- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-bugs] /tmp directory
by juan perin 05 Feb '10

05 Feb '10

Thanks for the answer! I've copied this response to the dev list email instead, after realizing its probably best there. I'm also having some trouble getting our PBS system configured. I have pbs://hostname/ as my pbs parameter in the universe file, as well as everything else specified in the documentation. I'm getting no error in the interface, and the backend never actually gets the job. The error I see in the logs says: galaxy.jobs.runners.pbs ERROR 2009-10-30 13:40:27,762 Uncaught exception queueing job Traceback (most recent call last): File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 144, in run_next self.queue_job( obj ) File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 219, in queue_job script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) TypeError: sequence item 1: expected string, DatasetPath found I'm guessing this has something to do with my config parameters, and the queue its trying to submit to. the pbs://hostname/ value was used under the assumption that it would default to the 'default' queue on our cluster, so I'm wondering if I need to hard code those values into the connection string? I'm a little confused as to how the syntax translates to the actual required string. My guess is, for our values: pbs://variome.chop.edu/default Perhaps its related to the scrambling of the egg instead? I simply passed LIBTORQUE_DIR to the directory containing my libtorqure.so etc... ? Thanks in advance. Juan Perin On Fri, Oct 30, 2009 at 12:07 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Juan Perin wrote: > > I'm hosting galaxy locally and am trying to figure out how to change the >> temporary upload location of files from the root / /tmp folder to something >> else. My /tmp partition is too small to handle large fastq files and this >> is causing me problems. I see where to change things in the universe file, >> but that's the final location, not the temporary space. >> > > Hi Juan, > > A quick solution is to set $TEMP in your shell environment. In the future, > we'll force uploads to honor new_file_path in universe_wsgi.ini. > > --nate >

5 7

Removing trailing white space on file upload
by Assaf Gordon 04 Feb '10

04 Feb '10

Hello, Would it be possible to ask to remove trailing white space when pasting data in the "upload" tool ? Couple of times our users pasted text in the edit-box which contained trailing spaces (usually after copying the text from a web page) - and this confuses other tools (specially 'join'). If "Convert Spaces to Tab" is checked, an extra empty column is created. If "Convert spaces to tab" is not checked (e.g. when pasting a list of gene names, single column) - each name contains a space which is very hard to detect unless you know exactly what you're looking for. The attached patch removes those white spaces (I hope I found all the right places). -gordon

1 0

minor issues with the latest UI improvements
by Assaf Gordon 04 Feb '10

04 Feb '10

Hi all, trying out the latest and greatest, here are couple of minor UI issues. All were tried on a recent clone (upto rev 3315:ac6e08aed7d4), without any modifications (just "sh setup.sh" and "sh run.sh"). 1. It is still possible to share histories without having a public name. ( maybe rev 3255:ea652508497a doesn't catch all possible cases ? ) the shared history gets a URL of "http://localhost:8080/u//h/unnamed-history" (which gives a "404 not found"). 2. The URL of a shared history contains the name of the history as the last part (e.g. "http://localhost:8080/u/gordon/h/unnamed-history"). But changing the history name (and unsharing + sharing again) does not update the URL. It will always use the original history name - very unfriendly if I publish first and then notice the bad name. 3. The opposite of 2: changing the "public user name" will cause a change in the shared history's URL. Since there's nothing preventing users from changing their public names, the published URLs are very volatile. If some day I will want to change my public name from "Gordon" to "Dr. Gordon", all the URL that I've sent or published (except on the "published histories" page) will become invalid (come to think about, the "Dr." part will never happen, so it's not critical (: ). 4. What stops a user from using somebody else's public name ? On my local galaxy I was able to give the same public name to two different email accounts. Worse: I was able to create two accounts with the same public name, and have them both public histories with the same name. Both histories got the same URL, and both appeared in the "published histories" view (but clicking on both got my to the same history). I'm not sure with public name take precedence, but if it's the last one set, then somebody can hijack all the published histories of a user by setting his public name to the other user's public name. 5. Taking items 2,3 and 4 together, I really dislike any public URL system that relies on user changeable information. I think the previous way (of using a hashed history ID) was much more robust. 6. Annotation feature: I was able to set annotations) for histories, workflows and workflows-steps, but not view them anywhere. Maybe that's just an alpha feature. but please note that I can put HTML code in the annotations, and it will be used without escaping/sanitzing. Example: create an empty history. Click on "Edit Tags and Annotation/Notes". Paste the following code in the annotation edit-box: <iframe src="http://cnn.com"></iframe> Press ENTER to save the annotation. The immediate refresh is probably done by AJAX or Javascript, so you see the HTML code. but click "refresh" and you'll see CNN inside an <iframe>. If you're going to display annotation/notes as part of published histories (where one user can publish his malicious history and other users will just view it without being able to block it) - it will be dangerous. 7. The "Edit Workflow Attributes" button is mis-placed on Firefox 3.0.6/Linux, see attached image. 8. Not UI issue, but still a bug: After uploading a wiggle file, I noticed a new file conversion option saying "Index Wiggle for Track Viewer" - obviously I clicked it ;) and got: Traceback (most recent call last): File "/home/gordon/temp/uitest/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py", line 8, in from bx.arrays.array_tree import * ImportError: No module named array_tree That's all for today, keep up the good work, -gordon

3 4

Mako/HTML bug with "use_remote_user"
by Assaf Gordon 03 Feb '10

03 Feb '10

Hello, Using the latest Galaxy, and with "use_remote_user" option turned on, the generated "User" menu is empty (see attached image). The problem is in "templates/base_panels.mako", starting at line 379: If "use_remote_user" is enabled, the only displayed option is the "logout" link (which I don't have - so the menu is empty). What I would expect is to see: 1. Optionally - a label saying: "logged in as {username}" - useful even if using remote_user. 2. preferences (to change the public name, and optionally the user address) 3. link to histories, datasets 4. if enabled - link to pages. I'm guessing "preferences" could be complicated (because one must not change email or password when using 'remote_user'), but it is required to be able to change the public-name (and adding optional address?). The attached patch enables the (easier to do) histories, datasets, and pages links. -gordon

1 0

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

03 Feb '10

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

1 0

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

02 Feb '10

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

1 0

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

02 Feb '10

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

1 0

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

02 Feb '10

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

1 0

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

02 Feb '10

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

1 0

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

02 Feb '10

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

1 0