- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba001f4c0326/ Changeset: ba001f4c0326 Branch: stable User: davebgx Date: 2014-02-19 21:23:45 Summary: Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script. Affected #: 9 files diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -186,8 +186,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter: + if file_path in tool_configs_to_filter: root.remove( elem ) persist_required = True elif elem.tag == 'section': @@ -196,8 +195,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: + if file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -221,8 +219,7 @@ if proprietary_tool_panel_elem.tag == 'tool': # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -233,8 +230,7 @@ if section_elem.tag == 'tool': # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -312,8 +308,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -322,8 +317,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) @@ -361,10 +355,8 @@ for tool_panel_dict in v: # Keep track of tool config file names associated with entries that have been made to the # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs. - tool_config_file = tool_panel_dict.get( 'tool_config', None ) - if tool_config_file: - if tool_config_file not in tool_configs_to_filter: - tool_configs_to_filter.append( tool_config_file ) + if tool_config not in tool_configs_to_filter: + tool_configs_to_filter.append( tool_config ) else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -2,112 +2,112 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"> - <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> - <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /> - <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" /> - <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_biosed.xml" /> - <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_btwisted.xml" /> - <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_cai_custom.xml" /> - <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_cai.xml" /> - <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_chaos.xml" /> - <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_charge.xml" /> - <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_checktrans.xml" /> - <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_chips.xml" /> - <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_cirdna.xml" /> - <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_codcmp.xml" /> - <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_coderet.xml" /> - <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_compseq.xml" /> - <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_cpgplot.xml" /> - <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_cpgreport.xml" /> - <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_cusp.xml" /> - <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_cutseq.xml" /> - <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_dan.xml" /> - <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_degapseq.xml" /> - <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_descseq.xml" /> - <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_diffseq.xml" /> - <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_digest.xml" /> - <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_dotmatcher.xml" /> - <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_dotpath.xml" /> - <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_dottup.xml" /> - <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_dreg.xml" /> - <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_einverted.xml" /> - <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_epestfind.xml" /> - <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_equicktandem.xml" /> - <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_est2genome.xml" /> - <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_etandem.xml" /> - <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_extractfeat.xml" /> - <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_extractseq.xml" /> - <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_freak.xml" /> - <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_fuzznuc.xml" /> - <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_fuzzpro.xml" /> - <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_fuzztran.xml" /> - <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_garnier.xml" /> - <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_geecee.xml" /> - <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_getorf.xml" /> - <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_helixturnhelix.xml" /> - <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_hmoment.xml" /> - <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_iep.xml" /> - <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_infoseq.xml" /> - <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_isochore.xml" /> - <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_lindna.xml" /> - <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_marscan.xml" /> - <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_maskfeat.xml" /> - <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_maskseq.xml" /> - <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_matcher.xml" /> - <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_megamerger.xml" /> - <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_merger.xml" /> - <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_msbar.xml" /> - <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_needle.xml" /> - <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_newcpgreport.xml" /> - <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_newcpgseek.xml" /> - <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_newseq.xml" /> - <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_noreturn.xml" /> - <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_notseq.xml" /> - <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_nthseq.xml" /> - <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_octanol.xml" /> - <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_oddcomp.xml" /> - <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_palindrome.xml" /> - <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_pasteseq.xml" /> - <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_patmatdb.xml" /> - <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_pepcoil.xml" /> - <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_pepinfo.xml" /> - <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_pepnet.xml" /> - <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_pepstats.xml" /> - <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_pepwheel.xml" /> - <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_pepwindow.xml" /> - <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_pepwindowall.xml" /> - <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_plotcon.xml" /> - <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_plotorf.xml" /> - <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_polydot.xml" /> - <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_preg.xml" /> - <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_prettyplot.xml" /> - <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_prettyseq.xml" /> - <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_primersearch.xml" /> - <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_revseq.xml" /> - <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_seqmatchall.xml" /> - <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_seqret.xml" /> - <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_showfeat.xml" /> - <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_shuffleseq.xml" /> - <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_sigcleave.xml" /> - <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_sirna.xml" /> - <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_sixpack.xml" /> - <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_skipseq.xml" /> - <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_splitter.xml" /> - <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_supermatcher.xml" /> - <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_syco.xml" /> - <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_tcode.xml" /> - <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_textsearch.xml" /> - <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_tmap.xml" /> - <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_tranalign.xml" /> - <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_transeq.xml" /> - <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_trimest.xml" /> - <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_trimseq.xml" /> - <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_twofeat.xml" /> - <tool id="EMBOSS: union105" version="5.0.0" file="emboss_union.xml" /> - <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_vectorstrip.xml" /> - <tool id="EMBOSS: water107" version="5.0.0" file="emboss_water.xml" /> - <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_wobble.xml" /> - <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_wordcount.xml" /> - <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_wordmatch.xml" /> + <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_5/emboss_antigenic.xml" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_5/emboss_backtranseq.xml" /> + <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_5/emboss_banana.xml" /> + <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_5/emboss_biosed.xml" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_5/emboss_btwisted.xml" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_5/emboss_cai_custom.xml" /> + <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_5/emboss_cai.xml" /> + <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_5/emboss_chaos.xml" /> + <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_5/emboss_charge.xml" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_5/emboss_checktrans.xml" /> + <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_5/emboss_chips.xml" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_5/emboss_cirdna.xml" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_5/emboss_codcmp.xml" /> + <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_5/emboss_coderet.xml" /> + <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_5/emboss_compseq.xml" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_5/emboss_cpgplot.xml" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_5/emboss_cpgreport.xml" /> + <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_5/emboss_cusp.xml" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_5/emboss_cutseq.xml" /> + <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_5/emboss_dan.xml" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_5/emboss_degapseq.xml" /> + <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_5/emboss_descseq.xml" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_5/emboss_diffseq.xml" /> + <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_5/emboss_digest.xml" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_5/emboss_dotmatcher.xml" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_5/emboss_dotpath.xml" /> + <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_5/emboss_dottup.xml" /> + <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_5/emboss_dreg.xml" /> + <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_5/emboss_einverted.xml" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_5/emboss_epestfind.xml" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_5/emboss_equicktandem.xml" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_5/emboss_est2genome.xml" /> + <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_5/emboss_etandem.xml" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_5/emboss_extractfeat.xml" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_5/emboss_extractseq.xml" /> + <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_5/emboss_freak.xml" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_5/emboss_fuzznuc.xml" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_5/emboss_fuzzpro.xml" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_5/emboss_fuzztran.xml" /> + <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_5/emboss_garnier.xml" /> + <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_5/emboss_geecee.xml" /> + <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_5/emboss_getorf.xml" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_5/emboss_helixturnhelix.xml" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_5/emboss_hmoment.xml" /> + <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_5/emboss_iep.xml" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_5/emboss_infoseq.xml" /> + <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_5/emboss_isochore.xml" /> + <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_5/emboss_lindna.xml" /> + <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_5/emboss_marscan.xml" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_5/emboss_maskfeat.xml" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_5/emboss_maskseq.xml" /> + <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_5/emboss_matcher.xml" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_5/emboss_megamerger.xml" /> + <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_5/emboss_merger.xml" /> + <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_5/emboss_msbar.xml" /> + <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_5/emboss_needle.xml" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_5/emboss_newcpgreport.xml" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_5/emboss_newcpgseek.xml" /> + <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_5/emboss_newseq.xml" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_5/emboss_noreturn.xml" /> + <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_5/emboss_notseq.xml" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_5/emboss_nthseq.xml" /> + <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_5/emboss_octanol.xml" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_5/emboss_oddcomp.xml" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_5/emboss_palindrome.xml" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_5/emboss_pasteseq.xml" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_5/emboss_patmatdb.xml" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_5/emboss_pepcoil.xml" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_5/emboss_pepinfo.xml" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_5/emboss_pepnet.xml" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_5/emboss_pepstats.xml" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_5/emboss_pepwheel.xml" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_5/emboss_pepwindow.xml" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_5/emboss_pepwindowall.xml" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_5/emboss_plotcon.xml" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_5/emboss_plotorf.xml" /> + <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_5/emboss_polydot.xml" /> + <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_5/emboss_preg.xml" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_5/emboss_prettyplot.xml" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_5/emboss_prettyseq.xml" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_5/emboss_primersearch.xml" /> + <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_5/emboss_revseq.xml" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_5/emboss_seqmatchall.xml" /> + <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_5/emboss_seqret.xml" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_5/emboss_showfeat.xml" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_5/emboss_shuffleseq.xml" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_5/emboss_sigcleave.xml" /> + <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_5/emboss_sirna.xml" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_5/emboss_sixpack.xml" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_5/emboss_skipseq.xml" /> + <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_5/emboss_splitter.xml" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_5/emboss_supermatcher.xml" /> + <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_5/emboss_syco.xml" /> + <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_5/emboss_tcode.xml" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_5/emboss_textsearch.xml" /> + <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_5/emboss_tmap.xml" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_5/emboss_tranalign.xml" /> + <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_5/emboss_transeq.xml" /> + <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_5/emboss_trimest.xml" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_5/emboss_trimseq.xml" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_5/emboss_twofeat.xml" /> + <tool id="EMBOSS: union105" version="5.0.0" file="emboss_5/emboss_union.xml" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_5/emboss_vectorstrip.xml" /> + <tool id="EMBOSS: water107" version="5.0.0" file="emboss_5/emboss_water.xml" /> + <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_5/emboss_wobble.xml" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_5/emboss_wordcount.xml" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_5/emboss_wordmatch.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"> - <tool id="freebayes" version="0.0.2 " file="freebayes.xml" /> + <tool id="freebayes" version="0.0.2 " file="variant_detection/freebayes.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0004_tools.xml --- a/scripts/migrate_tools/0004_tools.xml +++ b/scripts/migrate_tools/0004_tools.xml @@ -2,11 +2,11 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" /><repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1"> - <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/> - <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/> - <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/> - <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/> - <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/> - <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/> + <tool id="blastxml_to_tabular" version="0.0.8" file="ncbi_blast_plus/blastxml_to_tabular.xml"/> + <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastn_wrapper.xml"/> + <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastp_wrapper.xml"/> + <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastx_wrapper.xml"/> + <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml"/> + <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml"/></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0005_tools.xml --- a/scripts/migrate_tools/0005_tools.xml +++ b/scripts/migrate_tools/0005_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bwa_wrappers" description="Galaxy wrappers for the BWA short read aligner." changeset_revision="ffa8aaa14f7c"> - <tool id="bwa_wrapper" version="1.2.3" file="bwa_wrapper.xml"/> - <tool id="bwa_color_wrapper" version="1.0.2" file="bwa_color_wrapper.xml"/> + <tool id="bwa_wrapper" version="1.2.3" file="sr_mapping/bwa_wrapper.xml"/> + <tool id="bwa_color_wrapper" version="1.0.2" file="sr_mapping/bwa_color_wrapper.xml"/></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0006_tools.xml --- a/scripts/migrate_tools/0006_tools.xml +++ b/scripts/migrate_tools/0006_tools.xml @@ -1,18 +1,18 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="picard" description="Galaxy wrappers for the Picard SAM/BAM manipulation tools." changeset_revision="e0232cbac965"> - <tool id="picard_FastqToSam" version="1.56.0" file="picard_FastqToSam.xml" /> - <tool