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

[hg] galaxy 3411: Fix CheckboxField.is_checked(), which was brok...
by Greg Von Kuster 18 Feb '10

18 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0c07212afc00 changeset: 3411:0c07212afc00 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Feb 18 09:47:21 2010 -0500 description: Fix CheckboxField.is_checked(), which was broken if change set 3373. diffstat: lib/galaxy/web/form_builder.py | 2 -- templates/library/common/select_template.mako | 9 ++++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diffs (39 lines): diff -r 4a416d872806 -r 0c07212afc00 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Wed Feb 17 16:37:02 2010 -0500 +++ b/lib/galaxy/web/form_builder.py Thu Feb 18 09:47:21 2010 -0500 @@ -102,8 +102,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ) and value.lower() in ( "yes", "true", "on" ): - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not diff -r 4a416d872806 -r 0c07212afc00 templates/library/common/select_template.mako --- a/templates/library/common/select_template.mako Wed Feb 17 16:37:02 2010 -0500 +++ b/templates/library/common/select_template.mako Thu Feb 18 09:47:21 2010 -0500 @@ -1,6 +1,10 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<% + from galaxy.web.form_builder import CheckboxField + inheritable_check_box = CheckboxField( 'inheritable' ) +%> <script type="text/javascript"> $( function() { $( "select[refresh_on_change='true']").change( function() { @@ -50,10 +54,9 @@ <div class="form-row"> <label>Inherit template to contained folders and datasets?</label> %if inheritable_checked: - <input type="checkbox" name="inheritable" value="yes" checked/>Yes - %else: - <input type="checkbox" name="inheritable" value="yes"/>Yes + <% inheritable_check_box.checked = True %> %endif + ${inheritable_check_box.get_html()} <div class="toolParamHelp" style="clear: both;"> Check if you want this template to be used by other folders and datasets contained within this ${item_desc} </div>

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Re: [galaxy-dev] [galaxy-bugs] Fwd: Fwd: Installing data for Galaxy
by Daniel Blankenberg 18 Feb '10

18 Feb '10

Hi Iwe, > In the datatypes_conf.xml I added: > <datatype extension="fastabench" type="galaxy.sequence:Fasta" display_in_upload="true"/> All FASTA type files (fasta, fastabench, etc.) will be valid input for the 'fastabench' datatype. If you want to have a unique datatype that only includes 'fastabench' datatypes, you will need to create a new datatype class; if you want this datatype to be valid for 'fasta' input as well, this datatype should subclass Fasta. For example, in lib/galaxy/datatypes/sequence.py, add: class FastaBench( Fasta ): """Class representing a FASTA bench sequence""" file_ext = "fastabench" and change the entry in datatypes_conf.xml to (assuming you want it visible in the upload display): <datatype extension="fastabench" type="galaxy.sequence:FastaBench" display_in_upload="true"/> Also, confirm by looking at the screen output when starting the galaxy server via run.sh that the datatype is loading properly, if a datatype cannot be loaded properly it will default back to text. > Also when I choose an already existing (present in datatypes_conf.xml) format like "codcmp", and I add: > <param format="codcmp" name="input5" type="data" label="codcmp list example"/> > the list shows all the files in the file history tab. Correct, the codcmp datatype is of class galaxy.datatypes.data:Text, so all text files are valid codcmp files. Let us know how it goes and if we can be of further assistance. Thanks, Dan On Feb 18, 2010, at 7:09 AM, Iwe Muiser wrote: > Hey Dan, > > In the datatypes_conf.xml I added: > <datatype extension="fastabench" type="galaxy.sequence:Fasta" display_in_upload="true"/> > > Then in the XML file of the tool I added: > <param format="fastabench" name="input2" type="data" label="fastabench list example"/> > > Also when I choose an already existing (present in datatypes_conf.xml) format like "codcmp", and I add: > <param format="codcmp" name="input5" type="data" label="codcmp list example"/> > the list shows all the files in the file history tab. It seems to only work well with the very standard formats like fasta, BED, wig and so on. But I can not find the proper place to add my new datatype so that it will be shown in a list. > > Iwe > > > > 2010/2/17 Daniel Blankenberg <dan(a)bx.psu.edu> > Hi Iwe, > > Can you provide copies of the relevant sections of your datatypes_conf.xml, the actual datatype you created as well as the tool's xml file? > > Thanks, > > Dan > > On Feb 17, 2010, at 8:23 AM, Daniel Blankenberg wrote: > >> >> >> Begin forwarded message: >> >>> From: Iwe Muiser <e.c.muiser(a)gmail.com> >>> Date: February 17, 2010 6:14:24 AM EST >>> To: Daniel Blankenberg <dan(a)bx.psu.edu> >>> Subject: Re: [galaxy-bugs] Fwd: [galaxy-dev] Installing data for Galaxy >>> >>> Hello Dan, >>> >>> I tried and it's not working. I also deleted the underscores which also doesn't seem to help. A form keeps showing all the files in my history instead of the files with the new datatype I set. I have the idea I did not set the datatype correctly in a certain file, but I can't find which one it should be. >>> >>> Iwe >>> >>> 2010/2/16 Daniel Blankenberg <dan(a)bx.psu.edu> >>> Hello Iwe, >>> >>> Have you tried using all lowercase characters for the extension of your new datatype, including in the datatypes_conf.xml file? >>> >>> Thanks, >>> >>> Dan >>> >>> >>> >>> On Feb 16, 2010, at 10:55 AM, Guruprasad Ananda wrote: >>> >>>> Hi Iwe, >>>> >>>> I'm forwarding your message to galaxy-bugs mailing list so that the right person can help you. >>>> >>>> Thanks, >>>> Guru. >>>> >>>> Begin forwarded message: >>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Iwe Muiser <e.c.muiser(a)gmail.com> >>>>> Date: 2010/2/11 >>>>> Subject: Re: [galaxy-dev] Installing data for Galaxy >>>>> To: Guruprasad Ananda <gua110(a)bx.psu.edu> >>>>> >>>>> >>>>> Hello Guru, >>>>> >>>>> I have another question concerning adding a data format. I added a more stringent version of fasta to the datatypes as instructed on the website (adding to data_types.xml, building a sniffer, adding this to registry.py). Also I added a PWM datatype. I also installed a tool that needs PWM data as input (I set "format="PFMsimple""). If I upload a PWM file it will be automatically recognized as such. >>>>> However, when I want to make a file selection list for the tool that only shows the PWM files I run into problems. Instead of only showing the PWM format files, it shows all files present in the history. It does seem to work with fasta (or all regular file formats for that matter). I clearly forgot to set something right. Do you have a clue as to where to start? >>>>> >>>>> Thanks! >>>>> >>>>> Iwe >>>>> >>>>> >>>>> >>>>> On Feb 5, 2010, at 4:49 AM, Iwe Muiser wrote: >>>>> >>>>> > Hey Guru, >>>>> > >>>>> > Nate does not seem to answer. Is he absent or did something go wrong >>>>> > with the CC-ing? >>>>> > >>>>> > Greetings, >>>>> > >>>>> > Iwe >>>>> > >>>>> > 2010/2/3 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >> Hey Iwe, >>>>> >> >>>>> >> I'm glad you got it running! Please don't hesitate to email us if you have any questions in the future. >>>>> >> >>>>> >> Thanks for using Galaxy, >>>>> >> Guru. >>>>> >> >>>>> >> On Feb 3, 2010, at 4:59 AM, Iwe Muiser wrote: >>>>> >> >>>>> >>> Hey Guru, >>>>> >>> >>>>> >>> Thanks for the good description and cc-ing my other issue. I have >>>>> >>> installed several organisms now and it seems to be working perfectly. >>>>> >>> >>>>> >>> Greetings, >>>>> >>> >>>>> >>> Iwe >>>>> >>> >>>>> >>> 2010/2/2 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>> Hi Iwe, >>>>> >>>> >>>>> >>>> Yes, the path in alignseq.loc should contain the filename as well. For instance, here's how my alignseq.loc entry looks: >>>>> >>>> seq hg18 /Users/guru/Desktop/hg18.2bit.2bit >>>>> >>>> In fact, I tried downloading the 2bit file from UCSC just now, and updated my alignseq.loc and ran galaxy. The 'Extract genomic DNA' tool worked just fine and returned sequences. The only reason I could think why it isn't working for you is the alignseq.loc entry issue. Also, for some reason, the UCSC file has ".2bit" repeated twice in it's name. I'm sure you might have noticed that already. If not, please make sure the file name is ok. >>>>> >>>> >>>>> >>>> Also, I'm forwarding your email to Nate (on cc), who is the best person to help you with the issues you are facing with executing your binary. >>>>> >>>> >>>>> >>>> Please let us know if you have any further questions, >>>>> >>>> Guru. >>>>> >>>> >>>>> >>>> >>>>> >>>> On Feb 2, 2010, at 5:51 AM, Iwe Muiser wrote: >>>>> >>>> >>>>> >>>>> Hey Guru, >>>>> >>>>> >>>>> >>>>> There are some things I don't understand. I added the directory >>>>> >>>>> containing my binary executable to the PATH. if I open a terminal, it >>>>> >>>>> is able to find it by simply typing "32cotrasif_gw". When I make >>>>> >>>>> Galaxy execute the binary I get the following error: "An error >>>>> >>>>> occurred running this job: /bin/sh: 32cotrasif_gw: not found". it >>>>> >>>>> seems Galaxy uses sh to execute which does not seem to look at .bashrc >>>>> >>>>> or PATH variables. >>>>> >>>>> So I tried to set the interpreter to "bash". This gives the following >>>>> >>>>> error: "/home/muiser/Programs/galaxy_dist/tools/_motif_disc/32cotrasif_gw: >>>>> >>>>> /home/muiser/Programs/galaxy_dist/tools/_motif_disc/32cotrasif_gw: >>>>> >>>>> cannot execute binary file". >>>>> >>>>> >>>>> >>>>> "bash -c" needs quotes everywhere and makes the whole process >>>>> >>>>> unnecessarily complicated from my point of view (and has it never >>>>> >>>>> worked as well). >>>>> >>>>> >>>>> >>>>> A python wrapper script around cotrasif does make the output file >>>>> >>>>> (dataset_X.dat) but still gives me a red results item because it >>>>> >>>>> interprets the scripts standard output as faulty somehow. >>>>> >>>>> >>>>> >>>>> Do you have any ideas that might help me out? >>>>> >>>>> >>>>> >>>>> Also, the path to my hg18.2bit is set correctly. Mustn't I set the >>>>> >>>>> filename in this path as well? or just the path to the file itself? >>>>> >>>>> >>>>> >>>>> Greetings, >>>>> >>>>> >>>>> >>>>> Iwe >>>>> >>>>> >>>>> >>>>> 2010/2/1 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>>>> Hi Iwe, >>>>> >>>>>> >>>>> >>>>>> No, you don't need fasta files. Just the 2bit file should do. On looking at the python code for the tool, it seems like your PATH_TO_hg18.2bit may not be set correctly. Please make sure the path is right (and absolute) and try running the tool again. >>>>> >>>>>> >>>>> >>>>>> About your tool integration issue- please try using this format in the xml file, and let me know if it works fine: >>>>> >>>>>> <command> >>>>> >>>>>> myBinary $input $output >>>>> >>>>>> </command> >>>>> >>>>>> Also, please make sure that the binary is in your PATH. >>>>> >>>>>> >>>>> >>>>>> Thanks, >>>>> >>>>>> Guru. >>>>> >>>>>> >>>>> >>>>>> On Feb 1, 2010, at 1:17 PM, Iwe Muiser wrote: >>>>> >>>>>> >>>>> >>>>>>> Hello Guru, >>>>> >>>>>>> >>>>> >>>>>>> Thanks for the tip. It kind of works (no more red errors) except that >>>>> >>>>>>> it still doesn't actually fetches the sequences. >>>>> >>>>>>> The error is: >>>>> >>>>>>> "empty, format: fasta, database: hg18 >>>>> >>>>>>> Info: 55 warnings, 1st is: Chromosome by name 'chr1' was not found for >>>>> >>>>>>> build 'hg18'. >>>>> >>>>>>> Skipped 55 invalid lines, 1st is #1, "chr1 1259997 1260525 MACS_peak_6 0 +"" >>>>> >>>>>>> >>>>> >>>>>>> Do I also need the actual fasta files stored somewhere? I have them >>>>> >>>>>>> but I don't know where to put them so that galaxy can find them. >>>>> >>>>>>> >>>>> >>>>>>> Another problem I have is with integrating tools. I have a binary >>>>> >>>>>>> executable that gives a lot of trouble. I have tried everything from >>>>> >>>>>>> making a wrapper python script to all kinds of combinations with "./" >>>>> >>>>>>> and bash -c. Also I have put quotes pretty much everywhere. Now, >>>>> >>>>>>> finally, I have it working with a wrapper script only Galaxy gives me >>>>> >>>>>>> a message that the scripts stdout and sterror are actual errors while >>>>> >>>>>>> the file is being generated perfectly (dataset_X.dat). Do you know >>>>> >>>>>>> what is going on? >>>>> >>>>>>> I hope I made it clear enough because it is a nasty problem to explain. >>>>> >>>>>>> >>>>> >>>>>>> Iwe >>>>> >>>>>>> >>>>> >>>>>>> 2010/2/1 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>>>>>> Hello Iwe, >>>>> >>>>>>>> I apologise for not covering data integration in detail on our wiki. >>>>> >>>>>>>> Here's how you add a new sequence to your Galaxy instance. In your case, for >>>>> >>>>>>>> hg18, please download hg18.2bit file >>>>> >>>>>>>> from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/, and then >>>>> >>>>>>>> update tool-data/alignseq.loc file with the following line: >>>>> >>>>>>>> seq hg18 PATH_TO_hg18.2bit >>>>> >>>>>>>> Also, in future if you want to find out which ".loc" file to use, you can >>>>> >>>>>>>> check the validator tag under the input parameter in the tool's xml file. >>>>> >>>>>>>> Please let us know if you need any more information. >>>>> >>>>>>>> Thanks, >>>>> >>>>>>>> Guru >>>>> >>>>>>>> Galaxy team. >>>>> >>>>>>>> >>>>> >>>>>>>> On Feb 1, 2010, at 9:39 AM, Iwe Muiser wrote: >>>>> >>>>>>>> >>>>> >>>>>>>> Hello, >>>>> >>>>>>>> >>>>> >>>>>>>> I have some questions about installing data onto my Ubuntu linux box. Mainly >>>>> >>>>>>>> genomic data that can be used by the extract_genomic_dna.py script. I have >>>>> >>>>>>>> done some attempts to get this working but now I'm quite stuck. First I >>>>> >>>>>>>> downloaded this data from the UCSC ftp site. >>>>> >>>>>>>> (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes to be precise). >>>>> >>>>>>>> Then I added the following line to "faseq.loc" as instructed: "hg18 >>>>> >>>>>>>> /home/muiser/data/Human_data/HG18/chromosomes". >>>>> >>>>>>>> After this I restarted the galaxy deamon but nothing seems to have happened. >>>>> >>>>>>>> I have the idea that I am missing certain steps. >>>>> >>>>>>>> >>>>> >>>>>>>> The ultimate goal is to get a local galaxy install working like the one on >>>>> >>>>>>>> "http://main.g2.bx.psu.edu/" >>>>> >>>>>>>> >>>>> >>>>>>>> The wiki is helpful to install new tools and to get an idea of how stuff >>>>> >>>>>>>> works but sparsely mentions data integration. Except for MAFs which I tried >>>>> >>>>>>>> as well. I'm now building an index for these .maf files which I assume will >>>>> >>>>>>>> take quite some time. >>>>> >>>>>>>> >>>>> >>>>>>>> I hope you can help me out a bit. >>>>> >>>>>>>> >>>>> >>>>>>>> Thanks in advance, >>>>> >>>>>>>> >>>>> >>>>>>>> Iwe Muiser >>>>> >>>>>>>> _______________________________________________ >>>>> >>>>>>>> galaxy-dev mailing list >>>>> >>>>>>>> galaxy-dev(a)lists.bx.psu.edu >>>>> >>>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>>> >>>>>>>> >>>>> >>>>>>>> Guruprasad Ananda >>>>> >>>>>>>> Graduate Student >>>>> >>>>>>>> Bioinformatics and Genomics >>>>> >>>>>>>> The Pennsylvania State University >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> -- >>>>> >>>>>>> Master student >>>>> >>>>>>> Bioinformatics & Gene Regulation Group >>>>> >>>>>>> NTNU Trondheim >>>>> >>>>>>> +4594157082 >>>>> >>>>>>> >>>>> >>>>>> >>>>> >>>>>> Guruprasad Ananda >>>>> >>>>>> Graduate Student >>>>> >>>>>> Bioinformatics and Genomics >>>>> >>>>>> The Pennsylvania State University >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> Iwe EC Muiser >>>>> >>>>> Master student >>>>> >>>>> Bioinformatics & Gene Regulation Group >>>>> >>>>> NTNU Trondheim >>>>> >>>>> +4594157082 >>>>> >>>>> >>>>> >>>> >>>>> >>>> Guruprasad Ananda >>>>> >>>> Graduate Student >>>>> >>>> Bioinformatics and Genomics >>>>> >>>> The Pennsylvania State University >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> Iwe EC Muiser >>>>> >>> Master student >>>>> >>> Bioinformatics & Gene Regulation Group >>>>> >>> NTNU Trondheim >>>>> >>> +4594157082 >>>>> >>> >>>>> >> >>>>> >> Guruprasad Ananda >>>>> >> Graduate Student >>>>> >> Bioinformatics and Genomics >>>>> >> The Pennsylvania State University >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Iwe EC Muiser >>>>> > Master student >>>>> > Bioinformatics & Gene Regulation Group >>>>> > NTNU Trondheim >>>>> > +4594157082 >>>>> > >>>>> >>>>> Guruprasad Ananda >>>>> Graduate Student >>>>> Bioinformatics and Genomics >>>>> The Pennsylvania State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Iwe EC Muiser >>>>> Master student >>>>> NTNU - Department of Cancer Research and Molecular Medicine >>>>> Bioinformatics & Gene Regulation Group >>>>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>>>> Trondheim >>>>> +4594157082 >>>>> >>>>> >>>>> >>>>> -- >>>>> Iwe EC Muiser >>>>> Master student >>>>> NTNU - Department of Cancer Research and Molecular Medicine >>>>> Bioinformatics & Gene Regulation Group >>>>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>>>> Trondheim >>>>> +4594157082 >>>> >>>> >>>> Guruprasad Ananda >>>> Graduate Student >>>> Bioinformatics and Genomics >>>> The Pennsylvania State University >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> galaxy-bugs mailing list >>>> galaxy-bugs(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >>> >>> >>> >>> >>> -- >>> Iwe EC Muiser >>> Master student >>> NTNU - Department of Cancer Research and Molecular Medicine >>> Bioinformatics & Gene Regulation Group >>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>> Trondheim >>> +4594157082 >> >> _______________________________________________ >> galaxy-bugs mailing list >> galaxy-bugs(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-bugs > > > > > -- > Iwe EC Muiser > Master student > NTNU - Department of Cancer Research and Molecular Medicine > Bioinformatics & Gene Regulation Group > Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 > Trondheim > +4594157082

