galaxy-commits October 2013

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commit/galaxy-central: greg: Add an additional filter to correct improper image declarations so they will be displayed in tool config help sections or reqdme files contained in tool shed repositories.
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/836b6a16e5a9/ Changeset: 836b6a16e5a9 User: greg Date: 2013-10-04 16:13:44 Summary: Add an additional filter to correct improper image declarations so they will be displayed in tool config help sections or reqdme files contained in tool shed repositories. Affected #: 1 file diff -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac -r 836b6a16e5a9e499c0a07b23b69c25a3f17eba98 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1519,7 +1519,9 @@ route_to_images = '/repository/static/images/%s' % encoded_repository_id # We used to require $PATH_TO_IMAGES, but we now eliminate it if it's used. text = text.replace( '$PATH_TO_IMAGES', '' ) - # We can eliminate the default setting of /static/images since the routs will properly display images contained in that directory. + # Eliminate the invalid setting of ./static/images since the routes will properly display images contained in that directory. + text = text.replace( './static/images', '' ) + # Eliminate the default setting of /static/images since the routes will properly display images contained in that directory. text = text.replace( '/static/images', '' ) # Use regex to instantiate routes into the defined image paths. for match in re.findall( '.. image:: (?!http)/?(.+)', text ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the framework that display images declared in the help section of Galaxy tool configs contained in tool shed repositories to also work in README files with a .rst extension that are contained in repositories. Remote images that are available view http requests are supported as are any relative path for locating the image if it is contained within the repository hierarchy. The previously required $PATH_TO_IMAGES is no longer required, and is ignored if us
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bb04279216e/ Changeset: 1bb04279216e User: greg Date: 2013-10-04 16:04:25 Summary: Enhance the framework that display images declared in the help section of Galaxy tool configs contained in tool shed repositories to also work in README files with a .rst extension that are contained in repositories. Remote images that are available view http requests are supported as are any relative path for locating the image if it is contained within the repository hierarchy. The previously required $PATH_TO_IMAGES is no longer required, and is ignored if used. The following image declarations are all supported: .. image:: http://www.animalphotos.me/mammal/mammal-wcat_files/wildcat7.jpg .. image:: https://raw.github.com/peterjc/picobio/769e4a77194587207f50707939db42b9f04b… .. image:: $PATH_TO_IMAGES/count_modes.png .. image:: count_modes.png .. image:: /deep/Phyca11_example_output.png Affected #: 11 files diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -11,6 +11,7 @@ import shutil import sys import tempfile +import threading import traceback import types import urllib @@ -1333,19 +1334,16 @@ help_header = "" help_footer = "" if self.help is not None: - # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy. - # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk. - if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: - if self.app.name == 'galaxy': - repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/tool_runner/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) - elif self.app.name == 'tool_shed': - repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/repository/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) + if self.repository_id and self.help.text.find( '.. image:: ' ) >= 0: + # Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy. + lock = threading.Lock() + lock.acquire( True ) + try: + self.help.text = shed_util_common.set_image_paths( self.app, self.repository_id, self.help.text ) + except Exception, e: + log.exception( "Exception in parse_help, so images may not be properly displayed:\n%s" % str( e ) ) + finally: + lock.release() help_pages = self.help.findall( "page" ) help_header = self.help.text try: diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,8 +46,12 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # The following route will handle displaying tool shelp images for tools contained in repositories installed from the tool shed. - webapp.add_route( '/tool_runner/static/images/:repository_id/:image_file', controller='tool_runner', action='display_tool_help_image_in_repository', repository_id=None, image_file=None ) + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -285,6 +285,28 @@ status=status ) @web.expose + def display_image_in_repository( self, trans, **kwd ): + """ + Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The + image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that + is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer + required, and is now ignored. + .. image:: https://raw.github.com/galaxy/some_image.png + .. image:: $PATH_TO_IMAGES/some_image.png + .. image:: /static/images/some_image.gif + .. image:: some_image.jpg + .. image:: /deep/some_image.png + """ + repository_id = kwd.get( 'repository_id', None ) + relative_path_to_image_file = kwd.get( 'image_file', None ) + if repository_id and relative_path_to_image_file: + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + repo_files_dir = repository.repo_files_directory( trans.app ) + path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) + return open( path_to_file, 'r' ) + return None + + @web.expose @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -98,22 +98,6 @@ **vars ) @web.expose - def display_tool_help_image_in_repository( self, trans, **kwd ): - repository_id = kwd.get( 'repository_id', None ) - image_file = kwd.get( 'image_file', None ) - if repository_id and image_file: - repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) - repo_files_dir = os.path.join( repository.repo_files_directory( trans.app ) ) - default_path = os.path.abspath( os.path.join( repo_files_dir, 'static', 'images', image_file ) ) - if os.path.exists( default_path ): - return open( default_path, 'r' ) - else: - path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, image_file ) - if os.path.exists( path_to_file ): - return open( path_to_file, 'r' ) - return None - - @web.expose def rerun( self, trans, id=None, from_noframe=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -69,8 +69,12 @@ webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' ) webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' ) webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' ) - # The following route will handle displaying tool shelp images for tools contained in repositories. - webapp.add_route( '/repository/static/images/:repository_id/:image_file', controller='repository', action='display_tool_help_image_in_repository', repository_id=None, image_file=None ) + # Handle displaying tool help images and README file images for tools contained in repositories. + webapp.add_route( '/repository/static/images/:repository_id/:image_file', + controller='repository', + action='display_image_in_repository', + repository_id=None, + image_file=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -666,7 +666,7 @@ # Update repository files for browsing. suc.update_repository( repo ) changeset_revision = repository.tip( trans.app ) - metadata = self.get_metadata( trans, id, changeset_revision ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, @@ -897,7 +897,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) if trans.user and trans.user.email: return trans.fill_template( "/webapps/tool_shed/repository/contact_owner.mako", repository=repository, @@ -1015,6 +1018,27 @@ status=status ) ) @web.expose + def display_image_in_repository( self, trans, **kwd ): + """ + Open an image file that is contained in repository or that is referenced by a URL for display. The image can be defined in + either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. + The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. + .. image:: https://raw.github.com/galaxy/some_image.png + .. image:: $PATH_TO_IMAGES/some_image.png + .. image:: /static/images/some_image.gif + .. image:: some_image.jpg + .. image:: /deep/some_image.png + """ + repository_id = kwd.get( 'repository_id', None ) + relative_path_to_image_file = kwd.get( 'image_file', None ) + if repository_id and relative_path_to_image_file: + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repo_files_dir = os.path.join( repository.repo_path( trans.app ), repository.name ) + path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) + return open( path_to_file, 'r' ) + return None + + @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -1023,7 +1047,10 @@ if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) - metadata = self.get_metadata( trans, repository_id, changeset_revision ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + repository_id, + changeset_revision, + metadata_only=True ) try: return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, @@ -1052,22 +1079,6 @@ status='error' ) ) @web.expose - def display_tool_help_image_in_repository( self, trans, **kwd ): - repository_id = kwd.get( 'repository_id', None ) - image_file = kwd.get( 'image_file', None ) - if repository_id and image_file: - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - repo_files_dir = os.path.join( repository.repo_path( trans.app ), repository.name ) - default_path = os.path.abspath( os.path.join( repo_files_dir, 'static', 'images', image_file ) ) - if os.path.exists( default_path ): - return open( default_path, 'r' ) - else: - path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, image_file ) - if os.path.exists( path_to_file ): - return open( path_to_file, 'r' ) - return None - - @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): """Download an archive of the repository files compressed as zip, gz or bz2.""" # FIXME: thgis will currently only download the repository tip, no matter which installable changeset_revision is being viewed. @@ -1571,12 +1582,6 @@ pubdate=strftime( '%a, %d %b %Y %H:%M:%S UT', gmtime() ), items=functional_test_results ) - def get_metadata( self, trans, repository_id, changeset_revision ): - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - if repository_metadata and repository_metadata.metadata: - return repository_metadata.metadata - return None - @web.json def get_readme_files( self, trans, **kwd ): """ @@ -2409,7 +2414,10 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, @@ -2806,7 +2814,10 @@ 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + id, + repository.tip( trans.app ), + metadata_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/view_changelog.mako', repository=repository, metadata=metadata, @@ -2839,7 +2850,7 @@ diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( suc.to_html_string( diff ) ) - metadata = self.get_metadata( trans, id, ctx_str ) + metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: ctx_parent_rev = ctx_parent.rev() diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1072,13 +1072,15 @@ """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) -def get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision ): - """Get a specified metadata record for a specified repository.""