id="picard_SamToFastq" version="1.56.1" file="picard_SamToFastq.xml" /> - <tool id="picard_BamIndexStats" version="1.56.0" file="picard_BamIndexStats.xml" /> - <tool id="PicardASMetrics" version="1.56.0" file="rgPicardASMetrics.xml" /> - <tool id="PicardGCBiasMetrics" version="1.56.0" file="rgPicardGCBiasMetrics.xml" /> - <tool id="rgEstLibComp" version="1.56.0" file="rgPicardLibComplexity.xml" /> - <tool id="PicardInsertSize" version="1.56.0" file="rgPicardInsertSize.xml" /> - <tool id="PicardHsMetrics" version="1.56.0" file="rgPicardHsMetrics.xml" /> - <tool id="picard_ARRG" version="1.56.0" file="picard_AddOrReplaceReadGroups.xml" /> - <tool id="picard_ReorderSam" version="1.56.0" file="picard_ReorderSam.xml" /> - <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard_ReplaceSamHeader.xml" /> - <tool id="rgPicFixMate" version="1.56.0" file="rgPicardFixMate.xml" /> - <tool id="rgPicardMarkDups" version="1.56.0" file="rgPicardMarkDups.xml" /> + <tool id="picard_FastqToSam" version="1.56.0" file="picard/picard_FastqToSam.xml" /> + <tool id="picard_SamToFastq" version="1.56.1" file="picard/picard_SamToFastq.xml" /> + <tool id="picard_BamIndexStats" version="1.56.0" file="picard/picard_BamIndexStats.xml" /> + <tool id="PicardASMetrics" version="1.56.0" file="picard/rgPicardASMetrics.xml" /> + <tool id="PicardGCBiasMetrics" version="1.56.0" file="picard/rgPicardGCBiasMetrics.xml" /> + <tool id="rgEstLibComp" version="1.56.0" file="picard/rgPicardLibComplexity.xml" /> + <tool id="PicardInsertSize" version="1.56.0" file="picard/rgPicardInsertSize.xml" /> + <tool id="PicardHsMetrics" version="1.56.0" file="picard/rgPicardHsMetrics.xml" /> + <tool id="picard_ARRG" version="1.56.0" file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool id="picard_ReorderSam" version="1.56.0" file="picard/picard_ReorderSam.xml" /> + <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard/picard_ReplaceSamHeader.xml" /> + <tool id="rgPicFixMate" version="1.56.0" file="picard/rgPicardFixMate.xml" /> + <tool id="rgPicardMarkDups" version="1.56.0" file="picard/rgPicardMarkDups.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0007_tools.xml --- a/scripts/migrate_tools/0007_tools.xml +++ b/scripts/migrate_tools/0007_tools.xml @@ -1,15 +1,15 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bowtie_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools." changeset_revision="0c7e4eadfb3c"> - <tool id="bowtie_wrapper" version="1.1.2" file="bowtie_wrapper.xml" /> + <tool id="bowtie_wrapper" version="1.1.2" file="sr_mapping/bowtie_wrapper.xml" /></repository><repository name="bowtie_color_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools on color space reads" changeset_revision="fd0914e451c5"> - <tool id="bowtie_color_wrapper" version="1.1.2" file="bowtie_color_wrapper.xml" /> + <tool id="bowtie_color_wrapper" version="1.1.2" file="sr_mapping/bowtie_color_wrapper.xml" /></repository><repository name="lastz" description="Galaxy wrappers for the Lastz alignment tool" changeset_revision="0801f8207d30"> - <tool id="lastz_wrapper_2" version="1.1.2" file="lastz_wrapper.xml" /> + <tool id="lastz_wrapper_2" version="1.1.2" file="sr_mapping/lastz_wrapper.xml" /></repository><repository name="lastz_paired_reads" description="Galaxy wrapper for the Lastz alignment tool on paired reads" changeset_revision="96825cee5c25"> - <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="lastz_paired_reads_wrapper.xml" /> + <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="sr_mapping/lastz_paired_reads_wrapper.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -1,147 +1,147 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="dc20f447c0e2" name="bam_to_sam" description="Galaxy wrappers for the tool BAM-to-SAM: converts BAM format to SAM format"> - <tool id="bam_to_sam" version="1.0.3" file="bam_to_sam.xml" /> + <tool id="bam_to_sam" version="1.0.3" file="samtools/bam_to_sam.xml" /></repository><repository owner="devteam" changeset_revision="586c1f0e1515" name="categorize_elements_satisfying_criteria" description="Galaxy wrappers for the tool Categorize Elements: satisfying criteria"> - <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="categorize_elements_satisfying_criteria.xml" /> + <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="regVariation/categorize_elements_satisfying_criteria.xml" /></repository><repository owner="devteam" changeset_revision="acc3dc5d26e3" name="compute_motif_frequencies_for_all_motifs" description="Galaxy wrappers for the tool Compute Motif Frequencies For All Motifs: motif by motif"> - <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="compute_motif_frequencies_for_all_motifs.xml" /> + <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /></repository><repository owner="devteam" changeset_revision="46325357b948" name="compute_motifs_frequency" description="Galaxy wrappers for the tool Compute Motif Frequencies: in indel flanking regions"> - <tool id="compute_motifs_frequency" version="1.0.0" file="compute_motifs_frequency.xml" /> + <tool id="compute_motifs_frequency" version="1.0.0" file="regVariation/compute_motifs_frequency.xml" /></repository><repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"> - <tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /> + <tool id="ctdBatch_1" version="1.0.0" file="phenotype_association/ctd.xml" /></repository><repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> - <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + <tool id="cuffcompare" version="0.0.5" file="ngs_rna/cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> - <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + <tool id="cuffdiff" version="0.0.6" file="ngs_rna/cuffdiff_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> - <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + <tool id="cufflinks" version="0.0.6" file="ngs_rna/cufflinks_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> - <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + <tool id="cuffmerge" version="0.0.5" file="ngs_rna/cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> - <tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /> + <tool id="delete_overlapping_indels" version="1.0.0" file="regVariation/delete_overlapping_indels.xml" /></repository><repository owner="devteam" changeset_revision="de839553d2a2" name="divide_pg_snp" description="Galaxy wrappers for the tool Separate pgSnp alleles: into columns"> - <tool id="dividePgSnp" version="1.0.0" file="dividePgSnpAlleles.xml" /> + <tool id="dividePgSnp" version="1.0.0" file="phenotype_association/dividePgSnpAlleles.xml" /></repository><repository owner="devteam" changeset_revision="063ecbe59faf" name="draw_stacked_barplots" description="Galaxy wrappers for the tool Draw Stacked Bar Plots: for different categories and different criteria"> - <tool id="draw_stacked_barplots" version="1.0.0" file="draw_stacked_barplots.xml" /> + <tool id="draw_stacked_barplots" version="1.0.0" file="regVariation/draw_stacked_barplots.xml" /></repository><repository owner="devteam" changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" description="Galaxy wrappers for the tool Length Distribution chart"> - <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fasta_clipping_histogram.xml" /> + <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fastx_toolkit/fasta_clipping_histogram.xml" /></repository><repository owner="devteam" changeset_revision="8f0ae92440b8" name="fasta_formatter" description="Galaxy wrappers for the tool FASTA Width: formatter"> - <tool id="cshl_fasta_formatter" version="1.0.0" file="fasta_formatter.xml" /> + <tool id="cshl_fasta_formatter" version="1.0.0" file="fastx_toolkit/fasta_formatter.xml" /></repository><repository owner="devteam" changeset_revision="4b41e3076a50" name="fasta_nucleotide_changer" description="Galaxy wrappers for the tool RNA/DNA: converter"> - <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fasta_nucleotide_changer.xml" /> + <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fastx_toolkit/fasta_nucleotide_changer.xml" /></repository><repository owner="devteam" changeset_revision="e359ce20fbd9" name="fastq_quality_boxplot" description="Galaxy wrappers for the tool Draw quality score boxplot"> - <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastq_quality_boxplot.xml" /> + <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastx_toolkit/fastq_quality_boxplot.xml" /></repository><repository owner="devteam" changeset_revision="b87c74b61d81" name="fastq_quality_converter" description="Galaxy wrappers for the tool Quality format converter: (ASCII-Numeric)"> - <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastq_quality_converter.xml" /> + <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastx_toolkit/fastq_quality_converter.xml" /></repository><repository owner="devteam" changeset_revision="b145b9b26648" name="fastq_quality_filter" description="Galaxy wrappers for the Filter by quality tool."> - <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastq_quality_filter.xml" /> + <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastx_toolkit/fastq_quality_filter.xml" /></repository><repository owner="devteam" changeset_revision="04614cf6ed39" name="fastq_to_fasta" description="Galaxy wrappers for the tool FASTQ to FASTA: converter"> - <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastq_to_fasta.xml" /> + <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastx_toolkit/fastq_to_fasta.xml" /></repository><repository owner="devteam" changeset_revision="7f9660a246c0" name="fastx_artifacts_filter" description="Galaxy wrappers for the Remove sequencing artifacts tool."> - <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_artifacts_filter.xml" /> + <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_toolkit/fastx_artifacts_filter.xml" /></repository><repository owner="devteam" changeset_revision="a12850d0559b" name="fastx_barcode_splitter" description="Galaxy wrappers for the Barcode Splitter tool."