Failed to make secondary dataset primary.
" ) - @web.expose - def masthead( self, trans, active_view=None ): - brand = trans.app.config.get( "brand", "" ) - if brand: - brand ="/%s" % brand - wiki_url = trans.app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" ) - bugs_email = trans.app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) - blog_url = trans.app.config.get( "blog_url", "http://g2.trac.bx.psu.edu/blog" ) - screencasts_url = trans.app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" ) - admin_user = "false" - admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) - user = trans.get_user() - if user: - user_email = trans.get_user().email - if user_email in admin_users: - admin_user = "true" - return trans.fill_template( "/root/masthead.mako", brand=brand, wiki_url=wiki_url, - blog_url=blog_url,bugs_email=bugs_email, screencasts_url=screencasts_url, admin_user=admin_user, active_view=active_view ) + # @web.expose + # def masthead( self, trans, active_view=None ): + # brand = trans.app.config.get( "brand", "" ) + # if brand: + # brand ="/%s" % brand + # wiki_url = trans.app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" ) + # bugs_email = trans.app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) + # blog_url = trans.app.config.get( "blog_url", "http://g2.trac.bx.psu.edu/blog" ) + # screencasts_url = trans.app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" ) + # admin_user = "false" + # admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + # user = trans.get_user() + # if user: + # user_email = trans.get_user().email + # if user_email in admin_users: + # admin_user = "true" + # return trans.fill_template( "/root/masthead.mako", brand=brand, wiki_url=wiki_url, + # blog_url=blog_url,bugs_email=bugs_email, screencasts_url=screencasts_url, admin_user=admin_user, active_view=active_view ) @web.expose def dataset_errors( self, trans, id=None, **kwd ): diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py new file mode 100644 index 00000000000..7c17b6d7af8 --- /dev/null +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -0,0 +1,162 @@ +from galaxy.model import * +from galaxy.model.orm import * + +from galaxy.web import url_for + +import sys + +class Grid( object ): + """ + Specifieds the content and format of a grid (data table). + """ + title = "" + exposed = True + model_class = None + columns = [] + standard_filters = [] + default_filter = None + default_sort_key = None + def __init__( self ): + pass + def __call__( self, trans, **kwargs ): + # Session + session = trans.sa_session + # Process any actions + status = message = None + ids = self.get_ids( **kwargs ) + operation = kwargs.get( 'operation', None ) + if operation: + operation = operation.lower() + status, message = self.handle_operation( trans, operation, ids ) + # Build initial query + query = self.build_initial_query( session ) + query = self.apply_default_filter( trans, query ) + # Maintain sort state in generated urls + extra_url_args = {} + # Process filtering arguments + filter_args = {} + if self.default_filter: + filter_args.update( self.default_filter ) + for column in self.columns: + if column.key: + if "f-" + column.key in kwargs: + column_filter = kwargs.get( "f-" + column.key ) + if column_filter == "True": + filter_args[column.key] = True + elif column_filter == "False": + filter_args[column.key] = False + elif column_filter == "All": + del filter_args[column.key] + # Carry filter along to newly generated urls + extra_url_args[ "f-" + column.key ] = column_filter + if filter_args: + query = query.filter_by( **filter_args ) + # Process sort arguments + sort_key = sort_order = None + if 'sort' in kwargs: + sort_key = kwargs['sort'] + elif self.default_sort_key: + sort_key = self.default_sort_key + encoded_sort_key = sort_key + if sort_key: + if sort_key.startswith( "-" ): + sort_key = sort_key[1:] + sort_order = 'desc' + query = query.order_by( self.model_class.c.get( sort_key ).desc() ) + else: + sort_order = 'asc' + query = query.order_by( self.model_class.c.get( sort_key ).asc() ) + extra_url_args['sort'] = encoded_sort_key + # There might be a current row + current_item = self.get_current_item( trans ) + # Render + def url( *args, **kwargs ): + new_kwargs = dict( extra_url_args ) + if len(args) > 0: + new_kwargs.update( args[0] ) + new_kwargs.update( kwargs ) + return url_for( **new_kwargs ) + return trans.fill_template( "grid.mako", + grid=self, + query=query, + sort_key=sort_key, + encoded_sort_key=encoded_sort_key, + sort_order=sort_order, + current_item=current_item, + ids = ids, + url = url, + message_type = status, + message = message ) + def get_ids( self, **kwargs ): + id = [] + if 'id' in kwargs: + id = kwargs['id'] + # Coerce ids to list + if not isinstance( id, list ): + id = id.split( "," ) + # Ensure ids are integers + try: + id = map( int, id ) + except: + error( "Invalid id" ) + return id + + # ---- Override these ---------------------------------------------------- + def handle_operation( self, trans, operation, ids ): + pass + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + def apply_default_filter( self, trans, query ): + return query + +class GridColumn( object ): + def __init__( self, label, key=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1 ): + self.label = label + self.key = key + self.method = method + self.format = format + self.link = link + self.attach_popup = attach_popup + self.visible = visible + self.ncells = ncells + # Currently can only sort of columns that have a database + # representation, not purely derived. + if