << ------------------------\n"
raise AssertionError( errmsg )
def check_metadata_for_string( self, patt, hid=None ):
"""Looks for 'patt' in the edit page when editing a dataset"""
data_list = self.get_history_as_data_list()
self.assertTrue( data_list )
if hid is None: # take last hid
elem = data_list[-1]
hid = int( elem.get('hid') )
self.assertTrue( hid )
self.visit_page( "edit?hid=%s" % hid )
for subpatt in patt.split():
tc.find(subpatt)
def delete_history_item( self, hda_id, strings_displayed=[] ):
"""Deletes an item from a history"""
try:
hda_id = int( hda_id )
except:
raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
self.visit_url( "%s/root/delete?show_deleted_on_refresh=False&id=%s" % ( self.url, hda_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def undelete_history_item( self, hda_id, strings_displayed=[] ):
"""Un-deletes a deleted item in a history"""
try:
hda_id = int( hda_id )
except:
raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, hda_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def display_history_item( self, hda_id, strings_displayed=[] ):
"""Displays a history item - simulates eye icon click"""
self.visit_url( '%s/datasets/%s/display/' % ( self.url, self.security.encode_id( hda_id ) ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.home()
def view_history( self, history_id, strings_displayed=[] ):
"""Displays a history for viewing"""
self.visit_url( '%s/history/view?id=%s' % ( self.url, self.security.encode_id( history_id ) ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.home()
def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='',
strings_displayed=[], strings_not_displayed=[] ):
"""Edit history_dataset_association attribute information"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
submit_required = False
self.check_page_for_string( 'Edit Attributes' )
if new_name:
tc.fv( 'edit_attributes', 'name', new_name )
submit_required = True
if new_info:
tc.fv( 'edit_attributes', 'info', new_info )
submit_required = True
if new_dbkey:
tc.fv( 'edit_attributes', 'dbkey', new_dbkey )
submit_required = True
if new_startcol:
tc.fv( 'edit_attributes', 'startCol', new_startcol )
submit_required = True
if submit_required:
tc.submit( 'save' )
self.check_page_for_string( 'Attributes updated' )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed on Edit Attributes page." % check_str
except:
pass
self.home()
def check_hda_attribute_info( self, hda_id, strings_displayed=[] ):
"""Edit history_dataset_association attribute information"""
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def auto_detect_metadata( self, hda_id ):
"""Auto-detect history_dataset_association metadata"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
self.check_page_for_string( 'This will inspect the dataset and attempt' )
tc.fv( 'auto_detect', 'id', hda_id )
tc.submit( 'detect' )
try:
self.check_page_for_string( 'Attributes have been queued to be updated' )
self.wait()
except AssertionError:
self.check_page_for_string( 'Attributes updated' )
#self.check_page_for_string( 'Attributes updated' )
self.home()
def convert_format( self, hda_id, target_type ):
"""Convert format of history_dataset_association"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
self.check_page_for_string( 'This will inspect the dataset and attempt' )
tc.fv( 'convert_data', 'target_type', target_type )
tc.submit( 'convert_data' )
self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' )
self.wait() #wait for the format convert tool to finish before returning
self.home()
def change_datatype( self, hda_id, datatype ):
"""Change format of history_dataset_association"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
self.check_page_for_string( 'This will change the datatype of the existing dataset but' )
tc.fv( 'change_datatype', 'datatype', datatype )
tc.submit( 'change' )
self.check_page_for_string( 'Changed the type of dataset' )
self.home()
def copy_history_item( self, source_dataset_ids='', target_history_ids=[], all_target_history_ids=[],
deleted_history_ids=[] ):
"""Copy 1 or more history_dataset_associations to 1 or more histories"""
self.home()
self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_ids ) )
self.check_page_for_string( 'Source History Items' )
# Make sure all of users active histories are displayed
for id in all_target_history_ids:
self.check_page_for_string( id )
# Make sure only active histories are displayed
for id in deleted_history_ids:
try:
self.check_page_for_string( id )
raise AssertionError, "deleted history id %d displayed in list of target histories" % id
except:
pass
# Check each history to which we want to copy the item
for id in target_history_ids:
tc.fv( '1', 'target_history_ids', id )
tc.submit( 'do_copy' )
no_source_ids = len( source_dataset_ids.split( ',' ) )
check_str = '%d datasets copied to %d histories.' % ( no_source_ids, len( target_history_ids ) )
self.check_page_for_string( check_str )
self.home()
def get_hids_in_history( self ):
"""Returns the list of hid values for items in a history"""
data_list = self.get_history_as_data_list()
hids = []
for elem in data_list:
hid = elem.get('hid')
hids.append(hid)
return hids
def get_hids_in_histories( self ):
"""Returns the list of hids values for items in all histories"""
data_list = self.get_histories_as_data_list()
hids = []
for elem in data_list:
hid = elem.get('hid')
hids.append(hid)
return hids
def makeTfname(self, fname=None):
"""
safe temp name - preserve the file extension for tools that interpret it
"""
suffix = os.path.split(fname)[-1] # ignore full path
fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix)
return temp_prefix
def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ):
"""Verifies that the attributes and contents of a history item meet expectations"""
if wait:
self.wait( maxseconds=maxseconds ) #wait for job to finish
data_list = self.get_history_as_data_list()
self.assertTrue( data_list )
if hid is None: # take last hid
elem = data_list[-1]
hid = str( elem.get('hid') )
else:
hid = str( hid )
elems = [ elem for elem in data_list if elem.get('hid') == hid ]
self.assertTrue( len(elems) == 1 )
elem = elems[0]
self.assertTrue( hid )
self._assert_dataset_state( elem, 'ok' )
if self.is_zipped( filename ):
errmsg = 'History item %s is a zip archive which includes invalid files:\n' % hid
zip_file = zipfile.ZipFile( filename, "r" )
name = zip_file.namelist()[0]
test_ext = name.split( "." )[1].strip().lower()
if not ( test_ext == 'scf' or test_ext == 'ab1' or test_ext == 'txt' ):
raise AssertionError( errmsg )
for name in zip_file.namelist():
ext = name.split( "." )[1].strip().lower()
if ext != test_ext:
raise AssertionError( errmsg )
else:
local_name = self.get_filename( filename )
temp_name = self.makeTfname(fname = filename)
self.home()
self.visit_page( "display?hid=" + hid )
data = self.last_page()
file( temp_name, 'wb' ).write(data)
try:
# have to nest try-except in try-finally to handle 2.4
try:
if attributes is None:
attributes = {}
compare = attributes.get( 'compare', 'diff' )
extra_files = attributes.get( 'extra_files', None )
if compare == 'diff':
self.files_diff( local_name, temp_name, attributes=attributes )
elif compare == 're_match':
self.files_re_match( local_name, temp_name, attributes=attributes )
elif compare == 're_match_multiline':
self.files_re_match_multiline( local_name, temp_name, attributes=attributes )
elif compare == 'sim_size':
delta = attributes.get('delta','100')
s1 = len(data)
s2 = os.path.getsize(local_name)
if abs(s1-s2) > int(delta):
raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta)
else:
raise Exception, 'Unimplemented Compare type: %s' % compare
if extra_files:
self.verify_extra_files_content( extra_files, elem.get( 'id' ) )
