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

mysql setup / upload speed for fastq
by Nathaniel Street 11 Mar '10

11 Mar '10

Hi I have set galaxy to use mysql on localhost but I could not workout the syntax for the database_connection line to specify a username and password. Is this possible? I'm using Ubuntu so as per the install guide I have this database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock I wanted to try mysql to see if it was faster for uploads of very large NGS files. At the moment even uploading a file from the localhost is very very slow. Is this normal or are there some ways to speed it up? My fastq files are all > 10GB. Maybe using Galaxy isn't the right way to go and I should use the tools locally but as NGS handling is in there I am guessing large files were in mind? Thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

2 2

Adding custom genome
by Nathaniel Street 11 Mar '10

11 Mar '10

Hi I'm trying to add a custom genome to a local galaxy install. So far I have done this: 1)Create a fasta file per scaffold (it's an unfinished genome) 2)Create a nib file per one of those scaffold fasta files 3)Add an entry to build.txt nis Test genome (nis) 4)Add a line to alignseq.loc seq nis /data/nib/nis 5)Add a line to faseq.loc nis /data/sequences/nis Is there more that I need to do to be able to extract sequences using the Extract Genomic DNA tool? I tried to use the tool by uploading a GFF3 file, extracting a small part of that for testing and then using that small part to extract genomic DNA. When I try this I get an error message returned AttributeError: 'tuple' object has no attribute 'iteritems' And the text version of the Traceback gives this URL: http://XXX:XXX:XX:XX:8080/tool_runner/index File '/home/nat/work/software/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 807 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 1079 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 140 in execute inp_data = self.collect_input_datasets( tool, incoming, trans ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 101 in collect_input_datasets tool.visit_inputs( param_values, visitor ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 754 in visit_inputs callback( "", input, value[input.name] ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 85 in visitor input_datasets[ prefix + input.name ] = process_dataset( value ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 47 in process_dataset new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] File '/home/nat/work/software/galaxy-dist/lib/galaxy/datatypes/data.py', line 264 in convert_dataset for name, value in converted_dataset.iteritems(): AttributeError: 'tuple' object has no attribute 'iteritems' Can anyone tell me what I'm doing wrong? Do I need more than only the nib files? Many thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

1 0

displaying R output
by Jeremy Goecks 10 Mar '10

10 Mar '10

Hi Zaky, There are people on the galaxy-dev list (cc'd) that will be better able to assist you with this problem than me. Best, J. On Mar 8, 2010, at 12:11 PM, ZAKY ADAM wrote: > Hi Jeremy, > > I am running a perl program that embeds some R commands. The R commands require > a package called "qvalue". Running the R commands included in this package > results in some graphics in PDF. The program works perfectly on my computer, > but does not work on my galaxy that I have on scofield. I need this to run on > scofield in order to complete my workflow. > > The R commands are the following: > > library(tcltk); > library(qvalue); > p <- scan("p_valuesInputFile.txt"); > qobj <- qvalue(p, fdr.level = 0.05); > > I am reading simply 104 p values (in statistics) and save them in the variable > p, then the last command from the "qvalue" package should convert them into > what is called q values, but requires a graphical device. This last line > generates always the following error message: > > Loading Tcl/Tk interface ... done > Warning message: > In fun(...) : no DISPLAY variable so TK is not available > Read 104 items > > You don't need to be concerned with the code itself because, as I said, it > works perfectly on my mac os x computer. The problem is that Galaxy can not > deal with this graphical issue. > I hope that you can be helpful on this. > > Zaky Adam > Postdoctoral Research Fellow > Center for Comparative Genomics and Bioinformatics > The Pennsylvania State University > 306 Wartik Lab > University Park, PA 16802 > (814) 863-2185 > zua4(a)psu.edu >

3 2

Error in parsing XML help
by Chris Cole 10 Mar '10

10 Mar '10

Hi, Me again. I don't know why I've suddenly got all these errors. Updates aren't normally this problematic. This time I've got a huge amount of these errors in my paster.log: galaxy.tools ERROR 2010-03-09 14:12:46,128 error in help for tool Upload File Traceback (most recent call last): File "/homes/www-galaxy/galaxy_live/lib/galaxy/tools/__init__.py", line 489, in parse_help self.help = util.rst_to_html(self.help.text) File "/homes/www-galaxy/galaxy_live/lib/galaxy/util/__init__.py", line 232, in rst_to_html return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) ) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string enable_exit_status=enable_exit_status) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 607, in publish_programmatically pub.set_components(reader_name, parser_name, writer_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 92, in set_components self.set_reader(reader_name, self.parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 82, in set_reader self.reader = reader_class(parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 51, in __init__ self.set_parser(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 62, in set_parser parser_class = parsers.get_parser_class(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/__init__.py", line 48, in get_parser_class module = __import__(parser_name, globals(), locals()) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/__init__.py", line 77, in <module> from docutils.parsers.rst import states File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 110, in <module> import roman ImportError: No module named roman As far as I can see there's an error (like above) for every tool and the help text for the tools is no longer displayed within Galaxy. Has something changed in how the XML files should be formatted or is it something in the egg that's not right? Thanks again for any help. Cheers, Chris

2 2

Re: [galaxy-dev] Google Summer of Code proposal for phylogeny work with NESCent
by Brad Chapman 10 Mar '10

10 Mar '10

Anton, Sergei and Kanwei; Thanks for all the interest and feedback on the GSoC idea. To be clear, I was hoping to spec out a project involving Galaxy along with NESCent's phyloinformatics group (https://www.nescent.org/wg_phyloinformatics/Main_Page) as opposed to applying separately for Galaxy as an organization. The latter is quite a bit more work and very competitive. I worked with NESCent last year and they are a great group. The initial organizational application is starting to come together, and I put together a project idea based on what we've discussed thus far: https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code… The project idea gives interested students a basis for which they'll write a formal proposal with full details about what they plan to accomplish on a week by week basis. For now, we want to have something that looks good for the application which is due this Friday. Sergei, I know you are busy this week so no worries; I've put together enough to get the proposal in if you don't have time to look until later. If NESCent is accepted as an organization, we have until March 26th to do additional edits on the project idea, and then students will start looking at them and developing full project proposals. Any feedback about the idea and direction is more than welcome. You can create a wiki account and edit directly, or send general comments to me. Putting together an interesting and clear project idea will help get us accepted and attract good students to the project. Thanks again. Excited about getting this together, Brad > > Anton and Sergei; > > > >> Yes! One of guys on the Galaxy team is Sergei Kosakovsky Pond (the > >> author of HyPhy and datamonkey.org) who will be able to play a > >> leading role here. What is the timeframe? > > > > Awesome. This sounds perfect; Sergei, I could definitely use your > > help in defining the specifics around what is most interesting to > > you and useful for Galaxy. > > > > In terms of dates, we need to have an initial proposal refined by > > March 12th. Google then judges the applications; if we get > > accepted we have until March 26th to refine the proposal. > > > > Student applications are from March 29th to April 9th, followed by > > judging and selection of students. The actual work period is from > > May 24th to August 16th. > > > > Once the 2010 wiki is up and running, I will put together some > > initial text and then follow up here looking for more specific > > input. Thanks for getting involved with this,

