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commit/galaxy-central: dan: Fix for lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/affd8fe24fc1/ Changeset: affd8fe24fc1 User: dan Date: 2013-10-09 16:52:36 Summary: Fix for lib/galaxy/datatypes/converters/fastq_to_fqtoc.py Affected #: 1 file diff -r 9741409d89322b3da25e13be8a65a062a688f823 -r affd8fe24fc149b354fa3b603d205f4539e0804d lib/galaxy/datatypes/converters/fastq_to_fqtoc.py --- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py @@ -28,7 +28,7 @@ lines_per_chunk = 4*sequences chunk_begin = 0 - in_file = open(input_name) + in_file = open(input_fname) out_file.write('{"sections" : ['); 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: dan: Remove references to g2.trac.bx.psu.edu. Several references still exist in rgenetics converter tools and rgenetics test-data.
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9741409d8932/ Changeset: 9741409d8932 User: dan Date: 2013-10-09 16:50:05 Summary: Remove references to g2.trac.bx.psu.edu. Several references still exist in rgenetics converter tools and rgenetics test-data. Affected #: 3 files diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -192,7 +192,7 @@ self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) + self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.library_import_dir = kwargs.get( 'library_import_dir', None ) diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 templates/webapps/galaxy/admin/center.mako --- a/templates/webapps/galaxy/admin/center.mako +++ b/templates/webapps/galaxy/admin/center.mako @@ -106,7 +106,7 @@ <p><strong>Data Security and Data Libraries</strong></p><p/><strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found - here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security + here or in our <a href="http://wiki.galaxyproject.org/Learn/Security%20Features" target="_blank">data security page</a>. The data security process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -368,7 +368,7 @@ #logo_url = / # The URL linked by the "Galaxy Wiki" link in the "Help" menu. -#wiki_url = http://wiki.g2.bx.psu.edu/ +#wiki_url = http://wiki.galaxyproject.org/ # The URL linked by the "Support" link in the "Help" menu. #support_url = http://wiki.g2.bx.psu.edu/Support Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Prevent duplicate lines from being written to an env.sh file when installing a tool dependency or re-running a tool migration script with tool dependencies specified to be installed.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8af9e0ac6d2a/ Changeset: 8af9e0ac6d2a User: Dave Bouvier Date: 2013-10-08 22:48:05 Summary: Prevent duplicate lines from being written to an env.sh file when installing a tool dependency or re-running a tool migration script with tool dependencies specified to be installed. Affected #: 3 files diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -19,12 +19,41 @@ from fabric.api import lcd from fabric.api import local from fabric.api import settings +from fabric.api import hide log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' +def add_to_env_shell_file( text, env_shell_file ): + ''' + Append a line to a file, if this line does not already exist in the file. Creates the file and sets the mode to + executable if the file does not exist. Equivalent to a local version of fabric.contrib.files.append. + ''' + if not os.path.exists( env_shell_file ): + local( 'touch %s' % env_shell_file ) + # Explicitly set env.sh executable. + with settings( hide( 'everything' ), warn_only=True ): + local( 'chmod +x %s' % env_shell_file ) + return_code = 0 + # Convert the contents to a list, in order to support adding one or more lines to env.sh. + if isinstance( text, basestring ): + text = [ text ] + for line in text: + # Build a regex to search for the relevant line in env.sh. + regex = td_common_util.egrep_escape( line ) + # If the line exists, egrep will return a success. + with settings( hide( 'everything' ), warn_only=True ): + egrep_cmd = 'egrep "^%s$" %s' % ( regex, env_shell_file ) + contains_line = local( egrep_cmd ).succeeded + if contains_line: + continue + # If not, then append the line, escaping any single quotes in the shell command. + line = line.replace( "'", r"'\\''" ) + return_code = local( "echo '%s' >> %s" % ( line, env_shell_file ) ).return_code + return return_code + def check_fabric_version(): version = env.version if int( version.split( "." )[ 0 ] ) < 1: @@ -301,8 +330,8 @@ for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. env_var_dict = handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) - env_command = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = handle_command( app, tool_dependency, install_dir, env_command ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + return_code = add_to_env_shell_file( env_entry, env_file ) if return_code: return elif action_type == 'set_environment_for_install': @@ -344,13 +373,13 @@ log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) return modify_env_command_dict = dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) - modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + return_code = add_to_env_shell_file( env_entry, env_file ) if return_code: return modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) - modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) + return_code = add_to_env_shell_file( env_entry, env_file ) if return_code: return elif action_type == 'shell_command': diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -820,10 +820,10 @@ type='set_environment', status=app.model.ToolDependency.installation_status.INSTALLING, set_status=True ) - cmd = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) if env_var_version == '1.0': # Handle setting environment variables using a fabric method. - fabric_util.handle_command( app, tool_dependency, install_dir, cmd ) + fabric_util.add_to_env_shell_file( env_entry, env_file ) sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -1,5 +1,6 @@ import logging import os +import re import shutil import sys import tarfile @@ -170,26 +171,9 @@ changed_value = '%s' % env_var_value elif env_var_action == 'append_to': changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - line = "%s=%s; export %s" % (env_var_name, changed_value, env_var_name) - return create_or_update_env_shell_file_with_command(install_dir, line) - - -def create_or_update_env_shell_file_with_command( install_dir, command ): - """ - Return a shell expression which when executed will create or update - a Galaxy env.sh dependency file in the specified install_dir containing - the supplied command. - """ - 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 %s;chmod +x %s" % ( __shellquote(command), - write_action, - __shellquote(env_shell_file_path), - __shellquote(env_shell_file_path)) - return cmd + line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) + env_shell_file_path = os.path.join( install_dir, 'env.sh' ) + return line, env_shell_file_path def download_binary( url, work_dir ): ''' @@ -199,6 +183,17 @@ dir = url_download( work_dir, downloaded_filename, url, extract=False ) return downloaded_filename +def egrep_escape( text ): + """Escape ``text`` to allow literal matching using egrep.""" + regex = re.escape( text ) + # Seems like double escaping is needed for \ + regex = regex.replace( '\\\\', '\\\\\\' ) + # Triple-escaping seems to be required for $ signs + regex = regex.replace( r'\$', r'\\\$' ) + # Whereas single quotes should not be escaped + regex = regex.replace( r"\'", "'" ) + return regex + def format_traceback(): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fixes for 82b1789: (a) incorporate default values correctly and (b) use Backbone-style gets to access config values.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b61927f340f3/ Changeset: b61927f340f3 User: jgoecks Date: 2013-10-08 18:25:10 Summary: Fixes for 82b1789: (a) incorporate default values correctly and (b) use Backbone-style gets to access config values. Affected #: 1 file diff -r 5d5729d40b4f394dc6884d22daa39e3696842b80 -r b61927f340f30a636204ec560522acf9b76fd262 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -222,7 +222,7 @@ ], saved_values: obj_dict.prefs, onchange: function() { - this.track.set_name(this.track.config.values.name); + this.track.set_name(this.track.config.get('values').name); } }); this.prefs = this.config.get('values'); @@ -1136,7 +1136,7 @@ }, get_base_color: function(base) { - return this.config.values[ base.toLowerCase() + '_color' ] || this.config.values[ 'n_color' ]; + return this.config.get('values')[ base.toLowerCase() + '_color' ] || this.config.get('values')[ 'n_color' ]; } }); @@ -1893,16 +1893,29 @@ */ var Config = Backbone.Model.extend({ initialize: function(options) { - // values is a simple param_key -- value dictionary shared with drawables. - this.set('values', {}); + // values is a simple param_key-to-value dictionary used to store + // param values. + var values = {}; + + // Set default values. + _.each(options.params, function(p) { + values[p.key] = p.default_value; + }); // Restore saved values. if (options.saved_values) { - this.restore_values(options.saved_values); + _.each( this.get('params'), function(p) { + if (p.key in options.saved_values) { + values[p.key] = options.saved_values[p.key]; + } + }); } + + this.set('values', values); + + // HACK: to make onchange work as written, attach track at the + // top level of model and call onchange on custom event. if (options.onchange) { - // HACK: to make onchange work as written, attach track at the - // top level of model and call onchange on custom event. this.track = options.track; this.on('change:values', options.onchange, this); } @@ -1955,18 +1968,7 @@ else { return false; } - }, - - /** - * Restore config values from a dictionary. - */ - restore_values: function( values ) { - var self = this; - _.each( this.get('params'), function(param) { - self.set_param_value(param.key, values[param.key] || param.default_value); - }); - }, - + } }); var ConfigView = Backbone.View.extend({ @@ -2563,7 +2565,7 @@ track.tile_cache.clear(); in_drag = false; if (!in_handle) { drag_control.hide(); } - track.config.values.height = track.visible_height_px; + track.config.get('values').height = track.visible_height_px; track.changed(); }).appendTo(track.container_div); }, @@ -2575,8 +2577,8 @@ // Set modes, init mode. this.display_modes = new_modes; this.mode = (init_mode ? init_mode : - (this.config && this.config.values['mode'] ? - this.config.values['mode'] : this.display_modes[0]) + (this.config && this.config.get('values')['mode'] ? + this.config.get('values')['mode'] : this.display_modes[0]) ); this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); @@ -2926,7 +2928,7 @@ var track = this; // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = new_mode; - track.config.values['mode'] = new_mode; + track.config.get('values')['mode'] = new_mode; // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the // data manager would work if Auto data were checked for compatibility when a specific // mode is chosen. @@ -3955,7 +3957,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { set_painter_from_config: function() { - if ( this.config.values['connector_style'] === 'arcs' ) { + if ( this.config.get('values')['connector_style'] === 'arcs' ) { this.painter = painters.ArcLinkedFeaturePainter; } else { this.painter = painters.LinkedFeaturePainter; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Update modal and upload
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d5729d40b4f/ Changeset: 5d5729d40b4f User: guerler Date: 2013-10-08 18:12:48 Summary: Update modal and upload Affected #: 2 files diff -r 125a7cafb851d9b70195466389acf08dd9b98fd6 -r 5d5729d40b4f394dc6884d22daa39e3696842b80 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -12,9 +12,10 @@ elMain: '#everything', // defaults inputs - optionsDefaults: { - title : "galaxy-modal", - body : "No content available." + optionsDefault: { + title : "galaxy-modal", + body : "", + backdrop : true }, // initialize @@ -30,8 +31,16 @@ this.initialize(options); // fix height - var body = (this.$el).find('.modal-body'); - body.css('max-height', $(document).height() / 2); + this.$body.css('max-height', $(document).height() / 2); + + // set max-height so that modal does not exceed window size and is in middle of page. + /*/ TODO: this could perhaps be handled better using CSS. + this.$body.css( "max-height", + $(window).height() - + this.$footer.outerHeight() - + this.$header.outerHeight() - + parseInt( this.$dialog.css( "padding-top" ), 10 ) - + parseInt( this.$dialog.css( "padding-bottom" ), 10 ));*/ // show if (this.visible) @@ -39,7 +48,7 @@ else this.$el.fadeIn('fast'); - // set visibility flag + // set flag this.visible = true; }, @@ -47,8 +56,8 @@ hide: function(){ // fade out this.$el.fadeOut('fast'); - - // set visibility flag + + // set flag this.visible = false; }, @@ -56,11 +65,11 @@ create: function(options) { // configure options options = _.defaults(options, this.optionsDefault); - + // check for progress bar request if (options.body == 'progress') - options.body = '<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'; - + options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); + // remove former element if (this.$el) this.$el.remove(); @@ -69,45 +78,54 @@ this.setElement(this.template(options.title)); // link elements - var body = (this.$el).find('.modal-body'); - var footer = (this.$el).find('.modal-footer'); - var buttons = (this.$el).find('.buttons'); + this.$body = (this.$el).find('.modal-body'); + this.$footer = (this.$el).find('.modal-footer'); + this.$buttons = (this.$el).find('.buttons'); + this.$backdrop = (this.$el).find('.modal-backdrop'); // append body - body.append($(options.body)); - + this.