November 2009 - galaxy-dev - lists.galaxyproject.org

Library upload from system path
by SHAUN WEBB 17 Nov '09

17 Nov '09

Hi, I have updated Galaxy today with the latest changes. While trying to upload a file from the system path without copying to Galaxy I am getting the following Server error: AttributeError: 'ScopedSession' object has no attribute 'data' The full message is below. This does not occur if the file is copied in to galaxy. I have made local changes to a few of the upload files to support an additional binary file type, but I can't see how these would affect upload from system path. Is any one else having a similar issue? Any help would be appreciated Thanks Shaun Webb URL: http://bifx3.bio.ed.ac.uk:8080/library_admin/upload_library_dataset Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ >> body = self.call_body_method( method, trans, kwargs ) Module galaxy.web.framework.base:144 in call_body_method >> return method( trans, **kwargs ) Module galaxy.web.framework:87 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.library_admin:712 in upload_library_dataset >> **kwd ) Module galaxy.web.controllers.library_common:87 in upload_dataset >> uploaded_datasets, err_redirect, msg = >> self.get_path_paste_uploaded_datasets( trans, params, >> library_bunch, err_redirect, msg ) Module galaxy.web.controllers.library_common:171 in get_path_paste_uploaded_datasets >> uploaded_datasets.append( self.make_library_uploaded_dataset( >> trans, params, name, path, 'path_paste', library_bunch ) ) Module galaxy.web.controllers.library_common:121 in make_library_uploaded_dataset >> trans.sa_session.data.flush() AttributeError: 'ScopedSession' object has no attribute 'data' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] Questions about Galaxy!
by Greg Von Kuster 17 Nov '09

