February 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3317: Improvements to text rendering in TextArea fie...
by Greg Von Kuster 03 Feb '10

03 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4a2a488e4fa0 changeset: 3317:4a2a488e4fa0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 03 09:32:37 2010 -0500 description: Improvements to text rendering in TextArea fields in libraries. Eliminate the Optional / Required words in forms if no help text. diffstat: lib/galaxy/model/__init__.py | 6 +++++- templates/library/common/common.mako | 15 +-------------- templates/library/common/ldda_info.mako | 2 +- 3 files changed, 7 insertions(+), 16 deletions(-) diffs (57 lines): diff -r 4686a93802c0 -r 4a2a488e4fa0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Feb 02 16:49:00 2010 -0500 +++ b/lib/galaxy/model/__init__.py Wed Feb 03 09:32:37 2010 -0500 @@ -1273,9 +1273,13 @@ req = 'Required' else: req = 'Optional' + if field[ 'helptext' ]: + helptext='%s (%s)' % ( field[ 'helptext' ], req ) + else: + helptext = '' widgets.append( dict( label=field[ 'label' ], widget=field_widget, - helptext='%s (%s)' % ( field[ 'helptext' ], req ) ) ) + helptext=helptext ) ) return widgets class FormDefinitionCurrent( object ): diff -r 4686a93802c0 -r 4a2a488e4fa0 templates/library/common/common.mako --- a/templates/library/common/common.mako Tue Feb 02 16:49:00 2010 -0500 +++ b/templates/library/common/common.mako Wed Feb 03 09:32:37 2010 -0500 @@ -36,22 +36,9 @@ %else: %for i, field in enumerate( widgets ): %if field[ 'widget' ].value: - <% - val = field[ 'widget' ].value - # Change new line chars to html - if val.find( '\r\n' ) >= 0: - val = val.replace( '\r\n', '<br/>' ) - if val.find( '\r' ) >= 0: - val = val.replace( '\r', '<br/>' ) - if val.find( '\n' ) >= 0: - val = val.replace( '\n', '<br/>' ) - # Convert to unicode to display non-ascii characters. - if type( val ) is not unicode: - val = unicode( val, 'utf-8' ) - %> <div class="form-row"> <label>${field[ 'label' ]}</label> - ${val} + <pre>${field[ 'widget' ].value}</pre> <div class="toolParamHelp" style="clear: both;"> ${field[ 'helptext' ]} </div> diff -r 4686a93802c0 -r 4a2a488e4fa0 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Tue Feb 02 16:49:00 2010 -0500 +++ b/templates/library/common/ldda_info.mako Wed Feb 03 09:32:37 2010 -0500 @@ -63,7 +63,7 @@ <div class="toolFormBody"> <div class="form-row"> <label>Message:</label> - ${ldda.message} + <pre>${ldda.message}</pre> <div style="clear: both"></div> </div> <div class="form-row">

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Re: [galaxy-dev] [galaxy-bugs] Fwd: bug: boolean parameters in conditions always false
by Greg Von Kuster 02 Feb '10

02 Feb '10

Hello Gunnar, This issue should be resolved in change set 3316:4686a93802c0, which is now available in the Galaxy distribution. Let me know if you still encounter problems. Thanks! On Feb 1, 2010, at 11:23 AM, Gunnar Raetsch wrote: > Hi Greg, > > thanks for opening the bitbucket issue. > The bug is still there in the current release and we are bothered by > it... > Is there an estimate when it will be fixed? > > Cheers, Gunnar > > > On 08.12.2009, at 19:34, Greg Von Kuster wrote: > >> Hello Gunnar, >> >> I've opened the following ticket for this issue - you can "follow" >> the ticket in bitbucket if you want. Thanks for reporting this. >> >> http://bitbucket.org/galaxy/galaxy-central/issue/257/boolean-parameters-in-… >> >> >> On Dec 1, 2009, at 10:40 AM, James Taylor wrote: >> >>> >>> >>> Begin forwarded message: >>> >>>> From: Gunnar Rätsch <Gunnar.Raetsch(a)tuebingen.mpg.de> >>>> Date: December 1, 2009 7:16:43 AM EST >>>> To: James Taylor <james(a)bx.psu.edu> >>>> Subject: bug: boolean parameters in conditions always false >>>> >>>> Hi James, >>>> >>>> I recently encountered a bug in galaxy where the boolean >>>> parameter passed to the command is always false (i.e. the value >>>> given in falsevalue), even if the box is checked (truevalue never >>>> shows up). >>>> This reproducibly happens whenever the parameter is inside of a >>>> conditional. >>>> I verified that it works when it is outside and also works when I >>>> replace the boolean parameter with a select-field (with two >>>> options: true and false). >>>> >>>> Is this enough information to reproduce and fix it? >>>> >>>> Thanks a lot in advance! >>>> >>>> Cheers, Gunnar >>>> >>>> >>> >>> >>> _______________________________________________ >>> galaxy-bugs mailing list >>> galaxy-bugs(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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[hg] galaxy 3316: Fix a bug in ChcekboxField.get_html() - need t...
by Greg Von Kuster 02 Feb '10

02 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4686a93802c0 changeset: 3316:4686a93802c0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Feb 02 16:49:00 2010 -0500 description: Fix a bug in ChcekboxField.get_html() - need to include the prefix in the hidden field so it will work inside conditionals. Fixes ticket # #257. diffstat: lib/galaxy/web/form_builder.py | 9 +++++---- 1 files changed, 5 insertions(+), 4 deletions(-) diffs (21 lines): diff -r ac6e08aed7d4 -r 4686a93802c0 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Tue Feb 02 12:23:50 2010 -0500 +++ b/lib/galaxy/web/form_builder.py Tue Feb 02 16:49:00 2010 -0500 @@ -104,12 +104,13 @@ """ def __init__( self, name, checked=None ): self.name = name - self.checked = (checked == True) or (type(checked) == type('a') and (checked.lower() in ( "yes", "true", "on" ))) + self.checked = ( checked == True ) or ( type( checked ) == type( 'a' ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) def get_html( self, prefix="" ): - if self.checked: checked_text = "checked" + if self.checked: + checked_text = "checked" else: checked_text = "" - return '<input type="checkbox" name="%s%s" value="true" %s><input type="hidden" name="%s" value="true">' \ - % ( prefix, self.name, checked_text, self.name ) + return '<input type="checkbox" name="%s%s" value="true" %s><input type="hidden" name="%s%s" value="true">' \ + % ( prefix, self.name, checked_text, prefix, self.name ) @staticmethod def is_checked( value ): if value == True: # wierd behaviour caused by following check for 2 valued list - wtf? ross august 22

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fastx-toolkit version 0.0.13
by Assaf Gordon 02 Feb '10