1 0

Changing wall times...
by Kyle Kurz 09 Mar '10

09 Mar '10

Hi, I was not the original installer of our Galaxy instance, but have been tasked with changing the wall time that is requested when a job is submitted to the pbs queue. I found the job_walltime option in the universe_wsgi.ini, but we seem to be using round robin submission which then, in turn, submits a job to the pbs queue, so this doesn't work for me. Does anyone know an easy way to change the default time of 1 hr on this? Thanks, Kyle -- *************************** Kyle Kurz EECS Box 142 Stocker Center Ohio University Athens, OH 45701 kyle.w.kurz(a)gmail.com 740.249.9729 ***************************

2 4

link to a file within the library information
by nsfox＠uwaterloo.ca 09 Mar '10

09 Mar '10

Hi, Within the information specified by a library information template or a sequence request form, is it possible to make a link to a file? So that the pdf with the Bioanalyzer Results can be attached to the dataset or so the form sent with the sample to the sequencing center can be attached to the sequence request. Thanks, Natalie

2 1

Visualization problems
by juan perin 09 Mar '10

09 Mar '10

I've just updated via 'hg pull -u', ran the update to the database and went through the steps of enabling the visualization tab for viewing my bed and wig files. Yesterday there were a few aesthetic issue which seem to have been fixed with todays update. But, the tracks still fail to load for me at all. I've tried wig, bed, and (although its not supposed to work) bam files, because they are included in the selection box, so i figured i'd try... I essentially just get "loading data". The job on the cluster for indexing seems to be running, but then when i go back to 'analyze' i notice the job in my history, reporting that the BED to Interval conversion failed "due to a cluster problem". Any ideas are sincerely appreciated. Thanks in advance. --Juan When i try to run the conversion manually again, i get a slew of errors, summed up by: UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 1: ordinal not in range(128) Full error output in txt: URL: http://variome.chop.edu:8082/datasets/6a8910163e5b1d35/display/?preview=Tru… '/home/perin/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/perin/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/perin/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/perin/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy-dist/lib/galaxy/web/framework/base.py', line 134 in __call__ return body( environ, start_response ) File '/home/perin/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 630 in render template.render_context( context ) File '/home/perin/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 146 in render_context runtime._render_context(self, self.callable_, context, *args, **kwargs) File '/home/perin/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/perin/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/perin/galaxy-dist/database/compiled_templates/base.mako.py', line 37 in render_body __M_writer(unicode(next.body())) File '/home/perin/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/perin/galaxy-dist/database/compiled_templates/dataset/ large_file.mako.py', line 43 in render_body __M_writer(filters.html_escape(unicode( truncated_data ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 1: ordinal not in range(128)

2 1

Multiple users view sequence request
by nsfox＠uwaterloo.ca 09 Mar '10

09 Mar '10

Hi, To my understanding, a sequence request can only be viewed by the person who has created it or under the Admin tab. Is it possible for a user different from the one who created the request to view the sequence request? I'd like to use this functionality for projects collaborators to have read only view of the sequence request in order to keep up to date on the sequence requests' status. Thanks, Natalie

2 1

[hg] galaxy 3495: Re-display private roles on permissions forms ...
by Greg Von Kuster 09 Mar '10

