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[hg] galaxy 2613: Remove logging from galaxy.base
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5f60d79f483f changeset: 2613:5f60d79f483f user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 14:01:08 2009 -0400 description: Remove logging from galaxy.base 2 file(s) affected in this change: static/scripts/galaxy.base.js static/scripts/packed/galaxy.base.js diffs (26 lines): diff -r 278df6aa7139 -r 5f60d79f483f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Aug 21 14:28:46 2009 -0400 +++ b/static/scripts/galaxy.base.js Sun Aug 23 14:01:08 2009 -0400 @@ -77,14 +77,12 @@ }; function attach_popupmenu( button_element, wrapper ) { - console.log( button_element, wrapper ); var clean = function() { wrapper.unbind().hide(); $("#popup-helper").unbind( "click.popupmenu" ).hide(); // $(document).unbind( "click.popupmenu" ); }; var click = function( e ) { - console.log( e ); var o = $(button_element).offset(); $("#popup-helper").bind( "click.popupmenu", clean ).show(); // $(document).bind( "click.popupmenu", clean ); diff -r 278df6aa7139 -r 5f60d79f483f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Aug 21 14:28:46 2009 -0400 +++ b/static/scripts/packed/galaxy.base.js Sun Aug 23 14:01:08 2009 -0400 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></div>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){console.log(b,d);var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){console.log(g);var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></div>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file

1 0

[hg] galaxy 2611: Merge
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/52a145b22b69 changeset: 2611:52a145b22b69 user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:31:20 2009 -0400 description: Merge 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0014_pages.py diffs (220 lines): diff -r 36c479b93d7e -r 52a145b22b69 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun Aug 23 12:28:36 2009 -0400 +++ b/lib/galaxy/model/__init__.py Sun Aug 23 12:31:20 2009 -0400 @@ -33,7 +33,6 @@ self.external = False self.deleted = False self.purged = False - self.username = None # Relationships self.histories = [] @@ -1119,20 +1118,7 @@ self.country+'<br/>'+ \ 'Phone: '+self.phone -class Page( object ): - def __init__( self ): - self.id = None - self.user = None - self.title = None - self.slug = None - self.latest_revision_id = None - self.revisions = [] -class PageRevision( object ): - def __init__( self ): - self.user = None - self.title = None - self.content = None diff -r 36c479b93d7e -r 52a145b22b69 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Sun Aug 23 12:28:36 2009 -0400 +++ b/lib/galaxy/model/mapping.py Sun Aug 23 12:31:20 2009 -0400 @@ -42,7 +42,6 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), - Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -524,26 +523,6 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) -Page.table = Table( "page", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), - Column( "latest_revision_id", Integer, - ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), - Column( "title", TEXT ), - Column( "slug", TEXT, unique=True, index=True ), - ) - -PageRevision.table = Table( "page_revision", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), - Column( "title", TEXT ), - Column( "content", TEXT ) - ) - # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -926,18 +905,6 @@ assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) -assign_mapper( context, PageRevision, PageRevision.table ) - -assign_mapper( context, Page, Page.table, - properties=dict( user=relation( User ), - revisions=relation( PageRevision, backref='page', - cascade="all, delete-orphan", - primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), - latest_revision=relation( PageRevision, post_update=True, - primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), - lazy=False ) - ) ) - def db_next_hid( self ): """ Override __next_hid to generate from the database in a concurrency diff -r 36c479b93d7e -r 52a145b22b69 lib/galaxy/model/migrate/versions/0014_pages.py --- a/lib/galaxy/model/migrate/versions/0014_pages.py Sun Aug 23 12:28:36 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -from sqlalchemy import * -from migrate import * -from migrate.changeset import * - -import datetime -now = datetime.datetime.utcnow - -import logging -log = logging.getLogger( __name__ ) - -metadata = MetaData( migrate_engine ) - -Page_table = Table( "page", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), - Column( "latest_revision_id", Integer, - ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), - Column( "title", TEXT ), - Column( "slug", TEXT, unique=True, index=True ), - ) - -PageRevision_table = Table( "page_revision", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), - Column( "title", TEXT ), - Column( "content", TEXT ) - ) - -def upgrade(): - metadata.reflect() - try: - Page_table.create() - except: - log.debug( "Could not create page table" ) - try: - PageRevision_table.create() - except: - log.debug( "Could not create page_revision table" ) - - # Add 1 column to the user table - User_table = Table( "galaxy_user", metadata, autoload=True ) - col = Column( 'username', String(255), index=True, unique=True, default=False ) - print type( col ), col - col.create( User_table ) - assert col is User_table.c.username - -def downgrade(): - metadata.reflect() - Page_table.drop() - PageRevision_table.drop() - User_table = Table( "galaxy_user", metadata, autoload=True ) - User_table.c.username.drop() \ No newline at end of file diff -r 36c479b93d7e -r 52a145b22b69 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sun Aug 23 12:28:36 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sun Aug 23 12:31:20 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util -import logging, os, string, re +import logging, os, string from random import choice log = logging.getLogger( __name__ ) @@ -19,8 +19,6 @@ """ require_login_nocreation_template = require_login_template % "" require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." - -VALID_USERNAME_RE = re.compile( "^[a-zA-Z0-9\-\_]+$" ) class User( BaseController ): edit_address_id = None @@ -80,37 +78,6 @@ .add_text( "email", "Email", value=email, error=email_err ) .add_text( "conf_email", "Confirm Email", value='', error=conf_email_err ) .add_password( "password", "Password", value='', error=pass_err ) ) - - @web.expose - def change_username(self, trans, username='', **kwd): - username_err = '' - user = trans.get_user() - if not user: - trans.response.send_redirect( web.url_for( action='login' ) ) - if trans.request.method == "POST": - if len( username ) < 4: - username_err = "Username must be at least 4 characters in length" - elif len( username ) > 255: - username_err = "USername must be at most 255 characters in length" - elif not( VALID_USERNAME_RE.match( username ) ): - username_err = "Username must contain only letters, numbers, '-', and '_'" - elif trans.app.model.User.filter_by( username=username ).first(): - username_err = "This username is not available" - else: - user.username = username - user.flush() - trans.log_event( "User change username" ) - return trans.show_ok_message( "Username been set to: " + user.username ) - else: - username = user.username or '' - return trans.show_form( - web.FormBuilder( web.url_for(), "Change username", submit_text="Submit" ) - .add_text( "username", "Username", value=username, error=username_err, - help="""Your username is an optional identifier that - will be used to generate adresses for information - you share publicly. Usernames must be at least - four characters in length and contain only letters, - numbers, and the '-' and '_' characters""" ) ) @web.expose def login( self, trans, email='', password='' ): diff -r 36c479b93d7e -r 52a145b22b69 templates/user/index.mako --- a/templates/user/index.mako Sun Aug 23 12:28:36 2009 -0400 +++ b/templates/user/index.mako Sun Aug 23 12:31:20 2009 -0400 @@ -9,7 +9,6 @@ <ul> <li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li> <li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li> - <li><a href="${h.url_for( action='change_username' )}">${_('Change your public username')}</a></li> <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li> <li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li>

1 0

[hg] galaxy 2609: Fix security problem with grids. Template shou...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/36c479b93d7e changeset: 2609:36c479b93d7e user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:28:36 2009 -0400 description: Fix security problem with grids. Template should not be passed at call time, it must be passed at configure time. 6 file(s) affected in this change: lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/framework/helpers/grids.py manage_db.sh templates/grid.mako diffs (325 lines): diff -r 19b86ccccf6f -r 36c479b93d7e lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Sun Aug 23 12:28:36 2009 -0400 @@ -39,6 +39,7 @@ # Grid definition title = "Stored histories" model_class = model.History + template='/history/grid.mako' default_sort_key = "-create_time" columns = [ grids.GridColumn( "Name", key="name", @@ -86,6 +87,7 @@ return history.user.email # Grid definition title = "Histories shared with you by others" + template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" columns = [ @@ -161,7 +163,7 @@ status, message = self._list_undelete( trans, histories ) trans.sa_session.flush() # Render the list view - return self.stored_list_grid( trans, status=status, message=message, template='/history/grid.mako', **kwargs ) + return self.stored_list_grid( trans, status=status, message=message, **kwargs ) def _list_delete( self, trans, histories ): """Delete histories""" n_deleted = 0 @@ -240,14 +242,14 @@ if operation == "clone": if not id: message = "Select a history to clone" - return self.shared_list_grid( trans, status='error', message=message, template='/history/grid.mako', **kwargs ) + return self.shared_list_grid( trans, status='error', message=message, **kwargs ) # When cloning shared histories, only copy active datasets new_kwargs = { 'clone_choice' : 'active' } return self.clone( trans, id, **new_kwargs ) elif operation == 'unshare': if not id: message = "Select a history to unshare" - return self.shared_list_grid( trans, status='error', message=message, template='/history/grid.mako', **kwargs ) + return self.shared_list_grid( trans, status='error', message=message, **kwargs ) ids = util.listify( id ) histories = [] for history_id in ids: @@ -261,7 +263,7 @@ message = "Unshared %d shared histories" % len( ids ) status = 'done' # Render the list view - return self.shared_list_grid( trans, status=status, message=message, template='/history/grid.mako', **kwargs ) + return self.shared_list_grid( trans, status=status, message=message, **kwargs ) @web.expose def delete_current( self, trans ): """Delete just the active history -- this does not require a logged in user.""" diff -r 19b86ccccf6f -r 36c479b93d7e lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Sun Aug 23 12:28:36 2009 -0400 @@ -16,6 +16,7 @@ class RequestsListGrid( grids.Grid ): title = "Sequencing Requests" + template = '/requests/grid.mako' model_class = model.Request default_sort_key = "-create_time" show_filter = model.Request.states.UNSUBMITTED @@ -103,7 +104,7 @@ self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.UNSUBMITTED) # Render the list view - return self.request_grid( trans, template='/requests/grid.mako', **kwargs ) + return self.request_grid( trans, **kwargs ) def __show_request(self, trans, id, add_sample=False): try: diff -r 19b86ccccf6f -r 36c479b93d7e lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Sun Aug 23 12:28:36 2009 -0400 @@ -14,6 +14,7 @@ class RequestsListGrid( grids.Grid ): title = "Sequencing Requests" + template = "admin/requests/grid.mako" model_class = model.Request default_sort_key = "-create_time" show_filter = model.Request.states.SUBMITTED @@ -101,7 +102,7 @@ self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) # Render the list view - return self.request_grid( trans, template='/admin/requests/grid.mako', **kwargs ) + return self.request_grid( trans, **kwargs ) @web.expose @web.require_admin def edit(self, trans, **kwd): diff -r 19b86ccccf6f -r 36c479b93d7e lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Sun Aug 23 12:28:36 2009 -0400 @@ -14,8 +14,9 @@ title = "" exposed = True model_class = None - template = None + template = "grid.mako" columns = [] + operations = [] standard_filters = [] default_filter = None default_sort_key = None @@ -25,7 +26,6 @@ def __call__( self, trans, **kwargs ): status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) - template = kwargs.get( 'template', None ) session = trans.sa_session # Build initial query query = self.build_initial_query( session ) @@ -77,7 +77,7 @@ else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - return trans.fill_template( template, + return trans.fill_template( self.template, grid=self, query=query, sort_key=sort_key, diff -r 19b86ccccf6f -r 36c479b93d7e templates/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/grid.mako Sun Aug 23 12:28:36 2009 -0400 @@ -0,0 +1,196 @@ +<%inherit file="/base.mako"/> +<%def name="title()">${grid.title}</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + </script> +</%def> + +<%def name="stylesheets()"> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +<div class="grid-header"> + <h2>${grid.title}</h2> + %if grid.standard_filters: + <span class="title">Filter:</span> + %for i, filter in enumerate( grid.standard_filters ): + %if i > 0: + <span>|</span> + %endif + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endfor + %endif +</div> + + +<form action="${url()}" method="post" > + <table class="grid"> + <thead> + <tr> + <th></th> + %for column in grid.columns: + %if column.visible: + <% + href = "" + extra = "" + if column.sortable: + if sort_key == column.key: + if sort_order == "asc": + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + %> + <th\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${extra}</span> + </th> + %endif + %endfor + <th></th> + </tr> + </thead> + <tbody> + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Item selection column + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i + else: + extra = "" + %> + %if href: + <td><div class="menubutton split"><a class="label" href="${href}">${v}${extra}</a></td> + %else: + <td >${v}${extra}</td> + %endif + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> + <tfoot> + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected items: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> + </table> +</form>

1 0

[hg] galaxy 2608: [mq]: pages
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/19b86ccccf6f changeset: 2608:19b86ccccf6f user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:26:46 2009 -0400 description: [mq]: pages 5 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0014_pages.py lib/galaxy/web/controllers/user.py templates/user/index.mako diffs (220 lines): diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/model/__init__.py Sun Aug 23 12:26:46 2009 -0400 @@ -33,6 +33,7 @@ self.external = False self.deleted = False self.purged = False + self.username = None # Relationships self.histories = [] @@ -1118,7 +1119,20 @@ self.country+'<br/>'+ \ 'Phone: '+self.phone +class Page( object ): + def __init__( self ): + self.id = None + self.user = None + self.title = None + self.slug = None + self.latest_revision_id = None + self.revisions = [] +class PageRevision( object ): + def __init__( self ): + self.user = None + self.title = None + self.content = None diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/model/mapping.py Sun Aug 23 12:26:46 2009 -0400 @@ -42,6 +42,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), + Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -523,6 +524,26 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) +Page.table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), + Column( "title", TEXT ), + Column( "slug", TEXT, unique=True, index=True ), + ) + +PageRevision.table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -905,6 +926,18 @@ assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) +assign_mapper( context, PageRevision, PageRevision.table ) + +assign_mapper( context, Page, Page.table, + properties=dict( user=relation( User ), + revisions=relation( PageRevision, backref='page', + cascade="all, delete-orphan", + primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), + latest_revision=relation( PageRevision, post_update=True, + primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), + lazy=False ) + ) ) + def db_next_hid( self ): """ Override __next_hid to generate from the database in a concurrency diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/model/migrate/versions/0014_pages.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0014_pages.py Sun Aug 23 12:26:46 2009 -0400 @@ -0,0 +1,56 @@ +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +Page_table = Table( "page", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), + Column( "latest_revision_id", Integer, + ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), + Column( "title", TEXT ), + Column( "slug", TEXT, unique=True, index=True ), + ) + +PageRevision_table = Table( "page_revision", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), + Column( "title", TEXT ), + Column( "content", TEXT ) + ) + +def upgrade(): + metadata.reflect() + try: + Page_table.create() + except: + log.debug( "Could not create page table" ) + try: + PageRevision_table.create() + except: + log.debug( "Could not create page_revision table" ) + + # Add 1 column to the user table + User_table = Table( "galaxy_user", metadata, autoload=True ) + col = Column( 'username', String(255), index=True, unique=True, default=False ) + print type( col ), col + col.create( User_table ) + assert col is User_table.c.username + +def downgrade(): + metadata.reflect() + Page_table.drop() + PageRevision_table.drop() + User_table = Table( "galaxy_user", metadata, autoload=True ) + User_table.c.username.drop() \ No newline at end of file diff -r 77b761ff6cd3 -r 19b86ccccf6f lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sun Aug 23 09:22:19 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sun Aug 23 12:26:46 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util -import logging, os, string +import logging, os, string, re from random import choice log = logging.getLogger( __name__ ) @@ -19,6 +19,8 @@ """ require_login_nocreation_template = require_login_template % "" require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." + +VALID_USERNAME_RE = re.compile( "^[a-zA-Z0-9\-\_]+$" ) class User( BaseController ): edit_address_id = None @@ -78,6 +80,37 @@ .add_text( "email", "Email", value=email, error=email_err ) .add_text( "conf_email", "Confirm Email", value='', error=conf_email_err ) .add_password( "password", "Password", value='', error=pass_err ) ) + + @web.expose + def change_username(self, trans, username='', **kwd): + username_err = '' + user = trans.get_user() + if not user: + trans.response.send_redirect( web.url_for( action='login' ) ) + if trans.request.method == "POST": + if len( username ) < 4: + username_err = "Username must be at least 4 characters in length" + elif len( username ) > 255: + username_err = "USername must be at most 255 characters in length" + elif not( VALID_USERNAME_RE.match( username ) ): + username_err = "Username must contain only letters, numbers, '-', and '_'" + elif trans.app.model.User.filter_by( username=username ).first(): + username_err = "This username is not available" + else: + user.username = username + user.flush() + trans.log_event( "User change username" ) + return trans.show_ok_message( "Username been set to: " + user.username ) + else: + username = user.username or '' + return trans.show_form( + web.FormBuilder( web.url_for(), "Change username", submit_text="Submit" ) + .add_text( "username", "Username", value=username, error=username_err, + help="""Your username is an optional identifier that + will be used to generate adresses for information + you share publicly. Usernames must be at least + four characters in length and contain only letters, + numbers, and the '-' and '_' characters""" ) ) @web.expose def login( self, trans, email='', password='' ): diff -r 77b761ff6cd3 -r 19b86ccccf6f templates/user/index.mako --- a/templates/user/index.mako Sun Aug 23 09:22:19 2009 -0400 +++ b/templates/user/index.mako Sun Aug 23 12:26:46 2009 -0400 @@ -9,6 +9,7 @@ <ul> <li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li> <li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li> + <li><a href="${h.url_for( action='change_username' )}">${_('Change your public username')}</a></li> <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li> <li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li>

1 0

[hg] galaxy 2607: Fix clone history tests
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/77b761ff6cd3 changeset: 2607:77b761ff6cd3 user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 09:22:19 2009 -0400 description: Fix clone history tests 1 file(s) affected in this change: templates/history/clone.mako diffs (12 lines): diff -r e6dda627e6b0 -r 77b761ff6cd3 templates/history/clone.mako --- a/templates/history/clone.mako Sat Aug 22 23:20:09 2009 -0400 +++ b/templates/history/clone.mako Sun Aug 23 09:22:19 2009 -0400 @@ -8,7 +8,7 @@ <form action="${h.url_for( controller='history', action='clone' )}" method="post" > <div class="form-row"> %if id_argument is not None: - <input type="hidden" name="id" value="${trans.security.encode_id( id_argument )}"> + <input type="hidden" name="id" value="${id_argument}"> %endif You can clone the history such that the clone will include all items in the original history, or you can eliminate the original history's deleted items from the clone.