17 Nov '09

Kathleen, Please install a local instance of Galaxy and develop a data source tool that works between your Galaxy instance and GMap. You can download Galaxy from http://bitbucket.org/galaxy/galaxy-central/wiki/ GetGalaxy. When you have your tool working, please submit it to us for possible inclusion in the public Galaxy instance. Thanks very much for your interest in doing this. Greg Von Kuster On Nov 17, 2009, at 11:27 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: > Hello Greg Von Kuster, > > You can access test GMap at http://202.38.125.5:8383/. > Click the big button "search" and submit using the default params, > then > you can see four tracks. You can click the entry of the second > track, for > example the red one, then you can see the detail info in the right > panel. > Click the "view sequence", there is a button "submit to Galaxy", > you can > try it. > > Thanks a lot! > Kathleen > >> Kathleen, sorry, I thought you had your own local Galaxy instance. >> Can you give us more information on GMap? Do you have a wiki or >> something we can access online to read about it? >> >> Thanks! >> >> On Nov 17, 2009, at 10:37 AM, wangjun(a)mail.cbi.pku.edu.cn wrote: >> >>> Hello Greg Von Kuster, >>> >>> I am talking about your public Galaxy instance, and we don't have >>> local one. >>> We find that UCSC's data can be saved in your site directly, so we >>> hope >>> that Galaxy can also save our GMap data directly. We use the same >>> post >>> method like UCSC and the data can be saved now, but the data >>> title is >>> wrong. So I am writing to you to hope that you can help us. >>> >>> Thanks you. >>> >>> Kathleen >>> >>>> Hello Kathleen, >>>> >>>> Are you talking about your own local Galaxy instance or our main >>>> public Galaxy instance that is hosted here at Penn State >>>> University? >>>> >>>> Greg Von Kuster >>>> >>>> On Nov 17, 2009, at 10:10 AM, WangJun wrote: >>>> >>>>> Hello Greg Von Kuster, >>>>> >>>>> Thanks for your reply, but I think you misunderstood my meaning. >>>>> I am now working on a genome browser project GMap, and I hope that >>>>> I can post request from GMap to Galaxy, then Galaxy can retrieve >>>>> and save the data in the History space like the UCSC request. >>>>> Untill now, I can post a request, including a url and params, and >>>>> Galaxy can retrieve the data and save it. However, the title of >>>>> the >>>>> data is still "UCSC Main". I think that's because of the tool_id >>>>> param's value is still "ucsc_table_direct1". I mean whether you >>>>> can >>>>> support us by adding a new tool_id named "CBI GMap". Then our post >>>>> data can be shown with title "CBI GMap", not "UCSC Main". >>>>> >>>>> Thanks a lot! >>>>> Kathleen >>>>> >>>>> >>>>> 发件人： Greg Von Kuster >>>>> 发送时间： 2009-11-17 21:49:22 >>>>> 收件人： WangJun >>>>> 抄送： >>>>> 主题： Re: [galaxy-dev] Questions about Galaxy! >>>>> Kathleen, >>>>> >>>>> I'm not sure I understand the question, but if you are simply >>>>> creating a new tool that is very similar to the >>>>> "ucsc_table_direct1" tool , and you want the ID of your new >>>>> tool to >>>>> be "CBIGMap" ( I would advise against space characters in the tool >>>>> ID ), then your tools config tag can be something like this: >>>>> >>>>>> <tool id="CBIGMap" name="CBIG Map" version="1.0.0" hidden="false" >>>>>> tool_type="data_source" URL_method="post"> >>>>> >>>>> If you have questions about how to add a new tool to your Galaxy >>>>> instance, see our wiki at http://bitbucket.org/galaxy/galaxy- >>>>> central/wiki/AddToolTutorial >>>>> >>>>> >>>>> On Nov 17, 2009, at 8:38 AM, WangJun wrote: >>>>> >>>>>> Hello Greg Von Kuster, >>>>>> >>>>>> Now I have solved the second problem.:) >>>>>> And for the first one, could you help me to add a new tool_id >>>>>> named "CBI GMap" to support our data source? >>>>>> This is a project in Center for Bioinformatics in Peking >>>>>> University in China. And I am a PhD student working on it. If you >>>>>> have other questions, please email me.:) >>>>>> <tool id="ucsc_table_direct1" name="UCSC Main" version="1.0.0" >>>>>> hidden="false" tool_type="data_source" URL_method="post"> >>>>>> Thanks a lot! >>>>>> >>>>>> Best, >>>>>> Kathleen >>>>>> 20091117 >>>>>> >>>>>> ================================================================= >>>>>> == >>>>>> = >>>>>> Hello Greg Von Kuster, >>>>>> >>>>>> Thanks a lot for your reply. >>>>>> But I still have a question: >>>>>> >>>>>> I have a url, and I include three necessary params in the >>>>>> following form. After I post it to Galaxy, I can see that Galaxy >>>>>> fetch the data. However, there are two point that I want to ask: >>>>>> 1. the "tool_id" param. My data's title is still "UCSC Main", I >>>>>> think that's because I use the "ucsc_table_direct1" value for >>>>>> "tool_id", right? Then how do I change this title? Can I >>>>>> adjust it >>>>>> by other param to change the title? >>>>>> 2. If I submit data from UCSC, then I can see a white box >>>>>> containing the data in the History part. However, I can only see >>>>>> the data info without data if I submit from my own site. (You can >>>>>> refer to attachment for detail. The No.20 data is from UCSC, >>>>>> and I >>>>>> can see the sequence. While the No.22 data is from my site, and I >>>>>> can not see the sequence.) And I don't know why. >>>>>> >>>>>> <form method="POST" action="http://main.g2.bx.psu.edu/ >>>>>> tool_runner"> >>>>>> <input type="HIDDEN" value="ucsc_table_direct1" >>>>>> name="tool_id"/> >>>>>> <input type="HIDDEN" value="http://202.38.125.5:8383/ >>>>>> entry/ >>>>>> rice_nucleotide_frame_galaxy.jsp" name="URL"/> >>>>>> <input type="HIDDEN" value="<%=id%>" name="id"/> >>>>>> <input type="HIDDEN" value="<%=trackName%>" >>>>>> name="trackName"/> >>>>>> <input type="HIDDEN" value="<%=type%>" name="type"/> >>>>>> <input type="HIDDEN" value="rice" name="db"/> >>>>>> <input type="HIDDEN" value="Rice" name="org"/> >>>>>> <input type="SUBMIT" value="Send query to Galaxy" >>>>>> name="submitGalaxy"/> >>>>>> </form> >>>>>> >>>>>> (test data: http://202.38.125.5:8383/entry/ >>>>>> rice_nucleotide_frame_galaxy.jsp? >>>>>> id=LOC_Os02g01370&trackName=MSU_Osa1_Rice_Loci&type=seq ) >>>>>> >>>>>> Thank a lot! >>>>>> Best, >>>>>> Kathleen >>>>>> 20091117 >>>>>> >>>>>> >>>>>> 发件人： Greg Von Kuster >>>>>> 发送时间： 2009-11-17 04:50:55 >>>>>> 收件人： WangJun >>>>>> 抄送： galaxy-user(a)bx.psu.edu; galaxy-dev(a)bx.psu.edu >>>>>> 主题： Re: [galaxy-dev] Questions about Galaxy! >>>>>> Hello Kathleen, >>>>>> >>>>>> Please see our wiki at http://bitbucket.org/galaxy/galaxy- >>>>>> central/ >>>>>> wiki/DataSources for details about how Galaxy communicates with >>>>>> external data sources. Your "dataset platform" will need to >>>>>> build >>>>>> an url that includes all of the parameters that are needed to >>>>>> retrieve the data, and send that url to Galaxy in the URL >>>>>> parameter so that Galaxy can execute the post. >>>>>> >>>>>> >>>>>> On Nov 16, 2009, at 9:06 AM, WangJun wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> This is a question about Galaxy interaction with UCSC data. >>>>>>> >>>>>>> I hava a dataset platform, and I want to add a button like the >>>>>>> UCSC's "Send query to Galaxy". >>>>>>> >>>>>>> I find that it's actually a form: >>>>>>> <form method="POST" action="http://main.g2.bx.psu.edu/ >>>>>>> tool_runner"> >>>>>>> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> >>>>>>> <input type="HIDDEN" value="http://genome.ucsc.edu/cgi-bin/ >>>>>>> hgTables" name="URL"/> >>>>>>> <input type="HIDDEN" value="296389734" name="hguid"/> >>>>>>> <input type="HIDDEN" value="hg18" name="db"/> >>>>>>> <input type="HIDDEN" value="Human" name="org"/> >>>>>>> <input type="HIDDEN" value="multiz28way" name="hgta_table"/> >>>>>>> <input type="HIDDEN" value="multiz28way" name="hgta_track"/> >>>>>>> <input type="HIDDEN" value="range" name="hgta_regionType"/> >>>>>>> <input type="HIDDEN" value="primaryTable" >>>>>>> name="hgta_outputType"/> >>>>>>> <input type="HIDDEN" value="chr3:130734948-130736581" >>>>>>> name="position"/> >>>>>>> <input type="HIDDEN" value="get output" >>>>>>> name="hgta_doTopSubmit"/> >>>>>>> <input type="HIDDEN" value="146683120" name="hgsid"/> >>>>>>> <input type="SUBMIT" value="Send query to Galaxy" >>>>>>> name="hgta_doGalaxyQuery"/> >>>>>>> </form> >>>>>>> >>>>>>> I have a url and three params, and I tried. But I can't see my >>>>>>> data in the right-side green box. >>>>>>> And what's the tool_id param used for? >>>>>>> >>>>>>> Thanks in advance! >>>>>>> >>>>>>> Best, >>>>>>> Kathleen >>>>>>> 2009-11-16 >>>>>>> _______________________________________________ >>>>>>> galaxy-dev mailing list >>>>>>> galaxy-dev(a)lists.bx.psu.edu >>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>>>> >>>>>> Greg Von Kuster >>>>>> Galaxy Development Team >>>>>> greg(a)bx.psu.edu >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> Greg Von Kuster >>>>> Galaxy Development Team >>>>> greg(a)bx.psu.edu >>>>> >>>>> >>>>> >>>>> >>>> >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> greg(a)bx.psu.edu >>>> >>>> >>>> >>>> >>> >>> >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> >> > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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required version of R
by Andreas Kuntzagk 17 Nov '09

