commit/galaxy-central: greg: Clean up page content rendering in the tool shed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cdbee5bc4a6d/
changeset: cdbee5bc4a6d
user: greg
date: 2012-12-03 15:31:52
summary: Clean up page content rendering in the tool shed.
affected #: 7 files
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -19,6 +19,9 @@
from elementtree import ElementTree, ElementInclude
from elementtree.ElementTree import Element, SubElement
+eggs.require( 'markupsafe' )
+import markupsafe
+
log = logging.getLogger( __name__ )
INITIAL_CHANGELOG_HASH = '000000000000'
@@ -1155,20 +1158,20 @@
return all_repository_dependencies
def get_repository_file_contents( file_path ):
if is_gzip( file_path ):
- safe_str = to_safe_str( '\ngzip compressed file\n' )
+ safe_str = to_safe_string( '\ngzip compressed file\n' )
elif is_bz2( file_path ):
- safe_str = to_safe_str( '\nbz2 compressed file\n' )
+ safe_str = to_safe_string( '\nbz2 compressed file\n' )
elif check_zip( file_path ):
- safe_str = to_safe_str( '\nzip compressed file\n' )
+ safe_str = to_safe_string( '\nzip compressed file\n' )
elif check_binary( file_path ):
- safe_str = to_safe_str( '\nBinary file\n' )
+ safe_str = to_safe_string( '\nBinary file\n' )
else:
safe_str = ''
for i, line in enumerate( open( file_path ) ):
- safe_str = '%s%s' % ( safe_str, to_safe_str( line ) )
+ safe_str = '%s%s' % ( safe_str, to_safe_string( line ) )
if len( safe_str ) > MAX_CONTENT_SIZE:
large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
- safe_str = '%s%s' % ( safe_str, to_safe_str( large_str ) )
+ safe_str = '%s%s' % ( safe_str, to_safe_string( large_str ) )
break
return safe_str
def get_repository_files( trans, folder_path ):
@@ -1631,7 +1634,7 @@
except:
file_name = fpath
return file_name
-def to_safe_str( text, to_html=True ):
+def to_safe_string( text, to_html=True ):
"""Translates the characters in text to an html string"""
translated = []
for c in text:
@@ -1639,25 +1642,29 @@
translated.append( c )
elif c in MAPPED_CHARS:
translated.append( MAPPED_CHARS[ c ] )
- elif c in [ '\n', '\r' ]:
+ elif c in [ '\n' ]:
if to_html:
translated.append( '<br/>' )
else:
translated.append( c )
+ elif c in [ '\r' ]:
+ continue
elif c in [ ' ', ' ' ]:
translated.append( c )
else:
translated.append( '' )
+ if to_html:
+ str( markupsafe.escape( ''.join( translated ) ) )
return ''.join( translated )
def tool_shed_is_this_tool_shed( toolshed_base_url ):
return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
def translate_string( raw_text, to_html=True ):
if raw_text:
if len( raw_text ) <= MAX_CONTENT_SIZE:
- translated_string = to_safe_str( raw_text, to_html=to_html )
+ translated_string = to_safe_string( raw_text, to_html=to_html )
else:
large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
- translated_string = to_safe_str( '%s%s' % ( raw_text[ 0:MAX_CONTENT_SIZE ], large_str ), to_html=to_html )
+ translated_string = to_safe_string( '%s%s' % ( raw_text[ 0:MAX_CONTENT_SIZE ], large_str ), to_html=to_html )
else:
translated_string = ''
return translated_string
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -2263,17 +2263,6 @@
if list:
return ','.join( list )
return ''
- 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( '' )
- return ''.join( translated )
def __validate_repository_name( self, name, user ):
