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

[hg] galaxy 2357: Add new migration script that creates missing ...
by Greg Von Kuster 21 Apr '09

21 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5a0100a94b12 changeset: 2357:5a0100a94b12 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Apr 21 10:26:58 2009 -0400 description: Add new migration script that creates missing indexes and default data on galaxy_user and history_dataset_association tables. Fix the change datatype display in the edit_attributes template. Fix the tool config for main. 4 file(s) affected in this change: lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py manage_db.sh templates/dataset/edit_attributes.mako tool_conf.xml.main diffs (191 lines): diff -r db86a8c5e9b0 -r 5a0100a94b12 lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Apr 21 10:26:58 2009 -0400 @@ -0,0 +1,61 @@ +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +User_table = Table( "galaxy_user", metadata, autoload=True ) +HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) + +def boolean_false(): + if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': + return False + elif migrate_engine.name == 'sqlite': + return 0 + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +def upgrade(): + # Load existing tables + metadata.reflect() + # Add 2 indexes to the galaxy_user table + i = Index( 'ix_galaxy_user_deleted', User_table.c.deleted ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_galaxy_user_deleted' to galaxy_user table failed: %s" % ( str( e ) ) ) + i = Index( 'ix_galaxy_user_purged', User_table.c.purged ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_galaxy_user_purged' to galaxy_user table failed: %s" % ( str( e ) ) ) + # Set the default data in the galaxy_user table, but only for null values + cmd = "UPDATE galaxy_user SET deleted = %s WHERE deleted is null" + cmd = cmd % boolean_false() + try: + db_session.execute( cmd ) + except Exception, e: + log.debug( "Setting default data for galaxy_user.deleted column failed: %s" % ( str( e ) ) ) + cmd = "UPDATE galaxy_user SET purged = %s WHERE purged is null" + cmd = cmd % boolean_false() + try: + db_session.execute( cmd ) + except Exception, e: + log.debug( "Setting default data for galaxy_user.purged column failed: %s" % ( str( e ) ) ) + # Add 1 index to the history_dataset_association table + i = Index( 'ix_hda_copied_from_library_dataset_dataset_association_id', HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_hda_copied_from_library_dataset_dataset_association_id' to history_dataset_association table failed: %s" % ( str( e ) ) ) +def downgrade(): + pass diff -r db86a8c5e9b0 -r 5a0100a94b12 manage_db.sh --- a/manage_db.sh Tue Apr 21 10:01:47 2009 -0400 +++ b/manage_db.sh Tue Apr 21 10:26:58 2009 -0400 @@ -1,4 +1,9 @@ #!/bin/sh + +####### +# NOTE: To downgrade to a specific version, use something like: +# sh manage_db.sh downgrade --version=3 +####### cd `dirname $0` python -ES ./scripts/manage_db.py $@ diff -r db86a8c5e9b0 -r 5a0100a94b12 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Tue Apr 21 10:01:47 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Tue Apr 21 10:26:58 2009 -0400 @@ -6,12 +6,11 @@ <%def name="datatype( dataset, datatypes )"> <select name="datatype"> - ## $datatypes.sort() %for ext in datatypes: %if dataset.ext == ext: - <option value="${ext}" selected="yes">${_(ext)}}</option> + <option value="${ext}" selected="yes">${_(ext)}</option> %else: - <option value="${ext}">${_(ext)}}</option> + <option value="${ext}">${_(ext)}</option> %endif %endfor </select> diff -r db86a8c5e9b0 -r 5a0100a94b12 tool_conf.xml.main --- a/tool_conf.xml.main Tue Apr 21 10:01:47 2009 -0400 +++ b/tool_conf.xml.main Tue Apr 21 10:26:58 2009 -0400 @@ -9,14 +9,6 @@ <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> - </section> - <section name="Get ENCODE Data" id="encode"> - <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/> - <tool file="data_source/encode_import_genes_and_transcripts.xml"/> - <tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/> - <tool file="data_source/encode_import_transcription_regulation.xml"/> - <tool file="data_source/encode_import_all_latest_datasets.xml" /> - <tool file="data_source/encode_import_gencode.xml" /> </section> <section name="Send Data" id="send"> <tool file="data_destination/epigraph.xml" /> @@ -42,17 +34,6 @@ <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> </section> - <section name="Filter and Sort" id="filter"> - <tool file="stats/filtering.xml" /> - <tool file="filters/sorter.xml" /> - <tool file="filters/grep.xml" /> - </section> - <section name="Join, Subtract and Group" id="group"> - <tool file="filters/joiner.xml" /> - <tool file="filters/compare.xml"/> - <tool file="new_operations/subtract_query.xml"/> - <tool file="stats/grouping.xml" /> - </section> <section name="Convert Formats" id="convert"> <tool file="filters/bed2gff.xml" /> <tool file="fasta_tools/fasta_to_tabular.xml" /> @@ -68,15 +49,21 @@ <tool file="fasta_tools/fasta_to_tabular.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> </section> + <section name="Filter and Sort" id="filter"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + </section> + <section name="Join, Subtract and Group" id="group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml"/> + <tool file="new_operations/subtract_query.xml"/> + <tool file="stats/grouping.xml" /> + </section> <section name="Extract Features" id="features"> <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> <tool file="extract/extract_GFF_Features.xml" /> </section> -  <section name="Fetch Sequences" id="fetchSeq"> <tool file="extract/extract_genomic_dna.xml" /> </section> @@ -149,12 +136,19 @@ <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> <tool file="hyphy/hyphy_dnds_wrapper.xml" /> </section> - <section name="Taxonomy manipulation" id="tax_manipulation"> + <section name="Metagenomic analyses" id="tax_manipulation"> <tool file="taxonomy/gi2taxonomy.xml" /> <tool file="taxonomy/t2t_report.xml" /> <tool file="taxonomy/t2ps_wrapper.xml" /> <tool file="taxonomy/find_diag_hits.xml" /> + <tool file="taxonomy/lca.xml" /> <tool file="taxonomy/poisson2test.xml" /> + </section> + <section name="Short Read Analysis" id="short_read_analysis"> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> </section> <section name="EMBOSS" id="EMBOSSLite"> <tool file="emboss_5/emboss_antigenic.xml" /> @@ -265,10 +259,4 @@ <tool file="emboss_5/emboss_wordcount.xml" /> <tool file="emboss_5/emboss_wordmatch.xml" /> </section> - <section name="Short Read Analysis" id="short_read_analysis"> - <tool file="metag_tools/short_reads_figure_score.xml" /> - <tool file="metag_tools/short_reads_trim_seq.xml" /> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> - </section> </toolbox>