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), - trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ - .first() - +def get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=False ): + """Get a specified metadata record for a specified repository in the tool shed.""" + if metadata_only: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata and repository_metadata.metadata: + return repository_metadata.metadata + return None + return suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + def get_repository_metadata_revisions_for_review( repository, reviewed=True ): repository_metadata_revisions = [] metadata_changeset_revision_hashes = [] diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -1,7 +1,11 @@ import logging import os +import threading +from mako.template import Template from galaxy import eggs +from galaxy import web from galaxy.util import json +from galaxy.util import rst_to_html from galaxy.util import unicodify import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util @@ -34,13 +38,39 @@ full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) ) else: full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file ) + text = None try: f = open( full_path_to_readme_file, 'r' ) text = unicodify( f.read() ) f.close() - readme_files_dict[ readme_file_name ] = suc.size_string( text ) except Exception, e: log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) ) + text = None + if text: + text_of_reasonable_length = suc.size_string( text ) + if text_of_reasonable_length.find( '.. image:: ' ) >= 0: + # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy. + lock = threading.Lock() + lock.acquire( True ) + try: + text_of_reasonable_length = suc.set_image_paths( trans.app, + trans.security.encode_id( repository.id ), + text_of_reasonable_length ) + except Exception, e: + log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) ) + finally: + lock.release() + if readme_file_name.endswith( '.rst' ): + text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ), + input_encoding='utf-8', + output_encoding='utf-8', + default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) + text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ), + host_url=web.url_for( '/', qualified=True ) ) + else: + text_of_reasonable_length = suc.to_html_string( text_of_reasonable_length ) + readme_files_dict[ readme_file_name ] = text_of_reasonable_length else: # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest. ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1,5 +1,6 @@ import logging import os +import re import shutil import string import tempfile @@ -1504,6 +1505,28 @@ """Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision.""" return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) +def set_image_paths( app, encoded_repository_id, text ): + """ + Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy as well as image + display in repository README files. This method will determine the location of the image file and return the path to it that will enable + the caller to open the file. + """ + if text: + if app.name == 'galaxy': + route_to_images = '/admin_toolshed/static/images/%s' % encoded_repository_id + else: + # We're in the tool shed. + route_to_images = '/repository/static/images/%s' % encoded_repository_id + # We used to require $PATH_TO_IMAGES, but we now eliminate it if it's used. + text = text.replace( '$PATH_TO_IMAGES', '' ) + # We can eliminate the default setting of /static/images since the routs will properly display images contained in that directory. + text = text.replace( '/static/images', '' ) + # Use regex to instantiate routes into the defined image paths. + for match in re.findall( '.. image:: (?!http)/?(.+)', text ): + text = text.replace( match, match.replace( '/', '%2F' ) ) + text = re.sub( '.. image:: (?!http)/?(.+)', '.. image:: %s/\\1' % route_to_images, text ) + return text + def set_only_if_compiling_contained_td( repository, required_repository ): """Return True if the received required_repository is only needed to compile a tool dependency defined for the received repository.""" # This method is called only from Galaxy when rendering repository dependencies for an installed tool shed repository. diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -584,12 +584,7 @@ </%def><%def name="render_readme( readme, pad, parent, row_counter )"> - <% - from tool_shed.util.shed_util_common import to_html_string - from galaxy.util import rst_to_html - encoded_id = trans.security.encode_id( readme.id ) - render_rst = readme.name.endswith( '.rst' ) - %> + <% encoded_id = trans.security.encode_id( readme.id ) %><tr class="datasetRow" %if parent is not None: parent="${parent}" @@ -597,11 +592,7 @@ id="libraryItem-rr-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="readme_files"> - %if render_rst: - <tr><td>${ rst_to_html( readme.text ) }</td></tr> - %else: - <tr><td>${ to_html_string( readme.text ) }</td></tr> - %endif + <tr><td>${ readme.text }</td></tr></table></td></tr> diff -r 288203bc6e4eac539ad2008ca088530cf2250cee -r 1bb04279216e0abf4e24b9299cccc06c10b9c0ac test/tool_shed/functional/test_1140_tool_help_images.py --- a/test/tool_shed/functional/test_1140_tool_help_images.py +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -109,10 +109,10 @@ In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: - src="/tool_runner/static/images/<id>/count_modes.png" + src="/admin_toolshed/static/images/<id>/count_modes.png" ''' repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - image_path = 'src="/tool_runner/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + image_path = 'src="/admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. repository_metadata = repository.metadata tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: to_dict fixes.