02 Feb '10

Hello, A new version of FASTX-Toolkit is available for download at http://hannonlab.cshl.edu/fastx_toolkit/download.html This version should be much easier to integrate with galaxy. New tools: fastq_masker (suggested by Ben Bimber) New features: fastx_trimmer can trim N nucleotides from the end of the sequences (a new command line option, and a separate tool in Galaxy) fastx_clipper accepts minimum adapter length to clip (requested by Erick Antezana, command line only) Improved Galaxy integration: Almost all tools have working functional tests (except the plotting tools and barcode splitter). Plotting tools (nucleotide distribution and quality boxplot) detect input file type and show a detailed warning if given a FASTA/Q file as input (hopefully reducing bug reports). Tools read the input FASTQ type (sanger or solexa) and use the correct quality ASCII offset (33 for sanger, 64 for solexa). Comments are welcomed, -gordon

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[hg] galaxy 3315: Map end-of-line chars so they can be correctly...
by Greg Von Kuster 02 Feb '10

02 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ac6e08aed7d4 changeset: 3315:ac6e08aed7d4 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Feb 02 12:23:50 2010 -0500 description: Map end-of-line chars so they can be correctly stored in the db and displayed in form fields. Fix library formfields to convert end-of-line chars to html. diffstat: lib/galaxy/util/__init__.py | 4 +++- templates/library/common/common.mako | 15 ++++++++++++++- 2 files changed, 17 insertions(+), 2 deletions(-) diffs (41 lines): diff -r 050b4ced619f -r ac6e08aed7d4 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Mon Feb 01 16:30:33 2010 -0500 +++ b/lib/galaxy/util/__init__.py Tue Feb 02 12:23:50 2010 -0500 @@ -120,7 +120,9 @@ ']' :'__cb__', '{' :'__oc__', '}' :'__cc__', - '@' : '__at__' + '@' : '__at__', + '\n' : '__cn__', + '\r' : '__cr__' } def restore_text(text): diff -r 050b4ced619f -r ac6e08aed7d4 templates/library/common/common.mako --- a/templates/library/common/common.mako Mon Feb 01 16:30:33 2010 -0500 +++ b/templates/library/common/common.mako Tue Feb 02 12:23:50 2010 -0500 @@ -36,9 +36,22 @@ %else: %for i, field in enumerate( widgets ): %if field[ 'widget' ].value: + <% + val = field[ 'widget' ].value + # Change new line chars to html + if val.find( '\r\n' ) >= 0: + val = val.replace( '\r\n', '<br/>' ) + if val.find( '\r' ) >= 0: + val = val.replace( '\r', '<br/>' ) + if val.find( '\n' ) >= 0: + val = val.replace( '\n', '<br/>' ) + # Convert to unicode to display non-ascii characters. + if type( val ) is not unicode: + val = unicode( val, 'utf-8' ) + %> <div class="form-row"> <label>${field[ 'label' ]}</label> - ${field[ 'widget' ].value} + ${val} <div class="toolParamHelp" style="clear: both;"> ${field[ 'helptext' ]} </div>

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[hg] galaxy 3314: merge
by Greg Von Kuster 02 Feb '10

02 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/050b4ced619f changeset: 3314:050b4ced619f user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 01 16:30:33 2010 -0500 description: merge diffstat: lib/galaxy/util/hash_util.py | 43 ++++++++++++++----------- lib/galaxy/web/controllers/library_common.py | 5 +-- lib/galaxy/web/framework/helpers/__init__.py | 4 +- templates/library/common/browse_library.mako | 4 +- templates/library/common/common.mako | 2 +- templates/library/common/ldda_info.mako | 26 +++++++++------ test/functional/test_security_and_libraries.py | 5 ++- 7 files changed, 49 insertions(+), 40 deletions(-) diffs (212 lines): diff -r 068d572a2bf8 -r 050b4ced619f lib/galaxy/util/hash_util.py --- a/lib/galaxy/util/hash_util.py Mon Feb 01 16:30:18 2010 -0500 +++ b/lib/galaxy/util/hash_util.py Mon Feb 01 16:30:33 2010 -0500 @@ -1,28 +1,33 @@ +""" +Utility functions for bi-directional Python version compatibility. Python 2.5 +introduced hashlib which replaced sha in Python 2.4 and previous versions. +""" + import sys, logging -using_24 = sys.version_info[:2] < ( 2, 5 ) -if using_24: - import sha -else: + +# Use hashlib module if for Python 2.5+, fall back on old sha and md5 modules +try: import hashlib + sha1 = hashlib.sha1 + md5 = hashlib.md5 +except ImportError, e: + import sha, md5 + sha1 = sha.new + md5 = md5.new + import hmac log = logging.getLogger( __name__ ) -""" -Utility functions for bi-directional Python version compatibility. Python 2.5 -introduced hashlib which replaced sha in Python 2.4 and previous versions. -""" def new_secure_hash( text_type=None ): - if using_24: - if text_type: - return sha.new( text_type ).hexdigest() - return sha.new() + """ + Returns either a sha1 hash object (if called with no arguments), or a + hexdigest of the sha1 hash of the argument `text_type`. + """ + if text_type: + return sha1( text_type ).hexdigest() else: - if text_type: - return hashlib.sha1( text_type ).hexdigest() - return hashlib.sha1() + return sha1() + def hmac_new( key, value ): - if using_24: - return hmac.new( key, value, sha ).hexdigest() - else: - return hmac.new( key, value, hashlib.sha1 ).hexdigest() + return hmac.new( key, value, sha1 ).hexdigest() diff -r 068d572a2bf8 -r 050b4ced619f lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Feb 01 16:30:18 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Feb 01 16:30:33 2010 -0500 @@ -491,7 +491,6 @@ show_deleted=show_deleted, widgets=widgets, current_user_roles=current_user_roles, - show_deleted=show_deleted, msg=msg, messagetype=messagetype ) @web.expose @@ -1288,8 +1287,7 @@ filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) if not forms: - msg = "There are no forms on which to base the template, so create a form and " - msg += "try again to add the information template to the %s." % library_item_desc + msg = "There are no forms on which to base the template, so create a form and try to add the template again." trans.response.send_redirect( web.url_for( controller='forms', action='new', msg=msg, @@ -1342,7 +1340,6 @@ cntrller=cntrller, library_item_name=item.name, library_item_desc=library_item_desc, - library_id=library_id, item_type=item_type, library_id=library_id, folder_id=folder_id, diff -r 068d572a2bf8 -r 050b4ced619f lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Mon Feb 01 16:30:18 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/__init__.py Mon Feb 01 16:30:33 2010 -0500 @@ -4,8 +4,8 @@ from webhelpers import * from galaxy.util.json import to_json_string +from galaxy.util import hash_util from datetime import datetime, timedelta -import hashlib # If the date is more than one week ago, then display the actual date instead of in words def time_ago( x ): @@ -50,6 +50,6 @@ """ Return hex encoded md5 hash of string s """ - m = hashlib.md5() + m = hash_util.md5() m.update( s ) return m.hexdigest() \ No newline at end of file diff -r 068d572a2bf8 -r 050b4ced619f templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Mon Feb 01 16:30:18 2010 -0500 +++ b/templates/library/common/browse_library.mako Mon Feb 01 16:30:33 2010 -0500 @@ -196,7 +196,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">View this dataset's information</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add a template to this dataset</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and cntrller == 'library_admin' and info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete this dataset's template</a> @@ -294,7 +294,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">Edit this folder's information</a> %endif %if not branch_deleted( folder ) and ( ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Add template to this folder</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Add a template to this folder</a> %endif %if not branch_deleted( folder ) and cntrller == 'library_admin' and info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Delete this folder's template</a> diff -r 068d572a2bf8 -r 050b4ced619f templates/library/common/common.mako --- a/templates/library/common/common.mako Mon Feb 01 16:30:18 2010 -0500 +++ b/templates/library/common/common.mako Mon Feb 01 16:30:33 2010 -0500 @@ -265,7 +265,7 @@ ${field[ 'widget' ].get_html()} </div> <div class="toolParamHelp" style="clear: both;"> - ${field[ 'helptext' ]} + ${field[ 'helptext' ]}, leave blank to add a different template to this dataset after upload. </div> <div style="clear: both"></div> </div> diff -r 068d572a2bf8 -r 050b4ced619f templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Mon Feb 01 16:30:18 2010 -0500 +++ b/templates/library/common/ldda_info.mako Mon Feb 01 16:30:33 2010 -0500 @@ -1,13 +1,19 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/library/common/common.mako" import="render_template_info" /> -<% from galaxy import util %> +<% + from galaxy import util + from galaxy.web.controllers.library_common import branch_deleted -<% if ldda == ldda.library_dataset.library_dataset_dataset_association: current_version = True else: current_version = False + if ldda.user: + uploaded_by = ldda.user.email + else: + uploaded_by = 'anonymous' + info_association, inherited = ldda.get_info_association( restrict=True ) %> %if current_version: @@ -27,24 +33,22 @@ ${render_msg( msg, messagetype )} %endif -<% - if ldda.user: - uploaded_by = ldda.user.email - else: - uploaded_by = 'anonymous' -%> - <div class="toolForm"> <div class="toolFormTitle"> Information about ${ldda.name} - %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: + %if not library.deleted and not branch_deleted( ldda.library_dataset.folder ) and not ldda.library_dataset.deleted: <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> %if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda.library_dataset ): <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's information</a> + %if not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add a template to this dataset</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete this dataset's template</a> + %endif %endif %if cntrller=='library_admin' or trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) and trans.app.security_agent.can_manage_library_item( current_user_roles, ldda.library_dataset ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's permissions</a> %endif %if current_version and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda.library_dataset ) ): <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> diff -r 068d572a2bf8 -r 050b4ced619f test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Feb 01 16:30:18 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Mon Feb 01 16:30:33 2010 -0500 @@ -118,7 +118,10 @@ dp = sa_session.query( galaxy.model.DatasetPermissions ) \ .filter( galaxy.model.DatasetPermissions.table.c.dataset_id==latest_dataset.id ) \ .first() - if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: + if not dp.action: + raise AssertionError( 'The Dataset id %d has no associated DatasetPermissions when is should have "manage permissions".' \ + % latest_dataset.id ) + elif not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \ % ( latest_dataset.id, dp.action ) ) # Change DefaultHistoryPermissions for regular_user1