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[hg] galaxy 2356: Some more adjustremnt for safari and new images
by Greg Von Kuster 21 Apr '09

21 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/db86a8c5e9b0 changeset: 2356:db86a8c5e9b0 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Apr 21 10:01:47 2009 -0400 description: Some more adjustremnt for safari and new images 10 file(s) affected in this change: static/images/qk/quickie1_lrg.png static/images/qk/quickie1_small.png static/images/qk/quickie2_lrg.png static/images/qk/quickie2_small.png static/images/qk/quickie3_lrg.png static/images/qk/quickie3_small.png static/images/qk/quickie4.jpg static/images/qk/quickie4_lrg.png static/images/qk/quickie4_small.png static/welcome.html diffs (76 lines): diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie1_lrg.png Binary file static/images/qk/quickie1_lrg.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie1_small.png Binary file static/images/qk/quickie1_small.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie2_lrg.png Binary file static/images/qk/quickie2_lrg.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie2_small.png Binary file static/images/qk/quickie2_small.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie3_lrg.png Binary file static/images/qk/quickie3_lrg.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie3_small.png Binary file static/images/qk/quickie3_small.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie4.jpg Binary file static/images/qk/quickie4.jpg has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie4_lrg.png Binary file static/images/qk/quickie4_lrg.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/images/qk/quickie4_small.png Binary file static/images/qk/quickie4_small.png has changed diff -r f9cc5deca786 -r db86a8c5e9b0 static/welcome.html --- a/static/welcome.html Tue Apr 21 09:36:42 2009 -0400 +++ b/static/welcome.html Tue Apr 21 10:01:47 2009 -0400 @@ -28,7 +28,6 @@ .previous { width: 100%; overflow: auto; - padding-bottom: 10px; } .previous .quickie { min-width: 150px; @@ -75,7 +74,7 @@ <tr> <td align="center"> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsnew/flow.html',width:640,height:500,scroll:'no'})"> - <img src="images/qk/quickie4.jpg" border="0"> + <img src="images/qk/quickie4_lrg.png" border="0"> <br> </a> @@ -84,33 +83,31 @@ </table> </div> -<h3>Previous Quickies:</h3> +<h3>Previous Quickies</h3> <hr> <div class="previous"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> - <td width="33%" style="border-right: solid white 20px; text-decoration:none;"> + <td width="32%" style="border-right: solid white 10px;"> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie1_small.png" border="0"> </div> </a> </td> - <td width="33%" style="border: solid white 10px;"> + <td width="32%" style="border-left: solid white 5px; border-right: solid white 5px"> <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie2_small.png" border="0"> - </div> </a> </div> </td> - <td width="33%" style="border-left: solid white 20px;" > + <td width="32%" style="border-left: solid white 10px;" > <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie3_small.png" border="0"> - </div> </a> </td>