self.key: + self.sortable = True + else: + self.sortable = False + def get_value( self, trans, grid, item ): + if self.method: + value = getattr( grid, self.method )( trans, item ) + elif self.key: + value = getattr( item, self.key ) + else: + value = None + if self.format: + value = self.format( value ) + return value + +class GridOperation( object ): + def __init__( self, label, key=None, condition=None, allow_multiple=True ): + self.label = label + self.key = key + self.allow_multiple = allow_multiple + self.condition = condition + def allowed( self, item ): + if self.condition: + return self.condition( item ) + else: + return True + +class GridColumnFilter( object ): + def __init__( self, label, args=None ): + self.label = label + self.args = args + def get_url_args( self ): + rval = {} + for k, v in self.args.items(): + rval[ "f-" + k ] = v + return rval + \ No newline at end of file diff --git a/scripts/set_metadata.py b/scripts/set_metadata.py new file mode 100644 index 00000000000..7cd7ad2cc0b --- /dev/null +++ b/scripts/set_metadata.py @@ -0,0 +1,38 @@ +""" +Execute an external process to set_meta() on a provided list of pickled datasets. + +This should not be called directly! Use the set_metadata.sh script in Galaxy's +top level directly. + +""" + +import os, sys, cPickle +assert sys.version_info[:2] >= ( 2, 4 ) + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers +galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here +galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid + +def __main__(): + file_path = sys.argv.pop( 1 ) + tmp_dir = sys.argv.pop( 1 ) + galaxy.model.Dataset.file_path = file_path + galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir + for pickled_filenames in sys.argv[1:]: + pickled_filename_in, pickled_filename_kwds, pickled_filename_out, pickled_filename_results_code = pickled_filenames.split( ',' ) + try: + data = cPickle.load( open( pickled_filename_in ) )#unpickle DatasetInstance + kwds = cPickle.load( open( pickled_filename_kwds ) )#unpickle kwds + data.datatype.set_meta( data, **kwds ) + data.metadata.to_pickled_dict( pickled_filename_out ) # write out results of set_meta + cPickle.dump( ( True, 'Metadata has been set successfully' ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has suceeded + except Exception, e: + cPickle.dump( ( False, e ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has failed somehow + +__main__() \ No newline at end of file diff --git a/scripts/update_database/update_database_with_security_libraries.py b/scripts/update_database/update_database_with_security_libraries.py index 4145107242f..547c2cda683 100644 --- a/scripts/update_database/update_database_with_security_libraries.py +++ b/scripts/update_database/update_database_with_security_libraries.py @@ -131,7 +131,12 @@ def main(): i.create() except Exception, e: print_warning( "Adding index failed: %s" % ( e ) ) - + try: + i = sqlalchemy.Index( 'ix_job_state', app.model.Job.table.c.state ) + i.create() + except Exception, e: + print_warning( "Adding index failed: %s" % ( e ) ) + # Shutdown the app app.shutdown() @@ -165,8 +170,8 @@ def main(): # For each user: # 1. make sure they have a private role # 2. set DefaultUserPermissions - # 3. set DefaultHisstoryPermissions on existing histories - # 4. set DatasetPermissionss on each history's activatable_datasets + # 3. set DefaultHistoryPermissions on existing histories + # 4. set DatasetPermissions on each history's activatable_datasets default_user_action = security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action for user in app.model.User.query().all(): @@ -175,7 +180,7 @@ def main(): print "Setting up user %s." % user.email private_role = security_agent.get_private_user_role( user ) if not private_role: - security_agent.create_private_user_role( user ) + private_role = security_agent.create_private_user_role( user ) print "Created private role for %s" % user.email else: print_warning( "%s already has a private role, re-setting defaults anyway" % user.email ) @@ -187,15 +192,8 @@ def main(): # Add the new default permissions for the user dup = app.model.DefaultUserPermissions( user, default_user_action, private_role ) dup.flush() - # Set DefaultHistoryPermissions on all of the user's active histories and associated datasets - # TODO: fix mapping for history.activatable_datasets so it doesn't throw an exception on the - # following query when eagerloading activatable_datasets. Fix all of the queries below that - # call history.active_datasets to be history.activatable_datasets when this works. - histories = app.model.History.filter( and_( app.model.History.table.c.user_id==user.id, - app.model.History.table.c.purged==False ) ) \ - .options( eagerload( 'active_datasets' ) ).all() - print "Setting DefaultHistoryPermissions for %d un-purged histories associated with %s" % ( len( histories ), user.email ) - for history in histories: + print "Setting DefaultHistoryPermissions for %d un-purged histories associated with %s" % ( len( user.histories ), user.email ) + for history in user.active_histories: # Delete all of the current default permissions for the history for dhp in history.default_permissions: dhp.delete() @@ -203,9 +201,10 @@ def main(): # Add the new default permissions for the history dhp = app.model.DefaultHistoryPermissions( history, default_user_action, private_role ) dhp.flush() - print "Setting DatasetPermissionss for %d un-purged datasets in history %d" % ( len( history.active_datasets ), history.id ) + activatable_datasets = history.activatable_datasets #store this list, so we don't generate it more than once + print "Setting DatasetPermissions for %d un-purged datasets in history %d" % ( len( activatable_datasets ), history.id ) # Set the permissions on the current history's datasets that are not purged - for hda in history.active_datasets: + for hda in activatable_datasets: dataset = hda.dataset if dataset.library_associations: # Don't change permissions on a dataset associated with a library diff --git a/scripts/yuicompressor.jar b/scripts/yuicompressor.jar index 3f92c3413c7..c29470bd0d0 100644 Binary files a/scripts/yuicompressor.jar and b/scripts/yuicompressor.jar differ diff --git a/set_metadata.sh b/set_metadata.sh new file mode 100755 index 00000000000..962c799e75c --- /dev/null +++ b/set_metadata.