September 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Circster enhancements: (a) dragging and zooming; and (b) fill complete palette.
by Bitbucket 08 Sep '12

08 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/51b24be13e90/ changeset: 51b24be13e90 user: jgoecks date: 2012-09-08 19:08:33 summary: Circster enhancements: (a) dragging and zooming; and (b) fill complete palette. affected #: 2 files diff -r 108cda8986460298279279fca9ae40661a8e6174 -r 51b24be13e9085b6fda294354e709d844e5da964 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -827,9 +827,11 @@ this.height = options.height; this.total_gap = options.total_gap; this.genome = options.genome; - this.radius_start = options.radius_start; this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; + + // Compute radius start based on model. + this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap); }, render: function() { @@ -841,8 +843,17 @@ .append("svg") .attr("width", self.width) .attr("height", self.height) - .append("g") - .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")"); + .attr("pointer-events", "all") + // Set up zooming, dragging. + .append('svg:g') + .call(d3.behavior.zoom().on('zoom', function() { + svg.attr("transform", + "translate(" + d3.event.translate + ")" + + " scale(" + d3.event.scale + ")"); + })) + .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")") + .append('svg:g') + // -- Render each dataset in the visualization. -- this.model.get('tracks').each(function(track, index) { @@ -889,8 +900,8 @@ .style("stroke", block_color) .style("fill", block_color); }); - }); - } + }); + } }); /** diff -r 108cda8986460298279279fca9ae40661a8e6174 -r 51b24be13e9085b6fda294354e709d844e5da964 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -69,14 +69,13 @@ var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')) visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')), viz_view = new CircsterView({ - width: 600, - height: 600, + width: 700, + height: 700, // Gap is difficult to set because it very dependent on chromosome size and organization. - total_gap: 2 * Math.PI * 0.2, + total_gap: 2 * Math.PI * 0.1, genome: genome, model: visualization, - radius_start: 100, - dataset_arc_height: 15 + dataset_arc_height: 25 }); // -- Render viz. -- 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: Enhancements to tool dependency installation when installing with a tool shed repository: multiple environment variables can now be set and a new "make_directory" tag is supported.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/108cda898646/ changeset: 108cda898646 user: greg date: 2012-09-07 20:49:46 summary: Enhancements to tool dependency installation when installing with a tool shed repository: multiple environment variables can now be set and a new "make_directory" tag is supported. affected #: 3 files diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -17,6 +17,9 @@ return tarfile.is_tarfile( file_path ) def iszip( file_path ): return check_zip( file_path ) +def make_directory( full_path ): + if not os.path.exists( full_path ): + os.makedirs( full_path ) def move_directory_files( current_dir, source_dir, destination_dir ): source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) ) destination_directory = os.path.join( destination_dir ) diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -88,7 +88,9 @@ for action_tup in actions[ 1: ]: action_type, action_dict = action_tup current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - if action_type == 'move_directory_files': + if action_type == 'make_directory': + common_util.make_directory( full_path=action_dict[ 'full_path' ] ) + elif action_type == 'move_directory_files': common_util.move_directory_files( current_dir=current_dir, source_dir=os.path.join( action_dict[ 'source_directory' ] ), destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) @@ -98,29 +100,36 @@ destination_dir=os.path.join( action_dict[ 'destination' ] ) ) elif action_type == 'set_environment': # Currently the only action supported in this category is "environment_variable". - env_var_dict = action_dict[ 'environment_variable' ] - env_var_name = env_var_dict[ 'name' ] - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - cmd = "echo '%s=%s; export %s' > %s/env.sh;chmod +x %s/env.sh" % ( env_var_name, - changed_value, - env_var_name, - install_dir, - install_dir ) - output = local( cmd, capture=True ) - log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( output.stderr ) - sa_session.add( tool_dependency ) - sa_session.flush() - return + env_var_dicts = action_dict[ 'environment_variable' ] + for env_var_dict in env_var_dicts: + env_var_name = env_var_dict[ 'name' ] + env_var_action = env_var_dict[ 'action' ] + env_var_value = env_var_dict[ 'value' ] + if env_var_action == 'prepend_to': + changed_value = '%s:$%s' % ( env_var_value, env_var_name ) + elif env_var_action == 'set_to': + changed_value = '%s' % env_var_value + elif env_var_action == 'append_to': + changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + env_shell_file_path = '%s/env.sh' % install_dir + if os.path.exists( env_shell_file_path ): + write_action = '>>' + else: + write_action = '>' + cmd = "echo '%s=%s; export %s' %s %s;chmod +x %s" % ( env_var_name, + changed_value, + env_var_name, + write_action, + env_shell_file_path, + env_shell_file_path ) + output = local( cmd, capture=True ) + log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) + if output.return_code: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = str( output.stderr ) + sa_session.add( tool_dependency ) + sa_session.flush() + return elif action_type == 'shell_command': action = action_dict[ 'command' ] with settings( warn_only=True ): diff -r 1475240809a7e9b996aa7b9026b33e20ea9209bd -r 108cda8986460298279279fca9ae40661a8e6174 lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -113,6 +113,12 @@ action_dict[ 'url' ] = action_elem.text else: continue + elif action_type == 'make_directory': + # <action type="make_directory">$INSTALL_DIR/lib/python</action> + if action_elem.text: + action_dict[ 'full_path' ] = action_elem.text.replace( '$INSTALL_DIR', install_dir ) + else: + continue elif action_type in [ 'move_directory_files', 'move_file' ]: # <action type="move_file"> # <source>misc/some_file</source> @@ -128,15 +134,21 @@ action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'set_environment': # <action type="set_environment"> + # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> + env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_name = env_elem.get( 'name', 'PATH' ) env_var_action = env_elem.get( 'action', 'prepend_to' ) env_var_text = env_elem.text.replace( '$INSTALL_DIR', install_dir ) if env_var_text: - action_dict[ env_elem.tag ] = dict( name=env_var_name, action=env_var_action, value=env_var_text ) + env_var_dicts.append( dict( name=env_var_name, action=env_var_action, value=env_var_text ) ) + if env_var_dicts: + action_dict[ env_elem.tag ] = env_var_dicts + else: + continue else: continue actions.append( ( action_type, action_dict ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Added an error message to the repository clone error handling.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1475240809a7/ changeset: 1475240809a7 user: inithello date: 2012-09-07 17:54:02 summary: Added an error message to the repository clone error handling. affected #: 2 files diff -r 0491c108154248cab0006533d30e462df3ade6f9 -r 1475240809a7e9b996aa7b9026b33e20ea9209bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -363,7 +363,8 @@ noupdate=False, rev=util.listify( str( ctx_rev ) ) ) return True - except: + except Exception, e: + log.debug( 'Encountered an exception while cloning the repository: %s' % e ) return False def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" diff -r 0491c108154248cab0006533d30e462df3ade6f9 -r 1475240809a7e9b996aa7b9026b33e20ea9209bd lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -772,15 +772,8 @@ repository_id = kwd[ 'id' ] repository = get_repository( trans, repository_id ) if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.CLONING ]: - message = "The repository '%s' is not yet cloned, please try again..." - status = 'warning' - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='monitor_repository_installation', - **kwd ) ) - if repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: - message = "There was an error installing the repository '%s', please try again..." - status = 'warning' + trans.model.ToolShedRepository.installation_status.CLONING, + trans.model.ToolShedRepository.installation_status.ERROR ]: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) 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: inithello: Handle errors when cloning a tool shed repository.