$body.html(options.body); + // fix height if available if (options.height) - body.css('height', options.height); + this.$body.css('height', options.height); + // fix min-width so that modal cannot shrink considerably if new content is loaded. + this.$body.css('min-width', this.$body.width()); + + // configure background + if (!options.backdrop) + this.$backdrop.removeClass('in'); + // append buttons if (options.buttons) { // link functions + var self = this; $.each(options.buttons, function(name, value) { - buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); + self.$buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else // hide footer - footer.hide(); + this.$footer.hide(); // append to main element $(this.elMain).append($(this.el)); }, // enable buttons - enable: function(name) { - $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', false); + enableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', false); }, // disable buttons - disable: function(name) { - $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true); + disableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, // returns scroll top for body element scrollTop: function() { - return $(this.el).find('.modal-body').scrollTop(); + return this.$body.scrollTop(); }, /* @@ -116,12 +134,13 @@ // fill regular modal template template: function(title) { - return '<div class="modal in">' + - '<div class="modal-backdrop in" style="z-index: -1;"></div>' + + return '<div class="modal">' + + '<div class="modal-backdrop fade in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + '<div class="modal-content">' + '<div class="modal-header">' + - '<span><h3 class="title">' + title + '</h3></span>' + + '<button type="button" class="close" style="display: none;">×</button>' + + '<h4 class="title">' + title + '</h4>' + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + diff -r 125a7cafb851d9b70195466389acf08dd9b98fd6 -r 5d5729d40b4f394dc6884d22daa39e3696842b80 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -426,21 +426,21 @@ // update reset button if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0) - this.modal.enable('Reset'); + this.modal.enableButton('Reset'); else - this.modal.disable('Reset'); + this.modal.disableButton('Reset'); // update upload button if (this.counter.running == 0 && this.counter.announce > 0) - this.modal.enable('Upload'); + this.modal.enableButton('Upload'); else - this.modal.disable('Upload'); + this.modal.disableButton('Upload'); // select upload button if (this.counter.running == 0) - this.modal.enable('Select'); + this.modal.enableButton('Select'); else - this.modal.disable('Select'); + this.modal.disableButton('Select'); }, // load html template Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/125a7cafb851/ Changeset: 125a7cafb851 User: greg Date: 2013-10-08 17:56:00 Summary: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular. Affected #: 1 file diff -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd -r 125a7cafb851d9b70195466389acf08dd9b98fd6 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1238,21 +1238,27 @@ log.debug( error_message ) is_valid = False return repository_dependency_tup, is_valid, error_message - # Find the specified changeset revision in the repository's changelog to see if it's valid. - found = False repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - if changeset_hash == changeset_revision: - found = True - break - if not found: - error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ - ( toolshed, name, owner, changeset_revision ) - error_message += "because the changeset revision is invalid. " - log.debug( error_message ) - is_valid = False - return repository_dependency_tup, is_valid, error_message + # The received changeset_revision may be None since defining it in the dependency definition is optional. If this is the case, + # the default will be to set it's value to the repository dependency tip revision. + if changeset_revision is None: + changeset_revision = str( repo.changectx( repo.changelog.tip() ) ) + repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required, str( only_if_compiling_contained_td ) ] + else: + # Find the specified changeset revision in the repository's changelog to see if it's valid. + found = False + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if changeset_hash == changeset_revision: + found = True + break + if not found: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( toolshed, name, owner, changeset_revision ) + error_message += "because the changeset revision is invalid. " + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message else: # Repository dependencies are currently supported within a single tool shed. error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: small fixes for calculating tile height.