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commit/galaxy-central: kanwei: Don't show a row that takes up space in tool_form for hidden elements. Fixes #397. Small reorganization
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/124f8bcea0ff/ changeset: 124f8bcea0ff user: kanwei date: 2011-06-15 23:36:38 summary: Don't show a row that takes up space in tool_form for hidden elements. Fixes #397. Small reorganization affected #: 1 file (5 bytes) --- a/templates/tool_form.mako Wed Jun 15 17:16:23 2011 -0400 +++ b/templates/tool_form.mako Wed Jun 15 17:36:38 2011 -0400 @@ -2,7 +2,7 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"><% -from galaxy.util.expressions import ExpressionContext +from galaxy.util.expressions import ExpressionContext %><html> @@ -160,34 +160,35 @@ cls = "form-row form-row-error" else: cls = "form-row" + + label = param.get_label() + + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if type( field_html ) is not unicode: + field_html = unicode( field_html, 'utf-8' ) + + if param.type == "hidden": + return field_html %><div class="${cls}"> - <% label = param.get_label() %> %if label: - <label> - ${label}: - </label> + <label for="${param.name}">${label}:</label> %endif - <% - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change - - # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. - field_html = field.get_html( prefix ) - if type( field_html ) is not unicode: - field_html = unicode( field_html, 'utf-8' ) - %><div class="form-row-input">${field_html}</div> %if parent_errors.has_key( param.name ): - <div class="form-row-error-message"> - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> - </div> + <div class="form-row-error-message"> + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + </div> %endif %if param.help: - <div class="toolParamHelp" style="clear: both;"> - ${param.help} - </div> + <div class="toolParamHelp" style="clear: both;"> + ${param.help} + </div> %endif <div style="clear: both"></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: uncommented genome diversity tools
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ea2fec8ff044/ changeset: ea2fec8ff044 user: richard_burhans date: 2011-06-15 23:16:23 summary: uncommented genome diversity tools affected #: 1 file (104 bytes) --- a/tool_conf.xml.sample Wed Jun 15 17:10:51 2011 -0400 +++ b/tool_conf.xml.sample Wed Jun 15 17:16:23 2011 -0400 @@ -412,21 +412,12 @@ <tool file="human_genome_variation/hilbertvis.xml" /><tool file="human_genome_variation/freebayes.xml" /></section> - - - - <section name="VCF Tools" id="vcf_tools"><tool file="vcf_tools/intersect.xml" /><tool file="vcf_tools/annotate.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: tweaks to get genome diversity tools to pass their functional tests
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7b1bc03240c8/ changeset: 7b1bc03240c8 user: richard_burhans date: 2011-06-15 23:10:51 summary: tweaks to get genome diversity tools to pass their functional tests affected #: 4 files (9 bytes) --- a/tools/genome_diversity/extract_flanking_dna.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/extract_flanking_dna.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@ <command interpreter="python2.5"> extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -18,7 +18,7 @@ <option value="primer3">Primer3 input</option></param><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -44,10 +44,10 @@ <tests><test> - <param name="input" value="gd.sample.wsf"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/><param name="output_format" value="primer3"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.extract_flanking_dna.txt"/> + <param name="choice" value="0"/> + <output name="output" file="gd.extract_flanking_dna.txt"/></test></tests> --- a/tools/genome_diversity/extract_primers.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/extract_primers.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@ <command interpreter="python2.5"> extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -13,7 +13,7 @@ <inputs><param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -39,9 +39,9 @@ <tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.extract_primers.txt"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="choice" value="0"/> + <output name="output" file="gd.extract_primers.txt"/></test></tests> --- a/tools/genome_diversity/select_restriction_enzymes.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/select_restriction_enzymes.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@ <command interpreter="python2.5"> select_restriction_enzymes.