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0491c1081542/ changeset: 0491c1081542 user: inithello date: 2012-09-07 17:22:09 summary: Handle errors when cloning a tool shed repository. affected #: 2 files diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -355,12 +355,16 @@ return tool_shed_url.rstrip( '/' ) def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" - commands.clone( get_configured_ui(), - str( repository_clone_url ), - dest=str( repository_file_dir ), - pull=True, - noupdate=False, - rev=util.listify( str( ctx_rev ) ) ) + try: + commands.clone( get_configured_ui(), + str( repository_clone_url ), + dest=str( repository_file_dir ), + pull=True, + noupdate=False, + rev=util.listify( str( ctx_rev ) ) ) + return True + except: + return False def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" if dest_path is None: diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -64,7 +64,8 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ), + link=( lambda item: iff( item.status == model.ToolShedRepository.installation_status.ERROR, \ + None, dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -86,17 +87,29 @@ global_actions = [] operations = [ grids.GridOperation( "Get updates", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ), grids.GridOperation( "Deactivate or uninstall", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), + grids.GridOperation( "Uninstall", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='uninstall' ) ), + grids.GridOperation( "Reset to install", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset status to new' ) ), grids.GridOperation( "Activate or reinstall", allow_multiple=False, - condition=( lambda item: item.deleted ), + condition=( lambda item: ( item.deleted or item.uninstalled ) ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ] standard_filters = [] @@ -342,6 +355,16 @@ return self.manage_repository( trans, **kwd ) if operation == "get updates": return self.check_for_updates( trans, **kwd ) + if operation == "uninstall": + kwd[ 'deactivate_or_uninstall_repository_button' ] = 'Deactivate or Uninstall' + kwd[ 'remove_from_disk' ] = [u'true', u'true'] + return self.deactivate_or_uninstall_repository( trans, **kwd ) + if operation == "reset status to new": + repository = get_repository( trans, kwd[ 'id' ] ) + repository.status = model.ToolShedRepository.installation_status.NEW + repository.deleted = False + repository.uninstalled = True + trans.app.model.context.current.flush() if operation == "activate or reinstall": repository = get_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: @@ -406,7 +429,7 @@ remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_install_dir = os.path.abspath ( relative_install_dir ) + repository_install_dir = os.path.abspath ( relative_install_dir ) if relative_install_dir is not None else None errors = '' if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools: @@ -426,8 +449,12 @@ log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) removed = True except Exception, e: - log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - removed = False + if repository_install_dir is not None: + removed = False + log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) + else: + log.debug( "Repository installation directory does not exist." ) + removed = True if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. @@ -610,7 +637,12 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + result = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + if not result: + update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.ERROR ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + tool_shed_repository_ids=[ trans.security.encode_id( tool_shed_repository.id ) ] ) ) if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) @@ -746,6 +778,12 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) + if repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: + message = "There was an error installing the repository '%s', please try again..." + status = 'warning' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + **kwd ) ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: rmarenco: Modified the good files instead of the auto-generated ones
by Bitbucket 07 Sep '12

07 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1a56c4b28c6b/ changeset: 1a56c4b28c6b user: rmarenco date: 2012-09-07 15:54:31 summary: Modified the good files instead of the auto-generated ones affected #: 5 files diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb database/compiled_templates/webapps/galaxy/base_panels.mako.py --- a/database/compiled_templates/webapps/galaxy/base_panels.mako.py +++ /dev/null @@ -1,415 +0,0 @@ -# -*- encoding:ascii -*- -from mako import runtime, filters, cache -UNDEFINED = runtime.UNDEFINED -__M_dict_builtin = dict -__M_locals_builtin = locals -_magic_number = 6 -_modified_time = 1346972736.51736 -_template_filename=u'templates/webapps/galaxy/base_panels.mako' -_template_uri=u'/webapps/galaxy/base_panels.mako' -_template_cache=cache.Cache(__name__, _modified_time) -_source_encoding='ascii' -_exports = ['masthead', 'javascripts', 'title'] - - -def _mako_get_namespace(context, name): - try: - return context.namespaces[(__name__, name)] - except KeyError: - _mako_generate_namespaces(context) - return context.namespaces[(__name__, name)] -def _mako_generate_namespaces(context): - pass -def _mako_inherit(template, context): - _mako_generate_namespaces(context) - return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) -def render_body(context,**pageargs): - context.caller_stack._push_frame() - try: - __M_locals = __M_dict_builtin(pageargs=pageargs) - __M_writer = context.writer() - # SOURCE LINE 1 - __M_writer(u'\n\n') - # SOURCE LINE 4 - __M_writer(u'\n\n') - # SOURCE LINE 8 - __M_writer(u'\n\n') - # SOURCE LINE 232 - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_masthead(context): - context.caller_stack._push_frame() - try: - AssertionError = context.get('AssertionError', UNDEFINED) - h = context.get('h', UNDEFINED) - app = context.get('app', UNDEFINED) - util = context.get('util', UNDEFINED) - def tab(id,display,href,target='_parent',visible=True,extra_class='',menu_options=None): - context.caller_stack._push_frame() - try: - self = context.get('self', UNDEFINED) - len = context.get('len', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 19 - __M_writer(u'\n') - # SOURCE LINE 22 - __M_writer(u' \n ') - # SOURCE LINE 23 - - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - - - # SOURCE LINE 38 - __M_writer(u'\n <li class="') - # SOURCE LINE 39 - __M_writer(unicode(cls)) - __M_writer(u'" style="') - __M_writer(unicode(style)) - __M_writer(u'">\n') - # SOURCE LINE 40 - if href: - # SOURCE LINE 41 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown" target="') - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(href)) - __M_writer(u'">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - # SOURCE LINE 42 - else: - # SOURCE LINE 43 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 45 - if menu_options: - # SOURCE LINE 46 - __M_writer(u' <ul class="dropdown-menu">\n') - # SOURCE LINE 47 - for menu_item in menu_options: - # SOURCE LINE 48 - if not menu_item: - # SOURCE LINE 49 - __M_writer(u' <li class="divider"></li>\n') - # SOURCE LINE 50 - else: - # SOURCE LINE 51 - __M_writer(u' <li>\n') - # SOURCE LINE 52 - if len ( menu_item ) == 1: - # SOURCE LINE 53 - __M_writer(u' ') - __M_writer(unicode(menu_item[0])) - __M_writer(u'\n') - # SOURCE LINE 54 - elif len ( menu_item ) == 2: - # SOURCE LINE 55 - __M_writer(u' ') - name, link = menu_item - - __M_writer(u'\n <a href="') - # SOURCE LINE 56 - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - # SOURCE LINE 57 - else: - # SOURCE LINE 58 - __M_writer(u' ') - name, link, target = menu_item - - __M_writer(u'\n <a target="') - # SOURCE LINE 59 - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 61 - __M_writer(u' </li>\n') - pass - pass - # SOURCE LINE 64 - __M_writer(u' </ul>\n') - pass - # SOURCE LINE 66 - __M_writer(u' </li>\n ') - return '' - finally: - context.caller_stack._pop_frame() - trans = context.get('trans', UNDEFINED) - _ = context.get('_', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 11 - __M_writer(u'\n\n') - # SOURCE LINE 14 - __M_writer(u' <div style="position: relative; right: -50%; float: left;">\n <div style="display: block; position: relative; right: 50%;">\n\n <ul class="nav" border="0" cellspacing="0">\n \n ') - # SOURCE LINE 67 - __M_writer(u'\n\n') - # SOURCE LINE 70 - __M_writer(u' ') - __M_writer(unicode(tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 73 - __M_writer(u' ') - __M_writer(unicode(tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 76 - __M_writer(u' ') - - menu_options = [ - [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], - None, - [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], - [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], - [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], - [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] - ] - tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 86 - __M_writer(u'\n \n') - # SOURCE LINE 89 - __M_writer(u' ') - - menu_options = [ - [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], - [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ], - [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] - ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) - - - # SOURCE LINE 96 - __M_writer(u'\n\n') - # SOURCE LINE 99 - __M_writer(u' ') - - menu_options = [ - [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] - ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) - - - # SOURCE LINE 105 - __M_writer(u'\n\n') - # SOURCE LINE 108 - if app.config.get_bool( 'enable_cloud_launch', False ): - # SOURCE LINE 109 - __M_writer(u' ') - - menu_options = [ - [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], - ] - tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 114 - __M_writer(u'\n') - pass - # SOURCE LINE 116 - __M_writer(u'\n') - # SOURCE LINE 118 - __M_writer(u' ') - __M_writer(unicode(tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 121 - __M_writer(u' ') - - menu_options = [ - [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] - if app.config.get( 'terms_url', None ) is not None: - menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) - tab( "help", _("Help"), None, menu_options=menu_options) - - - # SOURCE LINE 132 - __M_writer(u'\n \n') - # SOURCE LINE 135 - __M_writer(u' ') - - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) - else: - logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - - - # SOURCE LINE 172 - __M_writer(u'\n \n') - # SOURCE LINE 176 - __M_writer(u' </ul>\n\n </div>\n </div>\n \n') - # SOURCE LINE 182 - __M_writer(u' <div class="title">\n <a href="') - # SOURCE LINE 183 - __M_writer(unicode(h.url_for( app.config.get( 'logo_url', '/' ) ))) - __M_writer(u'">\n <img border="0" src="') - # SOURCE LINE 184 - __M_writer(unicode(h.url_for('/static/images/galaxyIcon_noText.png'))) - __M_writer(u'">\n Galaxy\n') - # SOURCE LINE 186 - if app.config.brand: - # SOURCE LINE 187 - __M_writer(u' <span>/ ') - __M_writer(unicode(app.config.brand)) - __M_writer(u'</span>\n') - pass - # SOURCE LINE 189 - __M_writer(u' </a>\n </div>\n\n') - # SOURCE LINE 193 - __M_writer(u' ') - - bar_style = "quota-meter-bar" - usage = 0 - percent = 0 - quota = None - try: - usage = trans.app.quota_agent.get_usage( trans=trans ) - quota = trans.app.quota_agent.get_quota( trans.user ) - percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota ) - if percent is not None: - if percent >= 100: - bar_style += " quota-meter-bar-error" - elif percent >= 85: - bar_style += " quota-meter-bar-warn" - else: - percent = 0 - except AssertionError: - pass # Probably no history yet - tooltip = None - if not trans.user and quota and trans.app.config.allow_user_creation: - if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota: - tooltip = "Your disk quota is %s. You can increase your quota by registering a Galaxy account." % util.nice_size( quota ) - - - # SOURCE LINE 215 - __M_writer(u'\n\n <div class="quota-meter-container">\n') - # SOURCE LINE 218 - if tooltip: - # SOURCE LINE 219 - __M_writer(u' <div id="quota-meter" class="quota-meter tooltip" title="') - __M_writer(unicode(tooltip)) - __M_writer(u'">\n') - # SOURCE LINE 220 - else: - # SOURCE LINE 221 - __M_writer(u' <div id="quota-meter" class="quota-meter">\n') - pass - # SOURCE LINE 223 - __M_writer(u' <div id="quota-meter-bar" class="') - __M_writer(unicode(bar_style)) - __M_writer(u'" style="width: ') - __M_writer(unicode(percent)) - __M_writer(u'px;"></div>\n') - # SOURCE LINE 224 - if quota is not None: - # SOURCE LINE 225 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(percent)) - __M_writer(u'%</div>\n') - # SOURCE LINE 226 - else: - # SOURCE LINE 227 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(util.nice_size( usage ))) - __M_writer(u'</div>\n') - pass - # SOURCE LINE 229 - __M_writer(u' </div>\n </div>\n \n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_javascripts(context): - context.caller_stack._push_frame() - try: - parent = context.get('parent', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 6 - __M_writer(u'\n ') - # SOURCE LINE 7 - __M_writer(unicode(parent.javascripts())) - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_title(context): - context.caller_stack._push_frame() - try: - __M_writer = context.writer() - # SOURCE LINE 4 - __M_writer(u'Galaxy') - return '' - finally: - context.caller_stack._pop_frame() - - diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -71,7 +71,8 @@ ## Help tab. <% - menu_options = [ + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "_blank" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,7 +120,7 @@ ## Help tab. <% menu_options = [ - [_('Galaxy Q&A'), app.config.get( "q&a", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini --- a/universe_wsgi.ini +++ /dev/null @@ -1,753 +0,0 @@ -# -# Galaxy is configured by default to be useable in a single-user development -# environment. To tune the application for a multi-user production -# environment, see the documentation at: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server -# - -# Throughout this sample configuration file, except where stated otherwise, -# uncommented values override the default if left unset, whereas commented -# values are set to the default value. -# Examples of many