17 Nov '09

Hi, some tools in Graph/Display Data give us error messages. Since our version of R is "not so fresh" (2.7.2) I suspect this is the reason. Can anybody confirm that a newer version of R is required? Problems: Histogramm: Error in hist.default(list(1, 2, 3, 4, 5), xlab = "V1", breaks = "Sturges", : 'x' must be numeric Scatterplot: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf Error in plot.window(...) : need finite 'xlim' values Bar chart requires python module Numeric which is quite dated and superseded by numpy. Are there any plans to fix that? I don't want to install an unsupported python module. regards, Andreas

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Cheetah Code
by SHAUN WEBB 17 Nov '09

17 Nov '09

Hi, Since updating Galaxy I am having issues running some of the tools I have created. The problem is with if statements in the code (I believe it is Cheetah) within the <command> tab. This is an example: #if $input_type.in_source == "user": #rand2_seq.pl --in $in --cutsites $cutsites --out $out --length $length #else: #rand2_seq.pl --in $in --out $out --length $length #end if I am receiving the following error: File "/opt/galaxy_dist/eggs/py2.5-linux-x86_64-ucs4/Cheetah-2.2.2-py2.5-linux-x86_64.egg/Cheetah/Parser.py", line 2645, in popFromOpenDirectivesStack raise ParseError(self, msg="#end found, but nothing to end") ParseError: #end found, but nothing to end Line 4, column 1 Line|Cheetah Code ----|------------------------------------------------------------- 2 | #else: #rand2_seq.pl --in $in --out $out --length $length 3 | #end if 4 | ^ I am guessing there has been some sort of update to the way these scripts are compiled as they worked fine before. Thanks for your help Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[hg] galaxy 3042: Enhance history item error reports that are em...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/df9814119044 changeset: 3042:df9814119044 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Nov 16 16:27:48 2009 -0500 description: Enhance history item error reports that are emailed - report form now defaults to include the users email address if they are logged in - email now includes the id of both the dataset and the history, the hid and hda.display_name(), and a link to the history - admin users now have "view" access to any history and dataset ( this uses the new ~/history/view?id=... feature ) diffstat: lib/galaxy/web/controllers/dataset.py | 61 +++++++++++++++++++----------- lib/galaxy/web/controllers/history.py | 12 ++---- lib/galaxy/web/controllers/user.py | 2 - lib/galaxy/web/framework/__init__.py | 10 +---- templates/dataset/errors.mako | 17 +++++--- templates/mobile/history/detail.mako | 2 +- templates/root/history_common.mako | 4 +- test/base/twilltestcase.py | 6 +++ test/functional/test_history_functions.py | 6 +++ 9 files changed, 70 insertions(+), 50 deletions(-) diffs (319 lines): diff -r 2eb1e3c4d143 -r df9814119044 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Nov 16 15:06:07 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Mon Nov 16 16:27:48 2009 -0500 @@ -20,25 +20,38 @@ This error report was sent from the Galaxy instance hosted on the server "${host}" ----------------------------------------------------------------------------- -This is in reference to output dataset ${dataset_id}. +This is in reference to dataset id ${dataset_id} from history id ${history_id} +----------------------------------------------------------------------------- +You should be able to view the history containing the related history item + +${hid}: ${history_item_name} + +by logging in as a Galaxy admin user to the Galaxy instance referenced above +and pointing your browser to the following link. + +${history_view_link} ----------------------------------------------------------------------------- The user '${email}' provided the following information: + ${message} ----------------------------------------------------------------------------- job id: ${job_id} -tool id: ${tool_id} +tool id: ${job_tool_id} +----------------------------------------------------------------------------- +job command line: +${job_command_line} ----------------------------------------------------------------------------- job stderr: -${stderr} +${job_stderr} ----------------------------------------------------------------------------- job stdout: -${stdout} +${job_stdout} ----------------------------------------------------------------------------- job info: -${info} +${job_info} ----------------------------------------------------------------------------- job traceback: -${traceback} +${job_traceback} ----------------------------------------------------------------------------- (This is an automated message). """ @@ -103,41 +116,45 @@ @web.expose def errors( self, trans, id ): - dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - return trans.fill_template( "dataset/errors.mako", dataset=dataset ) - + hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + return trans.fill_template( "dataset/errors.mako", hda=hda ) @web.expose def stderr( self, trans, id ): dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) job = dataset.creating_job_associations[0].job trans.response.set_content_type( 'text/plain' ) return job.stderr - @web.expose def report_error( self, trans, id, email='', message="" ): smtp_server = trans.app.config.smtp_server if smtp_server is None: - return trans.show_error_message( "Sorry, mail is not configured for this galaxy instance" ) + return trans.show_error_message( "Mail is not configured for this galaxy instance" ) to_address = trans.app.config.error_email_to if to_address is None: - return trans.show_error_message( "Sorry, error reporting has been disabled for this galaxy instance" ) + return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" ) # Get the dataset and associated job - dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - job = dataset.creating_job_associations[0].job + hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + job = hda.creating_job_associations[0].job # Get the name of the server hosting the Galaxy instance from which this report originated host = trans.request.host + history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) ) # Build the email message msg = MIMEText( string.Template( error_report_template ) .safe_substitute( host=host, - dataset_id=dataset.id, + dataset_id=hda.dataset_id, + history_id=hda.history_id, + hid=hda.hid, + history_item_name=hda.get_display_name(), + history_view_link=history_view_link, + job_id=job.id, + job_tool_id=job.tool_id, + job_command_line=job.command_line, + job_stderr=job.stderr, + job_stdout=job.stdout, + job_info=job.info, + job_traceback=job.traceback, email=email, - message=message, - job_id=job.id, - tool_id=job.tool_id, - stderr=job.stderr, - stdout=job.stdout, - traceback=job.traceback, - info=job.info ) ) + message=message ) ) frm = to_address # Check email a bit email = email.strip() diff -r 2eb1e3c4d143 -r df9814119044 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Nov 16 15:06:07 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Nov 16 16:27:48 2009 -0500 @@ -438,23 +438,20 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) - @web.expose def view( self, trans, id=None ): """View a history. If a history is importable, then it is viewable by any user.""" - # Get history to view. if not id: return trans.show_error_message( "You must specify a history you want to view." ) history_to_view = get_history( trans, id, False) - # Integrity checks. if not history_to_view: - return trans.show_error_message( "The specified history does not exist.") + return trans.show_error_message( "The specified history does not exist." ) + # Admin users can view any history # TODO: Use a new flag to determine if history is viewable? - if not history_to_view.importable: - error( "The owner of this history has not published this history." ) - + if not trans.user_is_admin and not history_to_view.importable: + error( "Either you are not allowed to view this history or the owner of this history has not published it." ) # View history. query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ .filter( model.HistoryDatasetAssociation.history == history_to_view ) \ @@ -469,7 +466,6 @@ datasets = query.all(), user_owns_history = user_owns_history, show_deleted = False ) - @web.expose @web.require_login( "share histories with other users" ) def share( self, trans, id=None, email="", **kwd ): diff -r 2eb1e3c4d143 -r df9814119044 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Mon Nov 16 15:06:07 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Mon Nov 16 16:27:48 2009 -0500 @@ -181,9 +181,7 @@ refresh_frames = [ 'masthead', 'history' ] if not trans.app.config.allow_user_creation and not trans.user_is_admin(): return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) - # # Create the user, save all the user info and login to Galaxy - # if params.get('create_user_button', None) == "Submit": # check email and password validity error = self.__validate(trans, params, email, password, confirm) diff -r 2eb1e3c4d143 -r df9814119044 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Nov 16 15:06:07 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Nov 16 16:27:48 2009 -0500 @@ -446,13 +446,11 @@ self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) - def get_galaxy_session( self ): """ Return the current galaxy session """ return self.galaxy_session - def get_history( self, create=False ): """ Load the current history, creating a new one only if there is not @@ -497,7 +495,6 @@ self.sa_session.add_all( ( self.galaxy_session, history ) ) self.sa_session.flush() return history - def get_user( self ): """Return the current user if logged in or None.""" return self.galaxy_session.user @@ -507,7 +504,6 @@ self.sa_session.add( self.galaxy_session ) self.sa_session.flush() user = property( get_user, set_user ) - def get_user_and_roles( self ): user = self.get_user() if user: @@ -515,13 +511,9 @@ else: roles = [] return user, roles - def user_is_admin( self ): admin_users = self.app.config.get( "admin_users", "" ).split( "," ) - if self.user and admin_users and self.user.email in admin_users: - return True - return False - + return self.user and admin_users and self.user.email in admin_users def get_toolbox(self): """Returns the application toolbox""" return self.app.toolbox diff -r 2eb1e3c4d143 -r df9814119044 templates/dataset/errors.mako --- a/templates/dataset/errors.mako Mon Nov 16 15:06:07 2009 -0500 +++ b/templates/dataset/errors.mako Mon Nov 16 16:27:48 2009 -0500 @@ -18,10 +18,10 @@ <body> <h2>Dataset generation errors</h2> - <p><b>Dataset ${dataset.hid}: ${dataset.display_name()}</b></p> + <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> - %if dataset.creating_job_associations: - <% job = dataset.creating_job_associations[0].job %> + %if hda.creating_job_associations: + <% job = hda.creating_job_associations[0].job %> %if job.traceback: The Galaxy framework encountered the following error while attempting to run the tool: <pre>${job.traceback}</pre> @@ -43,7 +43,12 @@ %else: The tool did not create any additional job / error info. %endif - + <% + if trans.user: + user_email = trans.user.email + else: + user_email = '' + %> <h2>Report this error to the Galaxy Team</h2> <p> The Galaxy team regularly reviews errors that occur in the application. @@ -56,10 +61,10 @@ <div class="toolFormTitle">Error Report</div> <div class="toolFormBody"> <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > - <input type="hidden" name="id" value="${dataset.id}" /> + <input type="hidden" name="id" value="${hda.id}" /> <div class="form-row"> <label>Your email</label> - <input type="text" name="email" size="40" /> + <input type="text" name="email" size="40" value="${user_email}" /> </div> <div class="form-row"> <label>Message</label> diff -r 2eb1e3c4d143 -r df9814119044 templates/mobile/history/detail.mako --- a/templates/mobile/history/detail.mako Mon Nov 16 15:06:07 2009 -0500 +++ b/templates/mobile/history/detail.mako Mon Nov 16 16:27:48 2009 -0500 @@ -37,7 +37,7 @@ <div class="secondary"> ## Body for history items, extra info and actions, data "peek" <% user, roles = trans.get_user_and_roles() %> - %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): + %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div>You do not have permission to view this dataset.</div> %elif data_state == "queued": <div>Job is waiting to run</div> diff -r 2eb1e3c4d143 -r df9814119044 templates/root/history_common.mako --- a/templates/root/history_common.mako Mon Nov 16 15:06:07 2009 -0500 +++ b/templates/root/history_common.mako Mon Nov 16 16:27:48 2009 -0500 @@ -9,7 +9,7 @@ data_state = data.state user, roles = trans.get_user_and_roles() %> - %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): + %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${data.id}"> %else: <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}"> @@ -49,7 +49,7 @@ ## Body for history items, extra info and actions, data "peek" <div id="info${data.id}" class="historyItemBody"> - %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ): + %if not trans.user_is_admin() and not trans.app.security_agent.can_access_dataset( roles, data.dataset ): <div>You do not have permission to view this dataset.</div> %elif data_state == "upload": <div>Dataset is uploading</div> diff -r 2eb1e3c4d143 -r df9814119044 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 16 15:06:07 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 16 16:27:48 2009 -0500 @@ -430,6 +430,12 @@ if check_str: self.check_page_for_string( check_str ) self.home() + def view_history( self, history_id, check_str='' ): + """Displays a history for viewing""" + self.visit_url( '%s/history/view?id=%s' % ( self.url, self.security.encode_id( history_id ) ) ) + if check_str: + self.check_page_for_string( check_str ) + self.home() def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='' ): """Edit history_dataset_association attribute information""" self.home() diff -r 2eb1e3c4d143 -r df9814119044 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Nov 16 15:06:07 2009 -0500 +++ b/test/functional/test_history_functions.py Mon Nov 16 16:27:48 2009 -0500 @@ -603,6 +603,12 @@ except: pass self.check_history_for_string( 'You do not have permission to view this dataset' ) + # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin + self.logout() + self.login( email=admin_user.email ) + self.view_history( str( hda_2_bed.history_id ), check_str='<td>NM_005997_cds_0_0_chr1_147962193_r</td>' ) + self.logout() + self.login( email=regular_user3.email ) # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone4.id ) ) def test_065_sharing_private_history_by_choosing_to_not_share( self ):