# Repository names must be unique for each user, must be at least four characters
# in length and must contain only lower-case letters, numbers, and the '_' character.
@@ -2347,7 +2336,7 @@
anchors = modified + added + removed + deleted + unknown + ignored + clean
diffs = []
for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ):
- diffs.append( self.to_html_escaped( diff ) )
+ diffs.append( to_safe_string( diff, to_html=True ) )
is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) )
metadata = self.get_metadata( trans, id, ctx_str )
return trans.fill_template( '/webapps/community/repository/view_changeset.mako',
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 templates/webapps/community/common/common.mako
--- a/templates/webapps/community/common/common.mako
+++ b/templates/webapps/community/common/common.mako
@@ -31,16 +31,6 @@
</script></%def>
-<%def name="escape_html_add_breaks( value )">
- <%
- from galaxy import eggs
- eggs.require('markupsafe')
- import markupsafe
- value = str( markupsafe.escape( value ) ).replace( '\n', '<br/>' )
- %>
- ${value}
-</%def>
-
<%def name="render_star_rating( name, rating, disabled=False )"><%
if disabled:
@@ -71,7 +61,7 @@
<div class="form-row"><label>Detailed description:</label><table id="description_table">
- <tr><td>${ escape_html_add_breaks( description_text ) }</td></tr>
+ <tr><td>${description_text}</td></tr></table><div style="clear: both"></div></div>
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -1,4 +1,3 @@
-<%namespace file="/webapps/community/common/common.mako" import="escape_html_add_breaks" /><%def name="common_javascripts(repository)"><script type="text/javascript">
@@ -316,14 +315,17 @@
</%def><%def name="render_readme( readme, pad, parent, row_counter )">
- <% encoded_id = trans.security.encode_id( readme.id ) %>
+ <%
+ from galaxy.util.shed_util_common import to_safe_string
+ encoded_id = trans.security.encode_id( readme.id )
+ %><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- ${escape_html_add_breaks( readme.text )}
+ ${ to_safe_string( readme.text, to_html=True ) }
</td></tr><%
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 templates/webapps/community/repository/view_changeset.mako
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -185,7 +185,7 @@
ctr += 1
%><tr><td bgcolor="#E0E0E0">${anchor_str}</td></tr>
- <tr><td>${ escape_html_add_breaks( diff ) }</td></tr>
+ <tr><td>${diff}</td></tr>
%endfor
</table></div>
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 templates/webapps/community/repository/view_repository.mako
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -5,6 +5,7 @@
<%
from galaxy.web.framework.helpers import time_ago
+ from galaxy.util.shed_util_common import to_safe_string
has_readme = metadata and 'readme' in metadata
has_metadata = repository.metadata_revisions
@@ -157,7 +158,7 @@
${repository.description | h}
</div>
%if repository.long_description:
- ${render_long_description( repository.long_description )}
+ ${render_long_description( to_safe_string( repository.long_description, to_html=True ) )}
%endif
<div class="form-row"><label>Revision:</label>
diff -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 -r cdbee5bc4a6d2140401ba0ab1ce7de3e9b9882b0 templates/webapps/community/repository_review/browse_review.mako
--- a/templates/webapps/community/repository_review/browse_review.mako
+++ b/templates/webapps/community/repository_review/browse_review.mako
@@ -5,6 +5,7 @@
<%
from galaxy.web.form_builder import CheckboxField
from galaxy.webapps.community.util.container_util import STRSEP
+ from galaxy.util.shed_util_common import to_safe_string
can_manage_repository = is_admin or repository.user == trans.user
%>
@@ -93,7 +94,7 @@
<tr><td><div overflow-wrap:normal;overflow:hidden;word-break:keep-all;word-wrap:break-word;line-break:strict;>
- ${ escape_html_add_breaks( component_review.comment ) }
+ ${ to_safe_string( component_review.comment, to_html=True ) }
</div></td></tr>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Fixes for rendering certain tool shed repository content.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/20a25a4f989d/
changeset: 20a25a4f989d
user: greg
date: 2012-12-01 01:37:37
summary: Fixes for rendering certain tool shed repository content.