09 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3b1be99d1f62 changeset: 3495:3b1be99d1f62 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Mar 09 11:28:21 2010 -0500 description: Re-display private roles on permissions forms *only if* woring in the admin view. A lot of code cleanup and bug fixes related to uploading library datasets and setting access permissions on them at upload as well as some security cleanup and fixes. Fix the "Your changes completed successfully." message in the Edit Attributes page. Pass the "use_panels" param around the library methods so the matshead will re-appear when the user browses the library ( obvioulsy needs improvement, but at least for now there is now a way to get eh masthead back ). diffstat: lib/galaxy/security/__init__.py | 133 ++++++---- lib/galaxy/tools/actions/upload.py | 4 +- lib/galaxy/tools/actions/upload_common.py | 13 +- lib/galaxy/web/controllers/library_common.py | 166 ++++++++++--- lib/galaxy/web/controllers/root.py | 30 +- lib/galaxy/web/controllers/tool_runner.py | 5 +- templates/base_panels.mako | 4 +- templates/library/common/browse_library.mako | 64 ++-- templates/library/common/common.mako | 1 + templates/library/common/edit_template.mako | 4 +- templates/library/common/folder_info.mako | 4 +- templates/library/common/folder_permissions.mako | 2 +- templates/library/common/ldda_edit_info.mako | 8 +- templates/library/common/ldda_info.mako | 20 +- templates/library/common/ldda_permissions.mako | 2 +- templates/library/common/library_dataset_info.mako | 2 +- templates/library/common/library_dataset_permissions.mako | 2 +- templates/library/common/library_info.mako | 12 +- templates/library/common/library_permissions.mako | 2 +- templates/library/common/new_folder.mako | 2 +- templates/library/common/select_template.mako | 4 +- templates/library/common/upload.mako | 12 +- templates/mobile/manage_library.mako | 2 +- 23 files changed, 294 insertions(+), 204 deletions(-) diffs (1581 lines): diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/security/__init__.py Tue Mar 09 11:28:21 2010 -0500 @@ -18,8 +18,6 @@ class RBACAgent: """Class that handles galaxy security""" - IN_ACCESSIBLE = 'access_error' - ILL_LEGITIMATE = 'legitimate_error' permitted_actions = Bunch( DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with permissions on this dataset", "grant" ), DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), @@ -79,9 +77,9 @@ raise "Unimplemented Method" def get_permissions( self, library_dataset ): raise "Unimplemented Method" - def get_legitimate_roles( self, trans, item ): + def get_legitimate_roles( self, trans, item, cntrller ): raise "Unimplemented Method" - def derive_roles_from_access( self, trans, item_id, library=False, **kwd ): + def derive_roles_from_access( self, trans, item_id, cntrller, library=False, **kwd ): raise "Unimplemented Method" def get_component_associations( self, **kwd ): raise "Unimplemented Method" @@ -109,15 +107,26 @@ def sa_session( self ): """Returns a SQLAlchemy session""" return self.model.context - def get_legitimate_roles( self, trans, item ): + def get_legitimate_roles( self, trans, item, cntrller ): """ Return a sorted list of legitimate roles that can be associated with a permission on - item where item is a Library or a Dataset. If item is public, all non-private roles, - except for the current user's private role, are legitimate. If item is restricted, - legitimate roles are derived from the users and groups associated with each role that - is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or - LIBRARY_MANAGE ) on item. + item where item is a Library or a Dataset. The cntrller param is the controller from + which the request is sent. We cannot use trans.user_is_admin() because the controller is + what is important since admin users do not necessarily have permission to do things + on items outside of the admin view. + If cntrller is from the admin side ( e.g., library_admin ): + -if item is public, all roles, including private roles, are legitimate. + -if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or + LIBRARY_MANAGE ) on item. Legitimate roles will include private roles. + If cntrller is not from the admin side ( e.g., root, library ): + -if item is public, all non-private roles, except for the current user's private role, + are legitimate. + -if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission on item. Private roles, except + for the current user's private role, will be excluded. """ + admin_controller = cntrller in [ 'library_admin' ] def sort_by_attr( seq, attr ): """ Sort the sequence of objects by object's attribute @@ -142,29 +151,37 @@ self.model.Role.table.c.type != self.model.Role.types.PRIVATE, self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ .order_by( self.model.Role.table.c.name ) - # Add the current user's private role - roles.add( self.get_private_user_role( trans.user ) ) - # Add the current user's sharing roles - for role in self.get_sharing_roles( trans.user ): - roles.add( role ) - # Add all remaining non-private, non-sharing roles - for role in trans.sa_session.query( trans.app.model.Role ) \ - .filter( and_( self.model.Role.table.c.deleted==False, - self.model.Role.table.c.type != self.model.Role.types.PRIVATE, - self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ - .order_by( self.model.Role.table.c.name ): - roles.add( role ) - return sort_by_attr( [ role for role in roles ], 'name' ) + if admin_controller: + # The library is public and the user is an admin, so all roles are legitimate + for role in trans.sa_session.query( trans.app.model.Role ) \ + .filter( self.model.Role.table.c.deleted==False ) \ + .order_by( self.model.Role.table.c.name ): + roles.add( role ) + return sort_by_attr( [ role for role in roles ], 'name' ) + else: + # Add the current user's private role + roles.add( self.get_private_user_role( trans.user ) ) + # Add the current user's sharing roles + for role in self.get_sharing_roles( trans.user ): + roles.add( role ) + # Add all remaining non-private, non-sharing roles + for role in trans.sa_session.query( trans.app.model.Role ) \ + .filter( and_( self.model.Role.table.c.deleted==False, + self.model.Role.table.c.type != self.model.Role.types.PRIVATE, + self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ + .order_by( self.model.Role.table.c.name ): + roles.add( role ) + return sort_by_attr( [ role for role in roles ], 'name' ) # If item has roles associated with the access permission, we need to start with them. access_roles = item.get_access_roles( trans ) for role in access_roles: - if self.ok_to_display( trans, role ): + if admin_controller or self.ok_to_display( trans.user, role ): roles.add( role ) # Each role potentially has users. We need to find all roles that each of those users have. for ura in role.users: user = ura.user for ura2 in user.roles: - if self.ok_to_display( trans, ura2.role ): + if admin_controller or self.ok_to_display( trans.user, ura2.role ): roles.add( ura2.role ) # Each role also potentially has groups which, in turn, have members ( users ). We need to # find all roles that each group's members have. @@ -173,20 +190,20 @@ for uga in group.users: user = uga.user for ura in user.roles: - if self.ok_to_display( trans, ura.role ): + if admin_controller or self.ok_to_display( trans.user, ura.role ): roles.add( ura.role ) return sort_by_attr( [ role for role in roles ], 'name' ) - def ok_to_display( self, trans, role ): + def ok_to_display( self, user, role ): """ Method for checking if: - a role is private and is the current user's private role - a role is a sharing role and belongs to the current user """ - if trans.user: + if user: if role.type == self.model.Role.types.PRIVATE: - return role == self.get_private_user_role( trans.user ) + return role == self.get_private_user_role( user ) if role.type == self.model.Role.types.SHARING: - return role in self.get_sharing_roles( trans.user ) + return role in self.get_sharing_roles( user ) # If role.type is neither private nor sharing, it's ok to display return True return role.type != self.model.Role.types.PRIVATE and role.type != self.model.Role.types.SHARING @@ -490,17 +507,21 @@ if lp.action == self.permitted_actions.LIBRARY_ACCESS.action: self.sa_session.delete( lp ) self.sa_session.flush() - def derive_roles_from_access( self, trans, item_id, library=False, **kwd ): + def derive_roles_from_access( self, trans, item_id, cntrller, library=False, **kwd ): # Check the access permission on a dataset. If library is true, item_id refers to a library. If library - # is False, item_id refers to a dataset ( item_id must currently be decoded before being sent ). + # is False, item_id refers to a dataset ( item_id must currently be decoded before being sent ). The + # cntrller param is the calling controller, which needs to be passed to get_legitimate_roles(). msg = '' permissions = {} # accessible will be True only if at least 1 user has every role in DATASET_ACCESS_in accessible = False - # legitimate will be True only if all roles in DATASET_ACCESS_in are in the set - # of roles returned from self.get_legitimate_roles() + # legitimate will be True only if all roles in DATASET_ACCESS_in are in the set of roles returned from + # get_legitimate_roles() legitimate = False - error = None + # private_role_found will be true only if more than 1 role is being associated with the DATASET_ACCESS + # permission on item, and at least 1 of the roles is private. + private_role_found = False + error = False for k, v in get_permitted_actions( filter='DATASET' ).items(): in_roles = [ self.sa_session.query( self.model.Role ).get( x ) for x in listify( kwd.get( k + '_in', [] ) ) ] if