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[hg] galaxy 3313: Added UI support for annotating histories, HDA...
by Greg Von Kuster 02 Feb '10

02 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/068d572a2bf8 changeset: 3313:068d572a2bf8 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 01 16:30:18 2010 -0500 description: Added UI support for annotating histories, HDAs, workflows, and workflow steps. Numerous small changes as well: (a) added an 'edit workflow attributes' to workflow editor; (b) added 'Edit tags and Annotation' area to history panel; (c) added generic javascript method to ajax text updates. Also fixed public URL column bug. diffstat: lib/galaxy/web/base/controller.py | 57 ++++++++++- lib/galaxy/web/controllers/history.py | 13 ++- lib/galaxy/web/controllers/root.py | 4 + lib/galaxy/web/controllers/workflow.py | 67 +++++++++++- static/june_2007_style/base.css.tmpl | 42 +++++++ static/june_2007_style/blue/base.css | 7 + static/june_2007_style/blue/history.css | 7 - static/june_2007_style/history.css.tmpl | 40 ------- static/scripts/galaxy.base.js | 44 ++++++++ static/scripts/galaxy.workflow_editor.canvas.js | 5 +- static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/galaxy.workflow_editor.canvas.js | 2 +- templates/dataset/edit_attributes.mako | 39 ++++-- templates/grid_base.mako | 2 +- templates/root/history.mako | 80 ++++++++------ templates/sharing_base.mako | 8 +- templates/tagging_common.mako | 10 +- templates/workflow/edit_attributes.mako | 66 ++++++++++++ templates/workflow/editor.mako | 96 +++++++++++++++-- 19 files changed, 461 insertions(+), 130 deletions(-) diffs (993 lines): diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Feb 01 13:34:44 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Feb 01 16:30:18 2010 -0500 @@ -25,9 +25,13 @@ # Item's public URL based on username and slug. class PublicURLColumn( grids.TextColumn ): def get_link( self, trans, grid, item ): - if item.user.username: + if item.user.username and item.slug: return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - else: + elif not item.user.username: + # TODO: provide link to set username. + return None + elif not item.user.slug: + # TODO: provide link to set slg return None class BaseController( object ): @@ -73,6 +77,55 @@ item_class = None return item_class + def get_item_annotation_str( self, db_session, user, item ): + """ Returns a user's annotation string for an item. """ + annotation_obj = self.get_item_annotation_obj( db_session, user, item ) + if annotation_obj: + return annotation_obj.annotation + return None + + def get_item_annotation_obj( self, db_session, user, item ): + """ Returns a user's annotation object for an item. """ + # Get annotation association. TODO: we could replace this eval() with a long if/else stmt, but this is more general without sacrificing + try: + annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item.__class__.__name__ ) + except: + # Item doesn't have an annotation association class and cannot be annotated. + return False + + # Get annotation association object. + annotation_assoc = db_session.query( annotation_assoc_class ).filter_by( user=user ) + if item.__class__ == model.History: + annotation_assoc = annotation_assoc.filter_by( history=item ) + elif item.__class__ == model.HistoryDatasetAssociation: + annotation_assoc = annotation_assoc.filter_by( hda=item ) + elif item.__class__ == model.StoredWorkflow: + annotation_assoc = annotation_assoc.filter_by( stored_workflow=item ) + elif item.__class__ == model.WorkflowStep: + annotation_assoc = annotation_assoc.filter_by( workflow_step=item ) + return annotation_assoc.first() + + def add_item_annotation( self, trans, item, annotation ): + """ Add or update an item's annotation; a user can only have a single annotation for an item. """ + + # Get/create annotation association object. + annotation_assoc = self.get_item_annotation_obj( trans.sa_session, trans.get_user(), item ) + if not annotation_assoc: + # Create association. + # TODO: we could replace this eval() with a long if/else stmt, but this is more general without sacrificing + try: + annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item.__class__.__name__ ) + except: + # Item doesn't have an annotation association class and cannot be annotated. + return False + annotation_assoc = annotation_assoc_class() + item.annotations.append( annotation_assoc ) + annotation_assoc.user = trans.get_user() + + # Set annotation. + annotation_assoc.annotation = annotation + return True + Root = BaseController class SharingStatusColumn( grids.GridColumn ): diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Feb 01 13:34:44 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 01 16:30:18 2010 -0500 @@ -353,7 +353,7 @@ return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) @web.expose def rename_async( self, trans, id=None, new_name=None ): - history = trans.sa_session.query( model.History ).get( id ) + history = self.get_history( trans, id ) # Check that the history exists, and is either owned by the current # user (if logged in) or the current history assert history is not None @@ -365,6 +365,17 @@ history.name = new_name trans.sa_session.add( history ) trans.sa_session.flush() + + @web.expose + @web.require_login( "use Galaxy histories" ) + def annotate_async( self, trans, id, new_annotation=None, **kwargs ): + history = self.get_history( trans, id ) + if new_annotation: + self.add_item_annotation( trans, history, new_annotation ) + trans.sa_session.flush() + return + else: + return "failed" @web.expose @web.json diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Feb 01 13:34:44 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Mon Feb 01 16:30:18 2010 -0500 @@ -78,6 +78,7 @@ query = query.filter( model.HistoryDatasetAssociation.deleted == False ) return trans.stream_template_mako( "root/history.mako", history = history, + annotation = self.get_item_annotation_str( trans.sa_session, trans.get_user(), history ), datasets = query.all(), hda_id = hda_id, show_deleted = show_deleted ) @@ -304,6 +305,8 @@ else: setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_setting_metadata( data ) + self.add_item_annotation( trans, data, params.annotation ) + else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' trans.sa_session.flush() @@ -383,6 +386,7 @@ messagetype = 'done' return trans.fill_template( "/dataset/edit_attributes.mako", data=data, + data_annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), data ), datatypes=ldatatypes, current_user_roles=current_user_roles, all_roles=all_roles, diff -r d24f0190c2a8 -r 068d572a2bf8 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Feb 01 13:34:44 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 01 16:30:18 2010 -0500 @@ -303,6 +303,28 @@ session.flush() # Redirect to load galaxy frames. return trans.response.send_redirect( url_for( controller='workflow' ) ) + + @web.expose + @web.require_login( "use Galaxy workflows" ) + def edit_attributes( self, trans, id, **kwargs ): + # Get workflow and do error checking. + stored = get_stored_workflow( trans, id ) + if not stored: + error( "You do not own this workflow or workflow ID is invalid." ) + + # Update workflow attributes if new values submitted. + if 'name' in kwargs: + # Rename workflow. + stored.name = kwargs[ 'name' ] + if 'annotation' in kwargs: + # Set workflow annotation. + self.add_item_annotation( trans, stored, kwargs[ 'annotation' ] ) + trans.sa_session.flush() + + return trans.fill_template( 'workflow/edit_attributes.mako', + stored=stored, + annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), stored ) + ) @web.expose @web.require_login( "use Galaxy workflows" ) @@ -320,7 +342,29 @@ else: return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ .add_text( "new_name", "Workflow Name", value=stored.name ) - + + @web.expose + @web.require_login( "use Galaxy workflows" ) + def rename_async( self, trans, id, new_name=None, **kwargs ): + stored = get_stored_workflow( trans, id ) + if new_name: + stored.name = new_name + trans.sa_session.flush() + return + else: + return "failed" + + @web.expose + @web.require_login( "use Galaxy workflows" ) + def annotate_async( self, trans, id, new_annotation=None, **kwargs ): + stored = get_stored_workflow( trans, id ) + if new_annotation: + self.add_item_annotation( trans, stored, new_annotation ) + trans.sa_session.flush() + return + else: + return "failed" + @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): @@ -400,11 +444,11 @@ """ if not id: error( "Invalid workflow id" ) - id = trans.security.decode_id( id ) - return trans.fill_template( "workflow/editor.mako", workflow_id=id ) + stored = get_stored_workflow( trans, id ) + return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.get_user(), stored ) ) @web.json - def editor_form_post( self, trans, type='tool', tool_id=None, **incoming ): + def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ): """ Accepts a tool state and incoming values, and generates a new tool form and some additional information, packed into a json dictionary. @@ -423,7 +467,8 @@ 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'tool_errors': module.get_errors(), - 'form_html': module.get_config_form() + 'form_html': module.get_config_form(), + 'annotation': annotation } @web.json @@ -445,7 +490,8 @@ 'tooltip': module.get_tooltip(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), - 'form_html': module.get_config_form() + 'form_html': module.get_config_form(), + 'annotation': "" } @web.json @@ -477,6 +523,11 @@ # FIXME: Frontend should be able to handle workflow messages # as a dictionary not just the values data['upgrade_messages'][step.order_index] = upgrade_message.values() + # Get user annotation. + step_annotation = self.get_item_annotation_obj ( trans.sa_session, trans.get_user(), step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation # Pack attributes into plain dictionary step_dict = { 'id': step.order_index, @@ -489,6 +540,7 @@ 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'form_html': module.get_config_form(), + 'annotation' : annotation_str } # Connections input_connections = step.input_connections @@ -551,6 +603,9 @@ workflow.has_errors = True # Stick this in the step temporarily step.temp_input_connections = step_dict['input_connections'] + + # Save step annotation. + self.add_item_annotation( trans, step, step_dict[ 'annotation' ] ) # Second pass to deal with connections between steps for step in steps: # Input connections diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Mon Feb 01 13:34:44 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Feb 01 16:30:18 2010 -0500 @@ -656,3 +656,45 @@ } } + +## Icon buttons. + +.icon-button { + width: 16px; + height: 16px; + display: block; + float: left; + margin-left: 2px; + ## Allow alt text for screen readers + text-indent: 20px; +} + +.icon-button.display { + -sprite-group: history-buttons; + -sprite-image: eye_icon.png; +} + +.icon-button.display:hover { + -sprite-group: history-buttons; + -sprite-image: eye_icon_dark.png; +} + +.icon-button.delete { + -sprite-group: history-buttons; + -sprite-image: delete_icon.png; +} + +.icon-button.delete:hover { + -sprite-group: history-buttons; + -sprite-image: delete_icon_dark.png; +} + +.icon-button.edit { + -sprite-group: history-buttons; + -sprite-image: pencil_icon.png; +} + +.icon-button.edit:hover { + -sprite-group: history-buttons; + -sprite-image: pencil_icon_dark.png; +} \ No newline at end of file diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Mon Feb 01 13:34:44 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Feb 01 16:30:18 2010 -0500 @@ -110,3 +110,10 @@ .text-content fieldset{border-color:#ccc;border:1px solid #ccc;} .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} +.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;} +.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -52px;} +.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -78px;} +.icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} +.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} +.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;} +.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} \ No newline at end of file diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Mon Feb 01 13:34:44 2010 -0500 +++ b/static/june_2007_style/blue/history.css Mon Feb 01 16:30:18 2010 -0500 @@ -22,13 +22,6 @@ div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} div.historyItemButtons{float:right;} -.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;} -.icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} -.icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} -.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -52px;} -.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -78px;} -.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} div.historyItemBody div{padding-top:2px;} pre.peek{background:white;color:black;width:100%;overflow:auto;} pre.peek th{color:white;background:#023858;} diff -r d24f0190c2a8 -r 068d572a2bf8 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Mon Feb 01 13:34:44 2010 -0500 +++ b/static/june_2007_style/history.css.tmpl Mon Feb 01 16:30:18 2010 -0500 @@ -120,46 +120,6 @@ float: right; } -.icon-button { - width: 16px; - height: 16px; - display: block; - float: left; - margin-left: 2px; - ## Allow alt text for screen readers - text-indent: 20px; -} - -.icon-button.display { - -sprite-group: history-buttons; - -sprite-image: eye_icon.png; -} - -.icon-button.display:hover { - -sprite-group: history-buttons; - -sprite-image: eye_icon_dark.png; -} - -.icon-button.edit { - -sprite-group: history-buttons; - -sprite-image: pencil_icon.png; -} - -.icon-button.edit:hover { - -sprite-group: history-buttons; - -sprite-image: pencil_icon_dark.png; -} - -.icon-button.delete { - -sprite-group: history-buttons; - -sprite-image: delete_icon.png; -} - -.icon-button.delete:hover { - -sprite-group: history-buttons; - -sprite-image: delete_icon_dark.png; -} - div.historyItemBody div { padding-top: 2px; } diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Mon Feb 01 13:34:44 2010 -0500 +++ b/static/scripts/galaxy.base.js Mon Feb 01 16:30:18 2010 -0500 @@ -207,3 +207,47 @@ }); } } // end replace_dbkey_select() + +// +// Edit and save text asynchronously. +// +function async_save_text(click_to_edit_elt, text_elt_id, save_url, text_parm_name, use_textarea, num_rows) +{ + $("#" + click_to_edit_elt).click( function() { + var old_text = $("#" + text_elt_id).text() + if (use_textarea) + var t = $("<textarea rows='" + num_rows + "'>" + old_text + "</textarea>" ); + else + var t = $("<input type='text' value='" + old_text + "'></input>" ); + t.blur( function() { + $(this).remove(); + $("#" + text_elt_id).show(); + }); + t.keyup( function( e ) { + if ( e.keyCode == 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode == 13 ) { + // Enter key + new_text = this.value; + $(this).trigger( "blur" ); + var ajax_data = new Object(); + ajax_data[text_parm_name] = new_text; + $.ajax({ + url: save_url, + data: ajax_data, + error: function() { alert( "Text editing for elt " + text_elt_id + " failed" ) }, + success: function() { + $("#" + text_elt_id).text( new_text ); + } + }); + } + }); + $("#" + text_elt_id).hide(); + t.insertAfter( $("#" + text_elt_id) ); + t.focus(); + t.select(); + return false; + }); + +} diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Mon Feb 01 13:34:44 2010 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Mon Feb 01 16:30:18 2010 -0500 @@ -272,6 +272,7 @@ this.tool_state = data.tool_state; this.tool_errors = data.tool_errors; this.tooltip = data.tooltip ? data.tooltip : "" + this.annotation = data.annotation; if ( this.tool_errors ) { f.addClass( "tool-node-error" ); @@ -306,6 +307,7 @@ node = this; this.tool_state = data.tool_state; this.form_html = data.form_html; + this.annotation = data.annotation; this.tool_errors = data.tool_errors; if ( this.tool_errors ) { el.addClass( "tool-node-error" ); @@ -405,7 +407,8 @@ tool_state : node.tool_state, tool_errors : node.tool_errors, input_connections : input_connections, - position : $(node.element).position() + position : $(node.element).position(), + annotation: node.annotation }; nodes[ node.id ] = node_data; }); diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Mon Feb 01 13:34:44 2010 -0500 +++ b/static/scripts/packed/galaxy.base.js Mon Feb 01 16:30:18 2010 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var 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attr("value","?")}}}})}};function async_save_text(d,c,a,e,f,b){$("#"+d).click(function(){var h=$("#"+c).text();if(f){var g=$("<textarea rows='"+b+"'>"+h+"</textarea>")}else{var g=$("<input type='text' value='"+h+"'></input>")}g.blur(function(){$(this).remove();$("#"+c).show()});g.keyup(function(j){if(j.keyCode==27){$(this).trigger("blur")}else{if(j.keyCode==13){new_text=this.value;$(this).trigger("blur");var i=new Object();i[e]=new_text;$.ajax({url:a,data:i,error:function(){alert("Text editing for elt "+c+" failed")},success:function(){$("#"+c).text(new_text)}})}}});$("#"+c).hide();g.insertAfter($("#"+c));g.focus();g.select();return false})}; \ No newline at end of file diff -r d24f0190c2a8 -r 068d572a2bf8 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Feb 01 13:34:44 2010 -0500 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Feb 01 16:30:18 2010 -0500 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.