- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 56431b214df1: Don't 'use strict' as FF4 beta doesn't support it
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '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 1289944688 18000 # Node ID 56431b214df16653a966b96bf399c7646da267b8 # Parent 394d8186f666b506cd0a93aefb7a079e0c9ec59b Don't 'use strict' as FF4 beta doesn't support it --- a/static/scripts/jquery.jstore.js +++ b/static/scripts/jquery.jstore.js @@ -15,7 +15,7 @@ * http://creativecommons.org/licenses/by/3.0/us */ -"use strict"; +//"use strict"; /*global Class, window, jQuery, ActiveXObject, google */ --- a/static/scripts/class.js +++ b/static/scripts/class.js @@ -5,7 +5,7 @@ * Inspired by base2 and Prototype */ -"use strict"; +//"use strict"; (function () { --- a/static/scripts/packed/jquery.jstore.js +++ b/static/scripts/packed/jquery.jstore.js @@ -14,4 +14,4 @@ * Licensed under the Creative Commons Attribution 3.0 United States License: * http://creativecommons.org/licenses/by/3.0/us */ -"use strict";(function(i,n){var 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B("9.0.0")});e(G,{limit:-1,init:function(J,I){this.database=google.gears.factory.create("beta.database");this.database.open("jstore-"+J);this.database.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this._super(J,I)},updateCache:function(){var I=this.database.execute("SELECT k,v FROM jstore");while(I.isValidRow()){this.data[I.field(0)]=k(I.field(1));I.next()}I.close();this._super()},__set:function(I,J){this.database.execute("BEGIN");this.database.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)]);this.database.execute("COMMIT")},__remove:function(I){this.database.execute("BEGIN");this.database.execute("DELETE FROM jstore WHERE k = ?",[I]);this.database.execute("COMMIT")}},function(){return n.google!==undefined&&n.google.gears!==undefined});e(A,{limit:parseInt(10000,16),init:function(J,I){this.database=i('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+ J+'"></div>').appendTo(document.body).get(0);this._super(J,I)},updateCache:function(){this.database.load(this.project);var K=document.getElementById("jstore-"+this.project),L=K.XMLDocument,I,J=0;if(L&&L.documentElement&&L.documentElement.attributes){I=L.documentElement;for(;J<I.attributes.length;++J){this.data[I.attributes.item(J).nodeName]=k(I.attributes.item(J).nodeValue)}}this._super()},__set:function(I,J){this.database.setAttribute(I,x(J));this.database.save(this.project)},__remove:function(I){this.database.removeAttribute(I);this.database.save(this.project)}},function(){return n.ActiveXObject!==undefined})}(jQuery,window)); --- a/static/scripts/packed/class.js +++ b/static/scripts/packed/class.js @@ -4,4 +4,4 @@ * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) * Inspired by base2 and Prototype */ -"use strict";(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}()); +(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}());