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[hg] galaxy 2354: Fix for tool parameters - objects should now b...
by Greg Von Kuster 20 Apr '09

20 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/91e55ed1a0bd changeset: 2354:91e55ed1a0bd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Apr 20 18:34:58 2009 -0400 description: Fix for tool parameters - objects should now be correctly tranlsated to strings, and functional tests should now pass. 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (12 lines): diff -r 588b0ebb7451 -r 91e55ed1a0bd lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Apr 20 14:28:08 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Apr 20 18:34:58 2009 -0400 @@ -569,7 +569,7 @@ def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } - return super( SelectToolParameter, self ).value_to_basic( value, app ) + return value def value_from_basic( self, value, app, ignore_errors=False ): if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue": return UnvalidatedValue( value["value"] )

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[hg] galaxy 2350: Fix a bug in workflow sharing
by Nate Coraor 20 Apr '09

20 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f447719533f3 changeset: 2350:f447719533f3 user: James Taylor <james(a)jamestaylor.org> date: Mon Apr 20 13:07:25 2009 -0400 description: Fix a bug in workflow sharing 1 file(s) affected in this change: lib/galaxy/web/controllers/workflow.py diffs (12 lines): diff -r 2f4d3387c589 -r f447719533f3 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Apr 17 13:54:00 2009 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon Apr 20 13:07:25 2009 -0400 @@ -76,7 +76,7 @@ if not other: mtype = "error" msg = ( "User '%s' does not exist" % email ) - if other == trans.get_user(): + elif other == trans.get_user(): mtype = "error" msg = ( "You cannot share a workflow with yourself" ) elif trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \

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[hg] galaxy 2352: Fix bug in DrillDownSelectToolParamter
by Nate Coraor 20 Apr '09

20 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/15743050a944 changeset: 2352:15743050a944 user: James Taylor <james(a)jamestaylor.org> date: Mon Apr 20 13:22:19 2009 -0400 description: Fix bug in DrillDownSelectToolParamter 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (12 lines): diff -r 9c185604c32a -r 15743050a944 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Apr 20 13:14:06 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Apr 20 13:22:19 2009 -0400 @@ -990,7 +990,7 @@ initial_values.append( option['value'] ) recurse_options( initial_values, option['options'] ) # More working around dynamic options for workflow - if self.need_late_validation( trans, other_values ): + if self.need_late_validation( trans, context ): # Really the best we can do? return UnvalidatedValue( None ) initial_values = []

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[hg] galaxy 2351: Remove beta message from workflow views
by Nate Coraor 20 Apr '09

20 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9c185604c32a changeset: 2351:9c185604c32a user: James Taylor <james(a)jamestaylor.org> date: Mon Apr 20 13:14:06 2009 -0400 description: Remove beta message from workflow views 2 file(s) affected in this change: templates/workflow/editor.mako templates/workflow/index.mako diffs (46 lines): diff -r f447719533f3 -r 9c185604c32a templates/workflow/editor.mako --- a/templates/workflow/editor.mako Mon Apr 20 13:07:25 2009 -0400 +++ b/templates/workflow/editor.mako Mon Apr 20 13:14:06 2009 -0400 @@ -3,16 +3,8 @@ <%def name="init()"> <% self.active_view="workflow" - self.message_box_visible=True - self.message_box_class="warning" self.overlay_visible=True %> -</%def> - -<%def name="message_box_content()"> - Workflow support is currently in <b><i>beta</i></b> testing. - Workflows may not work with all tools, may fail unexpectedly, and may - not be compatible with future updates to <b>Galaxy</b>. </%def> <%def name="late_javascripts()"> diff -r f447719533f3 -r 9c185604c32a templates/workflow/index.mako --- a/templates/workflow/index.mako Mon Apr 20 13:07:25 2009 -0400 +++ b/templates/workflow/index.mako Mon Apr 20 13:14:06 2009 -0400 @@ -5,19 +5,12 @@ self.has_left_panel=False self.has_right_panel=False self.active_view="workflow" - self.message_box_visible=True - self.message_box_class="warning" + self.message_box_visible=False %> -</%def> - -<%def name="message_box_content()"> - Workflow support is currently in <b><i>beta</i></b> testing. - Workflows may not work with all tools, may fail unexpectedly, and may - not be compatible with future updates to <b>Galaxy</b>. </%def> <%def name="center_panel()"> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="workflow", action="list" )}"> </iframe> -</%def> \ No newline at end of file +</%def>