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[hg] galaxy 3041: Unicode fix: allow non-ascii characters to be ...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2eb1e3c4d143 changeset: 3041:2eb1e3c4d143 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 16 15:06:07 2009 -0500 description: Unicode fix: allow non-ascii characters to be displayed in tool help. diffstat: templates/tool_form.mako | 16 +++++++++++----- 1 files changed, 11 insertions(+), 5 deletions(-) diffs (26 lines): diff -r 84f96ae27ef4 -r 2eb1e3c4d143 templates/tool_form.mako --- a/templates/tool_form.mako Mon Nov 16 14:52:51 2009 -0500 +++ b/templates/tool_form.mako Mon Nov 16 15:06:07 2009 -0500 @@ -221,11 +221,17 @@ %if tool.help: <div class="toolHelp"> <div class="toolHelpBody"> - %if tool.has_multiple_pages: - ${tool.help_by_page[tool_state.page]} - %else: - ${tool.help} - %endif + <% + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + %> + ${tool_help} </div> </div> %endif

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[hg] galaxy 3036: Have Extract Genomic DNA tool copy metadata fr...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b7c6a418c571 changeset: 3036:b7c6a418c571 user: dan date: Mon Nov 16 10:57:31 2009 -0500 description: Have Extract Genomic DNA tool copy metadata from input file. This will allow the tool to keep column assignments when outputing interval format. diffstat: tools/extract/extract_genomic_dna.xml | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (18 lines): diff -r 1f8542d78671 -r b7c6a418c571 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Sat Nov 14 20:32:41 2009 -0500 +++ b/tools/extract/extract_genomic_dna.xml Mon Nov 16 10:57:31 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.0"> +<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"> <description>using coordinates from assembled/unassembled genomes</description> <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command> <inputs> @@ -12,7 +12,7 @@ </param> </inputs> <outputs> - <data format="fasta" name="out_file1"> + <data format="fasta" name="out_file1" metadata_source="input"> <change_format> <when input="out_format" value="interval" format="interval" /> </change_format>

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[hg] galaxy 3037: Fix unicode error in data.display_info(). Fixe...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3d0e1bdd6ce1 changeset: 3037:3d0e1bdd6ce1 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 16 11:27:30 2009 -0500 description: Fix unicode error in data.display_info(). Fixes #226. diffstat: lib/galaxy/datatypes/data.py | 5 +++++ 1 files changed, 5 insertions(+), 0 deletions(-) diffs (15 lines): diff -r b7c6a418c571 -r 3d0e1bdd6ce1 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Nov 16 10:57:31 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Mon Nov 16 11:27:30 2009 -0500 @@ -160,6 +160,11 @@ info = info.replace( '\r', '<br/>' ) if info.find( '\n' ) >= 0: info = info.replace( '\n', '<br/>' ) + + # Convert to unicode to display non-ascii characters. + if type( info ) is not unicode: + info = unicode( info, 'utf-8') + return info except: return "info unavailable"