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0` +python -ES ./scripts/set_metadata.py $@ diff --git a/static/fastx_icons/barcode_splitter_output_example.png b/static/fastx_icons/barcode_splitter_output_example.png new file mode 100644 index 00000000000..49dfd6c4cdb Binary files /dev/null and b/static/fastx_icons/barcode_splitter_output_example.png differ diff --git a/static/fastx_icons/fasta_clipping_histogram_1.png b/static/fastx_icons/fasta_clipping_histogram_1.png new file mode 100644 index 00000000000..a9416f68d9d Binary files /dev/null and b/static/fastx_icons/fasta_clipping_histogram_1.png differ diff --git a/static/fastx_icons/fasta_clipping_histogram_2.png b/static/fastx_icons/fasta_clipping_histogram_2.png new file mode 100644 index 00000000000..471be686bc1 Binary files /dev/null and b/static/fastx_icons/fasta_clipping_histogram_2.png differ diff --git a/static/fastx_icons/fastq_nucleotides_distribution_1.png b/static/fastx_icons/fastq_nucleotides_distribution_1.png new file mode 100644 index 00000000000..f238587ad02 Binary files /dev/null and b/static/fastx_icons/fastq_nucleotides_distribution_1.png differ diff --git a/static/fastx_icons/fastq_nucleotides_distribution_2.png b/static/fastx_icons/fastq_nucleotides_distribution_2.png new file mode 100644 index 00000000000..e935576e64c Binary files /dev/null and b/static/fastx_icons/fastq_nucleotides_distribution_2.png differ diff --git a/static/fastx_icons/fastq_nucleotides_distribution_3.png b/static/fastx_icons/fastq_nucleotides_distribution_3.png new file mode 100644 index 00000000000..cae0c53a88c Binary files /dev/null and b/static/fastx_icons/fastq_nucleotides_distribution_3.png differ diff --git a/static/fastx_icons/fastq_nucleotides_distribution_4.png b/static/fastx_icons/fastq_nucleotides_distribution_4.png new file mode 100644 index 00000000000..7f8369e57f4 Binary files /dev/null and b/static/fastx_icons/fastq_nucleotides_distribution_4.png differ diff --git a/static/fastx_icons/fastq_quality_boxplot_1.png b/static/fastx_icons/fastq_quality_boxplot_1.png new file mode 100644 index 00000000000..c3621fabf6c Binary files /dev/null and b/static/fastx_icons/fastq_quality_boxplot_1.png differ diff --git a/static/fastx_icons/fastq_quality_boxplot_2.png b/static/fastx_icons/fastq_quality_boxplot_2.png new file mode 100644 index 00000000000..95af2c1a648 Binary files /dev/null and b/static/fastx_icons/fastq_quality_boxplot_2.png differ diff --git a/static/fastx_icons/fastq_quality_boxplot_3.png b/static/fastx_icons/fastq_quality_boxplot_3.png new file mode 100644 index 00000000000..6121c84edbe Binary files /dev/null and b/static/fastx_icons/fastq_quality_boxplot_3.png differ diff --git a/static/fastx_icons/fastx_clipper_example.png b/static/fastx_icons/fastx_clipper_example.png new file mode 100644 index 00000000000..8d4ff4cc21a Binary files /dev/null and b/static/fastx_icons/fastx_clipper_example.png differ diff --git a/static/fastx_icons/fastx_clipper_illustration.png b/static/fastx_icons/fastx_clipper_illustration.png new file mode 100644 index 00000000000..5acf892fac9 Binary files /dev/null and b/static/fastx_icons/fastx_clipper_illustration.png differ diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl index fc06c2008ff..e0c9bb86022 100644 --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -65,22 +65,20 @@ div.toolParamHelp a div.toolFormBody { - background: $form_body_bg_bottom; - background-image: url(form_body_bg.png); - background-repeat: repeat-x; - background-position: top; - padding: 5px; - padding-left: 10px; - padding-right: 10px; + background: $form_body_bg_bottom; + background-image: url(form_body_bg.png); + background-repeat: repeat-x; + background-position: top; + padding: 5px 0; } div.toolFormBody div.toolFormTitle { background: transparent; - border: none; - font-weight: bold; - border-bottom: solid $form_border 1px; - margin-bottom: 5px; + border: none; + font-weight: bold; + border-bottom: solid $form_border 1px; + margin-bottom: 5px; } div.toolFormDisabled div.toolFormTitle { @@ -98,8 +96,8 @@ div.toolHelp div.toolHelpBody { - width: 100%; - overflow: auto; + width: 100%; + overflow: auto; } div.titleRow { @@ -111,9 +109,30 @@ div.titleRow { /* Forms */ +div.form +{ + border: solid $form_border 1px; +} + +div.form-title +{ + font-weight: bold; + padding: 5px 10px; + background: $form_title_bg_bottom; + background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid $form_border 1px; +} + +div.form-body +{ + padding: 5px 0; +} + div.form-row { - margin-bottom: 1em; + padding: 5px 10px; } div.form-title-row @@ -130,7 +149,6 @@ div.repeat-group-item div.form-row-error { background: $error_message_bg; - padding: 5px; } div.form-row label @@ -140,14 +158,35 @@ div.form-row label margin-bottom: .2em; } +div.form-row-input +{ + float: left; + width: 300px; +} + +div.form-row-input > input +{ + max-width: 300px; +} + +div.form-row-error-message +{ + width: 300px; + float: left; + color: red; + font-weight: bold; + padding: 3px 0 0 1em; +} + select, input, textarea { font: inherit; font-size: 115%; } -select, textarea, input[type="text"], input[type="file"] +select, textarea, input[type="text"], input[type="file"], input[type="password"] { + -webkit-box-sizing: border-box; max-width: 300px; } @@ -467,13 +506,26 @@ ul.manage-table-actions li { background: $history_running_bg; } +.state-fg-queued { + color: #888888; +} +.state-fg-ok { + color: #66AA66; +} +.state-fg-running { + color: #AAAA66; +} +.state-fg-error { + color: #AA6666; +} + ## Button styles .action-button { background: #eeeeee; color: #333; text-decoration: none; - font-size: 90%; + font-size: 95%; font-weight: bold; display: inline-block; cursor: pointer; @@ -508,13 +560,11 @@ div.popupmenu { display: none; background: #eeeeee; color: #333; - font-size: 90%; font-weight: bold; position: absolute; z-index: 20000; border: solid #aaaaaa 1px; - padding-top: 3px; - padding-bottom: 3px; + padding: 3px 0; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; @@ -524,9 +574,7 @@ div.popupmenu { } div.popupmenu-item { - padding: 3px; - padding-left: 1em; - padding-right: 1em; + padding: 3px 1em; cursor: pointer; } @@ -551,6 +599,19 @@ div.permissionContainer { ## Data grid style +.grid-header { + padding-bottom: 1em; +} + +.grid-header h2 { + margin: 0; + margin-bottom: 0.5em; +} + +.grid-header .title { + font-weight: bold; +} + .grid { padding-top: 1em; border-collapse: collapse; @@ -561,6 +622,9 @@ div.permissionContainer { border-bottom: solid #DDDDDD 1px; padding: 0.5em 1em; } +.grid tbody td:empty { + padding: 0; +} .grid thead th { background: $table_header_bg; background-image: url(form_title_bg.png); diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css index 2962cfb40b2..4d68feb9571 100644 --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -65,22 +65,20 @@ div.toolParamHelp a div.toolFormBody { - background: #FFFFFF; - background-image: url(form_body_bg.png); - background-repeat: repeat-x; - background-position: top; - padding: 5px; - padding-left: 10px; - padding-right: 10px; + background: #FFFFFF; + background-image: url(form_body_bg.png); + background-repeat: repeat-x; + background-position: top; + padding: 5px 0; } div.toolFormBody div.toolFormTitle { background: transparent; - border: none; - font-weight: bold; - border-bottom: solid #d8b365 1px; - margin-bottom: 5px; + border: none; + font-weight: bold; + border-bottom: solid #d8b365 1px; + margin-bottom: 5px; } div.toolFormDisabled div.toolFormTitle { @@ -98,8 +96,8 @@ div.toolHelp div.toolHelpBody { - width: 100%; - overflow: auto; + width: 100%; + overflow: auto; } div.titleRow { @@ -111,9 +109,30 @@ div.titleRow { /* Forms */ +div.form +{ + border: solid #d8b365 1px; +} + +div.form-title +{ + font-weight: bold; + padding: 5px 10px; + background: #d2c099; + background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid #d8b365 1px; +} + +div.form-body +{ + padding: 5px 0; +} + div.form-row { - margin-bottom: 1em; + padding: 5px 10px; } div.form-title-row @@ -130,7 +149,6 @@ div.repeat-group-item div.form-row-error { background: #FFCCCC; - padding: 5px; } div.form-row label @@ -140,14 +158,35 @@ div.form-row label margin-bottom: .2em; } +div.form-row-input +{ + float: left; + width: 300px; +} + +div.form-row-input > input +{ + max-width: 300px; +} + +div.form-row-error-message +{ + width: 300px; + float: left; + color: red; + font-weight: bold; + padding: 3px 0 0 1em; +} + select, input, textarea { font: inherit; font-size: 115%; } -select, textarea, input[type="text"], input[type="file"] +select, textarea, input[type="text"], input[type="file"], input[type="password"] { + -webkit-box-sizing: border-box; max-width: 300px; } @@ -465,12 +504,25 @@ ul.manage-table-actions li { background: #FFFFCC; } +.state-fg-queued { + color: #888888; +} +.state-fg-ok { + color: #66AA66; +} +.state-fg-running { + color: #AAAA66; +} +.state-fg-error { + color: #AA6666; +} + .action-button { background: #eeeeee; color: #333; text-decoration: none; - font-size: 90%; + font-size: 95%; font-weight: bold; display: inline-block; cursor: pointer; @@ -504,13 +556,11 @@ div.popupmenu { display: none; background: #eeeeee; color: #333; - font-size: 90%; font-weight: bold; position: absolute; z-index: 20000; border: solid #aaaaaa 1px; - padding-top: 3px; - padding-bottom: 3px; + padding: 3px 0; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; @@ -520,9 +570,7 @@ div.popupmenu { } div.popupmenu-item { - padding: 3px; - padding-left: 1em; - padding-right: 1em; + padding: 3px 1em; cursor: pointer; } @@ -546,6 +594,19 @@ div.permissionContainer { } +.grid-header { + padding-bottom: 1em; +} + +.grid-header h2 { + margin: 0; + margin-bottom: 0.5em; +} + +.grid-header .title { + font-weight: bold; +} + .grid { padding-top: 1em; border-collapse: collapse; @@ -556,6 +617,9 @@ div.permissionContainer { border-bottom: solid #DDDDDD 1px; padding: 0.5em 1em; } +.grid tbody td:empty { + padding: 0; +} .grid thead th { background: #ebd9b2; background-image: url(form_title_bg.png); diff --git a/static/june_2007_style/blue/panel_layout.css b/static/june_2007_style/blue/panel_layout.css index e48f52009af..77b4fa60a14 100644 --- a/static/june_2007_style/blue/panel_layout.css +++ b/static/june_2007_style/blue/panel_layout.css @@ -23,27 +23,6 @@ body width: 100%; height: 100%; } -#masthead -{ - position:absolute; - top:0; - left:0; - width:100%; - height:32px; - background: url(masthead_bg.png); - overflow: hidden; - color:#fff; - font-weight: bold; - border-bottom: solid #444 1px; -} - -#masthead div.title -{ - margin: 3px; - margin-right: 10px; - font-size: 182%; - font-weight: bold; -} #messagebox { @@ -254,4 +233,101 @@ div.unified-panel-body { { background-image: url(info_small.png); background-color: #CCCCFF; -} \ No newline at end of file +} + + +#masthead +{ + position:absolute; + top:0; + left:0; + width:100%; + height:32px; + background: #2C3143; + color:#fff; + border-bottom: solid #444 1px; + z-index: 15000; + padding: 0; +} + +#masthead a +{ + color: #eeeeee; +} + +#masthead .title +{ + padding: 3px 10px; + font-size: 175%; + font-weight: bold; +} + +#masthead a +{ + text-decoration: none; +} + +#masthead a:hover +{ + text-decoration: underline; +} + +div.tab-group +{ + margin: 0; + padding: 0 10px; + height: 100%; + white-space: nowrap; +} + +div.tab-group span.tab +{ + position: relative; + display: block; + float: left; + margin: 0; + padding: 0 1em; + height: 32px; + line-height: 32px; + text-align: left; +} + +div.tab-group > span.tab:hover > a +{ + color: gold !important; +} + +div.tab-group > span.active +{ + background: rgb(1,1,1); +} + +div.tab-group span.tab div.submenu { + display: none; + position: absolute; + z-index: 16000; + left: 0; + top: 32px; + padding: 1em; + margin: -1em; + padding-top: 0; + margin-top: 0; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 0 0 1em 1em; + -webkit-border-bottom-right-radius: 1em; + -webkit-border-bottom-left-radius: 1em; +} + +div.tab-group span.tab div.submenu ul { + display: block; + margin: 0; + padding: 0; + list-style-type: none; + background: #2C3143; +} + +div.tab-group span.tab div.submenu ul li { + display: block; + padding: 0 1em; + white-space: nowrap; +} diff --git a/static/june_2007_style/blue/reset.css b/static/june_2007_style/blue/reset.css index 0eb970e56bf..1c958c2a9b6 100644 --- a/static/june_2007_style/blue/reset.css +++ b/static/june_2007_style/blue/reset.css @@ -1,3 +1,3 @@ -/* Copyright (c) 2007, Yahoo! Inc. All rights reserved. */ -body {font:13px arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}table {font-size:inherit;font:100%;}select, input, textarea {font:99% arial,helvetica,clean,sans-serif;}pre, code {font:115% monospace;*font-size:100%;}body * {line-height:1.22em;} +/* Copyright (c) 2008, Yahoo! Inc. All rights reserved. */ +body{font:13px/1.231 arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea{font:99% arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} /*body,div,dl,dt,dd,ul,ol,li,h1,h2,h3,h4,h5,h6,pre,form,fieldset,input,textarea,p,blockquote,th,td{margin:0;padding:0;}table{border-collapse:collapse;border-spacing:0;}fieldset,img{border:0;}address,caption,cite,code,dfn,em,strong,th,var{font-style:normal;font-weight:normal;}ol,ul {list-style:none;}caption,th {text-align:left;}h1,h2,h3,h4,h5,h6{font-size:100%;font-weight:normal;}q:before,q:after{content:'';}abbr,acronym {border:0;}*/ diff --git a/static/june_2007_style/panel_layout.css.tmpl b/static/june_2007_style/panel_layout.css.tmpl index 016b228a0e0..81da6eff586 100644 --- a/static/june_2007_style/panel_layout.css.tmpl +++ b/static/june_2007_style/panel_layout.css.tmpl @@ -23,27 +23,6 @@ body width: 100%; height: 100%; } -#masthead -{ - position:absolute; - top:0; - left:0; - width:100%; - height:32px; - background: url(masthead_bg.png); - overflow: hidden; - color:#fff; - font-weight: bold; - border-bottom: solid ${layout_masthead_border} 1px; -} - -#masthead div.title -{ - margin: 3px; - margin-right: 10px; - font-size: 182%; - font-weight: bold; -} #messagebox { @@ -255,4 +234,102 @@ div.unified-panel-body { { background-image: url(info_small.png); background-color: $info_message_bg; -} \ No newline at end of file +} + +## ---- Masthead styles ---- + +#masthead +{ + position:absolute; + top:0; + left:0; + width:100%; + height:32px; + background: ${masthead_bg}; + color:#fff; + border-bottom: solid ${layout_masthead_border} 1px; + z-index: 15000; + padding: 0; +} + +#masthead a +{ + color: $masthead_link; +} + +#masthead .title +{ + padding: 3px 10px; + font-size: 175%; + font-weight: bold; +} + +#masthead a +{ + text-decoration: none; +} + +#masthead a:hover +{ + text-decoration: underline; +} + +div.tab-group +{ + margin: 0; + padding: 0 10px; + height: 100%; + white-space: nowrap; +} + +div.tab-group span.tab +{ + position: relative; + display: block; + float: left; + margin: 0; + padding: 0 1em; + height: 32px; + line-height: 32px; + text-align: left; +} + +div.tab-group > span.tab:hover > a +{ + color: gold !important; +} + +div.tab-group > span.active +{ + background: rgb(1,1,1); +} + +div.tab-group span.tab div.submenu { + display: none; + position: absolute; + z-index: 16000; + left: 0; + top: 32px; + padding: 1em; + margin: -1em; + padding-top: 0; + margin-top: 0; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 0 0 1em 1em; + -webkit-border-bottom-right-radius: 1em; + -webkit-border-bottom-left-radius: 1em; +} + +div.tab-group span.tab div.submenu ul { + display: block; + margin: 0; + padding: 0; + list-style-type: none; + background: ${masthead_bg}; +} + +div.tab-group span.tab div.submenu ul li { + display: block; + padding: 0 1em; + white-space: nowrap; +} diff --git a/static/june_2007_style/reset.css.tmpl b/static/june_2007_style/reset.css.tmpl index 0eb970e56bf..a13abe4b1c2 100644 --- a/static/june_2007_style/reset.css.tmpl +++ b/static/june_2007_style/reset.css.tmpl @@ -1,3 +1,5 @@ -/* Copyright (c) 2007, Yahoo! Inc. All rights reserved. */ -body {font:13px arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}table {font-size:inherit;font:100%;}select, input, textarea {font:99% arial,helvetica,clean,sans-serif;}pre, code {font:115% monospace;*font-size:100%;}body * {line-height:1.22em;} +/* Copyright (c) 2008, Yahoo! Inc. All rights reserved. */ +## yui fonts +body{font:13px/1.231 arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea{font:99% arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} +## yui reset... commented out??? /*body,div,dl,dt,dd,ul,ol,li,h1,h2,h3,h4,h5,h6,pre,form,fieldset,input,textarea,p,blockquote,th,td{margin:0;padding:0;}table{border-collapse:collapse;border-spacing:0;}fieldset,img{border:0;}address,caption,cite,code,dfn,em,strong,th,var{font-style:normal;font-weight:normal;}ol,ul {list-style:none;}caption,th {text-align:left;}h1,h2,h3,h4,h5,h6{font-size:100%;font-weight:normal;}q:before,q:after{content:'';}abbr,acronym {border:0;}*/ diff --git a/static/scripts/galaxy.panels.js b/static/scripts/galaxy.panels.js index efe2ccb0a2a..1729fe5a2b4 100644 --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -245,3 +245,35 @@ function make_popupmenu( button_element, options ) { }; $( button_element ).click( click ); }; + +// Tab management + + +$(function() { + $("span.tab").each( function() { + var submenu = $(this).children( "div.submenu" ); + if ( submenu.length > 0 ) { + if ( $.browser.msie ) { + // Vile IE iframe hack -- even IE7 needs this + submenu.prepend( "" ); + } + $(this).hoverIntent( function() { submenu.show(); }, function() { submenu.hide(); } ); + submenu.click( function() { submenu.hide(); } ); + } + }); +}); + +function user_changed( user_email, is_admin ) { + if ( user_email ) { + $(".loggedin-only").show(); + $(".loggedout-only").hide(); + $("#user-email").text( user_email ); + if ( is_admin ) { + $(".admin-only").show(); + } + } else { + $(".loggedin-only").hide(); + $(".loggedout-only").show(); + $(".admin-only").hide(); + } +} \ No newline at end of file diff --git a/static/scripts/jquery.hoverIntent.js b/static/scripts/jquery.hoverIntent.js index 43cb7850539..d7b32d9027c 100644 --- a/static/scripts/jquery.hoverIntent.js +++ b/static/scripts/jquery.hoverIntent.js @@ -109,4 +109,4 @@ // bind the function to the two event listeners return this.mouseover(handleHover).mouseout(handleHover); }; -})(jQuery); \ No newline at end of file +})(jQuery); diff --git a/static/scripts/pack_scripts.py b/static/scripts/pack_scripts.py index 0bf5ac4e68b..a678cb84a29 100755 --- a/static/scripts/pack_scripts.py +++ b/static/scripts/pack_scripts.py @@ -10,7 +10,7 @@ from os import path # Scripts that should not be packed -- just copied do_not_pack = set( [ "ie_pngfix.js", "aflax.js" ] ) -cmd = "java -jar ../../scripts/yuicompressor.jar --type js -v %(fname)s -o packed/%(fname)s" +cmd = "java -jar ../../scripts/yuicompressor.jar --type js %(fname)s -o packed/%(fname)s" # If specific scripts specified on command line, just pack them, otherwise pack # all. diff --git a/static/scripts/packed/IE7.js b/static/scripts/packed/IE7.js index 4bd659cca95..a7d3ad9bd5e 100644 --- a/static/scripts/packed/IE7.js +++ b/static/scripts/packed/IE7.js @@ -1 +1 @@ -(function(){IE7={toString:function(){return"IE7 version 2.0 (beta3)"}};var appVersion=IE7.appVersion=navigator.appVersion.match(/MSIE (\d\.\d)/)[1];if(/ie7_off/.test(top.location.search)||appVersion<5){return }var Undefined=K();var quirksMode=document.compatMode!="CSS1Compat";var documentElement=document.documentElement,body,viewport;var ANON="!";var HEADER=":link{ie7-link:link}:visited{ie7-link:visited}";var RELATIVE=/^[\w\.]+[^:]*$/;function makePath(href,path){if(RELATIVE.test(href)){href=(path||"")+href}return href}function getPath(href,path){href=makePath(href,path);return href.slice(0,href.lastIndexOf("/")+1)}var script=document.scripts[document.scripts.length-1];var path=getPath(script.src);try{var httpRequest=new ActiveXObject("Microsoft.XMLHTTP")}catch(e){}var fileCache={};function loadFile(href,path){try{href=makePath(href,path);if(!fileCache[href]){httpRequest.open("GET",href,false);httpRequest.send();if(httpRequest.status==0||httpRequest.status==200){fileCache[href]=httpRequest.responseText}}}catch(e){}finally{return fileCache[href]||""}}if(appVersion<5.5){undefined=Undefined();ANON="HTML:!";var GLOBAL=/(g|gi)$/;var _String_replace=String.prototype.replace;String.prototype.replace=function(expression,replacement){if(typeof replacement=="function"){if(expression&&expression.constructor==RegExp){var regexp=expression;var global=regexp.global;if(global==null){global=GLOBAL.test(regexp)}if(global){regexp=new RegExp(regexp.source)}}else{regexp=new RegExp(rescape(expression))}var match,string=this,result="";while(string&&(match=regexp.exec(string))){result+=string.slice(0,match.index)+replacement.apply(this,match);string=string.slice(match.index+match[0].length);if(!global){break}}return result+string}return _String_replace.apply(this,arguments)};Array.prototype.pop=function(){if(this.length){var i=this[this.length-1];this.length--;return i}return undefined};Array.prototype.push=function(){for(var i=0;i
")}$(".dialog-box").find(".body").html(B);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function make_popupmenu(D,B){var A=$("").appendTo("body");$.each(B,function(G,F){$("").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)};
\ No newline at end of file