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galaxy-dist commit 1bf064c8ab88: Fixed functional tests and samples grid alignment bug
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289928056 18000 # Node ID 1bf064c8ab88621dd58890f6cd56ad4900d10d6b # Parent 2e2ee0289d67d244954aa05bfe315dbb5ff413eb Fixed functional tests and samples grid alignment bug --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -341,7 +341,7 @@ class TestFormsAndRequests( TwillTestCas request_id=self.security.encode_id( request1.id ), strings_displayed=[ 'History of sequencing request "%s"' % request1.name, request1.states.NEW, - 'Request created' ], + 'Sequencing request created' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.REJECTED ] ) @@ -412,7 +412,7 @@ class TestFormsAndRequests( TwillTestCas self.add_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'Add Samples to Request "%s"' % request1.name, + strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # check the new sample field values on the request page @@ -446,7 +446,7 @@ class TestFormsAndRequests( TwillTestCas self.edit_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), sample_value_tuples=new_sample_value_tuples, - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name, + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # check the changed sample field values on the request page @@ -465,14 +465,14 @@ class TestFormsAndRequests( TwillTestCas self.submit_request( cntrller='requests', request_id=self.security.encode_id( request1.id ), request_name=request1.name, - strings_displayed_after_submit=[ 'The request has been submitted.' ] ) + strings_displayed_after_submit=[ 'The sequencing request has been submitted.' ] ) refresh( request1 ) # Make sure the request is showing in the 'submitted' filter self.check_request_grid( cntrller='requests', state=request1.states.SUBMITTED, strings_displayed=[ request1.name ] ) # Make sure the request's state is now set to 'submitted' - assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ + assert request1.state is not request1.states.SUBMITTED, "The state of the sequencing request '%s' should be set to '%s'" \ % ( request1.name, request1.states.SUBMITTED ) # the sample state should appear once for each sample strings_displayed_count = [ ( request1.type.states[0].name, len( request1.samples ) ) ] @@ -485,8 +485,8 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_count=strings_displayed_count, strings_not_displayed=strings_not_displayed ) strings_displayed=[ 'History of sequencing request "%s"' % request1.name, - 'Request submitted by %s' % regular_user1.email, - 'Request created' ] + 'Sequencing request submitted by %s' % regular_user1.email, + 'Sequencing request created' ] strings_displayed_count = [ ( request1.states.SUBMITTED, 1 ) ] self.view_request_history( cntrller='requests', request_id=self.security.encode_id( request1.id ), @@ -519,7 +519,7 @@ class TestFormsAndRequests( TwillTestCas self.add_bar_codes( cntrller='requests_admin', request_id=self.security.encode_id( request1.id ), bar_codes=bar_codes, - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], strings_displayed_after_submit=strings_displayed_after_submit ) # the second sample state should appear once for each sample strings_displayed_count = [ ( request1.type.states[1].name, len( request1.samples ) ), @@ -538,7 +538,7 @@ class TestFormsAndRequests( TwillTestCas # check history of each sample for sample in request1.samples: strings_displayed = [ 'Events for Sample "%s"' % sample.name, - 'Request submitted and sample state set to %s' % request1.type.states[0].name, + 'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name, request1.type.states[0].name, request1.type.states[1].name ] self.view_sample_history( cntrller='requests_admin', @@ -558,9 +558,9 @@ class TestFormsAndRequests( TwillTestCas if index > 1: # status message if index == len( request_type1.states ) - 1: - status_msg = 'All samples of this request are in the final sample state (%s).' % state.name + status_msg = 'All samples of this sequencing request are in the final sample state (%s).' % state.name else: - status_msg = 'All samples of this request are in the (%s) sample state. ' % state.name + status_msg = 'All samples of this sequencing request are in the (%s) sample state. ' % state.name # check email notification message email_msg = '' if state.id in [ email_state.id for email_state in email_notification_sample_states ]: @@ -568,7 +568,7 @@ class TestFormsAndRequests( TwillTestCas self.change_sample_state( request_id=self.security.encode_id( request1.id ), sample_ids=[ sample.id for sample in request1.samples ], new_sample_state_id=self.security.encode_id( state.id ), - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], strings_displayed_after_submit = [ status_msg, email_msg ] ) # check request history page if index == len( request_type1.states ) - 1: @@ -584,7 +584,7 @@ class TestFormsAndRequests( TwillTestCas self.check_request_grid( cntrller='requests_admin', state='Complete', strings_displayed=[ request1.name ] ) - assert request1.state is not request1.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ + assert request1.state is not request1.states.COMPLETE, "The state of the sequencing request '%s' should be set to '%s'" \ % ( request1.name, request1.states.COMPLETE ) # def test_045_admin_create_request_on_behalf_of_regular_user( self ): --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -113,27 +113,23 @@ </script></%def> -<%def name="render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"> +<%def name="render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"><% + trans.sa_session.refresh( request ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_rejected = request.is_rejected + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted if sample: - trans.sa_session.refresh( sample.request ) - is_complete = sample.request.is_complete - is_rejected = request.is_rejected - is_submitted = sample.request.is_submitted - is_unsubmitted = sample.request.is_unsubmitted can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) - display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) else: - is_complete = False - is_submitted = False - is_unsubmitted = False can_delete_samples = False display_checkboxes = False - display_bar_code = False display_datasets = False + display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) %><% if display_checkboxes and trans.security.encode_id( sample.id ) in encoded_selected_sample_ids: @@ -152,15 +148,13 @@ </td> %if display_bar_code: <td valign="top"> - %if is_admin: + %if is_admin and is_submitted: <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> %else: ${sample_widget['bar_code']} <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> %endif </td> - %else: - <td></td> %endif %if sample: %if is_unsubmitted: @@ -305,7 +299,7 @@ sample = None %> %if editing_samples: - <tr>${render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %elif sample: <tr><td> @@ -401,7 +395,7 @@ </tr> %else: ## The Add sample button was clicked for this sample_widget - <tr>${render_editable_sample_row( cntrller, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %endif %endfor </tbody>