of these options are explained in more detail in the wiki: -# -# http://wiki.g2.bx.psu.edu/Admin/Config -# -# Config hackers are encouraged to check there before asking for help. - -# ---- HTTP Server ---------------------------------------------------------- - -# Configuration of the internal HTTP server. - -[server:main] - -# The internal HTTP server to use. Currently only Paste is provided. This -# option is required. -use = egg:Paste#http - -# The port on which to listen. -#port = 8080 - -# The address on which to listen. By default, only listen to localhost (Galaxy -# will not be accessible over the network). Use '0.0.0.0' to listen on all -# available network interfaces. -#host = 127.0.0.1 - -# Use a threadpool for the web server instead of creating a thread for each -# request. -use_threadpool = True - -# Number of threads in the web server thread pool. -#threadpool_workers = 10 - -# ---- Filters -------------------------------------------------------------- - -# Filters sit between Galaxy and the HTTP server. - -# These filters are disabled by default. They can be enabled with -# 'filter-with' in the [app:main] section below. - -# Define the gzip filter. -[filter:gzip] -use = egg:Paste#gzip - -# Define the proxy-prefix filter. -[filter:proxy-prefix] -use = egg:PasteDeploy#prefix -prefix = /galaxy - -# ---- Galaxy --------------------------------------------------------------- - -# Configuration of the Galaxy application. - -[app:main] - -# -- Application and filtering - -# The factory for the WSGI application. This should not be changed. -paste.app_factory = galaxy.web.buildapp:app_factory - -# If not running behind a proxy server, you may want to enable gzip compression -# to decrease the size of data transferred over the network. If using a proxy -# server, please enable gzip compression there instead. -#filter-with = gzip - -# If running behind a proxy server and Galaxy is served from a subdirectory, -# enable the proxy-prefix filter and set the prefix in the -# [filter:proxy-prefix] section above. -#filter-with = proxy-prefix - -# If proxy-prefix is enabled and you're running more than one Galaxy instance -# behind one hostname, you will want to set this to the same path as the prefix -# in the filter above. This value becomes the "path" attribute set in the -# cookie so the cookies from each instance will not clobber each other. -#cookie_path = None - -# -- Database - -# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You -# may use a SQLAlchemy connection string to specify an external database -# instead. This string takes many options which are explained in detail in the -# config file documentation. -#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE - -# If the server logs errors about not having enough database pool connections, -# you will want to increase these values, or consider running more Galaxy -# processes. -#database_engine_option_pool_size = 5 -#database_engine_option_max_overflow = 10 - -# If using MySQL and the server logs the error "MySQL server has gone away", -# you will want to set this to some positive value (7200 should work). -#database_engine_option_pool_recycle = -1 - -# If large database query results are causing memory or response time issues in -# the Galaxy process, leave the result on the server instead. This option is -# only available for PostgreSQL and is highly recommended. -#database_engine_option_server_side_cursors = False - -# Create only one connection to the database per thread, to reduce the -# connection overhead. Recommended when not using SQLite: -#database_engine_option_strategy = threadlocal - -# Log all database transactions, can be useful for debugging and performance -# profiling. Logging is done via Python's 'logging' module under the qualname -# 'galaxy.model.orm.logging_connection_proxy' -#database_query_profiling_proxy = False - -# -- Files and directories - -# Path where genome builds are stored. This defaults to tool-data/genome -#genome_data_path = tool-data/genome - -# URL for rsync server to download pre-built indexes. -#rsync_url = rsync://scofield.bx.psu.edu/indexes - -# Dataset files are stored in this directory. -#file_path = database/files - -# Temporary files are stored in this directory. -#new_file_path = database/tmp - -# Tool config files, defines what tools are available in Galaxy. -# Tools can be locally developed or installed from Galaxy tool sheds. -#tool_config_file = tool_conf.xml,shed_tool_conf.xml - -# Default path to the directory containing the tools defined in tool_conf.xml. -# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. -#tool_path = tools - -# Path to the directory in which managed tool dependencies are placed. To use -# the dependency system, see the documentation at: -# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies -#tool_dependency_dir = None - -# Enable automatic polling of relative tool sheds to see if any updates -# are available for installed repositories. Ideally only one Galaxy -# server process should be able to check for repository updates. The -# setting for hours_between_check should be an integer between 1 and 24. -#enable_tool_shed_check = False -#hours_between_check = 12 - -# Directory where data used by tools is located, see the samples in that -# directory and the wiki for help: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration -#tool_data_path = tool-data - -# Directory where chrom len files are kept, currently mainly used by trackster -#len_file_path = tool-data/shared/ucsc/chrom - -# Datatypes config file, defines what data (file) types are available in -# Galaxy. -#datatypes_config_file = datatypes_conf.xml - -# Each job is given a unique empty directory as its current working directory. -# This option defines in what parent directory those directories will be -# created. -#job_working_directory = database/job_working_directory - -# If using a cluster, Galaxy will write job scripts and stdout/stderr to this -# directory. -#cluster_files_directory = database/pbs - -# External service types config file, defines what types of external_services configurations -# are available in Galaxy. -#external_service_type_config_file = external_service_types_conf.xml - -# Path to the directory containing the external_service_types defined in the config. -#external_service_type_path = external_service_types - -# Tools with a number of outputs not known until runtime can write these -# outputs to a directory for collection by Galaxy when the job is done. -# Previously, this directory was new_file_path, but using one global directory -# can cause performance problems, so using job_working_directory ('.' or cwd -# when a job is run) is encouraged. By default, both are checked to avoid -# breaking existing tools. -#collect_outputs_from = new_file_path,job_working_directory - -# -- Mail and notification - -# Galaxy sends mail for various things: Subscribing users to the mailing list -# if they request it, emailing password resets, notification from the Galaxy -# Sample Tracking system, and reporting dataset errors. To do this, it needs -# to send mail through an SMTP server, which you may define here (host:port). -# Galaxy will automatically try STARTTLS but will continue upon failure. -#smtp_server = None - -# If your SMTP server requires a username and password, you can provide them -# here (password in cleartext here, but if your server supports STARTTLS it -# will be sent over the network encrypted). -#smtp_username = None -#smtp_password = None - -# On the user registration form, users may choose to join the mailing list. -# This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu - -# Datasets in an error state include a link to report the error. Those reports -# will be sent to this address. Error reports are disabled if no address is set. -#error_email_to = None - -# -- Display sites - -# Galaxy can display data at various external browsers. These options specify -# which browsers should be available. URLs and builds available at these -# browsers are defined in the specifield files. - -# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - -# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt -#genetrack_display_sites = main,test - -# If use_remote_user = True, display application servers will be denied access -# to Galaxy and so displaying datasets in these sites will fail. -# display_servers contains a list of hostnames which should be allowed to -# bypass security to display datasets. Please be aware that there are security -# implications if this is allowed. More details (including required changes to -# the proxy server config) are available in the Apache proxy documentation on -# the wiki. -# -# The list of servers in this sample config are for the UCSC Main, Test and -# Archaea browsers, but the default if left commented is to not allow any -# display sites to bypass security (you must uncomment the line below to allow -# them). -#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… - -# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. - -use_nglims = False -nglims_config_file = tool-data/nglims.yaml - -# -- UI Localization - -# Append "/{brand}" to the "Galaxy" text in the masthead. -#brand = None - -# The URL linked by the "Galaxy/brand" text. -#logo_url = / - -# The URL linked by the "Galaxy Wiki" link in the "Help" menu. -#wiki_url = http://wiki.g2.bx.psu.edu/ - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support - -# The URL linked by the "How to Cite..." link in the "Help" menu. -#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy - -# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well -# as on the user registration and login forms. -#terms_url = None - -# The URL linked by the "Galaxy Q&A" link in the "Help" menu -qa_url = http://slyfox.bx.psu.edu:8080/ - -# Serve static content, which must be enabled if you're not serving it via a -# proxy server. These options should be self explanatory and so are not -# documented individually. You can use these paths (or ones in the proxy -# server) to point to your own styles. -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue -static_robots_txt = %(here)s/static/robots.txt - -# Pack javascript at launch (/static/scripts/*.js) -# This only happens if the modified timestamp of the source .js is newer -# than the version (if it exists) in /static/scripts/packed/ -# Note that this requires java > 1.4 for executing yuicompressor.jar -#pack_scripts = False - -# Enable Cloud Launch - -#enable_cloud_launch = False - -# -- Advanced proxy features - -# For help on configuring the Advanced proxy features, see: -# http://usegalaxy.org/production - -# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set -# this to True to inform Galaxy that mod_xsendfile is enabled upstream. -#apache_xsendfile = False - -# The same download handling can be done by nginx using X-Accel-Redirect. This -# should be set to the path defined in the nginx config as an internal redirect -# with access to Galaxy's data files (see documentation linked above). -#nginx_x_accel_redirect_base = False - -# nginx can make use of mod_zip to create zip files containing multiple library -# files. If using X-Accel-Redirect, this can be the same value as that option. -#nginx_x_archive_files_base = False - -# If using compression in the upstream proxy server, use this option to disable -# gzipping of library .tar.gz and .zip archives, since the proxy server will do -# it faster on the fly. -#upstream_gzip = False - -# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. -# Configuration for this is complex and explained in detail in the -# documentation linked above. The upload store is a temporary directory in -# which files uploaded by the upload module will be placed. -#nginx_upload_store = False - -# This value overrides the action set on the file upload form, e.g. the web -# path where the nginx_upload_module has been configured to intercept upload -# requests. -#nginx_upload_path = False - -# -- Logging and Debugging - -# Verbosity of console log messages. Acceptable values can be found here: -# http://docs.python.org/library/logging.html#logging-levels -#log_level = DEBUG - -# Print database operations to the server log (warning, quite verbose!). -#database_engine_option_echo = False - -# Print database pool operations to the server log (warning, quite verbose!). -#database_engine_option_echo_pool = False - -# Turn on logging of application events and some user events to the database. -#log_events = True - -# Turn on logging of user actions to the database. Actions currently logged are -# grid views, tool searches, and use of "recently" used tools menu. The -# log_events and log_actions functionality will eventually be merged. -#log_actions = True - -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. -#sanitize_all_html = True - -# Debug enables access to various config options useful for development and -# debugging: use_lint, use_profile, use_printdebug and use_interactive. It -# also causes the files used by PBS/SGE (submission script, output, and error) -# to remain on disk after the job is complete. Debug mode is disabled if -# commented, but is uncommented by default in the sample config. -debug = True - -# Check for WSGI compliance. -#use_lint = False - -# Run the Python profiler on each request. -#use_profile = False - -# Intercept print statements and show them on the returned page. -#use_printdebug = True - -# Enable live debugging in your browser. This should NEVER be enabled on a -# public site. Enabled in the sample config for development. -use_interactive = True - -# Write thread status periodically to 'heartbeat.log', (careful, uses disk -# space rapidly!). Useful to determine why your processes may be consuming a -# lot of CPU. -#use_heartbeat = False - -# Enable the memory debugging interface (careful, negatively impacts server -# performance). -#use_memdump = False - -# -- Data Libraries - -# These library upload options are described in much more detail in the wiki: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files - -# Add an option to the library upload form which allows administrators to -# upload a directory of files. -#library_import_dir = None - -# Add an option to the library upload form which allows authorized -# non-administrators to upload a directory of files. The configured directory -# must contain sub-directories named the same as the non-admin user's Galaxy -# login ( email ). The non-admin user is restricted to