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galaxy-dist commit 2c99bd86765f: Add RGENETICS section label to main tool conf
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1275924412 14400 # Node ID 2c99bd86765fc2665cfa6bea98b4ebae7fc3d6c8 # Parent f08dff0dd4ac92c5d9b75792c2c5c38eb280e81b Add RGENETICS section label to main tool conf --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -333,6 +333,7 @@ <tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> + <label text="RGENETICS" id="rgenetics" /><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /><tool file="data_source/upload.xml"/>

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galaxy-dist commit f08dff0dd4ac: Allow disabling of library download compression types
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1275924310 14400 # Node ID f08dff0dd4ac92c5d9b75792c2c5c38eb280e81b # Parent 4fb747f317d0b2c36ffb5fbf4b815caf4cb6ace1 Allow disabling of library download compression types --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -109,6 +109,13 @@ class LibraryCommon( BaseController ): comptypes_t = comptypes if trans.app.config.nginx_x_archive_files_base: comptypes_t = ['ngxzip'] + for comptype in trans.app.config.disable_library_comptypes: + # TODO: do this once, not every time (we're gonna raise an + # exception every time after the first time) + try: + comptypes_t.remove( comptype ) + except: + pass return trans.fill_template( '/library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -98,6 +98,7 @@ class Configuration( object ): if self.user_library_import_dir is not None and not os.path.exists( self.user_library_import_dir ): raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) + self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) # Configuration options for taking advantage of nginx features self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) ) self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )

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galaxy-dist commit 9114bd088776: Better handling of return key in search+select.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1275753610 14400 # Node ID 9114bd0887769b9ffe570b71f90ab95be68baa44 # Parent 21ddc9f843be29515ea6f260a73a710288606104 Better handling of return key in search+select. --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -287,9 +287,16 @@ function replace_big_select_inputs(min_l // case a user may have manually entered a value that needs to be refreshed). text_input_elt.bind("result", try_refresh_fn); text_input_elt.keyup( function(e) { - try_refresh_fn(); + if ( e.keyCode === 13 ) // Return key + try_refresh_fn(); }); - + + // Disable return key so that it does not submit the form automatically. This is done because elememnt should behave like a + // select (enter = select), not text input (enter = submit form). + text_input_elt.keydown( function(e) { + if ( e.keyCode === 13 ) // Return key + return false; + }); } }); } --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var 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a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); +$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var 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k=g[l];if(k!==null&&k!==undefined){b.attr("value",k)}else{if(j!=""){b.attr("value",j)}else{b.attr("value","?")}}};b.parents("form").submit(function(){i()});$(document).bind("convert_dbkeys",function(){i()});if(d.attr("refresh_on_change")=="true"){var c=d.attr("refresh_on_change_values");if(c!==undefined){c=c.split(",")}var h=function(){var m=b.attr("value");var l=g[m];if(l!==null&&l!==undefined){refresh=false;if(c!==undefined){for(var k=0;k<c.length;k++){if(l==c[k]){refresh=true;break}}}else{refresh=true}if(refresh){b.attr("value",l);b.parents("for m").submit()}}};b.bind("result",h);b.keyup(function(k){if(k.keyCode===13){h()}});b.keydown(function(k){if(k.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input 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href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_sta te");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()});