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);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<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.ext ension!="input"){f=f+" ("+b.extension+")"}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.destroy()});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.connectors,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;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear _active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.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){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.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=Mat h.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.red raw()})});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.time out=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_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 +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);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<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.ext ension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}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.annotation=f.annotation;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.destroy()});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.connectors,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:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.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;$( "#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.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){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)} }if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.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/l oading_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;$(thi s).css({left:b,top:p});$(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.mi n(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_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 d24f0190c2a8 -r 068d572a2bf8 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/dataset/edit_attributes.mako Mon Feb 01 16:30:18 2010 -0500 @@ -58,21 +58,32 @@ <div style="clear: both"></div> </div> %if trans.get_user() is not None: - <%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> - <div class="form-row"> - <label> - Tags: - </label> - <div style="float: left; width: 295px; margin-right: 10px; border-style: inset; border-width: 1px"> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")} + <%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> + <div class="form-row"> + <label> + Tags: + </label> + <div style="float: left; width: 295px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")} + </div> + <div style="clear: both"></div> + <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> </div> - <div style="clear: both"></div> - </div> + <div class="form-row"> + <label> + Annotation / Notes: + </label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <textarea name="annotation" cols="40" rows="2">${data_annotation}</textarea> + </div> + <div style="clear: both"></div> + <div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div> + </div> %endif %for name, spec in data.metadata.spec.items(): %if spec.visible: diff -r d24f0190c2a8 -r 068d572a2bf8 templates/grid_base.mako --- a/templates/grid_base.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/grid_base.mako Mon Feb 01 16:30:18 2010 -0500 @@ -844,7 +844,7 @@ ## Item selection column %if show_item_checkboxes: <td style="width: 1.5em;"> - <input type="checkbox" id="${encoded_id}" name="id" value="${encoded_id}" class="grid-row-select-checkbox" /> + <input type="checkbox" name="id" value="${encoded_id}" id="${encoded_id}" class="grid-row-select-checkbox" /> </td> %endif ## Data columns diff -r d24f0190c2a8 -r 068d572a2bf8 templates/root/history.mako --- a/templates/root/history.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/root/history.mako Mon Feb 01 16:30:18 2010 -0500 @@ -15,7 +15,7 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history", "autocomplete_tagging" )} -${h.js( "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} +${h.js( "galaxy.base", "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> $(function() { @@ -42,36 +42,20 @@ $.jStore.remove("history_expand_state"); })); - $("#history-rename").click( function() { - var old_name = $("#history-name").text() - var t = $("<input type='text' value='" + old_name + "'></input>" ); - t.blur( function() { - $(this).remove(); - $("#history-name").show(); - }); - t.keyup( function( e ) { - if ( e.keyCode == 27 ) { - // Escape key - $(this).trigger( "blur" ); - } else if ( e.keyCode == 13 ) { - // Enter key - new_value = this.value; - $(this).trigger( "blur" ); - $.ajax({ - url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", - data: { "_": true, new_name: new_value }, - error: function() { alert( "Rename failed" ) }, - success: function() { - $("#history-name").text( new_value ); - } - }); - } - }); - $("#history-name").hide(); - $("#history-name-area").append( t ); - t.focus(); - return false; - }); + // Rename async. + async_save_text("history-rename", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name"); + + // Annotation async. + // Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging. + $('#workflow-tag').click( function() + { + $('.tag-area').click(); + return false; + }); + + // Annotate async. + async_save_text("history-annotate", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", true, 4); + // Updater updater({ <% updateable = [data for data in reversed( datasets ) if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]] %> @@ -266,6 +250,9 @@ .historyItemBody { display: none; } +div.form-row { + padding: 5px 5px 5px 0px; +} </style> <noscript> @@ -303,12 +290,31 @@ <%namespace file="history_common.mako" import="render_dataset" /> %if trans.get_user() is not None: - <style> - .tag-element { - margin-bottom: 0.5em; - } - </style> - ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='history.mako' )} + <div style="margin: 0px 0px 5px 10px"> + <a href="#" onclick="$('#tags-and-annotation').toggle('fast')">Edit Tags and Annotation/Notes</a> + <div id="tags-and-annotation" style="display: none"> + ## Tagging elt. + <div class="form-row"> + <label>Tags:</label> + <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)} + <div style="clear: both"></div> + </div> + + ## Annotation elt. + <div id="history-annotation-area" class="form-row"> + <label>Annotation / Notes:</label> + <div style="float: right"><a id="history-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='annotate_async' )}"></a></div> + <div id="history-annotation">${annotation}</div> + <div style="clear: both"></div> + </div> + </div> + </div> %endif %if not datasets: diff -r d24f0190c2a8 -r 068d572a2bf8 templates/sharing_base.mako --- a/templates/sharing_base.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/sharing_base.mako Mon Feb 01 16:30:18 2010 -0500 @@ -67,7 +67,7 @@ <div class="indent" style="margin-top: 2em"> <h3>Making ${item_class_name} Accessible via Link and Publishing It</h3> - <div class="indent"> + <div> %if item.importable: <% item_status = "accessible via link" @@ -75,7 +75,7 @@ item_status = item_status + " and published" %> This ${item_class_name_lc} <strong>${item_status}</strong>. - <div class="indent"> + <div> <p>Anyone can view and import this ${item_class_name_lc} by visiting the following URL: <% url = h.url_for( action='display_by_username_and_slug', username=trans.get_user().username, slug=item.slug, qualified=True ) %> <blockquote> @@ -88,7 +88,7 @@ </div> <p>You can: - <div class="indent"> + <div> <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" method="POST"> %if not item.published: @@ -130,7 +130,7 @@ <h3>Sharing ${item_class_name} with Specific Users</h3> - <div class="indent"> + <div> %if item.users_shared_with: <p> diff -r d24f0190c2a8 -r 068d572a2bf8 templates/tagging_common.mako --- a/templates/tagging_common.