1 0

[hg] galaxy 2610: Backed out changeset 19b86ccccf6f (not quite r...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3e9b7ec9a305 changeset: 2610:3e9b7ec9a305 user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:31:05 2009 -0400 description: Backed out changeset 19b86ccccf6f (not quite ready yet) 5 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0014_pages.py lib/galaxy/web/controllers/user.py templates/user/index.mako diffs (220 lines): diff -r 19b86ccccf6f -r 3e9b7ec9a305 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/model/__init__.py Sun Aug 23 12:31:05 2009 -0400 @@ -33,7 +33,6 @@ self.external = False self.deleted = False self.purged = False - self.username = None # Relationships self.histories = [] @@ -1119,20 +1118,7 @@ self.country+'<br/>'+ \ 'Phone: '+self.phone -class Page( object ): - def __init__( self ): - self.id = None - self.user = None - self.title = None - self.slug = None - self.latest_revision_id = None - self.revisions = [] -class PageRevision( object ): - def __init__( self ): - self.user = None - self.title = None - self.content = None diff -r 19b86ccccf6f -r 3e9b7ec9a305 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/model/mapping.py Sun Aug 23 12:31:05 2009 -0400 @@ -42,7 +42,6 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "email", TrimmedString( 255 ), nullable=False ), - Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), @@ -524,26 +523,6 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) -Page.table = Table( "page", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), - Column( "latest_revision_id", Integer, - ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), - Column( "title", TEXT ), - Column( "slug", TEXT, unique=True, index=True ), - ) - -PageRevision.table = Table( "page_revision", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), - Column( "title", TEXT ), - Column( "content", TEXT ) - ) - # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -926,18 +905,6 @@ assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) -assign_mapper( context, PageRevision, PageRevision.table ) - -assign_mapper( context, Page, Page.table, - properties=dict( user=relation( User ), - revisions=relation( PageRevision, backref='page', - cascade="all, delete-orphan", - primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), - latest_revision=relation( PageRevision, post_update=True, - primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), - lazy=False ) - ) ) - def db_next_hid( self ): """ Override __next_hid to generate from the database in a concurrency diff -r 19b86ccccf6f -r 3e9b7ec9a305 lib/galaxy/model/migrate/versions/0014_pages.py --- a/lib/galaxy/model/migrate/versions/0014_pages.py Sun Aug 23 12:26:46 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -from sqlalchemy import * -from migrate import * -from migrate.changeset import * - -import datetime -now = datetime.datetime.utcnow - -import logging -log = logging.getLogger( __name__ ) - -metadata = MetaData( migrate_engine ) - -Page_table = Table( "page", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), - Column( "latest_revision_id", Integer, - ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), - Column( "title", TEXT ), - Column( "slug", TEXT, unique=True, index=True ), - ) - -PageRevision_table = Table( "page_revision", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), - Column( "title", TEXT ), - Column( "content", TEXT ) - ) - -def upgrade(): - metadata.reflect() - try: - Page_table.create() - except: - log.debug( "Could not create page table" ) - try: - PageRevision_table.create() - except: - log.debug( "Could not create page_revision table" ) - - # Add 1 column to the user table - User_table = Table( "galaxy_user", metadata, autoload=True ) - col = Column( 'username', String(255), index=True, unique=True, default=False ) - print type( col ), col - col.create( User_table ) - assert col is User_table.c.username - -def downgrade(): - metadata.reflect() - Page_table.drop() - PageRevision_table.drop() - User_table = Table( "galaxy_user", metadata, autoload=True ) - User_table.c.username.drop() \ No newline at end of file diff -r 19b86ccccf6f -r 3e9b7ec9a305 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sun Aug 23 12:26:46 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sun Aug 23 12:31:05 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util -import logging, os, string, re +import logging, os, string from random import choice log = logging.getLogger( __name__ ) @@ -19,8 +19,6 @@ """ require_login_nocreation_template = require_login_template % "" require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." - -VALID_USERNAME_RE = re.compile( "^[a-zA-Z0-9\-\_]+$" ) class User( BaseController ): edit_address_id = None @@ -80,37 +78,6 @@ .add_text( "email", "Email", value=email, error=email_err ) .add_text( "conf_email", "Confirm Email", value='', error=conf_email_err ) .add_password( "password", "Password", value='', error=pass_err ) ) - - @web.expose - def change_username(self, trans, username='', **kwd): - username_err = '' - user = trans.get_user() - if not user: - trans.response.send_redirect( web.url_for( action='login' ) ) - if trans.request.method == "POST": - if len( username ) < 4: - username_err = "Username must be at least 4 characters in length" - elif len( username ) > 255: - username_err = "USername must be at most 255 characters in length" - elif not( VALID_USERNAME_RE.match( username ) ): - username_err = "Username must contain only letters, numbers, '-', and '_'" - elif trans.app.model.User.filter_by( username=username ).first(): - username_err = "This username is not available" - else: - user.username = username - user.flush() - trans.log_event( "User change username" ) - return trans.show_ok_message( "Username been set to: " + user.username ) - else: - username = user.username or '' - return trans.show_form( - web.FormBuilder( web.url_for(), "Change username", submit_text="Submit" ) - .add_text( "username", "Username", value=username, error=username_err, - help="""Your username is an optional identifier that - will be used to generate adresses for information - you share publicly. Usernames must be at least - four characters in length and contain only letters, - numbers, and the '-' and '_' characters""" ) ) @web.expose def login( self, trans, email='', password='' ): diff -r 19b86ccccf6f -r 3e9b7ec9a305 templates/user/index.mako --- a/templates/user/index.mako Sun Aug 23 12:26:46 2009 -0400 +++ b/templates/user/index.mako Sun Aug 23 12:31:05 2009 -0400 @@ -9,7 +9,6 @@ <ul> <li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li> <li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li> - <li><a href="${h.url_for( action='change_username' )}">${_('Change your public username')}</a></li> <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li> <li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li>

