galaxy-dev August 2009

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[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 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 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 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 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 2600: Remove redundant auto-save js
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/97170896bb91 changeset: 2600:97170896bb91 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 20 11:04:45 2009 -0400 description: Remove redundant auto-save js 2 file(s) affected in this change: templates/workflow/editor_generic_form.mako templates/workflow/editor_tool_form.mako diffs (23 lines): diff -r bedfce38e652 -r 97170896bb91 templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Thu Aug 20 10:59:13 2009 -0400 +++ b/templates/workflow/editor_generic_form.mako Thu Aug 20 11:04:45 2009 -0400 @@ -40,7 +40,3 @@ </form> </div> </div> - -<script type="text/javascript"> - workflow.enable_auto_save(); -</script> diff -r bedfce38e652 -r 97170896bb91 templates/workflow/editor_tool_form.mako --- a/templates/workflow/editor_tool_form.mako Thu Aug 20 10:59:13 2009 -0400 +++ b/templates/workflow/editor_tool_form.mako Thu Aug 20 11:04:45 2009 -0400 @@ -108,8 +108,3 @@ </form> </div> </div> - -<script type="text/javascript"> - workflow.enable_auto_save(); -</script> -

1 0

[hg] galaxy 2601: Use JSON2.js for all JSON operations, and remo...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0517fd342fc8 changeset: 2601:0517fd342fc8 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 20 12:41:37 2009 -0400 description: Use JSON2.js for all JSON operations, and remove unused javascript files 7 file(s) affected in this change: static/scripts/cookie_set.js static/scripts/jquery.cookie.js static/scripts/jquery.json.js static/scripts/packed/cookie_set.js static/scripts/packed/jquery.cookie.js static/scripts/packed/jquery.json.js templates/workflow/editor.mako diffs (270 lines): diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/cookie_set.js --- a/static/scripts/cookie_set.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -function CookieSet( cookie_name ) { - this.cookie_name = cookie_name; - this.store = store = {}; - jQuery.each( ( jQuery.cookie( cookie_name) || "" ).split( "|" ), function( k, v ) { - store[ v ] = true; - }); -}; -CookieSet.prototype.add = function( value ) { - this.store[value] = true; - return this; -}; -CookieSet.prototype.remove = function( value ) { - delete this.store[value]; - return this; -}; -CookieSet.prototype.removeAll = function( value ) { - this.store = {}; - return this; -}; -CookieSet.prototype.contains = function( value ) { - return ( value in this.store ); -}; -CookieSet.prototype.save = function() { - t = []; - for ( key in this.store ) { - if ( key != "" ) { t.push( key ) } - } - jQuery.cookie( this.cookie_name, t.join( "|" ) ); - return this; -}; \ No newline at end of file diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/jquery.cookie.js --- a/static/scripts/jquery.cookie.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -/** - * Cookie plugin - * - * Copyright (c) 2006 Klaus Hartl (stilbuero.de) - * Dual licensed under the MIT and GPL licenses: - * http://www.opensource.org/licenses/mit-license.php - * http://www.gnu.org/licenses/gpl.html - * - */ - -/** - * Create a cookie with the given name and value and other optional parameters. - * - * @example $.cookie('the_cookie', 'the_value'); - * @desc Set the value of a cookie. - * @example $.cookie('the_cookie', 'the_value', {expires: 7, path: '/', domain: 'jquery.com', secure: true}); - * @desc Create a cookie with all available options. - * @example $.cookie('the_cookie', 'the_value'); - * @desc Create a session cookie. - * @example $.cookie('the_cookie', null); - * @desc Delete a cookie by passing null as value. - * - * @param String name The name of the cookie. - * @param String value The value of the cookie. - * @param Object options An object literal containing key/value pairs to provide optional cookie attributes. - * @option Number|Date expires Either an integer specifying the expiration date from now on in days or a Date object. - * If a negative value is specified (e.g. a date in the past), the cookie will be deleted. - * If set to null or omitted, the cookie will be a session cookie and will not be retained - * when the the browser exits. - * @option String path The value of the path atribute of the cookie (default: path of page that created the cookie). - * @option String domain The value of the domain attribute of the cookie (default: domain of page that created the cookie). - * @option Boolean secure If true, the secure attribute of the cookie will be set and the cookie transmission will - * require a secure protocol (like HTTPS). - * @type undefined - * - * @name $.cookie - * @cat Plugins/Cookie - * @author Klaus Hartl/klaus.hartl(a)stilbuero.de - */ - -/** - * Get the value of a cookie with the given name. - * - * @example $.cookie('the_cookie'); - * @desc Get the value of a cookie. - * - * @param String name The name of the cookie. - * @return The value of the cookie. - * @type String - * - * @name $.cookie - * @cat Plugins/Cookie - * @author Klaus Hartl/klaus.hartl(a)stilbuero.de - */ -jQuery.cookie = function(name, value, options) { - if (typeof value != 'undefined') { // name and value given, set cookie - options = options || {}; - if (value === null) { - value = ''; - options.expires = -1; - } - var expires = ''; - if (options.expires && (typeof options.expires == 'number' || options.expires.toUTCString)) { - var date; - if (typeof options.expires == 'number') { - date = new Date(); - date.setTime(date.getTime() + (options.expires * 24 * 60 * 60 * 1000)); - } else { - date = options.expires; - } - expires = '; expires=' + date.toUTCString(); // use expires attribute, max-age is not supported by IE - } - var path = options.path ? '; path=' + options.path : ''; - var domain = options.domain ? '; domain=' + options.domain : ''; - var secure = options.secure ? '; secure' : ''; - document.cookie = [name, '=', encodeURIComponent(value), expires, path, domain, secure].join(''); - } else { // only name given, get cookie - var cookieValue = null; - if (document.cookie && document.cookie != '') { - var cookies = document.cookie.split(';'); - for (var i = 0; i < cookies.length; i++) { - var cookie = jQuery.trim(cookies[i]); - // Does this cookie string begin with the name we want? - if (cookie.substring(0, name.length + 1) == (name + '=')) { - cookieValue = decodeURIComponent(cookie.substring(name.length + 1)); - break; - } - } - } - return cookieValue; - } -}; \ No newline at end of file diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/jquery.json.js --- a/static/scripts/jquery.json.