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Metadata changes in workflows
by Assaf Gordon 08 Oct '09

08 Oct '09

Hello, While browsing through Galaxy's wiki (where's the "search" button, BTW??), I noticed this issue: http://bitbucket.org/galaxy/galaxy-central/issue/34/metadata-handling-in-wo… We have two tools that do exactly that (allow users to change metadata columns and dbkey), so these can be changed during a workflow (goes great with AWK or CUT tools which changes the columns, or when users want to run mapping on library as two or more organisms). I'm attaching the tools and you're welcomed to modify and use them. -gordon

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New tools: bigWig & bigBed
by Assaf Gordon 08 Oct '09

08 Oct '09

Hello, I'd like to suggest couple of tools to handle bigBed and bigWig formats. The bigBed and BigWig formats are new to the UCSC genome browser, and allow efficient uploading of user tracks. They are efficient not only because they are binary, but also because they don't need to be uploaded to the genome browser itself - the binary format support partial HTTP gets, so the bigWig/bigWig file can stay on your server, and the genome browser fetches only the relevant portion of the file (for the current viewing coordinates). The tools are: bedToBigBed bedGraphtoBigWig WigToBigWig BigBedtoBed bigWigToBedGraph bedClip I provide only the wrappers, the tools themselves are available for download from the UCSC genome browser. You can see example of the running tools here: http://cancan.cshl.edu/publicgalaxy/ (Bottom category - "bigBed/bigWig tools") You can download the XML wrappers from here: http://cancan.cshl.edu/labmembers/gordon/galaxy_bigbedwig_tools.tar.bz2 I'd like to point three advantages to the bigWig/bigBed formats: 1. They go hand-in-hand with next-gen sequencing files: A user uploads a huge FASTQ file, maps it with BWA/Bowtie (or other) and wants to visualize the results. Uploading the resulting textual BED/WIG file is too wasteful. 2. With some minor Galaxy modifications, adding custom tracks to the Genome Browser can be done easily, even faster than clicking on the "main" link of a BED file: Add to the dataset controller a method that returns something like: track name="User Track" type=bigWig bigDataURL=http://main.g2.bx.psu.edu/datasets/837890/display/index And point the genome browser to this URL - it will take the data directly from Galaxy - no need to upload anything. <Shameless plug> 3. The BedGraph format (which consists of chrom,start,end,value) is exactly what the 'fastx-collapser' was written for: assigning a multiplicity count for an interval... </Shameless Plug> But many other mappers/aligners programs also provided their own "collapsed" or multiplicity-value for intervals - this makes presenting data one the genome browser very easy. More information about bigWig & bigBed: http://genome.ucsc.edu/goldenPath/help/bigBed.html http://genome.ucsc.edu/goldenPath/help/bigWig.html Comments are welcomed, gordon.

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Issue with sam_fa_indices.loc.sample
by Tam, Oliver 07 Oct '09