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -14,7 +14,7 @@ <inputs><param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -47,10 +47,10 @@ <tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="override_metadata" value="0"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="choice" value="0"/><param name="enzymes" value="BanI,BstOI,Hsp92II"/> - <output name="output" value="gd.select_restrictionenzymes.wsf"/> + <output name="output" file="gd.select_restriction_enzymes.wsf"/></test></tests> --- a/tools/genome_diversity/select_snps.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/select_snps.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@ <command interpreter="python"> select_snps.py "--input=$input" "--output=$output" "--chrlens_loc=${GALAXY_DATA_INDEX_DIR}/gd.chrlens.loc" "--num_snps=$num_snps" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--species=${input.metadata.species}" #else "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--species=$species" @@ -14,7 +14,7 @@ <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -40,10 +40,10 @@ <tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="num_snps" value="9"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.select_snps.wsf"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="num_snps" value="5"/> + <param name="choice" value="0"/> + <output name="output" file="gd.select_snps.wsf"/></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Show tool search by default. Fixes #575
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/381908d91275/ changeset: 381908d91275 user: jgoecks date: 2011-06-15 19:42:39 summary: Show tool search by default. Fixes #575 affected #: 2 files (2 bytes) --- a/templates/root/index.mako Wed Jun 15 13:22:18 2011 -0400 +++ b/templates/root/index.mako Wed Jun 15 13:42:39 2011 -0400 @@ -144,11 +144,11 @@ ## Search tools menu item. %if trans.app.toolbox_search.enabled: <% - show_tool_search = False + show_tool_search = True if trans.user: - show_tool_search = trans.user.preferences.get( "show_tool_search", "False" ) + show_tool_search = trans.user.preferences.get( "show_tool_search", "False" ) == "True" - if show_tool_search == "True": + if show_tool_search: action = "HIDE_TOOL" else: action = "SHOW_TOOL" --- a/templates/root/tool_menu.mako Wed Jun 15 13:22:18 2011 -0400 +++ b/templates/root/tool_menu.mako Wed Jun 15 13:42:39 2011 -0400 @@ -312,11 +312,11 @@ ## Tool search. <% - show_tool_search = False + show_tool_search = True if trans.user: - show_tool_search = trans.user.preferences.get( "show_tool_search", "False" ) + show_tool_search = trans.user.preferences.get( "show_tool_search", "False" ) == "True" - if show_tool_search == "True": + if show_tool_search: display = "block" else: display = "none" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Improve filtering tool's stdout reporting of lines filtered; fixes #536
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd656a54171b/ changeset: dd656a54171b user: jgoecks date: 2011-06-15 19:22:18 summary: Improve filtering tool's stdout reporting of lines filtered; fixes #536 affected #: 1 file (36 bytes) --- a/tools/stats/filtering.py Wed Jun 15 11:37:21 2011 -0400 +++ b/tools/stats/filtering.py Wed Jun 15 13:22:18 2011 -0400 @@ -130,7 +130,7 @@ valid_lines = total_lines - skipped_lines print 'Filtering with %s, ' % cond_text if valid_lines > 0: - print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines ) + print 'kept %4.2f%% of %d valid lines (%d total lines).' % ( 100.0*lines_kept/valid_lines, valid_lines, total_lines ) else: print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text if invalid_lines: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Do not assume that a library_dataset has a library_dataset_dataset_association when checking to see if a folder is public.
by Bitbucket 15 Jun '11

15 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ffa5a6d8215/ changeset: 0ffa5a6d8215 user: greg date: 2011-06-15 17:37:21 summary: Do not assume that a library_dataset has a library_dataset_dataset_association when checking to see if a folder is public. affected #: 1 file (51 bytes) --- a/lib/galaxy/security/__init__.py Tue Jun 14 16:42:11 2011 -0400 +++ b/lib/galaxy/security/__init__.py Wed Jun 15 11:37:21 2011 -0400 @@ -649,7 +649,8 @@ if not self.folder_is_public( sub_folder ): return False for library_dataset in folder.datasets: - if not self.dataset_is_public( library_dataset.library_dataset_dataset_association.dataset ): + ldda = library_dataset.library_dataset_dataset_association + if ldda and ldda.dataset and not self.dataset_is_public( ldda.dataset ): return False return True def make_folder_public( self, folder ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add Pacific Biosciences tools.