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/288203bc6e4e/ Changeset: 288203bc6e4e User: jgoecks Date: 2013-10-04 00:38:23 Summary: to_dict fixes. Affected #: 1 file diff -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b -r 288203bc6e4eac539ad2008ca088530cf2250cee lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2351,7 +2351,7 @@ self.tags.append(new_swta) def to_dict( self, view='collection', value_mapper = None ): - rval = super( StoredWorkflow, self ).to_dict(self, view=view, value_mapper = value_mapper) + rval = super( StoredWorkflow, self ).to_dict( view=view, value_mapper = value_mapper ) tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -3912,7 +3912,7 @@ return [ tool_version.tool_id for tool_version in self.get_versions( app ) ] def to_dict( self, view='element' ): - rval = super( ToolVersion, self ).to_dict( self, view ) + rval = super( ToolVersion, self ).to_dict( view=view ) rval['tool_name'] = self.tool_id for a in self.parent_tool_association: rval['parent_tool_id'] = a.parent_id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Enhance handling of downloaded compressed files based on their internal directory structure. Add rename_to attribute to the move_file action.
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8f2b1130bc52/ Changeset: 8f2b1130bc52 User: Dave Bouvier Date: 2013-10-03 20:17:19 Summary: Enhance handling of downloaded compressed files based on their internal directory structure. Add rename_to attribute to the move_file action. Affected #: 3 files diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -284,7 +284,8 @@ elif action_type == 'move_file': td_common_util.move_file( current_dir=current_dir, source=os.path.join( action_dict[ 'source' ] ), - destination_dir=os.path.join( action_dict[ 'destination' ] ) ) + destination=os.path.join( action_dict[ 'destination' ] ), + rename_to=action_dict[ 'rename_to' ] ) elif action_type == 'set_environment': # Currently the only action supported in this category is "environment_variable". # Build a command line from the prior_installation_required, in case an environment variable is referenced diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -464,7 +464,7 @@ is_binary_download = True else: is_binary_download = False - elif action_elem: + elif action_elem is not None: # We were provided with a single <action> element to perform certain actions after a platform-specific tarball was downloaded. elems = [ action_elem ] else: @@ -550,11 +550,7 @@ action_dict[ 'directory' ] = action_elem.text else: continue - elif action_type in [ 'move_directory_files', 'move_file' ]: - # <action type="move_file"> - # <source>misc/some_file</source> - # <destination>$INSTALL_DIR/bin</destination> - # </action> + elif action_type == 'move_directory_files': # <action type="move_directory_files"> # <source_directory>bin</source_directory> # <destination_directory>$INSTALL_DIR/bin</destination_directory> @@ -563,6 +559,14 @@ move_elem_text = evaluate_template( move_elem.text ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text + elif action_type == 'move_file': + # <action type="move_file" rename_to="new_file_name"> + # <source>misc/some_file</source> + # <destination>$INSTALL_DIR/bin</destination> + # </action> + action_dict[ 'source' ] = evaluate_template( action_elem.find( 'source' ).text ) + action_dict[ 'destination' ] = evaluate_template( action_elem.find( 'destination' ).text ) + action_dict[ 'rename_to' ] = action_elem.get( 'rename_to' ) elif action_type == 'set_environment': # <action type="set_environment"> # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> diff -r 84781f00ff8e57848397177511b77a400055b59f -r 8f2b1130bc523ba60731eb4c5cecfb004e7f9b1b lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -12,6 +12,109 @@ log = logging.getLogger( __name__ ) + +class CompressedFile( object ): + + def __init__( self, file_path, mode='r' ): + if istar( file_path ): + self.file_type = 'tar' + elif iszip( file_path ) and not isjar( file_path ): + self.file_type = 'zip' + self.file_name = os.path.splitext( file_path )[ 0 ] + if self.file_name.endswith( '.tar' ): + self.file_name = os.path.splitext( self.file_name )[ 0 ] + self.type = self.file_type + method = 'open_%s' % self.file_type + if hasattr( self, method ): + self.archive = getattr( self, method )( file_path, mode ) + else: + raise NameError( 'File type %s specified, no open method found.' % self.file_type ) + + def extract( self, path ): + full_path = self.extraction_path( path ) + self.archive.extractall( full_path ) + return full_path + + def extraction_path( self, path ): + '''Determine the path to which the archive should be extracted.''' + contents = self.getmembers() + extraction_path = path + if len( contents ) == 1: + # The archive contains a single file, return the extraction path. + if self.isfile( contents[ 0 ] ): + extraction_path = os.path.join( path, self.file_name ) + else: + # Sort filenames within the archive by