uploading files or -# sub-directories of files contained in their directory. -#user_library_import_dir = None - -# Add an option to the admin library upload tool allowing admins to paste -# filesystem paths to files and directories in a box, and these paths will be -# added to a library. Set to True to enable. Please note the security -# implication that this will give Galaxy Admins access to anything your Galaxy -# user has access to. -#allow_library_path_paste = False - -# Users may choose to download multiple files from a library in an archive. By -# default, Galaxy allows users to select from a few different archive formats -# if testing shows that Galaxy is able to create files using these formats. -# Specific formats can be disabled with this option, separate more than one -# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. -#disable_library_comptypes = - -# Some sequencer integration features in beta allow you to automatically -# transfer datasets. This is done using a lightweight transfer manager which -# runs outside of Galaxy (but is spawned by it automatically). Galaxy will -# communicate with this manager over the port specified here. -#transfer_manager_port = 8163 - -# Search data libraries with whoosh -#enable_whoosh_library_search = True -# Whoosh indexes are stored in this directory. -#whoosh_index_dir = database/whoosh_indexes - -# Search data libraries with lucene -#enable_lucene_library_search = False -# maxiumum file size to index for searching, in MB -#fulltext_max_size = 500 -#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger -# base URL of server providing search functionality using lucene -#fulltext_url = http://localhost:8081 - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -#id_secret = USING THE DEFAULT IS NOT SECURE! - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy -#use_remote_user = False - -# If use_remote_user is enabled and your external authentication -# method just returns bare usernames, set a default mail domain to be appended -# to usernames, to become your Galaxy usernames (email addresses). -#remote_user_maildomain = None - -# If use_remote_user is enabled, you can set this to a URL that will log your -# users out. -#remote_user_logout_href = None - -# Administrative users - set this to a comma-separated list of valid Galaxy -# users (email addresses). These users will have access to the Admin section -# of the server, and will have access to create users, groups, roles, -# libraries, and more. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Interface -#admin_users = None - -# Force everyone to log in (disable anonymous access). -#require_login = False - -# Allow unregistered users to create new accounts (otherwise, they will have to -# be created by an admin). -#allow_user_creation = True - -# Allow administrators to delete accounts. -#allow_user_deletion = False - -# Allow administrators to log in as other users (useful for debugging) -#allow_user_impersonation = False - -# Allow users to remove their datasets from disk immediately (otherwise, -# datasets will be removed after a time period specified by an administrator in -# the cleanup scripts run via cron) -#allow_user_dataset_purge = False - -# By default, users' data will be public, but setting this to True will cause -# it to be private. Does not affect existing users and data, only ones created -# after this option is set. Users may still change their default back to -# public. -#new_user_dataset_access_role_default_private = False - -# -- Beta features - -# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) -#object_store = disk -#os_access_key = <your cloud object store access key> -#os_secret_key = <your cloud object store secret key> -#os_bucket_name = <name of an existing object store bucket or container> -# If using 'swift' object store, you must specify the following connection properties -#os_host = swift.rc.nectar.org.au -#os_port = 8888 -#os_is_secure = False -#os_conn_path = / -# Reduced redundancy can be used only with the 's3' object store -#os_use_reduced_redundancy = False -# Size (in GB) that the cache used by object store should be limited to. -# If the value is not specified, the cache size will be limited only by the -# file system size. The file system location of the cache is considered the -# configuration of the ``file_path`` directive defined above. -#object_store_cache_size = 100 - -# Configuration file for the distributed object store, if object_store = -# distributed. See the sample at distributed_object_store_conf.xml.sample -#distributed_object_store_config_file = None - -# Enable Galaxy to communicate directly with a sequencer -#enable_sequencer_communication = False - -# Enable authentication via OpenID. Allows users to log in to their Galaxy -# account by authenticating with an OpenID provider. -#enable_openid = False -#openid_config_file = openid_conf.xml - -# Optional list of email addresses of API users who can make calls on behalf of -# other users -#api_allow_run_as = None - -# Enable tool tags (associating tools with tags). This has its own option -# since its implementation has a few performance implications on startup for -# large servers. -#enable_tool_tags = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# The URL to the myExperiment instance being used (omit scheme but include port) -#myexperiment_url = www.myexperiment.org:80 - -# Enable Galaxy's "Upload via FTP" interface. You'll need to install and -# configure an FTP server (we've used ProFTPd since it can use Galaxy's -# database for authentication) and set the following two options. - -# This should point to a directory containing subdirectories matching users' -# email addresses, where Galaxy will look for files. -#ftp_upload_dir = None - -# This should be the hostname of your FTP server, which will be provided to -# users in the help text. -#ftp_upload_site = None - -# Enable enforcement of quotas. Quotas can be set from the Admin interface. -#enable_quotas = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# -- Job Execution - -# To increase performance of job execution and the web interface, you can -# separate Galaxy into multiple processes. There are more than one way to do -# this, and they are explained in detail in the documentation: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… -# -# By default, Galaxy manages and executes jobs from within a single process and -# notifies itself of new jobs via in-memory queues. If you change job_manager -# and job_handlers from their default values, notification will instead be done -# using the `state` and `handler` columns of the job table in the database. - -# Identify the server_name (the string following server: at the top of this -# file) which should be designated as the job manager (only one): -#job_manager = main - -# Identify the server_name(s) which should be designated as job handlers -# (responsible for starting, tracking, finishing, and cleaning up jobs) as a -# comma-separated list. -#job_handlers = main - -# By default, a handler from job_handlers will be selected at random if the -# tool to run does specify a handler below in [galaxy:tool_handlers]. If you -# want certain handlers to only handle jobs for tools/params explicitly -# assigned below, use default_job_handlers to specify which handlers should be -# used for jobs without explicit handlers. -#default_job_handlers = main - -# This enables splitting of jobs into tasks, if specified by the particular tool config. -# This is a new feature and not recommended for production servers yet. -#use_tasked_jobs = False -#local_task_queue_workers = 2 - -# Enable job recovery (if Galaxy is restarted while cluster jobs are running, -# it can "recover" them when it starts). This is not safe to use if you are -# running more than one Galaxy server using the same database. -#enable_job_recovery = True - -# Setting metadata on job outputs to in a separate process (or if using a -# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the -# hefty expense that setting metadata incurs, your Galaxy process may become -# unresponsive when this operation occurs internally. -#set_metadata_externally = False - -# Although it is fairly reliable, setting metadata can occasionally fail. In -# these instances, you can choose to retry setting it internally or leave it in -# a failed state (since retrying internally may cause the Galaxy process to be -# unresponsive). If this option is set to False, the user will be given the -# option to retry externally, or set metadata manually (when possible). -#retry_metadata_internally = True - -# If (for example) you run on a cluster and your datasets (by default, -# database/files/) are mounted read-only, this option will override tool output -# paths to write outputs to the working directory instead, and the job manager -# will move the outputs to their proper place in the dataset directory on the -# Galaxy server after the job completes. -#outputs_to_working_directory = False - -# If your network filesystem's caching prevents the Galaxy server from seeing -# the job's stdout and stderr files when it completes, you can retry reading -# these files. The job runner will retry the number of times specified below, -# waiting 1 second between tries. For NFS, you may want to try the -noac mount -# option (Linux) or -actimeo=0 (Solaris). -#retry_job_output_collection = 0 - -# Clean up various bits of jobs left on the filesystem after completion. These -# bits include the job working directory, external metadata temporary files, -# and DRM stdout and stderr files (if using a DRM). Possible values are: -# always, onsuccess, never -#cleanup_job = always - -# Number of concurrent jobs to run (local job runner) -#local_job_queue_workers = 5 - -# Jobs can be killed after a certain amount of execution time. Format is in -# hh:mm:ss. Currently only implemented for PBS. -#job_walltime = None - -# Jobs can be killed if any of their outputs grow over a certain size (in -# bytes). 0 for no limit. -#output_size_limit = 0 - -# Jobs can be held back from submission to a runner if a user already has more -# jobs queued or running than the number specified below. This prevents a -# single user from stuffing the queue and preventing other users from being -# able to run jobs. -#user_job_limit = None - -# Clustering Galaxy is not a straightforward process and requires some -# pre-configuration. See the the wiki before attempting to set any of these -# options: -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster - -# Comma-separated list of job runners to start. local is always started. If -# left commented, no jobs will be run on the cluster, even if a cluster URL is -# explicitly defined in the [galaxy:tool_runners] section below. The runners -# currently available are 'pbs' and 'drmaa'. -#start_job_runners = None - -# For sites where all users in Galaxy match users on the system on which Galaxy -# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the -# actual user instead of as the user running the Galaxy server process. For -# details on these options, see the documentation at: -# -# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster -# -#drmaa_external_runjob_script = scripts/drmaa_external_runner.py -#drmaa_external_killjob_script = scripts/drmaa_external_killer.py -#external_chown_script = scripts/external_chown_script.py - -# File to source to set up the environment when running jobs. By default, the -# environment in which the Galaxy server starts is used when running jobs -# locally, and the environment set up per the DRM's submission method and -# policy is used when running jobs on a cluster (try testing with `qsub` on the -# command line). environment_setup_file can be set to the path of a file on -# the cluster that should be sourced by the user to set up the environment -# prior to running tools. This can be especially useful for running jobs as -# the actual user, to remove the need to configure each user's environment -# individually. This only affects cluster jobs, not local jobs. -#environment_setup_file = None - -# The URL for the default runner to use when a tool doesn't explicitly define a -# runner below. -#default_cluster_job_runner = local:/// - -# The cluster runners have their own thread pools used to prepare and finish -# jobs (so that these sometimes lengthy operations do not block normal queue -# operation). The value here is the number of worker threads available to each -# started runner. -#cluster_job_queue_workers = 3 - -# These options are only used when using file staging with PBS. -#pbs_application_server = -#pbs_stage_path = -#pbs_dataset_server = - -# This option allows users to see the full path of datasets via the "View -# Details" option in the history. Administrators can always see this. -#expose_dataset_path = False - -# ---- Per-Tool Job Management ---------------------------------------------- - -# Per-tool job handler and runner overrides. Parameters can be included to define multiple -# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster -# differently than standard Cufflinks jobs: -# -# cufflinks = local:/// -# cufflinks[source@trackster] = local:/// - -[galaxy:tool_handlers] - -# By default, Galaxy will select a handler at random from the list of -# job_handlers set above. You can override as in the following examples: -# -#upload1 = upload_handler -#cufflinks[source@trackster] = realtime_handler - -[galaxy:tool_runners] - -# If not listed here, a tool will run with the runner defined with -# default_cluster_job_runner. These overrides for local:/// are done because -# these tools can fetch data from remote sites, which may not be suitable to -# run on a cluster (if it does not have access to the Internet, for example). - -biomart = local:/// -encode_db1 = local:/// -hbvar = local:/// -microbial_import1 = local:/// -ucsc_table_direct1 = local:/// -ucsc_table_direct_archaea1 = local:/// -ucsc_table_direct_test1 = local:/// -upload1 = local:/// - -# ---- Galaxy Message Queue ------------------------------------------------- - -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -[galaxy_amqp] - -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#rabbitmqctl_path = /path/to/rabbitmqctl - diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -263,6 +263,9 @@ # as on the user registration and login forms. #terms_url = None +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy 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.