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galaxy-dist commit 394d8186f666: tool_form: Make radio and select box labels explicitly inline. Workflow: add colons after parameter names where appropriate. Fixes #419
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '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 1289929775 18000 # Node ID 394d8186f666b506cd0a93aefb7a079e0c9ec59b # Parent 1bf064c8ab88621dd58890f6cd56ad4900d10d6b tool_form: Make radio and select box labels explicitly inline. Workflow: add colons after parameter names where appropriate. Fixes #419 --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -210,6 +210,10 @@ div.form-row label { margin-bottom: .2em; } +div.form-row label.inline { + display: inline; +} + div.form-row-input { float: left; } --- a/templates/workflow/editor_tool_form.mako +++ b/templates/workflow/editor_tool_form.mako @@ -7,8 +7,8 @@ from galaxy.util.expressions import Expr <% ctx = ExpressionContext( values, ctx ) %> %for input_index, input in enumerate( inputs.itervalues() ): %if input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><b>${input.title_plural}</b></div> + <div class="repeat-group form-row"> + <label>${input.title_plural}:</label><% repeat_values = values[input.name] %> %for i in range( len( repeat_values ) ): <% @@ -19,7 +19,7 @@ from galaxy.util.expressions import Expr index = repeat_values[i]['__index__'] %><div class="repeat-group-item"> - <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> + <div class="form-title-row"><label>${input.title} ${i + 1}</label></div> ${do_inputs( input.inputs, repeat_values[ i ], rep_errors, prefix + input.name + "_" + str(index) + "|", ctx )} <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div></div> @@ -63,7 +63,7 @@ from galaxy.util.expressions import Expr %else: %if isinstance( value, RuntimeValue ): <label> - ${param.get_label()} + ${param.get_label()}: <span class="popupmenu"><button type="submit" name="make_buildtime" value="${prefix}${param.name}">Set in advance</button></span> @@ -73,7 +73,7 @@ from galaxy.util.expressions import Expr </div> %else: <label> - ${param.get_label()} + ${param.get_label()}: %if allow_runtime: <span class="popupmenu"><button type="submit" name="make_runtime" value="${prefix}${param.name}">Set at runtime</button> --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -248,16 +248,16 @@ class SelectField(BaseField): >>> t.add_option( "tuti", 1 ) >>> t.add_option( "fruity", "x" ) >>> print t.get_html() - <div><input type="radio" name="foo" value="1" id="foo|1"><label for="foo|1">tuti</label></div> - <div><input type="radio" name="foo" value="x" id="foo|x"><label for="foo|x">fruity</label></div> + <div><input type="radio" name="foo" value="1" id="foo|1"><label class="inline" for="foo|1">tuti</label></div> + <div><input type="radio" name="foo" value="x" id="foo|x"><label class="inline" for="foo|x">fruity</label></div> >>> t = SelectField( "bar", multiple=True, display="checkboxes" ) >>> t.add_option( "automatic", 3 ) >>> t.add_option( "bazooty", 4, selected=True ) >>> print t.get_html() <div class="checkUncheckAllPlaceholder" checkbox_name="bar"></div> - <div><input type="checkbox" name="bar" value="3" id="bar|3"><label for="bar|3">automatic</label></div> - <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label for="bar|4">bazooty</label></div> + <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div> + <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): self.name = name @@ -302,7 +302,7 @@ class SelectField(BaseField): selected_text = "" if selected: selected_text = " checked='checked'" - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \ + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>' % \ ( style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str( disabled ), uniq_id, text ) ) ctr += 1 return "\n".join( rval ) @@ -318,7 +318,7 @@ class SelectField(BaseField): selected_text = "" if selected: selected_text = " checked='checked'" - rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label for="%s">%s</label></div>' % \ + rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>' % \ ( style, prefix, self.name, --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -39,6 +39,7 @@ div.form-title-row{padding:5px 10px;} div.repeat-group-item{border-left:solid #d8b365 5px;margin-left:10px;margin-bottom:10px;} div.form-row-error{background:#FFCCCC;} div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;} +div.form-row label.inline{display:inline;} div.form-row-input{float:left;} div.form-row-input label{font-weight:normal;display:inline;} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -515,14 +515,14 @@ class SelectToolParameter( ToolParameter blah >>> print p.get_html() <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> - <div><input type="checkbox" name="blah" value="x" id="blah|x"><label for="blah|x">I am X</label></div> - <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div> - <div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label for="blah|z">I am Z</label></div> + <div><input type="checkbox" name="blah" value="x" id="blah|x"><label class="inline" for="blah|x">I am X</label></div> + <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div> + <div><input type="checkbox" name="blah" value="z" id="blah|z" checked='checked'><label class="inline" for="blah|z">I am Z</label></div> >>> print p.get_html( value=["x","y"]) <div class="checkUncheckAllPlaceholder" checkbox_name="blah"></div> - <div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label for="blah|x">I am X</label></div> - <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label for="blah|y">I am Y</label></div> - <div><input type="checkbox" name="blah" value="z" id="blah|z"><label for="blah|z">I am Z</label></div> + <div><input type="checkbox" name="blah" value="x" id="blah|x" checked='checked'><label class="inline" for="blah|x">I am X</label></div> + <div class="odd_row"><input type="checkbox" name="blah" value="y" id="blah|y" checked='checked'><label class="inline" for="blah|y">I am Y</label></div> + <div><input type="checkbox" name="blah" value="z" id="blah|z"><label class="inline" for="blah|z">I am Z</label></div> >>> print p.to_param_dict_string( ["y", "z"] ) y,z """