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delete a galaxy user
by Emeric Dubois 18 Feb '10

18 Feb '10

Hello, I have installed Galaxy in a production environment for multiple users. My installation of Galaxy has been configured such that only users who are logged in may use it and only admin may create a new user. I have a problem, I can create but can't delete a account... For the moment, I use a mysql command to block account : UPDATE galaxy.galaxy_user SET deleted = 1 WHERE galaxy_user.email LIKE "emeric.dubois(a)gmail.com" ; By this command, the account is inactive but all data associated are in database and in dataset folder. To free disk space, a set of scripts exist to remove the data files (histories and deleted datasets) but I haven't found a script to delete a user and all his data in database and dataset folder. Can you tell me if you have a solution to cleanly delete a user and his data ? Thank you. Best regards Emeric -- ***************************************** Emeric Dubois Plateforme MGX Institut de Génomique Fonctionnelle UMR 5203 CNRS – U 661 INSERM – Universite de Montpellier 141 rue de la cardonille 34094 Montpellier Cedex 05, France Tel: 04 67 14 29 32 Emeric.Dubois(a)igf.cnrs.fr ***************************************** -- Ce message a été vérifié par MailScanner pour des virus ou des polluriels et rien de suspect n'a été trouvé.

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[hg] galaxy 3410: Fix bug introduced in change set 3408:6471c9b8...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4a416d872806 changeset: 3410:4a416d872806 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 16:37:02 2010 -0500 description: Fix bug introduced in change set 3408:6471c9b8149c when testing form fields with labels / values longer than 30 chars. diffstat: test/base/twilltestcase.py | 16 +++++++++------- 1 files changed, 9 insertions(+), 7 deletions(-) diffs (26 lines): diff -r a8b176655f0b -r 4a416d872806 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Feb 17 15:50:38 2010 -0500 +++ b/test/base/twilltestcase.py Wed Feb 17 16:37:02 2010 -0500 @@ -882,13 +882,15 @@ control.get( name=elem ).selected = True else: # control.is_of_kind( "singlelist" ) for elem in control_value: - # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py - if len( elem ) > 30: - elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) - else: - elem_name = elem - - tc.fv( f.name, control.name, str( elem_name ) ) + try: + tc.fv( f.name, control.name, str( elem ) ) + except Exception, e2: + # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + if len( elem ) > 30: + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + tc.fv( f.name, control.name, str( elem_name ) ) except Exception, exc: errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) errmsg += "control: %s\n" % str( control )

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[hg] galaxy 3409: Fix for bug introduced in change set 3386:8d9c...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a8b176655f0b changeset: 3409:a8b176655f0b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 15:50:38 2010 -0500 description: Fix for bug introduced in change set 3386:8d9c8cf65dee when downloading datasets from a library. diffstat: lib/galaxy/web/controllers/library_common.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (13 lines): diff -r 6471c9b8149c -r a8b176655f0b lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Feb 17 14:49:13 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Feb 17 15:50:38 2010 -0500 @@ -1274,8 +1274,7 @@ or ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: continue ext = ldda.extension - if ext in composite_extensions: - is_composite = True + is_composite = ext in composite_extensions path = "" parent_folder = ldda.library_dataset.folder while parent_folder is not None:

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[hg] galaxy 3408: Fix bug intorduced in change set 3404:1e85451c...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6471c9b8149c changeset: 3408:6471c9b8149c user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 14:49:13 2010 -0500 description: Fix bug intorduced in change set 3404:1e85451c9c86 if testing multiple check boxes. Functional tests will now correctly test uploaded file names longer than 30 characters. diffstat: test/base/twilltestcase.py | 17 ++++++++++++----- 1 files changed, 12 insertions(+), 5 deletions(-) diffs (32 lines): diff -r 68dac4d2d94a -r 6471c9b8149c test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Feb 17 13:54:44 2010 -0500 +++ b/test/base/twilltestcase.py Wed Feb 17 14:49:13 2010 -0500 @@ -872,16 +872,23 @@ try: checkbox = control.get() checkbox.selected = is_checked( control_value ) - except ClientForm.AmbiguityError: - # if there's more than one checkbox, use the behaviour for - # ClientForm.ListControl - see twill code.. - pass + except Exception, e1: + # if there's more than one checkbox, probably should use the behaviour for + # ClientForm.ListControl ( see twill code ), but this works for now... + for elem in control_value: + control.get( name=elem ).selected = True else: for elem in control_value: control.get( name=elem ).selected = True else: # control.is_of_kind( "singlelist" ) for elem in control_value: - tc.fv( f.name, control.name, str( elem ) ) + # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + if len( elem ) > 30: + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + + tc.fv( f.name, control.name, str( elem_name ) ) except Exception, exc: errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) errmsg += "control: %s\n" % str( control )

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Tool unit-testing with "boolean" parameter
by Assaf Gordon 17 Feb '10

17 Feb '10

Hello, I'm trying to add a <tests> section for a tool which has a boolean/checkbox parameter. If one of the tests set the parameter's value to "false", the test throws an exception (before starting the actual job). If changed to "true", the test works. I've seen only a few tools with a boolean parameter (grouping.xml, complement.xml, concat.xml, merge.xml, phastOdds_tool.xml) and all of them only test the "true" value. I've tried setting the value to "false", to an empty string, and removing the parameter entirely, but it always throws an exception similar to: ================= Traceback (most recent call last): File "/home/gordon/temp/galaxy/test/functional/test_toolbox.py", line 134, in test_tool self.do_it( td ) File "/home/gordon/temp/galaxy/test/functional/test_toolbox.py", line 56, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/home/gordon/temp/galaxy/test/base/twilltestcase.py", line 920, in run_tool self.submit_form( **kwd ) File "/home/gordon/temp/galaxy/test/base/twilltestcase.py", line 870, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'header' to value '['false']' in form 'tool_form' threw exception: id=None name='false' label=None control: <CheckboxControl(header=[true])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. ================= Any workarounds ? thanks, -gordon