by Bitbucket 14 Jun '11

14 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f6bbb5ee934d/ changeset: f6bbb5ee934d user: greg date: 2011-06-14 22:42:11 summary: Add Pacific Biosciences tools. affected #: 14 files (417 bytes) --- a/tool_conf.xml.sample Tue Jun 14 13:48:17 2011 -0400 +++ b/tool_conf.xml.sample Tue Jun 14 16:42:11 2011 -0400 @@ -433,7 +433,17 @@ <tool file="vcf_tools/filter.xml" /><tool file="vcf_tools/extract.xml" /></section> - + <section name="PacBio/Illumina Assembly" id="hybrid"> + <tool file="ilmn_pacbio/quake.xml"/> + <tool file="ilmn_pacbio/quake_pe.xml"/> + <tool file="ilmn_pacbio/soap_denovo.xml"/> + + <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/> + <tool file="ilmn_pacbio/assembly_stats.xml"/> + </section><!-- TODO: uncomment the following EMBOSS section whenever moving to test, but comment it in .sample to eliminate Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Disk usage: fix up css positioning
by Bitbucket 14 Jun '11

14 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9b05eeb6c7ad/ changeset: 9b05eeb6c7ad user: kanwei date: 2011-06-14 19:48:17 summary: Disk usage: fix up css positioning affected #: 1 file (80 bytes) --- a/templates/root/history.mako Tue Jun 14 13:41:58 2011 -0400 +++ b/templates/root/history.mako Tue Jun 14 13:48:17 2011 -0400 @@ -411,17 +411,17 @@ <div id="history-name-area" class="historyLinks"> - <div id="history-name-container"> + <div id="history-name-container" style="position: relative;"> %if trans.get_user(): - <div id="history-name" class="tooltip editable-text" style="display: inline;" title="Click to rename history">${history.get_display_name() | h}</div> - <div id="history-size" style="display: inline; float: right;">${history.get_disk_size(nice_size=True)}</div> + <div id="history-size" style="position: absolute; top: 3px; right: 0px;">${history.get_disk_size(nice_size=True)}</div> + <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">${history.get_display_name() | h}</div> + %else: - <div id="history-size">${history.get_disk_size(nice_size=True)}</div> + <div id="history-size">${history.get_disk_size(nice_size=True)}</div> %endif - </div> - <div style="clear: both;"></div> - + </div></div> +<div style="clear: both;"></div> %if history.deleted: <div class="warningmessagesmall"> @@ -443,15 +443,15 @@ ## Annotation elt. <div id="history-annotation-area" style="display: none"> - <b>Annotation / Notes:</b> - <div id="history-annotation-container"> - <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> - %if annotation: + <strong>Annotation / Notes:</strong> + <div id="history-annotation-container"> + <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + %if annotation: ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to history</em> %endif - </div> + </div></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add a "disk_usage" column to galaxy_session.
by Bitbucket 14 Jun '11

14 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ecb4c8f7cc6/ changeset: 0ecb4c8f7cc6 user: natefoo date: 2011-06-14 19:41:58 summary: Add a "disk_usage" column to galaxy_session. affected #: 3 files (930 bytes) --- a/lib/galaxy/jobs/__init__.py Tue Jun 14 13:22:12 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Jun 14 13:41:58 2011 -0400 @@ -424,6 +424,7 @@ dataset.blurb = 'tool error' dataset.info = message dataset.set_size() + dataset.dataset.set_total_size() if dataset.ext == 'auto': dataset.extension = 'data' self.sa_session.add( dataset ) --- a/lib/galaxy/model/mapping.py Tue Jun 14 13:22:12 2011 -0400 +++ b/lib/galaxy/model/mapping.py Tue Jun 14 13:41:58 2011 -0400 @@ -475,8 +475,8 @@ Column( "current_history_id", Integer, ForeignKey( "history.id" ), nullable=True ), Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string Column( "is_valid", Boolean, default=False ), - Column( "prev_session_id", Integer ) # saves a reference to the previous session so we have a way to chain them together - ) + Column( "prev_session_id", Integer ), # saves a reference to the previous session so we have a way to chain them together + Column( "disk_usage", Numeric( 15, 0 ), index=True ) ) GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata, Column( "id", Integer, primary_key=True ), --- a/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py Tue Jun 14 13:22:12 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py Tue Jun 14 13:41:58 2011 -0400 @@ -1,6 +1,7 @@ """ Migration script to add 'total_size' column to the dataset table, 'purged' -column to the HDA table, and 'disk_usage' column to the User table. +column to the HDA table, and 'disk_usage' column to the User and GalaxySession +tables. """ from sqlalchemy import * @@ -45,6 +46,15 @@ print "Adding disk_usage column to galaxy_user table failed: %s" % str( e ) log.debug( "Adding disk_usage column to galaxy_user table failed: %s" % str( e ) ) + try: + GalaxySession_table = Table( "galaxy_session", metadata, autoload=True ) + c = Column( 'disk_usage', Numeric( 15, 0 ), index=True ) + c.create( GalaxySession_table ) + assert c is GalaxySession_table.c.disk_usage + except Exception, e: + print "Adding disk_usage column to galaxy_session table failed: %s" % str( e ) + log.debug( "Adding disk_usage column to galaxy_session table failed: %s" % str( e ) ) + def downgrade(): metadata.reflect() try: @@ -67,3 +77,10 @@ except Exception, e: print "Dropping disk_usage column from galaxy_user table failed: %s" % str( e ) log.debug( "Dropping disk_usage column from galaxy_user table failed: %s" % str( e ) ) + + try: + GalaxySession_table = Table( "galaxy_session", metadata, autoload=True ) + GalaxySession_table.c.disk_usage.drop() + except Exception, e: + print "Dropping disk_usage column from galaxy_session table failed: %s" % str( e ) + log.debug( "Dropping disk_usage column from galaxy_session table failed: %s" % str( e ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Sniffers: Fix sniffers not being loaded from datatypes.conf file. Modify VCF sniffer to just check a simple header string.