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[hg] galaxy 3038: Explicitly check eggs and fetch when starting, ...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/56f0d16aa299 changeset: 3038:56f0d16aa299 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 16 14:42:09 2009 -0500 description: Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building diffstat: run.sh | 19 +++++++++++++++++++ scripts/check_eggs.py | 14 +++++++++++--- scripts/scramble/scripts/pysqlite.py | 2 +- 3 files changed, 31 insertions(+), 4 deletions(-) diffs (71 lines): diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 run.sh --- a/run.sh Mon Nov 16 11:27:30 2009 -0500 +++ b/run.sh Mon Nov 16 14:42:09 2009 -0500 @@ -1,4 +1,23 @@ #!/bin/sh cd `dirname $0` + +# explicitly attempt to fetch eggs before running +FETCH_EGGS=1 +for arg in "$@"; do + [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break +done +if [ $FETCH_EGGS -eq 1 ]; then + python -ES ./scripts/check_eggs.py quiet + if [ $? -ne 0 ]; then + echo "Some eggs are out of date, attempting to fetch..." + python -ES ./scripts/fetch_eggs.py + if [ $? -eq 0 ]; then + echo "Fetch successful." + else + echo "Fetch failed." + exit 1 + fi + fi +fi python -ES ./scripts/paster.py serve universe_wsgi.ini $@ diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 scripts/check_eggs.py --- a/scripts/check_eggs.py Mon Nov 16 11:27:30 2009 -0500 +++ b/scripts/check_eggs.py Mon Nov 16 14:42:09 2009 -0500 @@ -11,6 +11,12 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) +try: + assert sys.argv[1] == 'quiet' + quiet = True +except: + quiet = False + from galaxy.eggs import * c = Crate() @@ -21,7 +27,9 @@ if not galaxy_config.check_conditional( name ): ignore.append( name ) if not c.find( ignore=ignore ): - print "Some of your Galaxy eggs are out of date. Please update them" - print "by running:" - print " python scripts/fetch_eggs.py" + if not quiet: + print "Some of your Galaxy eggs are out of date. Please update them" + print "by running:" + print " python scripts/fetch_eggs.py" sys.exit( 1 ) +sys.exit( 0 ) diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 scripts/scramble/scripts/pysqlite.py --- a/scripts/scramble/scripts/pysqlite.py Mon Nov 16 11:27:30 2009 -0500 +++ b/scripts/scramble/scripts/pysqlite.py Mon Nov 16 14:42:09 2009 -0500 @@ -33,10 +33,10 @@ # tag me = sys.argv[0] sys.argv = [ me ] +sys.argv.append( "build_static" ) if tag is not None: sys.argv.append( "egg_info" ) sys.argv.append( "--tag-build=%s" %tag ) -sys.argv.append( "build_static" ) sys.argv.append( "bdist_egg" ) # go