1 0

commit/galaxy-central: rmarenco: When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in unverse
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/95d98a265183/ changeset: 95d98a265183 user: rmarenco date: 2012-09-07 02:55:35 summary: When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in unverse affected #: 3 files diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd database/compiled_templates/webapps/galaxy/base_panels.mako.py --- /dev/null +++ b/database/compiled_templates/webapps/galaxy/base_panels.mako.py @@ -0,0 +1,415 @@ +# -*- encoding:ascii -*- +from mako import runtime, filters, cache +UNDEFINED = runtime.UNDEFINED +__M_dict_builtin = dict +__M_locals_builtin = locals +_magic_number = 6 +_modified_time = 1346972736.51736 +_template_filename=u'templates/webapps/galaxy/base_panels.mako' +_template_uri=u'/webapps/galaxy/base_panels.mako' +_template_cache=cache.Cache(__name__, _modified_time) +_source_encoding='ascii' +_exports = ['masthead', 'javascripts', 'title'] + + +def _mako_get_namespace(context, name): + try: + return context.namespaces[(__name__, name)] + except KeyError: + _mako_generate_namespaces(context) + return context.namespaces[(__name__, name)] +def _mako_generate_namespaces(context): + pass +def _mako_inherit(template, context): + _mako_generate_namespaces(context) + return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) +def render_body(context,**pageargs): + context.caller_stack._push_frame() + try: + __M_locals = __M_dict_builtin(pageargs=pageargs) + __M_writer = context.writer() + # SOURCE LINE 1 + __M_writer(u'\n\n') + # SOURCE LINE 4 + __M_writer(u'\n\n') + # SOURCE LINE 8 + __M_writer(u'\n\n') + # SOURCE LINE 232 + __M_writer(u'\n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_masthead(context): + context.caller_stack._push_frame() + try: + AssertionError = context.get('AssertionError', UNDEFINED) + h = context.get('h', UNDEFINED) + app = context.get('app', UNDEFINED) + util = context.get('util', UNDEFINED) + def tab(id,display,href,target='_parent',visible=True,extra_class='',menu_options=None): + context.caller_stack._push_frame() + try: + self = context.get('self', UNDEFINED) + len = context.get('len', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 19 + __M_writer(u'\n') + # SOURCE LINE 22 + __M_writer(u' \n ') + # SOURCE LINE 23 + + cls = "" + a_cls = "" + extra = "" + if extra_class: + cls += " " + extra_class + if self.active_view == id: + cls += " active" + if menu_options: + cls += " dropdown" + a_cls += " dropdown-toggle" + extra = "<b class='caret'></b>" + style = "" + if not visible: + style = "display: none;" + + + # SOURCE LINE 38 + __M_writer(u'\n <li class="') + # SOURCE LINE 39 + __M_writer(unicode(cls)) + __M_writer(u'" style="') + __M_writer(unicode(style)) + __M_writer(u'">\n') + # SOURCE LINE 40 + if href: + # SOURCE LINE 41 + __M_writer(u' <a class="') + __M_writer(unicode(a_cls)) + __M_writer(u'" data-toggle="dropdown" target="') + __M_writer(unicode(target)) + __M_writer(u'" href="') + __M_writer(unicode(href)) + __M_writer(u'">') + __M_writer(unicode(display)) + __M_writer(unicode(extra)) + __M_writer(u'</a>\n') + # SOURCE LINE 42 + else: + # SOURCE LINE 43 + __M_writer(u' <a class="') + __M_writer(unicode(a_cls)) + __M_writer(u'" data-toggle="dropdown">') + __M_writer(unicode(display)) + __M_writer(unicode(extra)) + __M_writer(u'</a>\n') + pass + # SOURCE LINE 45 + if menu_options: + # SOURCE LINE 46 + __M_writer(u' <ul class="dropdown-menu">\n') + # SOURCE LINE 47 + for menu_item in menu_options: + # SOURCE LINE 48 + if not menu_item: + # SOURCE LINE 49 + __M_writer(u' <li class="divider"></li>\n') + # SOURCE LINE 50 + else: + # SOURCE LINE 51 + __M_writer(u' <li>\n') + # SOURCE LINE 52 + if len ( menu_item ) == 1: + # SOURCE LINE 53 + __M_writer(u' ') + __M_writer(unicode(menu_item[0])) + __M_writer(u'\n') + # SOURCE LINE 54 + elif len ( menu_item ) == 2: + # SOURCE LINE 55 + __M_writer(u' ') + name, link = menu_item + + __M_writer(u'\n <a href="') + # SOURCE LINE 56 + __M_writer(unicode(link)) + __M_writer(u'">') + __M_writer(unicode(name)) + __M_writer(u'</a>\n') + # SOURCE LINE 57 + else: + # SOURCE LINE 58 + __M_writer(u' ') + name, link, target = menu_item + + __M_writer(u'\n <a target="') + # SOURCE LINE 59 + __M_writer(unicode(target)) + __M_writer(u'" href="') + __M_writer(unicode(link)) + __M_writer(u'">') + __M_writer(unicode(name)) + __M_writer(u'</a>\n') + pass + # SOURCE LINE 61 + __M_writer(u' </li>\n') + pass + pass + # SOURCE LINE 64 + __M_writer(u' </ul>\n') + pass + # SOURCE LINE 66 + __M_writer(u' </li>\n ') + return '' + finally: + context.caller_stack._pop_frame() + trans = context.get('trans', UNDEFINED) + _ = context.get('_', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 11 + __M_writer(u'\n\n') + # SOURCE LINE 14 + __M_writer(u' <div style="position: relative; right: -50%; float: left;">\n <div style="display: block; position: relative; right: 50%;">\n\n <ul class="nav" border="0" cellspacing="0">\n \n ') + # SOURCE LINE 67 + __M_writer(u'\n\n') + # SOURCE LINE 70 + __M_writer(u' ') + __M_writer(unicode(tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 73 + __M_writer(u' ') + __M_writer(unicode(tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 76 + __M_writer(u' ') + + menu_options = [ + [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], + None, + [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], + [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], + [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], + [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] + ] + tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) + + + # SOURCE LINE 86 + __M_writer(u'\n \n') + # SOURCE LINE 89 + __M_writer(u' ') + + menu_options = [ + [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], + [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ], + [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] + ] + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) + + + # SOURCE LINE 96 + __M_writer(u'\n\n') + # SOURCE LINE 99 + __M_writer(u' ') + + menu_options = [ + [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] + ] + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + + + # SOURCE LINE 105 + __M_writer(u'\n\n') + # SOURCE LINE 108 + if app.config.get_bool( 'enable_cloud_launch', False ): + # SOURCE LINE 109 + __M_writer(u' ') + + menu_options = [ + [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], + ] + tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) + + + # SOURCE LINE 114 + __M_writer(u'\n') + pass + # SOURCE LINE 116 + __M_writer(u'\n') + # SOURCE LINE 118 + __M_writer(u' ') + __M_writer(unicode(tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) ))) + __M_writer(u'\n \n') + # SOURCE LINE 121 + __M_writer(u' ') + + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], + [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], + [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], + [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + ] + if app.config.get( 'terms_url', None ) is not None: + menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) + tab( "help", _("Help"), None, menu_options=menu_options) + + + # SOURCE LINE 132 + __M_writer(u'\n \n') + # SOURCE LINE 135 + __M_writer(u' ') + + # Menu for user who is not logged in. + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] + if app.config.allow_user_creation: + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + extra_class = "loggedout-only" + visible = ( trans.user == None ) + tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) + + # Menu for user who is logged in. + if trans.user: + email = trans.user.email + else: + email = "" + menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] + if app.config.use_remote_user: + if app.config.remote_user_logout_href: + menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) + else: + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) + if app.config.require_login: + logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) + else: + logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) + menu_options.append( None ) + menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + if app.config.use_remote_user: + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) + + extra_class = "loggedin-only" + visible = ( trans.user != None ) + tab( "user", "User", None, visible=visible, menu_options=menu_options ) + + + # SOURCE LINE 172 + __M_writer(u'\n \n') + # SOURCE LINE 176 + __M_writer(u' </ul>\n\n </div>\n </div>\n \n') + # SOURCE LINE 182 + __M_writer(u' <div class="title">\n <a href="') + # SOURCE LINE 183 + __M_writer(unicode(h.url_for( app.config.get( 'logo_url', '/' ) ))) + __M_writer(u'">\n <img border="0" src="') + # SOURCE LINE 184 + __M_writer(unicode(h.url_for('/static/images/galaxyIcon_noText.png'))) + __M_writer(u'">\n Galaxy\n') + # SOURCE LINE 186 + if app.config.brand: + # SOURCE LINE 187 + __M_writer(u' <span>/ ') + __M_writer(unicode(app.config.brand)) + __M_writer(u'</span>\n') + pass + # SOURCE LINE 189 + __M_writer(u' </a>\n </div>\n\n') + # SOURCE LINE 193 + __M_writer(u' ') + + bar_style = "quota-meter-bar" + usage = 0 + percent = 0 + quota = None + try: + usage = trans.app.quota_agent.get_usage( trans=trans ) + quota = trans.app.quota_agent.get_quota( trans.user ) + percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota ) + if percent is not None: + if percent >= 100: + bar_style += " quota-meter-bar-error" + elif percent >= 85: + bar_style += " quota-meter-bar-warn" + else: + percent = 0 + except AssertionError: + pass # Probably no history yet + tooltip = None + if not trans.user and quota and trans.app.config.allow_user_creation: + if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota: + tooltip = "Your disk quota is %s. You can increase your quota by registering a Galaxy account." % util.nice_size( quota ) + + + # SOURCE LINE 215 + __M_writer(u'\n\n <div class="quota-meter-container">\n') + # SOURCE LINE 218 + if tooltip: + # SOURCE LINE 219 + __M_writer(u' <div id="quota-meter" class="quota-meter tooltip" title="') + __M_writer(unicode(tooltip)) + __M_writer(u'">\n') + # SOURCE LINE 220 + else: + # SOURCE LINE 221 + __M_writer(u' <div id="quota-meter" class="quota-meter">\n') + pass + # SOURCE LINE 223 + __M_writer(u' <div id="quota-meter-bar" class="') + __M_writer(unicode(bar_style)) + __M_writer(u'" style="width: ') + __M_writer(unicode(percent)) + __M_writer(u'px;"></div>\n') + # SOURCE LINE 224 + if quota is not None: + # SOURCE LINE 225 + __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') + __M_writer(unicode(percent)) + __M_writer(u'%</div>\n') + # SOURCE LINE 226 + else: + # SOURCE LINE 227 + __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') + __M_writer(unicode(util.nice_size( usage ))) + __M_writer(u'</div>\n') + pass + # SOURCE LINE 229 + __M_writer(u' </div>\n </div>\n \n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_javascripts(context): + context.caller_stack._push_frame() + try: + parent = context.get('parent', UNDEFINED) + __M_writer = context.writer() + # SOURCE LINE 6 + __M_writer(u'\n ') + # SOURCE LINE 7 + __M_writer(unicode(parent.javascripts())) + __M_writer(u'\n') + return '' + finally: + context.caller_stack._pop_frame() + + +def render_title(context): + context.caller_stack._push_frame() + try: + __M_writer = context.writer() + # SOURCE LINE 4 + __M_writer(u'Galaxy') + return '' + finally: + context.caller_stack._pop_frame() + + diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -302,8 +302,8 @@ ${tool.name} ${tool_version_select_field.get_html()} %endif  - <a href="http://slyfox.bx.psu.edu:8081/new/post/" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> - <a href="http://slyfox.bx.psu.edu:8081/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> + <a href="http://slyfox.bx.psu.edu:8080/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8080/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a></div><div class="toolFormBody"> diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd universe_wsgi.ini --- /dev/null +++ b/universe_wsgi.ini @@ -0,0 +1,753 @@ +# +# Galaxy is configured by default to be useable in a single-user development +# environment. To tune the