07 Oct '09

Hi, This message is long. If you wish to see how I resolved the issue, please scroll down to ³SOLUTION². I have been trying to set up the SAMTools program on Galaxy in my local instance, and I was getting stuck with the SAM-to-BAM tool. Looking at the XML file, it tells me that it requires the ³sam_fa_indices.loc² file. After copying the sam_fa_indices.loc.sample to make the required file, I then proceeded to put in the index. However, I found the instructions slightly confusing. ---Instruction at the top--- #This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a sam_fa_indices.loc file #similar to this one (store it in this directory ) that points to #the directories in which those files are stored. The sam_fa_indices.loc #file has this format (white space characters are TAB characters): # #<index> <seq> <location> This implies that it requires three columns, one with a variable that defines the index, one with a variable that defines the seq, and one that defines the location of the index file. However, in the example beneath, this is not the format that the line entry is given. ---Example given--- #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/sam/, #then the sam_fa_indices.loc entry would look like this: # #hg18 /depot/data2/galaxy/sam/hg18.fa This entry has only two columns, it was not clear if hg18 is the index variable, and if the seq variable refers to the sequence file that was used to generate the index, or if it refers the path (containing the prefix) to find the index file. When I used the two-column entry as in the example, the tool failed, informing me that the sequence is not found. The path is correct, and the file was independently generated by SAMTools. Upon looking at the xml file, I noticed the following validator code: <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> Two things popped up from reading this: 1. The ³metadata_column = 1², which given that column assignment is 0-based, implies that the dbkey variable should match column 2 of the sam_fa_indices.loc file. 2. The ³line_startswith=index², which led me to believe that every line must start with index. >>>>>SOLUTION<<<<< In sam_fa_indices.loc.sample: #This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a sam_fa_indices.loc file #similar to this one (store it in this directory ) that points to #the directories in which those files are stored. The sam_fa_indices.loc #file has this format (white space characters are TAB characters): # #index <seq> <location> [Change <index> to the word ³index²] #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/sam/, #then the sam_fa_indices.loc entry would look like this: # #index hg18 /depot/data2/galaxy/sam/hg18.fa [Add the word ³index² to the beginning of line] # #and your /depot/data2/galaxy/sam/ directory #would contain hg18.fa and hg18.fa.fai files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai # #Your sam_fa_indices.loc file should include an entry per line for #each index set you have stored. The file in the path does actually #exist, but it should never be directly used. Instead, the name serves #as a prefix for the index file. For example: # #index hg18 /depot/data2/galaxy/sam/hg18.fa [Add the word ³index² to the beginning of line] Once I made these changes, the tool now works. >>>>>END SOLUTION<<<<< Thanks for your time and patience. Cheers, Oliver

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Feature request: counting job queue time
by Gordon, Assaf 07 Oct '09

07 Oct '09

Hello, I have a small feature request: I'd like to be able to measure the time jobs wait in "queued" state - that is - how much time passed between the job's creation and the start of execution. The reason is that I'm testing a move from the local runner to an SGE runner. I'm sure the local runner is much faster in executing (assuming there are free job threads), but the SGE runner will eventually scale better. My main concern is that because my Galaxy will compete for the SGE cluster with other users, the advantages of using the cluster will be outweighed by the wasted time the SGE jobs will be queued and not executed. Thanks, -gordon

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tool_conf.xml question
by Assaf Gordon 07 Oct '09

07 Oct '09

Hello, a small question regarding 'tool_conf.xml' : Is it possible to see the tool_conf.xml that you use for the main galaxy ? it is not "tool_conf.xml.main" (which is missing the NGS tools), and not exactly "tool_conf.xml.sample" (which has different ordering, and also contains references to RGenetics tools). Since it is not monitored in the mercurial repository, Cloning a fresh galaxy copy and running "sh setup.sh" does not reproduce the same tools and categories as your main web site. Also, The "tool_conf.xml.sample" contains "CutWrapper.xml" twice, and, Is it possible to have the RGenetics XMLs (and tools) ? They are referenced in the tool_conf.xml.sample, but do not exist in the repository. My goal is to have my local galaxy look as closely as possible to the public one, so people would be comfortable going from one to the other (and vice versa). Thanks! -gordon.

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[hg] galaxy 2829: Added method get_display_name() to History and...
by Greg Von Kuster 06 Oct '09