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -(function ($) { - var m = { - '\b': '\\b', - '\t': '\\t', - '\n': '\\n', - '\f': '\\f', - '\r': '\\r', - '"' : '\\"', - '\\': '\\\\' - }, - s = { - 'array': function (x) { - var a = ['['], b, f, i, l = x.length, v; - for (i = 0; i < l; i += 1) { - v = x[i]; - f = s[typeof v]; - if (f) { - v = f(v); - if (typeof v == 'string') { - if (b) { - a[a.length] = ','; - } - a[a.length] = v; - b = true; - } - } - } - a[a.length] = ']'; - return a.join(''); - }, - 'boolean': function (x) { - return String(x); - }, - 'null': function (x) { - return "null"; - }, - 'number': function (x) { - return isFinite(x) ? String(x) : 'null'; - }, - 'object': function (x) { - if (x) { - if (x instanceof Array) { - return s.array(x); - } - var a = ['{'], b, f, i, v; - for (i in x) { - v = x[i]; - f = s[typeof v]; - if (f) { - v = f(v); - if (typeof v == 'string') { - if (b) { - a[a.length] = ','; - } - a.push(s.string(i), ':', v); - b = true; - } - } - } - a[a.length] = '}'; - return a.join(''); - } - return 'null'; - }, - 'string': function (x) { - if (/["\\\x00-\x1f]/.test(x)) { - x = x.replace(/([\x00-\x1f\\"])/g, function(a, b) { - var c = m[b]; - if (c) { - return c; - } - c = b.charCodeAt(); - return '\\u00' + - Math.floor(c / 16).toString(16) + - (c % 16).toString(16); - }); - } - return '"' + x + '"'; - } - }; - - $.toJSON = function(v) { - var f = isNaN(v) ? s[typeof v] : s['number']; - if (f) return f(v); - }; - - $.parseJSON = function(v, safe) { - if (safe === undefined) safe = $.parseJSON.safe; - if (safe && !/^("(\\.|[^"\\\n\r])*?"|[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t])+?$/.test(v)) - return undefined; - return eval('('+v+')'); - }; - - $.parseJSON.safe = false; - -})(jQuery); diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/packed/cookie_set.js --- a/static/scripts/packed/cookie_set.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -function CookieSet(a){this.cookie_name=a;this.store=store={};jQuery.each((jQuery.cookie(a)||"").split("|"),function(c,b){store[b]=true})}CookieSet.prototype.add=function(a){this.store[a]=true;return this};CookieSet.prototype.remove=function(a){delete this.store[a];return this};CookieSet.prototype.removeAll=function(a){this.store={};return this};CookieSet.prototype.contains=function(a){return(a in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}jQuery.cookie(this.cookie_name,t.join("|"));return this}; \ No newline at end of file diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/packed/jquery.cookie.js --- a/static/scripts/packed/jquery.cookie.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -jQuery.cookie=function(b,j,m){if(typeof j!="undefined"){m=m||{};if(j===null){j="";m.expires=-1}var e="";if(m.expires&&(typeof m.expires=="number"||m.expires.toUTCString)){var f;if(typeof m.expires=="number"){f=new Date();f.setTime(f.getTime()+(m.expires*24*60*60*1000))}else{f=m.expires}e="; expires="+f.toUTCString()}var l=m.path?"; path="+m.path:"";var g=m.domain?"; domain="+m.domain:"";var a=m.secure?"; secure":"";document.cookie=[b,"=",encodeURIComponent(j),e,l,g,a].join("")}else{var d=null;if(document.cookie&&document.cookie!=""){var k=document.cookie.split(";");for(var h=0;h<k.length;h++){var c=jQuery.trim(k[h]);if(c.substring(0,b.length+1)==(b+"=")){d=decodeURIComponent(c.substring(b.length+1));break}}}return d}}; \ No newline at end of file diff -r 97170896bb91 -r 0517fd342fc8 static/scripts/packed/jquery.json.js --- a/static/scripts/packed/jquery.json.js Thu Aug 20 11:04:45 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -(function($){var m={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},s={array:function(x){var a=["["],b,f,i,l=x.length,v;for(i=0;i<l;i+=1){v=x[i];f=s[typeof v];if(f){v=f(v);if(typeof v=="string"){if(b){a[a.length]=","}a[a.length]=v;b=true}}}a[a.length]="]";return a.join("")},"boolean":function(x){return String(x)},"null":function(x){return"null"},number:function(x){return isFinite(x)?String(x):"null"},object:function(x){if(x){if(x instanceof Array){return s.array(x)}var a=["{"],b,f,i,v;for(i in x){v=x[i];f=s[typeof v];if(f){v=f(v);if(typeof v=="string"){if(b){a[a.length]=","}a.push(s.string(i),":",v);b=true}}}a[a.length]="}";return a.join("")}return"null"},string:function(x){if(/["\\\x00-\x1f]/.test(x)){x=x.replace(/([\x00-\x1f\\"])/g,function(a,b){var c=m[b];if(c){return c}c=b.charCodeAt();return"\\u00"+Math.floor(c/16).toString(16)+(c%16).toString(16)})}return'"'+x+'"'}};$.toJSON=function(v){var f=isNaN(v)?s[typeof v]:s.number;if(f){return f(v) }};$.parseJSON=function(v,safe){if(safe===undefined){safe=$.parseJSON.safe}if(safe&&!/^("(\\.|[^"\\\n\r])*?"|[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t])+?$/.test(v)){return undefined}return eval("("+v+")")};$.parseJSON.safe=false})(jQuery); \ No newline at end of file diff -r 97170896bb91 -r 0517fd342fc8 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Aug 20 11:04:45 2009 -0400 +++ b/templates/workflow/editor.mako Thu Aug 20 12:41:37 2009 -0400 @@ -30,7 +30,6 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.drop.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.json.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.jstore-all.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> @@ -350,7 +349,7 @@ type: "POST", data: { id: "${trans.security.encode_id( workflow_id )}", - workflow_data: function() { return $.toJSON( workflow.to_simple() ) }, + workflow_data: function() { return JSON.stringify( workflow.to_simple() ) }, "_": "true" }, dataType: 'json',