except AssertionError, err:
errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare )
errmsg += str( err )
raise AssertionError( errmsg )
finally:
os.remove( temp_name )
def verify_extra_files_content( self, extra_files, hda_id ):
files_list = []
for extra_type, extra_value, extra_name, extra_attributes in extra_files:
if extra_type == 'file':
files_list.append( ( extra_name, extra_value, extra_attributes ) )
elif extra_type == 'directory':
for filename in os.listdir( self.get_filename( extra_value ) ):
files_list.append( ( filename, os.path.join( extra_value, filename ), extra_attributes ) )
else:
raise ValueError, 'unknown extra_files type: %s' % extra_type
for filename, filepath, attributes in files_list:
self.verify_composite_datatype_file_content( filepath, hda_id, base_name = filename, attributes = attributes )
def verify_composite_datatype_file_content( self, file_name, hda_id, base_name = None, attributes = None ):
local_name = self.get_filename( file_name )
if base_name is None:
base_name = os.path.split(file_name)[-1]
temp_name = self.makeTfname(fname = base_name)
self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, self.security.encode_id( hda_id ), base_name ) )
data = self.last_page()
file( temp_name, 'wb' ).write( data )
try:
# have to nest try-except in try-finally to handle 2.4
try:
if attributes is None:
attributes = {}
compare = attributes.get( 'compare', 'diff' )
if compare == 'diff':
self.files_diff( local_name, temp_name, attributes=attributes )
elif compare == 're_match':
self.files_re_match( local_name, temp_name, attributes=attributes )
elif compare == 're_match_multiline':
self.files_re_match_multiline( local_name, temp_name, attributes=attributes )
elif compare == 'sim_size':
delta = attributes.get('delta','100')
s1 = len(data)
s2 = os.path.getsize(local_name)
if abs(s1-s2) > int(delta):
raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta)
else:
raise Exception, 'Unimplemented Compare type: %s' % compare
except AssertionError, err:
errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare )
errmsg += str( err )
raise AssertionError( errmsg )
finally:
os.remove( temp_name )
def is_zipped( self, filename ):
if not zipfile.is_zipfile( filename ):
return False
return True
def is_binary( self, filename ):
temp = open( filename, "U" ) # why is this not filename? Where did temp_name come from
lineno = 0
for line in temp:
lineno += 1
line = line.strip()
if line:
for char in line:
if ord( char ) > 128:
return True
if lineno > 10:
break
return False
def verify_genome_build( self, dbkey='hg17' ):
"""Verifies that the last used genome_build at history id 'hid' is as expected"""
data_list = self.get_history_as_data_list()
self.assertTrue( data_list )
elems = [ elem for elem in data_list ]
elem = elems[-1]
genome_build = elem.get('dbkey')
self.assertTrue( genome_build == dbkey )
# Functions associated with user accounts
def create( self, email='test@bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', referer='' ):
# HACK: don't use panels because late_javascripts() messes up the twill browser and it
# can't find form fields (and hence user can't be logged in).
self.visit_url( "%s/user/create?use_panels=False" % self.url )
tc.fv( '1', 'email', email )
tc.fv( '1', 'webapp', webapp )
tc.fv( '1', 'referer', referer )
tc.fv( '1', 'password', password )
tc.fv( '1', 'confirm', password )
tc.fv( '1', 'username', username )
tc.submit( 'create_user_button' )
previously_created = False
username_taken = False
invalid_username = False
try:
self.check_page_for_string( "Created new user account" )
except:
try:
# May have created the account in a previous test run...
self.check_page_for_string( "User with that email already exists" )
previously_created = True
except:
try:
self.check_page_for_string( 'This user name is not available' )
username_taken = True
except:
try:
# Note that we're only checking if the usr name is >< 4 chars here...
self.check_page_for_string( 'User name must be at least 4 characters in length' )
invalid_username = True
except:
pass
return previously_created, username_taken, invalid_username
def create_user_with_info( self, email, password, username, user_info_values, user_info_select='', admin_view='False',
strings_displayed=[], strings_displayed_after_submit=[] ):
# This method creates a new user with associated info
self.visit_url( "%s/user/create?admin_view=%s&use_panels=False" % ( self.url, admin_view ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str)
tc.fv( "1", "email", email )
tc.fv( "1", "password", password )
tc.fv( "1", "confirm", password )
tc.fv( "1", "username", username )
if user_info_select:
# The user_info_select SelectField requires a refresh_on_change
self.refresh_form( 'user_info_select', user_info_select )
for index, info_value in enumerate( user_info_values ):
tc.fv( "1", "field_%i" % index, info_value )
tc.submit( "create_user_button" )
def edit_user_info( self, new_email='', new_username='', password='', new_password='',
info_values=[], strings_displayed=[], strings_displayed_after_submit=[] ):
self.visit_url( "%s/user/show_info" % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
if new_email or new_username:
if new_email:
tc.fv( "login_info", "email", new_email )
if new_username:
tc.fv( "login_info", "username", new_username )
tc.submit( "login_info_button" )
if password and new_password:
tc.fv( "change_password", "current", password )
tc.fv( "change_password", "password", new_password )
tc.fv( "change_password", "confirm", new_password )
tc.submit( "change_password_button" )
if info_values:
for index, info_value in enumerate( info_values ):
tc.fv( "user_info", "field_%i" % index, info_value )
tc.submit( "edit_user_info_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id='2' ):
# role.id = 2 is Private Role for test2@bx.psu.edu
# NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value
# in each select list or twill throws an exception, which is: ParseError: OPTION outside of SELECT
# Due to this bug, we'll bypass visiting the page, and simply pass the permissions on to the
# /user/set_default_permissions method.
url = "user/set_default_permissions?update_roles_button=Save&id=None"
for po in permissions_out:
key = '%s_out' % po
url ="%s&%s=%s" % ( url, key, str( role_id ) )
for pi in permissions_in:
key = '%s_in' % pi
url ="%s&%s=%s" % ( url, key, str( role_id ) )
self.home()
self.visit_url( "%s/%s" % ( self.url, url ) )
self.last_page()
self.check_page_for_string( 'Default new history permissions have been changed.' )
self.home()
def history_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=3 ): # role.id = 3 is Private Role for test3@bx.psu.edu
# NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value
# in each select list or twill throws an exception, which is: ParseError: OPTION outside of SELECT
# Due to this bug, we'll bypass visiting the page, and simply pass the permissions on to the
# /user/set_default_permissions method.
url = "root/history_set_default_permissions?update_roles_button=Save&id=None&dataset=True"
for po in permissions_out:
key = '%s_out' % po
url ="%s&%s=%s" % ( url, key, str( role_id ) )
for pi in permissions_in:
key = '%s_in' % pi
url ="%s&%s=%s" % ( url, key, str( role_id ) )
self.home()
self.visit_url( "%s/%s" % ( self.url, url ) )
self.check_page_for_string( 'Default history permissions have been changed.' )
self.home()
def login( self, email='test@bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', referer='' ):
# test@bx.psu.edu is configured as an admin user
previously_created, username_taken, invalid_username = \
self.create( email=email, password=password, username=username, webapp=webapp, referer=referer )
if previously_created:
# The acount has previously been created, so just login.
# HACK: don't use panels because late_javascripts() messes up the twill browser and it
# can't find form fields (and hence user can't be logged in).
self.visit_url( "%s/user/login?use_panels=False" % self.url )
tc.fv( '1', 'email', email )
tc.fv( '1', 'webapp', webapp )
tc.fv( '1', 'referer', referer )
tc.fv( '1', 'password', password )
tc.submit( 'login_button' )
def logout( self ):
self.home()
self.visit_page( "user/logout" )
self.check_page_for_string( "You have been logged out" )
self.home()
# Functions associated with browsers, cookies, HTML forms and page visits
def check_page_for_string( self, patt ):
"""Looks for 'patt' in the current browser page"""
page = self.last_page()
for subpatt in patt.split():
if page.find( patt ) == -1:
fname = self.write_temp_file( page )
errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname )
raise AssertionError( errmsg )
def write_temp_file( self, content, suffix='.html' ):
fd, fname = tempfile.mkstemp( suffix=suffix, prefix='twilltestcase-' )
f = os.fdopen( fd, "w" )
f.write( content )
f.close()
return fname
def clear_cookies( self ):
tc.clear_cookies()
def clear_form( self, form=0 ):
"""Clears a form"""
tc.formclear(str(form))
def home( self ):
self.visit_url( self.url )
def last_page( self ):
return tc.browser.get_html()
def load_cookies( self, file ):
filename = self.get_filename(file)
tc.load_cookies(filename)
def reload_page( self ):
tc.reload()
tc.code(200)
def show_cookies( self ):
return tc.show_cookies()
def showforms( self ):
"""Shows form, helpful for debugging new tests"""
return tc.showforms()
def submit_form( self, form_no=0, button="runtool_btn", **kwd ):
"""Populates and submits a form from the keyword arguments."""
# An HTMLForm contains a sequence of Controls. Supported control classes are:
# TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl,
# SubmitControl, ImageControl
for i, f in enumerate( self.showforms() ):
if i == form_no:
break
# To help with debugging a tool, print out the form controls when the test fails
print "form '%s' contains the following controls ( note the values )" % f.name
controls = {}
hc_prefix = ' 30:
elem_name = '%s..%s' % ( elem[:17], elem[-11:] )
else:
elem_name = elem
tc.fv( f.name, control.name, str( elem_name ) )
except Exception, exc:
errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) )
errmsg += "control: %s\n" % str( control )
errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the tag set.\n"
raise AssertionError( errmsg )
else:
# Add conditions for other control types here when necessary.
pass
tc.submit( button )
def refresh_form( self, control_name, value, form_no=0, **kwd ):
"""Handles Galaxy's refresh_on_change for forms without ultimately submitting the form"""
# control_name is the name of the form field that requires refresh_on_change, and value is
# the value to which that field is being set.
for i, f in enumerate( self.showforms() ):
if i == form_no:
break
try:
control = f.find_control( name=control_name )
except:
# This assumes we always want the first control of the given name, which may not be ideal...
control = f.find_control( name=control_name, nr=0 )
# Check for refresh_on_change attribute, submit a change if required
if 'refresh_on_change' in control.attrs.keys():
# Clear Control and set to proper value
control.clear()
tc.fv( f.name, control.name, value )
# Create a new submit control, allows form to refresh, instead of going to next page
control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} )
control.add_to_form( f )
control.fixup()
# Submit for refresh
tc.submit( '___refresh_grouping___' )
def visit_page( self, page ):
# tc.go("./%s" % page)
if not page.startswith( "/" ):
page = "/" + page
tc.go( self.url + page )
tc.code( 200 )
def visit_url( self, url ):
tc.go("%s" % url)
tc.code( 200 )
"""Functions associated with Galaxy tools"""
def run_tool( self, tool_id, repeat_name=None, **kwd ):
tool_id = tool_id.replace(" ", "+")
"""Runs the tool 'tool_id' and passes it the key/values from the *kwd"""
self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) )
if repeat_name is not None:
repeat_button = '%s_add' % repeat_name
# Submit the "repeat" form button to add an input)
tc.submit( repeat_button )
print "button '%s' clicked" % repeat_button
tc.find( 'runtool_btn' )
self.submit_form( **kwd )
def run_ucsc_main( self, track_params, output_params ):
"""Gets Data From UCSC"""
tool_id = "ucsc_table_direct1"
track_string = urllib.urlencode( track_params )
galaxy_url = urllib.quote_plus( "%s/tool_runner/index?" % self.url )
self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=%s&hgta_compressType=none&tool_id=%s&%s" % ( galaxy_url, tool_id, track_string ) )
tc.fv( "mainForm", "hgta_doTopSubmit", "get output" )
self.submit_form( button="get output" )#, **track_params )
tc.fv( 2, "hgta_doGalaxyQuery", "Send query to Galaxy" )
self.submit_form( button="Send query to Galaxy" )#, **output_params ) #AssertionError: Attempting to set field 'fbQual' to value '['whole']' in form 'None' threw exception: no matching forms! control:
def wait( self, maxseconds=120 ):
"""Waits for the tools to finish"""
sleep_amount = 0.1
slept = 0
self.home()
while slept <= maxseconds:
self.visit_page( "history" )
page = tc.browser.get_html()
if page.find( '' ) > -1:
time.sleep( sleep_amount )
slept += sleep_amount
sleep_amount *= 2
if slept + sleep_amount > maxseconds:
sleep_amount = maxseconds - slept # don't overshoot maxseconds
else:
break
assert slept < maxseconds
# Dataset Security stuff
# Tests associated with users
def create_new_account_as_admin( self, email='test4@bx.psu.edu', password='testuser',
username='regular-user4', webapp='galaxy', referer='' ):
"""Create a new account for another user"""
# HACK: don't use panels because late_javascripts() messes up the twill browser and it
# can't find form fields (and hence user can't be logged in).
self.visit_url( "%s/user/create?admin_view=True" % self.url )
tc.fv( '1', 'email', email )
tc.fv( '1', 'webapp', webapp )
tc.fv( '1', 'referer', referer )
tc.fv( '1', 'password', password )
tc.fv( '1', 'confirm', password )
tc.fv( '1', 'username', username )
tc.submit( 'create_user_button' )
previously_created = False
username_taken = False
invalid_username = False
try:
self.check_page_for_string( "Created new user account" )
except:
try:
# May have created the account in a previous test run...
self.check_page_for_string( "User with that email already exists" )
previously_created = True
except:
try:
self.check_page_for_string( 'This user name is not available' )
username_taken = True
except:
try:
# Note that we're only checking if the usr name is >< 4 chars here...
self.check_page_for_string( 'User name must be at least 4 characters in length' )
invalid_username = True
except:
pass
return previously_created, username_taken, invalid_username
def reset_password_as_admin( self, user_id, password='testreset' ):
"""Reset a user password"""
self.home()
self.visit_url( "%s/admin/reset_user_password?id=%s" % ( self.url, user_id ) )
tc.fv( "1", "password", password )
tc.fv( "1", "confirm", password )
tc.submit( "reset_user_password_button" )
self.check_page_for_string( "Passwords reset for 1 users" )
self.home()
def mark_user_deleted( self, user_id, email='' ):
"""Mark a user as deleted"""
self.home()
self.visit_url( "%s/admin/users?operation=delete&id=%s" % ( self.url, user_id ) )
check_str = "Deleted 1 users"
self.check_page_for_string( check_str )
self.home()
def undelete_user( self, user_id, email='' ):
"""Undelete a user"""
self.home()
self.visit_url( "%s/admin/users?operation=undelete&id=%s" % ( self.url, user_id ) )
check_str = "Undeleted 1 users"
self.check_page_for_string( check_str )
self.home()
def purge_user( self, user_id, email ):
"""Purge a user account"""
self.home()
self.visit_url( "%s/admin/users?operation=purge&id=%s" % ( self.url, user_id ) )
check_str = "Purged 1 users"
self.check_page_for_string( check_str )
self.home()
def manage_roles_and_groups_for_user( self, user_id, in_role_ids=[], out_role_ids=[],
in_group_ids=[], out_group_ids=[], strings_displayed=[] ):
self.home()
url = "%s/admin/manage_roles_and_groups_for_user?id=%s" % ( self.url, user_id )
if in_role_ids:
url += "&in_roles=%s" % ','.join( in_role_ids )
if out_role_ids:
url += "&out_roles=%s" % ','.join( out_role_ids )
if in_group_ids:
url += "&in_groups=%s" % ','.join( in_group_ids )
if out_group_ids:
url += "&out_groups=%s" % ','.join( out_group_ids )
if in_role_ids or out_role_ids or in_group_ids or out_group_ids:
url += "&user_roles_groups_edit_button=Save"
self.visit_url( url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.home()
# Tests associated with roles
def browse_roles( self, strings_displayed=[] ):
self.visit_url( '%s/admin/roles' % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def create_role( self,
name='Role One',
description="This is Role One",
in_user_ids=[],
in_group_ids=[],
create_group_for_role='no',
private_role='' ):
"""Create a new role"""
url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) )
if in_user_ids:
url += "&in_users=%s" % ','.join( in_user_ids )
if in_group_ids:
url += "&in_groups=%s" % ','.join( in_group_ids )
if create_group_for_role == 'yes':
url += '&create_group_for_role=yes'
self.home()
self.visit_url( url )
if create_group_for_role == 'yes':
check_str = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \
( name, name, len( in_user_ids ), len( in_group_ids ) )
else:
check_str = "Role '%s' has been created with %d associated users and %d associated groups" % \
( name, len( in_user_ids ), len( in_group_ids ) )
self.check_page_for_string( check_str )
if private_role:
# Make sure no private roles are displayed
try:
self.check_page_for_string( private_role )
errmsg = 'Private role %s displayed on Roles page' % private_role
raise AssertionError( errmsg )
except AssertionError:
# Reaching here is the behavior we want since no private roles should be displayed
pass
self.home()
self.visit_url( "%s/admin/roles" % self.url )
self.check_page_for_string( name )
self.home()
def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ):
"""Rename a role"""
self.home()
self.visit_url( "%s/admin/roles?operation=rename&id=%s" % ( self.url, role_id ) )
self.check_page_for_string( 'Change role name and description' )
tc.fv( "1", "name", name )
tc.fv( "1", "description", description )
tc.submit( "rename_role_button" )
self.home()
def mark_role_deleted( self, role_id, role_name ):
"""Mark a role as deleted"""
self.home()
self.visit_url( "%s/admin/roles?operation=delete&id=%s" % ( self.url, role_id ) )
check_str = "Deleted 1 roles: %s" % role_name
self.check_page_for_string( check_str )
self.home()
def undelete_role( self, role_id, role_name ):
"""Undelete an existing role"""
self.home()
self.visit_url( "%s/admin/roles?operation=undelete&id=%s" % ( self.url, role_id ) )
check_str = "Undeleted 1 roles: %s" % role_name
self.check_page_for_string( check_str )
self.home()
def purge_role( self, role_id, role_name ):
"""Purge an existing role"""
self.home()
self.visit_url( "%s/admin/roles?operation=purge&id=%s" % ( self.url, role_id ) )
check_str = "Purged 1 roles: %s" % role_name
self.check_page_for_string( check_str )
self.home()
def associate_users_and_groups_with_role( self, role_id, role_name, user_ids=[], group_ids=[] ):
self.home()
url = "%s/admin/role?id=%s&role_members_edit_button=Save" % ( self.url, role_id )
if user_ids:
url += "&in_users=%s" % ','.join( user_ids )
if group_ids:
url += "&in_groups=%s" % ','.join( group_ids )
self.visit_url( url )
check_str = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role_name, len( user_ids ), len( group_ids ) )
self.check_page_for_string( check_str )
self.home()
# Tests associated with groups
def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[] ):
"""Create a new group"""
url = "%s/admin/groups?operation=create&create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) )
if in_user_ids:
url += "&in_users=%s" % ','.join( in_user_ids )
if in_role_ids:
url += "&in_roles=%s" % ','.join( in_role_ids )
self.home()
self.visit_url( url )
check_str = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_user_ids ), len( in_role_ids ) )
self.check_page_for_string( check_str )
self.home()
self.visit_url( "%s/admin/groups" % self.url )
self.check_page_for_string( name )
self.home()
def browse_groups( self, strings_displayed=[] ):
self.visit_url( '%s/admin/groups' % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def rename_group( self, group_id, name='Group One Renamed' ):
"""Rename a group"""
self.home()
self.visit_url( "%s/admin/groups?operation=rename&id=%s" % ( self.url, group_id ) )
self.check_page_for_string( 'Change group name' )
tc.fv( "1", "name", name )
tc.submit( "rename_group_button" )
self.home()
def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ):
self.home()
url = "%s/admin/manage_users_and_roles_for_group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id )
if user_ids:
url += "&in_users=%s" % ','.join( user_ids )
if role_ids:
url += "&in_roles=%s" % ','.join( role_ids )
self.visit_url( url )
check_str = "Group '%s' has been updated with %d associated roles and %d associated users" % ( group_name, len( role_ids ), len( user_ids ) )
self.check_page_for_string( check_str )
self.home()
def mark_group_deleted( self, group_id, group_name ):
"""Mark a group as deleted"""
self.home()
self.visit_url( "%s/admin/groups?operation=delete&id=%s" % ( self.url, group_id ) )
check_str = "Deleted 1 groups: %s" % group_name
self.check_page_for_string( check_str )
self.home()
def undelete_group( self, group_id, group_name ):
"""Undelete an existing group"""
self.home()
self.visit_url( "%s/admin/groups?operation=undelete&id=%s" % ( self.url, group_id ) )
check_str = "Undeleted 1 groups: %s" % group_name
self.check_page_for_string( check_str )
self.home()
def purge_group( self, group_id, group_name ):
"""Purge an existing group"""
self.home()
self.visit_url( "%s/admin/groups?operation=purge&id=%s" % ( self.url, group_id ) )
check_str = "Purged 1 groups: %s" % group_name
self.check_page_for_string( check_str )
self.home()
# Form stuff
def create_form( self, name, desc, form_type, field_type='TextField', form_layout_name='',
num_fields=1, num_options=0, strings_displayed=[], strings_displayed_after_submit=[] ):
"""Create a new form definition."""