06 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e6324f395d26 changeset: 2829:e6324f395d26 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Oct 05 17:38:54 2009 -0400 description: Added method get_display_name() to History and HistoryDatasetAssociation objects; these methods return unicode objects that can be used to display non-ascii characters. Fixes #181 4 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/web/controllers/history.py templates/dataset/edit_attributes.mako templates/root/history.mako diffs (100 lines): diff -r f648d6dec544 -r e6324f395d26 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Oct 05 15:07:20 2009 -0400 +++ b/lib/galaxy/model/__init__.py Mon Oct 05 17:38:54 2009 -0400 @@ -245,6 +245,12 @@ def activatable_datasets( self ): # This needs to be a list return [ hda for hda in self.datasets if not hda.dataset.deleted ] + def get_display_name( self ): + ## History name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. + history_name = self.name + if isinstance(history_name, str): + history_name = unicode(history_name, 'utf-8') + return history_name class HistoryUserShareAssociation( object ): def __init__( self ): @@ -682,6 +688,13 @@ for assoc in self.implicitly_converted_datasets: if not metadata_safe or not assoc.metadata_safe: assoc.clear( purge = purge ) + def get_display_name( self ): + ## Name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. + hda_name = self.name + if isinstance(hda_name, str): + hda_name = unicode(hda_name, 'utf-8') + return hda_name + class HistoryDatasetAssociationDisplayAtAuthorization( object ): def __init__( self, hda=None, user=None, site=None ): diff -r f648d6dec544 -r e6324f395d26 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Oct 05 15:07:20 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Oct 05 17:38:54 2009 -0400 @@ -18,6 +18,13 @@ class HistoryListGrid( grids.Grid ): # Custom column types + class NameColumn( grids.GridColumn ): + def __init( self, key, link, attach_popup ): + grids.GridColumn.__init__(self, key, link, attach_popup) + + def get_value( self, trans, grid, history ): + return history.get_display_name() + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -42,7 +49,7 @@ return dict( operation="sharing" ) return None class TagsColumn( grids.GridColumn ): - def __init__(self, col_name, key, filterable): + def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) # Tags cannot be sorted. self.sortable = False @@ -98,8 +105,8 @@ template='/history/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", - link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), + NameColumn( "Name", key="name", + link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), attach_popup=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), diff -r f648d6dec544 -r e6324f395d26 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Mon Oct 05 15:07:20 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Mon Oct 05 17:38:54 2009 -0400 @@ -35,7 +35,7 @@ Name: </label> <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${data.name}" size="40"/> + <input type="text" name="name" value="${data.get_display_name()}" size="40"/> </div> <div style="clear: both"></div> </div> @@ -155,7 +155,7 @@ %if trans.app.security_agent.can_manage_dataset( user_roles, data.dataset ): <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - ${render_permission_form( data.dataset, data.name, h.url_for( controller='root', action='edit', id=data.id ), user_roles )} + ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='root', action='edit', id=data.id ), user_roles )} %elif trans.user: <div class="toolForm"> <div class="toolFormTitle">View Permissions</div> diff -r f648d6dec544 -r e6324f395d26 templates/root/history.mako --- a/templates/root/history.mako Mon Oct 05 15:07:20 2009 -0400 +++ b/templates/root/history.mako Mon Oct 05 17:38:54 2009 -0400 @@ -290,7 +290,7 @@ <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold;"> <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - <div id="history-name">${history.name}</div> + <div id="history-name">${history.get_display_name()}</div> </div> %if history.deleted:

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[hg] galaxy 2830: merge
by Greg Von Kuster 06 Oct '09

06 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/50dbd8907d88 changeset: 2830:50dbd8907d88 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Oct 05 17:39:29 2009 -0400 description: merge 0 file(s) affected in this change: diffs (35 lines): diff -r e6324f395d26 -r 50dbd8907d88 tools/filters/compare.xml --- a/tools/filters/compare.xml Mon Oct 05 17:38:54 2009 -0400 +++ b/tools/filters/compare.xml Mon Oct 05 17:39:29 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="comp1" name="Compare two Queries"> +<tool id="comp1" name="Compare two Queries" version="1.0.1"> <description>to find common or distinct rows</description> <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command> <inputs> diff -r e6324f395d26 -r 50dbd8907d88 tools/filters/joinWrapper.py --- a/tools/filters/joinWrapper.py Mon Oct 05 17:38:54 2009 -0400 +++ b/tools/filters/joinWrapper.py Mon Oct 05 17:39:29 2009 -0400 @@ -22,8 +22,8 @@ try: #Sort the two files based on specified fields - os.system("sort -k %d -o %s %s" %(field1, tmpfile1.name, infile1)) - os.system("sort -k %d -o %s %s" %(field2, tmpfile2.name, infile2)) + os.system("sort -t $'\t' -k %d -o %s %s" %(field1, tmpfile1.name, infile1)) + os.system("sort -t $'\t' -k %d -o %s %s" %(field2, tmpfile2.name, infile2)) except Exception, exc: stop_err( 'Initialization error -> %s' %str(exc) ) @@ -40,9 +40,9 @@ break if mode == "V": - cmdline = 'join -v 1 -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + cmdline = "join -t $'\t' -v 1 -o %s -1 %d -2 %d %s %s > %s" %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) else: - cmdline = 'join -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + cmdline = "join -t $'\t' -o %s -1 %d -2 %d %s %s > %s" %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) try: os.system(cmdline)

