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Merge -dev.
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@davebx
davebx committed Feb 3, 2017
2 parents 8d5b154 + 0b074f3 commit e92fcf1
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Showing 308 changed files with 5,790 additions and 3,681 deletions.
56 changes: 5 additions & 51 deletions .ci/flake8_lint_include_list.txt
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Expand Up @@ -14,6 +14,7 @@ lib/galaxy/dataset_collections/__init__.py
lib/galaxy/dataset_collections/structure.py
lib/galaxy/dataset_collections/subcollections.py
lib/galaxy/dataset_collections/type_description.py
lib/galaxy/dataset_collections/types/__init__.py
lib/galaxy/datatypes/assembly.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/checkers.py
Expand Down Expand Up @@ -93,16 +94,7 @@ lib/galaxy/jobs/runners/pulsar.py
lib/galaxy/jobs/runners/slurm.py
lib/galaxy/jobs/runners/state_handlers/
lib/galaxy/jobs/runners/tasks.py
lib/galaxy/jobs/runners/util/cli/factory.py
lib/galaxy/jobs/runners/util/cli/job/__init__.py
lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
lib/galaxy/jobs/runners/util/cli/job/torque.py
lib/galaxy/jobs/runners/util/cli/shell/__init__.py
lib/galaxy/jobs/runners/util/drmaa/
lib/galaxy/jobs/runners/util/env.py
lib/galaxy/jobs/runners/util/external.py
lib/galaxy/jobs/runners/util/__init__.py
lib/galaxy/jobs/runners/util/job_script/
lib/galaxy/jobs/runners/util/
lib/galaxy/jobs/splitters/basic.py
lib/galaxy/jobs/splitters/__init__.py
lib/galaxy/jobs/stock_rules.py
Expand Down Expand Up @@ -264,46 +256,9 @@ lib/galaxy/sample_tracking/__init__.py
lib/galaxy/sample_tracking/sample.py
lib/galaxy/security/validate_user_input.py
lib/galaxy/tags/
lib/galaxy/tools/actions/
lib/galaxy/tools/cwl/
lib/galaxy/tools/data_manager/__init__.py
lib/galaxy/tools/deps/
lib/galaxy/tools/exception_handling.py
lib/galaxy/tools/execute.py
lib/galaxy/tools/filters/
lib/galaxy/tools/imp_exp/export_history.py
lib/galaxy/tools/imp_exp/__init__.py
lib/galaxy/tools/linters/
lib/galaxy/tools/lint.py
lib/galaxy/tools/lint_util.py
lib/galaxy/tools/loader_directory.py
lib/galaxy/tools/loader.py
lib/galaxy/tools/parameters/dataset_matcher.py
lib/galaxy/tools/parameters/history_query.py
lib/galaxy/tools/parameters/__init__.py
lib/galaxy/tools/parameters/input_translation.py
lib/galaxy/tools/parameters/sanitize.py
lib/galaxy/tools/parameters/validation.py
lib/galaxy/tools/parameters/wrapped_json.py
lib/galaxy/tools/parameters/wrapped.py
lib/galaxy/tools/parser/
lib/galaxy/tools/special_tools.py
lib/galaxy/tools/test.py
lib/galaxy/tools/toolbox/
lib/galaxy/tools/util/galaxyops/
lib/galaxy/tools/util/__init__.py
lib/galaxy/tools/verify/
lib/galaxy/tools/
lib/galaxy/util/
lib/galaxy_utils/__init__.py
lib/galaxy/util/sleeper.py
lib/galaxy/util/specs.py
lib/galaxy_utils/sequence/fasta.py
lib/galaxy_utils/sequence/fastq.py
lib/galaxy_utils/sequence/__init__.py
lib/galaxy_utils/sequence/transform.py
lib/galaxy_utils/sequence/vcf.py
lib/galaxy/util/template.py
lib/galaxy/util/ucsc.py
lib/galaxy_utils/
lib/galaxy/version.py
lib/galaxy/visualization/data_providers/basic.py
lib/galaxy/visualization/data_providers/cigar.py
Expand Down Expand Up @@ -472,7 +427,6 @@ scripts/tools/re_escape_output.py
test/api/__init__.py
test/api/test_dataset_collections.py
test/api/test_datasets.py
test/api/test_datatypes.py
test/api/test_framework.py
test/api/test_history_contents_provenance.py
test/api/test_jobs.py
Expand All @@ -483,7 +437,6 @@ test/api/test_tool_data.py
test/api/test_tours.py
test/api/test_workflow_extraction.py
test/api/test_workflows_from_yaml.py
test/api/workflows_format_2/
test/base/api_asserts.py
test/base/api.py
test/base/api_util.py
Expand All @@ -495,6 +448,7 @@ test/base/nose_util.py
test/base/test_logging.py
test/base/tool_shed_util.py
test/base/twilltestcase.py
test/base/workflows_format_2/
test/casperjs/
test/functional/database_contexts.py
test/functional/__init__.py
Expand Down
9 changes: 6 additions & 3 deletions .ci/jenkins/selenium/run_galaxy.bash
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Expand Up @@ -2,9 +2,12 @@

