September 2008 - galaxy-dev - lists.galaxyproject.org

Adding new interval datatype
by Assaf Gordon 05 Sep '08

05 Sep '08

Hello, I'd like to add a new datatype to galaxy. This datatype is just an textual interval file, with non-default columns assignment. For example, the chromosome is on column 4, start/end at columns 6/7. Is there a way to achieve this without inheriting a new class in "/lib/galaxy/datatypes/interval.py" ? I was hoping for something along the lines of adding the following in "datatypes_conf.xml": <datatype extension="MyNewType" type="galaxy.datatypes.interval:Interval" mimetype="text/text" display_in_upload="true"> <metadata name="chromCol" value="4" /> <metadata name="startCol" value="6" /> <metadata name="endCol" value="7" /> </datatype> If this isn't possible yet, and if I may suggest a code fragment, then at "/lib/galaxy/datatypes/registry.py", line 53, I'd add something like: ------------------- for metadata in elem.findall( 'metadata ): name = metadata.get( 'name', None ) value = metadata.get( 'value', None ) if name and value: self.somehow_change_metadata_value ( name, value) ------------------- Thanks, Gordon.

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Test is at rev 1553:5468a480c0d8
by Greg Von Kuster 04 Sep '08

04 Sep '08

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Test is at rev 1552:3af945fa486b
by Greg Von Kuster 03 Sep '08

03 Sep '08

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Test is at rev 1545:dcaed9f80caf
by Greg Von Kuster 02 Sep '08

02 Sep '08

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Main is at rev 1490:cefbb71490a2
by Greg Von Kuster 02 Sep '08

