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May 2009

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[hg] galaxy 2391: Fix for pasting data in the upload utility - n...
by Greg Von Kuster 01 May '09

01 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9ad7b4abbfc7 changeset: 2391:9ad7b4abbfc7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri May 01 10:11:00 2009 -0400 description: Fix for pasting data in the upload utility - no longer results in a UnicodeWarning, added new tests to cover case. 3 file(s) affected in this change: lib/galaxy/datatypes/sniff.py test/base/twilltestcase.py test/functional/test_get_data.py diffs (136 lines): diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Thu Apr 30 16:12:59 2009 -0400 +++ b/lib/galaxy/datatypes/sniff.py Fri May 01 10:11:00 2009 -0400 @@ -30,9 +30,11 @@ if zipfile.is_zipfile( temp_name ): is_compressed = True else: - magic_check = chunk[:2] - if magic_check == util.gzip_magic: - is_compressed = True + try: + if unicode( chunk[:2] ) == unicode( util.gzip_magic ): + is_compressed = True + except: + pass if not is_compressed: # See if we have a multi-byte character file chars = chunk[:100] diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Apr 30 16:12:59 2009 -0400 +++ b/test/base/twilltestcase.py Fri May 01 10:11:00 2009 -0400 @@ -82,6 +82,18 @@ errmsg = 'The file doesn\'t exsit. Please check' % file errmsg += str( err ) raise AssertionError( errmsg ) + 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 ) # Functions associated with histories def check_history_for_errors( self ): @@ -663,16 +675,23 @@ self.home() # Tests associated with roles - def create_role( self, name='Role One', description="This is Role One", in_user_ids=[], in_group_ids=[], private_role='' ): + 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/create_role?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 ) - check_str = "Role '%s' has been created with %d associated users and %d associated groups" % ( name, len( in_user_ids ), len( in_group_ids ) ) + 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 @@ -800,16 +819,35 @@ 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/admin/library?manage=True&id=%s" % ( self.url, library_id ) ) + self.visit_url( "%s/admin/library?information=True&id=%s" % ( 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/admin/library?manage=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \ + url = "%s/admin/library?information=True&id=%s&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 ): + """Add a new info template to a library""" + self.home() + url = "%s/admin/info_template?library_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % ( self.url, library_id ) + self.home() + self.visit_url( url ) + check_str = "Create a new information template for library '%s'" % library_name + self.check_page_for_string ( check_str ) + # TODO: finish this... + def add_folder_info_template( self, library_id, library_name, folder_id, folder_name ): + """Add a new info template to a folder""" + self.home() + url = "%s/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 ) + self.home() + self.visit_url( url ) + check_str = "Create a new information template for folder '%s'" % folder_name + self.check_page_for_string ( check_str ) + # TODO: finish this... def add_folder( self, library_id, folder_id, name='Folder One', description='NThis is Folder One' ): """Create a new folder""" self.home() diff -r ee9a29c9efc1 -r 9ad7b4abbfc7 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Thu Apr 30 16:12:59 2009 -0400 +++ b/test/functional/test_get_data.py Fri May 01 10:11:00 2009 -0400 @@ -3,7 +3,6 @@ """ Tests are executed in order, sorted by name""" class UploadData( TwillTestCase ): - def test_00_multi_upload( self ): """test_get_data.test_multi_upload: Testing multiple uploads""" self.login() @@ -19,12 +18,20 @@ self.verify_dataset_correctness('1.scf') self.upload_file('1.scf.zip', ftype='binseq.zip') self.verify_dataset_correctness('1.scf.zip') + self.upload_url_paste( 'hello world' ) + self.check_history_for_string( 'Pasted Entry' ) + self.check_history_for_string( 'hello world' ) self.delete_history_item( 1 ) self.delete_history_item( 2 ) self.delete_history_item( 3 ) self.delete_history_item( 4 ) self.delete_history_item( 5 ) self.delete_history_item( 6 ) + self.delete_history_item( 7 ) + self.upload_url_paste( u'hello world' ) + self.check_history_for_string( 'Pasted Entry' ) + self.check_history_for_string( 'hello world' ) + self.delete_history_item( 8 ) def test_9999_clean_up( self ): self.delete_history() self.logout()

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