1 0

[hg] galaxy 2606: Merge
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e6dda627e6b0 changeset: 2606:e6dda627e6b0 user: James Taylor <james(a)jamestaylor.org> date: Sat Aug 22 23:20:09 2009 -0400 description: Merge 2 file(s) affected in this change: templates/base_panels.mako templates/history/grid.mako diffs (2711 lines): diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Sat Aug 22 23:20:09 2009 -0400 @@ -9,6 +9,7 @@ from migrate.changeset import * import sys, logging from galaxy.model.custom_types import * +from sqlalchemy.exceptions import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Sat Aug 22 23:20:09 2009 -0400 @@ -1534,10 +1534,19 @@ child_dataset.flush() child_dataset.set_size() child_dataset.name = "Secondary Dataset (%s)" % ( designation ) - child_dataset.state = child_dataset.states.OK child_dataset.init_meta() child_dataset.set_meta() child_dataset.set_peek() + # Associate new dataset with job + job = None + for assoc in outdata.creating_job_associations: + job = assoc.job + break + if job: + assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset ) + assoc.job = job + assoc.flush() + child_dataset.state = outdata.state child_dataset.flush() # Add child to return dict children[name][designation] = child_dataset @@ -1550,7 +1559,7 @@ def collect_primary_datasets( self, output): primary_datasets = {} - #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension' + #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' for name, outdata in output.items(): for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ): if not name in primary_datasets: @@ -1563,19 +1572,32 @@ if visible == "visible": visible = True else: visible = False ext = fields.pop(0).lower() + dbkey = outdata.dbkey + if fields: + dbkey = fields[ 0 ] # Create new primary dataset - primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True ) + primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=dbkey, create_dataset=True ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, primary_data.dataset ) primary_data.flush() # Move data from temp location to dataset location shutil.move( filename, primary_data.file_name ) primary_data.set_size() - primary_data.name = dataset.name - primary_data.info = dataset.info - primary_data.state = primary_data.states.OK - primary_data.init_meta( copy_from=dataset ) + primary_data.name = outdata.name + primary_data.info = outdata.info + primary_data.init_meta( copy_from=outdata ) + primary_data.dbkey = dbkey primary_data.set_meta() primary_data.set_peek() + # Associate new dataset with job + job = None + for assoc in outdata.creating_job_associations: + job = assoc.job + break + if job: + assoc = self.app.model.JobToOutputDatasetAssociation( '__new_primary_file_%s|%s__' % ( name, designation ), primary_data ) + assoc.job = job + assoc.flush() + primary_data.state = outdata.state primary_data.flush() outdata.history.add_dataset( primary_data ) # Add dataset to return dict diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Sat Aug 22 23:20:09 2009 -0400 @@ -20,12 +20,10 @@ for upload_dataset in incoming['files']: f = upload_dataset['file_data'] if isinstance( f, FieldStorage ): - # very small files can be StringIOs - if 'name' in dir( f.file ) and f.file.name != '<fdopen>': - local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' ) - f.file.close() - else: - local_filename = datatypes.sniff.stream_to_file( f.file, prefix="strio_upload_file_" )[0] + assert not isinstance( f.file, StringIO.StringIO ) + assert f.file.name != '<fdopen>' + local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' ) + f.file.close() upload_dataset['file_data'] = dict( filename = f.filename, local_filename = local_filename ) if upload_dataset['url_paste'].strip() != '': diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Sat Aug 22 23:20:09 2009 -0400 @@ -242,6 +242,55 @@ rval.append( add_value ) return rval +class RemoveValueFilter( Filter ): + """ + Removes a value from an options list. + + Type: remove_value + + Required Attributes: + value: value to remove from select list + or + ref: param to refer to + or + meta_ref: dataset to refer to + key: metadata key to compare to + """ + def __init__( self, d_option, elem ): + Filter.__init__( self, d_option, elem ) + self.value = elem.get( "value", None ) + self.ref_name = elem.get( "ref", None ) + self.meta_ref = elem.get( "meta_ref", None ) + self.metadata_key = elem.get( "key", None ) + assert self.value is not None or ( ( self.ref_name is not None or self.meta_ref is not None )and self.metadata_key is not None ), ValueError( "Required 'value' or 'ref' and 'key' attributes missing from filter" ) + self.multiple = string_as_bool( elem.get( "multiple", "False" ) ) + self.separator = elem.get( "separator", "," ) + def filter_options( self, options, trans, other_values ): + if trans is not None and trans.workflow_building_mode: return options + assert self.value is not None or ( self.ref_name is not None and self.ref_name in other_values ) or (self.meta_ref is not None and self.meta_ref in other_values ) or ( trans is not None and trans.workflow_building_mode), Exception( "Required dependency '%s' or '%s' not found in incoming values" % ( self.ref_name, self.meta_ref ) ) + def compare_value( option_value, filter_value ): + if isinstance( filter_value, list ): + if self.multiple: + option_value = option_value.split( self.separator ) + for value in filter_value: + if value not in filter_value: + return False + return True + return option_value in filter_value + if self.multiple: + return filter_value in option_value.split( self.separator ) + return option_value == filter_value + value = self.value + if value is None: + if self.ref_name is not None: + value = other_values.get( self.ref_name ) + else: + data_ref = other_values.get( self.meta_ref ) + if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ): + return options #cannot modify options + value = data_ref.metadata.get( self.metadata_key, None ) + return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] + class SortByColumnFilter( Filter ): """ Sorts an options list by a column @@ -274,6 +323,7 @@ unique_value = UniqueValueFilter, multiple_splitter = MultipleSplitterFilter, add_value = AdditionalValueFilter, + remove_value = RemoveValueFilter, sort_by = SortByColumnFilter ) class DynamicOptions( object ): diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Sat Aug 22 23:20:09 2009 -0400 @@ -764,11 +764,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -965,11 +961,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -1220,11 +1212,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -2027,7 +2015,7 @@ num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) proceed = True for i in range( num_states ): - if not util.restore_text( params.get( 'new_element_name_%i' % i, None ) ): + if not util.restore_text( params.get( 'state_name_%i' % i, None ) ): proceed = False break if not proceed: @@ -2045,8 +2033,8 @@ ss.delete() ss.flush() for i in range( num_states ): - name = util.restore_text( params.get( 'new_element_name_%i' % i, None )) - desc = util.restore_text( params.get( 'new_element_description_%i' % i, None )) + name = util.restore_text( params.get( 'state_name_%i' % i, None )) + desc = util.restore_text( params.get( 'state_desc_%i' % i, None )) ss = trans.app.model.SampleState(name, desc, rt) ss.flush() msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Sat Aug 22 23:20:09 2009 -0400 @@ -175,7 +175,7 @@ 'visible': True, 'required': False, 'type': BaseField.form_field_types()[0], - 'selectlist': '' } + 'selectlist': [] } self.current_form['fields'].append(empty_field) def __get_field(self, index, **kwd): params = util.Params( kwd ) @@ -183,10 +183,10 @@ # To reproduce, create a new form, click the "add field" button, click the # browser back arrow, then click the "add field" button again. # You should never attempt to "restore_text()" on a None object... - name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) - helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) + name = util.restore_text( params.get( 'field_name_%i' % index, '' ) ) + helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) ) required = params.get( 'field_required_%i' % index, False ) - field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) ) + field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(index, **kwd) return {'label': name, @@ -419,22 +419,39 @@ else: fdc_list = trans.app.model.FormDefinitionCurrent.query().all() return [ fdc.latest_form for fdc in fdc_list ] -def get_form_widgets( trans, form, contents={} ): + + +def get_form_widgets( trans, form, contents=[], user=None, **kwd ): ''' Return the list of widgets that comprise a form definition, including field contents if any. ''' + params = util.Params( kwd ) + if not user: + user = trans.user widgets = [] for index, field in enumerate( form.fields ): field_name = 'field_%i' % index - if field_name in contents: - value = contents[ field_name ] - elif field[ 'type' ] == 'CheckboxField': - # Since we do not have contents, set checkbox value to False - value = False + # determine the value of the field + if field_name in kwd: + # the user had already filled out this field and the same form is re-rendered + # due to some reason like required fields have been left out. + if field[ 'type' ] == 'CheckboxField': + value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) + else: + value = util.restore_text( params.get( field_name, '' ) ) + elif contents: + # this field has a saved value + value = str(contents[ index ]) else: - # Set other field types to empty string - value = '' + # if none of the above, then leave the field empty + if field[ 'type' ] == 'CheckboxField': + # Since we do not have contents, set checkbox value to False + value = False + else: + # Set other field types to empty string + value = '' + # create the field widget field_widget = eval( field[ 'type' ] )( field_name ) if field[ 'type' ] == 'TextField': field_widget.set_size( 40 ) @@ -442,6 +459,10 @@ elif field[ 'type' ] == 'TextArea': field_widget.set_size( 3, 40 ) field_widget.value = value + elif field['type'] == 'AddressField': + field_widget.user = user + field_widget.value = value + field_widget.params = params elif field[ 'type' ] == 'SelectField': for option in field[ 'selectlist' ]: if option == value: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Sat Aug 22 23:20:09 2009 -0400 @@ -137,11 +137,7 @@ # See if we have any field contents info = library.info_association[0].info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -475,11 +471,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -996,11 +988,7 @@ # See if we have any field contents info = info_association.info if info: - field_contents = {} - for index, value in enumerate( info.content ): - key = 'field_%i' % index - field_contents[ key ] = value - widgets = get_form_widgets( trans, template, field_contents ) + widgets = get_form_widgets( trans, template, info.content ) else: widgets = get_form_widgets( trans, template ) else: @@ -1173,3 +1161,13 @@ edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) + + +def get_authorized_libs(trans, user): + all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + authorized_libraries = [] + for library in all_libraries: + if trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \ + or trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library): + authorized_libraries.append(library) + return authorized_libraries \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Sat Aug 22 23:20:09 2009 -0400 @@ -8,6 +8,8 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from cgi import escape, FieldStorage +from galaxy.web.controllers.forms import get_form_widgets +from galaxy.web.controllers.library import get_authorized_libs log = logging.getLogger( __name__ ) @@ -62,18 +64,12 @@ request_grid = RequestsListGrid() @web.expose + @web.require_login( "create/submit sequencing requests" ) def index( self, trans ): return trans.fill_template( "requests/index.mako" ) - - def get_authorized_libs(self, trans): - all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() - authorized_libraries = [] - for library in all_libraries: - if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \ - or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library): - authorized_libraries.append(library) - return authorized_libraries + @web.expose + @web.require_login( "create/submit sequencing requests" ) def list( self, trans, **kwargs ): ''' List all request made by the current user @@ -137,7 +133,6 @@ Shows the request details ''' request = trans.app.model.Request.get(id) - libraries = self.get_authorized_libs(trans) # list of widgets to be rendered on the request form request_details = [] # main details @@ -146,6 +141,9 @@ helptext='')) request_details.append(dict(label='Type', value=request.type.name, + helptext='')) + request_details.append(dict(label='State', + value=request.state, helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -201,6 +199,7 @@ copy_list.add_option(s[0], i) return copy_list @web.expose + @web.require_login( "create/submit sequencing requests" ) def show_request(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -326,6 +325,7 @@ @web.expose + @web.require_login( "create/submit sequencing requests" ) def delete_sample(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -348,6 +348,7 @@ edit_mode=self.edit_mode) @web.expose + @web.require_login( "create/submit sequencing requests" ) def toggle_request_details(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -384,6 +385,7 @@ select_reqtype.add_option(rt.name, rt.id) return select_reqtype @web.expose + @web.require_login( "create/submit sequencing requests" ) def new(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -413,8 +415,8 @@ if params.get('create_request_button', False) == 'Save': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - msg=msg , - messagetype='done') ) + message=msg , + status='done') ) elif params.get('create_request_samples_button', False) == 'Add samples': new_kwd = {} new_kwd['id'] = trans.security.encode_id(request.id) @@ -457,12 +459,10 @@ helptext='(Optional)')) # libraries selectbox - libraries = self.get_authorized_libs(trans) + libraries = get_authorized_libs(trans, trans.user) libui = self.__library_ui(libraries, **kwd) widgets = widgets + libui - widgets = self.__create_form(trans, request_type.request_form_id, widgets, - form_values, **kwd) - title = 'Add a new request of type: %s' % request_type.name + widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], **kwd) return trans.fill_template( '/requests/new_request.mako', select_request_type=select_request_type, request_type=request_type, @@ -502,58 +502,13 @@ return [widget, new_lib] else: return [widget] - - def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd): - # TODO: RC - replace this method by importing as follows: - # from galaxy.web.controllers.forms import get_form_widgets - params = util.Params( kwd ) - form = trans.app.model.FormDefinition.get(form_id) - # form fields - for index, field in enumerate(form.fields): - # value of the field - if field['type'] == 'CheckboxField': - value = util.restore_text( params.get( 'field_%i' % index, False ) ) - else: - value = util.restore_text( params.get( 'field_%i' % index, '' ) ) - if not value: - if form_values: - value = str(form_values.content[index]) - # create the field - fw = eval(field['type'])('field_%i' % index) - if field['type'] == 'TextField': - fw.set_size(40) - fw.value = value - elif field['type'] == 'TextArea': - fw.set_size(3, 40) - fw.value = value - elif field['type'] == 'AddressField': - fw.user = trans.user - fw.value = value - fw.params = params - elif field['type'] == 'SelectField': - for option in field['selectlist']: - if option == value: - fw.add_option(option, option, selected=True) - else: - fw.add_option(option, option) - elif field['type'] == 'CheckboxField': - fw.checked = value - # require/optional - if field['required'] == 'required': - req = 'Required' - else: - req = 'Optional' - widgets.append(dict(label=field['label'], - widget=fw, - helptext=field['helptext']+' ('+req+')')) - return widgets def __validate(self, trans, request): ''' Validates the request entered by the user ''' empty_fields = [] - if not request.library: - empty_fields.append('Data library') +# if not request.library: +# empty_fields.append('Data library') # check rest of the fields of the form for index, field in enumerate(request.type.request_form.fields): if field['required'] == 'required' and request.values.content[index] in ['', None]: @@ -622,6 +577,7 @@ request.flush() return request @web.expose + @web.require_login( "create/submit sequencing requests" ) def edit(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -698,11 +654,10 @@ helptext='(Optional)')) # libraries selectbox - libraries = self.get_authorized_libs(trans) + libraries = get_authorized_libs(trans, trans.user) libui = self.__library_ui(libraries, request, **kwd) widgets = widgets + libui - widgets = self.__create_form(trans, request.type.request_form_id, widgets, - request.values, **kwd) + widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, **kwd) return trans.fill_template( '/requests/edit_request.mako', select_request_type=select_request_type, request_type=request.type, @@ -735,6 +690,8 @@ kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', action='list', + status='done', + message='The request <b>%s</b> has been deleted.' % request.name, **kwd) ) def __undelete_request(self, trans, id): try: @@ -754,6 +711,8 @@ kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', action='list', + status='done', + message='The request <b>%s</b> has been undeleted.' % request.name, **kwd) ) def __submit(self, trans, id): try: @@ -784,10 +743,14 @@ request.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name return trans.response.send_redirect( web.url_for( controller='requests', action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) @web.expose + @web.require_login( "create/submit sequencing requests" ) def submit_request(self, trans, **kwd): params = util.Params( kwd ) try: @@ -817,13 +780,16 @@ # change request's submitted field request.state = request.states.SUBMITTED request.flush() - ## TODO kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name return trans.response.send_redirect( web.url_for( controller='requests', action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) @web.expose + @web.require_login( "create/submit sequencing requests" ) def show_events(self, trans, **kwd): params = util.Params( kwd ) try: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Sat Aug 22 23:20:09 2009 -0400 @@ -7,19 +7,20 @@ import logging, tempfile, zipfile, tarfile, os, sys from galaxy.web.form_builder import * from datetime import datetime, timedelta +from galaxy.web.controllers.forms import get_form_widgets +from galaxy.web.controllers.library import get_authorized_libs log = logging.getLogger( __name__ ) - -# States for passing messages -SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" class RequestsListGrid( grids.Grid ): title = "Sequencing Requests" model_class = model.Request default_sort_key = "-create_time" + show_filter = model.Request.states.SUBMITTED columns = [ grids.GridColumn( "Name", key="name", - link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) )), + link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), + attach_popup=True ), grids.GridColumn( "Description", key="desc"), grids.GridColumn( "Sample(s)", method='number_of_samples', link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), @@ -30,15 +31,18 @@ ] operations = [ -# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), -# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ), + grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Delete", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), ] standard_filters = [ + grids.GridColumnFilter( model.Request.states.UNSUBMITTED, + args=dict( state=model.Request.states.UNSUBMITTED, deleted=False ) ), grids.GridColumnFilter( model.Request.states.SUBMITTED, args=dict( state=model.Request.states.SUBMITTED, deleted=False ) ), grids.GridColumnFilter( model.Request.states.COMPLETE, args=dict( state=model.Request.states.COMPLETE, deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted=False ) ) ] def get_user(self, trans, request): @@ -48,9 +52,9 @@ def get_request_type(self, trans, request): request_type = trans.app.model.RequestType.get(request.request_type_id) return request_type.name - def apply_default_filter( self, trans, query ): - return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, - self.model_class.state==self.model_class.states.COMPLETE)) +# def apply_default_filter( self, trans, query ): +# return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, +# self.model_class.state==self.model_class.states.COMPLETE)) def number_of_samples(self, trans, request): return str(len(request.samples)) @@ -67,32 +71,277 @@ ''' List all request made by the current user ''' - status = message = None + message = util.restore_text( kwargs.get( 'message', '' ) ) + status = kwargs.get( 'status', 'done' ) self.request_grid.default_filter = dict(state=trans.app.model.Request.states.SUBMITTED, deleted=False) if 'operation' in kwargs: operation = kwargs['operation'].lower() if operation == "show_request": id = trans.security.decode_id(kwargs['id']) - return self.__show_request(trans, id) - + return self.__show_request(trans, id, status, message) + elif operation == "submit": + id = trans.security.decode_id(kwargs['id']) + return self.__submit(trans, id) + elif operation == "edit": + id = trans.security.decode_id(kwargs['id']) + return self.__edit_request(trans, id) + elif operation == "delete": + id = trans.security.decode_id(kwargs['id']) + return self.__delete_request(trans, id) + elif operation == "undelete": + id = trans.security.decode_id(kwargs['id']) + return self.__undelete_request(trans, id) if 'show_filter' in kwargs.keys(): if kwargs['show_filter'] == 'All': - self.request_grid.default_filter = dict(deleted=False) + self.request_grid.default_filter = {} + elif kwargs['show_filter'] == 'Deleted': + self.request_grid.default_filter = dict(deleted=True) else: - self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) + self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) + self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) # Render the list view return self.request_grid( trans, template='/admin/requests/grid.mako', **kwargs ) - def __show_request(self, trans, id): + @web.expose + @web.require_admin + def edit(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('show', False) == 'True': + return self.__edit_request(trans, request.id, **kwd) + elif params.get('save_changes_request_button', False) == 'Save changes' \ + or params.get('edit_samples_button', False) == 'Edit samples': + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if not util.restore_text(params.get('name', '')): + msg = 'Please enter the <b>Name</b> of the request' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['show'] = 'True' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + **kwd) ) + request = self.__save_request(trans, request, **kwd) + msg = 'The changes made to the request named %s has been saved' % request.name + if params.get('save_changes_request_button', False) == 'Save changes': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done') ) + elif params.get('edit_samples_button', False) == 'Edit samples': + new_kwd = {} + new_kwd['request_id'] = request.id + new_kwd['edit_samples_button'] = 'Edit samples' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_request', + msg=msg , + messagetype='done', + **new_kwd) ) + elif params.get('refresh', False) == 'true': + return self.__edit_request(trans, request.id, **kwd) + def __edit_request(self, trans, id, **kwd): try: request = trans.app.model.Request.get(id) except: - return trans.response.send_redirect( web.url_for( controller='requests', + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg) ) + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + select_request_type = self.__select_request_type(trans, request.type.id) + # list of widgets to be rendered on the request form + widgets = [] + if util.restore_text( params.get( 'name', '' ) ): + name = util.restore_text( params.get( 'name', '' ) ) + else: + name = request.name + widgets.append(dict(label='Name', + widget=TextField('name', 40, name), + helptext='(Required)')) + if util.restore_text( params.get( 'desc', '' ) ): + desc = util.restore_text( params.get( 'desc', '' ) ) + else: + desc = request.desc + widgets.append(dict(label='Description', + widget=TextField('desc', 40, desc), + helptext='(Optional)')) + # libraries selectbox + libui = self.__library_ui(trans, request.user, request, **kwd) + widgets = widgets + libui + widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, request.user, **kwd) + return trans.fill_template( '/admin/requests/edit_request.mako', + select_request_type=select_request_type, + request_type=request.type, + request=request, + widgets=widgets, + msg=msg, + messagetype=messagetype) + return self.__show_request_form(trans) + def __delete_request(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # change request's submitted field + if not request.unsubmitted(): + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message='This request cannot be deleted as it is already been submitted', + **kwd) ) + request.deleted = True + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + status='done', + message='The request <b>%s</b> has been deleted.' % request.name, + **kwd) ) + def __undelete_request(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # change request's submitted field + request.deleted = False + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + status='done', + message='The request <b>%s</b> has been undeleted.' % request.name, + **kwd) ) + def __submit(self, trans, id): + try: + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + msg = self.__validate(trans, request) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + messagetype = 'error', + msg=msg, + request_id=request.id, + show='True') ) + # get the new state + new_state = request.type.states[0] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') + event.flush() + # change request's submitted field + request.state = request.states.SUBMITTED + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, + **kwd) ) + @web.expose + @web.require_admin + def submit_request(self, trans, **kwd): + params = util.Params( kwd ) + try: + id = int(params.get('id', False)) + request = trans.app.model.Request.get(id) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + msg = self.__validate(trans, request) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + messagetype='error', + msg=msg, + request_id=request.id, + show='True') ) + # get the new state + new_state = request.type.states[0] + for s in request.samples: + event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') + event.flush() + # change request's submitted field + request.state = request.states.SUBMITTED + request.flush() + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.SUBMITTED, + **kwd) ) + def __copy_sample(self): + copy_list = SelectField('copy_sample') + copy_list.add_option('None', -1, selected=True) + for i, s in enumerate(self.current_samples): + copy_list.add_option(s[0], i) + return copy_list + def __update_samples(self, request, **kwd): + params = util.Params( kwd ) + num_samples = len(self.current_samples) + self.current_samples = [] + for s in request.samples: + self.current_samples.append([s.name, s.values.content]) + for index in range(num_samples-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + self.current_samples.append([sample_name, sample_values]) + def __show_request(self, trans, id, messagetype, msg): + try: + request = trans.app.model.Request.get(id) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", **kwd) ) self.current_samples = [] + self.edit_mode = False for s in request.samples: self.current_samples.append([s.name, s.values.content]) self.details_state = 'Show request details' @@ -100,8 +349,163 @@ request=request, request_details=self.request_details(trans, id), current_samples = self.current_samples, - details_state=self.details_state) + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode, + msg=msg, messagetype=messagetype) @web.expose + @web.require_admin + def show_request(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.app.model.Request.get(int(params.get('request_id', None))) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('import_samples_button', False) == 'Import samples': + try: + file_obj = params.get('file_data', '') + import csv + reader = csv.reader(file_obj.file) + for row in reader: + self.current_samples.append([row[0], row[1:]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + operation='show_request', + id=trans.security.encode_id(request.id), + message='Error in importing samples from the given file.', + **kwd)) + elif params.get('add_sample_button', False) == 'Add New': + # save the all (saved+unsaved) sample info in 'current_samples' + self.__update_samples(request, **kwd) + # add an empty or filled sample + # if the user has selected a sample no. to copy then copy the contents + # of the src sample to the new sample else an empty sample + src_sample_index = int(params.get( 'copy_sample', -1 )) + if src_sample_index == -1: + # empty sample + self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]]) + else: + self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1), + [val for val in self.current_samples[src_sample_index][1]]]) + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + elif params.get('save_samples_button', False) == 'Save': + # update current_samples + self.__update_samples(request, **kwd) + # check for duplicate sample names + msg = '' + for index in range(len(self.current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = self.current_samples[sample_index][0] + if not sample_name.strip(): + msg = 'Please enter the name of sample number %i' % sample_index + break + count = 0 + for i in range(len(self.current_samples)): + if sample_name == self.current_samples[i][0]: + count = count + 1 + if count > 1: + msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + break + if msg: + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = self.current_samples, + sample_copy=self.__copy_sample(), details_state=self.details_state, + messagetype='error', msg=msg) + # save all the new/unsaved samples entered by the user + if not self.edit_mode: + for index in range(len(self.current_samples)-len(request.samples)): + sample_index = index + len(request.samples) + sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) + form_values.flush() + s = trans.app.model.Sample(sample_name, '', request, form_values) + s.flush() + else: + for index in range(len(self.current_samples)): + sample_index = index + sample_name = self.current_samples[sample_index][0] + new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) + sample_values = [] + for field_index in range(len(request.type.sample_form.fields)): + sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) + sample = request.has_sample(sample_name) + if sample: + form_values = trans.app.model.FormValues.get(sample.values.id) + form_values.content = sample_values + form_values.flush() + sample.name = new_sample_name + sample.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + elif params.get('edit_samples_button', False) == 'Edit samples': + self.edit_mode = True + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples=self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + elif params.get('cancel_changes_button', False) == 'Cancel': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) + + + @web.expose + @web.require_admin + def delete_sample(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request = trans.app.model.Request.get(int(params.get('request_id', 0))) + sample_index = int(params.get('sample_id', 0)) + sample_name = self.current_samples[sample_index][0] + s = request.has_sample(sample_name) + if s: + s.delete() + s.flush() + request.flush() + del self.current_samples[sample_index] + return trans.fill_template( '/admin/requests/show_request.mako', + request=request, + request_details=self.request_details(trans, request.id), + current_samples = self.current_samples, + sample_copy=self.__copy_sample(), + details_state=self.details_state, + edit_mode=self.edit_mode) + + @web.expose + @web.require_admin def toggle_request_details(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -128,24 +532,28 @@ # list of widgets to be rendered on the request form request_details = [] # main details + request_details.append(dict(label='User', + value=str(request.user.email), + helptext='')) request_details.append(dict(label='Description', value=request.desc, helptext='')) request_details.append(dict(label='Type', value=request.type.name, helptext='')) + request_details.append(dict(label='State', + value=request.state, + helptext='')) request_details.append(dict(label='Date created', value=request.create_time, helptext='')) - request_details.append(dict(label='Date updated', - value=request.create_time, - helptext='')) - request_details.append(dict(label='User', - value=str(request.user.email), - helptext='')) # library associated + if request.library: + value=request.library.name + else: + value = None request_details.append(dict(label='Data library', - value=trans.app.model.Library.get(request.library_id).name, + value=value, helptext='Data library where the resultant dataset will be stored')) # form fields for index, field in enumerate(request.type.request_form.fields): @@ -167,15 +575,262 @@ value=request.values.content[index], helptext=field['helptext']+' ('+req+')')) return request_details + + def __select_request_type(self, trans, rtid): + rt_ids = ['none'] + for rt in trans.app.model.RequestType.query().all(): + if not rt.deleted: + rt_ids.append(str(rt.id)) + select_reqtype = SelectField('select_request_type', + refresh_on_change=True, + refresh_on_change_values=rt_ids[1:]) + if rtid == 'none': + select_reqtype.add_option('Select one', 'none', selected=True) + else: + select_reqtype.add_option('Select one', 'none') + for rt in trans.app.model.RequestType.query().all(): + if not rt.deleted: + if rtid == rt.id: + select_reqtype.add_option(rt.name, rt.id, selected=True) + else: + select_reqtype.add_option(rt.name, rt.id) + return select_reqtype + @web.expose + @web.require_admin + def new(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('select_request_type', False) == 'True': + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=self.__select_request_type(trans, 'none'), + widgets=[], + msg=msg, + messagetype=messagetype) + elif params.get('create', False) == 'True': + if params.get('create_request_button', False) == 'Save' \ + or params.get('create_request_samples_button', False) == 'Add samples': + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if not util.restore_text(params.get('name', '')) \ + or util.restore_text(params.get('select_user', '')) == unicode('none'): + msg = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request' + kwd['create'] = 'True' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['create_request_button'] = None + kwd['create_request_samples_button'] = None + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='new', + **kwd) ) + request = self.__save_request(trans, None, **kwd) + msg = 'The new request named %s has been created' % request.name + if params.get('create_request_button', False) == 'Save': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + message=msg , + status='done') ) + elif params.get('create_request_samples_button', False) == 'Add samples': + new_kwd = {} + new_kwd['id'] = trans.security.encode_id(request.id) + new_kwd['operation'] = 'show_request' + new_kwd['add_sample'] = True + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done', + **new_kwd) ) + else: + return self.__show_request_form(trans, **kwd) + elif params.get('refresh', False) == 'true': + return self.__show_request_form(trans, **kwd) + def __show_request_form(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + except: + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=self.__select_request_type(trans, 'none'), + widgets=[], + msg=msg, + messagetype=messagetype) + form_values = None + select_request_type = self.__select_request_type(trans, request_type.id) + # user + user_id = params.get( 'select_user', 'none' ) + try: + user = trans.app.model.User.get(int(user_id)) + except: + user = None + # list of widgets to be rendered on the request form + widgets = [] + widgets.append(dict(label='Select user', + widget=self.__select_user(trans, user_id), + helptext='The request would be submitted on behalf of this user (Required)')) + widgets.append(dict(label='Name', + widget=TextField('name', 40, + util.restore_text( params.get( 'name', '' ) )), + helptext='(Required)')) + widgets.append(dict(label='Description', + widget=TextField('desc', 40, + util.restore_text( params.get( 'desc', '' ) )), + helptext='(Optional)')) + # libraries selectbox + libui = self.__library_ui(trans, user, **kwd) + widgets = widgets + libui + widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], user=user, **kwd) + return trans.fill_template( '/admin/requests/new_request.mako', + select_request_type=select_request_type, + request_type=request_type, + widgets=widgets, + msg=msg, + messagetype=messagetype) + def __select_user(self, trans, userid): + user_ids = ['none'] + for user in trans.app.model.User.query().all(): + if not user.deleted: + user_ids.append(str(user.id)) + select_user = SelectField('select_user', + refresh_on_change=True, + refresh_on_change_values=user_ids[1:]) + if userid == 'none': + select_user.add_option('Select one', 'none', selected=True) + else: + select_user.add_option('Select one', 'none') + for user in trans.app.model.User.query().all(): + if not user.deleted: + if userid == str(user.id): + select_user.add_option(user.email, user.id, selected=True) + else: + select_user.add_option(user.email, user.id) + return select_user + + def __library_ui(self, trans, user, request=None, **kwd): + params = util.Params( kwd ) + lib_id = params.get( 'library_id', 'none' ) + if not user: + libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all() + else: + libraries = get_authorized_libs(trans, user) + lib_list = SelectField('library_id', refresh_on_change=True, + refresh_on_change_values=['new']) + if request and lib_id == 'none': + if request.library: + lib_id = str(request.library.id) + if lib_id == 'none': + lib_list.add_option('Select one', 'none', selected=True) + else: + lib_list.add_option('Select one', 'none') + for lib in libraries: + if str(lib.id) == lib_id: + lib_list.add_option(lib.name, lib.id, selected=True) + else: + lib_list.add_option(lib.name, lib.id) + if lib_id == 'new': + lib_list.add_option('Create a new data library', 'new', selected=True) + else: + lib_list.add_option('Create a new data library', 'new') + widget = dict(label='Data library', + widget=lib_list, + helptext='Data library where the resultant dataset will be stored.') + if lib_id == 'new': + new_lib = dict(label='Create a new Library', + widget=TextField('new_library_name', 40, + util.restore_text( params.get( 'new_library_name', '' ) )), + helptext='Enter a library name here to request a new library') + return [widget, new_lib] + else: + return [widget] + def __validate(self, trans, request): + ''' + Validates the request entered by the user + ''' + empty_fields = [] +# if not request.library: +# empty_fields.append('Library') + # check rest of the fields of the form + for index, field in enumerate(request.type.request_form.fields): + if field['required'] == 'required' and request.values.content[index] in ['', None]: + empty_fields.append(field['label']) + if empty_fields: + msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + for ef in empty_fields: + msg = msg + '<b>' +ef + '</b><br/>' + return msg + return None + def __save_request(self, trans, request=None, **kwd): + ''' + This method saves a new request if request_id is None. + ''' + params = util.Params( kwd ) + request_type = trans.app.model.RequestType.get(int(params.select_request_type)) + if request: + user = request.user + else: + user = trans.app.model.User.get(int(params.get('select_user', ''))) + name = util.restore_text(params.get('name', '')) + desc = util.restore_text(params.get('desc', '')) + # library + try: + library = trans.app.model.Library.get(int(params.get('library_id', None))) + except: + library = None + # fields + values = [] + for index, field in enumerate(request_type.request_form.fields): + if field['type'] == 'AddressField': + value = util.restore_text(params.get('field_%i' % index, '')) + if value == 'new': + # save this new address in the list of this user's addresses + user_address = trans.app.model.UserAddress( user=user ) + user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, '')) + user_address.name = util.restore_text(params.get('field_%i_name' % index, '')) + user_address.institution = util.restore_text(params.get('field_%i_institution' % index, '')) + user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, '')) + user_address.city = util.restore_text(params.get('field_%i_city' % index, '')) + user_address.state = util.restore_text(params.get('field_%i_state' % index, '')) + user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) + user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) + user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) + user_address.flush() + trans.user.refresh() + values.append(int(user_address.id)) + elif value == unicode('none'): + values.append('') + else: + values.append(int(value)) + else: + values.append(util.restore_text(params.get('field_%i' % index, ''))) + form_values = trans.app.model.FormValues(request_type.request_form, values) + form_values.flush() + if not request: + request = trans.app.model.Request(name, desc, request_type, + user, form_values, + library=library, + state=trans.app.model.Request.states.UNSUBMITTED) + request.flush() + else: + request.name = name + request.desc = desc + request.type = request_type + request.user = user + request.values = form_values + request.library = library + request.flush() + return request @web.expose @web.require_admin def bar_codes(self, trans, **kwd): params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) request_id = params.get( 'request_id', None ) if request_id: request = trans.app.model.Request.get( int( request_id )) if not request: - return trans.response.send_redirect( web.url_for( controller='requests', + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", @@ -191,7 +846,9 @@ bc)) return trans.fill_template( '/admin/samples/bar_codes.mako', samples_list=[s for s in request.samples], - user=request.user, request=request, widgets=widgets) + user=request.user, request=request, widgets=widgets, + messagetype=messagetype, + msg=msg) @web.expose @web.require_admin def save_bar_codes(self, trans, **kwd): @@ -199,7 +856,7 @@ try: request = trans.app.model.Request.get(int(params.get('request_id', None))) except: - return trans.response.send_redirect( web.url_for( controller='requests', + return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', message="Invalid request ID", @@ -255,9 +912,10 @@ sample.bar_code = bar_code sample.