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galaxy-dist commit 5610a35bf9a6: Add the CBI Rice Mart data source tool to the distribution.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275680998 14400 # Node ID 5610a35bf9a67b0e43f02a433163232ab3f7a998 # Parent 84880085415b7b53ead611ccffee39b0ab9e0d4b Add the CBI Rice Mart data source tool to the distribution. --- /dev/null +++ b/tools/data_source/cbi_rice_mart.xml @@ -0,0 +1,39 @@ +<?xml version="1.0"?> + +<tool name="CBI Rice Mart" id="cbi_rice_mart" tool_type="data_source" version="1.0.1"> + <description>rice mart</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ricemart.cbi.edu.cn/biomart/martview/" check_values="false" method="get" target="_top"> + <display>go to RMap rice mart $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="_export" missing="1" /> + <value name="GALAXY_URL" missing="0" /> + </append_param> + </request_param> + <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" > + <value_translation> + <value galaxy_value="tabular" remote_value="TSV" /> + </value_translation> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <request_param galaxy_name="table" remote_name="table" missing="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="Rice mart query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -9,6 +9,7 @@ <tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" /> + <tool file="data_source/cbi_rice_mart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/fly_modencode.xml" /><tool file="data_source/flymine.xml" />

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galaxy-dist commit 56e2793886dc: Fix for library dataset information page, link to history items using hda.history_id rather than hda.history.id.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275688990 14400 # Node ID 56e2793886dc2d1547bb86f32a13d0e365f8fecd # Parent 5610a35bf9a67b0e43f02a433163232ab3f7a998 Fix for library dataset information page, link to history items using hda.history_id rather than hda.history.id. --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -148,7 +148,7 @@ </thead> %for hda in associated_hdas: <tr> - <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history.id ) )}">${hda.history.get_display_name()}</a></td> + <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history_id ) )}">${hda.history.get_display_name()}</a></td><td>${hda.get_display_name()}</td><td>${time_ago( hda.update_time )}</td><td>

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galaxy-dist commit 21ddc9f843be: Prevent workflow forms from being submitted twice when dynamic options are refreshed, resulting in AJAX error and inability to savewq
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1275690470 14400 # Node ID 21ddc9f843be29515ea6f260a73a710288606104 # Parent 56e2793886dc2d1547bb86f32a13d0e365f8fecd Prevent workflow forms from being submitted twice when dynamic options are refreshed, resulting in AJAX error and inability to savewq --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -328,6 +328,7 @@ type: 'POST', dataType: 'json', success: function( data ) { + workflow.active_form_has_changes = false; node.update_field_data( data ); }, beforeSubmit: function( data ) {

1 0

galaxy-dist commit a76d05bb41e1: Fixes and enhancements to the reports webapp:
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275672554 14400 # Node ID a76d05bb41e1c1f1eeaa93a18289eeed1213199b # Parent dd69c382eff1d3c0c160bc3ec392b06671317fd0 Fixes and enhancements to the reports webapp: 0) The report that is initially displayed is now the number of jobs per day for the current month rather than the grid displaying all jobs for today. 1) Eliminate eagerloading when querying jobs so that queries are much faster 2) Fix the disk space ( system ) report, and add a new feature that displays all active ( undeleted ) hda and ldda pointers to a specific dataset. 3) Standardize request parameters so that queries can more easily be built using parameters from the request. 4) A few other miscellaneous bug fixes in the reports. --- a/templates/webapps/reports/registered_users.mako +++ b/templates/webapps/reports/registered_users.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -4,7 +4,7 @@ <% from galaxy import util %> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -27,7 +27,7 @@ <tr class="tr"> %endif <td>${job[2]} ${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='user_for_month', email=email, month=job[0] )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='user_for_month', email=email, specified_date=job[0]+'-01' )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -63,7 +63,7 @@ class SpecifiedDateListGrid( grids.Grid model_class=model.User, link=( lambda item: dict( operation="user_per_month", id=item.id, webapp="reports" ) ), attach_popup=False ), - grids.StateColumn( "All", key="state", model_class=model.Job, visible=False, filterable="advanced" ) + grids.StateColumn( "state", key="state", model_class=model.Job, visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[1], columns[2] ], @@ -78,45 +78,59 @@ class SpecifiedDateListGrid( grids.Grid def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class SpecifiedDateInErrorListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ).filter( self.model_class.table.c.state == model.Job.states.ERROR ) + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.state == model.Job.states.ERROR ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( self.model_class.table.c.state == model.Job.states.ERROR, - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.state == model.Job.states.ERROR, + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class AllUnfinishedListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ).filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, + model.Job.table.c.state == model.Job.states.ERROR, + model.Job.table.c.state == model.Job.states.DELETED ) ) ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ), - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( not_( or_( model.Job.table.c.state == model.Job.states.OK, + model.Job.table.c.state == model.Job.states.ERROR, + model.Job.table.c.state == model.Job.states.DELETED ) ), + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class UserForMonthListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): email = util.restore_text( kwd.get( 'email', '' ) ) - year, month = map( int, kwd.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) return trans.sa_session.query( model.Job ) \ @@ -127,19 +141,22 @@ class UserForMonthListGrid( SpecifiedDat model.User.table.c.email == email, model.Job.table.c.create_time >= start_date, model.Job.table.c.create_time < end_date ) ) \ - .order_by( desc( model.Job.table.c.create_time ) ) + .enable_eagerloads( False ) class ToolForMonthListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] tool_id = util.restore_text( kwd.get( 'tool_id', '' ) ) - year, month = map( int, kwd.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) - return trans.sa_session.query( model.Job ) \ - .filter( and_( model.Job.table.c.tool_id == tool_id, - model.Job.table.c.create_time >= start_date, - model.Job.table.c.create_time < end_date ) ) \ - .order_by( desc( model.Job.table.c.create_time ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.tool_id == tool_id, + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class Jobs( BaseController ): @@ -158,8 +175,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -194,8 +210,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -222,7 +237,10 @@ class Jobs( BaseController ): params = util.Params( kwd ) message = '' monitor_email = params.get( 'monitor_email', 'monitor(a)bx.psu.edu' ) - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -254,7 +272,10 @@ class Jobs( BaseController ): def specified_month_in_error( self, trans, **kwd ): params = util.Params( kwd ) message = '' - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -289,8 +310,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -332,7 +352,9 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', + jobs=jobs, + message=message ) @web.expose def per_month_in_error( self, trans, **kwd ): params = util.Params( kwd ) @@ -349,7 +371,9 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako', + jobs=jobs, + message=message ) @web.expose def per_user( self, trans, **kwd ): params = util.Params( kwd ) @@ -398,8 +422,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -434,12 +457,15 @@ class Jobs( BaseController ): for row in q.execute(): jobs.append( ( row.tool_id, row.total_jobs ) ) - return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', + jobs=jobs, + message=message ) @web.expose def tool_per_month( self, trans, **kwd ): params = util.Params( kwd ) message = '' tool_id = params.get( 'tool_id', 'Add a column1' ) + specified_date = params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause = model.Job.table.c.tool_id == tool_id, @@ -452,7 +478,11 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_tool_per_month.mako', tool_id=tool_id, jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_tool_per_month.mako', + specified_date=specified_date, + tool_id=tool_id, + jobs=jobs, + message=message ) @web.expose def tool_for_month( self, trans, **kwd ): if 'operation' in kwd: @@ -462,8 +492,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -497,7 +526,10 @@ class Jobs( BaseController ): .one() # TODO: for some reason the job_info.id is not the same as job_id in the template, so we need to pass job_id # This needs to be fixed ASAP! - return trans.fill_template( '/webapps/reports/job_info.mako', job_id=job_id, job_info=job_info, message=message ) + return trans.fill_template( '/webapps/reports/job_info.mako', + job_id=job_id, + job_info=job_info, + message=message ) @web.expose def per_domain( self, trans, **kwd ): # TODO: rewrite using alchemy --- a/templates/webapps/reports/system.mako +++ b/templates/webapps/reports/system.mako @@ -1,13 +1,17 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<% + from galaxy.web.framework.helpers import time_ago +%> + %if message: ${render_msg( message, 'done' )} %endif <div class="toolForm"><h3 