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[hg] galaxy 3407: Fix jquery script packing
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/68dac4d2d94a changeset: 3407:68dac4d2d94a user: James Taylor <james(a)jamestaylor.org> date: Wed Feb 17 13:54:44 2010 -0500 description: Fix jquery script packing diffstat: static/scripts/pack_scripts.py | 2 +- static/scripts/packed/jquery.js | 4365 +-------------------------------------- 2 files changed, 5 insertions(+), 4362 deletions(-) diffs (truncated from 4394 to 3000 lines): diff -r 297d8c9c5eb0 -r 68dac4d2d94a static/scripts/pack_scripts.py --- a/static/scripts/pack_scripts.py Wed Feb 17 12:45:32 2010 -0500 +++ b/static/scripts/pack_scripts.py Wed Feb 17 13:54:44 2010 -0500 @@ -8,7 +8,7 @@ from os import path # Scripts that should not be packed -- just copied -do_not_pack = ['jquery.js'] +do_not_pack = set() cmd = "java -jar ../../scripts/yuicompressor.jar --type js %(fname)s -o packed/%(fname)s" diff -r 297d8c9c5eb0 -r 68dac4d2d94a static/scripts/packed/jquery.js --- a/static/scripts/packed/jquery.js Wed Feb 17 12:45:32 2010 -0500 +++ b/static/scripts/packed/jquery.js Wed Feb 17 13:54:44 2010 -0500 @@ -1,4 +1,4 @@ -/*! +/* * jQuery JavaScript Library v1.3.2 * http://jquery.com/ * @@ -9,4368 +9,11 @@ * Date: 2009-02-19 17:34:21 -0500 (Thu, 19 Feb 2009) * Revision: 6246 */ -(function(){ - -var - // Will speed up references to window, and allows munging its name. - window = this, - // Will speed up references to undefined, and allows munging its name. - undefined, - // Map over jQuery in case of overwrite - _jQuery = window.jQuery, - // Map over the $ in case of overwrite - _$ = window.$, - - jQuery = window.jQuery = window.$ = function( selector, context ) { - // The jQuery object is actually just the init constructor 'enhanced' - return new jQuery.fn.init( selector, context ); - }, - - // A simple way to check for HTML strings or ID strings - // (both of which we optimize for) - quickExpr = /^[^<]*(<(.|\s)+>)[^>]*$|^#([\w-]+)$/, - // Is it a simple selector - isSimple = /^.[^:#\[\.,]*$/; - -jQuery.fn = jQuery.prototype = { - init: function( selector, context ) { - // Make sure that a selection was provided - selector = selector || document; - - // Handle $(DOMElement) - if ( selector.nodeType ) { - this[0] = selector; - this.length = 1; - this.context = selector; - return this; - } - // Handle HTML strings - if ( typeof selector === "string" ) { - // Are we dealing with HTML string or an ID? - var match = quickExpr.exec( selector ); - - // Verify a match, and that no context was specified for #id - if ( match && (match[1] || !context) ) { - - // HANDLE: $(html) -> $(array) - if ( match[1] ) - selector = jQuery.clean( [ match[1] ], context ); - - // HANDLE: $("#id") - else { - var elem = document.getElementById( match[3] ); - - // Handle the case where IE and Opera return items - // by name instead of ID - if ( elem && elem.id != match[3] ) - return jQuery().find( selector ); - - // Otherwise, we inject the element directly into the jQuery object - var ret = jQuery( elem || [] ); - ret.context = document; - ret.selector = selector; - return ret; - } - - // HANDLE: $(expr, [context]) - // (which is just equivalent to: $(content).find(expr) - } else - return jQuery( context ).find( selector ); - - // HANDLE: $(function) - // Shortcut for document ready - } else if ( jQuery.isFunction( selector ) ) - return jQuery( document ).ready( selector ); - - // Make sure that old selector state is passed along - if ( selector.selector && selector.context ) { - this.selector = selector.selector; - this.context = selector.context; - } - - return this.setArray(jQuery.isArray( selector ) ? - selector : - jQuery.makeArray(selector)); - }, - - // Start with an empty selector - selector: "", - - // The current version of jQuery being used - jquery: "1.3.2", - - // The number of elements contained in the matched element set - size: function() { - return this.length; - }, - - // Get the Nth element in the matched element set OR - // Get the whole matched element set as a clean array - get: function( num ) { - return num === undefined ? - - // Return a 'clean' array - Array.prototype.slice.call( this ) : - - // Return just the object - this[ num ]; - }, - - // Take an array of elements and push it onto the stack - // (returning the new matched element set) - pushStack: function( elems, name, selector ) { - // Build a new jQuery matched element set - var ret = jQuery( elems ); - - // Add the old object onto the stack (as a reference) - ret.prevObject = this; - - ret.context = this.context; - - if ( name === "find" ) - ret.selector = this.selector + (this.selector ? " " : "") + selector; - else if ( name ) - ret.selector = this.selector + "." + name + "(" + selector + ")"; - - // Return the newly-formed element set - return ret; - }, - - // Force the current matched set of elements to become - // the specified array of elements (destroying the stack in the process) - // You should use pushStack() in order to do this, but maintain the stack - setArray: function( elems ) { - // Resetting the length to 0, then using the native Array push - // is a super-fast way to populate an object with array-like properties - this.length = 0; - Array.prototype.push.apply( this, elems ); - - return this; - }, - - // Execute a callback for every element in the matched set. - // (You can seed the arguments with an array of args, but this is - // only used internally.) - each: function( callback, args ) { - return jQuery.each( this, callback, args ); - }, - - // Determine the position of an element within - // the matched set of elements - index: function( elem ) { - // Locate the position of the desired element - return jQuery.inArray( - // If it receives a jQuery object, the first element is used - elem && elem.jquery ? elem[0] : elem - , this ); - }, - - attr: function( name, value, type ) { - var options = name; - - // Look for the case where we're accessing a style value - if ( typeof name === "string" ) - if ( value === undefined ) - return this[0] && jQuery[ type || "attr" ]( this[0], name ); - - else { - options = {}; - options[ name ] = value; - } - - // Check to see if we're setting style values - return this.each(function(i){ - // Set all the styles - for ( name in options ) - jQuery.attr( - type ? - this.style : - this, - name, jQuery.prop( this, options[ name ], type, i, name ) - ); - }); - }, - - css: function( key, value ) { - // ignore negative width and height values - if ( (key == 'width' || key == 'height') && parseFloat(value) < 0 ) - value = undefined; - return this.attr( key, value, "curCSS" ); - }, - - text: function( text ) { - if ( typeof text !== "object" && text != null ) - return this.empty().append( (this[0] && this[0].ownerDocument || document).createTextNode( text ) ); - - var ret = ""; - - jQuery.each( text || this, function(){ - jQuery.each( this.childNodes, function(){ - if ( this.nodeType != 8 ) - ret += this.nodeType != 1 ? - this.nodeValue : - jQuery.fn.text( [ this ] ); - }); - }); - - return ret; - }, - - wrapAll: function( html ) { - if ( this[0] ) { - // The elements to wrap the target around - var wrap = jQuery( html, this[0].ownerDocument ).clone(); - - if ( this[0].parentNode ) - wrap.insertBefore( this[0] ); - - wrap.map(function(){ - var elem = this; - - while ( elem.firstChild ) - elem = elem.firstChild; - - return elem; - }).append(this); - } - - return this; - }, - - wrapInner: function( html ) { - return this.each(function(){ - jQuery( this ).contents().wrapAll( html ); - }); - }, - - wrap: function( html ) { - return this.each(function(){ - jQuery( this ).wrapAll( html ); - }); - }, - - append: function() { - return this.domManip(arguments, true, function(elem){ - if (this.nodeType == 1) - this.appendChild( elem ); - }); - }, - - prepend: function() { - return this.domManip(arguments, true, function(elem){ - if (this.nodeType == 1) - this.insertBefore( elem, this.firstChild ); - }); - }, - - before: function() { - return this.domManip(arguments, false, function(elem){ - this.parentNode.insertBefore( elem, this ); - }); - }, - - after: function() { - return this.domManip(arguments, false, function(elem){ - this.parentNode.insertBefore( elem, this.nextSibling ); - }); - }, - - end: function() { - return this.prevObject || jQuery( [] ); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: [].push, - sort: [].sort, - splice: [].splice, - - find: function( selector ) { - if ( this.length === 1 ) { - var ret = this.pushStack( [], "find", selector ); - ret.length = 0; - jQuery.find( selector, this[0], ret ); - return ret; - } else { - return this.pushStack( jQuery.unique(jQuery.map(this, function(elem){ - return jQuery.find( selector, elem ); - })), "find", selector ); - } - }, - - clone: function( events ) { - // Do the clone - var ret = this.map(function(){ - if ( !jQuery.support.noCloneEvent && !jQuery.isXMLDoc(this) ) { - // IE copies events bound via attachEvent when - // using cloneNode. Calling detachEvent on the - // clone will also remove the events from the orignal - // In order to get around this, we use innerHTML. - // Unfortunately, this means some modifications to - // attributes in IE that are actually only stored - // as properties will not be copied (such as the - // the name attribute on an input). - var html = this.outerHTML; - if ( !html ) { - var div = this.ownerDocument.createElement("div"); - div.appendChild( this.cloneNode(true) ); - html = div.innerHTML; - } - - return jQuery.clean([html.replace(/ jQuery\d+="(?:\d+|null)"/g, "").replace(/^\s*/, "")])[0]; - } else - return this.cloneNode(true); - }); - - // Copy the events from the original to the clone - if ( events === true ) { - var orig = this.find("*").andSelf(), i = 0; - - ret.find("*").andSelf().each(function(){ - if ( this.nodeName !== orig[i].nodeName ) - return; - - var events = jQuery.data( orig[i], "events" ); - - for ( var type in events ) { - for ( var handler in events[ type ] ) { - jQuery.event.add( this, type, events[ type ][ handler ], events[ type ][ handler ].data ); - } - } - - i++; - }); - } - - // Return the cloned set - return ret; - }, - - filter: function( selector ) { - return this.pushStack( - jQuery.isFunction( selector ) && - jQuery.grep(this, function(elem, i){ - return selector.call( elem, i ); - }) || - - jQuery.multiFilter( selector, jQuery.grep(this, function(elem){ - return elem.nodeType === 1; - }) ), "filter", selector ); - }, - - closest: function( selector ) { - var pos = jQuery.expr.match.POS.test( selector ) ? jQuery(selector) : null, - closer = 0; - - return this.map(function(){ - var cur = this; - while ( cur && cur.ownerDocument ) { - if ( pos ? pos.index(cur) > -1 : jQuery(cur).is(selector) ) { - jQuery.data(cur, "closest", closer); - return cur; - } - cur = cur.parentNode; - closer++; - } - }); - }, - - not: function( selector ) { - if ( typeof selector === "string" ) - // test special case where just one selector is passed in - if ( isSimple.test( selector ) ) - return this.pushStack( jQuery.multiFilter( selector, this, true ), "not", selector ); - else - selector = jQuery.multiFilter( selector, this ); - - var isArrayLike = selector.length && selector[selector.length - 1] !