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - operation='show_request', - id=trans.security.encode_id(request.id)) ) + action='bar_codes', + request_id=request.id, + msg='Bar codes has been saved for this request', + messagetype='done')) def __set_request_state(self, request): # check if all the samples of the current request are in the final state complete = True diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Sat Aug 22 23:20:09 2009 -0400 @@ -82,7 +82,7 @@ job = assoc.job break if not job: - raise Exception("Failed to get job information for dataset hid %d" % hid) + raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id try: diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Sat Aug 22 23:20:09 2009 -0400 @@ -229,6 +229,8 @@ def manage_addresses(self, trans, **kwd): if trans.user: params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) if show_filter == 'All': addresses = [address for address in trans.user.addresses] @@ -238,7 +240,9 @@ addresses = [address for address in trans.user.addresses if not address.deleted] return trans.fill_template( 'user/address.mako', addresses=addresses, - show_filter=show_filter) + show_filter=show_filter, + msg=msg, + messagetype=messagetype) else: # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Sat Aug 22 23:18:47 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Sat Aug 22 23:20:09 2009 -0400 @@ -216,11 +216,18 @@ # tempfiles. Necessary for externalizing the upload tool. It's a little hacky # but for performance reasons it's way better to use Paste's tempfile than to # create a new one and copy. -import cgi +import cgi, tempfile class FieldStorage( cgi.FieldStorage ): def make_file(self, binary=None): - import tempfile return tempfile.NamedTemporaryFile() + def read_lines(self): + # Always make a new file + self.file = self.make_file() + self.__file = None + if self.outerboundary: + self.read_lines_to_outerboundary() + else: + self.read_lines_to_eof() cgi.FieldStorage = FieldStorage class Request( webob.Request ): diff -r fbad627b45ac -r e6dda627e6b0 static/welcome.html --- a/static/welcome.html Sat Aug 22 23:18:47 2009 -0400 +++ b/static/welcome.html Sat Aug 22 23:20:09 2009 -0400 @@ -71,7 +71,7 @@ <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.flv',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie1_small.png" border="0"> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/forms/edit_form.mako --- a/templates/admin/forms/edit_form.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/forms/edit_form.mako Sat Aug 22 23:20:09 2009 -0400 @@ -70,7 +70,7 @@ </%def> <div class="toolForm"> - <div class="toolFormTitle">Edit form definition '${form.name}'</div> + <div class="toolFormTitle">Edit form definition "${form.name}"</div> <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" > %for label, input in form_details: <div class="form-row"> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/add_states.mako --- a/templates/admin/requests/add_states.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/add_states.mako Sat Aug 22 23:20:09 2009 -0400 @@ -12,9 +12,9 @@ %for element_count in range( num_states ): <div class="form-row"> <label>${1+element_count}) State name:</label> - <input type="text" name="new_element_name_${element_count}" value="" size="40"/> + <input type="text" name="state_name_${element_count}" value="" size="40"/> <label>State help text (optional):</label> - <input type="text" name="new_element_description_${element_count}" value="" size="40"/> + <input type="text" name="state_desc_${element_count}" value="" size="40"/> </div> <div style="clear: both"></div> %endfor diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/edit_request.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/edit_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,88 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#edit_request" ).submit(); + } + }); +}); +</script> + +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}"> + <span>Browse requests</span></a> + </li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div> + %if len(select_request_type.options) == 1: + There are no request types created for a new request. + %else: + <div class="toolFormBody"> + <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" > + <div class="form-row"> + <label> + Select Request Type: + </label> + ${select_request_type.get_html()} + </div> + + %if select_request_type.get_selected() != ('Select one', 'none'): + %for i, field in enumerate(widgets): + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + %if field['label'] == 'Library' and new_library: + ${new_library.get_html()} + %endif + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="save_changes_request_button" value="Save changes"/> + ##<input type="submit" name="edit_samples_button" value="Edit samples"/> + </div> + %endif + </form> + </div> +</div> +%endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/grid.mako --- a/templates/admin/requests/grid.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/grid.mako Sat Aug 22 23:20:09 2009 -0400 @@ -76,29 +76,28 @@ <div class="grid-header"> <h2>${grid.title}</h2> - ##%if len(query.all()): + %if len(trans.app.model.Request.query().all()): ##<span class="title">Filter:</span> %for i, filter in enumerate( grid.standard_filters ): %if i > 0: <span>|</span> %endif - %if 'state' in grid.default_filter: - %if grid.default_filter['state'] == filter.label: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> - %endif + %if grid.show_filter == filter.label: + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> %else: - %if filter.label == 'All': - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> - %endif + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span> %endif %endfor - ##%endif + %endif </div> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='new', select_request_type=True )}"> + <img src="${h.url_for('/static/images/silk/add.png')}" /> + <span>Create a new request</span></a> + </li> +</ul> %if not len(query.all()): There are no requests. diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/new_request.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/new_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,84 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#new_request" ).submit(); + } + }); +}); +</script> + +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}"> + <span>Browse requests</span></a> + </li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">Add a new request</div> + %if len(select_request_type.options) == 1: + There are no request types created for a new request. + %else: + <div class="toolFormBody"> + <form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" > + <div class="form-row"> + <label> + Select Request Type + </label> + ${select_request_type.get_html()} + </div> + + %if select_request_type.get_selected() != ('Select one', 'none'): + %for i, field in enumerate(widgets): + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + %if field['label'] == 'Library' and new_library: + ${new_library.get_html()} + %endif + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="create_request_button" value="Save"/> + <input type="submit" name="create_request_samples_button" value="Add samples"/> + </div> + %endif + </form> + </div> +</div> +%endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/requests/show_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -12,18 +12,49 @@ </div> <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> - <span>Bar codes</span></a> - </li> + %if request.unsubmitted() and request.samples: + <li> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='submit_request', id=request.id)}"> + <span>Submit request</span></a> + </li> + %endif + %if request.submitted() and request.samples: + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> + <span>Bar codes</span></a> + </li> + %endif </ul> + +<%def name="render_sample_form( index, sample_name, sample_values )"> + <td> + <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${' (required)' }</i> + </div> + </td> + <td> + </td> + %for field_index, field in enumerate(request.type.sample_form.fields): + <td> + <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${'('+field['required']+')' }</i> + </div> + </td> + %endfor +</%def> <%def name="render_sample( index, sample )"> <td> ${sample.name} </td> <td> - <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %if sample.request.unsubmitted(): + Unsubmitted + %else: + <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %endif </td> %for field_index, field in enumerate(request.type.sample_form.fields): <td> @@ -34,10 +65,10 @@ %endif </td> %endfor + </%def> <div class="toolForm"> - ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div> <div class="form-row"> <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a> </div> @@ -57,13 +88,21 @@ </div> <div style="clear: both"></div> %endfor + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}"> + <span>Edit request details</span></a> + </li> + </ul> + </div> %endif </div> </div> <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> - <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests', action='show_request', request_id=request.id )}" method="post" > + <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: <table class="grid"> @@ -80,22 +119,88 @@ </div> </th> %endfor + <th></th> </tr> <thead> <tbody> + <% + request.refresh() + %> %for sample_index, sample in enumerate(current_samples): - <tr> - <td>${sample_index+1}</td> - ${render_sample( sample_index, request.samples[sample_index] )} - </tr> + %if edit_mode: + <tr> + <td>${sample_index+1}</td> + ${render_sample_form( sample_index, sample[0], sample[1])} + </tr> + %else: + <tr> + <td>${sample_index+1}</td> + %if sample_index in range(len(request.samples)): + ${render_sample( sample_index, request.samples[sample_index] )} + %else: + ${render_sample_form( sample_index, sample[0], sample[1])} + %endif + <td> + %if request.unsubmitted(): + <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %endif %endfor </tbody> </table> %else: <label>There are no samples.</label> %endif - </div> - ##</div> + %if not edit_mode: + <table class="grid"> + <tbody> + <tr> + <div class="form-row"> + <td> + %if current_samples and not request.complete(): + <input type="submit" name="edit_samples_button" value="Edit samples"/> + %endif + </td> + %if request.unsubmitted(): + <td> + <label>Import from csv file</label> + <input type="file" name="file_data" /> + <input type="submit" name="import_samples_button" value="Import samples"/> + </td> + <td> + %if current_samples: + <label>Copy from sample</label> + ${sample_copy.get_html()} + %endif + <input type="submit" name="add_sample_button" value="Add New"/> + </td> + %endif + </div> + </tr> + </tbody> + </table> + %endif + %if request.samples or current_samples: + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="refresh" value="true" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + %if edit_mode: + <input type="submit" name="save_samples_button" value="Save"/> + <input type="submit" name="cancel_changes_button" value="Cancel"/> + %elif request.unsubmitted(): + <input type="submit" name="save_samples_button" value="Save"/> + %endif + </div> + %endif + <input type="hidden" name="request_id" value="${request.id}" /> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/bar_codes.mako --- a/templates/admin/samples/bar_codes.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/samples/bar_codes.mako Sat Aug 22 23:20:09 2009 -0400 @@ -40,7 +40,7 @@ </tbody> </table> <div class="form-row"> - <input type="submit" name="save_new_sample_type" value="Save"/> + <input type="submit" name="save_bar_codes" value="Save"/> </div> </form> </div> \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/events.mako --- a/templates/admin/samples/events.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/admin/samples/events.mako Sat Aug 22 23:20:09 2009 -0400 @@ -56,7 +56,7 @@ </div> %endfor <div class="form-row"> - <input type="submit" name="add_event" value="Save"/> + <input type="submit" name="add_event_button" value="Save"/> </div> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/base_panels.mako --- a/templates/base_panels.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/base_panels.mako Sat Aug 22 23:20:09 2009 -0400 @@ -138,7 +138,7 @@ ${tab( "libraries", "Data Libraries", h.url_for( controller='library', action='index' ))} - %if trans.request_types(): + %if trans.user and trans.request_types(): <td class="tab"> <a>Lab</a> <div class="submenu"> diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/grid.mako --- a/templates/requests/grid.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/requests/grid.mako Sat Aug 22 23:20:09 2009 -0400 @@ -76,7 +76,7 @@ <div class="grid-header"> <h2>${grid.title}</h2> - ##%if len(query.all()): + %if len(trans.user.requests): ##<span class="title">Filter:</span> %for i, filter in enumerate( grid.standard_filters ): %if i > 0: @@ -88,17 +88,16 @@ <span class="filter"><a href="${h.url_for( controller='requests', action='list', show_filter=filter.label )}">${filter.label}</a></span> %endif %endfor - ##%endif + %endif </div> <ul class="manage-table-actions"> <li> <a class="action-button" href="${h.url_for( controller='requests', action='new', select_request_type=True )}"> <img src="${h.url_for('/static/images/silk/add.png')}" /> - <span>New request</span></a> + <span>Create a new request</span></a> </li> </ul> - %if not len(query.all()): There are no request(s). @@ -215,4 +214,4 @@ </tfoot> </table> </form> -%endif \ No newline at end of file +%endif diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/requests/show_request.mako Sat Aug 22 23:20:09 2009 -0400 @@ -68,7 +68,6 @@ </%def> <div class="toolForm"> - ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div> <div class="form-row"> <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a> </div> @@ -217,7 +216,6 @@ %endif </div> %endif - ##</div> - <input type="hidden" name="request_id" value="${request.id}" /> + <input type="hidden" name="request_id" value="${request.id}" /> </form> </div> diff -r fbad627b45ac -r e6dda627e6b0 templates/user/address.mako --- a/templates/user/address.mako Sat Aug 22 23:18:47 2009 -0400 +++ b/templates/user/address.mako Sat Aug 22 23:20:09 2009 -0400 @@ -33,51 +33,48 @@ </div> - -<div class="toolForm"> - ##<div class="toolFormTitle">Addresses</div> - <div class="toolFormBody"> - <% trans.user.refresh() %> - %if not trans.user.addresses: - <label>There are no addresses</label> - %else: - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - - <td> - <div class="form-row"> - <label>${address.desc}</label> - ${address.display()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id, - short_desc=address.desc, - name=address.name, institution=address.institution, - address1=address.address, city=address.city, - state=address.state, postal_code=address.postal_code, - country=address.country, phone=address.phone)}"> - <span>Edit</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}"> - <span>Delete address</span></a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}"> - <span>Undelete address</span></a> - %endif - - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> - %endif +%if not addresses: + <label>There are no addresses</label> +%else: + <div class="toolForm"> + <div class="toolFormBody"> + <% trans.user.refresh() %> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}</label> + ${address.display()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id, + short_desc=address.desc, + name=address.name, institution=address.institution, + address1=address.address, city=address.city, + state=address.state, postal_code=address.postal_code, + country=address.country, phone=address.phone)}"> + <span>Edit</span></a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}"> + <span>Delete</span></a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}"> + <span>Undelete</span></a> + %endif + + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + </div> </div> -</div> %endif \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Sat Aug 22 23:18:47 2009 -0400 +++ b/test/base/twilltestcase.py Sat Aug 22 23:20:09 2009 -0400 @@ -972,7 +972,7 @@ self.home() # Form stuff - def create_form( self, name='Form One', description='This is Form One', num_fields=1 ): + def create_form( self, name='Form One', desc='This is Form One', num_fields=1 ): """ Create a new form definition. Testing framework is still limited to only testing one instance for each repeat. This has to do with the 'flat' nature of defining @@ -988,7 +988,7 @@ self.visit_url( "%s/forms/new" % self.url ) self.check_page_for_string( 'Create a new form definition' ) tc.fv( "1", "name", name ) # form field 1 is the field named name... - tc.fv( "1", "description", description ) # form field 1 is the field named name... + tc.fv( "1", "description", desc ) # form field 1 is the field named name... tc.submit( "create_form_button" ) for index in range( num_fields ): field_name = 'field_name_%i' % index @@ -1001,7 +1001,140 @@ check_str = "The form '%s' has been updated with the changes." % name self.check_page_for_string( check_str ) self.home() - + def edit_form( self, form_id, form_name, new_form_name="Form One's Name (Renamed)", new_form_desc="This is Form One's description (Re-described)"): + """ + Edit form details; name & description + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name ) + tc.fv( "1", "name", new_form_name ) + tc.fv( "1", "description", new_form_desc ) + tc.submit( "save_changes_button" ) + self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name ) + self.home() + def form_add_field( self, form_id, form_name, field_index, fields): + """ + Add a new fields to the form definition + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name) + for i, field in enumerate(fields): + index = i+field_index + tc.submit( "add_field_button" ) + tc.fv( "1", "field_name_%i" % index, field['name'] ) + tc.fv( "1", "field_helptext_%i" % index, field['desc'] ) + tc.fv( "1", "field_type_%i" % index, field['type'] ) + tc.fv( "1", "field_required_%i" % index, field['required'] ) +# if field['type'] == 'SelectField': +# for option_index, option in enumerate(field['selectlist']): +# self.visit_url( "%s/forms/edit?select_box_options=add&form_id=%i&field_index=%i" % \ +# (self.url, form_id, index)) +# #data = self.last_page() +# #file( "rc.html", 'wb' ).write(data) +# tc.fv( "1", "field_%i_option_%i" % (index, option_index), option ) + tc.submit( "save_changes_button" ) + check_str = "The form '%s' has been updated with the changes." % form_name + self.check_page_for_string( check_str ) + self.home() + def form_remove_field( self, form_id, form_name, field_name): + """ + Remove a field from the form definition + """ + self.home() + self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) ) + self.check_page_for_string( 'Edit form definition "%s"' % form_name) + tc.submit( "remove_button" ) + tc.submit( "save_changes_button" ) + check_str = "The form '%s' has been updated with the changes." % form_name + self.check_page_for_string( check_str ) + self.home() + # Requests stuff + def create_request_type( self, name, desc, request_form_id, sample_form_id, states ): + self.home() + self.visit_url( "%s/admin/request_type?create=True" % self.url ) + self.check_page_for_string( 'Create a new request type' ) + tc.fv( "1", "name", name ) + tc.fv( "1", "description", desc ) + tc.fv( "1", "request_form_id", request_form_id ) + tc.fv( "1", "sample_form_id", sample_form_id ) + tc.fv( "1", "num_states", str( len( states ) ) ) + tc.submit( "define_states_button" ) + self.check_page_for_string( "Create %i states for the '%s' request type" % ( len(states), name )) + for index, state in enumerate(states): + tc.fv("1", "state_name_%i" % index, state[0]) + tc.fv("1", "state_desc_%i" % index, state[1]) + tc.submit( "save_request_type" ) + self.check_page_for_string( "Request type <b>%s</b> has been created" % name ) + def create_request( self, request_type_id, name, desc, library_id, fields ): + self.home() + self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.check_page_for_string( 'Add a new request' ) + tc.fv( "1", "name", name ) + tc.fv( "1", "desc", desc ) + tc.fv( "1", "library_id", str(library_id) ) + for index, field_value in enumerate(fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "create_request_button" ) + def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ): + self.home() + self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) + self.check_page_for_string( 'Add a new request' ) + tc.fv( "1", "select_user", str(user_id) ) + tc.fv( "1", "name", name ) + tc.fv( "1", "desc", desc ) + tc.fv( "1", "library_id", str(library_id) ) + for index, field_value in enumerate(fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "create_request_button" ) + def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_fields): + self.home() + self.visit_url( "%s/requests/edit?request_id=%i&show=True" % (self.url, request_id) ) + self.check_page_for_string( 'Edit request "%s"' % name ) + tc.fv( "1", "name", new_name ) + tc.fv( "1", "desc", new_desc ) + tc.fv( "1", "library_id", str(new_library_id) ) + for index, field_value in enumerate(new_fields): + tc.fv( "1", "field_%i" % index, field_value ) + tc.submit( "save_changes_request_button" ) + def add_samples( self, request_id, request_name, samples ): + self.home() + self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + self.check_page_for_string( 'Sequencing Request "%s"' % request_name ) + for sample_index, sample in enumerate(samples): + tc.submit( "add_sample_button" ) + sample_name, fields = sample + tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + for field_index, field_value in enumerate(fields): + tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.submit( "save_samples_button" ) + def submit_request( self, request_id, request_name ): + self.home() + self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id )) + self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) + def add_bar_codes( self, request_id, request_name, bar_codes ): + self.home() + self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) ) + self.check_page_for_string( 'Bar codes for Samples of Request "%s"' % request_name ) + for index, bar_code in enumerate(bar_codes): + tc.fv( "1", "sample_%i_bar_code" % index, bar_code ) + tc.submit( "save_bar_codes" ) + def change_sample_state( self, sample_name, sample_id, new_state_id, comment='' ): + self.home() + self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) ) + self.check_page_for_string( 'Events for Sample "%s"' % sample_name ) + tc.fv( "1", "select_state", str(new_state_id) ) + tc.fv( "1", "comment", comment ) + tc.submit( "add_event_button" ) + # Address stuff + def create_address( self, address ): + self.home() + self.visit_url( "%s/user/new_address" % self.url ) + self.check_page_for_string( 'New address' ) + for name, value in address.iteritems(): + tc.fv( "1", name, value ) + tc.submit( "Save_button" ) # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_forms_and_requests.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/functional/test_forms_and_requests.py Sat Aug 22 23:20:09 2009 -0400 @@ -0,0 +1,274 @@ +import galaxy.model +from galaxy.model.orm import * +from base.twilltestcase import * + +not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.' +logged_in_as_admin_security_msg = 'You must be an administrator to access this feature.' +not_logged_in_security_msg = 'You must be logged in to create/submit sequencing requests' +form_one_name = "Request Form" +form_two_name = "Sample Form" +request_type_name = 'Test Requestype' +sample_states = [ ( 'New', 'Sample entered into the system' ), + ( 'Received', 'Sample tube received' ), + ( 'Done', 'Sequence run complete' ) ] +address1 = dict( short_desc="Office", + name="James Bond", + institution="MI6" , + address1="MI6 Headquaters", + address2="", + city="London", + state="London", + postal_code="007", + country="United Kingdom", + phone="007-007-0007" ) + + +def get_latest_form(form_name): + fdc_list = galaxy.model.FormDefinitionCurrent.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False )\ + .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) + for fdc in fdc_list: + if form_name == fdc.latest_form.name: + return fdc.latest_form + return None + + +class TestFormsAndRequests( TwillTestCase ): + def test_000_create_form( self ): + """Testing creating a new form and editing it""" + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # create a form + global form_one_name + name = form_one_name + desc = "This is Form One's description" + self.create_form( name=name, desc=desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + # Get the form_definition object for later tests + form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name, + galaxy.model.FormDefinition.table.c.desc==desc ) ).all()[-1] + assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name + # edit form & add few more fields + new_name = "Request Form (Renamed)" + new_desc = "This is Form One's Re-described" + self.edit_form( form_one.id, form_one.name, new_form_name=new_name, new_form_desc=new_desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( new_name ) + self.check_page_for_string( new_desc ) + form_one_name = new_name + def test_005_add_form_fields( self ): + """Testing adding fields to a form definition""" + fields = [dict(name='Test field name one', + desc='Test field description one', + type='TextField', + required='required'), + dict(name='Test field name two', + desc='Test field description two', + type='AddressField', + required='optional')] + form_one = get_latest_form(form_one_name) + self.form_add_field(form_one.id, form_one.name, field_index=len(form_one.fields), fields=fields) + form_one_latest = get_latest_form(form_one_name) + assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) +#This following test has been commented out as it is causing: +#TwillException: multiple matches to "remove_button" +# def test_010_remove_form_fields( self ): +# """Testing removing fields from a form definition""" +# form_one = get_latest_form(form_one_name) +# self.form_remove_field( form_one.id, form_one.name, 'Test field name one' ) +# form_one_latest = get_latest_form(form_one_name) +# assert len(form_one_latest.fields) == len(form_one.fields)-1 + def test_015_create_sample_form( self ): + """Testing creating another form (for samples)""" + global form_two_name + name = form_two_name + desc = "This is Form One's description" + self.create_form( name=name, desc=desc ) + self.home() + self.visit_page( 'forms/manage' ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + def test_020_create_request_type( self ): + """Testing creating a new requestype""" + request_form = get_latest_form(form_one_name) + sample_form = get_latest_form(form_two_name) + self.create_request_type(request_type_name, "test request type", + str(request_form.id), str(sample_form.id), sample_states ) + global request_type + request_type = galaxy.model.RequestType.filter( and_( galaxy.model.RequestType.table.c.name==request_type_name ) ).all()[-1] + assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name + def test_025_create_address_and_library( self ): + """Testing address & library creation""" + # first create a regular user + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # first create a library for the request so that it can be submitted later + lib_name = 'TestLib001' + self.create_library( lib_name, '' ) + self.visit_page( 'admin/browse_libraries' ) + self.check_page_for_string( lib_name ) + # Get the library object for later tests + global library_one + library_one = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==lib_name, + galaxy.model.Library.table.c.deleted==False ) ).first() + assert library_one is not None, 'Problem retrieving library named "%s" from the database' % lib_name + global admin_user + admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() + assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + # Get the admin user's private role for later use + global admin_user_private_role + admin_user_private_role = None + for role in admin_user.all_roles(): + if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email: + admin_user_private_role = role + break + if not admin_user_private_role: + raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) + global regular_user1 + regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + # Get the regular user's private role for later use + global regular_user1_private_role + regular_user1_private_role = None + for role in regular_user1.all_roles(): + if role.name == regular_user1.email and role.description == 'Private Role for %s' % regular_user1.email: + regular_user1_private_role = role + break + if not regular_user1_private_role: + raise AssertionError( "Private role not found for user '%s'" % regular_user1.email ) + # Set permissions on the library, sort for later testing + permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] + permissions_out = [] + # Role one members are: admin_user, regular_user1. Each of these users will be permitted to + # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items. + self.set_library_permissions( str( library_one.id ), library_one.name, str( regular_user1_private_role.id ), permissions_in, permissions_out ) + # create address + #self.create_address( user_address1 ) + #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] ) + ## TODO: FIX HACK + ## the user address creation should be done as a test. + global user_address + user_address = galaxy.model.UserAddress() + user_address.user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + user_address.desc = address1[ 'short_desc' ] + user_address.name = address1[ 'name' ] + user_address.institution = address1[ 'institution' ] + user_address.address = address1[ 'address1' ]+' '+address1[ 'address2' ] + user_address.city = address1[ 'city' ] + user_address.state = address1[ 'state' ] + user_address.postal_code = address1[ 'postal_code' ] + user_address.country = address1[ 'country' ] + user_address.phone = address1[ 'phone' ] + user_address.flush() + user_address.user.refresh() + def test_030_create_request( self ): + """Testing creating, editing and submitting a request as a regular user""" + # login as a regular user + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + # set field values + fields = ['field one value', 'field two value', str(user_address.id)] + # create the request + request_name, request_desc = 'Request One', 'Request One Description' + self.create_request(request_type.id, request_name, request_desc, library_one.id, fields) + self.check_page_for_string( request_name ) + self.check_page_for_string( request_desc ) + global request_one + request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, + galaxy.model.Request.table.c.deleted==False ) ).first() + # check if the request's state is now set to 'unsubmitted' + assert request_one.state is not request_one.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.UNSUBMITTED ) + # sample fields + samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), + ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] + # add samples to this request + self.add_samples( request_one.id, request_one.name, samples ) + for sample_name, fields in samples: + self.check_page_for_string( sample_name ) + self.check_page_for_string( 'Unsubmitted' ) + for field_value in fields: + self.check_page_for_string( field_value ) + # edit this request + fields = ['field one value (editted)', 'field two value (editted)', str(user_address.id)] + self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, fields) + request_one.refresh() + self.check_page_for_string( request_name+' (Renamed)' ) + self.check_page_for_string( request_desc+' (Re-described)' ) + # submit the request + self.submit_request( request_one.id, request_one.name ) + request_one.refresh() + # check if the request's state is now set to 'submitted' + assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.SUBMITTED ) + def test_035_request_lifecycle( self ): + """Testing request lifecycle as it goes through all the states""" + # goto admin manage requests page + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.home() + self.visit_page( 'requests_admin/list' ) + self.check_page_for_string( request_one.name ) + self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \ + % ( self.url, self.security.encode_id( request_one.id ) )) + self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name ) + # set bar codes for the samples + bar_codes = [ '1234567890', '0987654321' ] + self.add_bar_codes( request_one.id, request_one.name, bar_codes ) + self.check_page_for_string( 'Bar codes has been saved for this request' ) + # change the states of all the samples of this request + for sample in request_one.samples: + self.change_sample_state( sample.name, sample.id, request_type.states[1].id ) + self.check_page_for_string( request_type.states[1].name ) + self.check_page_for_string( request_type.states[1].desc ) + self.change_sample_state( sample.name, sample.id, request_type.states[2].id ) + self.check_page_for_string( request_type.states[2].name ) + self.check_page_for_string( request_type.states[2].desc ) + self.home() + request_one.refresh() + # check if the request's state is now set to 'complete' + assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE ) +# def test_40_admin_create_request_on_behalf_of_regular_user( self ): +# """Testing creating and submitting a request as an admin on behalf of a regular user""" +# self.logout() +# self.login( email='test(a)bx.psu.edu' ) +## permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] +## permissions_out = [] +## self.set_library_permissions( str( library_one.id ), library_one.name, str( admin_user_private_role.id ), permissions_in, permissions_out ) +# # set field values +# fields = ['field one value', 'field two value', str(user_address.id)] +# # create the request +# request_name, request_desc = 'Request Two', 'Request Two Description' +# self.create_request_admin(request_type.id, regular_user1.id, request_name, request_desc, library_one.id, fields) +# self.check_page_for_string( request_name ) +# self.check_page_for_string( request_desc ) +# global request_two +# request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, +# galaxy.model.Request.table.c.deleted==False ) ).first() +# # check if the request's state is now set to 'unsubmitted' +# assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.UNSUBMITTED ) +# # sample fields +# samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), +# ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] +# # add samples to this request +# self.add_samples( request_two.id, request_two.name, samples ) +# for sample_name, fields in samples: +# self.check_page_for_string( sample_name ) +# self.check_page_for_string( 'Unsubmitted' ) +# for field_value in fields: +# self.check_page_for_string( field_value ) +# # submit the request +# self.submit_request( request_two.id, request_two.name ) +# request_two.refresh() +# # check if the request's state is now set to 'submitted' +# assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.SUBMITTED ) + + + + + + + \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Sat Aug 22 23:18:47 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Sat Aug 22 23:20:09 2009 -0400 @@ -196,7 +196,7 @@ dhps.sort() # Compare DefaultHistoryPermissions and actions_in - should be the same if dhps != actions_in: - raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \ + raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \ % ( str( dhps ), latest_history.id, str( actions_in ) ) ) # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): @@ -209,7 +209,7 @@ dps.sort() # Compare DatasetPermissionss and DefaultHistoryPermissions - should be the same if dps != dhps: - raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \ + raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \ % ( str( dps ), latest_dataset.id, str( dhps ) ) ) self.logout() def test_020_create_new_user_account_as_admin( self ): diff -r fbad627b45ac -r e6dda627e6b0 tools/extract/liftOver_wrapper_code.py --- a/tools/extract/liftOver_wrapper_code.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/extract/liftOver_wrapper_code.py Sat Aug 22 23:20:09 2009 -0400 @@ -3,7 +3,6 @@ to_dbkey = param_dict['to_dbkey'].split('.')[0].split('To')[1] to_dbkey = to_dbkey[0].lower()+to_dbkey[1:] out_data['out_file1'].set_dbkey(to_dbkey) - out_data['out_file2'].set_dbkey(to_dbkey) out_data['out_file1'].name = out_data['out_file1'].name + " [ MAPPED COORDINATES ]" out_data['out_file2'].name = out_data['out_file2'].name + " [ UNMAPPED COORDINATES ]" diff -r fbad627b45ac -r e6dda627e6b0 tools/metag_tools/split_paired_reads.py --- a/tools/metag_tools/split_paired_reads.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.py Sat Aug 22 23:20:09 2009 -0400 @@ -1,7 +1,7 @@ #! /usr/bin/python """ -Split Solexa paired end reads +Split fixed length paired end reads """ import os, sys @@ -12,9 +12,13 @@ outfile_end1 = open(sys.argv[2], 'w') outfile_end2 = open(sys.argv[3], 'w') - for i, line in enumerate(file(infile)): + i = 0 + + for line in file( infile ): line = line.rstrip() - if not line or line.startswith('#'): continue + + if not line: + continue end1 = '' end2 = '' @@ -42,5 +46,9 @@ outfile_end1.write('%s\n' %(end1)) outfile_end2.write('%s\n' %(end2)) + i += 1 + + if i % 4 != 0 : + sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n") outfile_end1.close() outfile_end2.close() \ No newline at end of file diff -r fbad627b45ac -r e6dda627e6b0 tools/solid_tools/maq_cs_wrapper.py --- a/tools/solid_tools/maq_cs_wrapper.py Sat Aug 22 23:18:47 2009 -0400 +++ b/tools/solid_tools/maq_cs_wrapper.py Sat Aug 22 23:20:09 2009 -0400 @@ -48,9 +48,9 @@ cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname) try: os.system(cmd1) - os.system('zcat -f %s >> %s' %(tmpf.name,tmpffastq.name)) - os.system('zcat -f %s >> %s' %(tmpr.name,tmprfastq.name)) - os.system('zcat -f %s >> %s' %(tmps.name,tmpsfastq.name)) + os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name)) + os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name)) + os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name)) except Exception, eq: stop_err("Error converting data to fastq format." + str(eq)) @@ -135,7 +135,7 @@ cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None) try: os.system(cmd1) - os.system('zcat -f %s >> %s' %(tmpf.name,tmpfastq.name)) + os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name)) tmpf.close() except: stop_err("Error converting data to fastq format.")