align="center">Old Histories and Datasets</h3> - <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> + <table align="center" width="90%" class="border" cellpadding="5" cellspacing="5"><tr><td><form method="post" action="system"> @@ -33,10 +37,14 @@ </td></tr></table> - <br clear="left" /><br /> + <br clear="left" /><h3 align="center">Current Disk Space Where Datasets are Stored</h3> - <table align="center" width="60%" class="colored"> - <tr><td colspan="5"><div class="toolFormTitle">Disk Usage for ${file_path}</div></td></tr> + <table align="center" width="90%" class="colored"> + <tr> + <td colspan="5"> + <b>Disk Usage for ${file_path}</b> + </td> + </tr><tr class="header"><td>File System</td><td>Disk Size</td> @@ -51,16 +59,16 @@ <td>${disk_usage[3]}</td><td>${disk_usage[4]}</td></tr> - %if len( datasets ) == 0: - <tr class="header"><td colspan="5">There are no datasets larger than ${file_size_str}</td></tr> - %else: - <tr><td colspan="5"><div class="toolFormTitle">${len( datasets )} largest datasets over ${file_size_str}</div></td></tr> + </table> + <br clear="left" /> + %if datasets.count() > 0: + <h3 align="center">${datasets.count()} largest unpurged data files over ${file_size_str}</h3> + <table align="center" width="90%" class="colored"><tr class="header"><td>File</td><td>Last Updated</td> - <td>History ID</td><td>Deleted</td> - <td>Size on Disk</td> + <td>File Size</td></tr><% ctr = 0 %> %for dataset in datasets: @@ -69,14 +77,19 @@ %else: <tr class="tr"> %endif - <td>dataset_${dataset[0]}.dat</td> - <td>${dataset[1]}</td> - <td>${dataset[2]}</td> - <td>${dataset[3]}</td> - <td>${dataset[4]}</td> + <td> + <% dataset_label = 'dataset%d_.dat' % dataset.id %> + <a href="${h.url_for( controller='system', action='dataset_info', id=trans.security.encode_id( dataset.id ) )}">${dataset_label}</a> + </td> + <td>${time_ago( dataset.update_time )}</td> + <td>${dataset.deleted}</td> + <td>${dataset.file_size}</td></tr><% ctr += 1 %> %endfor - %endif - </table> + </table> + <br clear="left" /> + %else: + <h3 align="center">There are no unpurged data files larger than ${file_size_str}</h3> + %endif </div> --- /dev/null +++ b/templates/webapps/reports/dataset_info.mako @@ -0,0 +1,119 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% + from galaxy.web.framework.helpers import time_ago + from galaxy.web.controllers.library_common import get_containing_library_from_library_dataset +%> + +%if message: + ${render_msg( message, 'done' )} +%endif + +<div class="toolForm"> + <h3 align="center">Dataset Information</h3> + <div class="toolFormBody"> + <div class="form-row"> + <label>Date uploaded:</label> + ${time_ago( dataset.create_time )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Last updated:</label> + ${time_ago( dataset.update_time )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>File size:</label> + ${dataset.get_size( nice_size=True )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>State:</label> + ${dataset.state} + <div style="clear: both"></div> + </div> + </div> +</div> +%if associated_hdas: + <p/> + <b>Active (undeleted) history items that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>History</th> + <th>History Item</th> + <th>Last Updated</th> + <th>User</th> + </tr> + </thead> + %for hda in associated_hdas: + <tr> + <td>${hda.history.get_display_name()}</td> + <td>${hda.get_display_name()}</td> + <td>${time_ago( hda.update_time )}</td> + <td> + %if hda.history.user: + ${hda.history.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> +%endif +%if associated_lddas: + <p/> + <b>Other active (undeleted) library datasets that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>Library</th> + <th>Folder</th> + <th>Library Dataset</th> + <th>Last Updated</th> + <th>Uploaded By</th> + </tr> + </thead> + %for ldda in associated_lddas: + <% containing_library = get_containing_library_from_library_dataset( trans, ldda.library_dataset ) %> + <tr> + <td> + <% + if containing_library: + library_display_name = containing_library.get_display_name() + else: + library_display_name = 'error finding library' + %> + ${library_display_name} + </td> + <td> + <% + library_dataset = ldda.library_dataset + folder = library_dataset.folder + folder_display_name = folder.get_display_name() + if folder_display_name == library_display_name: + folder_display_name = 'library root' + %> + ${folder_display_name} + </td> + <td>${ldda.get_display_name()}</td> + <td>${time_ago( ldda.update_time )}</td> + <td> + %if ldda.user: + ${ldda.