> - <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_barcode_splitter.xml" /> + <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_toolkit/fastx_barcode_splitter.xml" /></repository><repository owner="devteam" changeset_revision="2fe2d2b9e8e4" name="fastx_clipper" description="Galaxy wrappers for the tool Clip: adapter sequences"> - <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_clipper.xml" /> + <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_toolkit/fastx_clipper.xml" /></repository><repository owner="devteam" changeset_revision="e942fd3a76a5" name="fastx_collapser" description="Galaxy wrappers for the tool Collapse: sequences"> - <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_collapser.xml" /> + <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_toolkit/fastx_collapser.xml" /></repository><repository owner="devteam" changeset_revision="bcc5424a4a3c" name="fastx_nucleotides_distribution" description="Galaxy wrappers for the Draw nucleotides distribution chart tool."> - <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_nucleotides_distribution.xml" /> + <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" 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file="fastx_reverse_complement.xml" /> + <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_toolkit/fastx_reverse_complement.xml" /></repository><repository owner="devteam" changeset_revision="9cb372481a71" name="fastx_trimmer" description="Galaxy wrappers for the Trim sequences tool."> - <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_trimmer.xml" /> + <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_toolkit/fastx_trimmer.xml" /></repository><repository owner="devteam" changeset_revision="64133669255f" name="hgv_fundo" description="Galaxy wrappers for the tool FunDO: human genes associated with disease terms"> - <tool id="hgv_funDo" version="1.0.0" file="funDo.xml" /> + <tool id="hgv_funDo" version="1.0.0" file="phenotype_association/funDo.xml" /></repository><repository owner="devteam" changeset_revision="0e80ffa5b7f7" name="hgv_hilbertvis" description="Galaxy wrappers for the tool HVIS: visualization of genomic data with the Hilbert curve"> - 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tool."> - <tool id="t_test_two_samples" version="1.0.0" file="t_test_two_samples.xml" /> + <tool id="t_test_two_samples" version="1.0.0" file="regVariation/t_test_two_samples.xml" /></repository><repository owner="devteam" changeset_revision="acf952549b53" name="xy_plot" description="Galaxy wrappers for the tool Plotting tool: for multiple series and graph types"> - <tool id="XY_Plot_1" version="1.0.1" file="xy_plot.xml" /> + <tool id="XY_Plot_1" version="1.0.1" file="plotting/xy_plot.xml" /></repository></toolshed> \ No newline at end of file diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0009_tools.xml --- a/scripts/migrate_tools/0009_tools.xml +++ b/scripts/migrate_tools/0009_tools.xml @@ -1,132 +1,132 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> - <tool id="bowtie2" version="0.2" 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description="GMAJ Multiple Alignment Viewer"> - <tool id="gmaj_1" version="2.0.1" file="GMAJ.xml" /> + <tool id="gmaj_1" version="2.0.1" file="visualization/GMAJ.xml" /></repository><repository owner="devteam" changeset_revision="33e8ed5a4601" name="lca_wrapper" description="Find lowest diagnostic rank"> - <tool id="lca1" version="1.0.1" file="lca.xml" /> + <tool id="lca1" version="1.0.1" file="taxonomy/lca.xml" /></repository><repository owner="devteam" changeset_revision="ae2ec275332a" name="macs" description="Model-based Analysis of ChIP-Seq"> - <tool id="peakcalling_macs" version="1.0.1" file="macs_wrapper.xml" /> + <tool id="peakcalling_macs" version="1.0.1" file="peak_calling/macs_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="8cd5945559b8" name="poisson2test" description="Poisson two-sample test"> - <tool id="poisson2test" version="1.0.0" file="poisson2test.xml" /> + <tool id="poisson2test" version="1.0.0" file="taxonomy/poisson2test.xml" /></repository><repository owner="devteam" changeset_revision="82a8234e03f2" name="sicer" description="Statistical approach for the Identification of ChIP-Enriched Regions"> - <tool id="peakcalling_sicer" version="0.0.1" file="sicer_wrapper.xml" /> + <tool id="peakcalling_sicer" version="0.0.1" file="peak_calling/sicer_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="9e2b9ca7f33a" name="t2ps" description="Draw phylogeny"> - <tool id="Draw_phylogram" version="1.0.0" file="t2ps_wrapper.xml" /> + <tool id="Draw_phylogram" version="1.0.0" file="taxonomy/t2ps_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="592acb9505fc" name="t2t_report" description="Summarize taxonomy"> - <tool id="t2t_report" version="1.0.0" file="t2t_report.xml" /> + <tool id="t2t_report" version="1.0.0" file="taxonomy/t2t_report.xml" /></repository><repository owner="devteam" changeset_revision="b334cd1095ea" name="tabular_to_fastq" description="Tabular to FASTQ converter"> - <tool id="tabular_to_fastq" version="1.0.0" file="tabular_to_fastq.xml" /> + <tool id="tabular_to_fastq" version="1.0.0" file="fastq/tabular_to_fastq.xml" /></repository><repository owner="devteam" changeset_revision="1030acbecce6" name="tophat" description="Find splice junctions using RNA-seq data"> - <tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" /> + <tool id="tophat" version="1.5.0" file="ngs_rna/tophat_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="ffa30bedbee3" name="tophat2" description="Gapped-read mapper for RNA-seq data"> - <tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" /> + <tool id="tophat2" version="0.6" file="ngs_rna/tophat2_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b001b50f2009" name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)"> - <tool id="vcf_annotate" version="1.0.0" file="annotate.xml" /> + <tool id="vcf_annotate" version="1.0.0" file="vcf_tools/annotate.xml" /></repository><repository owner="devteam" changeset_revision="76ad0b7865b9" name="vcf_extract" description="Extract reads from a specified region"> - <tool id="vcf_extract" version="1.0.0" file="extract.xml" /> + <tool id="vcf_extract" version="1.0.0" file="vcf_tools/extract.xml" /></repository><repository owner="devteam" changeset_revision="da1a6f33b504" name="vcf_filter" description="Filter a VCF file"> - <tool id="vcf_filter" version="1.0.0" file="filter.xml" /> + <tool id="vcf_filter" version="1.0.0" file="vcf_tools/filter.xml" /></repository><repository owner="devteam" changeset_revision="9d162bde4113" name="vcf_intersect" description="Generate the intersection of two VCF files"><tool id="vcf_intersect" version="1.0.0" file="vcf_tools/intersect.xml" /></repository><repository owner="devteam" changeset_revision="66253fc0a69b" name="weblogo3" description="Sequence Logo generator for fasta (eg Clustal alignments)"> - <tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" /> + <tool id="rgweblogo3" version="0.4" file="rgenetics/rgWebLogo3.xml" /></repository></toolshed> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/d20888b2d96c/ Changeset: d20888b2d96c Branch: stable User: davebgx Date: 2014-02-21 00:01:05 Summary: Fix path for bowtie2. Affected #: 1 file diff -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 -r d20888b2d96c8a021871a4252b5cc74e09578f07 scripts/migrate_tools/0009_tools.xml --- a/scripts/migrate_tools/0009_tools.xml +++ b/scripts/migrate_tools/0009_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> - <tool id="bowtie2" version="0.2" file="ngs_rna/bowtie2_wrapper.xml" /> + <tool id="bowtie2" version="0.2" file="sr_mapping/bowtie2_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="a0c8dc671a23" name="ccat" description="Control-based ChIP-seq Analysis Tool"><tool id="peakcalling_ccat" version="0.0.1" file="peak_calling/ccat_wrapper.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/6f9d716d0009/ Changeset: 6f9d716d0009 User: davebgx Date: 2014-02-21 18:38:04 Summary: Merge stable. Affected #: 0 files 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.

1 0

commit/galaxy-central: martenson: data libraries: ui improvements, sorting, bugfix
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ab1e13eab15/ Changeset: 3ab1e13eab15 User: martenson Date: 2014-02-21 17:26:52 Summary: data libraries: ui improvements, sorting, bugfix Affected #: 6 files diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -95,7 +95,6 @@ time_created = '' # Go through every item in the folder and include its meta-data. for content_item in self.load_folder_contents( trans, folder ): -# rval = content_item.to_dict() return_item = {} encoded_id = trans.security.encode_id( content_item.id ) time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) @@ -104,7 +103,6 @@ # For folder return also hierarchy values if content_item.api_type == 'folder': encoded_id = 'F' + encoded_id -# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) return_item.update ( dict ( item_count = content_item.item_count ) ) if content_item.api_type == 'file': diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -21,44 +21,50 @@ // LIBRARY var Library = Backbone.Model.extend({ urlRoot: '/api/libraries' - }); + }); // FOLDER AS MODEL var FolderAsModel = Backbone.Model.extend({ urlRoot: '/api/folders' - }); + }); // LIBRARIES var Libraries = Backbone.Collection.extend({ url: '/api/libraries', - model: Library - }); + + model: Library, + + sort_key: 'name', // default + + sort_order: null, // default + + }); // ITEM var Item = Backbone.Model.extend({ urlRoot : '/api/libraries/datasets' - }) + }); // FOLDER AS COLLECTION var Folder = Backbone.Collection.extend({ model: Item - }) + }); // CONTAINER for folder contents (folders, items and metadata). var FolderContainer = Backbone.Model.extend({ - defaults : { - folder : new Folder(), - full_path : "unknown", - urlRoot : "/api/folders/", - id : "unknown" - }, + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, parse : function(obj) { this.full_path = obj[0].full_path; // update the inner collection