length, because if the shortest path entry in the archive is a directory, + # and the next entry has the directory prepended, then everything following that entry must be within that directory. + # For example, consider tarball for BWA 0.5.9: + # bwa-0.5.9.tar.bz2: + # bwa-0.5.9/ + # bwa-0.5.9/bwt.c + # bwa-0.5.9/bwt.h + # bwa-0.5.9/Makefile + # bwa-0.5.9/bwt_gen/ + # bwa-0.5.9/bwt_gen/Makefile + # bwa-0.5.9/bwt_gen/bwt_gen.c + # bwa-0.5.9/bwt_gen/bwt_gen.h + # When sorted by length, one sees a directory at the root of the tarball, and all other tarball contents as + # children of that directory. + filenames = sorted( [ self.getname( item ) for item in contents ], cmp=lambda a,b: cmp( len( a ), len( b ) ) ) + parent_name = filenames[ 0 ] + parent = self.getmember( parent_name ) + first_child = filenames[ 1 ] + if first_child.startswith( parent_name ) and parent is not None and self.isdir( parent ): + extraction_path = os.path.join( path, self.getname( parent ) ) + else: + extraction_path = os.path.join( path, self.file_name ) + if not os.path.exists( extraction_path ): + os.makedirs( extraction_path ) + return os.path.abspath( extraction_path ) + + def getmembers_tar( self ): + return self.archive.getmembers() + + def getmembers_zip( self ): + return self.archive.infolist() + + def getname_tar( self, item ): + return item.name + + def getname_zip( self, item ): + return item.filename + + def getmember( self, name ): + for member in self.getmembers(): + if self.getname( member ) == name: + return member + + def getmembers( self ): + return getattr( self, 'getmembers_%s' % self.type )() + + def getname( self, member ): + return getattr( self, 'getname_%s' % self.type )( member ) + + def isdir( self, member ): + return getattr( self, 'isdir_%s' % self.type )( member ) + + def isdir_tar( self, member ): + return member.isdir() + + def isdir_zip( self, member ): + if member.filename.endswith( os.sep ): + return True + return False + + def isfile( self, member ): + if not self.isdir( member ): + return True + return False + + def open_tar( self, filepath, mode ): + return tarfile.open( filepath, mode ) + + def open_zip( self, filepath, mode ): + return zipfile.ZipFile( filepath, mode ) + def clean_tool_shed_url( base_url ): if base_url: if base_url.find( '://' ) > -1: @@ -92,30 +195,6 @@ dir = url_download( work_dir, downloaded_filename, url, extract=False ) return downloaded_filename -def extract_tar( file_name, file_path ): - if isgzip( file_name ) or isbz2( file_name ): - # Open for reading with transparent compression. - tar = tarfile.open( file_name, 'r:*', errorlevel=0 ) - else: - tar = tarfile.open( file_name, errorlevel=0 ) - tar.extractall( path=file_path ) - tar.close() - -def extract_zip( archive_path, extraction_path ): - # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. - if not zipfile_ok( archive_path ): - return False - zip_archive = zipfile.ZipFile( archive_path, 'r' ) - for name in zip_archive.namelist(): - uncompressed_path = os.path.join( extraction_path, name ) - if uncompressed_path.endswith( '/' ): - if not os.path.isdir( uncompressed_path ): - os.makedirs( uncompressed_path ) - else: - file( uncompressed_path, 'wb' ).write( zip_archive.read( name ) ) - zip_archive.close() - return True - def format_traceback(): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) @@ -232,12 +311,18 @@ destination_file = os.path.join( destination_directory, file_name ) shutil.move( source_file, destination_file ) -def move_file( current_dir, source, destination_dir ): +def move_file( current_dir, source, destination, rename_to=None ): source_file = os.path.abspath( os.path.join( current_dir, source ) ) - destination_directory = os.path.join( destination_dir ) - if not os.path.isdir( destination_directory ): + if rename_to is not None: + destination_file = rename_to + destination_directory = os.path.join( destination ) + destination_path = os.path.join( destination_directory, destination_file ) + else: + destination_directory = os.path.join( destination ) + destination_path = os.path.join( destination_directory, source_file ) + if not os.path.exists( destination_directory ): os.makedirs( destination_directory ) - shutil.move( source_file, destination_directory ) + shutil.move( source_file, destination_path ) def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ @@ -340,19 +425,6 @@ continue return actions_elem_tuples -def tar_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - file_name = file_name.strip() - extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.tar', '.zip' ] - for extension in extensions: - if file_name.find( extension ) > 0: - dir_name = file_name[ :-len( extension ) ] - if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ): - return dir_name - if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ): - return os.path.abspath( file_path ) - raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) - def url_download( install_dir, downloaded_file_name, download_url, extract=True ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None @@ -374,32 +446,14 @@ if dst: dst.close() if extract: - if istar( file_path ): - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - extract_tar( file_path, install_dir ) - dir = tar_extraction_directory( install_dir, downloaded_file_name ) - elif isjar( file_path ): - dir = os.path.curdir - elif iszip( file_path ): - # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> - zip_archive_extracted = extract_zip( file_path, install_dir ) - dir = zip_extraction_directory( install_dir, downloaded_file_name ) + if istar( file_path ) or iszip( file_path ): + archive = CompressedFile( file_path ) + extraction_path = archive.extract( install_dir ) else: - dir = os.path.abspath( install_dir ) + extraction_path = os.path.abspath( install_dir ) else: - dir = os.path.abspath( install_dir ) - return dir - -def zip_extraction_directory( file_path, file_name ): - """Try to return the correct extraction directory.""" - files = [ filename for filename in os.listdir( file_path ) if not filename.endswith( '.zip' ) ] - if len( files ) > 1: - return os.path.abspath( file_path ) - elif len( files ) == 1: - # If there is only on file it should be a directory. - if os.path.isdir( os.path.join( file_path, files[ 0 ] ) ): - return os.path.abspath( os.path.join( file_path, files[ 0 ] ) ) - raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) ) + extraction_path = os.path.abspath( install_dir ) + return extraction_path def zipfile_ok( path_to_archive ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Trackster: Fix cell content if metadata is inconsistent
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/84781f00ff8e/ Changeset: 84781f00ff8e User: guerler Date: 2013-10-03 19:21:59 Summary: Trackster: Fix cell content if metadata is inconsistent Affected #: 1 file diff -r a1c04a1b716a2c83f821b08f5ca18ace27fcfe21 -r 84781f00ff8e57848397177511b77a400055b59f static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -183,7 +183,7 @@ var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { $cell.attr('colspan', colspan).addClass('stringalign'); - } else if (index < column_types.length) { + } else if (column_types !== undefined && index < column_types.length) { if (column_types[index] === 'str' || column_types === 'list') { /* Left align all str columns, right align the rest */ $cell.addClass('stringalign'); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Trackster: Fix cell content if metadata is inconsistent
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a1c04a1b716a/ Changeset: a1c04a1b716a User: guerler Date: 2013-10-03 19:11:43 Summary: Trackster: Fix cell content if metadata is inconsistent Affected #: 1 file diff -r e55c7a4a88e076f163949381937d38d11e48c74a -r a1c04a1b716a2c83f821b08f5ca18ace27fcfe21 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -179,17 +179,17 @@ // -- Helper functions. -- _renderCell: function(cell_contents, index, colspan) { + var $cell = $('<td>').text(cell_contents); var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); + $cell.attr('colspan', colspan).addClass('stringalign'); + } else if (index < column_types.length) { + if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + $cell.addClass('stringalign'); + } } - else if (column_types[index] === 'str' || column_types === 'list') { - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents); - } - else { - return $('<td>').text(cell_contents); - } + return $cell; }, _renderRow: function(line) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update universe sample with new inactivity box content default text
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e55c7a4a88e0/ Changeset: e55c7a4a88e0 User: dannon Date: 2013-10-03 18:18:50 Summary: Update universe sample with new inactivity box content default text Affected #: 1 file diff -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd -r e55c7a4a88e076f163949381937d38d11e48c74a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -299,7 +299,7 @@ # Used for warning box for inactive accounts (unable to run jobs). # In use only if activation_grace_period is set. -#inactivity_box_content = Your account has not been activated yet. Please activate your account by verifying your email address. For now you can access everything at Galaxy but your jobs won't run. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. # -- Display sites Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal
by commits-noreply＠bitbucket.org 04 Oct '13