self.visit_url( "%s/forms/create_form" % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( "1", "name", name )
tc.fv( "1", "description", desc )
tc.fv( "1", "form_type_selectbox", form_type )
tc.submit( "create_form_button" )
if form_type == "Sequencing Sample Form":
tc.submit( "add_layout_grid" )
tc.fv( "1", "grid_layout0", form_layout_name )
# Add fields to the new form definition
for index1 in range( num_fields ):
field_name = 'field_name_%i' % index1
field_contents = field_type
field_help_name = 'field_helptext_%i' % index1
field_help_contents = 'Field %i help' % index1
field_default = 'field_default_0'
field_default_contents = '%s default contents' % form_type
tc.fv( "1", field_name, field_contents )
tc.fv( "1", field_help_name, field_help_contents )
if field_type == 'SelectField':
# SelectField field_type requires a refresh_on_change
self.refresh_form( 'field_type_0', field_type )
# Add options so our select list is functional
if num_options == 0:
# Default to 2 options
num_options = 2
for index2 in range( 1, num_options+1 ):
tc.submit( "addoption_0" )
# Add contents to the new options fields
for index2 in range( num_options ):
option_field_name = 'field_0_option_%i' % index2
option_field_value = 'Option%i' % index2
tc.fv( "1", option_field_name, option_field_value )
else:
tc.fv( "1", "field_type_0", field_type )
tc.fv( "1", field_default, field_default_contents )
tc.submit( "save_changes_button" )
if num_fields == 0:
self.visit_url( "%s/forms/manage" % self.url )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
def edit_form( self, id, form_type='', new_form_name='', new_form_desc='', field_dicts=[], field_index=0,
strings_displayed=[], strings_not_displayed=[], strings_displayed_after_submit=[] ):
"""Edit form details; name and description"""
self.home()
self.visit_url( "%s/forms/manage?operation=Edit&id=%s" % ( self.url, id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
if new_form_name:
tc.fv( "1", "name", new_form_name )
if new_form_desc:
tc.fv( "1", "description", new_form_desc )
for i, field_dict in enumerate( field_dicts ):
index = i + field_index
tc.submit( "add_field_button" )
field_name = "field_name_%i" % index
field_value = field_dict[ 'name' ]
field_help = "field_helptext_%i" % index
field_help_value = field_dict[ 'desc' ]
field_type = "field_type_%i" % index
field_type_value = field_dict[ 'type' ]
field_required = "field_required_%i" % index
field_required_value = field_dict[ 'required' ]
tc.fv( "1", field_name, field_value )
tc.fv( "1", field_help, field_help_value )
tc.fv( "1", field_required, field_required_value )
if field_type_value.lower() == 'selectfield':
# SelectFields require a refresh_on_change
self.refresh_form( field_type, field_type_value )
for option_index, option in enumerate( field_dict[ 'selectlist' ] ):
tc.submit( "addoption_0" )
tc.fv( "1", "field_%i_option_%i" % ( index, option_index ), option )
else:
tc.fv( "1", field_type, field_type_value )
tc.submit( "save_changes_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
def mark_form_deleted( self, form_id ):
"""Mark a form_definition as deleted"""
self.home()
url = "%s/forms/manage?operation=delete&id=%s" % ( self.url, form_id )
self.visit_url( url )
check_str = "1 forms have been deleted."
self.check_page_for_string( check_str )
self.home()
# Requests stuff
def check_request_grid( self, cntrller, state, deleted=False, strings_displayed=[] ):
self.visit_url( '%s/%s/browse_requests?sort=create_time&f-state=%s&f-deleted=%s' % \
( self.url, cntrller, state.replace( ' ', '+' ), str( deleted ) ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def create_request_type( self, name, desc, request_form_id, sample_form_id, states, strings_displayed=[], strings_displayed_after_submit=[] ):
self.home()
self.visit_url( "%s/requests_admin/create_request_type" % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( "1", "name", name )
tc.fv( "1", "desc", desc )
tc.fv( "1", "request_form_id", request_form_id )
tc.fv( "1", "sample_form_id", sample_form_id )
for index, state in enumerate(states):
tc.submit( "add_state_button" )
tc.fv("1", "state_name_%i" % index, state[0])
tc.fv("1", "state_desc_%i" % index, state[1])
tc.submit( "save_request_type" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def request_type_permissions( self, request_type_id, request_type_name, role_ids_str, permissions_in, permissions_out ):
# role_ids_str must be a comma-separated string of role ids
url = "requests_admin/request_type_permissions?id=%s&update_roles_button=Save" % ( request_type_id )
for po in permissions_out:
key = '%s_out' % po
url ="%s&%s=%s" % ( url, key, role_ids_str )
for pi in permissions_in:
key = '%s_in' % pi
url ="%s&%s=%s" % ( url, key, role_ids_str )
self.home()
self.visit_url( "%s/%s" % ( self.url, url ) )
check_str = "Permissions updated for sequencer configuration '%s'" % request_type_name
self.check_page_for_string( check_str )
self.home()
def create_request( self, cntrller, request_type_id, name, desc, field_value_tuples, other_users_id='',
strings_displayed=[], strings_displayed_after_submit=[] ):
self.visit_url( "%s/requests_common/create_request?cntrller=%s" % ( self.url, cntrller ) )
# The request_type SelectList requires a refresh_on_change
self.refresh_form( 'request_type_id', request_type_id )
if cntrller == 'requests_admin' and other_users_id:
# The admin is creating a request on behalf of another user
# The user_id SelectField requires a refresh_on_change so that the selected
# user's addresses will be populated in the AddressField widget
self.refresh_form( "user_id", other_users_id )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( "1", "name", name )
tc.fv( "1", "desc", desc )
for index, field_value_tuple in enumerate( field_value_tuples ):
field_name = "field_%i" % index
field_value, refresh_on_change = field_value_tuple
if refresh_on_change:
# TODO: If the field is an AddressField, we should test for adding a new address
# which would need to be handled here. This currently only allows an existing
# user_address to be selected.
self.refresh_form( field_name, field_value )
else:
tc.fv( "1", field_name, field_value )
tc.submit( "create_request_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
self.home()
def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[],
strings_displayed=[], strings_displayed_after_submit=[] ):
self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.check_page_for_string( 'Edit sequencing request "%s"' % name )
if new_name:
tc.fv( "1", "name", new_name )
if new_desc:
tc.fv( "1", "desc", new_desc )
for index, field_value in enumerate( new_fields ):
tc.fv( "1", "field_%i" % index, field_value )
tc.submit( "edit_basic_request_info_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ):
self.visit_url( "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
# Simulate clicking the add-sample_button on the form. (gvk: 9/21/10 - TODO : There must be a bug in the mako template
# because twill cannot find any forms on the page, but I cannot find it although I've spent time cleaning up the
# template code and looking for any problems.
url = "%s/requests_common/manage_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id )