02 Sep '08

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[hg] galaxy 1489: Add a metadata parameter to Alignment datatype...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/21534250600b changeset: 1489:21534250600b user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Aug 28 15:12:53 2008 -0400 description: Add a metadata parameter to Alignment datatypes which stores chromosome information found in the alignment for each species. GMAJ tool no longer needs to have the chromosome specified for annotations. 4 file(s) affected in this change: lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/sequence.py templates/dataset/edit_attributes.mako tools/visualization/GMAJ.xml diffs (192 lines): diff -r dcaed9f80caf -r 21534250600b lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Thu Aug 28 13:57:23 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu Aug 28 15:12:53 2008 -0400 @@ -66,6 +66,7 @@ value = str( value ) self.value = value self.context = context + self.display = True def __str__(self): if self.value is None: @@ -264,4 +265,24 @@ def __str__(self): return ",".join( map( str, self.value ) ) +class PythonObjectParameter( MetadataParameter ): + def __init__( self, spec, value, context ): + MetadataParameter.__init__( self, spec, value, context ) + self.value = value + self.display = False + + def __str__(self): + if not self.value: + return self.spec.to_string( self.spec.no_value ) + return self.spec.to_string( self.value ) + + def get_html_field( self, value=None, other_values={} ): + return form_builder.TextField( self.spec.name, value=str( self ) ) + def get_html( self ): + return str( self ) + + @classmethod + def marshal( cls, value ): + return value + diff -r dcaed9f80caf -r 21534250600b lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Aug 28 13:57:23 2008 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Aug 28 15:12:53 2008 -0400 @@ -24,6 +24,7 @@ """Add metadata elements""" MetadataElement( name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None ) + MetadataElement( name="species_chromosomes", desc="Species Chromosomes", value={}, param=metadata.PythonObjectParameter, readonly=True, no_value={}, to_string=str ) class Fasta( Sequence ): """Class representing a FASTA sequence""" @@ -165,9 +166,10 @@ def set_meta( self, dataset, first_line_is_header=False, **kwd ): """ - Parses and returns species from MAF files. + Parses and sets species and chromosomes from MAF files. """ species = [] + species_chromosomes = {} try: for i, m in enumerate( bx.align.maf.Reader( open(dataset.file_name) ) ): for c in m.components: @@ -176,15 +178,20 @@ # "src_split" finds the rightmost dot, which is probably # wrong in general, and certainly here. spec = c.src + chrom = None if "." in spec: - spec = spec.split( "." )[0] + spec, chrom = spec.split( ".", 1 ) if spec not in species: species.append(spec) + species_chromosomes[spec] = [] + if chrom and chrom not in species_chromosomes[spec]: + species_chromosomes[spec].append( chrom ) # only check first 100,000 blocks for species if i > 100000: break except: pass dataset.metadata.species = species + dataset.metadata.species_chromosomes = species_chromosomes def missing_meta( self, dataset ): """Checks to see if species is set""" diff -r dcaed9f80caf -r 21534250600b templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Thu Aug 28 13:57:23 2008 -0400 +++ b/templates/dataset/edit_attributes.mako Thu Aug 28 15:12:53 2008 -0400 @@ -39,15 +39,17 @@ <div style="clear: both"></div> </div> %for element in metadata: - <div class="form-row"> - <label> - ${element.spec.desc}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${element.get_html()} + %if element.display: + <div class="form-row"> + <label> + ${element.spec.desc}: + </label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${element.get_html()} + </div> + <div style="clear: both"></div> </div> - <div style="clear: both"></div> - </div> + %endif %endfor <div class="form-row"> <input type="submit" name="save" value="Save"> diff -r dcaed9f80caf -r 21534250600b tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Thu Aug 28 13:57:23 2008 -0400 +++ b/tools/visualization/GMAJ.xml Thu Aug 28 15:12:53 2008 -0400 @@ -10,7 +10,6 @@ <filter type="data_meta" ref="maf_input" key="species" /> </options> </param> - <param name="chromosome" label="Chromosome" value="" type="text"/> <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> @@ -81,48 +80,53 @@ nowarn = $nowarn #end if -#for $seq_count, $annotation in $enumerate( $annotations ): +#set $seq_count = 0 +#for $spec_count, $annotation in $enumerate( $annotations ): +#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] +#else +#set $seq_names = [$annotation['species'].value] +#end if +#for $seq_name in $seq_names: seq ${seq_count}: -#if $annotation['chromosome'].value: -seqname = $annotation['species'].$annotation['chromosome'] -#else: -seqname = $annotation['species'] -#end if +seqname = $seq_name #if $annotation['exons_file'].dataset: -exons = ${seq_count}.exons.${annotation['exons_file'].extension} +exons = ${spec_count}.exons.${annotation['exons_file'].extension} #end if #if $annotation['repeats_file'].dataset: -repeats = ${seq_count}.repeats.${annotation['repeats_file'].extension} +repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension} #end if #if $annotation['links_file'].dataset: -links = ${seq_count}.links.${annotation['links_file'].extension} +links = ${spec_count}.links.${annotation['links_file'].extension} #end if #if $annotation['underlays_file'].dataset: -underlays = ${seq_count}.underlays.${annotation['underlays_file'].extension} +underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension} #end if #if $annotation['highlights_file'].dataset: -highlights = ${seq_count}.highlights.${annotation['highlights_file'].extension} +highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension} #end if offset = $annotation['offset'] +#set $seq_count = $seq_count + 1 +#end for #end for </configfile> <configfile name="filenames_file"> -#for $seq_count, $annotation in $enumerate( $annotations ): +#for $spec_count, $annotation in $enumerate( $annotations ): #if $annotation['exons_file'].dataset: -$annotation['exons_file'] = ${seq_count}.exons.${annotation['exons_file'].extension} +$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension} #end if #if $annotation['repeats_file'].dataset: -$annotation['repeats_file'] = ${seq_count}.repeats.${annotation['repeats_file'].extension} +$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension} #end if #if $annotation['links_file'].dataset: -$annotation['links_file'] = ${seq_count}.links.${annotation['links_file'].extension} +$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension} #end if #if $annotation['underlays_file'].dataset: -$annotation['underlays_file'] = ${seq_count}.underlays.${annotation['underlays_file'].extension} +$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension} #end if #if $annotation['highlights_file'].dataset: -$annotation['highlights_file'] = ${seq_count}.highlights.${annotation['highlights_file'].extension} +$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension} #end if #end for </configfile>