application for a multi-user production +# environment, see the documentation at: +# +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server +# + +# Throughout this sample configuration file, except where stated otherwise, +# uncommented values override the default if left unset, whereas commented +# values are set to the default value. +# Examples of many of these options are explained in more detail in the wiki: +# +# http://wiki.g2.bx.psu.edu/Admin/Config +# +# Config hackers are encouraged to check there before asking for help. + +# ---- HTTP Server ---------------------------------------------------------- + +# Configuration of the internal HTTP server. + +[server:main] + +# The internal HTTP server to use. Currently only Paste is provided. This +# option is required. +use = egg:Paste#http + +# The port on which to listen. +#port = 8080 + +# The address on which to listen. By default, only listen to localhost (Galaxy +# will not be accessible over the network). Use '0.0.0.0' to listen on all +# available network interfaces. +#host = 127.0.0.1 + +# Use a threadpool for the web server instead of creating a thread for each +# request. +use_threadpool = True + +# Number of threads in the web server thread pool. +#threadpool_workers = 10 + +# ---- Filters -------------------------------------------------------------- + +# Filters sit between Galaxy and the HTTP server. + +# These filters are disabled by default. They can be enabled with +# 'filter-with' in the [app:main] section below. + +# Define the gzip filter. +[filter:gzip] +use = egg:Paste#gzip + +# Define the proxy-prefix filter. +[filter:proxy-prefix] +use = egg:PasteDeploy#prefix +prefix = /galaxy + +# ---- Galaxy --------------------------------------------------------------- + +# Configuration of the Galaxy application. + +[app:main] + +# -- Application and filtering + +# The factory for the WSGI application. This should not be changed. +paste.app_factory = galaxy.web.buildapp:app_factory + +# If not running behind a proxy server, you may want to enable gzip compression +# to decrease the size of data transferred over the network. If using a proxy +# server, please enable gzip compression there instead. +#filter-with = gzip + +# If running behind a proxy server and Galaxy is served from a subdirectory, +# enable the proxy-prefix filter and set the prefix in the +# [filter:proxy-prefix] section above. +#filter-with = proxy-prefix + +# If proxy-prefix is enabled and you're running more than one Galaxy instance +# behind one hostname, you will want to set this to the same path as the prefix +# in the filter above. This value becomes the "path" attribute set in the +# cookie so the cookies from each instance will not clobber each other. +#cookie_path = None + +# -- Database + +# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You +# may use a SQLAlchemy connection string to specify an external database +# instead. This string takes many options which are explained in detail in the +# config file documentation. +#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE + +# If the server logs errors about not having enough database pool connections, +# you will want to increase these values, or consider running more Galaxy +# processes. +#database_engine_option_pool_size = 5 +#database_engine_option_max_overflow = 10 + +# If using MySQL and the server logs the error "MySQL server has gone away", +# you will want to set this to some positive value (7200 should work). +#database_engine_option_pool_recycle = -1 + +# If large database query results are causing memory or response time issues in +# the Galaxy process, leave the result on the server instead. This option is +# only available for PostgreSQL and is highly recommended. +#database_engine_option_server_side_cursors = False + +# Create only one connection to the database per thread, to reduce the +# connection overhead. Recommended when not using SQLite: +#database_engine_option_strategy = threadlocal + +# Log all database transactions, can be useful for debugging and performance +# profiling. Logging is done via Python's 'logging' module under the qualname +# 'galaxy.model.orm.logging_connection_proxy' +#database_query_profiling_proxy = False + +# -- Files and directories + +# Path where genome builds are stored. This defaults to tool-data/genome +#genome_data_path = tool-data/genome + +# URL for rsync server to download pre-built indexes. +#rsync_url = rsync://scofield.bx.psu.edu/indexes + +# Dataset files are stored in this directory. +#file_path = database/files + +# Temporary files are stored in this directory. +#new_file_path = database/tmp + +# Tool config files, defines what tools are available in Galaxy. +# Tools can be locally developed or installed from Galaxy tool sheds. +#tool_config_file = tool_conf.xml,shed_tool_conf.xml + +# Default path to the directory containing the tools defined in tool_conf.xml. +# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +#tool_path = tools + +# Path to the directory in which managed tool dependencies are placed. To use +# the dependency system, see the documentation at: +# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies +#tool_dependency_dir = None + +# Enable automatic polling of relative tool sheds to see if any updates +# are available for installed repositories. Ideally only one Galaxy +# server process should be able to check for repository updates. The +# setting for hours_between_check should be an integer between 1 and 24. +#enable_tool_shed_check = False +#hours_between_check = 12 + +# Directory where data used by tools is located, see the samples in that +# directory and the wiki for help: +# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration +#tool_data_path = tool-data + +# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + +# Datatypes config file, defines what data (file) types are available in +# Galaxy. +#datatypes_config_file = datatypes_conf.xml + +# Each job is given a unique empty directory as its current working directory. +# This option defines in what parent directory those directories will be +# created. +#job_working_directory = database/job_working_directory + +# If using a cluster, Galaxy will write job scripts and stdout/stderr to this +# directory. +#cluster_files_directory = database/pbs + +# External service types config file, defines what types of external_services configurations +# are available in Galaxy. +#external_service_type_config_file = external_service_types_conf.xml + +# Path to the directory containing the external_service_types defined in the config. +#external_service_type_path = external_service_types + +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + +# -- Mail and notification + +# Galaxy sends mail for various things: Subscribing users to the mailing list +# if they request it, emailing password resets, notification from the Galaxy +# Sample Tracking system, and reporting dataset errors. To do this, it needs +# to send mail through an SMTP server, which you may define here (host:port). +# Galaxy will automatically try STARTTLS but will continue upon failure. +#smtp_server = None + +# If your SMTP server requires a username and password, you can provide them +# here (password in cleartext here, but if your server supports STARTTLS it +# will be sent over the network encrypted). +#smtp_username = None +#smtp_password = None + +# On the user registration form, users may choose to join the mailing list. +# This is the address of the list they'll be subscribed to. +#mailing_join_addr = galaxy-announce-join(a)bx.psu.edu + +# Datasets in an error state include a link to report the error. Those reports +# will be sent to this address. Error reports are disabled if no address is set. +#error_email_to = None + +# -- Display sites + +# Galaxy can display data at various external browsers. These options specify +# which browsers should be available. URLs and builds available at these +# browsers are defined in the specifield files. + +# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt +#ucsc_display_sites = main,test,archaea,ucla + +# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt +#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 + +# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt +#genetrack_display_sites = main,test + +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. + +use_nglims = False +nglims_config_file = tool-data/nglims.yaml + +# -- UI Localization + +# Append "/{brand}" to the "Galaxy" text in the masthead. +#brand = None + +# The URL linked by the "Galaxy/brand" text. +#logo_url = / + +# The URL linked by the "Galaxy Wiki" link in the "Help" menu. +#wiki_url = http://wiki.g2.bx.psu.edu/ + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support + +# The URL linked by the "How to Cite..." link in the "Help" menu. +#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy + +# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well +# as on the user registration and login forms. +#terms_url = None + +# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + +# Serve static content, which must be enabled if you're not serving it via a +# proxy server. These options should be self explanatory and so are not +# documented individually. You can use these paths (or ones in the proxy +# server) to point to your own styles. +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue +static_robots_txt = %(here)s/static/robots.txt + +# Pack javascript at launch (/static/scripts/*.js) +# This only happens if the modified timestamp of the source .js is newer +# than the version (if it exists) in /static/scripts/packed/ +# Note that this requires java > 1.4 for executing yuicompressor.jar +#pack_scripts = False + +# Enable Cloud Launch + +#enable_cloud_launch = False + +# -- Advanced proxy features + +# For help on configuring the Advanced proxy features, see: +# http://usegalaxy.org/production + +# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set +# this to True to inform Galaxy that mod_xsendfile is enabled upstream. +#apache_xsendfile = False + +# The same download handling can be done by nginx using X-Accel-Redirect. This +# should be set to the path defined in the nginx config as an internal redirect +# with access to Galaxy's data files (see documentation linked above). +#nginx_x_accel_redirect_base = False + +# nginx can make use of mod_zip to create zip files containing multiple library +# files. If using X-Accel-Redirect, this can be the same value as that option. +#nginx_x_archive_files_base = False + +# If using compression in the upstream proxy server, use this option to disable +# gzipping of library .tar.gz and .zip archives, since the proxy server will do +# it faster on the fly. +#upstream_gzip = False + +# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. +# Configuration for this is complex and explained in detail in the +# documentation linked above. The upload store is a temporary directory in +# which files uploaded by the upload module will be placed. +#nginx_upload_store = False + +# This value overrides the action set on the file upload form, e.g. the web +# path where the nginx_upload_module has been configured to intercept upload +# requests. +#nginx_upload_path = False + +# -- Logging and Debugging + +# Verbosity of console log messages. Acceptable values can be found here: +# http://docs.python.org/library/logging.html#logging-levels +#log_level = DEBUG + +# Print database operations to the server log (warning, quite verbose!). +#database_engine_option_echo = False + +# Print database pool operations to the server log (warning, quite verbose!). +#database_engine_option_echo_pool = False + +# Turn on logging of application events and some user events to the database. +#log_events = True + +# Turn on logging of user actions to the database. Actions currently logged are +# grid views, tool searches, and use of "recently" used tools menu. The +# log_events and log_actions functionality will eventually be merged. +#log_actions = True + +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + +# Debug enables access to various config options useful for development and +# debugging: use_lint, use_profile, use_printdebug and use_interactive. It +# also causes the files used by PBS/SGE (submission script, output, and error) +# to remain on disk after the job is complete. Debug mode is disabled if +# commented, but is uncommented by default in the sample config. +debug = True + +# Check for WSGI compliance. +#use_lint = False + +# Run the Python profiler on each request. +#use_profile = False + +# Intercept print statements and show them on the returned page. +#use_printdebug = True + +# Enable live debugging in your browser. This should NEVER be enabled on a +# public site. Enabled in the sample config for development. +use_interactive = True + +# Write thread status periodically to 'heartbeat.log', (careful, uses disk +# space rapidly!). Useful to determine why your processes may be consuming a +# lot of CPU. +#use_heartbeat = False + +# Enable the memory debugging interface (careful, negatively impacts server +# performance). +#use_memdump = False + +# -- Data Libraries + +# These library upload options are described in much more detail in the wiki: +# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files + +# Add an option to the library upload form which allows administrators to +# upload a directory of files. +#library_import_dir = None + +# Add an option to the library upload form which allows authorized +# non-administrators to upload a directory of files. The configured directory +# must contain sub-directories named the same as the non-admin user's Galaxy +# login ( email ). The non-admin user is restricted to uploading files or +# sub-directories of files contained in their directory. +#user_library_import_dir = None + +# Add an option to the admin library upload tool allowing admins to paste +# filesystem paths to files and directories in a box, and these paths will be +# added to a library. Set to True to enable. Please note the security +# implication that this will give Galaxy Admins access to anything your Galaxy +# user has access to. +#allow_library_path_paste = False + +# Users may choose to download multiple files from a library in an archive. By +# default, Galaxy allows users to select from a few different archive formats +# if testing shows that Galaxy is able to create files using these formats. +# Specific formats can be disabled with this option, separate more than one +# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. +#disable_library_comptypes = + +# Some sequencer integration features in beta allow you to automatically +# transfer datasets. This is done using a lightweight transfer manager which +# runs outside of Galaxy (but is spawned by it automatically). Galaxy will +# communicate with this manager over the port specified here. +#transfer_manager_port = 8163 + +# Search data libraries with whoosh +#enable_whoosh_library_search = True +# Whoosh indexes are stored in this directory. +#whoosh_index_dir = database/whoosh_indexes + +# Search data libraries with lucene +#enable_lucene_library_search = False +# maxiumum file size to index for searching, in MB +#fulltext_max_size = 500 +#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +#id_secret = USING THE DEFAULT IS NOT SECURE! + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +#use_remote_user = False + +# If use_remote_user is enabled and your external authentication +# method just returns bare usernames, set a default mail domain to be appended +# to usernames, to become your Galaxy usernames (email addresses). +#remote_user_maildomain = None + +# If use_remote_user is enabled, you can set this to a URL that will log your +# users out. +#remote_user_logout_href = None + +# Administrative users - set this to a comma-separated list of valid Galaxy +# users (email addresses). These users will have access to the Admin section +# of the server, and will have access to create users, groups, roles, +# libraries, and more. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Interface +#admin_users = None + +# Force everyone to log in (disable anonymous access). +#require_login = False + +# Allow unregistered users to create new accounts (otherwise, they will have to +# be created by an admin). +#allow_user_creation = True + +# Allow administrators to delete accounts. +#allow_user_deletion = False + +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + +# Allow users to remove their datasets from disk immediately (otherwise, +# datasets will be removed after a time period specified by an administrator in +# the cleanup scripts run via cron) +#allow_user_dataset_purge = False + +# By default, users' data will be public, but setting this to True will cause +# it to be private. Does not affect existing users and data, only ones created +# after this option is set. Users may still change their default back to +# public. +#new_user_dataset_access_role_default_private = False + +# -- Beta features + +# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) +#object_store = disk +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> +# If using 'swift' object store, you must specify the following connection properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. The file system location of the cache is considered the +# configuration of the ``file_path`` directive defined above. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + +# Enable Galaxy to communicate directly with a sequencer +#enable_sequencer_communication = False + +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False +#openid_config_file = openid_conf.xml + +# Optional list of email addresses of API users who can make calls on behalf of +# other users +#api_allow_run_as = None + +# Enable tool tags (associating tools with tags). This has its own option +# since its implementation has a few performance implications on startup for +# large servers. +#enable_tool_tags = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + +# Enable Galaxy's "Upload via FTP" interface. You'll need to install and +# configure an FTP server (we've used ProFTPd since it can use Galaxy's +# database for authentication) and set the following two options. + +# This should point to a directory containing subdirectories matching users' +# email addresses, where Galaxy will look for files. +#ftp_upload_dir = None + +# This should be the hostname of your FTP server, which will be provided to +# users in the help text. +#ftp_upload_site = None + +# Enable enforcement of quotas. Quotas can be set from the Admin interface. +#enable_quotas = False + +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + +# -- Job Execution + +# To increase performance of job execution and the web interface, you can +# separate Galaxy into multiple processes. There are more than one way to do +# this, and they are explained in detail in the documentation: +# +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… +# +# By default, Galaxy manages and executes jobs from within a single process and +# notifies itself of new jobs via in-memory queues. If you change job_manager +# and job_handlers from their default values, notification will instead be done +# using the `state` and `handler` columns of the job table in the database. + +# Identify the server_name (the string following server: at the top of this +# file) which should be designated as the job manager (only one): +#job_manager = main + +# Identify the server_name(s) which should be designated as job handlers +# (responsible for starting, tracking, finishing, and cleaning up jobs) as a +# comma-separated list. +#job_handlers = main + +# By default, a handler from job_handlers will be selected at random if the +# tool to run does specify a handler below in [galaxy:tool_handlers]. If you +# want certain handlers to only handle jobs for tools/params explicitly +# assigned below, use default_job_handlers to specify which handlers should be +# used for jobs without explicit handlers. +#default_job_handlers = main + +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = False +#local_task_queue_workers = 2 + +# Enable job recovery (if Galaxy is restarted while cluster jobs are running, +# it can "recover" them when it starts). This is not safe to use if you are +# running more than one Galaxy server using the same database. +#enable_job_recovery = True + +# Setting metadata on job outputs to in a separate process (or if using a +# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the +# hefty expense that setting metadata incurs, your Galaxy process may become +# unresponsive when this operation occurs internally. +#set_metadata_externally = False + +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + +# If (for example) you run on a cluster and your datasets (by default, +# database/files/) are mounted read-only, this option will override tool output +# paths to write outputs to the working directory instead, and the job manager +# will move the outputs to their proper place in the dataset directory on the +# Galaxy server after the job completes. +#outputs_to_working_directory = False + +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + +# Clean up various bits of jobs left on the filesystem after completion. These +# bits include the job working directory, external metadata temporary files, +# and DRM stdout and stderr files (if using a DRM). Possible values are: +# always, onsuccess, never +#cleanup_job = always + +# Number of concurrent jobs to run (local job runner) +#local_job_queue_workers = 5 + +# Jobs can be killed after a certain amount of execution time. Format is in +# hh:mm:ss. Currently only implemented for PBS. +#job_walltime = None + +# Jobs can be killed if any of their outputs grow over a certain size (in +# bytes). 0 for no limit. +#output_size_limit = 0 + +# Jobs can be held back from submission to a runner if a user already has more +# jobs queued or running than the number specified below. This prevents a +# single user from stuffing the queue and preventing other users from being +# able to run jobs. +#user_job_limit = None + +# Clustering Galaxy is not a straightforward process and requires some +# pre-configuration. See the the wiki before attempting to set any of these +# options: +# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster + +# Comma-separated list of job runners to start. local is always started. If +# left commented, no jobs will be run on the cluster, even if a cluster URL is +# explicitly defined in the [galaxy:tool_runners] section below. The runners +# currently available are 'pbs' and 'drmaa'. +#start_job_runners = None + +# For sites where all users in Galaxy match users on the system on which Galaxy +# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the +# actual user instead of as the user running the Galaxy server process. For +# details on these options, see the documentation at: +# +# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster +# +#drmaa_external_runjob_script = scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = scripts/drmaa_external_killer.py +#external_chown_script = scripts/external_chown_script.py + +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. This only affects cluster jobs, not local jobs. +#environment_setup_file = None + +# The URL for the default runner to use when a tool doesn't explicitly define a +# runner below. +#default_cluster_job_runner = local:/// + +# The cluster runners have their own thread pools used to prepare and finish +# jobs (so that these sometimes lengthy operations do not block normal queue +# operation). The value here is the number of worker threads available to each +# started runner. +#cluster_job_queue_workers = 3 + +# These options are only used when using file staging with PBS. +#pbs_application_server = +#pbs_stage_path = +#pbs_dataset_server = + +# This option allows users to see the full path of datasets via the "View +# Details" option in the history. Administrators can always see this. +#expose_dataset_path = False + +# ---- Per-Tool Job Management ---------------------------------------------- + +# Per-tool job handler and runner overrides. Parameters can be included to define multiple +# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster +# differently than standard Cufflinks jobs: +# +# cufflinks = local:/// +# cufflinks[source@trackster] = local:/// + +[galaxy:tool_handlers] + +# By default, Galaxy will select a handler at random from the list of +# job_handlers set above. You can override as in the following examples: +# +#upload1 = upload_handler +#cufflinks[source@trackster] = realtime_handler + +[galaxy:tool_runners] + +# If not listed here, a tool will run with the runner defined with +# default_cluster_job_runner. These overrides for local:/// are done because +# these tools can fetch data from remote sites, which may not be suitable to +# run on a cluster (if it does not have access to the Internet, for example). + +biomart = local:/// +encode_db1 = local:/// +hbvar = local:/// +microbial_import1 = local:/// +ucsc_table_direct1 = local:/// +ucsc_table_direct_archaea1 = local:/// +ucsc_table_direct_test1 = local:/// +upload1 = local:/// + +# ---- Galaxy Message Queue ------------------------------------------------- + +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +[galaxy_amqp] + +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +#rabbitmqctl_path = /path/to/rabbitmqctl + 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: rmarenco: Added links to BioStar in the Help Menu and in tool forms