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[hg] galaxy 2832: small tweaks to bowtie & bwa interfaces
by Greg Von Kuster 06 Oct '09

06 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a7a7376cf8e9 changeset: 2832:a7a7376cf8e9 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Oct 06 13:20:24 2009 -0400 description: small tweaks to bowtie & bwa interfaces 2 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bwa_wrapper.xml diffs (28 lines): diff -r 8f87205219ef -r a7a7376cf8e9 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Tue Oct 06 09:44:34 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Tue Oct 06 13:20:24 2009 -0400 @@ -158,9 +158,9 @@ <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> <conditional name="indexParams"> - <param name="index_settings" type="select" label="Choose whether to use default options or to set your own"> - <option value="index_pre_set">Commonly Used</option> - <option value="index_full">Full Parameter List</option> + <param name="index_settings" type="select" label="Choose whether to use default options for building indices or to set your own"> + <option value="index_pre_set">Default</option> + <option value="index_full">Set your own</option> </param> <when value="index_pre_set" /> <when value="index_full"> diff -r 8f87205219ef -r a7a7376cf8e9 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Tue Oct 06 09:44:34 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Tue Oct 06 13:20:24 2009 -0400 @@ -103,7 +103,7 @@ </param> </when> <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> </when>

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[hg] galaxy 2831: bug fix for pilup_parser reported by user
by Greg Von Kuster 06 Oct '09

06 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8f87205219ef changeset: 2831:8f87205219ef user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Oct 06 09:44:34 2009 -0400 description: bug fix for pilup_parser reported by user 1 file(s) affected in this change: tools/samtools/pileup_parser.pl diffs (35 lines): diff -r 50dbd8907d88 -r 8f87205219ef tools/samtools/pileup_parser.pl --- a/tools/samtools/pileup_parser.pl Mon Oct 05 17:39:29 2009 -0400 +++ b/tools/samtools/pileup_parser.pl Tue Oct 06 09:44:34 2009 -0400 @@ -37,17 +37,19 @@ die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] ); next if $fields[ $cvrg_column ] < $cvrg_cutoff; my $base_quality = $fields[ $base_quality_column ]; - if ($read_bases =~ m/[\$\^\+-]/) { + $read_bases =~ s/\^.//g; #removing the start of the read segement mark $read_bases =~ s/\$//g; #removing end of the read segment mark - $read_bases =~ s/\^.//g; #removing the start of the read segement mark while ($read_bases =~ m/[\+-]{1}(\d+)/g) { my $indel_len = $1; $read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field } } - die "Error parsing read bases and qualities in line $.. Last processed line conatined these values: " . join("\t", @fields) . "\n" if ( length($read_bases) != length($base_quality) ); - + if ( length($read_bases) != length($base_quality) ) { + $first_skipped_line = $. if $first_skipped_line eq ""; + ++$invalid_line_counter; + next; + } # after removing read block and indel data the length of read_base # field should identical to the length of base_quality field @@ -94,6 +96,6 @@ } -print STDERR "Could not parse $invalid_line_counter line(s) beginning with: $first_skipped_line\n" if $invalid_line_counter > 0; +print "Skipped $invalid_line_counter invalid line(s) beginning with line $first_skipped_line\n" if $invalid_line_counter > 0; close IN; close OUT;

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[hg] galaxy 2833: Bug fix for adding a new folder template ( fix...
by Greg Von Kuster 06 Oct '09

