1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/040d6f59f464/ changeset: r5095:040d6f59f464 user: kanwei date: 2011-02-18 23:47:07 summary: Update distutils egg to 0.7, and use the provided HTML output writer to do rst->html conversion. Remove old code that previously did this. This fixes a bug where an extra "</div>" was appended after every output, resulting in the tool config not showing in workflows, in IE. affected #: 5 files (115 bytes)

--- a/eggs.ini Fri Feb 18 16:21:11 2011 -0500 +++ b/eggs.ini Fri Feb 18 17:47:07 2011 -0500 @@ -32,7 +32,7 @@ amqplib = 0.6.1 Beaker = 1.4 decorator = 3.1.2 -docutils = 0.4 +docutils = 0.7 drmaa = 0.4b3 elementtree = 1.2.6_20050316 GeneTrack = 2.0.0_beta_1

--- a/lib/galaxy/util/__init__.py Fri Feb 18 16:21:11 2011 -0500 +++ b/lib/galaxy/util/__init__.py Fri Feb 18 17:47:07 2011 -0500 @@ -19,7 +19,7 @@

pkg_resources.require( 'docutils' ) import docutils.core -from galaxy.util.docutils_ext.htmlfrag import Writer as HTMLFragWriter +import docutils.writers.html4css1

pkg_resources.require( 'elementtree' ) from elementtree import ElementTree, ElementInclude @@ -252,7 +252,9 @@ def write( self, str ): if len( str ) > 0 and not str.isspace(): log.warn( str ) - return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) ) + return docutils.core.publish_string(s, + writer=docutils.writers.html4css1.Writer(), + settings_overrides={"embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream()})

def xml_text(root, name=None): """Returns the text inside an element"""

--- a/lib/galaxy/util/docutils_ext/htmlfrag.py Fri Feb 18 16:21:11 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -# Author: Ollie Rutherfurd -# Contact: oliver@rutherfurd.net -# Revision: $Revision: 2884 $ -# Date: $Date: 2004-12-08 20:49:05 +0100 (Wed, 08 Dec 2004) $ -# Copyright: This module has been placed in the public domain. - -""" -Simple .ht (HyperText Template) document tree Writer. - -.ht tmeplate files are essentially normal HTML, with -an option set of RFC 2822-like headers at the top of -the file. There must be at least one blank line between -the last header and the start of the body HTML. - -See http://ht2html.sf.net/ for more information on -.ht files and ht2html.. -""" - -__docformat__ = 'reStructuredText' - -import os -from docutils import nodes -from docutils import writers -from docutils import frontend -from docutils.writers.html4css1 import HTMLTranslator, utils - - -class Writer(writers.Writer): - - supported = ('htmlfrag',) - """Formats this writer supports.""" - - settings_spec = ( - 'HTML-Specific Options', - None, - (('Specify a stylesheet URL, used verbatim. Default is ' - '"default.css". Overrides --stylesheet-path.', - ['--stylesheet'], - {'default': 'default.css', 'metavar': '<URL>', - 'overrides': 'stylesheet_path'}), - ('Specify a stylesheet file, relative to the current working ' - 'directory. The path is adjusted relative to the output HTML ' - 'file. Overrides --stylesheet.', - ['--stylesheet-path'], - {'metavar': '<file>', 'overrides': 'stylesheet'}), - ('Link to the stylesheet in the output HTML file. This is the ' - 'default.', - ['--link-stylesheet'], - {'dest': 'embed_stylesheet', 'action': 'store_false', - 'validator': frontend.validate_boolean}), - ('Embed the stylesheet in the output HTML file. The stylesheet ' - 'file must be accessible during processing (--stylesheet-path is ' - 'recommended). Default: link the stylesheet, do not embed it.', - ['--embed-stylesheet'], - {'action': 'store_true', 'validator': frontend.validate_boolean}), - ('Specify the initial header level. Default is 1 for "<h1>". ' - 'Does not affect document title & subtitle (see --no-doc-title).', - ['--initial-header-level'], - {'choices': '1 2 3 4 5 6'.split(), 'default': '3', - 'metavar': '<level>'}), - ('Specify the maximum width (in characters) for one-column field ' - 'names. Longer field names will span an entire row of the table ' - 'used to render the field list. Default is 14 characters. ' - 'Use 0 for "no limit".', - ['--field-name-limit'], - {'default': 14, 'metavar': '<level>', - 'validator': frontend.validate_nonnegative_int}), - ('Specify the maximum width (in characters) for options in option ' - 'lists. Longer options will span an entire row of the table used ' - 'to render the option list. Default is 14 characters. ' - 'Use 0 for "no limit".', - ['--option-limit'], - {'default': 14, 'metavar': '<level>', - 'validator': frontend.validate_nonnegative_int}), - ('Format for footnote references: one of "superscript" or ' - '"brackets". Default is "brackets".', - ['--footnote-references'], - {'choices': ['superscript', 'brackets'], 'default': 'brackets', - 'metavar': '<format>', - 'overrides': 'trim_footnote_reference_space'}), - ('Format for block quote attributions: one of "dash" (em-dash ' - 'prefix), "parentheses"/"parens", or "none". Default is "dash".', - ['--attribution'], - {'choices': ['dash', 'parentheses', 'parens', 'none'], - 'default': 'dash', 'metavar': '<format>'}), - ('Remove extra vertical whitespace between items of bullet lists ' - 'and enumerated lists, when list items are "simple" (i.e., all ' - 'items each contain one paragraph and/or one "simple" sublist ' - 'only). Default: enabled.', - ['--compact-lists'], - {'default': 1, 'action': 'store_true', - 'validator': frontend.validate_boolean}), - ('Disable compact simple bullet and enumerated lists.', - ['--no-compact-lists'], - {'dest': 'compact_lists', 'action': 'store_false'}), - ('Omit the XML declaration. Use with caution.', - ['--no-xml-declaration'], - {'dest': 'xml_declaration', 'default': 1, 'action': 'store_false', - 'validator': frontend.validate_boolean}), - ('Scramble email addresses to confuse harvesters. ' - 'For example, "abc@example.org" will become ' - '``<a href="mailto:%61%62%63%40...">abc at example dot org</a>``.', - ['--cloak-email-addresses'], - {'action': 'store_true', 'validator': frontend.validate_boolean}),)) - - - relative_path_settings = ('stylesheet_path',) - - output = None - - def __init__(self): - writers.Writer.__init__(self) - self.translator_class = HTMLFragTranslator - - def translate(self): - visitor = self.translator_class(self.document) - self.document.walkabout(visitor) - self.output = visitor.astext() - self.stylesheet = visitor.stylesheet - self.body = visitor.body - - -class HTMLFragTranslator(HTMLTranslator): - - def __init__(self, document): - # I don't believe we can embed any style content - # the header, so always link to the stylesheet. - document.settings.embed_stylesheet = 0 - HTMLTranslator.__init__(self, document) - - def astext(self): - # kludge! want footer, but not '</body></html>' - body = self.body_pre_docinfo + self.docinfo + self.body + \ - self.body_suffix[:-1] - return ''.join(body) - -# :indentSize=4:lineSeparator=\n:noTabs=true:tabSize=4:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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