# This should work, but although twill does not thorw any exceptions, the button click never occurs
# There are multiple forms on this page, and we'll only be using the form named manage_request.
# for sample_index, sample_value_tuple in enumerate( sample_value_tuples ):
# # Add the following form value to the already populated hidden field so that the manage_request
# # form is the current form
# tc.fv( "1", "id", request_id )
# tc.submit( 'add_sample_button' )
for sample_index, sample_value_tuple in enumerate( sample_value_tuples ):
sample_name, field_values = sample_value_tuple
sample_name = sample_name.replace( ' ', '+' )
field_name = "sample_%i_name" % sample_index
# The following form_value setting should work but since twill barfed on submitting the add_sample_button
# above, we have to simulate it by appending to the url.
# tc.fv( "1", field_name, sample_name )
url += "&%s=%s" % ( field_name, sample_name )
for field_index, field_value in enumerate( field_values ):
field_name = "sample_%i_field_%i" % ( sample_index, field_index )
field_value = field_value.replace( ' ', '+' )
# The following form_value setting should work but since twill barfed on submitting the add_sample_button
# above, we have to simulate it by appending to the url.
# tc.fv( "1", field_name, field_value )
url += "&%s=%s" % ( field_name , field_value )
# The following button submit should work but since twill barfed on submitting the add_sample_button
# above, we have to simulate it by appending to the url.
# tc.submit( "save_samples_button" )
url += "&save_samples_button=Save"
self.visit_url( url )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def submit_request( self, cntrller, request_id, request_name, strings_displayed_after_submit=[] ):
self.visit_url( "%s/requests_common/submit_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def reject_request( self, request_id, request_name, comment, strings_displayed=[], strings_displayed_after_submit=[] ):
self.visit_url( "%s/requests_admin/reject?id=%s" % ( self.url, request_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.fv( "1", "comment", comment )
tc.submit( "reject_button" )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def add_bar_codes( self, request_id, request_name, bar_codes, samples, strings_displayed_after_submit=[] ):
# We have to simulate the form submission here since twill barfs on the page
# gvk - 9/22/10 - TODO: make sure the mako template produces valid html
url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s&managing_samples=True" % ( self.url, request_id )
for index, field_value in enumerate( bar_codes ):
sample_field_name = "sample_%i_name" % index
sample_field_value = samples[ index ].name.replace( ' ', '+' )
field_name = "sample_%i_barcode" % index
url += "&%s=%s" % ( field_name, field_value )
url += "&%s=%s" % ( sample_field_name, sample_field_value )
url += "&save_samples_button=Save"
self.visit_url( url )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
def change_sample_state( self, request_id, request_name, sample_names, sample_ids, new_sample_state_id, new_state_name, comment='',
strings_displayed=[], strings_displayed_after_submit=[] ):
# We have to simulate the form submission here since twill barfs on the page
# gvk - 9/22/10 - TODO: make sure the mako template produces valid html
url = "%s/requests_common/manage_request?cntrller=requests_admin&id=%s" % ( self.url, request_id )
url += "&comment=%s&sample_state_id=%s" % ( comment, self.security.encode_id( new_sample_state_id ) )
# select_sample_%i=true must be included twice for each sample to simulate a CheckboxField checked setting.
for sample_id in sample_ids:
url += "&select_sample_%i=true&select_sample_%i=true" % ( sample_id, sample_id )
url += "&sample_operation=Change%20state&refresh=true"
url += "&change_state_button=Save"
self.visit_url( url )
self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
for sample_id, sample_name in zip( sample_ids, sample_names ):
self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%s" % ( self.url, self.security.encode_id( sample_id ) ) )
self.check_page_for_string( 'Events for Sample "%s"' % sample_name )
self.check_page_for_string( new_state_name )
def add_user_address( self, user_id, address_dict ):
self.home()
self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) )
self.check_page_for_string( 'Add new address' )
for field_name, value in address_dict.items():
tc.fv( "1", field_name, value )
tc.submit( "new_address_button" )
self.check_page_for_string( 'Address (%s) has been added' % address_dict[ 'short_desc' ] )
# Library stuff
def add_library_template( self, cntrller, item_type, library_id, form_id, form_name, folder_id=None, ldda_id=None ):
"""
Add a new info template to a library item - the template will ALWAYS BE SET TO INHERITABLE here. If you want to
dis-inherit your template, call the manage_library_template_inheritance() below immediately after you call this
method in your test code.
"""
self.home()
if item_type == 'library':
url = "%s/library_common/add_template?cntrller=%s&item_type=%s&library_id=%s" % \
( self.url, cntrller, item_type, library_id )
elif item_type == 'folder':
url = "%s/library_common/add_template?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id )
elif item_type == 'ldda':
url = "%s/library_common/add_template?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id, ldda_id )
self.visit_url( url )
self.check_page_for_string ( "Select a template for the" )
self.refresh_form( "form_id", form_id )
# For some unknown reason, twill barfs if the form number ( 1 ) is used in the following
# rather than the form anme ( select_template ), so we have to use the form name.
tc.fv( "select_template", "inheritable", '1' )
tc.submit( "add_template_button" )
self.check_page_for_string = 'A template based on the form "%s" has been added to this' % form_name
self.home()
def manage_library_template_inheritance( self, cntrller, item_type, library_id, folder_id=None, ldda_id=None, inheritable=True ):
# If inheritable is True, the item is currently inheritable.
self.home()
if item_type == 'library':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s" % \
( self.url, cntrller, item_type, library_id )
elif item_type == 'folder':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id )
elif item_type == 'ldda':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id, ldda_id )
self.visit_url( url )
if inheritable:
self.check_page_for_string = 'will no longer be inherited to contained folders and datasets'
else:
self.check_page_for_string = 'will now be inherited to contained folders and datasets'
self.home()
def browse_libraries_admin( self, deleted=False, strings_displayed=[], strings_not_displayed=[] ):
self.visit_url( '%s/library_admin/browse_libraries?sort=name&f-description=All&f-name=All&f-deleted=%s' % ( self.url, str( deleted ) ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed when browing library." % check_str
except:
pass
def browse_libraries_regular_user( self, strings_displayed=[], strings_not_displayed=[] ):
self.visit_url( '%s/library/browse_libraries' % self.url )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed when browing library." % check_str
except:
pass
def browse_library( self, cntrller, id, show_deleted=False, strings_displayed=[], strings_not_displayed=[] ):
self.visit_url( '%s/library_common/browse_library?cntrller=%s&id=%s&show_deleted=%s' % ( self.url, cntrller, id, str( show_deleted ) ) )
data=self.last_page()
file( 'greg.html', 'wb' ).write( data )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed when browing library." % check_str
except:
pass
def create_library( self, name='Library One', description='This is Library One', synopsis='Synopsis for Library One' ):
"""Create a new library"""
self.visit_url( "%s/library_admin/create_library" % self.url )
self.check_page_for_string( 'Create a new data library' )
tc.fv( "1", "name", name )
tc.fv( "1", "description", description )
tc.fv( "1", "synopsis", synopsis )
tc.submit( "create_library_button" )
check_str = "The new library named '%s' has been created" % name
self.check_page_for_string( check_str )
self.home()
def edit_template( self, cntrller, item_type, library_id, field_type, field_name_1, field_helptext_1, field_default_1,
folder_id='', ldda_id='', action='add_field' ):
"""Edit the form fields defining a library template"""
self.visit_url( "%s/library_common/edit_template?cntrller=%s&item_type=%s&library_id=%s" % \
( self.url, cntrller, item_type, library_id ) )
self.check_page_for_string( "Edit form definition" )
if action == 'add_field':
tc.submit( "add_field_button" )
tc.fv( "edit_form", "field_name_1", field_name_1 )
tc.fv( "edit_form", "field_helptext_1", field_helptext_1 )
if field_type == 'SelectField':
# Performs a refresh_on_change in this case
self.refresh_form( "field_type_1", field_type )
else:
tc.fv( "edit_form", "field_type_1", field_type )
tc.fv( "edit_form", "field_default_1", field_default_1 )
tc.submit( 'save_changes_button' )
self.check_page_for_string( "The template for this data library has been updated with your changes." )
def library_info( self, cntrller, library_id, library_name='', new_name='', new_description='', new_synopsis='',
template_fields=[], strings_displayed=[] ):
"""Edit information about a library, optionally using an existing template with up to 2 elements"""
self.visit_url( "%s/library_common/library_info?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
if new_name and new_description and new_synopsis:
tc.fv( '1', 'name', new_name )
tc.fv( '1', 'description', new_description )
tc.fv( '1', 'synopsis', new_synopsis )
tc.submit( 'library_info_button' )
self.check_page_for_string( "Information updated for library" )
if template_fields:
for field_name, field_value in template_fields:
# The 2nd form on the page contains the template, and the form is named edit_info.
# Set the template field value
tc.fv( "edit_info", field_name, field_value )
tc.submit( 'edit_info_button' )
self.home()
def library_permissions( self, library_id, library_name, role_ids_str, permissions_in, permissions_out, cntrller='library_admin' ):
# role_ids_str must be a comma-separated string of role ids
url = "library_common/library_permissions?id=%s&cntrller=%s&update_roles_button=Save" % ( library_id, cntrller )
for po in permissions_out:
key = '%s_out' % po
url ="%s&%s=%s" % ( url, key, role_ids_str )
for pi in permissions_in:
key = '%s_in' % pi
url ="%s&%s=%s" % ( url, key, role_ids_str )
self.home()
self.visit_url( "%s/%s" % ( self.url, url ) )
check_str = "Permissions updated for library '%s'." % library_name
self.check_page_for_string( check_str )
self.home()
def make_library_item_public( self, library_id, id, cntrller='library_admin', item_type='library',
contents=False, library_name='', folder_name='', ldda_name='' ):
url = "%s/library_common/make_library_item_public?cntrller=%s&library_id=%s&item_type=%s&id=%s&contents=%s" % \
( self.url, cntrller, library_id, item_type, id, str( contents ) )
self.visit_url( url )
if item_type == 'library':
if contents:
check_str = "The data library (%s) and all it's contents have been made publicly accessible." % library_name
else:
check_str = "The data library (%s) has been made publicly accessible, but access to it's contents has been left unchanged." % library_name
elif item_type == 'folder':
check_str = "All of the contents of folder (%s) have been made publicly accessible." % folder_name
elif item_type == 'ldda':
check_str = "The libary dataset (%s) has been made publicly accessible." % ldda_name
self.check_page_for_string( check_str )
# Library folder stuff
def add_folder( self, cntrller, library_id, folder_id, name='Folder One', description='This is Folder One' ):
"""Create a new folder"""
url = "%s/library_common/create_folder?cntrller=%s&library_id=%s&parent_id=%s" % ( self.url, cntrller, library_id, folder_id )
self.visit_url( url )
self.check_page_for_string( 'Create a new folder' )
tc.fv( "1", "name", name )
tc.fv( "1", "description", description )
tc.submit( "new_folder_button" )
check_str = "The new folder named '%s' has been added to the data library." % name
self.check_page_for_string( check_str )
self.home()
def folder_info( self, cntrller, folder_id, library_id, name='', new_name='', description='',
template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[],
strings_displayed_after_submit=[], strings_not_displayed_after_submit=[] ):
"""Add information to a library using an existing template with 2 elements"""
self.visit_url( "%s/library_common/folder_info?cntrller=%s&id=%s&library_id=%s" % \
( self.url, cntrller, folder_id, library_id ) )
if name and new_name and description:
tc.fv( '1', "name", new_name )
tc.fv( '1', "description", description )
tc.submit( 'rename_folder_button' )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed." % check_str
except:
pass
if template_refresh_field_contents:
# A template containing an AddressField is displayed on the form, so we need to refresh the form
# with the received template_refresh_field_contents. There are 2 forms on the folder_info page
# when in edit mode, and the 2nd one is the one we want.
self.refresh_form( "field_0", template_refresh_field_contents, form_no=2 )
if template_fields:
# We have an information template associated with the folder, so
# there are 2 forms on this page and the template is the 2nd form
for field_name, field_value in template_fields:
tc.fv( "edit_info", field_name, field_value )
tc.submit( 'edit_info_button' )
for check_str in strings_displayed_after_submit:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed_after_submit:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) incorrectly displayed." % check_str
except:
pass
self.home()
# Library dataset stuff
def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='',
upload_option='upload_file', file_type='auto', dbkey='hg18', space_to_tab='',
link_data_only='', dont_preserve_dirs='', roles=[], ldda_message='', hda_ids='',
template_refresh_field_contents='', template_fields=[], show_deleted='False', strings_displayed=[] ):
"""Add datasets to library using any upload_option"""
# NOTE: due to the library_wait() method call at the end of this method, no tests should be done
# for strings_displayed_after_submit.
url = "%s/library_common/upload_library_dataset?cntrller=%s&library_id=%s&folder_id=%s" % \
( self.url, cntrller, library_id, folder_id )
if replace_id:
# If we're uploading a new version of a library dataset, we have to include the replace_id param in the
# request because the form field named replace_id will not be displayed on the upload form if we dont.
url += "&replace_id=%s" % replace_id
self.visit_url( url )
if template_refresh_field_contents:
# A template containing an AddressField is displayed on the upload form, so we need to refresh the form
# with the received template_refresh_field_contents.
self.refresh_form( "field_0", template_refresh_field_contents )
for tup in template_fields:
tc.fv( "1", tup[0], tup[1] )
tc.fv( "1", "library_id", library_id )
tc.fv( "1", "folder_id", folder_id )
tc.fv( "1", "show_deleted", show_deleted )
tc.fv( "1", "ldda_message", ldda_message )
tc.fv( "1", "file_type", file_type )
tc.fv( "1", "dbkey", dbkey )
if space_to_tab:
tc.fv( "1", "space_to_tab", space_to_tab )
if link_data_only:
tc.fv( "1", "link_data_only", link_data_only )
if dont_preserve_dirs:
tc.fv( "1", "dont_preserve_dirs", dont_preserve_dirs )
for role_id in roles:
tc.fv( "1", "roles", role_id )