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/36577eb9f7a4/ Changeset: 36577eb9f7a4 User: jgoecks Date: 2013-10-08 17:45:49 Summary: Trackster: small fixes for calculating tile height. Affected #: 1 file diff -r c0f049223e27a3984dab6b018afa1fce440e6288 -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2128,9 +2128,9 @@ this.low = region.get('start'); this.high = region.get('end'); this.w_scale = w_scale; - // Wrap element in div for background and explicitly set height. Use canvas - // height attribute because canvas may not have height if it is not in document yet. - this.html_elt = $("<div class='track-tile'/>").append(canvas).height( $(canvas).attr("height") ); + this.canvas = canvas; + // Wrap element in div for background and to provide container for tile-specific elements. + this.html_elt = $("<div class='track-tile'/>").append(canvas); this.data = data; this.stale = false; }; @@ -3371,14 +3371,11 @@ // -- Update track, tile heights based on new tile. -- - // Clear any previous height settings for tile. - tile.html_elt.height('auto'); - - // Update max height based on current tile. - this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); + // Update max height based on current tile's canvas. + this.max_height_px = Math.max(this.max_height_px, $(tile.canvas).height()); // Update height for all tiles based on max height. - tile.html_elt.parent().children().css("height", this.max_height_px + "px"); + tile_element.parent().children().css("height", this.max_height_px + "px"); // Update track height based on max height and visible height. var track_height = this.max_height_px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fix for a bug introduced with the rename_to option for the move_file action.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c0f049223e27/ Changeset: c0f049223e27 User: Dave Bouvier Date: 2013-10-08 17:12:10 Summary: Fix for a bug introduced with the rename_to option for the move_file action. Affected #: 1 file diff -r 82b1789621244bd81bf68c28fbe42a29931efee1 -r c0f049223e27a3984dab6b018afa1fce440e6288 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -316,7 +316,8 @@ shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): - source_file = os.path.abspath( os.path.join( current_dir, source ) ) + source_path = os.path.abspath( os.path.join( current_dir, source ) ) + source_file = os.path.basename( source_path ) if rename_to is not None: destination_file = rename_to destination_directory = os.path.join( destination ) @@ -326,7 +327,7 @@ destination_path = os.path.join( destination_directory, source_file ) if not os.path.exists( destination_directory ): os.makedirs( destination_directory ) - shutil.move( source_file, destination_path ) + shutil.move( source_path, destination_path ) def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82b178962124/ Changeset: 82b178962124 User: jgoecks Date: 2013-10-08 16:55:43 Summary: Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view. Affected #: 1 file diff -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 -r 82b1789621244bd81bf68c28fbe42a29931efee1 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -215,7 +215,7 @@ this.name = obj_dict.name; this.view = view; this.container = container; - this.config = new DrawableConfig({ + this.config = new Config({ track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name } @@ -225,7 +225,7 @@ this.track.set_name(this.track.config.values.name); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.drag_handle_class = obj_dict.drag_handle_class; this.is_overview = false; this.action_icons = {}; @@ -285,24 +285,10 @@ title: "Edit settings", css_class: "settings-icon", on_click_fn: function(drawable) { - var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - drawable.config.update_from_form( $(Galaxy.modal.el) ); - Galaxy.modal.hide(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - - // show dialog - Galaxy.modal.show({title: "Configure", body: drawable.config.build_form(), buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); + var view = new ConfigView({ + model: drawable.config + }); + view.render(); } }, // Remove. @@ -911,7 +897,7 @@ this.reset(); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, @@ -1903,22 +1889,30 @@ }; /** - * Container for Drawable configuration data. + * Configuration object. */ -var DrawableConfig = function( options ) { - this.track = options.track; - this.params = options.params; - this.values = {}; - this.restore_values( (options.saved_values ? options.saved_values : {}) ); - this.onchange = options.onchange; -}; - -extend(DrawableConfig.prototype, { +var Config = Backbone.Model.extend({ + initialize: function(options) { + // values is a simple param_key -- value dictionary shared with drawables. + this.set('values', {}); + + // Restore saved values. + if (options.saved_values) { + this.restore_values(options.saved_values); + } + if (options.onchange) { + // HACK: to make onchange work as written, attach track at the + // top level of model and call onchange on custom event. + this.track = options.track; + this.on('change:values', options.onchange, this); + } + }, + /** * Set default value for parameter. */ set_param_default_value: function(key, default_value) { - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1932,7 +1926,7 @@ */ set_param_value: function(key, value) { // Find param. - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1952,8 +1946,10 @@ } // Set value and return true if changed, false otherwise. - if (this.values[key] !== value) { - this.values[key] = value; + if (this.get('values')[key] !== value) { + this.get('values')[key] = value; + // HACK: custom event trigger needed to indicate that values were updated. + this.trigger('change:values'); return true; } else { @@ -1965,21 +1961,25 @@ * Restore config values from a dictionary. */ restore_values: function( values ) { - var track_config = this; - $.each( this.params, function( index, param ) { - if ( values[ param.key ] !== undefined ) { - track_config.values[ param.key ] = values[ param.key ]; - } else { - track_config.values[ param.key ] = param.default_value; - } + var self = this; + _.each( this.get('params'), function(param) { + self.set_param_value(param.key, values[param.key] || param.default_value); }); }, +}); + +var ConfigView = Backbone.View.extend({ + /** - * Build form for modifying parameters. + * Build and show form for modifying configuration. Currently uses Galaxy modals. */ - build_form: function() { - var track_config = this; + render: function() { + // + // Build config selection UI. + // + + var track_config = this.model; var container = $("<div />"); var param; // Function to process parameters recursively @@ -1990,17 +1990,19 @@ if ( param.hidden ) { continue; } // Build row for param var id = 'param_' + index; - var value = track_config.values[ param.key ]; + var value = track_config.get('values')[ param.key ]; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); // Draw parameter as checkbox if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); // Draw parameter as textbox - } else if ( param.type === 'text' ) { + } + else if ( param.type === 'text' ) { row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); // Draw paramter as select area - } else if ( param.type === 'select' ) { + } + else if ( param.type === 'select' ) { var select = $('<select />').attr("id", id); for ( var i = 0; i < param.options.length; i++ ) { $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); @@ -2008,7 +2010,8 @@ select.val( value ); row.append( select ); // Draw parameter as color picker - } else if ( param.type === 'color' ) { + } + else if ( param.type === 'color' ) { var container_div = $("<div/>").appendTo(row), input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") @@ -2071,32 +2074,48 @@ } } // Handle top level parameters in order - handle_params( this.params, container ); - // Return element containing constructed form - return container; + handle_params( track_config.get('params'), container ); + + // + // Use Galaxy modal to display config. + // + + var self = this, + cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + self.update_from_form( $(Galaxy.modal.el) ); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + Galaxy.modal.show({title: "Configure", body: container, buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); }, /** * Update configuration from form. */ update_from_form: function( container ) { - var track_config = this; + var model = this.model; var changed = false; - $.each( this.params, function( index, param ) { - if ( ! param.hidden ) { + _.each(model.get('params'), function(param, index) { + if ( !param.hidden ) { // Get value from form element. var id = 'param_' + index; var value = container.find( '#' + id ).val(); if ( param.type === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } - changed = track_config.set_param_value(param.key, value) || changed; + changed = model.set_param_value(param.key, value) || changed; } }); - if ( changed ) { - this.onchange(); - this.track.changed(); - } } }); @@ -3785,7 +3804,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3793,7 +3812,7 @@ { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: 32, hidden: true } + { key: 'height', type: 'int', default_value: 30, hidden: true } ], saved_values: obj_dict.prefs, onchange: function() { @@ -3802,8 +3821,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { @@ -3844,7 +3863,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3862,8 +3881,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** @@ -3899,7 +3918,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3922,8 +3941,8 @@ track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; this.container_div.addClass( "feature-track" ); this.show_labels_scale = 0.001; @@ -4207,7 +4226,7 @@ this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; TiledTrack.call(this, view, container, obj_dict); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4223,7 +4242,7 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.painter = painters.VariantPainter; this.summary_draw_height = 30; @@ -4363,7 +4382,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4383,8 +4402,8 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - + this.prefs = this.config.get('values'); + // Choose painter based on whether there is reference data. this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter); 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: carlfeberhard: History panel: better reconciling of hda states within history and hda collection
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/402c90f647b6/ Changeset: 402c90f647b6 User: carlfeberhard Date: 2013-10-08 16:47:43 Summary: History panel: better reconciling of hda states within history and hda collection Affected #: 3 files diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -48,7 +48,7 @@ /** HDACollection of the HDAs contained in this history. */ this.hdas = new HDACollection(); - + /** the setTimeout id for any updater currently set */ this.updateTimeoutId = null; // if we've got hdas passed in the constructor, load them and set up updates if needed @@ -57,10 +57,14 @@ this.checkForUpdates(); //TODO: don't call if force_history_refresh if( this.hdas.length > 0 ){ - this.updateDisplayApplications(); + this.fetchDisplayApplications(); } } + this.setHdaEventHandlers(); + this.setOwnEventHandlers(); + }, + setHdaEventHandlers : function(){ // if an hda moves into the ready state and has the force_history_refresh flag (often via tool.xml) // then: refresh the panel this.hdas.bind( 'state:ready', function( hda, newState, oldState ){ @@ -68,7 +72,9 @@ this.updateAfterDelay(); } }, this ); + }, + setOwnEventHandlers : function(){ if( this.logger ){ this.bind( 'all', function( event ){ this.log( this + '', arguments ); @@ -88,84 +94,86 @@ updateAfterDelay : function(){ var history = this; this.updateTimeoutId = setTimeout( function(){ + history.updateTimeoutId = null; history.stateUpdater(); }, History.UPDATE_DELAY ); return this.updateTimeoutId; }, - // get the history's state from it's cummulative ds states, delay + update if needed - // events: ready + isRunning : function(){ + var historyState = this.get( 'state' ); + // set up to keep pulling if this history in run/queue state + //note: the state strings btwn history & hda are shared on the server (or a subset of) + return ( ( historyState === HistoryDatasetAssociation.STATES.RUNNING ) + ||( historyState === HistoryDatasetAssociation.STATES.QUEUED ) ); + }, + + isReady : function(){ + return !this.isRunning(); + }, + checkForUpdates : function(){ - // get overall History state from collection, run updater if History has running/queued hdas - // boiling it down on the client to running/not - if( this.hdas.running().length ){ + // set up to keep pulling if this history in run/queue state + if( this.isRunning() ){ this.updateAfterDelay(); + // otherwise, we're now in a 'ready' state (no hdas running) } else { this.trigger( 'ready' ); } return this; }, - // update this history, find any hda's running/queued, update ONLY those that have changed states, - // set up to run this again in some interval of time + findHdasToUpdate : function(){ + var history = this, + state_ids = history.get( 'state_ids' ), + changedIds = []; + + // get a list of hda ids for hdas we need to get more info on + _.each( state_ids, function( list, stateAccrdToHistory ){ + _.each( list, function( id ){ + var hda = history.hdas.get( id ); + // if the id is not in the current hda list + // or the state doesn't match the state rpt. by the history - save that id + if( !hda || hda.get( 'state' ) !