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> +%endif --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -432,13 +432,19 @@ class Dataset( object ): path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) # Make path absolute return os.path.abspath( path ) - def get_size( self ): + def get_size( self, nice_size=False ): """Returns the size of the data on disk""" if self.file_size: - return self.file_size + if nice_size: + return galaxy.datatypes.data.nice_size( self.file_size ) + else: + return self.file_size else: try: - return os.path.getsize( self.file_name ) + if nice_size: + return galaxy.datatypes.data.nice_size( os.path.getsize( self.file_name ) ) + else: + return os.path.getsize( self.file_name ) except OSError: return 0 def set_size( self ): --- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/users_last_access_date.mako +++ b/templates/webapps/reports/users_last_access_date.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_month_in_error.mako +++ b/templates/webapps/reports/jobs_per_month_in_error.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='jobs', action='specified_month_in_error', month=job[0] )}">${job[2]} ${job[3]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_month_in_error', specified_date=job[0]+'-01' )}">${job[2]} ${job[3]}</a></td><td>${job[1]}</td></tr><% ctr += 1 %> --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,10 +1,6 @@ import operator, os from datetime import datetime, timedelta from galaxy.web.base.controller import * -#import pkg_resources -#pkg_resources.require( "SQLAlchemy >= 0.4" ) -#from sqlalchemy.orm import eagerload -#from sqlalchemy import desc from galaxy import model from galaxy.model.orm import * import logging @@ -44,7 +40,6 @@ class System( BaseController ): deleted_histories_days=deleted_histories_days, deleted_datasets_days=deleted_datasets_days, message=message ) - def userless_histories( self, trans, **kwd ): """The number of userless histories and associated datasets that have not been updated for the specified number of days.""" params = util.Params( kwd ) @@ -54,11 +49,6 @@ class System( BaseController ): cutoff_time = datetime.utcnow() - timedelta( days=userless_histories_days ) history_count = 0 dataset_count = 0 - #h = self.app.model.History - #where = ( h.table.c.user_id==None ) & ( h.table.c.deleted=='f' ) & ( h.table.c.update_time < cutoff_time ) - #histories = h.query().filter( where ).options( eagerload( 'datasets' ) ) - - #for history in histories: for history in trans.sa_session.query( model.History ) \ .filter( and_( model.History.table.c.user_id == None, model.History.table.c.deleted == True, @@ -71,7 +61,6 @@ class System( BaseController ): else: message = "Enter the number of days." return str( userless_histories_days ), message - def deleted_histories( self, trans, **kwd ): """ The number of histories that were deleted more than the specified number of days ago, but have not yet been purged. @@ -104,7 +93,6 @@ class System( BaseController ): else: message = "Enter the number of days." return str( deleted_histories_days ), message - def deleted_datasets( self, trans, **kwd ): """The number of datasets that were deleted more than the specified number of days ago, but have not yet been purged.""" params = util.Params( kwd ) @@ -128,6 +116,25 @@ class System( BaseController ): else: message = "Enter the number of days." return str( deleted_datasets_days ), message + @web.expose + def dataset_info( self, trans, **kwd ): + params = util.Params( kwd ) + message = '' + dataset = trans.sa_session.query( model.Dataset ).get( trans.security.decode_id( kwd.get( 'id', '' ) ) ) + # Get all associated hdas and lddas that use the same disk file. + associated_hdas = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ + .filter( and_( trans.model.HistoryDatasetAssociation.deleted == False, + trans.model.HistoryDatasetAssociation.dataset_id == dataset.id ) ) \ + .all() + associated_lddas = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ) \ + .filter( and_( trans.model.LibraryDatasetDatasetAssociation.deleted == False, + trans.model.LibraryDatasetDatasetAssociation.dataset_id == dataset.id ) ) \ + .all() + return trans.fill_template( '/webapps/reports/dataset_info.mako', + dataset=dataset, + associated_hdas=associated_hdas, + associated_lddas=associated_lddas, + message=message ) def get_disk_usage( self, file_path ): df_cmd = 'df -h ' + file_path is_sym_link = os.path.islink( file_path ) @@ -163,13 +170,13 @@ class System( BaseController ): def disk_usage( self, trans, **kwd ): file_path = trans.app.config.file_path disk_usage = self.get_disk_usage( file_path ) - min_file_size = 2**32 # 4 Gb + #min_file_size = 2**32 # 4 Gb + min_file_size = 0 file_size_str = nice_size( min_file_size ) - datasets = [] - for dataset in trans.sa_session.query( model.Dataset ) \ - .filter( model.Dataset.table.c.file_size > min_file_size ) \ - .order_by( desc( model.Dataset.table.c.file_size ) ): - datasets.append( ( dataset.id, str( dataset.update_time )[0:10], dataset.history.history_id, dataset.deleted, dataset.file_size ) ) + datasets = trans.sa_session.query( model.Dataset ) \ + .filter( and_( model.Dataset.table.c.purged == False, + model.Dataset.table.c.file_size > min_file_size ) ) \ + .order_by( desc( model.Dataset.table.c.file_size ) ) return file_path, disk_usage, datasets, file_size_str def nice_size( size ): --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -13,14 +13,12 @@ log = logging.getLogger( __name__ ) class Users( BaseController ): @web.expose def registered_users( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) + message = util.restore_text( kwd.get( 'message', '' ) ) num_users = trans.sa_session.query( galaxy.model.User ).count() return trans.fill_template( '/webapps/reports/registered_users.mako', num_users=num_users, message=message ) @web.expose def registered_users_per_month( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) + message = util.restore_text( kwd.get( 'message', '' ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), from_obj = [ galaxy.model.User.table ], @@ -29,15 +27,19 @@ class Users( BaseController ): users = [] for row in q.execute(): users.append( ( row.date.strftime( "%Y-%m" ), - row.num_users, - row.date.strftime( "%B" ), - row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/registered_users_per_month.mako', users=users, message=message ) + row.num_users, + row.date.strftime( "%B" ), + row.date.strftime( "%Y" ) ) ) + return trans.fill_template( '/webapps/reports/registered_users_per_month.mako', + users=users, + message=message ) @web.expose def specified_month( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + message = util.restore_text( kwd.get( 'message', '' ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -63,9 +65,10 @@ class Users( BaseController ): message=message ) @web.expose def specified_date( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - year, month, day = map( int, params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ).split( "-" ) ) + message = util.restore_text( kwd.get( 'message', '' ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) day_of_month = start_date.strftime( "%d" ) @@ -91,9 +94,8 @@ class Users( BaseController ): message=message ) @web.expose def last_access_date( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - not_logged_in_for_days = params.get( 'not_logged_in_for_days', 90 ) + message = util.restore_text( kwd.get( 'message', '' ) ) + not_logged_in_for_days = kwd.get( 'not_logged_in_for_days', 90 ) if not not_logged_in_for_days: not_logged_in_for_days = 0 cutoff_time = datetime.utcnow() - timedelta( days=int( not_logged_in_for_days ) ) --- a/templates/webapps/reports/registered_users_specified_month.mako +++ b/templates/webapps/reports/registered_users_specified_month.mako @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='users', action='specified_date', specified_date=user[0], day_label=user[3], month_label=month_label, year_label=year_label, day_of_month=user[1] )}">${user[3]}, ${month_label} ${user[1]}, ${year_label}</a></td> + <td><a href="${h.url_for( controller='users', action='specified_date', specified_date=user[0] )}">${user[3]}, ${month_label} ${user[1]}, ${year_label}</a></td><td>${user[2]}</td></tr><% ctr += 1 %> --- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -73,14 +73,14 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='today_all' )}">Number of jobs today</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_all' )}">Number of jobs per day for current month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Number of jobs in error per day for current month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='today_all' )}">Today's jobs</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_all' )}">Jobs per day this month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Jobs in error per day this month</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='all_unfinished' )}">All unfinished jobs</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_all' )}">Number of jobs per month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Number of jobs in error per month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user' )}">Number of jobs per user</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_tool' )}">Number of jobs per tool</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_all' )}">Jobs per month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Jobs in error per month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user' )}">Jobs per user</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_tool' )}">Jobs per tool</a></div></div></div><div class="toolSectionPad"></div> @@ -101,7 +101,7 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='system', action='index' )}">Disk space, old histories and datasets</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='system', action='index' )}">Disk space maintenance</a></div></div></div></div> @@ -110,6 +110,6 @@ </%def><%def name="center_panel()"> - <% center_url = h.url_for( controller='jobs', action='today_all' ) %> + <% center_url = h.url_for( controller='jobs', action='specified_month_all' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> --- a/templates/webapps/reports/jobs_per_domain.mako +++ b/templates/webapps/reports/jobs_per_domain.