affected #: 2 files
diff -r 03ec137ca8a3148aa771769e80963b65194b7895 -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -1064,19 +1064,6 @@
return removed, error_message
def tool_shed_from_repository_clone_url( repository_clone_url ):
return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' )
-def translate_string( raw_text, to_html=True ):
- if raw_text:
- if to_html:
- if len( raw_text ) <= MAX_CONTENT_SIZE:
- translated_string = to_html_str( raw_text )
- else:
- large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
- translated_string = to_html_str( '%s%s' % ( raw_text[ 0:MAX_CONTENT_SIZE ], large_str ) )
- else:
- raise Exception( "String translation currently only supports text to HTML." )
- else:
- translated_string = ''
- return translated_string
def update_in_shed_tool_config( app, repository ):
# A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list
# of config_elems instead of using the in-memory list.
diff -r 03ec137ca8a3148aa771769e80963b65194b7895 -r 20a25a4f989d034c6be371ffa90947c8dc0269d3 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -62,7 +62,7 @@
f = open( full_path_to_readme_file, 'r' )
text = f.read()
f.close()
- readme_files_dict[ readme_file_name ] = str( text )
+ readme_files_dict[ readme_file_name ] = translate_string( text, to_html=False )
except Exception, e:
log.debug( "Error reading README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \
( str( relative_path_to_readme_file ), str( repository_name ), str( changeset_revision ), str( e ) ) )
@@ -1155,22 +1155,22 @@
return all_repository_dependencies
def get_repository_file_contents( file_path ):
if is_gzip( file_path ):
- to_html = to_html_str( '\ngzip compressed file\n' )
+ safe_str = to_safe_str( '\ngzip compressed file\n' )
elif is_bz2( file_path ):
- to_html = to_html_str( '\nbz2 compressed file\n' )
+ safe_str = to_safe_str( '\nbz2 compressed file\n' )
elif check_zip( file_path ):
- to_html = to_html_str( '\nzip compressed file\n' )
+ safe_str = to_safe_str( '\nzip compressed file\n' )
elif check_binary( file_path ):
- to_html = to_html_str( '\nBinary file\n' )
+ safe_str = to_safe_str( '\nBinary file\n' )
else:
- to_html = ''
+ safe_str = ''
for i, line in enumerate( open( file_path ) ):
- to_html = '%s%s' % ( to_html, to_html_str( line ) )
- if len( to_html ) > MAX_CONTENT_SIZE:
+ safe_str = '%s%s' % ( safe_str, to_safe_str( line ) )
+ if len( safe_str ) > MAX_CONTENT_SIZE:
large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
- to_html = '%s%s' % ( to_html, to_html_str( large_str ) )
+ safe_str = '%s%s' % ( safe_str, to_safe_str( large_str ) )
break
- return to_html
+ return safe_str
def get_repository_files( trans, folder_path ):
contents = []
for item in os.listdir( folder_path ):
@@ -1631,7 +1631,7 @@
except:
file_name = fpath
return file_name
-def to_html_str( text ):
+def to_safe_str( text, to_html=True ):
"""Translates the characters in text to an html string"""
translated = []
for c in text:
@@ -1639,17 +1639,28 @@
translated.append( c )
elif c in MAPPED_CHARS:
translated.append( MAPPED_CHARS[ c ] )
- elif c == ' ':
- translated.append( ' ' )
- elif c == '\t':
- translated.append( ' ' )
- elif c == '\n':
- translated.append( '<br/>' )
- elif c not in [ '\r' ]:
+ elif c in [ '\n', '\r' ]:
+ if to_html:
+ translated.append( '<br/>' )
+ else:
+ translated.append( c )
+ elif c in [ ' ', ' ' ]:
+ translated.append( c )
+ else:
translated.append( '' )
return ''.join( translated )
def tool_shed_is_this_tool_shed( toolshed_base_url ):
return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
+def translate_string( raw_text, to_html=True ):
+ if raw_text:
+ if len( raw_text ) <= MAX_CONTENT_SIZE:
+ translated_string = to_safe_str( raw_text, to_html=to_html )
+ else:
+ large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
+ translated_string = to_safe_str( '%s%s' % ( raw_text[ 0:MAX_CONTENT_SIZE ], large_str ), to_html=to_html )
+ else:
+ translated_string = ''
+ return translated_string
def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ):
"""
Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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