# Refresh the form by selecting the upload_option - we do this here to ensure
# all previously entered form contents are retained.
self.refresh_form( 'upload_option', upload_option )
if upload_option == 'import_from_history':
for check_str in strings_displayed:
self.check_page_for_string( check_str )
if hda_ids:
# Twill cannot handle multi-checkboxes, so the form can only have 1 hda_ids checkbox
try:
tc.fv( "add_history_datasets_to_library", "hda_ids", hda_ids )
except:
tc.fv( "add_history_datasets_to_library", "hda_ids", '1' )
tc.submit( 'add_history_datasets_to_library_button' )
else:
if filename:
filename = self.get_filename( filename )
tc.formfile( "1", "files_0|file_data", filename )
elif server_dir:
tc.fv( "1", "server_dir", server_dir )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
tc.submit( "runtool_btn" )
# Give the files some time to finish uploading
self.library_wait( library_id )
data = self.last_page()
file( 'greg1.html', 'wb' ).write( data )
self.home()
def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str,
permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ):
# role_ids_str must be a comma-separated string of role ids
url = "%s/library_common/ldda_permissions?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \
( self.url, cntrller, library_id, folder_id, id )
for po in permissions_out:
key = '%s_out' % po
url ="%s&%s=%s" % ( url, key, role_ids_str )
for pi in permissions_in:
key = '%s_in' % pi
url ="%s&%s=%s" % ( url, key, role_ids_str )
if permissions_in or permissions_out:
url += "&update_roles_button=Save"
self.visit_url( url )
if not strings_displayed:
strings_displayed = [ "Permissions updated for dataset '%s'." % ldda_name ]
for check_str in strings_displayed:
self.check_page_for_string( check_str )
self.home()
def ldda_edit_info( self, cntrller, library_id, folder_id, ldda_id, ldda_name, new_ldda_name='',
template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[] ):
"""Edit library_dataset_dataset_association information, optionally template element information"""
self.visit_url( "%s/library_common/ldda_edit_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \
( self.url, cntrller, library_id, folder_id, ldda_id ) )
check_str = 'Edit attributes of %s' % ldda_name
self.check_page_for_string( check_str )
if new_ldda_name:
tc.fv( '1', 'name', new_ldda_name )
tc.submit( 'save' )
check_str = "Attributes updated for library dataset '%s'." % new_ldda_name
self.check_page_for_string( check_str )
if template_refresh_field_contents:
# A template containing an AddressField is displayed on the upload form, so we need to refresh the form
# with the received template_refresh_field_contents. There are 4 forms on this page, and the template is
# contained in the 4th form named "edit_info".
self.refresh_form( "field_0", template_refresh_field_contents, form_no=4 )
if template_fields:
# We have an information template associated with the folder, so
# there are 2 forms on this page and the template is the 2nd form
for field_name, field_value in template_fields:
tc.fv( "edit_info", field_name, field_value )
tc.submit( 'edit_info_button' )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
try:
self.check_page_for_string( check_str )
raise AssertionError, "String (%s) should not have been displayed on ldda Edit Attributes page." % check_str
except:
pass
self.home()
def act_on_multiple_datasets( self, cntrller, library_id, do_action, ldda_ids='', strings_displayed=[] ):
# Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission
# by going directly to the form action
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&ldda_ids=%s&do_action=%s' \
% ( self.url, cntrller, library_id, ldda_ids, do_action ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
def download_archive_of_library_files( self, cntrller, library_id, ldda_ids, format ):
self.home()
# Here it would be ideal to have twill set form values and submit the form, but
# twill barfs on that due to the recently introduced page wrappers around the contents
# of the browse_library.mako template which enable panel layout when visiting the
# page from an external URL. By "barfs", I mean that twill somehow loses hod on the
# cntrller param. We'll just simulate the form submission by building the URL manually.
# Here's the old, better approach...
#self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) )
#for ldda_id in ldda_ids:
# tc.fv( "1", "ldda_ids", ldda_id )
#tc.fv( "1", "do_action", format )
#tc.submit( "action_on_datasets_button" )
# Here's the new approach...
url = "%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&do_action=%s" % ( self.url, cntrller, library_id, format )
for ldda_id in ldda_ids:
url += "&ldda_ids=%s" % ldda_id
self.visit_url( url )
tc.code( 200 )
archive = self.write_temp_file( self.last_page(), suffix='.' + format )
self.home()
return archive
def check_archive_contents( self, archive, lddas ):
def get_ldda_path( ldda ):
path = ""
parent_folder = ldda.library_dataset.folder
while parent_folder is not None:
if parent_folder.parent is None:
path = os.path.join( parent_folder.library_root[0].name, path )
break
path = os.path.join( parent_folder.name, path )
parent_folder = parent_folder.parent
path += ldda.name
return path
def mkdir( file ):
dir = os.path.join( tmpd, os.path.dirname( file ) )
if not os.path.exists( dir ):
os.makedirs( dir )
tmpd = tempfile.mkdtemp()
if tarfile.is_tarfile( archive ):
t = tarfile.open( archive )
for n in t.getnames():
mkdir( n )
t.extract( n, tmpd )
t.close()
elif zipfile.is_zipfile( archive ):
z = zipfile.ZipFile( archive, 'r' )
for n in z.namelist():
mkdir( n )
open( os.path.join( tmpd, n ), 'wb' ).write( z.read( n ) )
z.close()
else:
raise Exception( 'Unable to read archive: %s' % archive )
for ldda in lddas:
orig_file = self.get_filename( ldda.name )
downloaded_file = os.path.join( tmpd, get_ldda_path( ldda ) )
assert os.path.exists( downloaded_file )
try:
self.files_diff( orig_file, downloaded_file )
except AssertionError, err:
errmsg = 'Library item %s different than expected, difference:\n' % ldda.name
errmsg += str( err )
errmsg += 'Unpacked archive remains in: %s\n' % tmpd
raise AssertionError( errmsg )
shutil.rmtree( tmpd )
def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ):
"""Mark a library item as deleted"""
self.home()
self.visit_url( "%s/library_common/delete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \
% ( self.url, cntrller, library_id, item_id, item_type ) )
if item_type == 'library_dataset':
item_desc = 'Dataset'
else:
item_desc = item_type.capitalize()
check_str = "%s '%s' has been marked deleted" % ( item_desc, item_name )
self.check_page_for_string( check_str )
self.home()
def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ):
"""Mark a library item as deleted"""
self.home()
self.visit_url( "%s/library_common/undelete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \
% ( self.url, cntrller, library_id, item_id, item_type ) )
if item_type == 'library_dataset':
item_desc = 'Dataset'
else:
item_desc = item_type.capitalize()
check_str = "%s '%s' has been marked undeleted" % ( item_desc, item_name )
self.check_page_for_string( check_str )
self.home()
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 ) )
check_str = "Library '%s' and all of its contents have been purged" % library_name
self.check_page_for_string( check_str )
self.home()
def library_wait( self, library_id, cntrller='library_admin', maxiter=90 ):
"""Waits for the tools to finish"""
count = 0
sleep_amount = 1
while count < maxiter:
count += 1
self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) )
page = tc.browser.get_html()
if page.find( '' ) > -1:
time.sleep( sleep_amount )
sleep_amount += 1
else:
break
self.assertNotEqual(count, maxiter)
# Tests associated with tags
def add_tag( self, item_id, item_class, context, new_tag ):
self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" % \
( self.url, item_id, item_class, context, new_tag ) )