this.get("folder").reset(obj[1].folder_contents); return obj; } - }) + }); // HISTORY ITEM var HistoryItem = Backbone.Model.extend({ @@ -76,16 +82,6 @@ model : GalaxyHistory }); - //ROUTER - var LibraryRouter = Backbone.Router.extend({ - routes: { - "" : "libraries", - "folders/:id" : "folder_content", - "folders/:folder_id/download/:format" : "download" - } - }); - - // MMMMMMMMMMMMMM // === VIEWS ==== // MMMMMMMMMMMMMM @@ -121,15 +117,15 @@ var tmpl_array = []; // CONTAINER - tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); - // tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); - tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); - tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); @@ -142,19 +138,20 @@ tmpl_array.push('</div>'); // BREADCRUMBS - tmpl_array.push('<div class="library_breadcrumb">'); - tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); - tmpl_array.push('<% _.each(path, function(path_item) { %>'); - tmpl_array.push('<% if (path_item[0] != id) { %>'); - tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); - tmpl_array.push('<% } else { %>'); - tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); - tmpl_array.push('<% } %>'); - tmpl_array.push('<% }); %>'); - tmpl_array.push('</div>'); + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(path, function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); + // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="table table-condensed">'); + tmpl_array.push('<table id="folder_table" class="library_table table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); @@ -164,8 +161,7 @@ tmpl_array.push(' <th>date (UTC)</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); - tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' ..</td>'); + tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); @@ -173,29 +169,34 @@ tmpl_array.push(' <td></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder - tmpl_array.push(' <td>'); - tmpl_array.push(' <span class="fa fa-folder-open"></span></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td><%- content_item.get("name") %>'); - tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder - tmpl_array.push(' <span class="muted">(empty folder)</span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td>folder</td>'); - tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <span class="fa fa-file"></span>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset - tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type - tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size - tmpl_array.push(' <% } %> '); - tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated - tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %> '); tmpl_array.push(' <% }); %>'); tmpl_array.push(' '); tmpl_array.push(' </tbody>'); @@ -207,7 +208,7 @@ templateDatasetModal : function(){ var tmpl_array = []; - tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push('<div class="modal_table">'); tmpl_array.push(' <table class="table table-striped table-condensed">'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); @@ -329,12 +330,11 @@ // event binding events: { 'click #select-all-checkboxes' : 'selectAll', - 'click .folder_row' : 'selectClickedRow', 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click #toolbtn_dl' : 'bulkDownload', + 'click #toolbtn_create_folder' : 'createFolderFromModal', 'click .library-dataset' : 'showDatasetDetails', - 'click #toolbtn_create_folder' : 'createFolderFromModal', - 'click .btn_open_folder' : 'navigateToFolder' + 'click .dataset_row' : 'selectClickedRow' }, // MMMMMMMMMMMMMMMMMM @@ -397,18 +397,6 @@ return (Math.round(size) / 10) + unit; }, - // handles the click on 'open' and 'upper' folder icons - navigateToFolder : function(event){ - var folder_id = $(event.target).attr('data-id'); - if (typeof folder_id === 'undefined') { - return false; - } else if (folder_id === '0'){ - library_router.navigate('/', {trigger: true, replace: false}); - } else { - library_router.navigate('folders/' + folder_id, {trigger: true, replace: false}); - } - }, - //show modal with current dataset info showDatasetDetails : function(event){ // prevent default @@ -558,8 +546,6 @@ $row = $(event.target.parentElement); source = 'td'; } - if (checkbox === '') {event.stopPropagation(); return;} // button in row was clicked - if (checkbox === undefined) {event.stopPropagation(); return;} // folder row was clicked if (checkbox.checked){ if (source==='td'){ @@ -584,6 +570,9 @@ $row.find('a').removeClass('light'); $row.addClass('dark'); $row.find('a').addClass('dark'); + $row.find('span').removeClass('fa-file-o'); + $row.find('span').addClass('fa-file'); + }, makeWhiteRow: function($row){ @@ -591,6 +580,8 @@ $row.find('a').removeClass('dark'); $row.addClass('light'); $row.find('a').addClass('light'); + $row.find('span').addClass('fa-file-o'); + $row.find('span').removeClass('fa-file'); }, // show toolbar in case something is selected @@ -799,8 +790,72 @@ 'click #create_new_library_btn' : 'show_library_modal' }, + modal: null, + + collection: null, + // initialize initialize : function(){ + var viewContext = this; + this.collection = new Libraries(); + // this.collection.on('sort', this.render, this); + + this.collection.fetch({ + success: function(libraries){ + viewContext.render(); + }, + error: function(model, response){ + + if (response.statusCode().status === 403){ //TODO open to public + mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); + setTimeout(that.redirectToLogin, 3000); + } else { + mod_toastr.error('An error occured. Please try again.'); + } + } + }) + // modification of upper DOM element to show scrollbars due to the #center element inheritance + $("#center").css('overflow','auto'); + }, + + render: function (models) { + var template = this.templateLibraryList(); + var libraries_to_render = null; + + if (this.collection !== null && typeof models === 'undefined'){ + libraries_to_render = this.collection.models; + } else if (models !== null){ + libraries_to_render = models; + } else { + libraries_to_render = []; + } + + this.$el.html(template({libraries: libraries_to_render, order: this.collection.sort_order})); + + }, + + /** Sorts the underlying collection according to the parameters received through URL. + Currently supports only sorting by name. */ + sortLibraries: function(sort_by, order){ + if (sort_by === 'name'){ + if (order === 'asc'){ + this.collection.sort_order = 'asc'; + this.collection.comparator = function(libraryA, libraryB){ + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return 1; // after + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return -1; // before + return 0; // equal + } + } else if (order === 'desc'){ + this.collection.sort_order = 'desc'; + this.collection.comparator = function(libraryA, libraryB){ + if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return -1; // before + if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return 1; // after + return 0; // equal + } + } + this.collection.sort(); + } + }, // MMMMMMMMMMMMMMMMMM @@ -809,13 +864,13 @@ templateLibraryList: function(){ tmpl_array = []; - tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); + tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - // tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); - tmpl_array.push('<table class="table table-condensed">'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); + tmpl_array.push('<table class="library_table table table-condensed">'); tmpl_array.push(' <thead>'); - tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); tmpl_array.push(' </thead>'); @@ -831,7 +886,7 @@ tmpl_array.push('</table>'); tmpl_array.push('</div>'); - return tmpl_array.join(''); + return _.template(tmpl_array.join('')); }, templateNewLibraryInModal: function(){ @@ -848,29 +903,6 @@ return tmpl_array.join(''); }, - render: function () { - // modification of upper DOM element to show scrollbars due to the #center element inheritance - $("#center").css('overflow','auto'); - - var that = this; - libraries = new Libraries(); - - libraries.fetch({ - success: function (libraries) { - var template = _.template(that.templateLibraryList(), { libraries : libraries.models }); - that.$el.html(template); - }, - error: function(model, response){ - if (response.statusCode().status === 403){ //TODO open to public - mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); - setTimeout(that.redirectToLogin, 3000); - } else { - mod_toastr.error('An error occured. Please try again.'); - } - } - }) - }, - redirectToHome: function(){ window.location = '../'; }, @@ -878,9 +910,6 @@ window.location = '/user/login'; }, - // own modal - modal : null, - // show/hide create library modal show_library_modal : function (event){ event.preventDefault(); @@ -908,6 +937,7 @@ var self = this; library.save(libraryDetails, { success: function (library) { + self.collection.add(library); self.modal.hide(); self.clear_library_modal(); self.render(); @@ -945,23 +975,42 @@ } }); + +//ROUTER +var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "sort/:sort_by/:order" : "sort_libraries", + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" + } +}); + // galaxy library wrapper View var GalaxyLibrary = Backbone.View.extend({ - folderContentView : null, - galaxyLibraryview : null, + // folderContentView : null, + // galaxyLibraryview : null, initialize : function(){ - folderContentView = new FolderContentView(); galaxyLibraryview = new GalaxyLibraryview(); library_router = new LibraryRouter(); + folderContentView = new FolderContentView(); library_router.on('route:libraries', function() { // render libraries list galaxyLibraryview.render(); }); + library_router.on('route:sort_libraries', function(sort_by, order) { + // sort libraries list + galaxyLibraryview.sortLibraries(sort_by, order); + galaxyLibraryview.render(); + }); + library_router.on('route:folder_content', function(id) { + // if (this.folderContentView === null){ + // } // render folder's contents folderContentView.render({id: id}); }); @@ -978,10 +1027,8 @@ } }); -Backbone.history.start({pushState: false}); - -// return this -} + Backbone.history.start({pushState: false}); + } }); // return diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th class="button_heading"></th>');r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(" ..