v == self.permitted_actions.DATASET_ACCESS and in_roles: @@ -514,22 +535,18 @@ # will keep ill-legitimate roles from being associated with the DATASET_ACCESS permission on the # dataset (i.e., in the case where item is a library, if Role1 is associated with LIBRARY_ACCESS, # then only those users that have Role1 should be associated with DATASET_ACCESS. - legitimate_roles = self.get_legitimate_roles( trans, item ) + legitimate_roles = self.get_legitimate_roles( trans, item, cntrller ) ill_legitimate_roles = [] for role in in_roles: if role not in legitimate_roles: ill_legitimate_roles.append( role ) if ill_legitimate_roles: - # NOTE: this condition should never occur since ill-legitimate roles are filtered out of the set of - # roles displayed on the permissions forms, but just in case there is a bug somewhere that incorrectly + # This condition should never occur since ill-legitimate roles are filtered out of the set of + # roles displayed on the forms, but just in case there is a bug somewhere that incorrectly # filters, we'll display this message. - error = self.ILL_LEGITIMATE - if library: - msg += "The following roles are not associated with users that have the 'access library' permission on this " - msg += "library, so they cannot be associated with the 'access' permission on the datasets: " - else: - msg += "The following roles are not associated with users that have the 'access' permission on this " - msg += "dataset, so they were incorrectly displayed on the permission form: " + error = True + msg += "The following roles are not associated with users that have the 'access' permission on this " + msg += "item, so they were incorrectly displayed: " for role in ill_legitimate_roles: msg += "%s, " % role.name msg = msg.rstrip( ", " ) @@ -540,6 +557,14 @@ in_roles = new_in_roles else: legitimate = True + if len( in_roles ) > 1: + # At least 1 user must have every role associated with the access + # permission on this dataset, or the dataset is not accessible. + # Since we have more than 1 role, none of them can be private. + for role in in_roles: + if role.type == self.model.Role.types.PRIVATE: + private_role_found = True + break if len( in_roles ) == 1: accessible = True else: @@ -556,7 +581,7 @@ group = gra.group for uga in group.users: users_set.add( uga.user ) - # Make sure that at least 1 user has every role being associated with the dataset + # Make sure that at least 1 user has every role being associated with the dataset. for user in users_set: user_roles_set = set() for ura in user.roles: @@ -564,14 +589,16 @@ if in_roles_set.issubset( user_roles_set ): accessible = True break - if not accessible: - error = self.IN_ACCESSIBLE - # Don't set the permissions for DATASET_ACCESS if inaccessible, but set all other permissions + if private_role_found or not accessible: + error = True + # Don't set the permissions for DATASET_ACCESS if inaccessible or multiple roles with + # at least 1 private, but set all other permissions. permissions[ self.get_action( v.action ) ] = [] - msg += "At least 1 user must have every role associated with accessing datasets. The roles you " - msg += "attempted to associate for access would make the datasets in-accessible by everyone, " - msg += "so access permissions were left in their original state (or not set). All other " - msg += "permissions were updated for the datasets." + msg = "At least 1 user must have every role associated with accessing datasets. " + if private_role_found: + msg += "Since you are associating more than 1 role, no private roles are allowed." + if not accessible: + msg += "The roles you attempted to associate for access would make the datasets in-accessible by everyone." else: permissions[ self.get_action( v.action ) ] = in_roles else: diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Mar 09 11:28:21 2010 -0500 @@ -15,7 +15,9 @@ precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation ) incoming = upload_common.persist_uploads( incoming ) - uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) + # We can pass an empty string as the cntrller here since it is used to check whether we + # are in an admin view, and this tool is currently not used there. + uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if not uploaded_datasets: diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Mar 09 11:28:21 2010 -0500 @@ -121,10 +121,9 @@ trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) trans.sa_session.flush() return hda -def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): +def new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state=None ): current_user_roles = trans.get_current_user_roles() - if not ( trans.app.security_agent.can_add_library_item( current_user_roles, library_bunch.folder ) \ - or trans.user.email in trans.app.config.get( "admin_users", "" ).split( "," ) ): + if not ( cntrller in [ 'library_admin' ] or trans.app.security_agent.can_add_library_item( current_user_roles, library_bunch.folder ) ): # This doesn't have to be pretty - the only time this should happen is if someone's being malicious. raise Exception( "User is not authorized to add datasets to this library." ) folder = library_bunch.folder @@ -203,19 +202,19 @@ trans.sa_session.add( dp ) trans.sa_session.flush() return ldda -def new_upload( trans, uploaded_dataset, library_bunch=None, state=None ): +def new_upload( trans, cntrller, uploaded_dataset, library_bunch=None, state=None ): if library_bunch: - return new_library_upload( trans, uploaded_dataset, library_bunch, state ) + return new_library_upload( trans, cntrller, uploaded_dataset, library_bunch, state ) else: return new_history_upload( trans, uploaded_dataset, state ) -def get_uploaded_datasets( trans, params, precreated_datasets, dataset_upload_inputs, library_bunch=None ): +def get_uploaded_datasets( trans, cntrller, params, precreated_datasets, dataset_upload_inputs, library_bunch=None ): uploaded_datasets = [] for dataset_upload_input in dataset_upload_inputs: uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) for uploaded_dataset in uploaded_datasets: data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name ) if not data: - data = new_upload( trans, uploaded_dataset, library_bunch ) + data = new_upload( trans, cntrller, uploaded_dataset, library_bunch ) else: data.extension = uploaded_dataset.file_type data.dbkey = uploaded_dataset.dbkey diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Tue Mar 09 11:28:21 2010 -0500 @@ -107,18 +107,18 @@ msg += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." messagetype = "info" return trans.fill_template( '/library/common/browse_library.mako', + cntrller=cntrller, use_panels=use_panels, - cntrller=cntrller, library=library, created_ldda_ids=created_ldda_ids, hidden_folder_ids=hidden_folder_ids, - default_action=params.get( 'default_action', None ), show_deleted=show_deleted, comptypes=comptypes, current_user_roles=current_user_roles, msg=msg, messagetype=messagetype ) - return trans.response.send_redirect( web.url_for( controller=cntrller, + return trans.response.send_redirect( web.url_for( use_panels=use_panels, + controller=cntrller, action='browse_libraries', default_action=params.get( 'default_action', None ), msg=util.sanitize_text( msg ), @@ -128,6 +128,7 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) # See if we have any associated templates @@ -158,12 +159,14 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='library_info', cntrller=cntrller, + use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype='done' ) ) return trans.fill_template( '/library/common/library_info.mako', cntrller=cntrller, + use_panels=use_panels, library=library, widgets=widgets, current_user_roles=current_user_roles, @@ -177,6 +180,7 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) current_user_roles = trans.get_current_user_roles() @@ -195,13 +199,15 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, + use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype='done' ) ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_permissions.mako', cntrller=cntrller, + use_panels=use_panels, library=library, current_user_roles=current_user_roles, roles=roles, @@ -214,12 +220,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) parent_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( parent_id ) ) if not parent_folder: msg = "Invalid parent folder id (%s) specified" % str( parent_id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -248,6 +256,7 @@ msg += "Additional information about this folder may be added using the inherited template." return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, + use_panels=use_panels, folder=new_folder, library_id=library_id, widgets=widgets, @@ -262,6 +271,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -270,6 +280,7 @@ # cannot occur before the associated item is saved. return trans.fill_template( '/library/common/new_folder.mako', cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder=parent_folder, show_deleted=show_deleted, @@ -281,6 +292,7 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) current_user_roles = trans.get_current_user_roles() # See if we have any associated templates @@ -308,6 +320,7 @@ messagetype='error' return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, + use_panels=use_panels, folder=folder, library_id=library_id, widgets=widgets, @@ -323,12 +336,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) if not folder: msg = "Invalid folder specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -354,6 +369,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, + use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted, @@ -362,9 +378,10 @@ # If