1 0

[hg] galaxy 2604: Rework popup menu styles. Popups are now large...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/abdb523727ed changeset: 2604:abdb523727ed user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 06 10:29:51 2009 -0400 description: Rework popup menu styles. Popups are now larger, have borders, and have better highlight styles. The history options button is now a popup menu. (Also misc style fixes and improvements). 16 file(s) affected in this change: lib/galaxy/web/controllers/history.py static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/june_2007_style/blue/history-buttons.png static/june_2007_style/blue/history-states.png static/june_2007_style/blue/library.css static/june_2007_style/blue/panel_layout.css static/june_2007_style/blue_colors.ini static/june_2007_style/panel_layout.css.tmpl static/scripts/galaxy.base.js templates/base_panels.mako templates/history/clone.mako templates/history/grid.mako templates/root/index.mako templates/workflow/editor.mako templates/workflow/list.mako diffs (688 lines): diff -r 542471b183d7 -r abdb523727ed lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Aug 20 18:44:35 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Aug 06 10:29:51 2009 -0400 @@ -229,6 +229,7 @@ # No message return None, None @web.expose + @web.require_login( "work with shared histories" ) def list_shared( self, trans, **kwargs ): """List histories shared with current user by others""" msg = util.restore_text( kwargs.get( 'msg', '' ) ) @@ -617,6 +618,7 @@ if send_to_err: msg += send_to_err return self.sharing( trans, histories=shared_histories, msg=msg ) + @web.expose @web.require_login( "share histories with other users" ) def sharing( self, trans, histories=[], id=None, **kwd ): @@ -644,6 +646,7 @@ shared_msg = "History (%s) now shared with: %d users. " % ( history.name, len( history.users_shared_with ) ) msg = '%s%s' % ( shared_msg, msg ) return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='done' ) + @web.expose @web.require_login( "rename histories" ) def rename( self, trans, id=None, name=None, **kwd ): @@ -681,19 +684,26 @@ else: change_msg = change_msg + "<p>History: "+cur_names[i]+" does not appear to belong to you.</p>" return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) + @web.expose @web.require_login( "clone shared Galaxy history" ) - def clone( self, trans, id, **kwd ): + def clone( self, trans, id=None, **kwd ): """Clone a list of histories""" params = util.Params( kwd ) - ids = util.listify( id ) - histories = [] - for history_id in ids: - history = get_history( trans, history_id, check_ownership=False ) - histories.append( history ) + # If clone_choice was not specified, display form passing along id + # argument clone_choice = params.get( 'clone_choice', None ) if not clone_choice: - return trans.fill_template( "/history/clone.mako", history=history ) + return trans.fill_template( "/history/clone.mako", id_argument=id ) + # Extract histories for id argument, defaulting to current + if id is None: + histories = [ trans.history ] + else: + ids = util.listify( id ) + histories = [] + for history_id in ids: + history = get_history( trans, history_id, check_ownership=False ) + histories.append( history ) user = trans.get_user() for history in histories: if history.user == user: diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/base.css.tmpl Thu Aug 06 10:29:51 2009 -0400 @@ -2,6 +2,19 @@ body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,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{font-size:75%;} +## Mixins +.unselectable { + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +} + +.shadow { + -moz-box-shadow: 0 3px 30px black; + -webkit-box-shadow: 0 3px 30px black; +} + +## Real styles body { background: $base_bg_bottom; @@ -48,7 +61,7 @@ padding-left: 10px; padding-right: 10px; background: $form_title_bg_bottom; - background-image: url(form_title_bg.png); + ## background-image: url(form_title_bg.png); background-repeat: repeat-x; background-position: top; border-bottom: solid $form_border 1px; @@ -524,10 +537,11 @@ ## Button styles .action-button { - background: #eeeeee; + background: transparent; + line-height: 16px; color: #333; text-decoration: none; - font-size: 95%; + font-size: 100%; font-weight: bold; display: inline-block; cursor: pointer; @@ -556,39 +570,139 @@ background: #aaaaaa; } -## Popup menu styles +## A menu button is a button that has an attached popup menu -div.popupmenu { - display: none; - background: #eeeeee; - color: #333; - font-size: 110%; - font-weight: bold; - font-style: normal; - white-space: nowrap; - position: absolute; - z-index: 20000; - border: solid #aaaaaa 1px; - padding: 3px 0; +.menubutton { + display: inline-block; + cursor: pointer; + position: relative; + .unselectable; + + border: solid transparent 1px; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; + + padding: 3px 0.5em; + margin: -3px -0.5em; + padding-right: 1.5em; + + .label, .arrow { + position: relative; + display: block; + } + + .label { + border-right: none; + } + + .arrow { + padding-left: 2px; + width: 1em; + position: absolute; + top: 0; + right: 5px; + height: 100%; + } + + .arrow > span { + display: inline-block; + padding-top: 3px; + } + } -div.popupmenu-item { - padding: 3px 1em; - cursor: pointer; +.menubutton:hover { + border-color: #aaaaaa; + ## background: #eeeeee; + ## color: #333; } -div.popupmenu-item:hover { - background: #aaaaaa; +## A split menu button, the main button has an action, the arrow causes the +## popup menu to appear + +.menubutton.split { + padding-right: 2em; + .arrow { + border-left: solid transparent 1px; + } +} + +.menubutton.split:hover { + .arrow { + border-left: solid #aaaaaa 1px; + } +} + +## Popup menu styles + +.overlay-border { + position: absolute; + top: 0; + left: 0; + height: 100%; + width: 100%; + padding: 1em; + margin: -1em; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 1em; + -webkit-border-radius: 1em; + z-index: -1; +} + +div.popmenu-wrapper { + + position: absolute; + top: 100%; + z-index: 20000; + + ul { + + display: block; + margin: 0; + padding: 0; + + background: white; + color: #333; + font-weight: bold; + font-style: normal; + white-space: nowrap; + border: solid #aaaaaa 1px; + padding: 3px 0; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; + ## margin: -3px -0.5em; + ## min-width: 100%; + + .unselectable; + + li { + display: block; + padding: 3px 1em; + cursor: pointer; + border-top: solid transparent 1px; + border-bottom: solid transparent 1px; + } + + li.head { + color: #999; + font-style: italic; + } + } +} + +div.popmenu-wrapper ul li:hover { + background: #EEEEFF; + border-color: #aaa; +} + +div.popmenu-wrapper ul li.head:hover { + background: inherit; + border-color: transparent; } .popup-arrow { - font-size: 80%; cursor: pointer; text-decoration: none; color: #555; @@ -632,7 +746,7 @@ } .grid thead th { background: $table_header_bg; - background-image: url(form_title_bg.png); + ## background-image: url(form_title_bg.png); background-repeat: repeat-x; background-position: top; border-top: solid $table_border 1px; @@ -648,4 +762,4 @@ } .grid .current { background-color: #EEEEFF; -} \ No newline at end of file +} diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/blue/base.css Thu Aug 06 10:29:51 2009 -0400 @@ -3,13 +3,15 @@ table{font-size:inherit;font:100%;} pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} body{font-size:75%;} +.unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} +.shadow{-moz-box-shadow:0 3px 30px black;-webkit-box-shadow:0 3px 30px black;} body{background:#FFFFFF;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} a:link,a:visited,a:active{color:#303030;} h1,h2,h3,h4{color:#023858;} hr{border:none;height:0px;border-bottom:dotted #303030 1px;} div.toolForm{border:solid #d8b365 1px;} -div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#d2c099;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} +div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} div.toolParamHelp{color:#666;} div.toolParamHelp a{color:#666;} div.toolFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} @@ -20,7 +22,7 @@ div.toolHelpBody{width:100%;overflow:auto;} div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:0.5em;padding-bottom:0.25em;} 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-title{font-weight:bold;padding:5px 10px;background:#ebd9b2;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{padding:5px 10px;} div.form-title-row{padding:5px 10px;} @@ -77,14 +79,28 @@ .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:95%;font-weight:bold;display:inline-block;cursor:pointer;padding:2px;border:solid #aaaaaa 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} +.action-button{background:transparent;line-height:16px;color:#333;text-decoration:none;font-size:100%;font-weight:bold;display:inline-block;cursor:pointer;padding:2px;border:solid #aaaaaa 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} .action-button > *{vertical-align:middle;} .action-button:hover{color:black;background:#dddddd;} .action-button:active{color:white;background:#aaaaaa;} -div.popupmenu{display:none;background:#eeeeee;color:#333;font-size:110%;font-weight:bold;font-style:normal;white-space:nowrap;position:absolute;z-index:20000;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} -div.popupmenu-item{padding:3px 1em;cursor:pointer;} -div.popupmenu-item:hover{background:#aaaaaa;} -.popup-arrow{font-size:80%;cursor:pointer;text-decoration:none;color:#555;} +.menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;padding:3px 0.5em;margin:-3px -0.5em;padding-right:1.5em;} +.menubutton .label,.menubutton .arrow{position:relative;display:block;} +.menubutton .label{border-right:none;} +.menubutton .arrow{padding-left:2px;width:1em;position:absolute;top:0;right:5px;height:100%;} +.menubutton .arrow > span{display:inline-block;padding-top:3px;} +.menubutton:hover{border-color:#aaaaaa;} +.menubutton.split{padding-right:2em;} +.menubutton.split .arrow{border-left:solid transparent 1px;} +.menubutton.split:hover{} +.menubutton.split:hover .arrow{border-left:solid #aaaaaa 1px;} +.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} +div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;} +div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} +div.popmenu-wrapper ul li{display:block;padding:3px 1em;cursor:pointer;border-top:solid transparent 1px;border-bottom:solid transparent 1px;} +div.popmenu-wrapper ul li.head{color:#999;font-style:italic;} +div.popmenu-wrapper ul li:hover{background:#EEEEFF;border-color:#aaa;} +div.popmenu-wrapper ul li.head:hover{background:inherit;border-color:transparent;} +.popup-arrow{cursor:pointer;text-decoration:none;color:#555;} .popup-arrow:hover{color:black;} div.permissionContainer{padding-left:20px;} .grid-header{padding-bottom:1em;} @@ -93,6 +109,6 @@ .grid{padding-top:1em;border-collapse:collapse;width:100%;} .grid tbody td{border-top:solid #DDDDDD 1px;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);background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.5em 1em;text-align:left;} +.grid thead th{background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.5em 1em;text-align:left;} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.5em 1em;} .grid .current{background-color:#EEEEFF;} diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue/history-buttons.png Binary file static/june_2007_style/blue/history-buttons.png has changed diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue/history-states.png Binary file static/june_2007_style/blue/history-states.png has changed diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/blue/library.css Thu Aug 06 10:29:51 2009 -0400 @@ -1,4 +1,4 @@ -.libraryRow{background-color:#d2c099;} +.libraryRow{background-color:#ebd9b2;} .datasetHighlighted{background-color:#C1C9E5;} .libraryItemDeleted-True{font-style:italic;} div.historyItemBody{padding:4px 4px 2px 4px;} diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/blue/panel_layout.css Thu Aug 06 10:29:51 2009 -0400 @@ -24,7 +24,7 @@ .unified-panel-header-inner{padding-top:0.45em;} .menu-bg{background:#C1C9E5 url(menu_bg.png) top repeat-x;} div.unified-panel-body{position:absolute;top:2em;bottom:0;width:100%;margin-top:1px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;border:0px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;background:transparent;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;background:#bbb;} .panel-header-button:hover{color:black;background:#aaaaaa;} .panel-header-button:active{color:white;background:#aaaaaa;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} @@ -37,9 +37,8 @@ .panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;} .panel-info-message{background-image:url(info_small.png);background-color:#CCCCFF;} #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 a{color:#eeeeee;text-decoration:none;} #masthead .title{padding:3px 10px;font-size:175%;font-weight:bold;} -#masthead a{text-decoration:none;} #masthead a:hover{text-decoration:underline;} .tab-group{margin:0;padding:0 10px;height:100%;white-space:nowrap;cursor:default;background:transparent;} .tab-group .tab{background:#2C3143;position:relative;float:left;margin:0;padding:0 1em;height:32px;line-height:32px;text-align:left;} diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/blue_colors.ini --- a/static/june_2007_style/blue_colors.ini Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/blue_colors.ini Thu Aug 06 10:29:51 2009 -0400 @@ -9,7 +9,7 @@ #menu_bg_hatch=#AAAAFF # Forms form_title_bg_top=#ebd9b2 -form_title_bg_bottom=#d2c099 +form_title_bg_bottom=#ebd9b2 form_title_bg_hatch=- form_border=#d8b365 #form_body_bg=#FFFFFF diff -r 542471b183d7 -r abdb523727ed static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Thu Aug 20 18:44:35 2009 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Thu Aug 06 10:29:51 2009 -0400 @@ -144,13 +144,12 @@ display: inline-block; cursor: pointer; margin: -1px; padding: 1px; - border: 0px; padding-right: 0.5em; padding-left: 0.5em; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; - background: transparent; + background: #bbb; } .panel-header-button:hover { @@ -230,8 +229,7 @@ ## Masthead -#masthead -{ +#masthead { position:absolute; top:0; left:0; @@ -242,27 +240,20 @@ border-bottom: solid ${layout_masthead_border} 1px; z-index: 15000; padding: 0; + + a { + color: ${masthead_link}; + text-decoration: none; + } + + .title { + padding: 3px 10px; + font-size: 175%; + font-weight: bold; + } } -#masthead a -{ - color: $masthead_link; -} - -#masthead .title -{ - padding: 3px 10px; - font-size: 175%; - font-weight: bold; -} - -#masthead a -{ - text-decoration: none; -} - -#masthead a:hover -{ +#masthead a:hover { text-decoration: underline; } diff -r 542471b183d7 -r abdb523727ed static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Thu Aug 20 18:44:35 2009 -0400 +++ b/static/scripts/galaxy.base.js Thu Aug 06 10:29:51 2009 -0400 @@ -54,30 +54,52 @@ function make_popupmenu( button_element, options ) { ensure_popup_helper(); - $(button_element).css( "position", "relative" ); - var menu_element = $( "<div class='popupmenu' id='" + button_element.attr('id') + "-menu'></div>" ) - .css( "position", "absolute" ) - .appendTo( button_element ); + var container_element = $(button_element); + // if ( container_element.parent().hasClass( "combo-button" ) ) { + // container_element = container_element.parent(); + // } + // ontainer_element).css( "position", "relative" ); + var menu_element = $( "<ul id='" + button_element.attr('id') + "-menu'></div>" ); $.each( options, function( k, v ) { - $( "<div class='popupmenu-item' />" ).html( k ).click( v ).appendTo( menu_element ); + if ( v ) { + $( "<li/>" ).html( k ).click( v ).appendTo( menu_element ); + } else { + $( "<li class='head'/>" ).html( k ).appendTo( menu_element ); + } }); + var wrapper = $( "<div class='popmenu-wrapper'>" ); + wrapper.append( menu_element ) + .append( "<div class='overlay-border'>" ) + .css( "position", "absolute" ) + .appendTo( "body" ) + .hide(); + attach_popupmenu( button_element, wrapper ); +}; + +function attach_popupmenu( button_element, wrapper ) { + console.log( button_element, wrapper ); var clean = function() { - $(menu_element).unbind().hide(); - // $("#popup-helper").unbind().hide(); - $(document).unbind( "click.popupmenu" ); + wrapper.unbind().hide(); + $("#popup-helper").unbind( "click.popupmenu" ).hide(); + // $(document).unbind( "click.popupmenu" ); }; var click = function( e ) { + console.log( e ); var o = $(button_element).offset(); - // $("#popup-helper").mousedown( clean ).show(); - $(document).bind( "click.popupmenu", clean ); + $("#popup-helper").bind( "click.popupmenu", clean ).show(); + // $(document).bind( "click.popupmenu", clean ); // Show off screen to get size right - $( menu_element ).click( clean ).css( { left: 0, top: -1000 } ).show(); + wrapper.click( clean ).css( { left: 0, top: -1000 } ).show(); // console.log( e.pageX, $(document).scrollLeft() + $(window).width(), $(menu_element).width() ); - // var x = Math.min( e.pageX - 2, $(document).scrollLeft() + $(window).width() - $(menu_element).width() - 5 ); + var x = e.pageX - wrapper.width() / 2 + x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 20 ); + x = Math.max( x, $(document).scrollLeft() + 20 ); // console.log( e.pageX, $(document).scrollLeft() + $(window).width(), $(menu_element).width() ); - $( menu_element ).css( { - top: 0, //e.pageY - 2, - left: 0 // x + + + wrapper.css( { + top: e.pageY - 5, + left: x } ); return false; }; diff -r 542471b183d7 -r abdb523727ed templates/base_panels.mako --- a/templates/base_panels.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/base_panels.mako Thu Aug 06 10:29:51 2009 -0400 @@ -20,7 +20,7 @@ ## Default stylesheets <%def name="stylesheets()"> - ${h.css('panel_layout')} + ${h.css('base','panel_layout')} <style type="text/css"> #center { %if not self.has_left_panel: @@ -50,7 +50,7 @@ <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - ${h.js( 'jquery', 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'galaxy.panels' )} + ${h.js( 'jquery', 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'galaxy.base', 'galaxy.panels' )} <script type="text/javascript"> ensure_dd_helper(); diff -r 542471b183d7 -r abdb523727ed templates/history/clone.mako --- a/templates/history/clone.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/history/clone.mako Thu Aug 06 10:29:51 2009 -0400 @@ -7,7 +7,9 @@ <div class="toolFormBody"> <form action="${h.url_for( controller='history', action='clone' )}" method="post" > <div class="form-row"> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> + %if id_argument is not None: + <input type="hidden" name="id" value="${trans.security.encode_id( id_argument )}"> + %endif You can clone the history such that the clone will include all items in the original history, or you can eliminate the original history's deleted items from the clone. </div> diff -r 542471b183d7 -r abdb523727ed templates/history/grid.mako --- a/templates/history/grid.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/history/grid.mako Thu Aug 06 10:29:51 2009 -0400 @@ -153,16 +153,15 @@ <% # Attach popup menu? if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">▼</a>' % i + extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i else: extra = "" %> %if href: - <td><a href="${href}">${v}</a> ${extra}</td> + <td><div class="menubutton split"><a class="label" href="${href}">${v}${extra}</a></td> %else: <td >${v}${extra}</td> %endif - </td> %endfor %endif %endfor diff -r 542471b183d7 -r abdb523727ed templates/root/index.mako --- a/templates/root/index.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/root/index.mako Thu Aug 06 10:29:51 2009 -0400 @@ -1,4 +1,46 @@ <%inherit file="/base_panels.mako"/> + +<%def name="late_javascripts()"> + ${parent.late_javascripts()} + <script type="text/javascript"> + $(function(){ + $("#history-options-button").css( "position", "relative" ); + make_popupmenu( $("#history-options-button"), { + "List your histories": null, + "Stored by you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list')}"; + }, + "Shared with you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; + }, + "Current History": null, + "Create new": function() { + galaxy_history.location = "${h.url_for( controller='root', action='history_new' )}"; + }, + "Clone": function() { + galaxy_main.location = "${h.url_for( controller='history', action='clone')}"; + }, + "Manage sharing": function() { + galaxy_main.location = "${h.url_for( controller='history', action='share' )}"; + }, + "Extract workflow": function() { + galaxy_main.location = "${h.url_for( controller='workflow', action='build_from_current_history' )}"; + }, + "Dataset security": function() { + galaxy_main.location = "${h.url_for( controller='root', action='history_set_default_permissions' )}"; + }, + "Show deleted datasets": function() { + galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; + }, + "Delete": function() { + if ( confirm( "Really delete the current history?" ) ) { + galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; + } + } + }); + }); + </script> +</%def> <%def name="init()"> <% @@ -48,7 +90,7 @@ <div class="unified-panel-header" unselectable="on"> <div class="unified-panel-header-inner"> <div style="float: right"> - <a class='panel-header-button' href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"><span>${_('Options')}</span></a> + <a id="history-options-button" class='panel-header-button' href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"><span>${_('Options')}<span>▼</span></span></a> </div> <div class="panel-header-text">${_('History')}</div> </div> diff -r 542471b183d7 -r abdb523727ed templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/workflow/editor.mako Thu Aug 06 10:29:51 2009 -0400 @@ -677,9 +677,8 @@ <div class="unified-panel-header" unselectable="on"> <div class="unified-panel-header-inner" style="float: right"> - <span class="panel-header-button-group"> <a id="layout-button" class="panel-header-button">Layout</a> - </span> +    <a id="save-button" class="panel-header-button">Save</a> <a id="close-button" class="panel-header-button">Close</a> </div> diff -r 542471b183d7 -r abdb523727ed templates/workflow/list.mako --- a/templates/workflow/list.mako Thu Aug 20 18:44:35 2009 -0400 +++ b/templates/workflow/list.mako Thu Aug 06 10:29:51 2009 -0400 @@ -37,8 +37,10 @@ %for i, workflow in enumerate( workflows ): <tr> <td> + <div class="menubutton"> + <a id="wf-${i}-popup" class="arrow" style="display: none;"><span>▼</span></a> ${workflow.name} - <a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a> + </div> </td> <td>${len(workflow.latest_workflow.steps)}</td> ## <td>${str(workflow.update_time)[:19]}</td>