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1904,15 +1904,14 @@ def branch_deleted( folder ): def get_containing_library_from_library_dataset( trans, library_dataset ): """Given a library_dataset, get the containing library""" folder = library_dataset.folder - parent = folder while folder.parent: - parent = folder.parent - # We have parent set to the library's root folder, which has the - # same name as the library + folder = folder.parent + # We have folder set to the library's root folder, which has the same name as the library for library in trans.sa_session.query( trans.model.Library ) \ .filter( and_( trans.model.Library.table.c.deleted == False, - trans.model.Library.table.c.name == parent.name ) ): - if library.root_folder == parent: + trans.model.Library.table.c.name == folder.name ) ): + # Just to double-check + if library.root_folder == folder: return library return None --- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -25,7 +25,7 @@ <tr class="tr"> %endif <td>${job[2]} ${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='tool_for_month', tool_id=tool_id, month=job[0] )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='tool_for_month', tool_id=tool_id, specified_date=job[0]+'-01' )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor --- a/templates/webapps/reports/registered_users_per_month.mako +++ b/templates/webapps/reports/registered_users_per_month.mako @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='users', action='specified_month', month=user[0], month_label=user[2].strip(), year_label=user[3] )}">${user[2]} ${user[3]}</a></td> + <td><a href="${h.url_for( controller='users', action='specified_month', specified_date=user[0]+'-01' )}">${user[2]} ${user[3]}</a></td><td>${user[1]}</td></tr><% ctr += 1 %> --- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_month_all.mako +++ b/templates/webapps/reports/jobs_per_month_all.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -26,7 +26,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='jobs', action='specified_month_all', month=job[0] )}">${job[4]} ${job[5]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_month_all', specified_date=job[0]+'-01' )}">${job[4]} ${job[5]}</a></td><td>${job[1]}</td><td>${job[2]}</td><td>${job[3]}</td>

1 0

galaxy-dist commit 6dde140d0cfd: I forgot to change the disk file size from 0 back to 4 gb for the systems report before may last commit.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275676257 14400 # Node ID 6dde140d0cfd53820f9cbb83bbb44338ac8bd6aa # Parent a76d05bb41e1c1f1eeaa93a18289eeed1213199b I forgot to change the disk file size from 0 back to 4 gb for the systems report before may last commit. --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -170,8 +170,7 @@ class System( BaseController ): def disk_usage( self, trans, **kwd ): file_path = trans.app.config.file_path disk_usage = self.get_disk_usage( file_path ) - #min_file_size = 2**32 # 4 Gb - min_file_size = 0 + min_file_size = 2**32 # 4 Gb file_size_str = nice_size( min_file_size ) datasets = trans.sa_session.query( model.Dataset ) \ .filter( and_( model.Dataset.table.c.purged == False,

1 0

galaxy-dist commit dd69c382eff1: lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1275671936 14400 # Node ID dd69c382eff1d3c0c160bc3ec392b06671317fd0 # Parent d01207f24908bc3f6d5323689f0aa46557f4d254 lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -70,6 +70,15 @@ <input type="text" name="data_dir" value="" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><input type="hidden" name="new" value="submitted" size="40"/></div> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1476,6 +1476,9 @@ class RequestEvent( object ): self.comment = comment class RequestType( object ): + rename_dataset_options = Bunch( NO = 'Do not rename', + SAMPLE_NAME = 'Preprend sample name', + EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) def __init__(self, name=None, desc=None, request_form=None, sample_form=None, datatx_info=None): --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -62,6 +62,15 @@ <input type="text" name="data_dir" value="${request_type.datatx_info.get('data_dir', '')}" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><input type="submit" name="save_changes" value="Save changes"/></div></form> --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -221,7 +221,6 @@ class RequestsAdmin( BaseController ): @web.json def get_file_details( self, trans, id=None, file=None, folder_path=None ): - print >> sys.stderr, 'get_file_details', id, file def print_ticks(d): pass # Avoid caching @@ -1623,7 +1622,7 @@ class RequestsAdmin( BaseController ): else: sample.dataset_files.append(dict(filepath=filepath, status=sample.transfer_status.NOT_STARTED, - name=filepath.split('/')[-1], + name=self.