the library is public all roles are legitimate, but if the library is restricted, only those # roles associated with the LIBRARY_ACCESS permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/folder_permissions.mako', cntrller=cntrller, + use_panels=use_panels, folder=folder, library_id=library_id, current_user_roles=current_user_roles, @@ -378,12 +395,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -471,6 +490,7 @@ ldda.metadata.dbkey = ldda.dbkey return trans.fill_template( "/library/common/ldda_edit_info.mako", cntrller=cntrller, + use_panels=use_panels, ldda=ldda, library_id=library_id, file_formats=file_formats, @@ -487,12 +507,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -506,6 +528,7 @@ current_user_roles = trans.get_current_user_roles() return trans.fill_template( '/library/common/ldda_info.mako', cntrller=cntrller, + use_panels=use_panels, ldda=ldda, library=library, show_deleted=show_deleted, @@ -521,6 +544,7 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ids = util.listify( id ) lddas = [] for id in [ trans.security.decode_id( id ) for id in ids ]: @@ -530,6 +554,7 @@ trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -544,26 +569,25 @@ ldda = lddas[0] if trans.app.security_agent.dataset_is_public( ldda.dataset ): # The dataset is public, so check access to the library - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) else: - roles = trans.app.security_agent.get_legitimate_roles( trans, ldda.dataset ) + roles = trans.app.security_agent.get_legitimate_roles( trans, ldda.dataset, cntrller ) if params.get( 'update_roles_button', False ): current_user_roles = trans.get_current_user_roles() if cntrller=='library_admin' or ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \ trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ): + a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action ) permissions, in_roles, error, msg = \ - trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), library=True, **kwd ) + trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **kwd ) for ldda in lddas: # Set the DATASET permissions on the Dataset. - if error == trans.app.security_agent.IN_ACCESSIBLE: - # If derive_roles_from_access() returned an "in_accessible" error, then we keep the original role - # associations for the DATASET_ACCESS permission on each ldda. - a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action ) + if error: + # Keep the original role associations for the DATASET_ACCESS permission on the ldda. permissions[ a ] = ldda.get_access_roles( trans ) trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) trans.sa_session.refresh( ldda.dataset ) - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + # Set the LIBRARY permissions on the LibraryDataset. The LibraryDataset and + # LibraryDatasetDatasetAssociation will be set with the same permissions. permissions = {} for k, v in trans.app.model.Library.permitted_actions.items(): if k != 'LIBRARY_ACCESS': @@ -586,6 +610,7 @@ messagetype = 'error' return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, + use_panels=use_panels, lddas=lddas, library_id=library_id, roles=roles, @@ -613,6 +638,7 @@ trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -620,6 +646,7 @@ # Display permission form, permissions will be updated for all lddas simultaneously. return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, + use_panels=use_panels, lddas=lddas, library_id=library_id, roles=roles, @@ -632,7 +659,6 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) deleted = util.string_as_bool( params.get( 'deleted', False ) ) - show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): last_used_build = dbkey[0] @@ -662,19 +688,27 @@ ( replace_dataset and trans.app.security_agent.can_modify_library_item( current_user_roles, replace_dataset ) ) ): if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): # Check to see if the user selected roles to associate with the DATASET_ACCESS permission - # on the dataset that would make the dataset in-accessible to everyone. + # on the dataset that would cause accessibility issues. roles = params.get( 'roles', False ) error = None if roles: vars = dict( DATASET_ACCESS_in=roles ) permissions, in_roles, error, msg = \ - trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), library=True, **vars ) - if error: - if error == trans.app.security_agent.IN_ACCESSIBLE: - msg = "At least 1 user must have every role associated with accessing datasets. The roles you " - msg += "attempted to associate for access would make the datasets in-accessible by everyone." - messagetype = 'error' - if not error: + trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **vars ) + if error: + messagetype = 'error' + + trans.response.send_redirect( web.url_for( controller='library_common', + action='upload_library_dataset', + cntrller=cntrller, + library_id=library_id, + folder_id=folder_id, + replace_id=replace_id, + upload_option=upload_option, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + + else: # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) if info_association and info_association.inheritable: @@ -683,7 +717,7 @@ else: template_id = 'None' widgets = [] - created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, + created_outputs_dict = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, cntrller=cntrller, library_id=library_id, folder_id=folder_id, @@ -691,9 +725,10 @@ widgets=widgets, replace_dataset=replace_dataset, **kwd ) - if created_outputs: - total_added = len( created_outputs.values() ) - ldda_id_list = [ str( v.id ) for v in created_outputs.values() ] + if created_outputs_dict: + total_added = len( created_outputs_dict.keys() ) + ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] + created_ldda_ids=",".join( ldda_id_list ) if replace_dataset: msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: @@ -722,20 +757,19 @@ cntrller=cntrller, id=library_id, default_action=default_action, - created_ldda_ids=",".join( ldda_id_list ), - show_deleted=show_deleted, + created_ldda_ids=created_ldda_ids, msg=util.sanitize_text( msg ), messagetype='done' ) ) else: + created_ldda_ids = '' msg = "Upload failed" messagetype='error' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, - created_ldda_ids=",".join( [ str( v.id ) for v in created_outputs.values() ] ), - show_deleted=show_deleted, + created_ldda_ids=created_ldda_ids, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) # See if we have any inherited templates, but do not inherit contents. @@ -757,12 +791,12 @@ # If the library is public, all active roles are legitimate. If the library is restricted by the # LIBRARY_ACCESS permission, only those roles associated with that permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) # If we're using nginx upload, override the form action - action = web.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, show_deleted=show_deleted ) + action = web.url_for( controller='library_common', action='upload_library_dataset' ) if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: # url_for is intentionally not used on the base URL here - # nginx_upload_path is expected to include the proxy prefix if the @@ -785,7 +819,6 @@ roles=roles, history=history, widgets=widgets, - show_deleted=show_deleted, msg=msg, messagetype=messagetype ) def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ): @@ -833,11 +866,11 @@ precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller ) if upload_option == 'upload_file': tool_params = upload_common.persist_uploads( tool_params ) - uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) + uploaded_datasets = upload_common.get_uploaded_datasets( trans, cntrller, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) elif upload_option == 'upload_directory': - uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) elif upload_option == 'upload_paths': - uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, params, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, err_redirect, msg ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if upload_option == 'upload_file' and not uploaded_datasets: msg = 'Select a file, enter a URL or enter text' @@ -855,7 +888,7 @@ json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) - def make_library_uploaded_dataset( self, trans, params, name, path, type, library_bunch, in_folder=None ): + def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() uploaded_dataset.name = name @@ -867,14 +900,14 @@ uploaded_dataset.space_to_tab = params.space_to_tab if in_folder: uploaded_dataset.in_folder = in_folder - uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch ) + uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) if params.get( 'link_data_only', False ): uploaded_dataset.link_data_only = True uploaded_dataset.data.file_name = os.path.abspath( path ) trans.sa_session.add( uploaded_dataset.data ) trans.sa_session.flush() return uploaded_dataset - def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): + def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): files = [] try: for entry in os.listdir( full_dir ): @@ -900,9 +933,9 @@ uploaded_datasets = [] for file in files: name = os.path.basename( file ) - uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, name, file, 'server_dir', library_bunch ) ) + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, file, 'server_dir', library_bunch ) ) return uploaded_datasets, None, None - def get_path_paste_uploaded_datasets( self, trans, params, library_bunch, err_redirect, msg ): + def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, err_redirect, msg ): if params.get( 'filesystem_paths', '' ) == '': msg = "No paths entered in the upload form" err_redirect = True @@ -922,7 +955,7 @@ if not bad_paths: if os.path.isfile( path ): name = os.path.basename( path ) - uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, name, path, 'path_paste', library_bunch ) ) + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, path, 'path_paste', library_bunch ) ) for basedir, dirs, files in os.walk( line ): for file in files: file_path = os.path.abspath( os.path.join( basedir, file ) ) @@ -930,7 +963,14 @@ in_folder = os.path.dirname( file_path.replace( path, '', 1 ).lstrip( '/' ) ) else: in_folder = None - uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, file, file_path, 'path_paste', library_bunch, in_folder ) ) + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, + cntrller, + params, + file, + file_path, + 'path_paste', + library_bunch, + in_folder ) ) if bad_paths: msg = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) err_redirect = True @@ -1036,7 +1076,7 @@ dbkeys = get_dbkey_options( last_used_build ) # Send list of legitimate roles to the form so the dataset can be associated with 1 or more of them. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( "/library/common/upload.mako", upload_option=upload_option, library_id=library_id, @@ -1055,6 +1095,7 @@ def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ): """Catches the dataset id and displays file contents as directed""" show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda.dataset: msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) @@ -1083,6 +1124,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -1093,12 +1135,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( id ) ) if not library_dataset: msg = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -1130,6 +1174,7 @@ messagetype = "error" return trans.fill_template( '/library/common/library_dataset_info.mako', cntrller=cntrller, + use_panels=use_panels, library_dataset=library_dataset, library_id=library_id, current_user_roles=current_user_roles, @@ -1145,12 +1190,14 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( id ) if not library_dataset: msg = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -1179,9 +1226,10 @@ msg = "You are not authorized to managed the permissions of this dataset" messagetype = "error" library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) - roles = trans.app.security_agent.get_legitimate_roles( trans, library ) + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_dataset_permissions.mako', cntrller=cntrller, + use_panels=use_panels, library_dataset=library_dataset, library_id=library_id, roles=roles, @@ -1197,6 +1245,7 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) action = params.get( 'do_action', None ) if not ldda_ids: msg = "You must select at least one dataset" @@ -1208,6 +1257,17 @@ ldda_ids = util.listify( ldda_ids ) if action == 'add': history = trans.get_history() + if history is None: + # Must be a bot sending a request without having a history. + msg = "You do not have a current history" + return trans.response.send_redirect( web.url_for( controller='library_common', + action='browse_library', + cntrller=cntrller, + use_panels=use_panels, + id=library_id, + show_deleted=show_deleted, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) total_imported_lddas = 0 msg = '' messagetype = 'done' @@ -1229,6 +1289,7 @@ trans.response.send_redirect( web.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=",".join( ldda_ids ), @@ -1346,6 +1407,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, + use_panels=use_panels, id=library_id, show_deleted=show_deleted, msg=util.sanitize_text( msg ), @@ -1393,6 +1455,7 @@ else: params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) msg = util.restore_text( params.get( 'msg', '' ) ) action = '' messagetype = params.get( 'messagetype', 'done' ) @@ -1418,6 +1481,7 @@ trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=folder_id, id=id, @@ -1459,6 +1523,7 @@ template_ids, widgets, template_select_list = generate_template_stuff( trans, forms, 'none' ) return trans.fill_template( '/library/common/select_template.mako', cntrller=cntrller, + use_panels=use_panels, item_name=item.name, item_desc=item_desc, item_type=item_type, @@ -1476,6 +1541,7 @@ def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) @@ -1491,6 +1557,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=folder_id, id=id, @@ -1502,6 +1569,7 @@ # Edit the template itself, keeping existing field contents, if any. params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) @@ -1521,6 +1589,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=folder_id, id=id, @@ -1532,6 +1601,7 @@ response_redirect=web.url_for( controller='library_common', action='edit_template', cntrller=cntrller, + use_panels=use_panels, item_type=item_type, library_id=library_id, folder_id=folder_id, @@ -1544,6 +1614,7 @@ # Edit the contents of the template fields without altering the template itself. params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) @@ -1595,6 +1666,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=folder_id, id=id, @@ -1607,6 +1679,7 @@ # a future enhancement. params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) @@ -1623,6 +1696,7 @@ return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, + use_panels=use_panels, library_id=library_id, folder_id=folder_id, id=id, diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Mar 09 11:28:21 2010 -0500 @@ -335,31 +335,18 @@ if not trans.user: return trans.show_error_message( "You must be logged in if you want to change permissions." ) if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ): - # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles. We need - # to ensure that they did not associated roles that would make the dataset in-accessible by everyone. + # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles. We + # need to ensure that they did not associate roles that would cause accessibility problems. permissions, in_roles, error, msg = \ - trans.app.security_agent.derive_roles_from_access( trans, data.dataset.id, **kwd ) + trans.app.security_agent.derive_roles_from_access( trans, data.dataset.id, 'root', **kwd ) a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action ) - if error == trans.app.security_agent.IN_ACCESSIBLE: - # If derive_roles_from_access() returned an "in_accessible" error, then we keep the original role - # associations for the DATASET_ACCESS permission on the dataset. + if error: + # Keep the original role associations for the DATASET_ACCESS permission on the dataset. permissions[ a ] = data.dataset.get_access_roles( trans ) - # Make sure the user is not associating another user's private role with the DATASET_ACCESS permission. - # It would be better to filter out other user's private roles from the access box on the permission form, - # but that gets a bit tricky since we are not differentiating between permissions ( i.e., the same set of - # derived roles are used for both the manage permissions and the access box ). - current_user_private_role = trans.app.security_agent.get_private_user_role( trans.user ) - access_roles = permissions[ a ] - for role in access_roles: - if role.type == trans.app.model.Role.types.PRIVATE and role is not current_user_private_role: - error = trans.app.security_agent.IN_ACCESSIBLE - permissions[ a ] = data.dataset.get_access_roles( trans ) - msg = "You cannot associate another user's private role with the access permission on this dataset " - msg += "or it will become in-accessible to you. Access permissions were left in their original state." - messagetype = 'error' - break trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions ) trans.sa_session.refresh( data.dataset ) + if not msg: + msg = 'Your changes completed successfully.' else: return trans.show_error_message( "You are not authorized to change this dataset's permissions" ) if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey: @@ -374,11 +361,10 @@ # the built-in 'id' is overwritten in lots of places as well ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] ldatatypes.sort() - all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset ) + all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) if error: messagetype = 'error' else: - msg = 'Your changes completed successfully.' messagetype = 'done' return trans.fill_template( "/dataset/edit_attributes.mako", data=data, diff -r 00aab7119686 -r 3b1be99d1f62 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Mar 09 11:18:45 2010 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Mar 09 11:28:21 2010 -0500 @@ -142,6 +142,7 @@ """ Precreate datasets for asynchronous uploading. """ + cntrller = kwd.get( 'cntrller', '' ) roles = kwd.get( 'roles', False ) if roles: # The user associated the DATASET_ACCESS permission on the uploaded datasets with 1 or more roles. @@ -151,7 +152,7 @@ # did not associated roles that would make the dataset in-accessible by everyone. library_id = trans.app.security.decode_id( kwd.get( 'library_id', '' ) ) vars = dict( DATASET_ACCESS_in=roles ) - permissions, in_roles, error, msg = trans.app.security_agent.check_access_permission( trans, library_id, library=True, **vars ) + permissions, in_roles, error, msg = trans.app.security_agent.derive_roles_from_access( trans, library_id, cntrller, library=True, **vars ) if error: return [ 'error', msg ] permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) @@ -166,7 +167,7 @@ library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset ) else: library_bunch = None - return upload_common.new_upload( trans, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD ) + return upload_common.new_upload( trans, cntrller, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD ) tool = self.get_toolbox().tools_by_id.get( tool_id, None ) if not tool: return False # bad tool_id diff -r 00aab7119686 -r 3b1be99d1f62 templates/base_panels.mako --- a/templates/base_panels.