04 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fed7f7b23fd/ Changeset: 2fed7f7b23fd User: guerler Date: 2013-10-03 18:09:35 Summary: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal Affected #: 4 files diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -255,7 +255,8 @@ }); // Initialize ratings. - $('.community_rating_star').rating({}); + if ($('.community_rating_star').length !== 0) + $('.community_rating_star').rating({}); // Initialize item menu operations. make_popup_menus(); diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,47 +20,7 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, - { - "Cancel": function() { - hide_modal(); - }, - "Add": function() { - var requests = []; - $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data = { - data_type: 'track_config', - 'hda_ldda': 'hda' - }, - id = $(this).val(); - if ($(this).attr("name") !== "id") { - data.hda_ldda = 'ldda'; - } - requests[requests.length] = $.ajax({ - url: add_track_async_url + "/" + id, - data: data, - dataType: "json" - }); - }); - // To preserve order, wait until there are definitions for all tracks and then add - // them sequentially. - $.when.apply($, requests).then(function() { - // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to - // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? - $.map(arguments, function(arg) { return arg[0]; }) : - [ arguments[0] ] - ); - success_fn(track_defs); - }); - hide_modal(); - } - } - ); - /*Galaxy.modal.show({ + Galaxy.modal.show({ title : "Select datasets for new tracks", body : table_html, buttons : @@ -100,7 +60,7 @@ Galaxy.modal.hide(); } } - });*/ + }); } }); }; diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -86,7 +86,7 @@ // Create grid. var grid = new Grid({ - url_base: location.pathname, + url_base: '${trans.request.path_url}', async: is_true('${grid.use_async}'), async_ops: async_ops, categorical_filters: categorical_filters, @@ -102,6 +102,12 @@ // Initialize grid objects on load. // FIXME: use a grid view object eventually. $(document).ready(function() { + + // strip protocol and domain + var url = grid.get('url_base'); + url = url.replace(/^.*\/\/[^\/]+/, ''); + grid.set('url_base', url); + init_grid_elements(); init_grid_controls(); // Initialize text filters to select text on click and use normal font when user is typing. diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,38 +152,6 @@ </script></%def> -<%def name="overlay( title='', content='', visible=False )"> - <%def name="title()"></%def> - <%def name="content()"></%def> - - <% - if visible: - display = "style='display: block;'" - overlay_class = "in" - else: - display = "style='display: none;'" - overlay_class = "" - %> - - <div id="top-modal" class="modal fade ${overlay_class}" ${display}> - <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> - <div id="top-modal-dialog" class="modal-dialog"> - <div class="modal-content"> - <div class="modal-header"> - <button type='button' class='close' style="display: none;">×</button> - <h4 class='title'>${title}</h4> - </div> - <div class="modal-body">${content}</div> - <div class="modal-footer"> - <div class="buttons" style="float: right;"></div> - <div class="extra_buttons" style=""></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - </div> -</%def> - ## document <html><head> @@ -214,7 +182,6 @@ %if self.galaxy_config['message_box']: <div id="messagebox" class="panel-message"></div> %endif - ${self.overlay()} ## left panel %if self.galaxy_config['left_panel']: <div id="left"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: activation feature tweaks
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b714089d888c/ Changeset: b714089d888c User: martenson Date: 2013-10-03 17:18:59 Summary: activation feature tweaks Affected #: 2 files diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -133,7 +133,7 @@ self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) - self.user_activation_on = kwargs.get( 'user_activation_on', None ) + self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) ) self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -670,8 +670,10 @@ user = trans.app.model.User( email=email ) user.set_password_cleartext( password ) user.username = username - if trans.app.config.user_activation_on: # Do not set the active flag in case activation is OFF. + if trans.app.config.user_activation_on: user.active = False + else: + user.active = True # Activation is off, every new user is active by default. trans.sa_session.add( user ) trans.sa_session.flush() trans.app.security_agent.create_private_user_role( user ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Remove reference to removed select field in the repository write permission form.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/becb2b5d2d06/ Changeset: becb2b5d2d06 User: Dave Bouvier Date: 2013-10-03 16:45:39 Summary: Remove reference to removed select field in the repository write permission form. Affected #: 1 file diff -r 54673424aa68129d1bae517db268d571feb73fae -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -723,7 +723,6 @@ post_submit_strings_not_displayed=[] ): self.display_manage_repository_page( repository ) self.check_for_strings( strings_displayed, strings_not_displayed ) - tc.fv( "user_access", "allow_push", '-Select one' ) for username in usernames: tc.fv( "user_access", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits October 2013