1 0

[hg] galaxy 2605: Fixing styles for history rename and share int...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fbad627b45ac changeset: 2605:fbad627b45ac user: James Taylor <james(a)jamestaylor.org> date: Sat Aug 22 23:18:47 2009 -0400 description: Fixing styles for history rename and share interfaces 6 file(s) affected in this change: static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/scripts/packed/galaxy.base.js templates/history/rename.mako templates/history/share.mako templates/root/index.mako diffs (390 lines): diff -r abdb523727ed -r fbad627b45ac static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Thu Aug 06 10:29:51 2009 -0400 +++ b/static/june_2007_style/base.css.tmpl Sat Aug 22 23:18:47 2009 -0400 @@ -3,6 +3,7 @@ body{font-size:75%;} ## Mixins + .unselectable { user-select: none; -moz-user-select: none; @@ -15,8 +16,8 @@ } ## Real styles -body -{ + +body { background: $base_bg_bottom; color: $base_text; background-image: url(base_bg.png); @@ -25,60 +26,55 @@ margin: 10px; } -img -{ +img { border: 0; } -a:link, a:visited, a:active -{ +a:link, a:visited, a:active { color: $link_text; } -h1, h2, h3, h4 -{ +h1, h2, h3, h4 { color: $header_text; /*text-shadow: #bbb 2px 2px 1px;*/ } -hr -{ +hr { border: none; height: 0px; border-bottom: dotted $base_text 1px; } -div.toolForm -{ - border: solid $form_border 1px; +th { + text-align: left; } -div.toolFormTitle -{ - font-weight: bold; - padding: 5px; - padding-left: 10px; - padding-right: 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.toolForm { + border: solid $form_border 1px; } -div.toolParamHelp -{ - color: #666; +div.toolFormTitle { + font-weight: bold; + padding: 5px; + padding-left: 10px; + padding-right: 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.toolParamHelp a -{ - color: #666; +div.toolParamHelp { + color: #666; } -div.toolFormBody -{ +div.toolParamHelp a { + color: #666; +} + +div.toolFormBody { background: $form_body_bg_bottom; background-image: url(form_body_bg.png); background-repeat: repeat-x; @@ -86,8 +82,7 @@ padding: 5px 0; } -div.toolFormBody div.toolFormTitle -{ +div.toolFormBody div.toolFormTitle { background: transparent; border: none; font-weight: bold; @@ -104,12 +99,10 @@ border-color: ${layout_border}; } -div.toolHelp -{ +div.toolHelp { } -div.toolHelpBody -{ +div.toolHelpBody { width: 100%; overflow: auto; } @@ -121,15 +114,13 @@ padding-bottom: 0.25em; } -/* Forms */ +## Forms -div.form -{ +div.form { border: solid $form_border 1px; } -div.form-title -{ +div.form-title { font-weight: bold; padding: 5px 10px; background: $form_title_bg_bottom; @@ -139,53 +130,44 @@ border-bottom: solid $form_border 1px; } -div.form-body -{ +div.form-body { padding: 5px 0; } -div.form-row -{ +div.form-row { padding: 5px 10px; } -div.form-title-row -{ +div.form-title-row { padding: 5px 10px; } -div.repeat-group-item -{ +div.repeat-group-item { border-left: solid $form_border 5px; margin-left: 10px; margin-bottom: 10px; } -div.form-row-error -{ +div.form-row-error { background: $error_message_bg; } -div.form-row label -{ +div.form-row label { font-weight: bold; display: block; margin-bottom: .2em; } -div.form-row-input -{ +div.form-row-input { float: left; width: 300px; } -div.form-row-input > input -{ +div.form-row-input > input { max-width: 300px; } -div.form-row-error-message -{ +div.form-row-error-message { width: 300px; float: left; color: red; @@ -193,19 +175,17 @@ padding: 3px 0 0 1em; } -select, input, textarea -{ +select, input, textarea { font: inherit; font-size: 115%; } -select, textarea, input[type="text"], input[type="file"], input[type="password"] -{ +select, textarea, input[type="text"], input[type="file"], input[type="password"] { -webkit-box-sizing: border-box; max-width: 300px; } -/* Messages */ +## Messages .errormessage, .warningmessage, .donemessage, .infomessage, .welcomeBlue, .welcomeRed , .screencastBox, .yellowbox, .redbox, .bluebox, .greenbox { diff -r abdb523727ed -r fbad627b45ac static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Thu Aug 06 10:29:51 2009 -0400 +++ b/static/june_2007_style/blue/base.css Sat Aug 22 23:18:47 2009 -0400 @@ -10,6 +10,7 @@ a:link,a:visited,a:active{color:#303030;} h1,h2,h3,h4{color:#023858;} hr{border:none;height:0px;border-bottom:dotted #303030 1px;} +th{text-align:left;} div.toolForm{border:solid #d8b365 1px;} div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} div.toolParamHelp{color:#666;} diff -r abdb523727ed -r fbad627b45ac static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Thu Aug 06 10:29:51 2009 -0400 +++ b/static/scripts/packed/galaxy.base.js Sat Aug 22 23:18:47 2009 -0400 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,b){ens ure_popup_helper();$(d).css("position","relative");var a=$("<div class='popupmenu' id='"+d.attr("id")+"-menu'></div>").css("position","absolute").appendTo(d);$.each(b,function(g,f){$("<div class='popupmenu-item' />").html(g).click(f).appendTo(a)});var c=function(){$(a).unbind().hide();$(document).unbind("click.popupmenu")};var e=function(f){var g=$(d).offset();$(document).bind("click.popupmenu",c);$(a).click(c).css({left:0,top:-1000}).show();$(a).css({top:0,left:0});return false};$(d).click(e)}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></div>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){console.log(b,d);var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){console.log(g);var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file diff -r abdb523727ed -r fbad627b45ac templates/history/rename.mako --- a/templates/history/rename.mako Thu Aug 06 10:29:51 2009 -0400 +++ b/templates/history/rename.mako Sat Aug 22 23:18:47 2009 -0400 @@ -3,39 +3,37 @@ <%def name="title()">${_('Rename History')}</%def> <div class="toolForm"> - <div class="toolFormTitle">${_('Rename History')}</div> + <div class="toolFormTitle">${_('Rename')}</div> <div class="toolFormBody"> <form action="${h.url_for( controller='history', action='rename' )}" method="post" > - <table class="grid"> + <div class="form-row"> + <table> + <thead> + <tr> + <th>${_('Current Name')}</th> + <th>${_('New Name')}</th> + </tr> + </thead> + <tbody> %for history in histories: <tr> <td> - <div class="form-row"> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - <label>${_('Current Name')}</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${history.name} - </div> - </div> + <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> + ${history.name} </td> <td> - <div class="form-row"> - <label>${_('New Name')}</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${history.name}" size="40"> - </div> - </div> + <input type="text" name="name" value="${history.name}" size="40"> </td> </tr> %endfor + </tbody> <tr> <td colspan="2"> - <div class="form-row"> - <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> - </div> + <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> </td> </tr> </table> + </div> </form> </div> </div> diff -r abdb523727ed -r fbad627b45ac templates/history/share.mako --- a/templates/history/share.mako Thu Aug 06 10:29:51 2009 -0400 +++ b/templates/history/share.mako Sat Aug 22 23:18:47 2009 -0400 @@ -8,32 +8,32 @@ %if not can_change and not cannot_change and not no_change_needed: ## We are sharing histories that contain only public datasets <form name='share' id='share' action="${h.url_for( controller="history", action='share' )}" method="post" > - %for history in histories: - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - <div class="toolForm"> - <div class="form-row"> - <label>${_('History Name:')}</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${history.name} - </div> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>${_('Number of Datasets:')}</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - %if len( history.datasets ) < 1: - <div class="warningmark">${_('This history contains no data.')}</div> - %else: - ${len(history.datasets)} - %endif - </td> - </div> - </div> - <div style="clear: both"></div> - <p/> - </div> - %endfor - <p/> + <div class="form-title-row"><b>Histories to be shared:</b></div> + <div class="form-row" style="padding-left: 2em;"> + <table width="100%"> + <thead> + <th>${_('History Name')}</th> + <th>${_('Number of Datasets')}</th> + </thead> + <tbody> + %for history in histories: + <tr> + <td> + <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> + ${history.name} + </td> + <td> + %if len( history.datasets ) < 1: + <div class="warningmark">${_('This history contains no data.')}</div> + %else: + ${len(history.datasets)} + %endif + </td> + </tr> + %endfor + </tbody> + </table> + </div> <div style="clear: both"></div> <div class="form-row"> <label>Galaxy user emails with which to share histories</label> diff -r abdb523727ed -r fbad627b45ac templates/root/index.mako --- a/templates/root/index.mako Thu Aug 06 10:29:51 2009 -0400 +++ b/templates/root/index.mako Sat Aug 22 23:18:47 2009 -0400 @@ -20,7 +20,7 @@ "Clone": function() { galaxy_main.location = "${h.url_for( controller='history', action='clone')}"; }, - "Manage sharing": function() { + "Share": function() { galaxy_main.location = "${h.url_for( controller='history', action='share' )}"; }, "Extract workflow": function() {