== undefined && !selector.nodeType; - return this.filter(function() { - return isArrayLike ? jQuery.inArray( this, selector ) < 0 : this != selector; - }); - }, - - add: function( selector ) { - return this.pushStack( jQuery.unique( jQuery.merge( - this.get(), - typeof selector === "string" ? - jQuery( selector ) : - jQuery.makeArray( selector ) - ))); - }, - - is: function( selector ) { - return !!selector && jQuery.multiFilter( selector, this ).length > 0; - }, - - hasClass: function( selector ) { - return !!selector && this.is( "." + selector ); - }, - - val: function( value ) { - if ( value === undefined ) { - var elem = this[0]; - - if ( elem ) { - if( jQuery.nodeName( elem, 'option' ) ) - return (elem.attributes.value || {}).specified ? elem.value : elem.text; - - // We need to handle select boxes special - if ( jQuery.nodeName( elem, "select" ) ) { - var index = elem.selectedIndex, - values = [], - options = elem.options, - one = elem.type == "select-one"; - - // Nothing was selected - if ( index < 0 ) - return null; - - // Loop through all the selected options - for ( var i = one ? index : 0, max = one ? index + 1 : options.length; i < max; i++ ) { - var option = options[ i ]; - - if ( option.selected ) { - // Get the specifc value for the option - value = jQuery(option).val(); - - // We don't need an array for one selects - if ( one ) - return value; - - // Multi-Selects return an array - values.push( value ); - } - } - - return values; - } - - // Everything else, we just grab the value - return (elem.value || "").replace(/\r/g, ""); - - } - - return undefined; - } - - if ( typeof value === "number" ) - value += ''; - - return this.each(function(){ - if ( this.nodeType != 1 ) - return; - - if ( jQuery.isArray(value) && /radio|checkbox/.test( this.type ) ) - this.checked = (jQuery.inArray(this.value, value) >= 0 || - jQuery.inArray(this.name, value) >= 0); - - else if ( jQuery.nodeName( this, "select" ) ) { - var values = jQuery.makeArray(value); - - jQuery( "option", this ).each(function(){ - this.selected = (jQuery.inArray( this.value, values ) >= 0 || - jQuery.inArray( this.text, values ) >= 0); - }); - - if ( !values.length ) - this.selectedIndex = -1; - - } else - this.value = value; - }); - }, - - html: function( value ) { - return value === undefined ? - (this[0] ? - this[0].innerHTML.replace(/ jQuery\d+="(?:\d+|null)"/g, "") : - null) : - this.empty().append( value ); - }, - - replaceWith: function( value ) { - return this.after( value ).remove(); - }, - - eq: function( i ) { - return this.slice( i, +i + 1 ); - }, - - slice: function() { - return this.pushStack( Array.prototype.slice.apply( this, arguments ), - "slice", Array.prototype.slice.call(arguments).join(",") ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map(this, function(elem, i){ - return callback.call( elem, i, elem ); - })); - }, - - andSelf: function() { - return this.add( this.prevObject ); - }, - - domManip: function( args, table, callback ) { - if ( this[0] ) { - var fragment = (this[0].ownerDocument || this[0]).createDocumentFragment(), - scripts = jQuery.clean( args, (this[0].ownerDocument || this[0]), fragment ), - first = fragment.firstChild; - - if ( first ) - for ( var i = 0, l = this.length; i < l; i++ ) - callback.call( root(this[i], first), this.length > 1 || i > 0 ? - fragment.cloneNode(true) : fragment ); - - if ( scripts ) - jQuery.each( scripts, evalScript ); - } - - return this; - - function root( elem, cur ) { - return table && jQuery.nodeName(elem, "table") && jQuery.nodeName(cur, "tr") ? - (elem.getElementsByTagName("tbody")[0] || - elem.appendChild(elem.ownerDocument.createElement("tbody"))) : - elem; - } - } -}; - -// Give the init function the jQuery prototype for later instantiation -jQuery.fn.init.prototype = jQuery.fn; - -function evalScript( i, elem ) { - if ( elem.src ) - jQuery.ajax({ - url: elem.src, - async: false, - dataType: "script" - }); - - else - jQuery.globalEval( elem.text || elem.textContent || elem.innerHTML || "" ); - - if ( elem.parentNode ) - elem.parentNode.removeChild( elem ); -} - -function now(){ - return +new Date; -} - -jQuery.extend = jQuery.fn.extend = function() { - // copy reference to target object - var target = arguments[0] || {}, i = 1, length = arguments.length, deep = false, options; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - target = arguments[1] || {}; - // skip the boolean and the target - i = 2; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction(target) ) - target = {}; - - // extend jQuery itself if only one argument is passed - if ( length == i ) { - target = this; - --i; - } - - for ( ; i < length; i++ ) - // Only deal with non-null/undefined values - if ( (options = arguments[ i ]) != null ) - // Extend the base object - for ( var name in options ) { - var src = target[ name ], copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) - continue; - - // Recurse if we're merging object values - if ( deep && copy && typeof copy === "object" && !copy.nodeType ) - target[ name ] = jQuery.extend( deep, - // Never move original objects, clone them - src || ( copy.length != null ? [ ] : { } ) - , copy ); - - // Don't bring in undefined values - else if ( copy !== undefined ) - target[ name ] = copy; - - } - - // Return the modified object - return target; -}; - -// exclude the following css properties to add px -var exclude = /z-?index|font-?weight|opacity|zoom|line-?height/i, - // cache defaultView - defaultView = document.defaultView || {}, - toString = Object.prototype.toString; - -jQuery.extend({ - noConflict: function( deep ) { - window.$ = _$; - - if ( deep ) - window.jQuery = _jQuery; - - return jQuery; - }, - - // See test/unit/core.js for details concerning isFunction. - // Since version 1.3, DOM methods and functions like alert - // aren't supported. They return false on IE (#2968). - isFunction: function( obj ) { - return toString.call(obj) === "[object Function]"; - }, - - isArray: function( obj ) { - return toString.call(obj) === "[object Array]"; - }, - - // check if an element is in a (or is an) XML document - isXMLDoc: function( elem ) { - return elem.nodeType === 9 && elem.documentElement.nodeName !== "HTML" || - !!elem.ownerDocument && jQuery.isXMLDoc( elem.ownerDocument ); - }, - - // Evalulates a script in a global context - globalEval: function( data ) { - if ( data && /\S/.test(data) ) { - // Inspired by code by Andrea Giammarchi - // http://webreflection.blogspot.com/2007/08/global-scope-evaluation-and-dom.h… - var head = document.getElementsByTagName("head")[0] || document.documentElement, - script = document.createElement("script"); - - script.type = "text/javascript"; - if ( jQuery.support.scriptEval ) - script.appendChild( document.createTextNode( data ) ); - else - script.text = data; - - // Use insertBefore instead of appendChild to circumvent an IE6 bug. - // This arises when a base node is used (#2709). - head.insertBefore( script, head.firstChild ); - head.removeChild( script ); - } - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toUpperCase() == name.toUpperCase(); - }, - - // args is for internal usage only - each: function( object, callback, args ) { - var name, i = 0, length = object.length; - - if ( args ) { - if ( length === undefined ) { - for ( name in object ) - if ( callback.apply( object[ name ], args ) === false ) - break; - } else - for ( ; i < length; ) - if ( callback.apply( object[ i++ ], args ) === false ) - break; - - // A special, fast, case for the most common use of each - } else { - if ( length === undefined ) { - for ( name in object ) - if ( callback.call( object[ name ], name, object[ name ] ) === false ) - break; - } else - for ( var value = object[0]; - i < length && callback.call( value, i, value ) !== false; value = object[++i] ){} - } - - return object; - }, - - prop: function( elem, value, type, i, name ) { - // Handle executable functions - if ( jQuery.isFunction( value ) ) - value = value.call( elem, i ); - - // Handle passing in a number to a CSS property - return typeof value === "number" && type == "curCSS" && !exclude.test( name ) ? - value + "px" : - value; - }, - - className: { - // internal only, use addClass("class") - add: function( elem, classNames ) { - jQuery.each((classNames || "").split(/\s+/), function(i, className){ - if ( elem.nodeType == 1 && !jQuery.className.has( elem.className, className ) ) - elem.className += (elem.className ? " " : "") + className; - }); - }, - - // internal only, use removeClass("class") - remove: function( elem, classNames ) { - if (elem.nodeType == 1) - elem.className = classNames !== undefined ? - jQuery.grep(elem.className.split(/\s+/), function(className){ - return !jQuery.className.has( classNames, className ); - }).join(" ") : - ""; - }, - - // internal only, use hasClass("class") - has: function( elem, className ) { - return elem && jQuery.inArray( className, (elem.className || elem).toString().split(/\s+/) ) > -1; - } - }, - - // A method for quickly swapping in/out CSS properties to get correct calculations - swap: function( elem, options, callback ) { - var old = {}; - // Remember the old values, and insert the new ones - for ( var name in options ) { - old[ name ] = elem.style[ name ]; - elem.style[ name ] = options[ name ]; - } - - callback.call( elem ); - - // Revert the old values - for ( var name in options ) - elem.style[ name ] = old[ name ]; - }, - - css: function( elem, name, force, extra ) { - if ( name == "width" || name == "height" ) { - var val, props = { position: "absolute", visibility: "hidden", display:"block" }, which = name == "width" ? [ "Left", "Right" ] : [ "Top", "Bottom" ]; - - function getWH() { - val = name == "width" ? elem.offsetWidth : elem.offsetHeight; - - if ( extra === "border" ) - return; - - jQuery.each( which, function() { - if ( !extra ) - val -= parseFloat(jQuery.curCSS( elem, "padding" + this, true)) || 0; - if ( extra === "margin" ) - val += parseFloat(jQuery.curCSS( elem, "margin" + this, true)) || 0; - else - val -= parseFloat(jQuery.curCSS( elem, "border" + this + "Width", true)) || 0; - }); - } - - if ( elem.offsetWidth !== 0 ) - getWH(); - else - jQuery.swap( elem, props, getWH ); - - return Math.max(0, Math.round(val)); - } - - return jQuery.curCSS( elem, name, force ); - }, - - curCSS: function( elem, name, force ) { - var ret, style = elem.style; - - // We need to handle opacity special in IE - if ( name == "opacity" && !jQuery.support.opacity ) { - ret = jQuery.attr( style, "opacity" ); - - return ret == "" ? - "1" : - ret; - } - - // Make sure we're using the right name for getting the float value - if ( name.match( /float/i ) ) - name = styleFloat; - - if ( !force && style && style[ name ] ) - ret = style[ name ]; - - else if ( defaultView.getComputedStyle ) { - - // Only "float" is needed here - if ( name.match( /float/i ) ) - name = "float"; - - name = name.replace( /([A-Z])/g, "-$1" ).toLowerCase(); - - var computedStyle = defaultView.getComputedStyle( elem, null ); - - if ( computedStyle ) - ret = computedStyle.getPropertyValue( name ); - - // We should always get a number back from opacity - if ( name == "opacity" && ret == "" ) - ret = "1"; - - } else if ( elem.currentStyle ) { - var camelCase = name.replace(/\-(\w)/g, function(all, letter){ - return letter.toUpperCase(); - }); - - ret = elem.currentStyle[ name ] || elem.currentStyle[ camelCase ]; - - // From the awesome hack by Dean Edwards - // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291 - - // If we're not dealing with a regular pixel number - // but a number that has a weird ending, we need to convert it to pixels - if ( !/^\d+(px)?$/i.test( ret ) && /^\d/.test( ret ) ) { - // Remember the original values - var left = style.left, rsLeft = elem.runtimeStyle.left; - - // Put in the new values to get a computed value out - elem.runtimeStyle.left = elem.currentStyle.left; - style.left = ret || 0; - ret = style.pixelLeft + "px"; - - // Revert the changed values - style.left = left; - elem.runtimeStyle.left = rsLeft; - } - } - - return ret; - }, - - clean: function( elems, context, fragment ) { - context = context || document; - - // !context.createElement fails in IE with an error but returns typeof 'object' - if ( typeof context.createElement === "undefined" ) - context = context.ownerDocument || context[0] && context[0].ownerDocument || document; - - // If a single string is passed in and it's a single tag - // just do a createElement and skip the rest - if ( !fragment && elems.length === 1 && typeof elems[0] === "string" ) { - var match = /^<(\w+)\s*\/?>$/.exec(elems[0]); - if ( match ) - return [ context.createElement( match[1] ) ]; - } - - var ret = [], scripts = [], div = context.createElement("div"); - - jQuery.each(elems, function(i, elem){ - if ( typeof elem === "number" ) - elem += ''; - - if ( !elem ) - return; - - // Convert html string into DOM nodes - if ( typeof elem === "string" ) { - // Fix "XHTML"-style tags in all browsers - elem = elem.replace(/(<(\w+)[^>]*?)\/>/g, function(all, front, tag){ - return tag.match(/^(abbr|br|col|img|input|link|meta|param|hr|area|embed)$/i) ? - all : - front + "></" + tag + ">"; - }); - - // Trim whitespace, otherwise indexOf won't work as expected - var tags = elem.replace(/^\s+/, "").substring(0, 10).toLowerCase(); - - var wrap = - // option or optgroup - !tags.indexOf("<opt") && - [ 1, "<select multiple='multiple'>", "</select>" ] || - - !tags.indexOf("<leg") && - [ 1, "<fieldset>", "</fieldset>" ] || - - tags.match(/^<(thead|tbody|tfoot|colg|cap)/) && - [ 1, "<table>", "</table>" ] || - - !tags.indexOf("<tr") && - [ 2, "<table><tbody>", "</tbody></table>" ] || - - // <thead> matched above - (!tags.indexOf("<td") || !tags.indexOf("<th")) && - [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ] || - - !tags.indexOf("<col") && - [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ] || - - // IE can't serialize <link> and <script> tags normally - !jQuery.support.htmlSerialize && - [ 1, "div<div>", "</div>" ] || - - [ 0, "", "" ]; - - // Go to html and back, then peel off extra wrappers - div.innerHTML = wrap[1] + elem + wrap[2]; - - // Move to the right depth - while ( wrap[0]-- ) - div = div.lastChild; - - // Remove IE's autoinserted <tbody> from table fragments - if ( !jQuery.support.tbody ) { - - // String was a <table>, *may* have spurious <tbody> - var hasBody = /<tbody/i.test(elem), - tbody = !tags.indexOf("<table") && !hasBody ? 