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/tagging_common.mako Mon Feb 01 16:30:18 2010 -0500 @@ -20,7 +20,7 @@ %endif ## Render HTML for a list of tags. -<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual')"> +<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual', render_add_tag_button=True)"> ## Useful attributes. <% num_tags = len( tags ) @@ -79,7 +79,9 @@ <input class="tag-input" type='text' size='${input_size}'/> %endif ## Add "add tag" button. - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %if render_add_tag_button: + <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %endif %endif </div> </div> @@ -102,7 +104,7 @@ ## Render individual tagging element. -<%def name="render_individual_tagging_element(user=None, tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True)"> +<%def name="render_individual_tagging_element(user=None, tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True, render_add_tag_button=True)"> ## Useful attributes. <% # Useful ids. @@ -114,7 +116,7 @@ %> ## Build HTML. - ${self.render_tagging_element_html(elt_id, item_tags, editable, use_toggle_link, input_size, in_form)} + ${self.render_tagging_element_html(elt_id=elt_id, tags=item_tags, editable=editable, use_toggle_link=use_toggle_link, input_size=input_size, in_form=in_form, render_add_tag_button=render_add_tag_button)} ## Build script that augments tags using progressive javascript. <script type="text/javascript"> diff -r d24f0190c2a8 -r 068d572a2bf8 templates/workflow/edit_attributes.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/workflow/edit_attributes.mako Mon Feb 01 16:30:18 2010 -0500 @@ -0,0 +1,66 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="title()">${_('Edit Workflow Attributes')}</%def> + +<%def name="stylesheets()"> + ${h.css( "base", "autocomplete_tagging" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )} +</%def> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<%def name="body()"> + <div class="toolForm"> + <div class="toolFormTitle">${_('Edit Workflow Attributes')}</div> + <div class="toolFormBody"> + <form name="edit_attributes" action="${h.url_for( action='edit_attributes' )}" method="post"> + <input type="hidden" name="id" value="${trans.security.encode_id( stored.id )}"/> + <div class="form-row"> + <label> + Name: + </label> + <div style="float: left; width: 225px; margin-right: 10px;"> + <input type="text" name="name" value="${stored.name}" size="30"/> + </div> + <div style="clear: both"></div> + </div> + <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> + <div class="form-row"> + <label> + Tags: + </label> + <div style="float: left; width: 265px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="25")} + </div> + <div style="clear: both"></div> + <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> + </div> + <div class="form-row"> + <label> + Annotation / Notes: + </label> + <div style="float: left; width: 225px; margin-right: 10px;"> + <textarea name="annotation" cols="30" rows="2">${annotation}</textarea> + </div> + <div style="clear: both"></div> + <div class="toolParamHelp">Add an annotation notes to a workflow; annotations are available when a workflow is viewed.</div> + </div> + <div class="form-row"> + <input type="submit" name="save" value="${_('Save')}"/> + </div> + </form> + </div> + </div> +</%def> \ No newline at end of file diff -r d24f0190c2a8 -r 068d572a2bf8 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Mon Feb 01 13:34:44 2010 -0500 +++ b/templates/workflow/editor.mako Mon Feb 01 16:30:18 2010 -0500 @@ -34,7 +34,9 @@ "jquery.jstore-all", "json2", "galaxy.base", - "galaxy.workflow_editor.canvas" )} + "galaxy.workflow_editor.canvas", + "jquery.autocomplete", + "autocomplete_tagging")} <!--[if lt IE 7]> <script type='text/javascript'> @@ -77,7 +79,7 @@ // Load workflow definition $.ajax( { url: "${h.url_for( action='load_workflow' )}", - data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" }, + data: { id: "${trans.security.encode_id( stored.id )}", "_": "true" }, dataType: 'json', cache: false, success: function( data ) { @@ -142,6 +144,12 @@ canvas_manager.draw_overview(); }); + $('#edit-attributes-button').click( function() { + workflow.clear_active_node(); + $('#edit-attributes').show(); + $('#right-content').hide(); + }); + $.jStore.ready(function(engine) { engine.ready(function() { // On load, set the size to the pref stored in local storage if it exists @@ -209,6 +217,19 @@ } }); }); + + // Rename async. + async_save_text("workflow-rename", "workflow-name", "${h.url_for( action="rename_async", id=trans.security.encode_id(stored.id) )}", "new_name"); + + // Tag async. Simply have the workflow tag element generate a click on the tag element to activate tagging. + $('#workflow-tag').click( function() + { + $('.tag-area').click(); + return false; + }); + + // Annotate async. + async_save_text("workflow-annotate", "workflow-annotation", "${h.url_for( action="annotate_async", id=trans.security.encode_id(stored.id) )}", "new_annotation", true, 4); }); // Global state for the whole workflow @@ -285,7 +306,8 @@ }; function show_form_for_tool( text, node ) { - $("#right-content").html( text ); + $("#edit-attributes").hide(); + $("#right-content").show().html( text ); $("#right-content").find( "form" ).ajaxForm( { type: 'POST', dataType: 'json', @@ -316,6 +338,17 @@ $(this).remove(); make_popupmenu( b, options ); }); + // Add annotation field to form. + // TODO: need to set the annotation for this tool. + var annotation_div = + $( "<div class='form-row'> \ + <label>Annotation / Notes:</label> \ + <div style='margin-right: 10px;'> \ + <textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \ + <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \ + </div> \ + </div>"); + $(this).append( annotation_div ); // Implements auto-saving based on whether the inputs change. We consider // "changed" to be when a field is accessed and not necessarily modified // because of an issue where "onchange" is not triggered when activating @@ -366,7 +399,7 @@ url: "${h.url_for( action='save_workflow' )}", type: "POST", data: { - id: "${trans.security.encode_id( workflow_id )}", + id: "${trans.security.encode_id( stored.id )}", workflow_data: function() { return JSON.stringify( workflow.to_simple() ) }, "_": "true" }, @@ -421,10 +454,10 @@ <%def name="stylesheets()"> ## Include "base.css" for styling tool menu and forms (details) - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + ${h.css( "base", "autocomplete_tagging")} ## But make sure styles for the layout take precedence - ${parent.stylesheets()} + ${parent.stylesheets()} <style type="text/css"> body { margin: 0; padding: 0; overflow: hidden; } @@ -508,9 +541,8 @@ div.toolFormRow { position: relative; } - - - #right-content { + + .right-content { margin: 5px; } @@ -575,7 +607,6 @@ } .form-row { - } div.toolFormInCanvas div.toolFormBody { padding: 0; @@ -740,9 +771,52 @@ <div class="unified-panel-header" unselectable="on"> <div class="unified-panel-header-inner"> Details + <div style="float: right"> + <a id="edit-attributes-button" class="panel-header-button">Edit Workflow Attributes</a> + </div> </div> </div> <div class="unified-panel-body" style="overflow: auto;"> - <div id="right-content"></div> + ## Div for elements to modify workflow attributes. + <div id="edit-attributes" class="toolForm right-content"> + <div class="toolFormTitle">Edit Workflow Attributes</div> + <div class="toolFormBody"> + ## Workflow name. + <div id="workflow-name-area" class="form-row"> + <label>Name:</label> + <div style="float: right"><a id="workflow-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='rename_sync' )}"></a></div> + <div id="workflow-name">${stored.name}</div> + <div style="clear: both"></div> + </div> + ## Workflow tags. + <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> + <div class="form-row"> + <label> + Tags: + </label> + <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> + <div style="float: left; width: 225px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> + <style> + .tag-area { + border: none; + } + </style> + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)} + </div> + <div style="clear: both"></div> + <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> + </div> + ## Workflow annotation. + <div id="workflow-annotation-area" class="form-row"> + <label>Annotation / Notes:</label> + <div style="float: right"><a id="workflow-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> + <div id="workflow-annotation">${annotation}</div> + <div style="clear: both"></div> + <div class="toolParamHelp">Add an annotation or notes to a workflow; annotations are available when a workflow is viewed.</div> + </div> + </div> + </div> + ## Div where tool details are loaded and modified. + <div id="right-content" class="right-content"></div> </div> </%def>