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[hg] galaxy 2353: New welcome per james style but with images in...
by Nate Coraor 20 Apr '09

20 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/588b0ebb7451 changeset: 2353:588b0ebb7451 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Mon Apr 20 14:28:08 2009 -0400 description: New welcome per james style but with images instead. Everything is now .flv 6 file(s) affected in this change: static/images/qk/quickie1_small.png static/images/qk/quickie2_small.png static/images/qk/quickie3_small.png static/images/qk/quickie4.jpg static/images/welcomePhoto.jpg static/welcome.html diffs (115 lines): diff -r 15743050a944 -r 588b0ebb7451 static/images/qk/quickie1_small.png Binary file static/images/qk/quickie1_small.png has changed diff -r 15743050a944 -r 588b0ebb7451 static/images/qk/quickie2_small.png Binary file static/images/qk/quickie2_small.png has changed diff -r 15743050a944 -r 588b0ebb7451 static/images/qk/quickie3_small.png Binary file static/images/qk/quickie3_small.png has changed diff -r 15743050a944 -r 588b0ebb7451 static/images/qk/quickie4.jpg Binary file static/images/qk/quickie4.jpg has changed diff -r 15743050a944 -r 588b0ebb7451 static/images/welcomePhoto.jpg Binary file static/images/welcomePhoto.jpg has changed diff -r 15743050a944 -r 588b0ebb7451 static/welcome.html --- a/static/welcome.html Mon Apr 20 13:22:19 2009 -0400 +++ b/static/welcome.html Mon Apr 20 14:28:08 2009 -0400 @@ -13,6 +13,7 @@ } .current-quickie { width: 100%; + background: black; } .quickie .head { font-size: 200%; @@ -35,10 +36,12 @@ .previous .quickie .head { font-size: 120%; padding: 10px 10px; + text-decoration: none; } .previous .quickie .sub { font-size: 100%; padding: 10px 10px; + text-decoration: none; } #screencasts { max-width: 50em; @@ -62,7 +65,7 @@ <div id="screencasts"> <h2>Introducing Galactic Quickies</h2> - +<hr> <p> Galactic quickies are <i>super-short</i> screencasts that are <i>always</i> under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly. </p> @@ -70,13 +73,10 @@ <div class="current-quickie"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> - <td> - - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/min.html',width:640,height:496,scroll:'no'})"> - <div class="quickie"> - <div class="head">A word about interval data</div> - <div class="sub">Galactic quickie #3</div> - </div> + <td align="center"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsnew/flow.html',width:640,height:500,scroll:'no'})"> + <img src="images/qk/quickie4.jpg" border="0"> + <br> </a> </td> @@ -85,27 +85,36 @@ </div> <h3>Previous Quickies:</h3> +<hr> <div class="previous"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> - <td width="50%" style="border-right: solid white 25px;"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/min.html',width:640,height:496,scroll:'no'})"> + <td width="33%" style="border-right: solid white 20px; text-decoration:none;"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> - <div class="head">Sequences as tab data</div> - <div class="sub">Galactic quickie #1</div> + <img src="images/qk/quickie1_small.png" border="0"> </div> </a> </td> - <td width="50%"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/min.html',width:640,height:496,scroll:'no'})"> + <td width="33%" style="border: solid white 10px;"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> <div class="quickie"> - <div class="head">Grouping</div> - <div class="sub">Galactic quickie #2</div> + <img src="images/qk/quickie2_small.png" border="0"> + </div> </a> </div> </td> + <td width="33%" style="border-left: solid white 20px;" > + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie3_small.png" border="0"> + + </div> + </a> + </td> + </tr> </table> </div> @@ -118,7 +127,7 @@ <p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a> and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. +This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. <p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> </div> </div>

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[hg] galaxy 2349: Previous addition of check_newlines to sniff w...
by Nate Coraor 17 Apr '09