</td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td>");r.push(' <span class="fa fa-folder-open"></span></td>');r.push(" <td></td>");r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(" <td>");r.push(' <span class="fa fa-file"></span>');r.push(" </td>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().parent().attr("id");if(typeof v==="undefined"){v=$(u.target).parent().attr("id")}if(typeof v==="undefined"){v=$(u.target).parent().parent().attr("id")}var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<ol class="breadcrumb">');r.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');r.push(" <% _.each(path, function(path_item) { %>");r.push(" <% if (path_item[0] != id) { %>");r.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');r.push("<% } else { %>");r.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');r.push(" <% } %>");r.push(" <% }); %>");r.push("</ol>");r.push('<table id="folder_table" class="library_table table table-condensed">');r.push(" <thead>");r.push(' <th class="button_heading"></th>');r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Folder" class="fa fa-folder-o"></span>');r.push(" </td>");r.push(" <td></td>");r.push(" <td>");r.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } else { %>");r.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Dataset" class="fa fa-file-o"></span>');r.push(" </td>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } %> ");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div class="modal_table">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().parent().attr("id");if(typeof v==="undefined"){v=$(u.target).parent().attr("id")}if(typeof v==="undefined"){v=$(u.target).parent().parent().attr("id")}var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark");r.find("span").removeClass("fa-file-o");r.find("span").addClass("fa-file")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light");r.find("span").addClass("fa-file-o");r.find("span").removeClass("fa-file")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},modal:null,collection:null,initialize:function(){var r=this;this.collection=new o();this.collection.fetch({success:function(s){r.render()},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(that.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}});$("#center").css("overflow","auto")},render:function(t){var r=this.templateLibraryList();var s=null;if(this.collection!==null&&typeof t==="undefined"){s=this.collection.models}else{if(t!==null){s=t}else{s=[]}}this.$el.html(r({libraries:s,order:this.collection.sort_order}))},sortLibraries:function(s,r){if(s==="name"){if(r==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return -1}return 0}}else{if(r==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="library_table table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.collection.add(u);r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var q=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){galaxyLibraryview=new a();library_router=new q();folderContentView=new m();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:sort_libraries",function(s,r){galaxyLibraryview.sortLibraries(s,r);galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1286,15 +1286,19 @@ div.libraryItemBody{padding:4px 4px 2px 4px} li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} +.library_table td{border-top:1px solid #5f6990 !important} +.library_table th{border-bottom:2px solid #5f6990 !important} +.library_table a{color:#0A143D}.library_table a:hover{color:maroon} tr.light td{background-color:white;color:black} -tr.light:hover td{background-color:#f5f5f5;color:#8389a1} +tr.light:hover td{background-color:#A2A9C8} tr.dark td{background-color:#8389a1;color:white} tr.dark:hover td{background-color:#bbbfd0;color:white} -a.dark:hover{color:yellow} a.dark{color:white} +.modal_table tr{border-bottom:1px solid #5f6990 !important} +.modal_table th{border:none !important} +.modal_table td{border:none !important} th.button_heading{width:2em} -div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} -div.library_breadcrumb a:hover{color:green} +#library_folder_toolbar{margin-bottom:1em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -6,15 +6,19 @@ div.libraryItemBody{padding:4px 4px 2px 4px} li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} +.library_table td{border-top:1px solid #5f6990 !important} +.library_table th{border-bottom:2px solid #5f6990 !important} +.library_table a{color:#0A143D}.library_table a:hover{color:maroon} tr.light td{background-color:white;color:black} -tr.light:hover td{background-color:#f5f5f5;color:#8389a1} +tr.light:hover td{background-color:#A2A9C8} tr.dark td{background-color:#8389a1;color:white} tr.dark:hover td{background-color:#bbbfd0;color:white} -a.dark:hover{color:yellow} a.dark{color:white} +.modal_table tr{border-bottom:1px solid #5f6990 !important} +.modal_table th{border:none !important} +.modal_table td{border:none !important} th.button_heading{width:2em} -div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} -div.library_breadcrumb a:hover{color:green} +#library_folder_toolbar{margin-bottom:1em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} diff -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 -r 3ab1e13eab15408930e55fbc262addffd2bf1f6d static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -30,6 +30,21 @@ } +.library_table{ + td { + border-top:1px solid #5f6990 !important; + } + th { + border-bottom: 2px solid #5f6990 !important; + } + a { + color: #0A143D; + &:hover{ + color: maroon; + } + } +} + tr.light td { background-color: white; @@ -37,8 +52,8 @@ } tr.light:hover td { - background-color: #f5f5f5; - color: #8389a1; + background-color: #A2A9C8; + // color: #8389a1; } tr.dark td { @@ -50,28 +65,42 @@ background-color: #bbbfd0; color: white; } -a.dark:hover -{ - color: yellow; - // text-decoration: none; -} a.dark { color: white; - // text-decoration: none; } + + + +.modal_table{ + tr { + border-bottom: 1px solid #5f6990 !important; + } + th{ + border: none !important; + } + td{ + border: none !important; + } +} + + + + + + + + + + th.button_heading { width: 2em; } -div.library_breadcrumb{ - padding-top: 0.8em; - padding-bottom: 0.8em; + +#library_folder_toolbar { + margin-bottom: 1em; } -div.library_breadcrumb a:hover{ - color:green; -} - img.expanderIcon { padding-right: 4px; 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.

1 0

commit/galaxy-central: dan: remove extraneous comment from 7732e2da1563.
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bbd48fc01abd/ Changeset: bbd48fc01abd User: dan Date: 2014-02-21 16:42:23 Summary: remove extraneous comment from 7732e2da1563. Affected #: 1 file diff -r 7732e2da1563682b911e08e445f103e7e58af78b -r bbd48fc01abd9df25b1e0fa8e2bbe2727d252a88 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1781,7 +1781,7 @@ # Both of these values indicate that no dataset is selected. However, 'None' # indicates that the dataset is optional, while '' indicates that it is not. none_values = [ None, '', 'None' ] - if value in none_values:# is None or value == '' or value == 'None': + if value in none_values: return value if isinstance(value, str) and value.find(",") > -1: values = value.split(",") 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.

1 0

commit/galaxy-central: dan: More fixes for multiple datasets with None Datasets.
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7732e2da1563/ Changeset: 7732e2da1563 User: dan Date: 2014-02-21 16:39:28 Summary: More fixes for multiple datasets with None Datasets. Affected #: 1 file diff -r 320dca6064fcbb0381c8d4b75c92c91b02285e2e -r 7732e2da1563682b911e08e445f103e7e58af78b lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1780,12 +1780,13 @@ def to_python( self, value, app ): # Both of these values indicate that no dataset is selected. However, 'None' # indicates that the dataset is optional, while '' indicates that it is not. - if value is None or value == '' or value == 'None': + none_values = [ None, '', 'None' ] + if value in none_values:# is None or value == '' or value == 'None': return value if isinstance(value, str) and value.find(",") > -1: values = value.split(",") # TODO: Optimize. -John - return [app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( val ) ) for val in values] + return [ app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( val ) ) for val in values if val not in none_values ] return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) def to_param_dict_string( self, value, other_values={} ): 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.

1 0

commit/galaxy-central: davebgx: Fix missing import in install and test framework.
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/320dca6064fc/ Changeset: 320dca6064fc User: davebgx Date: 2014-02-21 14:57:49 Summary: Fix missing import in install and test framework. Affected #: 2 files diff -r b706c7c0844f3120952f39d6fc6826e111f267d3 -r 320dca6064fcbb0381c8d4b75c92c91b02285e2e test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -43,6 +43,7 @@ from galaxy.app import UniverseApplication from galaxy.util.json import from_json_string +from galaxy.util import asbool from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file diff -r b706c7c0844f3120952f39d6fc6826e111f267d3 -r 320dca6064fcbb0381c8d4b75c92c91b02285e2e test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -42,6 +42,7 @@ from base.tool_shed_util import parse_tool_panel_config from galaxy.app import UniverseApplication +from galaxy.util import asbool from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file 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.

1 0

commit/galaxy-central: jmchilton: Add functional tests for @kellrott's workflow usage additions.