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/base_panels.mako Tue Mar 09 11:28:21 2010 -0500 @@ -72,10 +72,10 @@ <![if !IE]> <script type="text/javascript"> var upload_form_error = function( msg ) { - if ( ! $("iframe#galaxy_main").contents().find("body").find("div[name='upload_error']").size() ) { + if ( ! $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").size() ) { $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage" name="upload_error">' + msg + '</div><p/>' ); } else { - $("iframe#galaxy_main").contents().find("body").find("div[name='upload_error']").text( msg ); + $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg ); } } jQuery( function() { diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/browse_library.mako Tue Mar 09 11:28:21 2010 -0500 @@ -166,7 +166,7 @@ <%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False )"> <% - ## The received data must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods + ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying ## children, which are always lddas ). We also need to make sure we're displaying the latest version of this ## library_dataset, so we display the attributes from the ldda. @@ -204,33 +204,33 @@ %if ldda.library_dataset.deleted: <span class="libraryItem-error"> %endif - <a href="${h.url_for( controller='library_common', action='ldda_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 )}"><b>${ldda.name[:50]}</b></a> + <a href="${h.url_for( controller='library_common', action='ldda_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 ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> %if ldda.library_dataset.deleted: </span> %endif <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${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( folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_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 information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_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</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_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 )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_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 ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${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( folder.id ), id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Edit permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): <a class="action-button" href="${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( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ) )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> %endif %if cntrller in [ 'library_admin', 'requests_admin' ]: %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: @@ -300,7 +300,7 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a> + <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a> %if folder.description: <i>- ${folder.description}</i> %endif @@ -310,21 +310,21 @@ <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="folder_img-${folder.id}-popup"> %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_add ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Add datasets</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=library_id )}">Add sub-folder</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${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 information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %endif %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_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</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> %endif %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_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 )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), show_deleted=show_deleted )}">Delete template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> %endif %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">Edit permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif %if cntrller in [ 'library_admin', 'requests_admin' ]: %if not library.deleted and not folder.deleted: @@ -404,8 +404,8 @@ <ul class="manage-table-actions"> %if not library.deleted and ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ): - <li><a class="action-button" href="${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( library.root_folder.id ), show_deleted=show_deleted )}"><span>Add datasets</span></a></li> - <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Add folder</a></li> + <li><a class="action-button" href="${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( library.root_folder.id ) )}"><span>Add datasets</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li> %endif </ul> @@ -420,47 +420,47 @@ <br/> %endif - <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ) )}" onSubmit="javascript:return checkForm();" method="post"> + <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> <thead> <tr class="libraryTitle"> %if cntrller == 'library_admin' or can_add or can_modify or can_manage: <th style="padding-left: 42px;"> - <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> %if not library.deleted: %if cntrller == 'library_admin' or can_modify: - <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %endif %if ( cntrller == 'library_admin' or can_modify ) and not library.info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Add template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> %endif %if ( cntrller == 'library_admin' or can_modify ) and info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Delete template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> %endif %if cntrller == 'library_admin' or can_manage: - <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif %if cntrller == 'library_admin': <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> %endif %if show_deleted: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=False )}">Hide deleted items</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=True )}">Show deleted items</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> %endif %elif cntrller == 'library_admin' and not library.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Undelete this data library</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> %elif library.purged: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">This data library has been purged</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> %endif </div> </th> %else: <th style="padding-left: 42px;"> - <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <a href="${h.url_for( controller='library_common', action='library_info', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> </th> %endif <th>Information</th> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/common.mako --- a/templates/library/common/common.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/common.mako Tue Mar 09 11:28:21 2010 -0500 @@ -102,6 +102,7 @@ <form name="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post"> <input type="hidden" name="tool_id" value="upload1"/> <input type="hidden" name="tool_state" value="None"/> + <input type="hidden" name="cntrller" value="${cntrller}"/> <input type="hidden" name="library_id" value="${library_id}"/> <input type="hidden" name="folder_id" value="${folder_id}"/> <input type="hidden" name="upload_option" value="${upload_option}"/> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/edit_template.mako --- a/templates/library/common/edit_template.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/edit_template.mako Tue Mar 09 11:28:21 2010 -0500 @@ -4,7 +4,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -14,7 +14,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit the template for the ${item_desc} '${item_name}'</div> - <form id="edit_template" name="edit_template" action="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" > + <form id="edit_template" name="edit_template" action="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, use_panels=use_panels, show_deleted=show_deleted )}" method="post" > <div class="toolFormBody"> %for i, field in enumerate( widgets ): <div class="form-row"> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/folder_info.mako --- a/templates/library/common/folder_info.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/folder_info.mako Tue Mar 09 11:28:21 2010 -0500 @@ -11,7 +11,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -23,7 +23,7 @@ <div class="toolFormTitle">Edit folder name and description</div> <div class="toolFormBody"> %if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, folder ): - <form name="folder" action="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}" method="post" > + <form name="folder" action="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}" method="post" > <div class="form-row"> <label>Name:</label> <input type="text" name="name" value="${folder_name}" size="40"/> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/folder_permissions.mako --- a/templates/library/common/folder_permissions.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/folder_permissions.mako Tue Mar 09 11:28:21 2010 -0500 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/ldda_edit_info.mako --- a/templates/library/common/ldda_edit_info.