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2f684dfa8d47/ changeset: 2f684dfa8d47 user: rmarenco date: 2012-09-07 01:08:27 summary: Added links to BioStar in the Help Menu and in tool forms affected #: 6 files diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1783,3 +1783,17 @@ .opacity(80); } } + +.icon-button.general-question{ + background: url(question-octagon-frame.png) no-repeat 0px 0px; + margin-top: 3px; + margin-right: 4px; + float: right; +} + +.icon-button.tag-question{ + background: url(question-balloon.png) no-repeat 0px 0px; + margin-top: 3px; + margin-right: 4px; + float: right; +} diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -910,3 +910,5 @@ div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} .text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} +.icon-button.general-question{background:url(question-octagon-frame.png) no-repeat 0px 0px;margin-top:3px;margin-right:4px;float:right;} +.icon-button.tag-question{background:url(question-balloon.png) no-repeat 0px 0px;margin-top:3px;margin-right:4px;float:right;} diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/question-balloon.png Binary file static/june_2007_style/blue/question-balloon.png has changed diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 static/june_2007_style/blue/question-octagon-frame.png Binary file static/june_2007_style/blue/question-octagon-frame.png has changed diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -12,7 +12,7 @@ </%def><%def name="javascripts()"> - ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )} + ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage", "libs/bootstrap" )} <script type="text/javascript"> $(function() { $(window).bind("refresh_on_change", function() { @@ -282,19 +282,30 @@ tool_url = tool.action[0] + h.url_for(tool.action[1]) %> +<% + # Set the tool name in lower case + low_tool_name = tool.name.lower() +%> + %if tool_id_version_message: ${render_msg( tool_id_version_message, 'warning' )} %endif <div class="toolForm" id="${tool.id}"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> - %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version})</div> - %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}</div> - %endif + <div class="toolFormTitle"> + %if tool.has_multiple_pages: + ${tool.name} (step ${tool_state.page+1} of ${tool.npages}) + %elif not tool_version_select_field: + ${tool.name} (version ${tool.version}) + %else: + ${tool.name} ${tool_version_select_field.get_html()} + %endif +  + <a href="http://slyfox.bx.psu.edu:8081/new/post/" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8081/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + </div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"><input type="hidden" name="tool_id" value="${tool.id}"> diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 2f684dfa8d474560f241388bbb1fec5c612eca75 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,6 +120,7 @@ ## Help tab. <% menu_options = [ + [_('Galaxy Q&A'), app.config.get( "q&a", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], 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: Fix bug introduced 2 commits ago.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c09dfcc62c2/ changeset: 5c09dfcc62c2 user: greg date: 2012-09-06 22:27:35 summary: Fix bug introduced 2 commits ago. affected #: 1 file diff -r f0fe84f46793708dc5eac02442e2e9a72e1d9c70 -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1427,10 +1427,7 @@ tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) invalid_file_tups = [] - if tool is None: - if not valid: - invalid_file_tups = [ ( name, error_message ) ] - else: + if tool: invalid_file_tups = check_tool_input_params( trans.app, repository.repo_path, tool_config, 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: Fix a mis-named variable.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f0fe84f46793/ changeset: f0fe84f46793 user: greg date: 2012-09-06 22:22:57 summary: Fix a mis-named variable. affected #: 1 file diff -r 42e544d00e75be44887b17f6985bcb251573e1de -r f0fe84f46793708dc5eac02442e2e9a72e1d9c70 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -266,7 +266,7 @@ if name.endswith( '.sample' ): relative_path = os.path.join( root, name ) copy_sample_file( trans.app, relative_path, dest_path=dest_path ) - sample_files_copied.append( name ) + sample_files.append( name ) return sample_files def copy_file_from_disk( filename, repo_dir, dir ): file_path = None 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: Fixes for displaying error messages when displaying invalid tools in tool shed repository changeset revisions.
by Bitbucket 06 Sep '12

06 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/42e544d00e75/ changeset: 42e544d00e75 user: greg date: 2012-09-06 22:17:15 summary: Fixes for displaying error messages when displaying invalid tools in tool shed repository changeset revisions. affected #: 2 files diff -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d -r 42e544d00e75be44887b17f6985bcb251573e1de lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -248,6 +248,34 @@ except: pass return converter_path, display_path +def can_generate_tool_dependency_metadata( root, metadata_dict ): + """ + Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml + file is defined in the <requirement> tag for at least one tool in the repository. + """ + can_generate_dependency_metadata = False + for elem in root: + can_generate_dependency_metadata = False + tool_dependency_name = elem.get( 'name', None ) + tool_dependency_version = elem.get( 'version', None ) + tool_dependency_type = elem.tag + if tool_dependency_name and tool_dependency_version and tool_dependency_type: + for tool_dict in metadata_dict[ 'tools' ]: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_version = requirement_dict.get( 'version', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: + can_generate_dependency_metadata = True + break + if requirements and not can_generate_dependency_metadata: + # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> + # tag for any tool in the repository. + break + if not can_generate_dependency_metadata: + break + return can_generate_dependency_metadata def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files, webapp='galaxy' ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make @@ -512,34 +540,6 @@ if tool_dependencies_dict: metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict return metadata_dict -def can_generate_tool_dependency_metadata( root, metadata_dict ): - """ - Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml - file is defined in the <requirement> tag for at least one tool in the repository. - """ - can_generate_dependency_metadata = False - for elem in root: - can_generate_dependency_metadata = False - tool_dependency_name = elem.get( 'name', None ) - tool_dependency_version = elem.get( 'version', None ) - tool_dependency_type = elem.tag - if tool_dependency_name and tool_dependency_version and tool_dependency_type: - for tool_dict in metadata_dict[ 'tools' ]: - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - req_name = requirement_dict.get( 'name', None ) - req_version = requirement_dict.get( 'version', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - if not can_generate_dependency_metadata: - break - return can_generate_dependency_metadata def generate_metadata_for_changeset_revision( app, repository_clone_url, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, webapp='galaxy' ): """ @@ -597,50 +597,53 @@ # Find all tool configs. if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - print "Error parsing %s", full_path, ", exception: ", str( e ) - is_tool = False - if is_tool: - tool, valid, error_message = load_tool_from_config( app, full_path ) - if tool is None: - if not valid: - invalid_file_tups.append( ( name, error_message ) ) - else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) - can_set_metadata = True - for tup in invalid_files_and_errors_tups: - if name in tup: - can_set_metadata = False - invalid_tool_configs.append( name ) - break - if can_set_metadata: - if resetting_all_metadata_on_repository: - full_path_to_tool_config = os.path.join( root, name ) - stripped_path_to_tool_config = full_path_to_tool_config.replace( work_dir, '' ) - if stripped_path_to_tool_config.startswith( '/' ): - stripped_path_to_tool_config = stripped_path_to_tool_config[ 1: ] - relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) + if os.path.getsize( full_path ) > 0: + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( full_path ) + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + except Exception, e: + print "Error parsing %s", full_path, ", exception: ", str( e ) + is_tool = False + if is_tool: + tool, valid, error_message = load_tool_from_config( app, full_path ) + if tool is None: + if not valid: + invalid_file_tups.append( ( name, error_message ) ) + else: + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) + can_set_metadata = True + for tup in invalid_files_and_errors_tups: + if name in tup: + can_set_metadata = False + invalid_tool_configs.append( name ) + break + if can_set_metadata: + if resetting_all_metadata_on_repository: + full_path_to_tool_config = os.path.join( root, name ) + stripped_path_to_tool_config = full_path_to_tool_config.replace( work_dir, '' ) + if stripped_path_to_tool_config.startswith( '/' ): + stripped_path_to_tool_config = stripped_path_to_tool_config[ 1: ] + relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) + else: + relative_path_to_tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) else: - relative_path_to_tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) - else: - invalid_file_tups.extend( invalid_files_and_errors_tups ) + for tup in invalid_files_and_errors_tups: + invalid_file_tups.append( tup ) # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) + if os.path.getsize( os.path.abspath( relative_path ) ) > 0: + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if 'tools' in metadata_dict: # This step must be done after metadata for tools has been defined. tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) diff -r b43eadc8cdb486b7bfa971ff89552ba04126ef0d -r 42e544d00e75be44887b17f6985bcb251573e1de lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1426,9 +1426,22 @@ repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + invalid_file_tups = [] + if tool is None: + if not valid: + invalid_file_tups = [ ( name, error_message ) ] + else: + invalid_file_tups = check_tool_input_params( trans.app, + repository.repo_path, + tool_config, + tool, + [], + webapp=webapp ) + if invalid_file_tups: + message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) + elif error_message: + message = error_message try: - if error_message: - message = error_message return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, @@ -1439,7 +1452,7 @@ message=message, status='error' ) except Exception, e: - message = "This tool is invalid because: %s." % str( e ) + message = "Exception thrown attempting to display tool: %s." % str( e ) if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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