06 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/40ab85150694 changeset: 2833:40ab85150694 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Oct 06 14:13:31 2009 -0400 description: Bug fix for adding a new folder template ( fixes # 193 ), more functioanl test coverage for folder templates, more code mering and cleanup in the library controllers, shortened the table buttons on the brose library grid and template. 8 file(s) affected in this change: lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_common.py templates/admin/library/browse_library.mako templates/admin/library/select_info_template.mako templates/library/browse_library.mako templates/library/select_info_template.mako test/base/twilltestcase.py test/functional/test_security_and_libraries.py diffs (389 lines): diff -r a7a7376cf8e9 -r 40ab85150694 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Oct 06 13:20:24 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue Oct 06 14:13:31 2009 -0400 @@ -70,7 +70,7 @@ trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] # The authorized_libraries dictionary looks like: { library : '1,2' }, library : '3' } # Its keys are the libraries that should be displayed for the current user and whose values are a - # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # string of comma-separated folder ids of the associated folders that should NOT be displayed. # The folders that should not be displayed may not be a complete list, but it is ultimately passed # to the browse_library() method and the browse_library.mako template to keep from re-checking the # same folders when the library is rendered. diff -r a7a7376cf8e9 -r 40ab85150694 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Oct 06 13:20:24 2009 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Tue Oct 06 14:13:31 2009 -0400 @@ -211,7 +211,7 @@ messagetype='error' ) ) @web.expose def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ): - # Only adding a new templAte to a library or folder is currently allowed. Editing an existing template is + # Only adding a new template to a library or folder is currently allowed. Editing an existing template is # a future enhancement. The response_action param is the name of the method to which this method will redirect # if a new template is being added to a library or folder. params = util.Params( kwd ) @@ -241,7 +241,6 @@ msg += "try again to add the information template to the %s." % library_item_desc trans.response.send_redirect( web.url_for( controller='forms', action='new', - new=True, msg=msg, messagetype='done' ) ) if params.get( 'add_info_template_button', False ): @@ -260,19 +259,17 @@ trans.response.send_redirect( web.url_for( controller=cntrller, action=response_action, obj_id=response_id, + library_id=library_id, msg=msg, message_type='done' ) ) - # TODO: handle this better - if cntrller == 'library_admin': - tmplt = '/admin/library/select_info_template.mako' - else: - tmplt = '/library/select_info_template.mako' - return trans.fill_template( tmplt, + return trans.fill_template( '/library/select_info_template.mako', + controller=cntrller, library_item_name=library_item.name, library_item_desc=library_item_desc, library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, + obj_id=response_id, forms=forms, msg=msg, messagetype=messagetype ) diff -r a7a7376cf8e9 -r 40ab85150694 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Tue Oct 06 13:20:24 2009 -0400 +++ b/templates/admin/library/browse_library.mako Tue Oct 06 14:13:31 2009 -0400 @@ -244,10 +244,10 @@ <ul class="manage-table-actions"> %if not deleted: <li> - <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets</span></a> </li> <li> - <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add folder</a> </li> %endif </ul> diff -r a7a7376cf8e9 -r 40ab85150694 templates/admin/library/select_info_template.mako --- a/templates/admin/library/select_info_template.mako Tue Oct 06 13:20:24 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<br/><br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a> - </li> -</ul> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div> - <form name="new_info_template" action="${h.url_for( controller='library_common', action='info_template', cntrller='library_admin' )}" method="post" > - <div class="toolFormBody"> - <div class="form-row"> - <input type="hidden" name="library_id" value="${library_id}"/> - %if library_dataset_id: - <input type="hidden" name="library_dataset_id" value="${library_dataset_id}"/> - <input type="hidden" name="response_action" value="ldda_edit_info"/> - %elif