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context.getElementsByTagName("*"); - } - - return {set: set, expr: expr}; -}; - -Sizzle.filter = function(expr, set, inplace, not){ - var old = expr, result = [], curLoop = set, match, anyFound, - isXMLFilter = set && set[0] && isXML(set[0]); - - while ( expr && set.length ) { - for ( var type in Expr.filter ) { - if ( (match = Expr.match[ type ].exec( expr )) != null ) { - var filter = Expr.filter[ type ], found, item; - anyFound = false; - - if ( curLoop == result ) { - result = []; - } - - if ( Expr.preFilter[ type ] ) { - match = Expr.preFilter[ type ]( match, curLoop, inplace, result, not, isXMLFilter ); - - if ( !match ) { - anyFound = found = true; - } else if ( match === true ) { - continue; - } - } - - if ( match ) { - for ( var i = 0; (item = curLoop[i]) != null; i++ ) { - if ( item ) { - found = filter( item, match, i, curLoop ); - var pass = not ^ !!found; - - if ( inplace && found != null ) { - if ( pass ) { - anyFound = true; - } else { - curLoop[i] = false; - } - } else if ( pass ) { - result.push( item ); - anyFound = true; - } - } - } - } - - if ( found !== undefined ) { - if ( !inplace ) { - curLoop = result; - } - - expr = expr.replace( Expr.match[ type ], "" ); - - if ( !anyFound ) { - return []; - } - - break; - } - } - } - - // Improper expression - if ( expr == old ) { - if ( anyFound == null ) { - throw "Syntax error, unrecognized expression: " + expr; - } else { - break; - } - } - - old = expr; - } - - return curLoop; -}; - -var Expr = Sizzle.selectors = { - order: [ "ID", "NAME", "TAG" ], - match: { - ID: /#((?:[\w\u00c0-\uFFFF_-]|\\.)+)/, - CLASS: /\.((?:[\w\u00c0-\uFFFF_-]|\\.)+)/, - NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF_-]|\\.)+)['"]*\]/, - ATTR: /\[\s*((?:[\w\u00c0-\uFFFF_-]|\\.)+)\s*(?:(\S?=)\s*(['"]*)(.*?)\3|)\s*\]/, - TAG: /^((?:[\w\u00c0-\uFFFF\*_-]|\\.)+)/, - CHILD: /:(only|nth|last|first)-child(?:$(even|odd|[\dn+-]*)$)?/, - POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:$(\d*)$)?(?=[^-]|$)/, - PSEUDO: /:((?:[\w\u00c0-\uFFFF_-]|\\.)+)(?:$(['"]*)((?:\([^$]+\)|[^\2]*)+)\2\))?/ - }, - attrMap: { - "class": "className", - "for": "htmlFor" - }, - attrHandle: { - href: function(elem){ - return elem.getAttribute("href"); - } - }, - relative: { - "+": function(checkSet, part, isXML){ - var isPartStr = typeof part === "string", - isTag = isPartStr && !/\W/.test(part), - isPartStrNotTag = isPartStr && !isTag; - - if ( isTag && !isXML ) { - part = part.toUpperCase(); - } - - for ( var i = 0, l = checkSet.length, elem; i < l; i++ ) { - if ( (elem = checkSet[i]) ) { - while ( (elem = elem.previousSibling) && elem.nodeType !== 1 ) {} - - checkSet[i] = isPartStrNotTag || elem && elem.nodeName === part ? - elem || false : - elem === part; - } - } - - if ( isPartStrNotTag ) { - Sizzle.filter( part, checkSet, true ); - } - }, - ">": function(checkSet, part, isXML){ - var isPartStr = typeof part === "string"; - - if ( isPartStr && !/\W/.test(part) ) { - part = isXML ? part : part.toUpperCase(); - - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - if ( elem ) { - var parent = elem.parentNode; - checkSet[i] = parent.nodeName === part ? parent : false; - } - } - } else { - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - if ( elem ) { - checkSet[i] = isPartStr ? - elem.parentNode : - elem.parentNode === part; - } - } - - if ( isPartStr ) { - Sizzle.filter( part, checkSet, true ); - } - } - }, - "": function(checkSet, part, isXML){ - var doneName = done++, checkFn = dirCheck; - - if ( !part.match(/\W/) ) { - var nodeCheck = part = isXML ? part : part.toUpperCase(); - checkFn = dirNodeCheck; - } - - checkFn("parentNode", part, doneName, checkSet, nodeCheck, isXML); - }, - "~": function(checkSet, part, isXML){ - var doneName = done++, checkFn = dirCheck; - - if ( typeof part === "string" && !part.match(/\W/) ) { - var nodeCheck = part = isXML ? part : part.toUpperCase(); - checkFn = dirNodeCheck; - } - - checkFn("previousSibling", part, doneName, checkSet, nodeCheck, isXML); - } - }, - find: { - ID: function(match, context, isXML){ - if ( typeof context.getElementById !== "undefined" && !isXML ) { - var m = context.getElementById(match[1]); - return m ? [m] : []; - } - }, - NAME: function(match, context, isXML){ - if ( typeof context.getElementsByName !== "undefined" ) { - var ret = [], results = context.getElementsByName(match[1]); - - for ( var i = 0, l = results.length; i < l; i++ ) { - if ( results[i].getAttribute("name") === match[1] ) { - ret.push( results[i] ); - } - } - - return ret.length === 0 ? null : ret; - } - }, - TAG: function(match, context){ - return context.getElementsByTagName(match[1]); - } - }, - preFilter: { - CLASS: function(match, curLoop, inplace, result, not, isXML){ - match = " " + match[1].replace(/\\/g, "") + " "; - - if ( isXML ) { - return match; - } - - for ( var i = 0, elem; (elem = curLoop[i]) != null; i++ ) { - if ( elem ) { - if ( not ^ (elem.className && (" " + elem.className + " ").indexOf(match) >= 0) ) { - if ( !inplace ) - result.push( elem ); - } else if ( inplace ) { - curLoop[i] = false; - } - } - } - - return false; - }, - ID: function(match){ - return match[1].replace(/\\/g, ""); - }, - TAG: function(match, curLoop){ - for ( var i = 0; curLoop[i] === false; i++ ){} - return curLoop[i] && isXML(curLoop[i]) ? match[1] : match[1].toUpperCase(); - }, - CHILD: function(match){ - if ( match[1] == "nth" ) { - // parse equations like 'even', 'odd', '5', '2n', '3n+2', '4n-1', '-n+6' - var test = /(-?)(\d*)n((?:\+|-)?\d*)/.exec( - match[2] == "even" && "2n" || match[2] == "odd" && "2n+1" || - !/\D/.test( match[2] ) && "0n+" + match[2] || match[2]); - - // calculate the numbers (first)n+(last) including if they are negative - match[2] = (test[1] + (test[2] || 1)) - 0; - match[3] = test[3] - 0; - } - - // TODO: Move to normal caching system - match[0] = done++; - - return match; - }, - ATTR: function(match, curLoop, inplace, result, not, isXML){ - var name = match[1].replace(/\\/g, ""); - - if ( !isXML && Expr.attrMap[name] ) { - match[1] = Expr.attrMap[name]; - } - - if ( match[2] === "~=" ) { - match[4] = " " + match[4] + " "; - } - - return match; - }, - PSEUDO: function(match, curLoop, inplace, result, not){ - if ( match[1] === "not" ) { - // If we're dealing with a complex expression, or a simple one - if ( match[3].match(chunker).length > 1 || /^\w/.test(match[3]) ) { - match[3] = Sizzle(match[3], null, null, curLoop); - } else { - var ret = Sizzle.filter(match[3], curLoop, inplace, true ^ not); - if ( !inplace ) { - result.push.apply( result, ret ); - } - return false; - } - } else if ( Expr.match.POS.test( match[0] ) || Expr.match.CHILD.test( match[0] ) ) { - return true; - } - - return match; - }, - POS: function(match){ - match.unshift( true ); - return match; - } - }, - filters: { - enabled: function(elem){ - return elem.disabled === false && elem.type !== "hidden"; - }, - disabled: function(elem){ - return elem.disabled === true; - }, - checked: function(elem){ - return elem.checked === true; - }, - selected: function(elem){ - // Accessing this property makes selected-by-default - // options in Safari work properly - elem.parentNode.selectedIndex; - return elem.selected === true; - }, - parent: function(elem){ - return !!elem.firstChild; - }, - empty: function(elem){ - return !elem.firstChild; - }, - has: function(elem, i, match){ - return !!Sizzle( match[3], elem ).length; - }, - header: function(elem){ - return /h\d/i.test( elem.nodeName ); - }, - text: function(elem){ - return "text" === elem.type; - }, - radio: function(elem){ - return "radio" === elem.type; - }, - checkbox: function(elem){ - return "checkbox" === elem.type; - }, - file: function(elem){ - return "file" === elem.type; - }, - password: function(elem){ - return "password" === elem.type; - }, - submit: function(elem){ - return "submit" === elem.type; - }, - image: function(elem){ - return "image" === elem.type; - }, - reset: function(elem){ - return "reset" === elem.type; - }, - button: function(elem){ - return "button" === elem.type || elem.nodeName.toUpperCase() === "BUTTON"; - }, - input: function(elem){ - return /input|select|textarea|button/i.test(elem.nodeName); - } - }, - setFilters: { - first: function(elem, i){ - return i === 0; - }, - last: function(elem, i, match, array){ - return i === array.length - 1; - }, - even: function(elem, i){ - return i % 2 === 0; - }, - odd: function(elem, i){ - return i % 2 === 1; - }, - lt: function(elem, i, match){ - return i < match[3] - 0; - }, - gt: function(elem, i, match){ - return i > match[3] - 0; - }, - nth: function(elem, i, match){ - return match[3] - 0 == i; - }, - eq: function(elem, i, match){ - return match[3] - 0 == i; - } - }, - filter: { - PSEUDO: function(elem, match, i, array){ - var name = match[1], filter = Expr.filters[ name ]; - - if ( filter ) { - return filter( elem, i, match, array ); - } else if ( name === "contains" ) { - return (elem.textContent || elem.innerText || "").indexOf(match[3]) >= 0; - } else if ( name === "not" ) { - var not = match[3]; - - for ( var i = 0, l = not.length; i < l; i++ ) { - if ( not[i] === elem ) { - return false; - } - } - - return true; - } - }, - CHILD: function(elem, match){ - var type = match[1], node = elem; - switch (type) { - case 'only': - case 'first': - while (node = node.previousSibling) { - if ( node.nodeType === 1 ) return false; - } - if ( type == 'first') return true; - node = elem; - case 'last': - while (node = node.nextSibling) { - if ( node.nodeType === 1 ) return false; - } - return true; - case 'nth': - var first = match[2], last = match[3]; - - if ( first == 1 && last == 0 ) { - return true; - } - - var doneName = match[0], - parent = elem.parentNode; - - if ( parent && (parent.sizcache !== doneName || !elem.nodeIndex) ) { - var count = 0; - for ( node = parent.firstChild; node; node = node.nextSibling ) { - if ( node.nodeType === 1 ) { - node.nodeIndex = ++count; - } - } - parent.sizcache = doneName; - } - - var diff = elem.nodeIndex - last; - if ( first == 0 ) { - return diff == 0; - } else { - return ( diff % first == 0 && diff / first >= 0 ); - } - } - }, - ID: function(elem, match){ - return elem.nodeType === 1 && elem.getAttribute("id") === match; - }, - TAG: function(elem, match){ - return (match === "*" && elem.nodeType === 1) || elem.nodeName === match; - }, - CLASS: function(elem, match){ - return (" " + (elem.className || elem.getAttribute("class")) + " ") - .indexOf( match ) > -1; - }, - ATTR: function(elem, match){ - var name = match[1], - result = Expr.attrHandle[ name ] ? - Expr.attrHandle[ name ]( elem ) : - elem[ name ] != null ? - elem[ name ] : - elem.getAttribute( name ), - value = result + "", - type = match[2], - check = match[4]; - - return result == null ? - type === "!=" : - type === "=" ? - value === check : - type === "*=" ? - value.indexOf(check) >= 0 : - type === "~=" ? - (" " + value + " ").indexOf(check) >= 0 : - !check ? - value && result !== false : - type === "!=" ? - value != check : - type === "^=" ? - value.indexOf(check) === 0 : - type === "$=" ? - value.substr(value.length - check.length) === check : - type === "|=" ? - value === check || value.substr(0, check.length + 1) === check + "-" : - false; - }, - POS: function(elem, match, i, array){ - var name = match[2], filter = Expr.setFilters[ name ]; - - if ( filter ) { - return filter( elem, i, match, array ); - } - } - } -}; - -var origPOS = Expr.match.POS; - -for ( var type in Expr.match ) { - Expr.match[ type ] = RegExp( Expr.match[ type ].source + /(?![^\[]*\])(?![^$]*$)/.source ); -} - -var makeArray = function(array, results) { - array = Array.prototype.slice.call( array ); - - if ( results ) { - results.push.apply( results, array ); - return results; - } - - return array; -}; - -// Perform a simple check to determine if the browser is capable of -// converting a NodeList to an array using builtin methods. -try { - Array.prototype.slice.call( document.documentElement.childNodes ); - -// Provide a fallback method if it does not work -} catch(e){ - makeArray = function(array, results) { - var ret = results || []; - - if ( toString.call(array) === "[object Array]" ) { - Array.prototype.push.apply( ret, array ); - } else { - if ( typeof array.length === "number" ) { - for ( var i = 0, l = array.length; i < l; i++ ) { - ret.push( array[i] ); - } - } else { - for ( var i = 0; array[i]; i++ ) { - ret.push( array[i] ); - } - } - } - - return ret; - }; -} - -var sortOrder; - -if ( document.documentElement.compareDocumentPosition ) { - sortOrder = function( a, b ) { - var ret = a.compareDocumentPosition(b) & 4 ? -1 : a === b ? 