1 0

galaxy-dist commit 918a25ed14f5: Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '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 1290008781 18000 # Node ID 918a25ed14f5427f70970b0c436159fc58fd111e # Parent 7bded9108bd8297ea609e9ec06bbe516b5f0b83a Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do. --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -601,7 +601,7 @@ class Forms( BaseController ): for ft in trans.model.Sample.supported_field_types: self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in trans.model.Request.supported_field_types: + for ft in trans.model.FormDefinition.supported_field_types: self.fieldtype.add_option( ft.__name__, ft__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') @@ -641,7 +641,7 @@ class Forms( BaseController ): else: self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in trans.model.Request.supported_field_types: + for ft in trans.model.FormDefinition.supported_field_types: if ft.__name__ == field[ 'type' ]: self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) if ft == 'SelectField':

1 0

galaxy-dist commit 2e2ee0289d67: Fix BLAST+ regression from changeset 535d276c92bc (loc file columns)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1289925107 0 # Node ID 2e2ee0289d67d244954aa05bfe315dbb5ff413eb # Parent d2d0c199c20ddf942e1e2587dc9aede8acd9cebc Fix BLAST+ regression from changeset 535d276c92bc (loc file columns) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -40,10 +40,13 @@ blastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -41,10 +41,13 @@ blastp </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> -  + <options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -39,10 +39,13 @@ tblastx </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -40,10 +40,13 @@ blastx </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> -  + <options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -40,10 +40,13 @@ tblastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" />