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b706c7c0844f/ Changeset: b706c7c0844f User: jmchilton Date: 2014-02-21 03:27:26 Summary: Add functional tests for @kellrott's workflow usage additions. Affected #: 1 file diff -r e87d6516105d6def9751cfb6df6e69b23bfacb14 -r b706c7c0844f3120952f39d6fc6826e111f267d3 test/functional/api/test_workflows.py --- a/test/functional/api/test_workflows.py +++ b/test/functional/api/test_workflows.py @@ -103,6 +103,29 @@ pja = pjas[ 0 ] self._assert_has_keys( pja, "action_type", "output_name", "action_arguments" ) + def test_invocation_usage( self ): + workflow = self.workflow_populator.load_workflow( name="test_usage" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_id = workflow_request[ "workflow_id" ] + response = self._get( "workflows/%s/usage" % workflow_id ) + self._assert_status_code_is( response, 200 ) + assert len( response.json() ) == 0 + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + + response = self._get( "workflows/%s/usage" % workflow_id ) + self._assert_status_code_is( response, 200 ) + usages = response.json() + assert len( usages ) == 1 + + usage_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, usages[ 0 ][ "id" ] ) ) + self._assert_status_code_is( usage_details_response, 200 ) + usage_details = usage_details_response.json() + # Assert some high-level things about the structure of data returned. + self._assert_has_keys( usage_details, "inputs", "steps" ) + for step in usage_details[ "steps" ].values(): + self._assert_has_keys( step, "workflow_step_id", "order_index" ) + def test_post_job_action( self ): """ Tests both import and execution of post job actions. """ 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.

1 0

commit/galaxy-central: kellrott: Merged galaxy/galaxy-central into default
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b304bf48192e/ Changeset: b304bf48192e User: kellrott Date: 2013-06-27 23:05:56 Summary: Merged galaxy/galaxy-central into default Affected #: 2 files diff -r 63b58d89dedd942ad9842958476dd9d364fe1fe0 -r b304bf48192eca003b434870f73f324639697c2c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1147,8 +1147,6 @@ Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as each repository's tool dependencies. """ - # TODO: figure out how to handle installing repositories and tool dependencies consecutively since each redirects to an ajaxian grid. This - # is not a problem in that Galaxy API. message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) @@ -1160,15 +1158,27 @@ message=message, status=status ) ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + if kwd.get( 'repair_repository_button', False ): + repair_dict = kwd.get( 'repair_dict', None ) + if not repair_dict: + repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + if ordered_tsr_ids and ordered_repo_info_dicts: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repositories', + operation='repair', + ordered_tsr_ids=ordered_tsr_ids, + ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) - if ordered_tsr_ids and ordered_repo_info_dicts: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repositories', - operation='repair', - ordered_tsr_ids=ordered_tsr_ids, - ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako', + repository=tool_shed_repository, + repair_dict=repair_dict, + message=message, + status=status ) @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): diff -r 63b58d89dedd942ad9842958476dd9d364fe1fe0 -r b304bf48192eca003b434870f73f324639697c2c templates/admin/tool_shed_repository/repair_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -0,0 +1,51 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} +</%def> + +${render_galaxy_repository_actions( repository )} + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are correctly + installed. Click <b>Repair</b> to inspect and repair these repositories. +</div> + +<div class="toolForm"> + <div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div> + <br/><br/> + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=repair_dict )}" method="post" > + <% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %> + <table class="grid"> + <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> + %for repo_info_dict in ordered_repo_info_dicts: + <% + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + break + %> + <tr> + <td>${name | h}</td> + <td>${repository_owner | h}</td> + <td>${changeset_revision | h}</td> + </tr> + %endfor + </table> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="repair_repository_button" value="Repair"/> + </div> + </form> + </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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a561dea97563/ Changeset: a561dea97563 Branch: /use-placeholder-instead-of-value-in-html-1392839097891 User: trevorw Date: 2014-02-19 20:46:26 Summary: use `placeholder` instead of `value` in html5 - editor.mako Affected #: 1 file diff -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 -r a561dea97563b04d0cff617f1692ede4438fafe3 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -302,7 +302,7 @@ <div class="unified-panel-body" style="overflow: auto;"><div class="toolMenu"><div id="tool-search" style="padding-bottom: 5px; position: relative; display: block; width: 100%"> - <input type="text" name="query" value="search tools" id="tool-search-query" class="search-query parent-width" /> + <input type="text" name="query" placeholder="search tools" id="tool-search-query" class="search-query parent-width" /><img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner" /></div><div class="toolSectionList"> https://bitbucket.org/galaxy/galaxy-central/commits/65de107dc224/ Changeset: 65de107dc224 User: jmchilton Date: 2014-02-21 03:25:31 Summary: Merged in trevorw/galaxy-central-1//use-placeholder-instead-of-value-in-html-1392839097891 (pull request #325) use `placeholder` instead of `value` in html5 - editor.mako Affected #: 1 file diff -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f -r 65de107dc224a90943057b9df2b1de521b26544d templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -302,7 +302,7 @@ <div class="unified-panel-body" style="overflow: auto;"><div class="toolMenu"><div id="tool-search" style="padding-bottom: 5px; position: relative; display: block; width: 100%"> - <input type="text" name="query" value="search tools" id="tool-search-query" class="search-query parent-width" /> + <input type="text" name="query" placeholder="search tools" id="tool-search-query" class="search-query parent-width" /><img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner" /></div><div class="toolSectionList"> 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bd6b50a9fc1/ Changeset: 8bd6b50a9fc1 User: trevorw Date: 2014-02-21 01:14:09 Summary: whitespace Affected #: 7 files diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -350,7 +350,7 @@ except Exception, e: self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) ) ok = False - if ok: + if ok: if deactivate: # We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers. sniffer_class = elem.get( 'type', None ) diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1850,7 +1850,7 @@ if hda.copied_from_library_dataset_dataset_association is not None: rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id - + if hda.history is not None: rval['history_id'] = hda.history.id diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1621,7 +1621,7 @@ if type( value ) != list: value = [ value ] field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) - + # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): current_user_roles = trans.get_current_user_roles() diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -501,7 +501,7 @@ else: input.visit_inputs( prefix, value[input.name], callback ) def get_initial_value( self, trans, context, history=None ): - # State for a conditional is a plain dictionary. + # State for a conditional is a plain dictionary. rval = {} # Get the default value for the 'test element' and use it # to determine the current case diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -138,9 +138,9 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) - webapp.mapper.resource( 'datatype', - 'datatypes', - path_prefix='/api', + webapp.mapper.resource( 'datatype', + 'datatypes', + path_prefix='/api', collection={ 'sniffers': 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) @@ -180,41 +180,41 @@ # ============================ webapp.mapper.connect( 'api_key_retrieval', - '/api/authenticate/baseauth/', - controller='authenticate', - action='get_api_key', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', conditions=dict( method=[ "GET" ] ) ) # ======================= # ===== LIBRARY API ===== # ======================= - + webapp.mapper.connect( 'show_lda_item', - '/api/libraries/datasets/:id', - controller='lda_datasets', - action='show', + '/api/libraries/datasets/:id', + controller='lda_datasets', + action='show', conditions=dict( method=[ "GET" ] ) ) - webapp.mapper.connect( 'download_lda_items', - '/api/libraries/datasets/download/:format', - controller='lda_datasets', - action='download', + webapp.mapper.connect( 'download_lda_items', + '/api/libraries/datasets/download/:format', + controller='lda_datasets', + action='download', conditions=dict( method=[ "POST", "GET" ] ) ) - webapp.mapper.connect( 'create_folder', - '/api/folders/:encoded_parent_folder_id', - controller='folders', - action='create', + webapp.mapper.connect( 'create_folder', + '/api/folders/:encoded_parent_folder_id', + controller='folders', + action='create', conditions=dict( method=[ "POST" ] ) ) webapp.mapper.resource_with_deleted( 'library', - 'libraries', + 'libraries', path_prefix='/api' ) - webapp.mapper.resource( 'folder', - 'folders', + webapp.mapper.resource( 