0 : 1; - if ( ret === 0 ) { - hasDuplicate = true; - } - return ret; - }; -} else if ( "sourceIndex" in document.documentElement ) { - sortOrder = function( a, b ) { - var ret = a.sourceIndex - b.sourceIndex; - if ( ret === 0 ) { - hasDuplicate = true; - } - return ret; - }; -} else if ( document.createRange ) { - sortOrder = function( a, b ) { - var aRange = a.ownerDocument.createRange(), bRange = b.ownerDocument.createRange(); - aRange.selectNode(a); - aRange.collapse(true); - bRange.selectNode(b); - bRange.collapse(true); - var ret = aRange.compareBoundaryPoints(Range.START_TO_END, bRange); - if ( ret === 0 ) { - hasDuplicate = true; - } - return ret; - }; -} - -// Check to see if the browser returns elements by name when -// querying by getElementById (and provide a workaround) -(function(){ - // We're going to inject a fake input element with a specified name - var form = document.createElement("form"), - id = "script" + (new Date).getTime(); - form.innerHTML = "<input name='" + id + "'/>"; - - // Inject it into the root element, check its status, and remove it quickly - var root = document.documentElement; - root.insertBefore( form, root.firstChild ); - - // The workaround has to do additional checks after a getElementById - // Which slows things down for other browsers (hence the branching) - if ( !!document.getElementById( id ) ) { - Expr.find.ID = function(match, context, isXML){ - if ( typeof context.getElementById !== "undefined" && !isXML ) { - var m = context.getElementById(match[1]); - return m ? m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ? [m] : undefined : []; - } - }; - - Expr.filter.ID = function(elem, match){ - var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); - return elem.nodeType === 1 && node && node.nodeValue === match; - }; - } - - root.removeChild( form ); -})(); - -(function(){ - // Check to see if the browser returns only elements - // when doing getElementsByTagName("*") - - // Create a fake element - var div = document.createElement("div"); - div.appendChild( document.createComment("") ); - - // Make sure no comments are found - if ( div.getElementsByTagName("*").length > 0 ) { - Expr.find.TAG = function(match, context){ - var results = context.getElementsByTagName(match[1]); - - // Filter out possible comments - if ( match[1] === "*" ) { - var tmp = []; - - for ( var i = 0; results[i]; i++ ) { - if ( results[i].nodeType === 1 ) { - tmp.push( results[i] ); - } - } - - results = tmp; - } - - return results; - }; - } - - // Check to see if an attribute returns normalized href attributes - div.innerHTML = "<a href='#'></a>"; - if ( div.firstChild && typeof div.firstChild.getAttribute !== "undefined" && - div.firstChild.getAttribute("href") !== "#" ) { - Expr.attrHandle.href = function(elem){ - return elem.getAttribute("href", 2); - }; - } -})(); - -if ( document.querySelectorAll ) (function(){ - var oldSizzle = Sizzle, div = document.createElement("div"); - div.innerHTML = "<p class='TEST'></p>"; - - // Safari can't handle uppercase or unicode characters when - // in quirks mode. - if ( div.querySelectorAll && div.querySelectorAll(".TEST").length === 0 ) { - return; - } - - Sizzle = function(query, context, extra, seed){ - context = context || document; - - // Only use querySelectorAll on non-XML documents - // (ID selectors don't work in non-HTML documents) - if ( !seed && context.nodeType === 9 && !isXML(context) ) { - try { - return makeArray( context.querySelectorAll(query), extra ); - } catch(e){} - } - - return oldSizzle(query, context, extra, seed); - }; - - Sizzle.find = oldSizzle.find; - Sizzle.filter = oldSizzle.filter; - Sizzle.selectors = oldSizzle.selectors; - Sizzle.matches = oldSizzle.matches; -})(); - -if ( document.getElementsByClassName && document.documentElement.getElementsByClassName ) (function(){ - var div = document.createElement("div"); - div.innerHTML = "<div class='test e'></div><div class='test'></div>"; - - // Opera can't find a second classname (in 9.6) - if ( div.getElementsByClassName("e").length === 0 ) - return; - - // Safari caches class attributes, doesn't catch changes (in 3.2) - div.lastChild.className = "e"; - - if ( div.getElementsByClassName("e").length === 1 ) - return; - - Expr.order.splice(1, 0, "CLASS"); - Expr.find.CLASS = function(match, context, isXML) { - if ( typeof context.getElementsByClassName !== "undefined" && !isXML ) { - return context.getElementsByClassName(match[1]); - } - }; -})(); - -function dirNodeCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { - var sibDir = dir == "previousSibling" && !isXML; - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - if ( elem ) { - if ( sibDir && elem.nodeType === 1 ){ - elem.sizcache = doneName; - elem.sizset = i; - } - elem = elem[dir]; - var match = false; - - while ( elem ) { - if ( elem.sizcache === doneName ) { - match = checkSet[elem.sizset]; - break; - } - - if ( elem.nodeType === 1 && !isXML ){ - elem.sizcache = doneName; - elem.sizset = i; - } - - if ( elem.nodeName === cur ) { - match = elem; - break; - } - - elem = elem[dir]; - } - - checkSet[i] = match; - } - } -} - -function dirCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) { - var sibDir = dir == "previousSibling" && !isXML; - for ( var i = 0, l = checkSet.length; i < l; i++ ) { - var elem = checkSet[i]; - if ( elem ) { - if ( sibDir && elem.nodeType === 1 ) { - elem.sizcache = doneName; - elem.sizset = i; - } - elem = elem[dir]; - var match = false; - - while ( elem ) { - if ( elem.sizcache === doneName ) { - match = checkSet[elem.sizset]; - break; - } - - if ( elem.nodeType === 1 ) { - if ( !isXML ) { - elem.sizcache = doneName; - elem.sizset = i; - } - if ( typeof cur !== "string" ) { - if ( elem === cur ) { - match = true; - break; - } - - } else if ( Sizzle.filter( cur, [elem] ).length > 0 ) { - match = elem; - break; - } - } - - elem = elem[dir]; - } - - checkSet[i] = match; - } - } -} - -var contains = document.compareDocumentPosition ? function(a, b){ - return a.compareDocumentPosition(b) & 16; -} : function(a, b){ - return a !== b && (a.contains ? a.contains(b) : true); -}; - -var isXML = function(elem){ - return elem.nodeType === 9 && elem.documentElement.nodeName !== "HTML" || - !!elem.ownerDocument && isXML( elem.ownerDocument ); -}; - -var posProcess = function(selector, context){ - var tmpSet = [], later = "", match, - root = context.nodeType ? [context] : context; - - // Position selectors must be done after the filter - // And so must :not(positional) so we move all PSEUDOs to the end - while ( (match = Expr.match.PSEUDO.exec( selector )) ) { - later += match[0]; - selector = selector.replace( Expr.match.PSEUDO, "" ); - } - - selector = Expr.relative[selector] ? selector + "*" : selector; - - for ( var i = 0, l = root.length; i < l; i++ ) { - Sizzle( selector, root[i], tmpSet ); - } - - return Sizzle.filter( later, tmpSet ); -}; - -// EXPOSE -jQuery.find = Sizzle; -jQuery.filter = Sizzle.filter; -jQuery.expr = Sizzle.selectors; -jQuery.expr[":"] = jQuery.expr.filters; - -Sizzle.selectors.filters.hidden = function(elem){ - return elem.offsetWidth === 0 || elem.offsetHeight === 0; -}; - -Sizzle.selectors.filters.visible = function(elem){ - return elem.offsetWidth > 0 || elem.offsetHeight > 0; -}; - -Sizzle.selectors.filters.animated = function(elem){ - return jQuery.grep(jQuery.timers, function(fn){ - return elem === fn.elem; - }).length; -}; - -jQuery.multiFilter = function( expr, elems, not ) { - if ( not ) { - expr = ":not(" + expr + ")"; - } - - return Sizzle.matches(expr, elems); -}; - -jQuery.dir = function( elem, dir ){ - var matched = [], cur = elem[dir]; - while ( cur && cur != document ) { - if ( cur.nodeType == 1 ) - matched.push( cur ); - cur = cur[dir]; - } - return matched; -}; - -jQuery.nth = function(cur, result, dir, elem){ - result = result || 1; - var num = 0; - - for ( ; cur; cur = cur[dir] ) - if ( cur.nodeType == 1 && ++num == result ) - break; - - return cur; -}; - -jQuery.sibling = function(n, elem){ - var r = []; - - for ( ; n; n = n.nextSibling ) { - if ( n.nodeType == 1 && n != elem ) - r.push( n ); - } - - return r; -}; - -return; - -window.Sizzle = Sizzle; - -})(); -/* - * A number of helper functions used for managing events. - * Many of the ideas behind this code originated from - * Dean Edwards' addEvent library. - */ -jQuery.event = { - - // Bind an event to an element - // Original by Dean Edwards - add: function(elem, types, handler, data) { - if ( elem.nodeType == 3 || elem.nodeType == 8 ) - return; - - // For whatever reason, IE has trouble passing the window object - // around, causing it to be cloned in the process - if ( elem.setInterval && elem != window ) - elem = window; - - // Make sure that the function being executed has a unique ID - if ( !handler.guid ) - handler.guid = this.guid++; - - // if data is passed, bind to handler - if ( data !== undefined ) { - // Create temporary function pointer to original handler - var fn = handler; - - // Create unique handler function, wrapped around original handler - handler = this.proxy( fn ); - - // Store data in unique handler - handler.data = data; - } - - // Init the element's event structure - var events = jQuery.data(elem, "events") || jQuery.data(elem, "events", {}), - handle = jQuery.data(elem, "handle") || jQuery.data(elem, "handle", function(){ - // Handle the second event of a trigger and when - // an event is called after a page has unloaded - return typeof jQuery !== "undefined" && !jQuery.event.triggered ? - jQuery.event.handle.apply(arguments.callee.elem, arguments) : - undefined; - }); - // Add elem as a property of the handle function - // This is to prevent a memory leak with non-native - // event in IE. - handle.elem = elem; - - // Handle multiple events separated by a space - // jQuery(...).bind("mouseover mouseout", fn); - jQuery.each(types.split(/\s+/), function(index, type) { - // Namespaced event handlers - var namespaces = type.split("."); - type = namespaces.shift(); - handler.type = namespaces.slice().sort().join("."); - - // Get the current list of functions bound to this event - var handlers = events[type]; - - if ( jQuery.event.specialAll[type] ) - jQuery.event.specialAll[type].setup.call(elem, data, namespaces); - - // Init the event handler queue - if (!handlers) { - handlers = events[type] = {}; - - // Check for a special event handler - // Only use addEventListener/attachEvent if the special - // events handler returns false - if ( !jQuery.event.special[type] || jQuery.event.special[type].setup.call(elem, data, namespaces) === false ) { - // Bind the global event handler to the element - if (elem.addEventListener) - elem.addEventListener(type, handle, false); - else if (elem.attachEvent) - elem.attachEvent("on" + type, handle); - } - } - - // Add the function to the element's handler list - handlers[handler.guid] = handler; - - // Keep track of which events have been used, for global triggering - jQuery.event.global[type] = true; - }); - - // Nullify elem to prevent memory leaks in IE - elem = null; - }, - - guid: 1, - global: {}, - - // Detach an event or set of events from an element - remove: function(elem, types, handler) { - // don't do events on text and comment nodes - if ( elem.nodeType == 3 || elem.nodeType == 8 ) - return; - - var events = jQuery.data(elem, "events"), ret, index; - - if ( events ) { - // Unbind all events for the element - if ( types === undefined || (typeof types === "string" && types.charAt(0) == ".") ) - for ( var type in events ) - this.remove( elem, type + (types || "") ); - else { - // types is actually an event object here - if ( types.type ) { - handler = types.handler; - types = types.type; - } - - // Handle multiple events seperated by a space - // jQuery(...).unbind("mouseover mouseout", fn); - jQuery.each(types.split(/\s+/), function(index, type){ - // Namespaced event handlers - var namespaces = type.split("."); - type = namespaces.shift(); - var namespace = RegExp("(^|\\.)" + namespaces.slice().sort().join(".