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 ]">

1 0

[hg] galaxy 2602: Require json2.js
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/62e24f51b518 changeset: 2602:62e24f51b518 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 20 12:51:39 2009 -0400 description: Require json2.js 2 file(s) affected in this change: static/scripts/packed/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako diffs (19 lines): diff -r 0517fd342fc8 -r 62e24f51b518 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 20 12:41:37 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 20 12:51:39 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio 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oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connecto 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.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></d iv>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this). offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.c ss("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_n odes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connecto rs,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.acti ve_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];fo r(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_ up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type =null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:functi on(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f* j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent ().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r 0517fd342fc8 -r 62e24f51b518 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Aug 20 12:41:37 2009 -0400 +++ b/templates/workflow/editor.mako Thu Aug 20 12:51:39 2009 -0400 @@ -31,6 +31,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.jstore-all.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/json2.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.workflow_editor.canvas.js')}"> </script>

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[hg] galaxy 2596: Fix collect_primary_datasets() and add collect...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b77721ef035d changeset: 2596:b77721ef035d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Aug 21 17:03:42 2009 -0400 description: Fix collect_primary_datasets() and add collected primary/child datasets to job. Add new filter to dynamic_options: remove_value. Fix error in exception when reruning a dataset with a JobToOutputDatasetAssociation but with no job. 3 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/dynamic_options.py lib/galaxy/web/controllers/tool_runner.py diffs (150 lines): diff -r 108533bf35b8 -r b77721ef035d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Aug 21 15:18:17 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Aug 21 17:03:42 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__' % 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__' % 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 108533bf35b8 -r b77721ef035d lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Fri Aug 21 15:18:17 2009 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Fri Aug 21 17:03:42 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 108533bf35b8 -r b77721ef035d lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Fri Aug 21 15:18:17 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Fri Aug 21 17:03:42 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:

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galaxy-dev August 2009