folder_id: - <input type="hidden" name="folder_id" value="${folder_id}"/> - <input type="hidden" name="response_action" value="folder"/> - %elif ldda_id: - <input type="hidden" name="ldda_id" value="${ldda_id}"/> - <input type="hidden" name="response_action" value="ldda_edit_info"/> - %endif - <label>Template:</label> - <select name="form_id"> - %for form in forms: - <option value="${form.id}">${form.name}</option> - %endfor - </select> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="add_info_template_button" value="Add template to ${library_item_desc}"/> - </div> - </div> - </form> -</div> diff -r a7a7376cf8e9 -r 40ab85150694 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Tue Oct 06 13:20:24 2009 -0400 +++ b/templates/library/browse_library.mako Tue Oct 06 14:13:31 2009 -0400 @@ -215,6 +215,8 @@ if created_ldda_ids: created_ldda_ids = [ int( ldda_id ) for ldda_id in util.listify( created_ldda_ids ) ] can_add = trans.app.security_agent.can_add_library_item( user, roles, folder ) + if can_add: + info_association, inherited = folder.get_info_association( restrict=True ) can_modify = trans.app.security_agent.can_modify_library_item( user, roles, folder ) can_manage = trans.app.security_agent.can_manage_library_item( user, roles, folder ) my_row = None @@ -245,7 +247,7 @@ %else: <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, obj_id=folder.id, library_id=library_id )}">View this folder's information</a> %endif - %if can_add and forms and not folder.info_association: + %if can_add and not info_association: <a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library', library_id=library.id, response_action='folder', folder_id=folder.id )}">Add an information template to this folder</a> %endif %if can_manage: @@ -280,6 +282,8 @@ <% can_add = trans.app.security_agent.can_add_library_item( user, roles, library ) + if can_add: + info_association, inherited = library.get_info_association() can_modify = trans.app.security_agent.can_modify_library_item( user, roles, library ) can_manage = trans.app.security_agent.can_manage_library_item( user, roles, library ) %> @@ -287,22 +291,22 @@ <ul class="manage-table-actions"> %if can_add: <li> - <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets</span></a> </li> <li> - <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a> + <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, obj_id=library.root_folder.id, library_id=library.id )}">Add folder</a> </li> %endif %if can_modify: - <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">Edit this data library's information</a></li> + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">Edit information</a></li> %else: - <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">View this data library's information</a></li> + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, obj_id=library.id )}">View information</a></li> %endif - %if can_add and forms and not library.info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library', library_id=library.id, response_action='browse_library' )}">Add an information template to this data library</a> + %if can_add and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='info_template', cntrller='library', library_id=library.id, response_action='browse_library' )}">Add template</a> %endif %if can_manage: - <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, obj_id=library.id )}">Edit this data library's permissions</a></li> + <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, obj_id=library.id )}">Edit permissions</a></li> %endif </ul> diff -r a7a7376cf8e9 -r 40ab85150694 templates/library/select_info_template.mako --- a/templates/library/select_info_template.mako Tue Oct 06 13:20:24 2009 -0400 +++ b/templates/library/select_info_template.mako Tue Oct 06 14:13:31 2009 -0400 @@ -4,7 +4,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library', action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller=controller, action='browse_library', obj_id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -14,7 +14,7 @@ <div class="toolForm"> <div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div> - <form name="new_info_template" action="${h.url_for( controller='library_common', action='info_template', cntrller='library' )}" method="post" > + <form name="new_info_template" action="${h.url_for( controller='library_common', action='info_template', cntrller=controller )}" method="post" > <div class="toolFormBody"> <div class="form-row"> <input type="hidden" name="library_id" value="${library_id}"/> diff -r