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[hg] galaxy 3039: Ajax support for grid operations. Preparations...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/052f6096e3cd changeset: 3039:052f6096e3cd user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 16 14:52:33 2009 -0500 description: Ajax support for grid operations. Preparations for ajaxing history grid. diffstat: lib/galaxy/web/controllers/history.py | 18 ++-- lib/galaxy/web/framework/helpers/grids.py | 3 +- templates/grid_base_async.mako | 135 +++++++++++++++++++++------------ 3 files changed, 95 insertions(+), 61 deletions(-) diffs (253 lines): diff -r 3d0e1bdd6ce1 -r 052f6096e3cd lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Nov 16 11:27:30 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Nov 16 14:52:33 2009 -0500 @@ -87,7 +87,7 @@ # Grid definition title = "Saved Histories" model_class = model.History - template='/history/grid.mako' + template='/grid_base.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", model_class=model.History, @@ -110,14 +110,14 @@ ) operations = [ - grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Share", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), - grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), - grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) + grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), + grids.GridOperation( "Share", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), async_compatible=True ), + grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ), async_compatible=True ), + grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ), async_compatible=True ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), diff -r 3d0e1bdd6ce1 -r 052f6096e3cd lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 16 11:27:30 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 16 14:52:33 2009 -0500 @@ -393,7 +393,7 @@ return query.filter( complete_filter ) class GridOperation( object ): - def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None ): + def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False ): self.label = label self.key = key self.allow_multiple = allow_multiple @@ -401,6 +401,7 @@ self.condition = condition self.target = target self.url_args = url_args + self.async_compatible = async_compatible def get_url_args( self, item ): if self.url_args: temp = dict( self.url_args ) diff -r 3d0e1bdd6ce1 -r 052f6096e3cd templates/grid_base_async.mako --- a/templates/grid_base_async.mako Mon Nov 16 11:27:30 2009 -0500 +++ b/templates/grid_base_async.mako Mon Nov 16 14:52:33 2009 -0500 @@ -33,6 +33,23 @@ $(document).ready(function() { // Initialize grid elements. init_grid_elements(); + + // Operations that are not async (AJAX) compatible. + var no_async_ops = new Object(); + %for operation in grid.operations: + %if not operation.async_compatible: + no_async_ops['${operation.label}'] = "True"; + %endif + %endfor + + // Initialize each operation button to do operation when clicked. + $('input[name=operation]:submit').each(function() { + $(this).click( function() { + var this_value = $(this).attr("value"); + var no_async = ( no_async_ops[this_value] != undefined && no_async_ops[this_value] != null); + do_operation(this_value, no_async); + }); + }); // Initialize autocomplete for text inputs in search UI. var t = $("#input-tags-filter"); @@ -227,13 +244,13 @@ } } - update_grid(true); + update_grid(); }); var container = $('#' + name + "-filtering-criteria"); container.append(t); - update_grid(true); + update_grid(); } // Set sort condition for grid. @@ -307,7 +324,7 @@ // Update grid. url_args["f-" + name] = new_value; - update_grid(true); + update_grid(); } var num_pages = ${num_pages}; @@ -354,11 +371,41 @@ { url_args['page'] = parseInt(new_page); } - update_grid(); + update_grid(true); + } + + // Perform a grid operation. TODO: this is not complete. + function do_operation(operation, no_async) + { + // For some reason, $('input[name=id]:checked').val() does not return all ids for checked boxes. + // The code below performs this function. + var item_ids = new Array() + $('input[name=id]:checked').each(function() { + item_ids[item_ids.length] = $(this).val(); + }); + + // Update URL args. + url_args['operation'] = operation; + url_args['id'] = item_ids; + + // If operation cannot be performed asynchronously, redirect to location. Otherwise do operation. + if (no_async) + { + var arg_str = ""; + var arg; + + for (arg in url_args) + arg_str = arg_str + arg + "=" + url_args[arg] + "&"; + + self.location = encodeURI( "${h.url_for()}?" + arg_str ); + } + else + update_grid(); + } // Update grid. - function update_grid() + function update_grid(maintain_page_links) { $.ajax({ url: "${h.url_for()}", @@ -381,61 +428,47 @@ var num_pages = parseInt( parsed_response_text[1] ); // Rebuild page links. - var page_link_container = $('#page-link-container'); - page_link_container.children().remove(); - if (num_pages > 1) + if (!maintain_page_links) { - // Show page link row. - $('#page-links-row').show(); + var page_link_container = $('#page-link-container'); + page_link_container.children().remove(); + if (num_pages > 1) + { + // Show page link row. + $('#page-links-row').show(); - // First page is the current page. - var t = $("<span>1</span>"); - t.addClass('page-link'); - t.addClass('inactive-link'); - t.attr('id', 'page-link-1'); - page_link_container.append(t); + // First page is the current page. + var t = $("<span>1</span>"); + t.addClass('page-link'); + t.addClass('inactive-link'); + t.attr('id', 'page-link-1'); + page_link_container.append(t); - // Subsequent pages are navigable. - for (var i = 2; i <= num_pages; i++) + // Subsequent pages are navigable. + for (var i = 2; i <= num_pages; i++) + { + var span = $("<span></span>"); + span.addClass('page-link'); + span.attr('id', 'page-link-' + i); + var t = $("<a href='#'>" + i + "</a>"); + var page_num = i + t.click(function() { + set_page(page_num); + }); + span.append(t) + page_link_container.append(span); + } + } + else { - var span = $("<span></span>"); - span.addClass('page-link'); - span.attr('id', 'page-link-' + i); - var t = $("<a href='#'>" + i + "</a>"); - var page_num = i - t.click(function() { - set_page(page_num); - }); - span.append(t) - page_link_container.append(span); + // Hide page link row. + $('#page-links-row').hide('slow'); } - } - else - { - // Hide page link row. - $('#page-links-row').hide('slow'); } } }); } - // Perform a grid operation. TODO: this is not complete. - function do_operation() - { - // Get grid form. - var form = $('#grid-form'); - var operation = $('input[name=operation]:submit').val(); - var item_ids = $('input[name=id]:checked').val(); - - // Update URL args. - url_args['operation'] = operation; - url_args['id'] = item_ids; - - //update_grid(); - - //document.location = ${h.url_for()} + "?" - } - </script> </%def> @@ -491,7 +524,7 @@ ## Print grid. <%def name="render_grid_table()"> - <form action="${url()}" method="post" onsubmit="do_operation();return false;"> + <form action="${url()}" method="post" onsubmit="return false;"> <table class="grid"> <thead id="grid-table-header"> <tr>

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