1 0

[hg] galaxy 3312: Rollback case-insensitive sorting on grids bec...
by Greg Von Kuster 02 Feb '10

02 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d24f0190c2a8 changeset: 3312:d24f0190c2a8 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 01 13:34:44 2010 -0500 description: Rollback case-insensitive sorting on grids because it doesn't work with postgres and mysql. diffstat: lib/galaxy/web/framework/helpers/grids.py | 7 +++++-- 1 files changed, 5 insertions(+), 2 deletions(-) diffs (19 lines): diff -r edfb84f6371e -r d24f0190c2a8 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Sat Jan 30 16:38:12 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Feb 01 13:34:44 2010 -0500 @@ -157,10 +157,13 @@ if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' - query = query.order_by( func.lower( self.model_class.table.c.get( sort_key ) ).desc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).desc() ) + # Can't use lower() on timestamp objects. + #query = query.order_by( func.lower( self.model_class.table.c.get( sort_key ) ).desc() ) else: sort_order = 'asc' - query = query.order_by( func.lower( self.model_class.table.c.get( sort_key ) ).asc() ) + # See reason for not using lower() to do case-insensitive search. + query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key # There might be a current row

1 0

[hg] galaxy 3311: Fix md5 hashing helper for Python 2.4
by Greg Von Kuster 01 Feb '10