1 0

galaxy-dist commit 94c2040e5825: More minor ui fixes in sample tracking
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289918776 18000 # Node ID 94c2040e58255136741d776de8401cfb4128133b # Parent 7cc69601ca2da9b6d21f980585b59d73c0133cba More minor ui fixes in sample tracking --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -220,7 +220,7 @@ %endif %if can_delete_samples: ## Delete button - <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + <td valign="top"><a class="action-button" confirm="This sample is not recoverable after deletion. Click Ok to delete." href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif </%def> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -12,19 +12,22 @@ <%def name="javascripts()"> ${parent.javascripts()} ${common_javascripts()} + ${local_javascripts()} </%def> -<script type="text/javascript"> - // This function stops the form from getting submitted when return key is pressed - // This is needed in this form as the barcode scanner (when in keyboard emulation mode) - // may send a return key appended to the scanned barcode string. - function stopRKey(evt) { - var evt = (evt) ? evt : ((event) ? event : null); - var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); - if ((evt.keyCode == 13) && (node.type=="text")) {return false;} - } - document.onkeypress = stopRKey -</script> +<%def name="local_javascripts()"> + <script type="text/javascript"> + // This function stops the form from getting submitted when return key is pressed + // This is needed in this form as the barcode scanner (when in keyboard emulation mode) + // may send a return key appended to the scanned barcode string. + function stopRKey(evt) { + var evt = (evt) ? evt : ((event) ? event : null); + var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); + if ((evt.keyCode == 13) && (node.type=="text")) {return false;} + } + document.onkeypress = stopRKey + </script> +</%def><% from galaxy.web.framework.helpers import time_ago @@ -68,7 +71,7 @@ %if request.samples_without_library_destinations: <p> - <font color="red"><b><i>Select a target data library and folder for a sample before selecting its datasets to transfer from the sequencer</i></b></font> + <font color="red"><b><i>Select a target data library and folder for a sample before selecting it's datasets to transfer from the sequencer</i></b></font></p> %endif --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -59,7 +59,7 @@ %if request.samples_without_library_destinations: <p> - <font color="red"><b><i>Select a target data library and folder for a sample before selecting its datasets to transfer from the sequencer</i></b></font> + <font color="red"><b><i>Select a target data library and folder for a sample before selecting it's datasets to transfer from the sequencer</i></b></font></p> %endif

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galaxy-dist commit 7cc69601ca2d: minor ui fixes in sample tracking
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289916735 18000 # Node ID 7cc69601ca2da9b6d21f980585b59d73c0133cba # Parent def13f052a4a22c46ec5be6481ad874ceb734799 minor ui fixes in sample tracking --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -4,8 +4,8 @@ %if message: ${render_msg( message, status )} %endif - -<h2>Reject Sequencing Request "${request.name}"</h2> +<br/><br/> +##<h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a> @@ -16,7 +16,7 @@ </ul><div class="toolForm"> - <div class="toolFormTitle">Reject request</div> + <div class="toolFormTitle">Reject sequencing request "${request.name}"</div><form name="event" action="${h.url_for( controller='requests_admin', action='reject_request', id=trans.security.encode_id( request.id ) )}" method="post" ><div class="form-row"> Rejecting this request will move the request state to <b>Rejected</b>. --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -58,9 +58,9 @@ %endif %if request.samples_without_library_destinations: - <br/> - <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> - <br/> + <p> + <font color="red"><b><i>Select a target data library and folder for a sample before selecting its datasets to transfer from the sequencer</i></b></font> + </p> %endif %if message: --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -67,9 +67,9 @@ </ul> %if request.samples_without_library_destinations: - <br/> - <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> - <br/> + <p> + <font color="red"><b><i>Select a target data library and folder for a sample before selecting its datasets to transfer from the sequencer</i></b></font> + </p> %endif %if request.is_rejected: --- a/templates/requests/common/view_request_history.mako +++ b/templates/requests/common/view_request_history.mako @@ -34,7 +34,7 @@ ${render_msg( message, status )} %endif -<h2>History of sequencing request "${request.name}"</h2> +<h3>History of sequencing request "${request.name}"</h3><div class="toolForm"><table class="grid">