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[hg] galaxy 1490: Remove node from workflow before removing asso...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cefbb71490a2 changeset: 1490:cefbb71490a2 user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 31 21:14:06 2008 -0400 description: Remove node from workflow before removing associated element from canvas, make sure to actually set "active_node" to null when clearing the active node. 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (21 lines): diff -r 21534250600b -r cefbb71490a2 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 28 15:12:53 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Sun Aug 31 21:14:06 2008 -0400 @@ -252,8 +252,8 @@ t.destroy(); $(t.element).draggable('destroy'); }); + workflow.remove_node( this ); $(this.element).draggable('destroy').remove(); - workflow.remove_node( this ); }, make_active : function () { $(this.element).addClass( "toolForm-active" ); @@ -442,6 +442,7 @@ 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>" ); },

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[hg] galaxy 1483: Allow the user to optionally set a reference s...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8e81eced2601 changeset: 1483:8e81eced2601 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 27 12:06:47 2008 -0400 description: Allow the user to optionally set a reference sequence in GMAJ. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (23 lines): diff -r c77dea3e745a -r 8e81eced2601 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Tue Aug 26 17:07:44 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Aug 27 12:06:47 2008 -0400 @@ -3,6 +3,7 @@ <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> + <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> <param name="species" type="select" label="Species of Annotation" multiple="False"> <options> @@ -70,7 +71,11 @@ title = "Galaxy: $maf_input.name" alignfile = input.maf +#if $refseq.value: +refseq = $refseq +#else: refseq = any +#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn

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[hg] galaxy 1484: More fixes for twill 0.9.
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/30fefdf743c2 changeset: 1484:30fefdf743c2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Aug 27 15:35:14 2008 -0400 description: More fixes for twill 0.9. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (47 lines): diff -r 8e81eced2601 -r 30fefdf743c2 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Aug 27 12:06:47 2008 -0400 +++ b/test/base/twilltestcase.py Wed Aug 27 15:35:14 2008 -0400 @@ -18,6 +18,7 @@ # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) +#log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): @@ -412,7 +413,7 @@ #Check for onchange attribute, submit a change if required for i, f in enumerate( tc.showforms() ): if i == form - 1: - break + break for i, control in enumerate( f.controls ): try: if 'refresh_on_change' in control.attrs.keys(): @@ -447,21 +448,19 @@ tc.formvalue(str(form), str(i+1), str(elem) ) #Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl('SubmitControl','___refresh_grouping___',{'name':'refresh_grouping'}) - control.add_to_form(tc.showforms()[form-1]) + control.add_to_form( f ) + control.fixup() #submit for refresh tc.submit('___refresh_grouping___') #start over submit_form() return self.submit_form(form, button, **kwd) - except: continue - + except Exception, e: + # Log.debug("In submit_form, caught exception: %s" %str( e )) + continue for key, value in kwd.items(): # needs to be able to handle multiple values per key if not isinstance(value, list): value = [ value ] - - for i, f in enumerate( tc.showforms() ): - if i == form - 1: - break for i, control in enumerate( f.controls ): if control.name == key: control.clear()

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[hg] galaxy 1485: Bugfix for workflow editor.
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/19c03a96b338 changeset: 1485:19c03a96b338 user: James Taylor <james(a)jamestaylor.org> date: Wed Aug 27 15:51:59 2008 -0400 description: Bugfix for workflow editor. 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (13 lines): diff -r 30fefdf743c2 -r 19c03a96b338 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 27 15:35:14 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 27 15:51:59 2008 -0400 @@ -483,7 +483,8 @@ // zIndex tracking for bring to front zmax = $("#canvas-container").data( "zmax" ) if ( ! zmax ) { - zmax = 0; + // Start above level where connectors are drawn + zmax = 20; } f.css( "zIndex", zmax + 1 ); $("#canvas-container").data( "zmax", zmax + 1 );

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