01 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/084973d2b331 changeset: 3311:084973d2b331 user: James Taylor <james(a)jamestaylor.org> date: Mon Feb 01 16:23:20 2010 -0500 description: Fix md5 hashing helper for Python 2.4 diffstat: lib/galaxy/util/hash_util.py | 43 +++++++++++++++------------ lib/galaxy/web/framework/helpers/__init__.py | 4 +- 2 files changed, 26 insertions(+), 21 deletions(-) diffs (78 lines): diff -r 5ea7bb062c22 -r 084973d2b331 lib/galaxy/util/hash_util.py --- a/lib/galaxy/util/hash_util.py Mon Feb 01 15:43:07 2010 -0500 +++ b/lib/galaxy/util/hash_util.py Mon Feb 01 16:23:20 2010 -0500 @@ -1,28 +1,33 @@ +""" +Utility functions for bi-directional Python version compatibility. Python 2.5 +introduced hashlib which replaced sha in Python 2.4 and previous versions. +""" + import sys, logging -using_24 = sys.version_info[:2] < ( 2, 5 ) -if using_24: - import sha -else: + +# Use hashlib module if for Python 2.5+, fall back on old sha and md5 modules +try: import hashlib + sha1 = hashlib.sha1 + md5 = hashlib.md5 +except ImportError, e: + import sha, md5 + sha1 = sha.new + md5 = md5.new + import hmac log = logging.getLogger( __name__ ) -""" -Utility functions for bi-directional Python version compatibility. Python 2.5 -introduced hashlib which replaced sha in Python 2.4 and previous versions. -""" def new_secure_hash( text_type=None ): - if using_24: - if text_type: - return sha.new( text_type ).hexdigest() - return sha.new() + """ + Returns either a sha1 hash object (if called with no arguments), or a + hexdigest of the sha1 hash of the argument `text_type`. + """ + if text_type: + return sha1( text_type ).hexdigest() else: - if text_type: - return hashlib.sha1( text_type ).hexdigest() - return hashlib.sha1() + return sha1() + def hmac_new( key, value ): - if using_24: - return hmac.new( key, value, sha ).hexdigest() - else: - return hmac.new( key, value, hashlib.sha1 ).hexdigest() + return hmac.new( key, value, sha1 ).hexdigest() diff -r 5ea7bb062c22 -r 084973d2b331 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Mon Feb 01 15:43:07 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/__init__.py Mon Feb 01 16:23:20 2010 -0500 @@ -4,8 +4,8 @@ from webhelpers import * from galaxy.util.json import to_json_string +from galaxy.util import hash_util from datetime import datetime, timedelta -import hashlib # If the date is more than one week ago, then display the actual date instead of in words def time_ago( x ): @@ -50,6 +50,6 @@ """ Return hex encoded md5 hash of string s """ - m = hashlib.md5() + m = hash_util.md5() m.update( s ) return m.hexdigest() \ No newline at end of file

1 0

[hg] galaxy 3310: A few improvements to library templates. Beha...
by Greg Von Kuster 01 Feb '10

01 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5ea7bb062c22 changeset: 3310:5ea7bb062c22 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Feb 01 15:43:07 2010 -0500 description: A few improvements to library templates. Behavior is still not optimal, but at least now functional. Functional tests still needed, and coming shortly. diffstat: lib/galaxy/web/controllers/library_common.py | 3 +-- templates/library/common/browse_library.mako | 4 ++-- templates/library/common/common.mako | 2 +- templates/library/common/ldda_info.mako | 26 +++++++++++++++----------- test/functional/test_security_and_libraries.py | 5 ++++- 5 files changed, 23 insertions(+), 17 deletions(-) diffs (118 lines): diff -r 25b70e6cdd85 -r 5ea7bb062c22 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Feb 01 14:56:23 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Feb 01 15:43:07 2010 -0500 @@ -1287,8 +1287,7 @@ filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) if not forms: - msg = "There are no forms on which to base the template, so create a form and " - msg += "try again to add the information template to the %s." % library_item_desc + msg = "There are no forms on which to base the template, so create a form and try to add the template again." trans.response.send_redirect( web.url_for( controller='forms', action='new', msg=msg, diff -r 25b70e6cdd85 -r 5ea7bb062c22 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Mon Feb 01 14:56:23 2010 -0500 +++ b/templates/library/common/browse_library.mako Mon Feb 01 15:43:07 2010 -0500 @@ -196,7 +196,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">View this dataset's information</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add a template to this dataset</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and cntrller == 'library_admin' and info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete this dataset's template</a> @@ -294,7 +294,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">Edit this folder's information</a> %endif %if not branch_deleted( folder ) and ( ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Add template to this folder</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Add a template to this folder</a> %endif %if not branch_deleted( folder ) and cntrller == 'library_admin' and info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Delete this folder's template</a> diff -r 25b70e6cdd85 -r 5ea7bb062c22 templates/library/common/common.mako --- a/templates/library/common/common.mako Mon Feb 01 14:56:23 2010 -0500 +++ b/templates/library/common/common.mako Mon Feb 01 15:43:07 2010 -0500 @@ -265,7 +265,7 @@ ${field[ 'widget' ].get_html()} </div> <div class="toolParamHelp" style="clear: both;"> - ${field[ 'helptext' ]} + ${field[ 'helptext' ]}, leave blank to add a different template to this dataset after upload. </div> <div style="clear: both"></div> </div> diff -r 25b70e6cdd85 -r 5ea7bb062c22 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Mon Feb 01 14:56:23 2010 -0500 +++ b/templates/library/common/ldda_info.mako Mon Feb 01 15:43:07 2010 -0500 @@ -1,13 +1,19 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/library/common/common.mako" import="render_template_info" /> -<% from galaxy import util %> +<% + from galaxy import util + from galaxy.web.controllers.library_common import branch_deleted -<% if ldda == ldda.library_dataset.library_dataset_dataset_association: current_version = True else: current_version = False + if ldda.user: + uploaded_by = ldda.user.email + else: + uploaded_by = 'anonymous' + info_association, inherited = ldda.get_info_association( restrict=True ) %> %if current_version: @@ -27,24 +33,22 @@ ${render_msg( msg, messagetype )} %endif -<% - if ldda.user: - uploaded_by = ldda.user.email - else: - uploaded_by = 'anonymous' -%> - <div class="toolForm"> <div class="toolFormTitle"> Information about ${ldda.name} - %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: + %if not library.deleted and not branch_deleted( ldda.library_dataset.folder ) and not ldda.library_dataset.deleted: <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> %if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda.library_dataset ): <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's information</a> + %if not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Add a template to this dataset</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_info_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete this dataset's template</a> + %endif %endif %if cntrller=='library_admin' or trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) and trans.app.security_agent.can_manage_library_item( current_user_roles, ldda.library_dataset ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit this dataset's permissions</a> %endif %if current_version and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda.library_dataset ) ): <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> diff -r 25b70e6cdd85 -r 5ea7bb062c22 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Feb 01 14:56:23 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Mon Feb 01 15:43:07 2010 -0500 @@ -118,7 +118,10 @@ dp = sa_session.query( galaxy.model.DatasetPermissions ) \ .filter( galaxy.model.DatasetPermissions.table.c.dataset_id==latest_dataset.id ) \ .first() - if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: + if not dp.action: + raise AssertionError( 'The Dataset id %d has no associated DatasetPermissions when is should have "manage permissions".' \ + % latest_dataset.id ) + elif not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \ % ( latest_dataset.id, dp.action ) ) # Change DefaultHistoryPermissions for regular_user1

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