1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c5dcf903d84/ changeset: 7c5dcf903d84 branches: user: greg date: 2011-06-03 22:46:14 summary: Clean up displaying content in the tool shed. affected #: 3 files (625 bytes) --- a/lib/galaxy/datatypes/checkers.py Fri Jun 03 16:22:02 2011 -0400 +++ b/lib/galaxy/datatypes/checkers.py Fri Jun 03 16:46:14 2011 -0400 @@ -25,9 +25,13 @@ temp.close() return False -def check_binary( file_path ): +def check_binary( name, file_path=True ): + # Handles files if file_path is True or text if file_path is False is_binary = False - temp = open( file_path, "U" ) + if file_path: + temp = open( name, "U" ) + else: + temp = name chars_read = 0 for chars in temp: for char in chars: @@ -39,7 +43,8 @@ break if chars_read > 100: break - temp.close() + if file_path: + temp.close() return is_binary def check_gzip( file_path ): @@ -94,6 +99,10 @@ return True return False +def is_bz2( file_path ): + is_bz2, is_valid = check_bz2( file_path ) + return is_bz2 + def is_gzip( file_path ): is_gzipped, is_valid = check_gzip( file_path ) - return is_gzipped and is_valid + return is_gzipped --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jun 03 16:22:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Jun 03 16:46:14 2011 -0400 @@ -3,6 +3,7 @@ from datetime import * from galaxy import util +from galaxy.datatypes.checkers import * from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.webapps.community.model import directory_hash_id @@ -13,12 +14,12 @@ log = logging.getLogger( __name__ ) -VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) -# Characters that are valid -VALID_CHARS = set( string.letters + string.digits ) # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', '<' :'<' } +MAX_CONTENT_SIZE = 32768 +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;" ) +VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): # TODO rename this class to be categoryListGrid when we eliminate all the tools stuff. @@ -173,17 +174,6 @@ repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() - # TODO: These translations are costly, so figure out a better way... - def from_html_escaped( self, text ): - """Restores sanitized text""" - for key, value in MAPPED_CHARS.items(): - text = text.replace( value, key ) - return text - def to_html_escape_code( self, text ): - """Restricts the characters that are allowed in a text""" - for key, value in MAPPED_CHARS.items(): - text = text.replace( key, value ) - return text @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) @@ -567,23 +557,9 @@ ctx_parent = ctx.parents()[0] modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean - def is_binary( chars ): - is_binary = False - chars_read = 0 - for char in chars: - chars_read += 1 - if ord( char ) > 128: - is_binary = True - break - return is_binary diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): - if not util.is_multi_byte( diff ) and not is_binary( diff ): - # TODO: is there a better way? - diffs.append( self.to_html_escape_code( diff ) ) - else: - fixed_diff = diff.split( '\n' )[0] + '\nFile contains non-ascii characters that cannot be displayed\n' - diffs.append( fixed_diff ) + diffs.append( self.to_html_escaped( diff ) ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, ctx=ctx, @@ -681,28 +657,60 @@ message=message ) ) @web.json def get_file_contents( self, trans, file_path ): - def print_ticks( d ): - # pexpect timeout method - pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - if os.stat( file_path ).st_size > 32768: - return 'File size larger than maximum viewing size of 32 kb' - cmd = "cat %s" % file_path - # Handle the authentication message if ssh keys are not set - the message is - # something like: "Are you sure you want to continue connecting (yes/no)." - output = pexpect.run( cmd, - events={ pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - output = self.to_html_escape_code( output ) - return unicode( output.replace( '\r\n', '<br/>' ).replace( ' ', ' ' ) ) + if is_gzip( file_path ): + to_html = self.to_html_str( '\ngzip compressed file\n' ) + elif is_bz2( file_path ): + to_html = self.to_html_str( '\nbz2 compressed file\n' ) + elif check_zip( file_path ): + to_html = self.to_html_str( '\nzip compressed file\n' ) + elif check_binary( file_path ): + to_html = self.to_html_str( '\nBinary file\n' ) + else: + to_html = '' + for i, line in enumerate( open( file_path ) ): + to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) + if len( to_html ) > MAX_CONTENT_SIZE: + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %d\n' % MAX_CONTENT_SIZE + to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) + break + return to_html @web.expose def help( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) + def to_html_escaped( self, text ): + """Translates the characters in text to html values""" + translated = [] + for c in text: + if c in [ '\r\n', '\n', ' ', '\t' ] or c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + else: + translated.append( 'X' ) + return ''.join( translated ) + def to_html_str( self, text ): + """Translates the characters in text to sn html string""" + translated = [] + for c in text: + if c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + elif c == ' ': + translated.append( ' ' ) + elif c == '\t': + translated.append( '    ' ) + elif c in [ '\r\n', '\n' ]: + translated.append( '<br/>' ) + else: + translated.append( 'X' ) + return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): options = [] for user in trans.sa_session.query( trans.model.User ): --- a/templates/webapps/community/repository/common.mako Fri Jun 03 16:22:02 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Fri Jun 03 16:46:14 2011 -0400 @@ -42,7 +42,6 @@ document.upload_form.upload_point.value = selKeys[0]; }, onActivate: function(dtnode) { - // TODO: certainly not ideal - find a better way to display the file contents. var cell = $("#file_contents"); var selected_value; if (dtnode.data.key == 'root') { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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