+var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){$("").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(f,b,c){var e=false;var d=null;resize=function(g){var h=g;if(g<0){g=0}jq(f).css("width",g);jq(c).css("left",h);jq(b).css("left",g+7);if(document.recalc){document.recalc()}};toggle=function(){if(e){jq(c).removeClass("hover");jq(c).animate({left:d},"fast");jq(f).css("left",-d).show().animate({left:0},"fast",function(){resize(d);jq(c).removeClass("hidden")});e=false}else{d=jq(c).position().left;jq(b).css("left",hidden_width);if(document.recalc){document.recalc()}jq(c).removeClass("hover");jq(f).animate({left:-d},"fast");jq(c).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});e=true}};jq(c).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(g,h){jq("#DD-helper").show()},stop:function(g,h){jq("#DD-helper").hide();return false},drag:function(g,h){x=h.position.left;x=Math.min(400,Math.max(100,x));if(e){jq(f).css("left",0);jq(c).removeClass("hidden");e=false}resize(x);h.position.left=x;h.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show();var a=function(g){if((e&&g=="show")||(!e&&g=="hide")){toggle()}};return{force_panel:a}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){jq(a).css("width",k);jq(e).css("right",k+9);jq(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){jq(h).removeClass("hover");jq(h).animate({right:c},"fast");jq(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);jq(h).removeClass("hidden")});j=false}else{c=jq(document).width()-jq(h).position().left-border_tweak;jq(e).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq(h).removeClass("hover");jq(a).animate({right:-c},"fast");jq(h).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=jq(e).width()-(j?c:0);if(l")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function make_popupmenu(d,b){var a=$("").appendTo("body");$.each(b,function(g,f){$("").html(g).click(f).appendTo(a)});var c=function(){$(a).unbind().hide();$("#popup-helper").unbind().hide()};var e=function(){var f=$(d).offset();$("#popup-helper").mousedown(c).show();$(a).click(c).css({top:-1000}).show().css({top:f.top+$(d).height()+9,left:f.left+$(d).width()-$(a).width()})};$(d).click(e)}$(function(){$("span.tab").each(function(){var a=$(this).children("div.submenu");if(a.length>0){if($.browser.msie){a.prepend("")}$(this).hoverIntent(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
diff --git a/static/scripts/packed/galaxy.ui.scrollPanel.js b/static/scripts/packed/galaxy.ui.scrollPanel.js
index fd0e8056d1d..fcfec80043f 100644
--- a/static/scripts/packed/galaxy.ui.scrollPanel.js
+++ b/static/scripts/packed/galaxy.ui.scrollPanel.js
@@ -1 +1 @@
-$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close_dist=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left
").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('').appendTo("#canvas-container").get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});workflow.remove_node(this);$(this.element).draggable("destroy").remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var A=this.element.get(0);(function(B){B.removeChild(A);B.appendChild(A)})(A.parentNode);$(A).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("");B.enable_input_terminal(G,F.name,F.extensions);E.append($(""+F.label+"
").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($(""))}$.each(D.data_outputs,function(I,F){var H=$("");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($(""+G+"
").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element),D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_errors=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($(""+G.label+"
").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B=""+C+"
";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("No node selected
")},activate_node:function(A){if(this.active_node!=A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A}},node_changed:function(A){this.has_changes=true;if(this.active_node==A){parent.show_form_for_tool(A.form_html,A)}}});function prebuild_node(H,F,K){var E=$("");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$(""+F+"
");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("");var D="
loading tool info...").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(M,L){workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes};
\ No newline at end of file
+function Terminal(a){this.element=a;this.connectors=[]}Terminal.prototype={connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}};function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal;function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(t in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[t])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var g=n(this.handle1.element)+5;var f=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var e=100;var k=Math.min(g,p);var a=Math.max(g,p);var j=Math.min(f,m);var u=Math.max(f,m);var b=Math.min(Math.max(Math.abs(u-j)/2,100),300);var o=k-e;var s=j-e;var q=a-k+2*e;var l=u-j+2*e;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);g-=o;f-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(g,f);r.bezierCurveTo(g+b,f,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(g,f);r.bezierCurveTo(g+b,f,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(c,a,b){node=this;$(c).each(function(){var d=this.terminal=new InputTerminal(this,b);d.node=node;d.name=a;$(this).droppable({tolerance:"intersect",accept:function(e){e=e.get(0);return(e.terminal)&&(d.can_accept(e.terminal))},activeClass:"input-terminal-active",over:function(g,f){f.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(g,f){f.