*\\.") + "(\\.|$)"); - - if ( events[type] ) { - // remove the given handler for the given type - if ( handler ) - delete events[type][handler.guid]; - - // remove all handlers for the given type - else - for ( var handle in events[type] ) - // Handle the removal of namespaced events - if ( namespace.test(events[type][handle].type) ) - delete events[type][handle]; - - if ( jQuery.event.specialAll[type] ) - jQuery.event.specialAll[type].teardown.call(elem, namespaces); - - // remove generic event handler if no more handlers exist - for ( ret in events[type] ) break; - if ( !ret ) { - if ( !jQuery.event.special[type] || jQuery.event.special[type].teardown.call(elem, namespaces) === false ) { - if (elem.removeEventListener) - elem.removeEventListener(type, jQuery.data(elem, "handle"), false); - else if (elem.detachEvent) - elem.detachEvent("on" + type, jQuery.data(elem, "handle")); - } - ret = null; - delete events[type]; - } - } - }); - } - - // Remove the expando if it's no longer used - for ( ret in events ) break; - if ( !ret ) { - var handle = jQuery.data( elem, "handle" ); - if ( handle ) handle.elem = null; - jQuery.removeData( elem, "events" ); - jQuery.removeData( elem, "handle" ); - } - } - }, - - // bubbling is internal - trigger: function( event, data, elem, bubbling ) { - // Event object or event type - var type = event.type || event; - - if( !bubbling ){ - event = typeof event === "object" ? - // jQuery.Event object - event[expando] ? event : - // Object literal - jQuery.extend( jQuery.Event(type), event ) : - // Just the event type (string) - jQuery.Event(type); - - if ( type.indexOf("!") >= 0 ) { - event.type = type = type.slice(0, -1); - event.exclusive = true; - } - - // Handle a global trigger - if ( !elem ) { - // Don't bubble custom events when global (to avoid too much overhead) - event.stopPropagation(); - // Only trigger if we've ever bound an event for it - if ( this.global[type] ) - jQuery.each( jQuery.cache, function(){ - if ( this.events && this.events[type] ) - jQuery.event.trigger( event, data, this.handle.elem ); - }); - } - - // Handle triggering a single element - - // don't do events on text and comment nodes - if ( !elem || elem.nodeType == 3 || elem.nodeType == 8 ) - return undefined; - - // Clean up in case it is reused - event.result = undefined; - event.target = elem; - - // Clone the incoming data, if any - data = jQuery.makeArray(data); - data.unshift( event ); - } - - event.currentTarget = elem; - - // Trigger the event, it is assumed that "handle" is a function - var handle = jQuery.data(elem, "handle"); - if ( handle ) - handle.apply( elem, data ); - - // Handle triggering native .onfoo handlers (and on links since we don't call .click() for links) - if ( (!elem[type] || (jQuery.nodeName(elem, 'a') && type == "click")) && elem["on"+type] && elem["on"+type].apply( elem, data ) === false ) - event.result = false; - - // Trigger the native events (except for clicks on links) - if ( !bubbling && elem[type] && !event.isDefaultPrevented() && !(jQuery.nodeName(elem, 'a') && type == "click") ) { - this.triggered = true; - try { - elem[ type ](); - // prevent IE from throwing an error for some hidden elements - } catch (e) {} - } - - this.triggered = false; - - if ( !event.isPropagationStopped() ) { - var parent = elem.parentNode || elem.ownerDocument; - if ( parent ) - jQuery.event.trigger(event, data, parent, true); - } - }, - - handle: function(event) { - // returned undefined or false - var all, handlers; - - event = arguments[0] = jQuery.event.fix( event || window.event ); - event.currentTarget = this; - - // Namespaced event handlers - var namespaces = event.type.split("."); - event.type = namespaces.shift(); - - // Cache this now, all = true means, any handler - all = !namespaces.length && !event.exclusive; - - var namespace = RegExp("(^|\\.)" + namespaces.slice().sort().join(".*\\.") + "(\\.|$)"); - - handlers = ( jQuery.data(this, "events") || {} )[event.type]; - - for ( var j in handlers ) { - var handler = handlers[j]; - - // Filter the functions by class - if ( all || namespace.test(handler.type) ) { - // Pass in a reference to the handler function itself - // So that we can later remove it - event.handler = handler; - event.data = handler.data; - - var ret = handler.apply(this, arguments); - - if( ret !== undefined ){ - event.result = ret; - if ( ret === false ) { - event.preventDefault(); - event.stopPropagation(); - } - } - - if( event.isImmediatePropagationStopped() ) - break; - - } - } - }, - - props: "altKey attrChange attrName bubbles button cancelable charCode clientX clientY ctrlKey currentTarget data detail eventPhase fromElement handler keyCode metaKey newValue originalTarget pageX pageY prevValue relatedNode relatedTarget screenX screenY shiftKey srcElement target toElement view wheelDelta which".split(" "), - - fix: function(event) { - if ( event[expando] ) - return event; - - // store a copy of the original event object - // and "clone" to set read-only properties - var originalEvent = event; - event = jQuery.Event( originalEvent ); - - for ( var i = this.props.length, prop; i; ){ - prop = this.props[ --i ]; - event[ prop ] = originalEvent[ prop ]; - } - - // Fix target property, if necessary - if ( !event.target ) - event.target = event.srcElement || document; // Fixes #1925 where srcElement might not be defined either - - // check if target is a textnode (safari) - if ( event.target.nodeType == 3 ) - event.target = event.target.parentNode; - - // Add relatedTarget, if necessary - if ( !event.relatedTarget && event.fromElement ) - event.relatedTarget = event.fromElement == event.target ? event.toElement : event.fromElement; - - // Calculate pageX/Y if missing and clientX/Y available - if ( event.pageX == null && event.clientX != null ) { - var doc = document.documentElement, body = document.body; - event.pageX = event.clientX + (doc && doc.scrollLeft || body && body.scrollLeft || 0) - (doc.clientLeft || 0); - event.pageY = event.clientY + (doc && doc.scrollTop || body && body.scrollTop || 0) - (doc.clientTop || 0); - } - - // Add which for key events - if ( !event.which && ((event.charCode || event.charCode === 0) ? event.charCode : event.keyCode) ) - event.which = event.charCode || event.keyCode; - - // Add metaKey to non-Mac browsers (use ctrl for PC's and Meta for Macs) - if ( !event.metaKey && event.ctrlKey ) - event.metaKey = event.ctrlKey; - - // Add which for click: 1 == left; 2 == middle; 3 == right - // Note: button is not normalized, so don't use it - if ( !event.which && event.button ) - event.which = (event.button & 1 ? 1 : ( event.button & 2 ? 3 : ( event.button & 4 ? 2 : 0 ) )); - - return event; - }, - - proxy: function( fn, proxy ){ - proxy = proxy || function(){ return fn.apply(this, arguments); }; - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || proxy.guid || this.guid++; - // So proxy can be declared as an argument - return proxy; - }, - - special: { - ready: { - // Make sure the ready event is setup - setup: bindReady, - teardown: function() {} - } - }, - - specialAll: { - live: { - setup: function( selector, namespaces ){ - jQuery.event.add( this, namespaces[0], liveHandler ); - }, - teardown: function( namespaces ){ - if ( namespaces.length ) { - var remove = 0, name = RegExp("(^|\\.)" + namespaces[0] + "(\\.|$)"); - - jQuery.each( (jQuery.data(this, "events").live || {}), function(){ - if ( name.test(this.type) ) - remove++; - }); - - if ( remove < 1 ) - jQuery.event.remove( this, namespaces[0], liveHandler ); - } - } - } - } -}; - -jQuery.Event = function( src ){ - // Allow instantiation without the 'new' keyword - if( !this.preventDefault ) - return new jQuery.Event(src); - - // Event object - if( src && src.type ){ - this.originalEvent = src; - this.type = src.type; - // Event type - }else - this.type = src; - - // timeStamp is buggy for some events on Firefox(#3843) - // So we won't rely on the native value - this.timeStamp = now(); - - // Mark it as fixed - this[expando] = true; -}; - -function returnFalse(){ - return false; -} -function returnTrue(){ - return true; -} - -// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding -// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-bindin… -jQuery.Event.prototype = { - preventDefault: function() { - this.isDefaultPrevented = returnTrue; - - var e = this.originalEvent; - if( !e ) - return; - // if preventDefault exists run it on the original event - if (e.preventDefault) - e.preventDefault(); - // otherwise set the returnValue property of the original event to false (IE) - e.returnValue = false; - }, - stopPropagation: function() { - this.isPropagationStopped = returnTrue; - - var e = this.originalEvent; - if( !e ) - return; - // if stopPropagation exists run it on the original event - if (e.stopPropagation) - e.stopPropagation(); - // otherwise set the cancelBubble property of the original event to true (IE) - e.cancelBubble = true; - }, - stopImmediatePropagation:function(){ - this.isImmediatePropagationStopped = returnTrue; - this.stopPropagation(); - }, - isDefaultPrevented: returnFalse, - isPropagationStopped: returnFalse, - isImmediatePropagationStopped: returnFalse -}; -// Checks if an event happened on an element within another element -// Used in jQuery.event.special.mouseenter and mouseleave handlers -var withinElement = function(event) { - // Check if mouse(over|out) are still within the same parent element - var parent = event.relatedTarget; - // Traverse up the tree - while ( parent && parent != this ) - try { parent = parent.parentNode; } - catch(e) { parent = this; } - - if( parent != this ){ - // set the correct event type - event.type = event.data; - // handle event if we actually just moused on to a non sub-element - jQuery.event.handle.apply( this, arguments ); - } -}; - -jQuery.each({ - mouseover: 'mouseenter', - mouseout: 'mouseleave' -}, function( orig, fix ){ - jQuery.event.special[ fix ] = { - setup: function(){ - jQuery.event.add( this, orig, withinElement, fix ); - }, - teardown: function(){ - jQuery.event.remove( this, orig, withinElement ); - } - }; -}); - -jQuery.fn.extend({ - bind: function( type, data, fn ) { - return type == "unload" ? this.one(type, data, fn) : this.each(function(){ - jQuery.event.add( this, type, fn || data, fn && data ); - }); - }, - - one: function( type, data, fn ) { - var one = jQuery.event.proxy( fn || data, function(event) { - jQuery(this).unbind(event, one); - return (fn || data).apply( this, arguments ); - }); - return this.each(function(){ - jQuery.event.add( this, type, one, fn && data); - }); - }, - - unbind: function( type, fn ) { - return this.each(function(){ - jQuery.event.remove( this, type, fn ); - }); - }, - - trigger: function( type, data ) { - return this.each(function(){ - jQuery.event.trigger( type, data, this ); - }); - }, - - triggerHandler: function( type, data ) { - if( this[0] ){ - var event = jQuery.Event(type); - event.preventDefault(); - event.stopPropagation(); - jQuery.event.trigger( event, data, this[0] ); - return event.result; - } - }, - - toggle: function( fn ) { - // Save reference to arguments for access in closure - var args = arguments, i = 1; - - // link all the functions, so any of them can unbind this click handler - while( i < args.length ) - jQuery.event.proxy( fn, args[i++] ); - - return this.click( jQuery.event.proxy( fn, function(event) { - // Figure out which function to execute - this.lastToggle = ( this.lastToggle || 0 ) % i; - - // Make sure that clicks stop - event.preventDefault(); - - // and execute the function - return args[ this.lastToggle++ ].apply( this, arguments ) || false; - })); - }, - - hover: function(fnOver, fnOut) { - return this.mouseenter(fnOver).mouseleave(fnOut); - }, - - ready: function(fn) { - // Attach the listeners - bindReady(); - - // If the DOM is already ready - if ( jQuery.isReady ) - // Execute the function immediately - fn.call( document, jQuery ); - - // Otherwise, remember the function for later - else - // Add the function to the wait list - jQuery.readyList.push( fn ); - - return this; - }, - - live: function( type, fn ){ - var proxy = jQuery.event.proxy( fn ); - proxy.guid += this.selector + type; - - jQuery(document).bind( liveConvert(type, this.selector), this.selector, proxy ); - - return this; - }, - - die: function( type, fn ){ - jQuery(document).unbind( liveConvert(type, this.selector), fn ? { guid: fn.guid + this.selector + type } : null );