1 0

[hg] galaxy 2603: Merge trunk
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/542471b183d7 changeset: 2603:542471b183d7 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 20 18:44:35 2009 -0400 description: Merge trunk 0 file(s) affected in this change: diffs (1505 lines): diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Aug 20 18:44:35 2009 -0400 @@ -6,6 +6,8 @@ from galaxy.datatypes.tabular import * from galaxy.datatypes.interval import * from galaxy.datatypes import metadata +from galaxy.util.json import from_json_string +from galaxy.util.expressions import ExpressionContext import pkg_resources pkg_resources.require( "PasteDeploy" ) @@ -18,6 +20,12 @@ # States for running a job. These are NOT the same as data states JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED, JOB_ADMIN_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted', 'admin_deleted' + +# This file, if created in the job's working directory, will be used for +# setting advanced metadata properties on the job and its associated outputs. +# This interface is currently experimental, is only used by the upload tool, +# and should eventually become API'd +TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json' class JobManager( object ): """ @@ -320,6 +328,7 @@ self.working_directory = \ os.path.join( self.app.config.job_working_directory, str( self.job_id ) ) self.output_paths = None + self.tool_provided_job_metadata = None self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) #wrapper holding the info required to restore and clean up from files used for setting metadata externally def get_param_dict( self ): @@ -422,6 +431,8 @@ dataset.blurb = 'tool error' dataset.info = message dataset.set_size() + if dataset.ext == 'auto': + dataset.extension = 'data' dataset.flush() job.state = model.Job.states.ERROR job.command_line = self.command_line @@ -486,16 +497,28 @@ except ( IOError, OSError ): self.fail( "Job %s's output dataset(s) could not be read" % job.id ) return + job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) for dataset_assoc in job.output_datasets: + context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running + if context.get( 'path', None ): + # The tool can set an alternate output path for the dataset. + try: + shutil.move( context['path'], dataset.file_name ) + except ( IOError, OSError ): + if not context['stderr']: + context['stderr'] = 'This dataset could not be processed' dataset.blurb = 'done' dataset.peek = 'no peek' - dataset.info = stdout + stderr + dataset.info = context['stdout'] + context['stderr'] dataset.set_size() - if stderr: + if context['stderr']: dataset.blurb = "error" elif dataset.has_data(): + # If the tool was expected to set the extension, attempt to retrieve it + if dataset.ext == 'auto': + dataset.extension = context.get( 'ext', 'data' ) #if a dataset was copied, it won't appear in our dictionary: #either use the metadata from originating output dataset, or call set_meta on the copies #it would be quicker to just copy the metadata from the originating output dataset, @@ -510,18 +533,39 @@ #the metadata that was stored to disk for use via the external process, #and the changes made by the user will be lost, without warning or notice dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset ).filename_out ) - if self.tool.is_multi_byte: - dataset.set_multi_byte_peek() - else: - dataset.set_peek() + try: + assert context.get( 'line_count', None ) is not None + if self.tool.is_multi_byte: + dataset.set_multi_byte_peek( line_count=context['line_count'] ) + else: + dataset.set_peek( line_count=context['line_count'] ) + except: + if self.tool.is_multi_byte: + dataset.set_multi_byte_peek() + else: + dataset.set_peek() + try: + # set the name if provided by the tool + dataset.name = context['name'] + except: + pass else: dataset.blurb = "empty" + if dataset.ext == 'auto': + dataset.extension = 'txt' dataset.flush() - if stderr: + if context['stderr']: dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR else: dataset_assoc.dataset.dataset.state = model.Dataset.states.OK - dataset_assoc.dataset.dataset.flush() + # If any of the rest of the finish method below raises an + # exception, the fail method will run and set the datasets to + # ERROR. The user will never see that the datasets are in error if + # they were flushed as OK here, since upon doing so, the history + # panel stops checking for updates. So allow the + # mapping.context.current.flush() at the bottom of this method set + # the state instead. + #dataset_assoc.dataset.dataset.flush() # Save stdout and stderr if len( stdout ) > 32768: @@ -591,7 +635,8 @@ return self.output_paths class DatasetPath( object ): - def __init__( self, real_path, false_path = None ): + def __init__( self, dataset_id, real_path, false_path = None ): + self.dataset_id = dataset_id self.real_path = real_path self.false_path = false_path def __str__( self ): @@ -605,10 +650,55 @@ self.output_paths = [] for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) - self.output_paths.append( DatasetPath( data.file_name, false_path ) ) + self.output_paths.append( DatasetPath( data.id, data.file_name, false_path ) ) else: - self.output_paths = [ DatasetPath( da.dataset.file_name ) for da in job.output_datasets ] + self.output_paths = [ DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) for da in job.output_datasets ] return self.output_paths + + def get_output_file_id( self, file ): + if self.output_paths is None: + self.get_output_fnames() + for dp in self.output_paths: + if self.app.config.outputs_to_working_directory and os.path.basename( dp.false_path ) == file: + return dp.dataset_id + elif os.path.basename( dp.real_path ) == file: + return dp.dataset_id + return None + + def get_tool_provided_job_metadata( self ): + if self.tool_provided_job_metadata is not None: + return self.tool_provided_job_metadata + + # Look for JSONified job metadata + self.tool_provided_job_metadata = [] + meta_file = os.path.join( self.working_directory, TOOL_PROVIDED_JOB_METADATA_FILE ) + if os.path.exists( meta_file ): + for line in open( meta_file, 'r' ): + try: + line = from_json_string( line ) + assert 'type' in line + except: + log.exception( '(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % self.job_id ) + log.debug( 'Offending data was: %s' % line ) + continue + # Set the dataset id if it's a dataset entry and isn't set. + # This isn't insecure. We loop the job's output datasets in + # the finish method, so if a tool writes out metadata for a + # dataset id that it doesn't own, it'll just be ignored. + if line['type'] == 'dataset' and 'dataset_id' not in line: + try: + line['dataset_id'] = self.get_output_file_id( line['dataset'] ) + except KeyError: + log.warning( '(%s) Tool provided job dataset-specific metadata without specifying a dataset' % self.job_id ) + continue + self.tool_provided_job_metadata.append( line ) + return self.tool_provided_job_metadata + + def get_dataset_finish_context( self, job_context, dataset ): + for meta in self.get_tool_provided_job_metadata(): + if meta['type'] == 'dataset' and meta['dataset_id'] == dataset.id: + return ExpressionContext( meta, job_context ) + return job_context def check_output_sizes( self ): sizes = [] diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Aug 20 18:44:35 2009 -0400 @@ -5,7 +5,7 @@ pkg_resources.require( "simplejson" ) -import logging, os, string, sys, tempfile, glob, shutil +import logging, os, string, sys, tempfile, glob, shutil, types import simplejson import binascii from UserDict import DictMixin @@ -415,6 +415,7 @@ output.metadata_source = data_elem.get("metadata_source", "") output.parent = data_elem.get("parent", None) output.label = util.xml_text( data_elem, "label" ) + output.count = int( data_elem.get("count", 1) ) output.filters = data_elem.findall( 'filter' ) self.outputs[ output.name ] = output # Any extra generated config files for the tool @@ -816,7 +817,11 @@ # If we've completed the last page we can execute the tool elif state.page == self.last_page: out_data = self.execute( trans, incoming=params ) - return 'tool_executed.mako', dict( out_data=out_data ) + try: + assert type( out_data ) is types.DictType + return 'tool_executed.mako', dict( out_data=out_data ) + except: + return 'message.mako', dict( message_type='error', message=out_data, refresh_frames=[] ) # Otherwise move on to the next page else: state.page += 1 @@ -824,15 +829,26 @@ self.fill_in_new_state( trans, self.inputs_by_page[ state.page ], state.inputs ) return 'tool_form.mako', dict( errors=errors, tool_state=state ) else: - if filter( lambda x: isinstance( x, FieldStorage ) and x.file, state.inputs.values() ): + try: + self.find_fieldstorage( state.inputs ) + except InterruptedUpload: # If inputs contain a file it won't persist. Most likely this # is an interrupted upload. We should probably find a more # standard method of determining an incomplete POST. return self.handle_interrupted( trans, state.inputs ) - else: - # Just a refresh, render the form with updated state and errors. - return 'tool_form.mako', dict( errors=errors, tool_state=state ) + except: + pass + # Just a refresh, render the form with updated state and errors. + return 'tool_form.mako', dict( errors=errors, tool_state=state ) + def find_fieldstorage( self, x ): + if isinstance( x, FieldStorage ): + raise InterruptedUpload( None ) + elif type( x ) is types.DictType: + [ self.find_fieldstorage( y ) for y in x.values() ] + elif type( x ) is types.ListType: + [ self.find_fieldstorage( y ) for y in x ] + def handle_interrupted( self, trans, inputs ): """ Upon handling inputs, if it appears that we have received an incomplete @@ -1704,3 +1720,6 @@ return value else: return incoming.get( key, default ) + +class InterruptedUpload( Exception ): + pass diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Aug 20 18:44:35 2009 -0400 @@ -1,8 +1,10 @@ import os, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile +from cgi import FieldStorage from __init__ import ToolAction from galaxy import datatypes, jobs from galaxy.datatypes import sniff from galaxy import model, util +from galaxy.util.json import to_json_string import sys, traceback @@ -11,14 +13,28 @@ class UploadToolAction( ToolAction ): # Action for uploading files - def __init__( self ): - self.empty = False - self.line_count = None - def remove_tempfile( self, filename ): - try: - os.unlink( filename ) - except: - log.exception( 'failure removing temporary file: %s' % filename ) + def persist_uploads( self, incoming ): + if 'files' in incoming: + new_files = [] + temp_files = [] + for upload_dataset in incoming['files']: + f = upload_dataset['file_data'] + if isinstance( f, FieldStorage ): + # very small files can be StringIOs + if 'name' in dir( f.file ) and f.file.name != '<fdopen>': + local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' ) + f.file.close() + else: + local_filename = datatypes.sniff.stream_to_file( f.file, prefix="strio_upload_file_" )[0] + upload_dataset['file_data'] = dict( filename = f.filename, + local_filename = local_filename ) + if upload_dataset['url_paste'].strip() != '': + upload_dataset['url_paste'] = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" )[0] + else: + upload_dataset['url_paste'] = None + new_files.append( upload_dataset ) + incoming['files'] = new_files + return incoming def execute( self, tool, trans, incoming={}, set_output_hid = True ): dataset_upload_inputs = [] for input_name, input in tool.inputs.iteritems(): @@ -42,330 +58,100 @@ log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, trans.user.id ) ) else: self.precreated_datasets.append( data ) + data_list = [] + + incoming = self.persist_uploads( incoming ) + + json_file = tempfile.mkstemp() + json_file_path = json_file[1] + json_file = os.fdopen( json_file[0], 'w' ) for dataset_upload_input in dataset_upload_inputs: uploaded_datasets = dataset_upload_input.get_uploaded_datasets( trans, incoming ) for uploaded_dataset in uploaded_datasets: - precreated_dataset = self.get_precreated_dataset( uploaded_dataset.precreated_name ) - dataset = self.add_file( trans, uploaded_dataset.primary_file, uploaded_dataset.name, uploaded_dataset.file_type, uploaded_dataset.is_multi_byte, uploaded_dataset.dbkey, space_to_tab = uploaded_dataset.space_to_tab, info = uploaded_dataset.info, precreated_dataset = precreated_dataset, metadata = uploaded_dataset.metadata, uploaded_dataset = uploaded_dataset ) - #dataset state is now set, we should not do anything else to this dataset - data_list.append( dataset ) - #clean up extra temp names - uploaded_dataset.clean_up_temp_files() - + data = self.get_precreated_dataset( uploaded_dataset.name ) + if not data: + data = trans.app.model.HistoryDatasetAssociation( history = trans.history, create_dataset = True ) + data.name = uploaded_dataset.name + data.state = data.states.QUEUED + data.extension = uploaded_dataset.file_type + data.dbkey = uploaded_dataset.dbkey + data.flush() + trans.history.add_dataset( data, genome_build = uploaded_dataset.dbkey ) + permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) + trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions ) + else: + data.extension = uploaded_dataset.file_type + data.dbkey = uploaded_dataset.dbkey + data.flush() + trans.history.genome_build = uploaded_dataset.dbkey + if uploaded_dataset.type == 'composite': + # we need to init metadata before the job is dispatched + data.init_meta() + for meta_name, meta_value in uploaded_dataset.metadata.iteritems(): + setattr( data.metadata, meta_name, meta_value ) + data.flush() + json = dict( file_type = uploaded_dataset.file_type, + dataset_id = data.dataset.id, + dbkey = uploaded_dataset.dbkey, + type = uploaded_dataset.type, + metadata = uploaded_dataset.metadata, + primary_file = uploaded_dataset.primary_file, + extra_files_path = data.extra_files_path, + composite_file_paths = uploaded_dataset.composite_files, + composite_files = dict( [ ( k, v.__dict__ ) for k, v in data.datatype.get_composite_files( data ).items() ] ) ) + else: + try: + is_binary = uploaded_dataset.datatype.is_binary + except: + is_binary = None + json = dict( file_type = uploaded_dataset.file_type, + name = uploaded_dataset.name, + dataset_id = data.dataset.id, + dbkey = uploaded_dataset.dbkey, + type = uploaded_dataset.type, + is_binary = is_binary, + space_to_tab = uploaded_dataset.space_to_tab, + path = uploaded_dataset.path ) + json_file.write( to_json_string( json ) + '\n' ) + data_list.append( data ) + json_file.close() + #cleanup unclaimed precreated datasets: for data in self.precreated_datasets: log.info( 'Cleaned up unclaimed precreated dataset (%s).' % ( data.id ) ) data.state = data.states.ERROR data.info = 'No file contents were available.' - if data_list: - trans.app.model.flush() + if not data_list: + try: + os.remove( json_file_path ) + except: + pass + return 'No data was entered in the upload form, please go back and choose data to upload.' # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id - try: - # For backward compatibility, some tools may not have versions yet. - job.tool_version = tool.version - except: - job.tool_version = "1.0.1" + job.tool_version = tool.version job.state = trans.app.model.Job.states.UPLOAD job.flush() log.info( 'tool %s created job id %d' % ( tool.id, job.id ) ) trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) + + for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + job.add_parameter( name, value ) + job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) + for i, dataset in enumerate( data_list ): + job.add_output_dataset( i, dataset ) + trans.app.model.flush() - #if we could make a 'real' job here, then metadata could be set before job.finish() is called - hda = data_list[0] #only our first hda is being added as output for the job, why? - job.state = trans.app.model.Job.states.OK - file_size_str = datatypes.data.nice_size( hda.dataset.file_size ) - job.info = "%s, size: %s" % ( hda.info, file_size_str ) - job.add_output_dataset( hda.name, hda ) - job.flush() - log.info( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ) ) - trans.log_event( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ), tool_id=tool.id ) - return dict( output=hda ) - - def upload_empty(self, trans, job, err_code, err_msg, precreated_dataset = None): - if precreated_dataset is not None: - data = precreated_dataset - else: - data = trans.app.model.HistoryDatasetAssociation( create_dataset=True ) - trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) ) - data.name = err_code - data.extension = "txt" - data.dbkey = "?" - data.info = err_msg - data.file_size = 0 - data.state = data.states.EMPTY - data.flush() - if precreated_dataset is None: - trans.history.add_dataset( data ) - trans.app.model.flush() - # Indicate job failure by setting state and info - job.state = trans.app.model.Job.states.ERROR - job.info = err_msg - job.add_output_dataset( data.name, data ) - job.flush() - log.info( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ) ) - trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) - return dict( output=data ) - - def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None, metadata = {}, uploaded_dataset = None ): - def dataset_no_data_error( data, message = 'there was an error uploading your file' ): - data.info = "No data: %s." % message - data.state = data.states.ERROR - if data.extension is None: - data.extension = 'data' - return data - data_type = None - - if precreated_dataset is not None: - data = precreated_dataset - else: - data = trans.app.model.HistoryDatasetAssociation( history = trans.history, create_dataset = True ) - trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) ) - - # See if we have an empty file - if not os.path.getsize( temp_name ) > 0: - return dataset_no_data_error( data, message = 'you attempted to upload an empty file' ) - #raise BadFileException( "you attempted to upload an empty file." ) - if is_multi_byte: - ext = sniff.guess_ext( temp_name, is_multi_byte=True ) - else: - if not data_type: #at this point data_type is always None (just initialized above), so this is always True...lots of cleanup needed here - # See if we have a gzipped file, which, if it passes our restrictions, - # we'll decompress on the fly. - is_gzipped, is_valid = self.check_gzip( temp_name ) - if is_gzipped and not is_valid: - return dataset_no_data_error( data, message = 'you attempted to upload an inappropriate file' ) - #raise BadFileException( "you attempted to upload an inappropriate file." ) - elif is_gzipped and is_valid: - # We need to uncompress the temp_name file - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp() - gzipped_file = gzip.GzipFile( temp_name ) - while 1: - try: - chunk = gzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - return dataset_no_data_error( data, message = 'problem decompressing gzipped data' ) - #raise BadFileException( 'problem decompressing gzipped data.' ) - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - gzipped_file.close() - # Replace the gzipped file with the decompressed file - shutil.move( uncompressed, temp_name ) - file_name = file_name.rstrip( '.gz' ) - data_type = 'gzip' - ext = '' - if not data_type: - # See if we have a zip archive - is_zipped, is_valid, test_ext = self.check_zip( temp_name ) - if is_zipped and not is_valid: - return dataset_no_data_error( data, message = 'you attempted to upload an inappropriate file' ) - #raise BadFileException( "you attempted to upload an inappropriate file." ) - elif is_zipped and is_valid: - # Currently, we force specific tools to handle this case. We also require the user - # to manually set the incoming file_type - if ( test_ext == 'ab1' or test_ext == 'scf' ) and file_type != 'binseq.zip': - return dataset_no_data_error( data, message = "Invalid 'File Format' for archive consisting of binary files - use 'Binseq.zip'" ) - #raise BadFileException( "Invalid 'File Format' for archive consisting of binary files - use 'Binseq.zip'." ) - elif test_ext == 'txt' and file_type != 'txtseq.zip': - return dataset_no_data_error( data, message = "Invalid 'File Format' for archive consisting of text files - use 'Txtseq.zip'" ) - #raise BadFileException( "Invalid 'File Format' for archive consisting of text files - use 'Txtseq.zip'." ) - if not ( file_type == 'binseq.zip' or file_type == 'txtseq.zip' ): - return dataset_no_data_error( data, message = "you must manually set the 'File Format' to either 'Binseq.zip' or 'Txtseq.zip' when uploading zip files" ) - #raise BadFileException( "you must manually set the 'File Format' to either 'Binseq.zip' or 'Txtseq.zip' when uploading zip files." ) - data_type = 'zip' - ext = file_type - if not data_type: - if self.check_binary( temp_name ): - if uploaded_dataset and uploaded_dataset.datatype and uploaded_dataset.datatype.is_binary: - #we need a more generalized way of checking if a binary upload is of the right format for a datatype...magic number, etc - data_type = 'binary' - ext = uploaded_dataset.file_type - else: - parts = file_name.split( "." ) - if len( parts ) > 1: - ext = parts[1].strip().lower() - if not( ext == 'ab1' or ext == 'scf' ): - return dataset_no_data_error( data, message = "you attempted to upload an inappropriate file" ) - #raise BadFileException( "you attempted to upload an inappropriate file." ) - if ext == 'ab1' and file_type != 'ab1': - return dataset_no_data_error( data, message = "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files" ) - #raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) - elif ext == 'scf' and file_type != 'scf': - return dataset_no_data_error( data, message = "you must manually set the 'File Format' to 'Scf' when uploading scf files" ) - #raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) - data_type = 'binary' - if not data_type: - # We must have a text file - if trans.app.datatypes_registry.get_datatype_by_extension( file_type ).composite_type != 'auto_primary_file' and self.check_html( temp_name ): - return dataset_no_data_error( data, message = "you attempted to upload an inappropriate file" ) - #raise BadFileException( "you attempted to upload an inappropriate file." ) - #if data_type != 'binary' and data_type != 'zip' and not trans.app.datatypes_registry.get_datatype_by_extension( ext ).is_binary: - if data_type != 'binary' and data_type != 'zip': - if space_to_tab: - self.line_count = sniff.convert_newlines_sep2tabs( temp_name ) - else: - self.line_count = sniff.convert_newlines( temp_name ) - if file_type == 'auto': - ext = sniff.guess_ext( temp_name, sniff_order=trans.app.datatypes_registry.sniff_order ) - else: - ext = file_type - data_type = ext - if info is None: - info = 'uploaded %s file' %data_type - data.extension = ext - data.name = file_name - data.dbkey = dbkey - data.info = info - data.flush() - shutil.move( temp_name, data.file_name ) - dataset_state = data.states.OK #don't set actual state here, only set to OK when finished setting attributes of the dataset - data.set_size() - data.init_meta() - #need to set metadata, has to be done after extention is set - for meta_name, meta_value in metadata.iteritems(): - setattr( data.metadata, meta_name, meta_value ) - if self.line_count is not None: - try: - if is_multi_byte: - data.set_multi_byte_peek( line_count=self.line_count ) - else: - data.set_peek( line_count=self.line_count ) - except: - if is_multi_byte: - data.set_multi_byte_peek() - else: - data.set_peek() - else: - if is_multi_byte: - data.set_multi_byte_peek() - else: - data.set_peek() - - # validate incomming data - # Commented by greg on 3/14/07 - # for error in data.datatype.validate( data ): - # data.add_validation_error( - # model.ValidationError( message=str( error ), err_type=error.__class__.__name__, attributes=util.object_to_string( error.