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(k,i){var f=$(this).data("droppable");var g=i.draggable.get(0).terminal;var j=f.element.get(0).terminal;var l=new Connector();l.connect(g,j);l.redraw()}});$(this).hoverIntent(function(){if(d.connectors.length>0){var e=$("").css({display:"none"}).appendTo("body").append($("").append($("").click(function(){$.each(d.connectors,function(g,f){f.destroy()});e.remove()}))).bind("mouseleave",function(){$(this).remove()});e.css({top:$(this).offset().top-2,left:$(this).offset().left-e.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[a]=d})},enable_output_terminal:function(c,a,b){node=this;$(c).each(function(){var d=this.terminal=new OutputTerminal(this,b);d.node=node;d.name=a;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var e=$('').appendTo("#canvas-container").get(0);e.terminal=new OutputTerminal(e);var f=new Connector();this.drag_temp_connector=f;f.dragging=true;f.connect(this.terminal,e.terminal);return e},drag:function(g,f){h=f.helper.get(0);h.terminal.redraw()},stop:function(g,f){this.drag_temp_connector.destroy()}});node.output_terminals[a]=d})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy();$(b.element).droppable("destroy")});$.each(this.output_terminals,function(a,b){b.destroy();$(b.element).draggable("destroy")});workflow.remove_node(this);$(this.element).draggable("destroy").remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(e){var d=this.element;if(e.type){this.type=e.type}this.form_html=e.form_html;this.tool_state=e.tool_state;this.tool_errors=e.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var g=$("").appendTo(a);$.each(e.data_inputs,function(j,b){var f=$("");c.enable_input_terminal(f,b.name,b.extensions);g.append($(""+b.label+"
").prepend(f))});if((e.data_inputs.length>0)&&(e.data_outputs.length>0)){a.append($(""))}$.each(e.data_outputs,function(k,b){var j=$("");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($(""+f+"
").append(j))});workflow.node_changed(this)},update_field_data:function(e){var c=$(this.element),d=this;this.tool_state=e.tool_state;this.form_html=e.form_html;this.tool_errors=e.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var f=c.find("div.inputs");var b=$("");var a=f.find("div.input-data-row");$.each(e.data_inputs,function(k,g){var j=$("");d.enable_input_terminal(j,g.name,g.extensions);f.find("div[name="+g.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($(""+g.label+"
").prepend(j))});f.replaceWith(b);f.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c=""+d+"
";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var e={};$.each(d.input_terminals,function(f,g){e[g.name]=null;$.each(g.connectors,function(j,k){e[g.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:e,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(e,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(e))});wf.id_counter=b+1;$.each(a.steps,function(e,d){var c=wf.nodes[e];$.each(d.input_connections,function(g,f){if(f){var i=wf.nodes[f.id];var j=new Connector();j.connect(i.output_terminals[f.output_name],c.input_terminals[g]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("No node selected
")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}}});function prebuild_node(k,i,n){var g=$("");var d=new Node(g);d.type=k;if(k=="tool"){d.tool_id=n}var m=$(""+i+"
");g.append(m);g.css("left",$(window).scrollLeft()+20);g.css("top",$(window).scrollTop()+20);var l=$("");var e=" loading tool info...").click(function(b){d.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));g.appendTo("#canvas-container");var c=$("#canvas-container").position();g.css({left:(-c.left)+10,top:(-c.top)+10});var a=g.width();j.prependTo(m);a+=(j.width()+10);g.css("width",a);$(g).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(f,b){workflow.activate_node(d)},start:function(f,b){workflow.activate_node(d)},drag:function(f,b){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(f,b){$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return d}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes};
\ No newline at end of file
diff --git a/static/scripts/packed/ie7-recalc.js b/static/scripts/packed/ie7-recalc.js
index 86a27f6ee1c..60192641791 100644
--- a/static/scripts/packed/ie7-recalc.js
+++ b/static/scripts/packed/ie7-recalc.js
@@ -1 +1 @@
-(function(){if(!IE7.loaded){return }CLASSES=/\sie7_class\d+/g;IE7.CSS.extend({elements:{},handlers:[],reset:function(){this.removeEventHandlers();var elements=this.elements;for(var i in elements){elements[i].runtimeStyle.cssText=""}this.elements={};var elements=IE7.Rule.elements;for(var i in elements){with(elements[i]){className=className.replace(CLASSES,"")}}IE7.Rule.elements={}},reload:function(){this.rules=[];this.getInlineStyles();this.screen.load();if(this.print){this.print.load()}this.refresh();this.trash()},addRecalc:function(propertyName,test,handler,replacement){this.base(propertyName,test,function(element){handler(element);IE7.CSS.elements[element.uniqueID]=element},replacement)},recalc:function(){this.reset();this.base()},addEventHandler:function(element,type,handler){element.attachEvent(type,handler);this.handlers.push(arguments)},removeEventHandlers:function(){var handler;while(handler=this.handlers.pop()){handler[0].detachEvent(handler[1],handler[2])}},getInlineStyles:function(){var styleSheets=document.getElementsByTagName("style"),styleSheet;for(var i=styleSheets.length-1;(styleSheet=styleSheets[i]);i--){if(!styleSheet.disabled&&!styleSheet.ie7){var cssText=styleSheet.cssText||styleSheet.innerHTML;this.styles.push(cssText);styleSheet.cssText=cssText}}},trash:function(){var styleSheets=document.styleSheets,styleSheet,i;for(i=0;i- + +
+
+
+
+
+
+
+
+ Galaxy quickie
+ click to play
+ Grouping
+ })
})
})
})
}){kind=icon}
})