1 0

[hg] galaxy 3405: Update to workflow UI: (1) made options menu; ...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/43249ea9d72a changeset: 3405:43249ea9d72a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Feb 17 12:25:17 2010 -0500 description: Update to workflow UI: (1) made options menu; (2) created styles for item metadata; and (3) put item annotations in own metadata form below tool form. diffstat: lib/galaxy/web/controllers/page.py | 3 +- static/june_2007_style/base.css.tmpl | 44 +++++++ static/june_2007_style/blue/base.css | 7 + static/scripts/autocomplete_tagging.js | 2 + static/scripts/galaxy.workflow_editor.canvas.js | 1 - static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/galaxy.workflow_editor.canvas.js | 2 +- templates/workflow/editor.mako | 103 ++++++++-------- 8 files changed, 109 insertions(+), 55 deletions(-) diffs (355 lines): diff -r 1e85451c9c86 -r 43249ea9d72a lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Wed Feb 17 11:07:08 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Wed Feb 17 12:25:17 2010 -0500 @@ -570,7 +570,6 @@ @web.expose def display_by_username_and_slug( self, trans, username, slug ): """ Display page based on a username and slug. """ - session = trans.sa_session # Get page. session = trans.sa_session @@ -588,7 +587,7 @@ # Process page content. processor = _PageContentProcessor( trans, 'utf-8', 'text/html', self._get_embed_html ) processor.feed( page.latest_revision.content ) - # Output is string, so convert to unicode. + # Output is string, so convert to unicode for display. page_content = unicode( processor.output(), 'utf-8' ) return trans.fill_template_mako( "page/display.mako", item=page, item_data=page_content, content_only=True ) diff -r 1e85451c9c86 -r 43249ea9d72a static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Wed Feb 17 11:07:08 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Wed Feb 17 12:25:17 2010 -0500 @@ -111,6 +111,50 @@ overflow: auto; } +div.metadataForm { + border:solid #aaaaaa 1px; +} + +div.metadataFormTitle { + font-weight:bold; + padding:5px; + padding-left:10px; + padding-right:10px; + background:#cccccc; + background-repeat:repeat-x; + background-position:top; + border-bottom:solid #aaaaaa 1px; +} + +div.metadataFormBody { + background:#FFFFFF; + background-image:url(form_body_bg.png); + background-repeat:repeat-x; + background-position:top; + padding:5px 0; +} + +div.metadataFormBody div.metadataFormTitle { + background:transparent; + border:none; + font-weight:bold; + border-bottom:solid #dcb790 1px; + margin-bottom:5px; +} + +div.metadataFormDisabled div.metadataFormTitle { + background:#eee; + border-color:#999; +} + +div.metadataFormDisabled { + border-color:#999; +} + +div.metadataHelpBody { + width:100%;overflow:auto; +} + div.titleRow { font-weight: bold; border-bottom: dotted gray 1px; diff -r 1e85451c9c86 -r 43249ea9d72a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Wed Feb 17 11:07:08 2010 -0500 +++ b/static/june_2007_style/blue/base.css Wed Feb 17 12:25:17 2010 -0500 @@ -22,6 +22,13 @@ div.toolFormDisabled{border-color:#999;} div.toolHelp{} div.toolHelpBody{width:100%;overflow:auto;} +div.metadataForm{border:solid #aaaaaa 1px;} +div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} +div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.metadataFormBody div.metadataFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #dcb790 1px;margin-bottom:5px;} +div.metadataFormDisabled div.metadataFormTitle{background:#eee;border-color:#999;} +div.metadataFormDisabled{border-color:#999;} +div.metadataHelpBody{width:100%;overflow:auto;} div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:0.5em;padding-bottom:0.25em;} div.form{border:solid #d8b365 1px;} div.form-title{font-weight:bold;padding:5px 10px;background:#ebd9b2;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} diff -r 1e85451c9c86 -r 43249ea9d72a static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Wed Feb 17 11:07:08 2010 -0500 +++ b/static/scripts/autocomplete_tagging.js Wed Feb 17 12:25:17 2010 -0500 @@ -323,12 +323,14 @@ tag_area.hide(); else { + /* var num_tags = array_length(settings.tags); if (num_tags == 0) { add_tag_button.hide(); tag_input_field.show(); } + */ } // Initialize tag names. diff -r 1e85451c9c86 -r 43249ea9d72a static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Feb 17 11:07:08 2010 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Feb 17 12:25:17 2010 -0500 @@ -307,7 +307,6 @@ node = this; this.tool_state = data.tool_state; this.form_html = data.form_html; - this.annotation = data.annotation; this.tool_errors = data.tool_errors; if ( this.tool_errors ) { el.addClass( "tool-node-error" ); diff -r 1e85451c9c86 -r 43249ea9d72a static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Wed Feb 17 11:07:08 2010 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Wed Feb 17 12:25:17 2010 -0500 @@ -1,1 +1,1 @@ -function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" 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failed")},success:function(){u.flushCache()}});return false}}});var j=function(s,r,q,u,t){tag_name_and_value=u.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var i={selectFirst:false,formatItem:j,autoFill:false,highlight:false};b.autocomplete(e.ajax_autocomplete_tag_url,i);h.find(".delete-tag-img").each(function(){d($(this))});init_tag_click_function($(this),e.tag_click_fn);n.click(function(){$(this).hide();c.click();return false});if(e.editable){c.blur(function(q){num_tags=o(e.tags);if(num_tags!=0){n.show();b.hide();c.removeClass("active-tag-area");c.addClass("tooltip")}else{}});c.click(function(s){var r=$(this).hasClass("active-tag-area");if($(s.target).hasClass("delete-tag-img")&&!r){return false}if($(s.target).hasClass("tag-name")&&!r){return false}$(this).removeClass("tooltip");$(this).addClass("active-tag-area");n.hide();b.show();b.focus();var q=function(u){var t=c.attr("id");if(($(u.t 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unction(){}});return true})}function a(q){var r=new Array();for(key in q){r[r.length]=key+"-->"+q[key]}return"{"+r.join(",")+"}"}function m(q){return q.split(":")}function k(q){var r=$("<img src='"+e.delete_tag_img+"'/>").addClass("delete-tag-img");d(r);var s=$("<span>").text(q).addClass("tag-name");s.click(function(){tag_name_and_value=q.split(":");e.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var t=$("<span></span>").addClass("tag-button");t.append(s);if(e.editable){t.append(r)}return t}}; \ No newline at end of file diff -r 1e85451c9c86 -r 43249ea9d72a static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Feb 17 11:07:08 2010 -0500 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Feb 17 12:25:17 2010 -0500 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.ext ension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.annotation=f.annotation;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))}) ;g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes, function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$( "#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)} }if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent(); var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/l oading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(thi s).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.mi n(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b .cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b) {k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.ext ension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extension+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div .input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each (d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position(),annotation:d.annotation};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form" ).submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){ break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);v ar h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this ).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.t op-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f =b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a= (m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r 1e85451c9c86 -r 43249ea9d72a templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Feb 17 11:07:08 2010 -0500 +++ b/templates/workflow/editor.mako Wed Feb 17 12:25:17 2010 -0500 @@ -26,7 +26,8 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"> </script> <![endif]--> - ${h.js( "jquery", + ${h.js( "jquery", + "jquery.tipsy", "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", @@ -128,27 +129,27 @@ return false; }); - ## make_popupmenu( "#optionsbutton", { - ## "Create <b>new</b> workflow" : create_new_workflow_dialog, - ## "<b>Save</b> current workflow" : save_current_workflow, - ## "<b>Load</b> a stored workflow" : load_workflow - ## }); + make_popupmenu( $("#workflow-options-button"), { + ##"Create New" : create_new_workflow_dialog, + "Edit Attributes" : edit_workflow_attributes, + "Layout": layout_editor, + "Save" : save_current_workflow, + ##"Load a Workflow" : load_workflow, + "Close": close_editor, + }); - $("#save-button").click( function() { save_current_workflow(); } ); - $("#close-button").click( function() { close_editor(); } ); - - $("#layout-button").click( function() { + function layout_editor() { workflow.layout(); workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - }); + }; - $('#edit-attributes-button').click( function() { + function edit_workflow_attributes() { workflow.clear_active_node(); $('#edit-attributes').show(); - $('#right-content').hide(); - }); + $('#right-content').hide(); + }; $.jStore.ready(function(engine) { engine.ready(function() { @@ -219,7 +220,7 @@ }); // Rename async. - async_save_text("workflow-rename", "workflow-name", "${h.url_for( action="rename_async", id=trans.security.encode_id(stored.id) )}", "new_name"); + async_save_text("workflow-name", "workflow-name", "${h.url_for( action="rename_async", id=trans.security.encode_id(stored.id) )}", "new_name"); // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging. $('#workflow-tag').click( function() @@ -228,7 +229,7 @@ return false; }); // Annotate async. - async_save_text("workflow-annotate", "workflow-annotation", "${h.url_for( action="annotate_async", id=trans.security.encode_id(stored.id) )}", "new_annotation", true, 4); + async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( action="annotate_async", id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4); }); // Global state for the whole workflow @@ -306,7 +307,7 @@ function show_form_for_tool( text, node ) { $("#edit-attributes").hide(); - $("#right-content").show().html( text ); + $("#right-content").show().html( text ); $("#right-content").find( "form" ).ajaxForm( { type: 'POST', dataType: 'json', @@ -337,17 +338,7 @@ $(this).remove(); make_popupmenu( b, options ); }); - // Add annotation field to form. - // TODO: need to set the annotation for this tool. - var annotation_div = - $( "<div class='form-row'> \ - <label>Annotation / Notes:</label> \ - <div style='margin-right: 10px;'> \ - <textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \ - <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \ - </div> \ - </div>"); - $(this).append( annotation_div ); + // Implements auto-saving based on whether the inputs change. We consider // "changed" to be when a field is accessed and not necessarily modified // because of an issue where "onchange" is not triggered when activating @@ -358,6 +349,30 @@ }); }); }); + + + // Add metadata form to tool. + if ( node ) + { + var metadata_div = + $( "<p><div class='metadataForm'> \ + <div class='metadataFormTitle'>Edit Step Attributes</div> \ + <div class='form-row'> \ + <label>Annotation / Notes:</label> \ + <div style='margin-right: 10px;'> \ + <textarea name='annotation' rows='3' style='width: 100%'>" + node.annotation + "</textarea> \ + <div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div> \ + </div> \ + </div> \ + </div>"); + // When metadata is changed, update node and set workflow changes flag. + var textarea = $(metadata_div).find("textarea"); + textarea.change( function () { + node.annotation = $(this).val(); + workflow.has_changes = true; + }); + $("#right-content").find(".toolForm").after( metadata_div ); + } } var close_editor = function() { @@ -373,7 +388,7 @@ { "Cancel" : hide_modal, "Save Changes" : function() { - save_current_workflow( do_close ); + save_current_workflow( null, do_close ); } }, { "Don't Save": do_close @@ -383,7 +398,7 @@ } } - var save_current_workflow = function ( success_callback ) { + var save_current_workflow = function ( eventObj, success_callback ) { show_modal( "Saving workflow", "progress" ); workflow.check_changes_in_active_form(); if (!workflow.has_changes) { @@ -739,13 +754,10 @@ <div class="unified-panel-header" unselectable="on"> <div class="unified-panel-header-inner" style="float: right"> - <a id="layout-button" class="panel-header-button">Layout</a> -    - <a id="save-button" class="panel-header-button">Save</a> - <a id="close-button" class="panel-header-button">Close</a> + <a id="workflow-options-button" class="panel-header-button popup" href="#">Options</a> </div> <div class="unified-panel-header-inner"> - Workflow canvas + Workflow Canvas | ${stored.name | h} </div> </div> @@ -770,22 +782,17 @@ <div class="unified-panel-header" unselectable="on"> <div class="unified-panel-header-inner"> Details - <div style="float: right"> - <a id="edit-attributes-button" class="panel-header-button">Edit Workflow Attributes</a> - </div> </div> </div> <div class="unified-panel-body" style="overflow: auto;"> ## Div for elements to modify workflow attributes. - <div id="edit-attributes" class="toolForm right-content"> - <div class="toolFormTitle">Edit Workflow Attributes</div> - <div class="toolFormBody"> + <div id="edit-attributes" class="metadataForm right-content"> + <div class="metadataFormTitle">Edit Workflow Attributes</div> + <div class="metadataFormBody"> ## Workflow name. <div id="workflow-name-area" class="form-row"> <label>Name:</label> - <div style="float: right"><a id="workflow-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='rename_sync' )}"></a></div> - <div id="workflow-name">${stored.name | h}</div> - <div style="clear: both"></div> + <span id="workflow-name" class="tooltip editable-text" original-title="Click to rename workflow">${stored.name | h}</span> </div> ## Workflow tags. <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> @@ -793,24 +800,20 @@ <label> Tags: </label> - <div style="float: right"><a id="workflow-tag" title="Tag" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> <div style="float: left; width: 225px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> <style> .tag-area { border: none; } </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, input_size="20", render_add_tag_button=False)} + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, input_size="20")} </div> - <div style="clear: both"></div> <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> </div> ## Workflow annotation. <div id="workflow-annotation-area" class="form-row"> <label>Annotation / Notes:</label> - <div style="float: right"><a id="workflow-annotate" title="Annotate" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='workflow', action='annotate_async' )}"></a></div> - <div id="workflow-annotation">${annotation | h}</div> - <div style="clear: both"></div> + <span id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation">${annotation | h}</span> <div class="toolParamHelp">Add an annotation or notes to a workflow; annotations are available when a workflow is viewed.</div> </div> </div>

1 0

[hg] galaxy 3406: Add the bx browser as a display app for builds...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/297d8c9c5eb0 changeset: 3406:297d8c9c5eb0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 12:45:32 2010 -0500 description: Add the bx browser as a display app for builds hg18,hg19.mm8.mm9, and add the bx browser to the tool config for main. diffstat: lib/galaxy/config.py | 1 + lib/galaxy/datatypes/interval.py | 24 ++++++++++++++++++++++++ lib/galaxy/datatypes/tabular.py | 2 ++ lib/galaxy/util/__init__.py | 8 +++++++- tool-data/shared/bx/bx_build_sites.txt | 1 + tool_conf.xml.main | 1 + universe_wsgi.ini.sample | 3 ++- 7 files changed, 38 insertions(+), 2 deletions(-) diffs (118 lines): diff -r 43249ea9d72a -r 297d8c9c5eb0 lib/galaxy/config.py --- a/lib/galaxy/config.py Wed Feb 17 12:25:17 2010 -0500 +++ b/lib/galaxy/config.py Wed Feb 17 12:45:32 2010 -0500 @@ -81,6 +81,7 @@ self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) + self.bx_display_sites = kwargs.get( 'bx_display_sites', "main" ).lower().split(",") self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") diff -r 43249ea9d72a -r 297d8c9c5eb0 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Wed Feb 17 12:25:17 2010 -0500 +++ b/lib/galaxy/datatypes/interval.py Wed Feb 17 12:45:32 2010 -0500 @@ -54,6 +54,7 @@ """Initialize interval datatype, by adding UCSC display apps""" Tabular.__init__(self, **kwd) self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) + self.add_display_app ( 'main', 'BX', 'as_bx_display_file', 'bx_links' ) def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) @@ -246,6 +247,29 @@ link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val + def bx_links( self, dataset, type, app, base_url ): + # TODO: abstract these methods to eliminate duplicate code. + ret_val = [] + if dataset.has_data: + viewport_tuple = self.get_estimated_display_viewport(dataset) + if viewport_tuple: + chrom = viewport_tuple[0] + start = viewport_tuple[1] + stop = viewport_tuple[2] + for site_name, site_url in util.get_bx_by_build(dataset.dbkey): + if site_name in app.config.bx_display_sites: + # HACK: UCSC doesn't support https, so force http even + # if our URL scheme is https. Making this work + # requires additional hackery in your upstream proxy. + # If UCSC ever supports https, remove this hack. + internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='bx_' + site_name ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) + return ret_val def validate( self, dataset ): """Validate an interval file using the bx GenomicIntervalReader""" diff -r 43249ea9d72a -r 297d8c9c5eb0 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Wed Feb 17 12:25:17 2010 -0500 +++ b/lib/galaxy/datatypes/tabular.py Wed Feb 17 12:45:32 2010 -0500 @@ -214,6 +214,8 @@ return open( dataset.file_name ) def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) + def as_bx_display_file( self, dataset, **kwd ): + return open( dataset.file_name ) class Taxonomy( Tabular ): def __init__(self, **kwd): diff -r 43249ea9d72a -r 297d8c9c5eb0 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Wed Feb 17 12:25:17 2010 -0500 +++ b/lib/galaxy/util/__init__.py Wed Feb 17 12:45:32 2010 -0500 @@ -278,7 +278,12 @@ def string_to_object( s ): return pickle.loads( binascii.unhexlify( s ) ) - +def get_bx_by_build(build): + sites = [] + for site in bx_build_sites: + if build in site['builds']: + sites.append((site['name'],site['url'])) + return sites def get_ucsc_by_build(build): sites = [] for site in ucsc_build_sites: @@ -471,6 +476,7 @@ galaxy_root_path = os.path.join(__path__[0], "..","..","..") # The dbnames list is used in edit attributes and the upload tool dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) +bx_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "bx", "bx_build_sites.txt" ) ) ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False ) diff -r 43249ea9d72a -r 297d8c9c5eb0 tool-data/shared/bx/bx_build_sites.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/shared/bx/bx_build_sites.txt Wed Feb 17 12:45:32 2010 -0500 @@ -0,0 +1,1 @@ +main http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 diff -r 43249ea9d72a -r 297d8c9c5eb0 tool_conf.xml.main --- a/tool_conf.xml.main Wed Feb 17 12:25:17 2010 -0500 +++ b/tool_conf.xml.main Wed Feb 17 12:45:32 2010 -0500 @@ -4,6 +4,7 @@ <tool file="data_source/upload.xml"/> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> + <tool file="data_source/bx_browser.xml" /> <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/gramene_mart.xml" /> diff -r 43249ea9d72a -r 297d8c9c5eb0 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed Feb 17 12:25:17 2010 -0500 +++ b/universe_wsgi.ini.sample Wed Feb 17 12:45:32 2010 -0500 @@ -105,7 +105,8 @@ # Use the new iframe / javascript based layout use_new_layout = true -# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing +# Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing +bx_display_sites = main ucsc_display_sites = main,test,archaea,ucla gbrowse_display_sites = main,test,tair # Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt

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