__dict__ ) ) ) - if data.missing_meta(): - data.datatype.set_meta( data ) - dbkey_to_store = dbkey - if type( dbkey_to_store ) == type( [] ): - dbkey_to_store = dbkey[0] - if precreated_dataset is not None: - trans.history.genome_build = dbkey_to_store - else: - trans.history.add_dataset( data, genome_build=dbkey_to_store ) - #set up composite files - if uploaded_dataset is not None: - composite_files = data.datatype.get_composite_files( data ) - if composite_files: - os.mkdir( data.extra_files_path ) #make extra files path - for name, value in composite_files.iteritems(): - if uploaded_dataset.composite_files[ value.name ] is None and not value.optional: - data.info = "A required composite data file was not provided (%s)" % name - dataset_state = data.states.ERROR - break - elif uploaded_dataset.composite_files[ value.name] is not None: - if not value.is_binary: - if uploaded_dataset.composite_files[ value.name ].space_to_tab: - sniff.convert_newlines_sep2tabs( uploaded_dataset.composite_files[ value.name ].filename ) - else: - sniff.convert_newlines( uploaded_dataset.composite_files[ value.name ].filename ) - shutil.move( uploaded_dataset.composite_files[ value.name ].filename, os.path.join( data.extra_files_path, name ) ) - if data.datatype.composite_type == 'auto_primary_file': - #now that metadata was set above, we should create the primary file as required - open( data.file_name, 'wb+' ).write( data.datatype.generate_primary_file( dataset = data ) ) - data.state = dataset_state #Always set dataset state LAST - trans.app.model.flush() - trans.log_event( "Added dataset %d to history %d" %( data.id, trans.history.id ), tool_id="upload" ) - return data - - def check_gzip( self, temp_name ): - temp = open( temp_name, "U" ) - magic_check = temp.read( 2 ) - temp.close() - if magic_check != util.gzip_magic: - return ( False, False ) - CHUNK_SIZE = 2**15 # 32Kb - gzipped_file = gzip.GzipFile( temp_name ) - chunk = gzipped_file.read( CHUNK_SIZE ) - gzipped_file.close() - if self.check_html( temp_name, chunk=chunk ) or self.check_binary( temp_name, chunk=chunk ): - return( True, False ) - return ( True, True ) - - def check_zip( self, temp_name ): - if not zipfile.is_zipfile( temp_name ): - return ( False, False, None ) - zip_file = zipfile.ZipFile( temp_name, "r" ) - # Make sure the archive consists of valid files. The current rules are: - # 1. Archives can only include .ab1, .scf or .txt files - # 2. All file extensions within an archive must be the same - name = zip_file.namelist()[0] - test_ext = name.split( "." )[1].strip().lower() - if not ( test_ext == 'scf' or test_ext == 'ab1' or test_ext == 'txt' ): - return ( True, False, test_ext ) - for name in zip_file.namelist(): - ext = name.split( "." )[1].strip().lower() - if ext != test_ext: - return ( True, False, test_ext ) - return ( True, True, test_ext ) - - def check_html( self, temp_name, chunk=None ): - if chunk is None: - temp = open(temp_name, "U") - else: - temp = chunk - regexp1 = re.compile( "<A\s+[^>]*HREF[^>]+>", re.I ) - regexp2 = re.compile( "<IFRAME[^>]*>", re.I ) - regexp3 = re.compile( "<FRAMESET[^>]*>", re.I ) - regexp4 = re.compile( "<META[^>]*>", re.I ) - lineno = 0 - for line in temp: - lineno += 1 - matches = regexp1.search( line ) or regexp2.search( line ) or regexp3.search( line ) or regexp4.search( line ) - if matches: - if chunk is None: - temp.close() - return True - if lineno > 100: - break - if chunk is None: - temp.close() - return False - def check_binary( self, temp_name, chunk=None ): - if chunk is None: - temp = open( temp_name, "U" ) - else: - temp = chunk - lineno = 0 - for line in temp: - lineno += 1 - line = line.strip() - if line: - if util.is_multi_byte( line ): - return False - for char in line: - if ord( char ) > 128: - if chunk is None: - temp.close() - return True - if lineno > 10: - break - if chunk is None: - temp.close() - return False + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + return dict( [ ( i, v ) for i, v in enumerate( data_list ) ] ) def get_precreated_dataset( self, name ): """ @@ -378,7 +164,3 @@ return self.precreated_datasets.pop( names.index( name ) ) else: return None - -class BadFileException( Exception ): - pass - diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Aug 20 18:44:35 2009 -0400 @@ -304,21 +304,22 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.FileField( self.name, ajax = self.ajax, value = value ) def from_html( self, value, trans=None, other_values={} ): + # TODO: Fix nginx upload module support # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) - if type( value ) == dict: - upload_location = self.tool.app.config.nginx_upload_location - assert upload_location, \ - "Request appears to have been processed by nginx_upload_module \ - but Galaxy is not configured to recgonize it" - # Check that the file is in the right location - local_filename = os.path.abspath( value['path'] ) - assert local_filename.startswith( upload_location ), \ - "Filename provided by nginx is not in correct directory" - value = Bunch( - filename = value["name"], - local_filename = local_filename - ) + #if type( value ) == dict: + # upload_location = self.tool.app.config.nginx_upload_location + # assert upload_location, \ + # "Request appears to have been processed by nginx_upload_module \ + # but Galaxy is not configured to recgonize it" + # # Check that the file is in the right location + # local_filename = os.path.abspath( value['path'] ) + # assert local_filename.startswith( upload_location ), \ + # "Filename provided by nginx is not in correct directory" + # value = Bunch( + # filename = value["name"], + # local_filename = local_filename + # ) return value def get_required_enctype( self ): """ @@ -330,10 +331,18 @@ return None elif isinstance( value, unicode ) or isinstance( value, str ): return value + elif isinstance( value, dict ): + # or should we jsonify? + try: + return value['local_filename'] + except: + return None raise Exception( "FileToolParameter cannot be persisted" ) def to_python( self, value, app ): if value is None: return None + elif isinstance( value, unicode ) or isinstance( value, str ): + return value else: raise Exception( "FileToolParameter cannot be persisted" ) def get_initial_value( self, trans, context ): diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Thu Aug 20 18:44:35 2009 -0400 @@ -12,6 +12,7 @@ from galaxy.datatypes import sniff from galaxy.util.bunch import Bunch from galaxy.util.odict import odict +from galaxy.util import json class Group( object ): def __init__( self ): @@ -167,33 +168,30 @@ rval.append( rval_dict ) return rval def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ): - def get_data_file_filename( data_file, is_multi_byte = False, override_name = None, override_info = None ): + def get_data_file_filename( data_file, override_name = None, override_info = None ): dataset_name = override_name dataset_info = override_info def get_file_name( file_name ): file_name = file_name.split( '\\' )[-1] file_name = file_name.split( '/' )[-1] return file_name - if 'local_filename' in dir( data_file ): + try: # Use the existing file - return data_file.local_filename, get_file_name( data_file.filename ), is_multi_byte - elif 'filename' in dir( data_file ): - #create a new tempfile - try: - temp_name, is_multi_byte = sniff.stream_to_file( data_file.file, prefix='upload' ) - precreated_name = get_file_name( data_file.filename ) - if not dataset_name: - dataset_name = precreated_name - if not dataset_info: - dataset_info = 'uploaded file' - return temp_name, get_file_name( data_file.filename ), is_multi_byte, dataset_name, dataset_info - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) - self.remove_temp_file( temp_name ) - return None, None, is_multi_byte, None, None - def filenames_from_url_paste( url_paste, group_incoming, override_name = None, override_info = None ): + if not dataset_name and 'filename' in data_file: + dataset_name = get_file_name( data_file['filename'] ) + if not dataset_info: + dataset_info = 'uploaded file' + return Bunch( type='file', path=data_file['local_filename'], name=get_file_name( data_file['filename'] ) ) + #return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info + except: + # The uploaded file should've been persisted by the upload tool action + return Bunch( type=None, path=None, name=None ) + #return None, None, None, None, None + def get_url_paste_urls_or_filename( group_incoming, override_name = None, override_info = None ): filenames = [] - if url_paste not in [ None, "" ]: + url_paste_file = group_incoming.get( 'url_paste', None ) + if url_paste_file is not None: + url_paste = open( url_paste_file, 'r' ).read( 1024 ) if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): url_paste = url_paste.replace( '\r', '' ).split( '\n' ) for line in url_paste: @@ -208,114 +206,54 @@ dataset_info = override_info if not dataset_info: dataset_info = 'uploaded url' - try: - temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) - except Exception, e: - temp_name = None - precreated_name = str( e ) - log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) - try: - self.remove_temp_file( temp_name ) - except: - pass - yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) - #yield ( None, str( e ), False, dataset_name, dataset_info ) + yield Bunch( type='url', path=line, name=precreated_name ) + #yield ( 'url', line, precreated_name, dataset_name, dataset_info ) else: dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here if override_name: dataset_name = override_name if override_info: dataset_info = override_info - is_valid = False - for line in url_paste: #Trim off empty lines from begining - line = line.rstrip( '\r\n' ) - if line: - is_valid = True - break - if is_valid: - try: - temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) - temp_name = None - precreated_name = str( e ) - try: - self.remove_temp_file( temp_name ) - except: - pass - yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) - #yield ( None, str( e ), False, dataset_name, dataset_info ) - + yield Bunch( type='file', path=url_paste_file, name=precreated_name ) + #yield ( 'file', url_paste_file, precreated_name, dataset_name, dataset_info ) def get_one_filename( context ): data_file = context['file_data'] url_paste = context['url_paste'] name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) warnings = [] - is_multi_byte = False space_to_tab = False if context.get( 'space_to_tab', None ) not in ["None", None]: space_to_tab = True - temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) - if temp_name: + file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) + if file_bunch.path: if url_paste.strip(): warnings.append( "All file contents specified in the paste box were ignored." ) else: #we need to use url_paste - #file_names = filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ) - for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ):#file_names: - if temp_name: + for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): + if file_bunch.path: break - ###this check will cause an additional file to be retrieved and created...so lets not do that - #try: #check to see if additional paste contents were available - # file_names.next() - # warnings.append( "Additional file contents were specified in the paste box, but ignored." ) - #except StopIteration: - # pass - return temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings - + return file_bunch, warnings def get_filenames( context ): rval = [] data_file = context['file_data'] url_paste = context['url_paste'] name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) - warnings = [] - is_multi_byte = False space_to_tab = False if context.get( 'space_to_tab', None ) not in ["None", None]: space_to_tab = True - temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) - if temp_name: - rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) - for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ): - if temp_name: - rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) + warnings = [] + file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) + if file_bunch.path: + file_bunch.space_to_tab = space_to_tab + rval.append( file_bunch ) + #rval.append( ( type, temp_name, precreated_name, space_to_tab, dataset_name, dataset_info ) ) + for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): + if file_bunch.path: + file_bunch.space_to_tab = space_to_tab + rval.append( file_bunch ) return rval - class UploadedDataset( Bunch ): - def __init__( self, **kwd ): - Bunch.__init__( self, **kwd ) - self.primary_file = None - self.composite_files = odict() - self.dbkey = None - self.warnings = [] - self.metadata = {} - - self._temp_filenames = [] #store all created filenames here, delete on cleanup - def register_temp_file( self, filename ): - if isinstance( filename, list ): - self._temp_filenames.extend( filename ) - else: - self._temp_filenames.append( filename ) - def remove_temp_file( self, filename ): - try: - os.unlink( filename ) - except Exception, e: - pass - #log.warning( str( e ) ) - def clean_up_temp_files( self ): - for filename in self._temp_filenames: - self.remove_temp_file( filename ) - file_type = self.get_file_type( context ) d_type = self.get_datatype( trans, context ) dbkey = context.get( 'dbkey', None ) @@ -325,51 +263,50 @@ for group_incoming in context.get( self.name, [] ): i = int( group_incoming['__index__'] ) groups_incoming[ i ] = group_incoming - if d_type.composite_type is not None: #handle uploading of composite datatypes #Only one Dataset can be created + ''' dataset = UploadedDataset() + dataset.datatype = d_type + ''' + dataset = Bunch() + dataset.type = 'composite' dataset.file_type = file_type + dataset.dbkey = dbkey dataset.datatype = d_type - dataset.dbkey = dbkey + dataset.warnings = [] + dataset.metadata = {} + dataset.composite_files = {} #load metadata files_metadata = context.get( self.metadata_ref, {} ) - for meta_name, meta_spec in d_type.metadata_spec.iteritems(): + for meta_name, meta_spec in d_type.metadata_spec.iteritems(): if meta_spec.set_in_upload: if meta_name in files_metadata: dataset.metadata[ meta_name ] = files_metadata[ meta_name ] - - temp_name = None - precreated_name = None - is_multi_byte = False - space_to_tab = False - warnings = [] dataset_name = None dataset_info = None if dataset.datatype.composite_type == 'auto_primary_file': #replace sniff here with just creating an empty file temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file() ), prefix='upload_auto_primary_file' ) - precreated_name = dataset_name = 'Uploaded Composite Dataset (%s)' % ( file_type ) + dataset.primary_file = temp_name + dataset.space_to_tab = False + dataset.precreated_name = dataset.name = 'Uploaded Composite Dataset (%s)' % ( file_type ) else: - temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( groups_incoming[ 0 ] ) + file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] ) if dataset.datatype.composite_type: precreated_name = 'Uploaded Composite Dataset (%s)' % ( file_type ) writable_files_offset = 1 - if temp_name is None:#remove this before finish, this should create an empty dataset + dataset.primary_file = file_bunch.path + dataset.space_to_tab = file_bunch.space_to_tab + dataset.precreated_name = file_bunch.precreated_name + dataset.name = file_bunch.precreated_name + dataset.warnings.extend( file_bunch.warnings ) + if dataset.primary_file is None:#remove this before finish, this should create an empty dataset raise Exception( 'No primary dataset file was available for composite upload' ) - dataset.primary_file = temp_name - dataset.is_multi_byte = is_multi_byte - dataset.space_to_tab = space_to_tab - dataset.precreated_name = precreated_name - dataset.name = dataset_name - dataset.info = dataset_info - dataset.warnings.extend( warnings ) - dataset.register_temp_file( temp_name ) - keys = [ value.name for value in writable_files.values() ] for i, group_incoming in enumerate( groups_incoming[ writable_files_offset : ] ): key = keys[ i + writable_files_offset ] @@ -377,37 +314,22 @@ dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) dataset.composite_files[ key ] = None else: - temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( group_incoming ) - if temp_name: - dataset.composite_files[ key ] = Bunch( filename = temp_name, precreated_name = precreated_name, is_multi_byte = is_multi_byte, space_to_tab = space_to_tab, warnings = warnings, info = dataset_info, name = dataset_name ) - dataset.register_temp_file( temp_name ) + file_bunch, warnings = get_one_filename( group_incoming ) + if file_bunch.path: + dataset.composite_files[ key ] = file_bunch.__dict__ else: dataset.composite_files[ key ] = None if not writable_files[ writable_files.keys()[ keys.index( key ) ] ].optional: dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) return [ dataset ] else: + datasets = get_filenames( context[ self.name ][0] ) rval = [] - for temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, in get_filenames( context[ self.name ][0] ): - dataset = UploadedDataset() + for dataset in datasets: dataset.file_type = file_type - dataset.datatype = d_type dataset.dbkey = dbkey - dataset.primary_file = temp_name - dataset.is_multi_byte = is_multi_byte - dataset.space_to_tab = space_to_tab - dataset.name = dataset_name - dataset.info = dataset_info - dataset.precreated_name = precreated_name - dataset.register_temp_file( temp_name ) rval.append( dataset ) - return rval - def remove_temp_file( self, filename ): - try: - os.unlink( filename ) - except Exception, e: - log.warning( str( e ) ) - + return rval class Conditional( Group ): type = "conditional" diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/util/__init__.py Thu Aug 20 18:44:35 2009 -0400 @@ -3,7 +3,7 @@ """ import logging -import threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys +import threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile # Older py compatibility try: @@ -454,6 +454,26 @@ out_dict[ str( key ) ] = value return out_dict +def mkstemp_ln( src, prefix='mkstemp_ln_' ): + """ + From tempfile._mkstemp_inner, generate a hard link in the same dir with a + random name. Created so we can persist the underlying file of a + NamedTemporaryFile upon its closure. + """ + dir = os.path.dirname(src) + names = tempfile._get_candidate_names() + for seq in xrange(tempfile.TMP_MAX): + name = names.next() + file = os.path.join(dir, prefix + name) + try: + linked_path = os.link( src, file ) + return (os.path.abspath(file)) + except OSError, e: + if e.errno == errno.EEXIST: + continue # try again + raise + raise IOError, (errno.EEXIST, "No usable temporary file name found") + galaxy_root_path = os.path.join(__path__[0], "..","..","..") dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) #this list is used in edit attributes and the upload tool ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) #this list is used in history.tmpl diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Thu Aug 20 18:44:35 2009 -0400 @@ -136,6 +136,7 @@ """ Precreate datasets for asynchronous uploading. """ + permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) def create_dataset( name, history ): data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) data.name = name @@ -143,6 +144,7 @@ data.history = history data.flush() history.add_dataset( data ) + trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions ) return data tool = self.get_toolbox().tools_by_id.get( tool_id, None ) if not tool: diff -r 62e24f51b518 -r 542471b183d7 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Thu Aug 20 12:51:39 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Thu Aug 20 18:44:35 2009 -0400 @@ -212,6 +212,17 @@ else: return None +# For request.params, override cgi.FieldStorage.make_file to create persistent +# tempfiles. Necessary for externalizing the upload tool. It's a little hacky +# but for performance reasons it's way better to use Paste's tempfile than to +# create a new one and copy. +import cgi +class FieldStorage( cgi.FieldStorage ): + def make_file(self, binary=None): + import tempfile + return tempfile.NamedTemporaryFile() +cgi.FieldStorage = FieldStorage + class Request( webob.Request ): """ Encapsulates an HTTP request. diff -r 62e24f51b518 -r 542471b183d7 templates/base_panels.mako --- a/templates/base_panels.mako Thu Aug 20 12:51:39 2009 -0400 +++ b/templates/base_panels.mako Thu Aug 20 18:44:35 2009 -0400 @@ -72,9 +72,6 @@ <script type="text/javascript"> jQuery( function() { $("iframe#galaxy_main").load( function() { - ##$(this.contentDocument).find("input[galaxy-ajax-upload]").each( function() { - ##$("iframe")[0].contentDocument.body.innerHTML = "HELLO" - ##$(this.contentWindow.document).find("input[galaxy-ajax-upload]").each( function() { $(this).contents().find("form").each( function() { if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){ $(this).submit( function() { diff -r 62e24f51b518 -r 542471b183d7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Aug 20 12:51:39 2009 -0400 +++ b/test/base/twilltestcase.py Thu Aug 20 18:44:35 2009 -0400 @@ -93,6 +93,8 @@ valid_hid = int( hid ) except: raise AssertionError, "Invalid hid (%s) created when uploading file %s" % ( hid, filename ) + # Wait for upload processing to finish (TODO: this should be done in each test case instead) + self.wait() def upload_url_paste( self, url_paste, ftype='auto', dbkey='unspecified (?)' ): """Pasted data in the upload utility""" self.visit_page( "tool_runner/index?tool_id=upload1" ) @@ -112,6 +114,8 @@ valid_hid = int( hid ) except: raise AssertionError, "Invalid hid (%s) created when pasting %s" % ( hid, url_paste ) + # Wait for upload processing to finish (TODO: this should be done in each test case instead) + self.wait() # Functions associated with histories def check_history_for_errors( self ): diff -r 62e24f51b518 -r 542471b183d7 tools/data_source/upload.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/upload.py Thu Aug 20 18:44:35 2009 -0400 @@ -0,0 +1,280 @@ +#!/usr/bin/env python +#Processes uploads from the user. + +# WARNING: Changes in this tool (particularly as related to parsing) may need +# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools + +import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile +from galaxy import eggs +# need to import model before sniff to resolve a circular import dependency +import galaxy.model +from galaxy.datatypes import sniff +from galaxy import util +from galaxy.util.json import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg, ret=1 ): + sys.stderr.write( msg ) + sys.exit( ret ) + +def file_err( msg, dataset, json_file ): + json_file.write( to_json_string( dict( type = 'dataset', + ext = 'data', + dataset_id = dataset.dataset_id, + stderr = msg ) ) + "\n" ) + try: + os.remove( dataset.path ) + except: + pass + +def safe_dict(d): + """ + Recursively clone json structure with UTF-8 dictionary keys + http://mellowmachines.com/blog/2009/06/exploding-dictionary-with-unicode-ke… + """ + if isinstance(d, dict): + return dict([(k.encode('utf-8'), safe_dict(v)) for k,v in d.iteritems()]) + elif isinstance(d, list): + return [safe_dict(x) for x in d] + else: + return d + +def check_html( temp_name, chunk=None ): + if chunk is None: + temp = open(temp_name, "U") + else: + temp = chunk + regexp1 = re.compile( "<A\s+[^>]*HREF[^>]+>", re.I ) + regexp2 = re.compile( "<IFRAME[^>]*>", re.I ) + regexp3 = re.compile( "<FRAMESET[^>]*>", re.I ) + regexp4 = re.compile( "<META[^>]*>", re.I ) + lineno = 0 + for line in temp: + lineno += 1 + matches = regexp1.search( line ) or regexp2.search( line ) or regexp3.search( line ) or regexp4.search( line ) + if matches: + if chunk is None: + temp.close() + return True + if lineno > 100: + break + if chunk is None: + temp.close() + return False + +def check_binary( temp_name, chunk=None ): + if chunk is None: + temp = open( temp_name, "U" ) + else: + temp = chunk + lineno = 0 + for line in temp: + lineno += 1 + line = line.strip() + if line: + for char in line: + if ord( char ) > 128: + if chunk is None: + temp.close() + return True + if lineno > 10: + break + if chunk is None: + temp.close() + return False + +def check_gzip( temp_name ): + temp = open( temp_name, "U" ) + magic_check = temp.read( 2 ) + temp.close() + if magic_check != util.gzip_magic: + return ( False, False ) + CHUNK_SIZE = 2**15 # 32Kb + gzipped_file = gzip.GzipFile( temp_name ) + chunk = gzipped_file.read( CHUNK_SIZE ) + gzipped_file.close() + if check_html( temp_name, chunk=chunk ) or check_binary( temp_name, chunk=chunk ): + return( True, False ) + return ( True, True ) + +def check_zip( temp_name ): + if not zipfile.is_zipfile( temp_name ): + return ( False, False, None ) + zip_file = zipfile.ZipFile( temp_name, "r" ) + # Make sure the archive consists of valid files. The current rules are: + # 1. Archives can only include .ab1, .scf or .txt files + # 2. All file extensions within an archive must be the same + name = zip_file.namelist()[0] + test_ext = name.split( "." )[1].strip().lower() + if not ( test_ext == 'scf' or test_ext == 'ab1' or test_ext == 'txt' ): + return ( True, False, test_ext ) + for name in zip_file.namelist(): + ext = name.split( "." )[1].strip().lower() + if ext != test_ext: + return ( True, False, test_ext ) + return ( True, True, test_ext ) + +def add_file( dataset, json_file ): + data_type = None + line_count = None + + if dataset.type == 'url': + try: + temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( dataset.path ), prefix='url_paste' ) + except Exception, e: + file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file ) + return + dataset.path = temp_name + dataset.is_multi_byte = is_multi_byte + + # See if we have an empty file + if not os.path.exists( dataset.path ): + file_err( 'Uploaded temporary file (%s) does not exist. Please' % dataset.path, dataset, json_file ) + return + if not os.path.getsize( dataset.path ) > 0: + file_err( 'The uploaded file is empty', dataset, json_file ) + return + if 'is_multi_byte' not in dir( dataset ): + dataset.is_multi_byte = util.is_multi_byte( open( dataset.path, 'r' ).read( 1024 )[:100] ) + if dataset.is_multi_byte: + ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) + data_type = ext + else: + # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress + is_gzipped, is_valid = check_gzip( dataset.path ) + if is_gzipped and not is_valid: + file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + return + elif is_gzipped and is_valid: + # We need to uncompress the temp_name file + CHUNK_SIZE = 2**20 # 1Mb + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ) ) + gzipped_file = gzip.GzipFile( dataset.path ) + while 1: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing gzipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + # Replace the gzipped file with the decompressed file + shutil.move( uncompressed, dataset.path ) + dataset.name = dataset.name.rstrip( '.gz' ) + data_type = 'gzip' + if not data_type: + # See if we have a zip archive + is_zipped, is_valid, test_ext = check_zip( dataset.path ) + if is_zipped and not is_valid: + file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + return + elif is_zipped and is_valid: + # Currently, we force specific tools to handle this case. We also require the user + # to manually set the incoming file_type + if ( test_ext == 'ab1' or test_ext == 'scf' ) and dataset.file_type != 'binseq.zip': + file_err( "Invalid 'File Format' for archive consisting of binary files - use 'Binseq.zip'", dataset, json_file ) + return + elif test_ext == 'txt' and dataset.file_type != 'txtseq.zip': + file_err( "Invalid 'File Format' for archive consisting of text files - use 'Txtseq.zip'", dataset, json_file ) + return + if not ( dataset.file_type == 'binseq.zip' or dataset.file_type == 'txtseq.zip' ): + file_err( "You must manually set the 'File Format' to either 'Binseq.zip' or 'Txtseq.zip' when uploading zip files", dataset, json_file ) + return + data_type = 'zip' + ext = dataset.file_type + if not data_type: + if check_binary( dataset.path ): + if dataset.is_binary is not None: + data_type = 'binary' + ext = dataset.file_type + else: + parts = dataset.name.split( "." ) + if len( parts ) > 1: + ext = parts[1].strip().lower() + if not( ext == 'ab1' or ext == 'scf' ): + file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + return + if ext == 'ab1' and dataset.file_type != 'ab1': + file_err( "You must manually set the 'File Format' to 'Ab1' when uploading ab1 files.", dataset, json_file ) + return + elif ext == 'scf' and dataset.file_type != 'scf': + file_err( "You must manually set the 'File Format' to 'Scf' when uploading scf files.", dataset, json_file ) + return + data_type = 'binary' + if not data_type: + # We must have a text file + if check_html( dataset.path ): + file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + return + if data_type != 'binary' and data_type != 'zip': + if dataset.space_to_tab: + line_count = sniff.convert_newlines_sep2tabs( dataset.path ) + else: + line_count = sniff.convert_newlines( dataset.path ) + if dataset.file_type == 'auto': + ext = sniff.guess_ext( dataset.path ) + else: + ext = dataset.file_type + data_type = ext + # Save job info for the framework + info = dict( type = 'dataset', + dataset_id = dataset.dataset_id, + path = dataset.path, + ext = ext, + stdout = 'uploaded %s file' % data_type, + name = dataset.name, + line_count = line_count ) + json_file.write( to_json_string( info ) + "\n" ) + +def add_composite_file( dataset, json_file ): + if dataset.composite_files: + os.mkdir( dataset.extra_files_path ) + for name, value in dataset.composite_files.iteritems(): + value = util.bunch.Bunch( **value ) + if dataset.composite_file_paths[ value.name ] is None and not value.optional: + file_err( 'A required composite data file was not provided (%s)' % name, dataset, json_file ) + break + elif dataset.composite_file_paths[value.name] is not None: + if not value.is_binary: + if uploaded_dataset.composite_files[ value.name ].space_to_tab: + sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] ) + else: + sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) + shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + info = dict( type = 'dataset', + dataset_id = dataset.dataset_id, + path = dataset.primary_file, + stdout = 'uploaded %s file' % dataset.file_type ) + json_file.write( to_json_string( info ) + "\n" ) + +def __main__(): + + if len( sys.argv ) != 2: + print >>sys.stderr, 'usage: upload.py <json paramfile>' + sys.exit( 1 ) + + json_file = open( 'galaxy.json', 'w' ) + + for line in open( sys.argv[1], 'r' ): + dataset = from_json_string( line ) + dataset = util.bunch.Bunch( **safe_dict( dataset ) ) + + if dataset.type == 'composite': + add_composite_file( dataset, json_file ) + else: + add_file( dataset, json_file ) + + # clean up paramfile + try: + os.remove( sys.argv[1] ) + except: + pass + +if __name__ == '__main__': + __main__() diff -r 62e24f51b518 -r 542471b183d7 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Aug 20 12:51:39 2009 -0400 +++ b/tools/data_source/upload.xml Thu Aug 20 18:44:35 2009 -0400 @@ -1,10 +1,13 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.0.2"> +<tool name="Upload File" id="upload1" version="1.0.3"> <description> from your computer </description> <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> + <command interpreter="python"> + upload.py $paramfile + </command> <inputs> <param name="file_type" type="select" label="File Format" help="Which format? See help below"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">

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