by Bitbucket 14 Jun '11

14 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d7c529fa8e96/ changeset: d7c529fa8e96 user: kanwei date: 2011-06-14 19:22:12 summary: Sniffers: Fix sniffers not being loaded from datatypes.conf file. Modify VCF sniffer to just check a simple header string. affected #: 3 files (559 bytes) --- a/datatypes_conf.xml.sample Tue Jun 14 13:17:34 2011 -0400 +++ b/datatypes_conf.xml.sample Tue Jun 14 13:22:12 2011 -0400 @@ -280,6 +280,7 @@ defined format first, followed by next-most rigidly defined, and so on. --> + <sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/> @@ -303,7 +304,6 @@ <sniffer type="galaxy.datatypes.tabular:Pileup"/><sniffer type="galaxy.datatypes.interval:Interval"/><sniffer type="galaxy.datatypes.tabular:Sam"/> - <sniffer type="galaxy.datatypes.tabular:Vcf"/><!-- Keep this commented until the sniff method in the assembly.py module is fixed to not read the entire file. --- a/lib/galaxy/datatypes/registry.py Tue Jun 14 13:17:34 2011 -0400 +++ b/lib/galaxy/datatypes/registry.py Tue Jun 14 13:22:12 2011 -0400 @@ -122,32 +122,22 @@ if current_app is None and isinstance( d_type1, type( d_type2 ) ): d_type1.add_display_application( display_app ) # Load datatype sniffers from the config - sniff_order = [] sniffers = root.find( 'sniffers' ) for elem in sniffers.findall( 'sniffer' ): dtype = elem.get( 'type', None ) if dtype: - sniff_order.append( dtype ) - for dtype in sniff_order: - try: - fields = dtype.split( ":" ) - datatype_module = fields[0] - datatype_class = fields[1] - fields = datatype_module.split( "." ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - aclass = getattr( module, datatype_class )() - included = False - for atype in self.sniff_order: - if not issubclass( atype.__class__, aclass.__class__ ) and isinstance( atype, aclass.__class__ ): - included = True - break - if not included: + try: + fields = dtype.split( ":" ) + datatype_module = fields[0] + datatype_class = fields[1] + module = __import__( datatype_module ) + for comp in datatype_module.split('.')[1:]: + module = getattr(module, comp) + aclass = getattr( module, datatype_class )() self.sniff_order.append( aclass ) self.log.debug( 'Loaded sniffer for datatype: %s' % dtype ) - except Exception, exc: - self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) + except Exception, exc: + self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) #default values if len(self.datatypes_by_extension) < 1: self.datatypes_by_extension = { --- a/lib/galaxy/datatypes/tabular.py Tue Jun 14 13:17:34 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Tue Jun 14 13:22:12 2011 -0400 @@ -479,13 +479,8 @@ MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True ) def sniff( self, filename ): - try: - # If reader can read and parse file, it's VCF. - for line in list( galaxy_utils.sequence.vcf.Reader( open( filename ) ) ): - pass - return True - except: - return False + headers = get_headers( filename, '\n', count=1 ) + return headers[0][0].startswith("##fileformat=VCF") def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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