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/ldda_edit_info.mako Tue Mar 09 11:28:21 2010 -0500 @@ -29,7 +29,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -53,7 +53,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit attributes of ${ldda.name}</div> <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), show_deleted=show_deleted, )}" method="post"> + <form name="edit_attributes" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), use_panels=use_panels, show_deleted=show_deleted, )}" method="post"> <input type="hidden" name="id" value="${trans.security.encode_id( ldda.id )}"/> <div class="form-row"> <label>Name:</label> @@ -90,7 +90,7 @@ <input type="submit" name="save" value="Save"/> </div> </form> - <form name="auto_detect" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), show_deleted=show_deleted, )}" method="post"> + <form name="auto_detect" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), use_panels=use_panels, show_deleted=show_deleted, )}" method="post"> <div class="form-row"> <input type="hidden" name="id" value="${trans.security.encode_id( ldda.id )}"/> <input type="submit" name="detect" value="Auto-detect"/> @@ -106,7 +106,7 @@ <div class="toolFormTitle">Change data type</div> <div class="toolFormBody"> %if ldda.datatype.allow_datatype_change: - <form name="change_datatype" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), show_deleted=show_deleted, )}" method="post"> + <form name="change_datatype" action="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), use_panels=use_panels, show_deleted=show_deleted, )}" method="post"> <div class="form-row"> <label>New Type:</label> ${datatype( ldda, file_formats )} diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/ldda_info.mako Tue Mar 09 11:28:21 2010 -0500 @@ -27,7 +27,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -42,23 +42,23 @@ <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> %if cntrller=='library_admin' or can_modify: - <a class="action-button" href="${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 information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %if not info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='add_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 template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_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 )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), show_deleted=show_deleted )}">Delete template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_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 ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> %endif %endif %if cntrller=='library_admin' or can_manage: - <a class="action-button" href="${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 permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif %if current_version and ( cntrller=='library_admin' or can_modify ): - <a class="action-button" href="${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> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ) )}">Upload a new version of this dataset</a> %endif %if cntrller=='library' and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> %endif </div> %endif @@ -111,7 +111,7 @@ <div class="toolFormTitle">Expired versions of ${ldda.name}</div> %for expired_ldda in expired_lddas: <div class="form-row"> - <a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), show_deleted=show_deleted )}">${expired_ldda.name}</a> + <a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( expired_ldda.library_dataset.folder.id ), id=trans.security.encode_id( expired_ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${expired_ldda.name}</a> </div> %endfor %endif diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/ldda_permissions.mako --- a/templates/library/common/ldda_permissions.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/ldda_permissions.mako Tue Mar 09 11:28:21 2010 -0500 @@ -13,7 +13,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/library_dataset_info.mako --- a/templates/library/common/library_dataset_info.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/library_dataset_info.mako Tue Mar 09 11:28:21 2010 -0500 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/library_dataset_permissions.mako --- a/templates/library/common/library_dataset_permissions.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/library_dataset_permissions.mako Tue Mar 09 11:28:21 2010 -0500 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/library_info.mako --- a/templates/library/common/library_info.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/library_info.mako Tue Mar 09 11:28:21 2010 -0500 @@ -16,7 +16,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -27,15 +27,15 @@ <div class="toolForm"> %if cntrller == 'library_admin' or can_add or can_modify or can_manage: <div class="toolFormTitle"> - <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> %if not library.deleted: %if ( cntrller == 'library_admin' or can_add ) and not library.info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Add template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='library', library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> %endif %if cntrller == 'library_admin' or can_manage: - <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">Edit permissions</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif %if cntrller == 'library_admin': <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> @@ -43,14 +43,14 @@ %elif cntrller == 'library_admin' and not library.purged: <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Undelete this data library</a> %elif library.purged: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">This data library has been purged</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">This data library has been purged</a> %endif </div> </div> %endif <div class="toolFormBody"> %if not library.deleted and ( cntrller == 'library_admin' or can_modify ): - <form name="library" action="${h.url_for( controller='library_common', action='library_info', id=trans.security.encode_id( library.id ), cntrller=cntrller, show_deleted=show_deleted )}" method="post" > + <form name="library" action="${h.url_for( controller='library_common', action='library_info', id=trans.security.encode_id( library.id ), cntrller=cntrller, use_panels=use_panels, show_deleted=show_deleted )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/library_permissions.mako --- a/templates/library/common/library_permissions.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/library_permissions.mako Tue Mar 09 11:28:21 2010 -0500 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/new_folder.mako --- a/templates/library/common/new_folder.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/new_folder.mako Tue Mar 09 11:28:21 2010 -0500 @@ -5,7 +5,7 @@ <br/<br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/select_template.mako --- a/templates/library/common/select_template.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/select_template.mako Tue Mar 09 11:28:21 2010 -0500 @@ -33,7 +33,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, use_panels=use_panels, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -44,7 +44,7 @@ <div class="toolForm"> <div class="toolFormTitle">Select a template for the ${item_desc} '${item_name}'</div> <div class="toolFormBody"> - <form id="select_template" name="select_template" action="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, show_deleted=show_deleted )}" method="post" > + <form id="select_template" name="select_template" action="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type=item_type, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, use_panels=use_panels, show_deleted=show_deleted )}" method="post" > <div class="form-row"> <input type="hidden" name="refresh" value="true" size="40"/> <label>Template:</label> diff -r 00aab7119686 -r 3b1be99d1f62 templates/library/common/upload.mako --- a/templates/library/common/upload.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/library/common/upload.mako Tue Mar 09 11:28:21 2010 -0500 @@ -26,26 +26,26 @@ ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="upload-librarydataset--popup"> - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file', show_deleted=show_deleted )}">Upload files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> %if cntrller == 'library_admin': %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> %endif %if trans.app.config.allow_library_path_paste: - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths', show_deleted=show_deleted )}">Upload files from filesystem paths</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a> %endif %elif cntrller == 'library': %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> %endif %endif - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history', show_deleted=show_deleted )}">Import datasets from your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> </div> %endif <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id )}"><span>Browse this data library</span></a> </li> </ul> diff -r 00aab7119686 -r 3b1be99d1f62 templates/mobile/manage_library.mako --- a/templates/mobile/manage_library.mako Tue Mar 09 11:18:45 2010 -0500 +++ b/templates/mobile/manage_library.mako Tue Mar 09 11:28:21 2010 -0500 @@ -64,7 +64,7 @@ </div> %endif %if trans.app.security_agent.can_manage_library_item( current_user_roles, library ): - <% roles = trans.app.security_agent.get_legitimate_roles( trans, library ) %> + <% roles = trans.app.security_agent.get_legitimate_roles( trans, library, 'mobile' ) %> ${render_permission_form( library, library.name, h.url_for( controller='library_common', cntrller='mobile', action='library_permissions', id=trans.security.encode_id( library.id ) ), roles )} %endif

1 0