== stateAccrdToHistory ){ + changedIds.push( id ); + } + }); + }); + return changedIds; + }, + + // fetch new data for this history, + // compare the state_ids from that with the current list and fetch updates for new or changed hdas + // if the history still has non-ready hdas, set up to run this again in some interval of time // events: ready stateUpdater : function(){ //TODO: we need to get states from one location: history_contents (right now it's both history and contents) var history = this, oldState = this.get( 'state' ), - // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state - oldStateIds = this.get( 'state_ids' ); + historyXhr = this.fetch(); // pull from the history api - //TODO: fetch? - jQuery.ajax( 'api/histories/' + this.get( 'id' ) - - ).success( function( response ){ + historyXhr.done( function( newHistoryModel ){ //this.log( 'historyApiRequest, response:', response ); - history.set( response ); - history.log( 'current history state:', history.get( 'state' ), - '(was)', oldState, + history.set( newHistoryModel ); + history.log( 'current history state:', history.get( 'state' ), '(was)', oldState, 'new size:', history.get( 'nice_size' ) ); - //TODO: revisit this - seems too elaborate, need something straightforward - // for each state, check for the difference between old dataset states and new - // the goal here is to check ONLY those datasets that have changed states (not all datasets) - var changedIds = []; - _.each( _.keys( response.state_ids ), function( state ){ - var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); - // aggregate those changed ids - changedIds = changedIds.concat( diffIds ); - }); - // send the changed ids (if any) to dataset collection to have them fetch their own model changes - if( changedIds.length ){ - history.fetchHdaUpdates( changedIds ) - .done( function(){ - furtherUpdatesOrReady( history ); + var hdaIdsToUpdate = history.findHdasToUpdate(); + if( hdaIdsToUpdate.length ){ + // simplify with empty promise when no ids + history.fetchHdaUpdates( hdaIdsToUpdate ) + .done( function( models ){ + history.checkForUpdates(); }); } else { - furtherUpdatesOrReady( history ); + history.checkForUpdates(); } - function furtherUpdatesOrReady( history ){ - var timeout; - // set up to keep pulling if this history in run/queue state - if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.SETTING_METADATA )){ - //|| ( history.hdas.running() ) ){ - timeout = history.updateAfterDelay(); - - // otherwise, we're now in a 'ready' state (no hdas running) - } else { - this.updateTimeoutId = null; - history.trigger( 'ready' ); - } - return timeout; - } - - }).error( function( xhr, status, error ){ + }); + historyXhr.fail( function( xhr, status, error ){ //TODO: use ajax.status handlers here // keep rolling on a bad gateway - server restart if( xhr.status === 502 ){ @@ -197,9 +205,7 @@ xhr = jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), - /** - * @inner - */ + /** @inner */ error : function( xhr, status, error ){ if( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ){ return; } @@ -286,11 +292,10 @@ * @param {String[]} ids an array of hda ids to update (optional, defaults to all hdas) * @returns {HistoryDatasetAssociation[]} hda models that were updated */ - updateDisplayApplications : function( ids ){ - this.log( this + 'updateDisplayApplications:', ids ); + fetchDisplayApplications : function( ids ){ + this.log( this + '.fetchDisplayApplications:', ids ); var history = this, - // data = { id: this.get( 'id' ) }; - //if( ids && _.isArray( ids ) ){ data.hda_ids = ids.join( ',' ); } + // if any ids passed place them in the query string data data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); //TODO: hardcoded diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)||(h.get("state")===HistoryDatasetAssociation.STATES.SETTING_METADATA)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -198,8 +198,11 @@ // 2. from console: new PersistentStorage( '__history_panel' ).set( 'debugging', true ) // -> history panel and hdas will display console logs in console var debugging = false; - if( jQuery.jStorage.get( '__history_panel' ) ){ + if( sessionStorage.getItem( '__history_panel' ) ){ debugging = new PersistentStorage( '__history_panel' ).get( 'debugging' ); + if( debugging ){ + console.debug( '(debugging)' ); + } } // get the current user (either from the top frame's Galaxy or if in tab via the bootstrap) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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