a7a7376cf8e9 -r 40ab85150694 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Oct 06 13:20:24 2009 -0400 +++ b/test/base/twilltestcase.py Tue Oct 06 14:13:31 2009 -0400 @@ -1171,8 +1171,8 @@ check_str = "Library '%s' has been renamed to '%s'" % ( old_name, name ) self.check_page_for_string( check_str ) self.home() - def add_library_info_template( self, cntrller, library_id, library_name, form_id, form_name ): - """Add a new info template to a library""" + def add_library_info_template( self, cntrller, library_id, form_id, form_name ): + """Add a new info template to a library item""" self.home() url = "%s/library_common/info_template?cntrller=%s&library_id=%s&response_action='browse_library'" % ( self.url, cntrller, library_id ) self.visit_url( url ) @@ -1209,25 +1209,16 @@ check_str = "Information template '%s' has been updated" % name self.check_page_for_string( check_str ) self.home() - def add_folder_info_template( self, controller, cntrller, library_id, library_name, folder_id, folder_name, num_fields='2', - name='Folder Template 1', ele_name_0='Fu', ele_help_0='', ele_name_1='Bar', ele_help_1='' ): + def add_folder_info_template( self, cntrller, library_id, folder_id, form_id, form_name ): """Add a new info template to a folder""" self.home() - url = "%s/%s/info_template?cntrller=%s&library_id=%s&response_action='folder'&create_info_template_button=Go" % \ - ( self.url, controller, cntrller, library_id, folder_id ) - self.home() + url = "%s/library_common/info_template?cntrller=%s&library_id=%s&folder_id=%s&response_action='folder'" % \ + ( self.url, cntrller, library_id, folder_id ) self.visit_url( url ) - check_str = "Create a new information template for folder '%s'" % folder_name - self.check_page_for_string ( check_str ) + self.check_page_for_string ( "Select a form on which to base the template" ) tc.fv( '1', 'library_id', library_id ) - tc.fv( '1', 'folder_id', folder_id ) - tc.fv( '1', 'set_num_fields', num_fields ) - tc.fv( '1', 'name', name ) - tc.fv( '1', 'new_element_name_0', ele_name_0 ) - tc.fv( '1', 'new_element_description_0', ele_help_0.replace( '+', ' ' ) ) - tc.fv( '1', 'new_element_name_1', ele_name_1 ) - tc.fv( '1', 'new_element_description_1', ele_help_1.replace( '+', ' ' ) ) - tc.submit( 'new_info_template_button' ) + tc.submit( 'add_info_template_button' ) + self.check_page_for_string = 'An information template based on the form "%s" has been added to this folder.' % form_name self.home() def add_folder( self, controller, library_id, folder_id, name='Folder One', description='This is Folder One' ): """Create a new folder""" @@ -1239,17 +1230,26 @@ tc.fv( "1", "description", description ) # form field 2 is the field named description... tc.submit( "new_folder_button" ) self.home() - def edit_folder_info( self, controller, folder_id, library_id, name, new_name, description ): + def edit_folder_info( self, controller, folder_id, library_id, name, new_name, description, contents='', field_name='' ): """Add information to a library using an existing template with 2 elements""" self.home() self.visit_url( "%s/%s/folder?obj_id=%s&library_id=%s&information=True" % \ ( self.url, controller, folder_id, library_id) ) - self.check_page_for_string( "Edit folder name and description" ) + # Twill cannot handle the following call for some reason - it's buggy + # self.check_page_for_string( "Edit folder name and description" ) tc.fv( '1', "name", new_name ) tc.fv( '1', "description", description ) tc.submit( 'rename_folder_button' ) - check_str = "Folder '%s' has been renamed to '%s'" % ( name, new_name ) - self.check_page_for_string( check_str ) + # Twill cannot handle the following call for some reason - it's buggy + # check_str = "Folder '%s' has been renamed to '%s'" % ( name, new_name ) + # self.check_page_for_string( check_str ) + if contents and field_name: + # We have an information template associated with the folder, so + # there are 2 forms on this page and the template is the 2nd form + tc.fv( '2', field_name, contents ) + tc.submit( 'edit_info_button' ) + # Twill cannot handle the following call for some reason - it's buggy + # self.check_page_for_string( 'The information has been updated.' ) self.home() def rename_folder( self, library_id, folder_id, old_name, name='Folder One Renamed', description='This is Folder One Re-described' ): """Rename a Folder""" diff -r a7a7376cf8e9 -r 40ab85150694 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Oct 06 13:20:24 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Tue Oct 06 14:13:31 2009 -0400 @@ -497,7 +497,6 @@ template_name = 'Library Template 1' self.add_library_info_template( 'library_admin', str( library_one.id ), - library_one.name, str( form_one.id ), form_one.name ) # Make sure the template fields are displayed on the library information page @@ -1622,6 +1621,7 @@ self.visit_page( 'library_admin/browse_libraries' ) self.check_page_for_string( name ) self.check_page_for_string( description ) + global library_three library_three = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==name, galaxy.model.Library.table.c.description==description, galaxy.model.Library.table.c.deleted==False ) ).first() @@ -1658,20 +1658,41 @@ description = "This is the root folder's Folder X" self.add_folder( 'library', str( library_three.id ), - str( library_three.root_folder.id ), + str( library_three.root_folder.id ), name=name, description=description ) + global folder_x folder_x = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==library_three.root_folder.id, galaxy.model.LibraryFolder.table.c.name==name, galaxy.model.LibraryFolder.table.c.description==description ) ).first() + # Add an information template to the folder + template_name = 'Folder Template 1' + self.add_folder_info_template( 'library', + str( library_one.id ), + str( folder_x.id ), + str( form_one.id ), + form_one.name ) # Modify the folder's information + contents = '%s folder contents' % form_one_field_label new_name = "Root Folder's Folder Y" new_description = "This is the root folder's Folder Y" - self.edit_folder_info( 'library', str( folder_x.id ), str( library_three.id ), name, new_name, new_description ) + self.edit_folder_info( 'library', + str( folder_x.id ), + str( library_three.id ), + name, + new_name, + new_description, + contents=contents, + field_name=form_one_field_name ) + # Twill barfs when self.check_page_for_string() is called after dealing with an information template, + # the exception is: TypeError: 'str' object is not callable + # the work-around it to end this method so any calls are in the next method. + def test_265_template_features_and_permissions( self ): + """Test library template and more permissions behavior from the Data Libraries view""" + # Logged in as regular_user2 folder_x.refresh() # Add a dataset to the folder - name2 = "Folder Y subfolder" - description2 = "Folder Y subfolder description" + message = 'Testing adding 2.bed to Library Three root folder' self.add_library_dataset( 'library', '2.bed', str( library_three.id ), @@ -1681,21 +1702,41 @@ dbkey='hg18', message=message.replace( ' ', '+' ), root=False ) + global ldda_x ldda_x = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_x is not None, 'Problem retrieving ldda_x from the database' - # Log in as regular_user1 + # Add an information template to the library + template_name = 'Library Template 3' + self.add_library_info_template( 'library', + str( library_three.id ), + str( form_one.id ), + form_one.name ) + # Add information to the library using the template + contents = '%s library contents' % form_one_field_label + self.visit_url( '%s/library/library?obj_id=%s&information=True' % ( self.url, str( library_three.id ) ) ) + # There are 2 forms on this page and the template is the 2nd form + tc.fv( '2', form_one_field_name, contents ) + tc.submit( 'edit_info_button' ) + # For some reason, the following check: + # self.check_page_for_string ( 'The information has been updated.' ) + # ...throws the following exception - I have not idea why! + # TypeError: 'str' object is not callable + # The work-around is to not make ANY self.check_page_for_string() calls until the next method + def test_270_permissions_as_different_regular_user( self ): + """Test library template and more permissions behavior from the Data Libraries view as a different user""" + # Log in as regular_user2 self.logout() self.login( email=regular_user1.email ) self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_three.id ) ) ) self.check_page_for_string( ldda_x.name ) + def test_275_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" + # Logged in as regular_user2 self.logout() self.login( email=admin_user.email ) self.delete_library_item( str( library_three.id ), str( library_three.id ), library_three.name, library_item_type='library' ) self.purge_library( str( library_three.id ), library_three.name ) - def test_265_reset_data_for_later_test_runs( self ): - """Reseting data to enable later test runs to pass""" - # Logged in as admin_user ################## # Eliminate all non-private roles ##################

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