'folder', + 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', + webapp.mapper.resource( 'content', 'contents', controller='folder_contents', name_prefix='folder_', @@ -233,9 +233,9 @@ 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) - - webapp.mapper.resource( 'job', - 'jobs', + + webapp.mapper.resource( 'job', + 'jobs', path_prefix='/api' ) webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) ) @@ -243,7 +243,7 @@ _add_item_extended_metadata_controller( webapp, name_prefix="library_dataset_", path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - + _add_item_extended_metadata_controller( webapp, name_prefix="history_dataset_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -251,14 +251,14 @@ # ==================== # ===== TOOLSHED ===== # ==================== - + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, image_file=None ) - + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -239,7 +239,7 @@ Redirects a user accessing a Data Source tool to its target action link. This method will subvert mix-mode content blocking in several browsers when accessing non-https data_source tools from an https galaxy server. - + Tested as working on Safari 7.0 and FireFox 26 Subverting did not work on Chrome 31 """ @@ -255,13 +255,13 @@ trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) - + if isinstance( tool, DataSourceTool ): link = url_for( tool.action, **tool.get_static_param_values( trans ) ) else: link = url_for( controller='tool_runner', tool_id=tool.id ) return trans.response.send_redirect( link ) - + @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: diff -r 0f65411e40224e7a9b32f3273896113654a742ce -r 8bd6b50a9fc10b334647a5df755d845d341612ee tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -126,7 +126,7 @@ elif is_gzipped and is_valid: if link_data_only == 'copy_files': # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb + CHUNK_SIZE = 2**20 # 1Mb fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) while 1: @@ -159,7 +159,7 @@ elif is_bzipped and is_valid: if link_data_only == 'copy_files': # We need to uncompress the temp_name file - CHUNK_SIZE = 2**20 # 1Mb + CHUNK_SIZE = 2**20 # 1Mb fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) while 1: https://bitbucket.org/galaxy/galaxy-central/commits/1f2383ac9a8e/ Changeset: 1f2383ac9a8e User: jmchilton Date: 2014-02-21 03:25:04 Summary: Merged in trevorw/galaxy-central (pull request #331) whitespace Affected #: 7 files diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -350,7 +350,7 @@ except Exception, e: self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) ) ok = False - if ok: + if ok: if deactivate: # We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers. sniffer_class = elem.get( 'type', None ) diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1850,7 +1850,7 @@ if hda.copied_from_library_dataset_dataset_association is not None: rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id - + if hda.history is not None: rval['history_id'] = hda.history.id diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1621,7 +1621,7 @@ if type( value ) != list: value = [ value ] field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) - + # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): current_user_roles = trans.get_current_user_roles() diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -501,7 +501,7 @@ else: input.visit_inputs( prefix, value[input.name], callback ) def get_initial_value( self, trans, context, history=None ): - # State for a conditional is a plain dictionary. + # State for a conditional is a plain dictionary. rval = {} # Get the default value for the 'test element' and use it # to determine the current case diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -138,9 +138,9 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) - webapp.mapper.resource( 'datatype', - 'datatypes', - path_prefix='/api', + webapp.mapper.resource( 'datatype', + 'datatypes', + path_prefix='/api', collection={ 'sniffers': 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) @@ -180,41 +180,41 @@ # ============================ webapp.mapper.connect( 'api_key_retrieval', - '/api/authenticate/baseauth/', - controller='authenticate', - action='get_api_key', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', conditions=dict( method=[ "GET" ] ) ) # ======================= # ===== LIBRARY API ===== # ======================= - + webapp.mapper.connect( 'show_lda_item', - '/api/libraries/datasets/:id', - controller='lda_datasets', - action='show', + '/api/libraries/datasets/:id', + controller='lda_datasets', + action='show', conditions=dict( method=[ "GET" ] ) ) - webapp.mapper.connect( 'download_lda_items', - '/api/libraries/datasets/download/:format', - controller='lda_datasets', - action='download', + webapp.mapper.connect( 'download_lda_items', + '/api/libraries/datasets/download/:format', + controller='lda_datasets', + action='download', conditions=dict( method=[ "POST", "GET" ] ) ) - webapp.mapper.connect( 'create_folder', - '/api/folders/:encoded_parent_folder_id', - controller='folders', - action='create', + webapp.mapper.connect( 'create_folder', + '/api/folders/:encoded_parent_folder_id', + controller='folders', + action='create', conditions=dict( method=[ "POST" ] ) ) webapp.mapper.resource_with_deleted( 'library', - 'libraries', + 'libraries', path_prefix='/api' ) - webapp.mapper.resource( 'folder', - 'folders', + webapp.mapper.resource( 'folder', + 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', + webapp.mapper.resource( 'content', 'contents', controller='folder_contents', name_prefix='folder_', @@ -233,9 +233,9 @@ 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) - - webapp.mapper.resource( 'job', - 'jobs', + + webapp.mapper.resource( 'job', + 'jobs', path_prefix='/api' ) webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) ) @@ -243,7 +243,7 @@ _add_item_extended_metadata_controller( webapp, name_prefix="library_dataset_", path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - + _add_item_extended_metadata_controller( webapp, name_prefix="history_dataset_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -251,14 +251,14 @@ # ==================== # ===== TOOLSHED ===== # ==================== - + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', controller='admin_toolshed', action='display_image_in_repository', repository_id=None, image_file=None ) - + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -239,7 +239,7 @@ Redirects a user accessing a Data Source tool to its target action link. This method will subvert mix-mode content blocking in several browsers when accessing non-https data_source tools from an https galaxy server. - + Tested as working on Safari 7.0 and FireFox 26 Subverting did not work on Chrome 31 """ @@ -255,13 +255,13 @@ trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) - + if isinstance( tool, DataSourceTool ): link = url_for( tool.action, **tool.get_static_param_values( trans ) ) else: link = url_for( controller='tool_runner', tool_id=tool.id ) return trans.response.send_redirect( link ) - + @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: diff -r d7c8982b89def2729638c5c4fad3fa14325f608e -r 1f2383ac9a8ec518f4c91a4c5c2de825f4ddf36f tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -126,7 +126,7 @@ elif is_gzipped and is_valid: if link_data_only == 'copy_files': # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb + CHUNK_SIZE = 2**20 # 1Mb fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) while 1: @@ -159,7 +159,7 @@ elif is_bzipped and is_valid: if link_data_only == 'copy_files': # We need to uncompress the temp_name file - CHUNK_SIZE = 2**20 # 1Mb + CHUNK_SIZE = 2**20 # 1Mb fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) while 1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Pack scripts
by commits-noreply＠bitbucket.org 21 Feb '14

21 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7c8982b89de/ Changeset: d7c8982b89de User: guerler Date: 2014-02-21 02:11:07 Summary: Pack scripts Affected #: 1 file diff -r 86f8a8311fec37d0cfcae2e919e37e96a31ca297 -r d7c8982b89def2729638c5c4fad3fa14325f608e static/scripts/packed/mvc/ui/ui-portlet.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-portlet.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{label:"",icon:"fa-tasks",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$content:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this.template(this.options));this.$content=this.$el.find("#content");if(this.options.height){this.$el.find("#body").css("height",this.options.height);this.$el.find("#content").css("overflow",this.options.overflow)}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(e,f){f.$el.prop("id",e);c.$buttons.append(f.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(e,f){f.$el.prop("id",e);c.$operations.append(f.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},label:function(c){var d=this.$el.find("#label");if(c){d.html(c)}return d.html()},template:function(d){var c='<div class="toolForm">';if(d.label||d.icon){c+='<div id="title" class="toolFormTitle" style="overflow:hidden;"><div id="operations" style="float: right;"></div><div style="overflow: hidden">';if(d.icon){c+='<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa '+d.icon+'"> </i>'}c+='<div id="label" style="padding-top: 2px; float: left;">'+d.label+"</div>";c+="</div></div>"}c+='<div id="body" class="toolFormBody">';if(d.placement=="top"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+='<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+="</div></div>";return c}});return{View:b}}); \ No newline at end of file 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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