17 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2f4d3387c589 changeset: 2349:2f4d3387c589 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 17 13:54:00 2009 -0400 description: Previous addition of check_newlines to sniff was lost at some point. 1 file(s) affected in this change: lib/galaxy/datatypes/sniff.py diffs (26 lines): diff -r 8d63860c3b83 -r 2f4d3387c589 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Thu Apr 16 14:01:10 2009 -0400 +++ b/lib/galaxy/datatypes/sniff.py Fri Apr 17 13:54:00 2009 -0400 @@ -51,6 +51,22 @@ os.write( fd, chunk ) os.close( fd ) return temp_name, is_multi_byte + +def check_newlines( fname, bytes_to_read=52428800 ): + """ + Determines if there are any non-POSIX newlines in the first + number_of_bytes (by default, 50MB) of the file. + """ + CHUNK_SIZE = 2 ** 20 + f = open( fname, 'r' ) + for chunk in f.read( CHUNK_SIZE ): + if f.tell() > bytes_to_read: + break + if chunk.count( '\r' ): + f.close() + return True + f.close() + return False def convert_newlines( fname ): """

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[hg] galaxy 2348: Fix some inexplicable bugs in the security/lib...
by Nate Coraor 16 Apr '09

16 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8d63860c3b83 changeset: 2348:8d63860c3b83 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Apr 16 14:01:10 2009 -0400 description: Fix some inexplicable bugs in the security/libraries migration script. 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0003_security_and_libraries.py diffs (39 lines): diff -r 0dde4843fa48 -r 8d63860c3b83 lib/galaxy/model/migrate/versions/0003_security_and_libraries.py --- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Wed Apr 15 15:46:12 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Thu Apr 16 14:01:10 2009 -0400 @@ -46,7 +46,7 @@ def localtimestamp(): if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': - return "LOCALTIMESTAMP %s" + return "LOCALTIMESTAMP" elif migrate_engine.name == 'sqlite': return "current_date || ' ' || current_time" else: @@ -477,7 +477,7 @@ "email AS name," + \ "email AS description," + \ "'private' As type," + \ - "%d AS deleted " + \ + "%s AS deleted " + \ "FROM galaxy_user " + \ "ORDER BY id;" cmd = cmd % ( nextval('role'), localtimestamp(), localtimestamp(), boolean_false() ) @@ -523,7 +523,7 @@ "user_role_association.role_id AS role_id " + \ "FROM history " + \ "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ - "WHERE history.purged = %d AND history.user_id IS NOT NULL;" + "WHERE history.purged = %s AND history.user_id IS NOT NULL;" cmd = cmd % ( nextval('default_history_permissions'), boolean_false() ) db_session.execute( cmd ) # Create "manage permissions" dataset_permissions for all activate-able datasets @@ -539,7 +539,7 @@ "JOIN history_dataset_association ON history_dataset_association.history_id = history.id " + \ "JOIN dataset ON history_dataset_association.dataset_id = dataset.id " + \ "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ - "WHERE dataset.purged = %d AND history.user_id IS NOT NULL;" + "WHERE dataset.purged = %s AND history.user_id IS NOT NULL;" cmd = cmd % ( nextval('dataset_permissions'), localtimestamp(), localtimestamp(), boolean_false() ) db_session.execute( cmd )

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Error while submitting a job to sge queue
by Akash Mohan 15 Apr '09

15 Apr '09

Hi All, I have encountered this strange problem while submitting a job to an sge queue. I have used the unified method wherein the galaxy setup is made available on NFS. I have mounted the galaxy directory on the execution host. As I submit a job through the web ui I could trace that the job does get submitted to the queue. But however it fails with an error as below: galaxy.jobs.runners.sge DEBUG 2009-04-14 08:36:09,252 (15/15) state change: job finished, but failed galaxy.jobs ERROR 2009-04-14 08:36:09,493 Unable to cleanup job 15 Traceback (most recent call last): File "/usr/galaxy/galaxy-6c555b0460f1/lib/galaxy/jobs/__init__.py", line 523, in cleanup shutil.rmtree( self.working_directory ) File "/usr/local/lib/python2.5/shutil.py", line 167, in rmtree onerror(os.listdir, path, sys.exc_info()) File "/usr/local/lib/python2.5/shutil.py", line 165, in rmtree names = os.listdir(path) OSError: [Errno 2] No such file or directory: './database/job_working_directory/15' Where could error be. Kindly let me know if anybody has faced error before. Thanks a ton Akash DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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