__dataset_name(sample, filepath.split('/')[-1]), error_msg='', size=sample.dataset_size(filepath))) trans.sa_session.add( sample ) @@ -1638,7 +1637,16 @@ class RequestsAdmin( BaseController ): action='show_datatx_page', sample_id=trans.security.encode_id(sample.id), folder_path=folder_path)) - + + def __dataset_name(self, sample, filepath): + name = filepath.split('/')[-1] + opt = sample.request.type.datatx_info.get('rename_dataset', sample.request.type.rename_dataset_options.NO) + if opt == sample.request.type.rename_dataset_options.NO: + return name + elif opt == sample.request.type.rename_dataset_options.SAMPLE_NAME: + return sample.name+'_'+name + elif opt == sample.request.type.rename_dataset_options.EXPERIMENT_AND_SAMPLE_NAME: + return sample.request.name+'_'+sample.name+'_'+name def __setup_datatx_user(self, trans, library, folder): ''' This method sets up the datatx user: @@ -1830,7 +1838,8 @@ class RequestsAdmin( BaseController ): return trans.fill_template( '/admin/requests/view_request_type.mako', request_type=rt, forms=get_all_forms( trans ), - states_list=rt.states ) + states_list=rt.states, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans, rt) ) def __view_form(self, trans, **kwd): try: fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id(kwd['id']) ) @@ -1855,7 +1864,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'remove_state_button', False ): rt_info, rt_states = self.__create_request_type_form(trans, **kwd) index = int(params.get( 'remove_state_button', '' ).split(" ")[2]) @@ -1864,7 +1874,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'save_request_type', False ): rt, message = self.__save_request_type(trans, **kwd) if not rt: @@ -1888,7 +1899,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', False) )) trans.sa_session.add( rt ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -1903,7 +1915,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) def __create_request_type_form(self, trans, **kwd): request_forms=get_all_forms( trans, filter=dict(deleted=False), @@ -1949,6 +1962,19 @@ class RequestsAdmin( BaseController ): break return rt_info, rt_states + def __rename_dataset_selectbox(self, trans, rt=None): + if rt: + sel_opt = rt.datatx_info.get('rename_dataset', trans.app.model.RequestType.rename_dataset_options.NO) + else: + sel_opt = trans.app.model.RequestType.rename_dataset_options.NO + rename_dataset_selectbox = SelectField('rename_dataset') + for opt, opt_name in trans.app.model.RequestType.rename_dataset_options.items(): + if sel_opt == opt_name: + rename_dataset_selectbox.add_option(opt_name, opt_name, selected=True) + else: + rename_dataset_selectbox.add_option(opt_name, opt_name) + return rename_dataset_selectbox + def __save_request_type(self, trans, **kwd): params = util.Params( kwd ) rt = trans.app.model.RequestType() @@ -1960,7 +1986,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', '') )) trans.sa_session.add( rt ) trans.sa_session.flush() # set sample states --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -55,6 +55,8 @@ <h2>Data transfer from Sequencer</h2><h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3> +<br/> +<br/><ul class="manage-table-actions"> %if sample.request.submitted() and sample.inprogress_dataset_files(): @@ -131,7 +133,7 @@ <input type="submit" name="open_folder" value="Open folder"/><input type="submit" name="folder_up" value="Up"/></div> - <div class="form-row"> + <div class="form-row"><select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple> %for index, f in enumerate(files): <option value="${f}">${f}</option>

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galaxy-dist commit 84880085415b: Add the ratmine datasource tool to main's tool config.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275677102 14400 # Node ID 84880085415b7b53ead611ccffee39b0ab9e0d4b # Parent 6dde140d0cfd53820f9cbb83bbb44338ac8bd6aa Add the ratmine datasource tool to main's tool config. --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -10,6 +10,7 @@ <tool file="data_source/gramene_mart.xml" /><tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/ratmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" />

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