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galaxy-dist commit def13f052a4a: Restored the function to stop the edit samples form from getting submitted when return key is pressed. This is needed in this form as the barcode scanner (when in keyboard emulation mode) may send a return key appended to the scanned barcode string.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289853524 18000 # Node ID def13f052a4a22c46ec5be6481ad874ceb734799 # Parent 02f6c9dae26e9aef40a44bc151ed07b457715839 Restored the function to stop the edit samples form from getting submitted when return key is pressed. This is needed in this form as the barcode scanner (when in keyboard emulation mode) may send a return key appended to the scanned barcode string. --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -68,7 +68,7 @@ def update_sample_state( message ): api_key = get_value(dom, 'api_key') log.debug('Barcode: ' + barcode) log.debug('State: ' + state) - log.debug('api_key: ' + api_key) + log.debug('API Key: ' + api_key) # validate if not barcode or not state or not api_key: log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -14,6 +14,18 @@ ${common_javascripts()} </%def> +<script type="text/javascript"> + // This function stops the form from getting submitted when return key is pressed + // This is needed in this form as the barcode scanner (when in keyboard emulation mode) + // may send a return key appended to the scanned barcode string. + function stopRKey(evt) { + var evt = (evt) ? evt : ((event) ? event : null); + var node = (evt.target) ? evt.target : ((evt.srcElement) ? evt.srcElement : null); + if ((evt.keyCode == 13) && (node.type=="text")) {return false;} + } + document.onkeypress = stopRKey +</script> + <% from galaxy.web.framework.helpers import time_ago

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galaxy-dist commit 0505090dbbe6: Changing back
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Anton Nekrutenko <anton(a)bx.psu.edu> # Date 1289851601 18000 # Node ID 0505090dbbe610741cacd7a9a1c2e79b8cc9ea5c # Parent 9a7482206be274678079271331171600a2023b03 Changing back --- a/tools/taxonomy/t2ps_wrapper.py +++ b/tools/taxonomy/t2ps_wrapper.py @@ -59,7 +59,7 @@ except OSError, e: # Convert PS to PDF try: - ps2pdf_cmd = 'pstopdf %s -o %s' % ( ps_file.name, pdf_file ) + ps2pdf_cmd = 'ps2pdf %s %s' % ( ps_file.name, pdf_file ) retcode = subprocess.call( ps2pdf_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode

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galaxy-dist commit 33dacaafc62e: Change in output redirect. Should fix drawing phylogeny bug. Thanks Nate for pointing this out.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User anton(a)grusha.bx.psu.edu # Date 1289920626 18000 # Node ID 33dacaafc62eac4a8940c4bc978da1d1a6c68af9 # Parent 94c2040e58255136741d776de8401cfb4128133b Change in output redirect. Should fix drawing phylogeny bug. Thanks Nate for pointing this out. --- a/tools/taxonomy/t2ps_wrapper.py +++ b/tools/taxonomy/t2ps_wrapper.py @@ -38,7 +38,7 @@ ps_file = tempfile.NamedTemporaryFile('w # Execute taxonomy2tree try: - t2t_cmd = 'taxonomy2tree %s %s %s /dev/null 1 &> /dev/null' % ( tree_file, max_tree_level, newick_file.name ) + t2t_cmd = 'taxonomy2tree %s %s %s /dev/null 1 > /dev/null 2>&1' % ( tree_file, max_tree_level, newick_file.name ) retcode = subprocess.call( t2t_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of taxonomy2tree terminated by signal", -retcode

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