set -e

sleep 30 # TODO: wait on something instead of just sleeping...

echo `df`
echo "Waiting for postgres to become available"
while ! nc -z postgres 5432;
do
sleep 1
printf "."
done

echo "Creating postgres database for Galaxy"
createdb -w -U postgres -h postgres galaxy
Expand Down
23 changes: 2 additions & 21 deletions .ci/py3_sources.txt
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Expand Up @@ -40,26 +40,7 @@ lib/galaxy/quota/
lib/galaxy/sample_tracking/
lib/galaxy/security/
lib/galaxy/tags/
lib/galaxy/tools/actions/
lib/galaxy/tools/cwl/
lib/galaxy/tools/deps/
lib/galaxy/tools/exception_handling.py
lib/galaxy/tools/execute.py
lib/galaxy/tools/lint.py
lib/galaxy/tools/lint_util.py
lib/galaxy/tools/linters/
lib/galaxy/tools/loader.py
lib/galaxy/tools/loader_directory.py
lib/galaxy/tools/parameters/dataset_matcher.py
lib/galaxy/tools/parameters/__init__.py
lib/galaxy/tools/parameters/input_translation.py
lib/galaxy/tools/parameters/sanitize.py
lib/galaxy/tools/parameters/validation.py
lib/galaxy/tools/parameters/wrapped_json.py
lib/galaxy/tools/parameters/wrapped.py
lib/galaxy/tools/parser/
lib/galaxy/tools/test.py
lib/galaxy/tools/toolbox/
lib/galaxy/tools/
lib/galaxy/tours/
lib/galaxy/util/
lib/galaxy/visualization/
Expand All @@ -84,7 +65,7 @@ lib/galaxy/webapps/tool_shed/util/ratings_util.py
lib/galaxy/work/
lib/galaxy/workflow/extract.py
lib/galaxy/workflow/run.py
lib/galaxy/workflow/schedulers/core.py
lib/galaxy/workflow/schedulers/
lib/galaxy/workflow/steps.py
lib/galaxy_ext/
lib/galaxy_utils/
Expand Down
8 changes: 6 additions & 2 deletions README.rst
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Expand Up @@ -9,9 +9,13 @@ The latest information about Galaxy is available via `https://galaxyproject.org/

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat with us
:alt: Chat on irc

.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter

.. image:: https://img.shields.io/badge/docs-release-green.svg
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation

Expand Down
1 change: 1 addition & 0 deletions client/galaxy/scripts/mvc/form/form-parameters.js
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Expand Up @@ -151,6 +151,7 @@ define(['utils/utils',
area : input_def.area,
readonly : input_def.readonly,
placeholder : input_def.placeholder,
datalist : input_def.datalist,
onchange : input_def.onchange
});
},
Expand Down
2 changes: 1 addition & 1 deletion client/galaxy/scripts/mvc/form/form-section.js
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Expand Up @@ -144,7 +144,7 @@ function( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {
this.app.field_list[ id ] = field;
var input_element = new InputElement( this.app, {
name : input_def.name,
label : input_def.label || input_def.name,
label : input_def.hide_label ? '' : input_def.label || input_def.name,
value : input_def.value,
text_value : input_def.text_value,
collapsible_value : input_def.collapsible_value,
Expand Down
9 changes: 5 additions & 4 deletions client/galaxy/scripts/mvc/form/form-view.js
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Expand Up @@ -9,7 +9,8 @@ function( Utils, Portlet, Ui, FormSection, FormData ) {
initial_errors : false,
cls : 'ui-portlet-limited',
icon : null,
always_refresh : true
always_refresh : true,
message_status : 'warning'
});
this.setElement( '<div/>' );
this.render();
Expand Down Expand Up @@ -123,7 +124,7 @@ function( Utils, Portlet, Ui, FormSection, FormData ) {
/** Renders/appends dom elements of the form */
_renderForm: function() {
$( '.tooltip' ).remove();
this.message = new Ui.Message();
this.message = new Ui.UnescapedMessage();
this.section = new FormSection.View( this, { inputs: this.options.inputs } );
this.portlet = new Portlet.View({
icon : this.options.icon,
Expand All @@ -138,8 +139,8 @@ function( Utils, Portlet, Ui, FormSection, FormData ) {
this.portlet.append( this.section.$el );
this.$el.empty();
this.options.inputs && this.$el.append( this.portlet.$el );
this.options.message && this.message.update( { persistent: true, status: 'warning', message: this.options.message } );
this.options.message && this.message.update( { persistent: true, status: this.options.message_status, message: this.options.message } );
Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );
}
});
});
});
13 changes: 8 additions & 5 deletions client/galaxy/scripts/mvc/tool/tool-form-composite.js
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@@ -1,6 +1,7 @@
/** This is the run workflow tool form view. */
define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-data', 'mvc/tool/tool-form-base', 'mvc/ui/ui-modal', 'mvc/webhooks' ],
function( Utils, Deferred, Ui, Form, FormData, ToolFormBase, Modal, Webhooks ) {
define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-data', 'mvc/tool/tool-form-base', 'mvc/ui/ui-modal', 'mvc/webhooks', 'mvc/workflow/workflow-icons' ],
function( Utils, Deferred, Ui, Form, FormData, ToolFormBase, Modal, Webhooks, WorkflowIcons ) {

var View = Backbone.View.extend({
initialize: function( options ) {
var self = this;
Expand Down Expand Up @@ -37,10 +38,11 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
this.parms = [];
_.each( this.model.get( 'steps' ), function( step, i ) {
Galaxy.emit.debug( 'tool-form-composite::initialize()', i + ' : Preparing workflow step.' );
var icon = WorkflowIcons[step.step_type];
step = Utils.merge( {
index : i,
name : 'Step ' + ( parseInt( i ) + 1 ) + ': ' + step.name,
icon : '',
name : step.name,
icon : icon || '',
help : null,
description : step.annotation && ' - ' + step.annotation || step.description,
citations : null,
Expand Down Expand Up @@ -270,7 +272,8 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
);
}
} else {
_.each( step.inputs, function( input ) { input.flavor = 'module' } );
var is_simple_input = ([ 'data_input', 'data_collection_input' ]).indexOf( step.step_type ) != -1;
_.each( step.inputs, function( input ) { input.flavor = 'module'; input.hide_label = is_simple_input; } );
form = new Form( Utils.merge({
title : '<b>' + step.name + '</b>',
onchange : function() { _.each( self.links[ step.index ], function( link ) { self._refreshStep( link ) } ) },
Expand Down
46 changes: 28 additions & 18 deletions client/galaxy/scripts/mvc/ui/ui-misc.js
View file
Expand Up @@ -62,7 +62,7 @@ define(['utils/utils',
this.$el.addClass( 'alert' ).addClass( 'alert-' + status );
}
if ( this.model.get( 'message' ) ) {
this.$el.html( this.model.get( 'message' ) );
this.$el.html( this.messageForDisplay() );
this.$el[ this.model.get( 'fade' ) ? 'fadeIn' : 'show' ]();
this.timeout && window.clearTimeout( this.timeout );
if ( !this.model.get( 'persistent' ) ) {
Expand All @@ -75,6 +75,15 @@ define(['utils/utils',
this.$el.fadeOut();
}
return this;
},
messageForDisplay: function() {
return _.escape( this.model.get( 'message' ) );
}
});

var UnescapedMessage = Message.extend({
messageForDisplay: function() {
return this.model.get( 'message' );
}
});

Expand Down Expand Up @@ -152,21 +161,22 @@ define(['utils/utils',
});

return {
Button : Buttons.ButtonDefault,
ButtonIcon : Buttons.ButtonIcon,
ButtonCheck : Buttons.ButtonCheck,
ButtonMenu : Buttons.ButtonMenu,
ButtonLink : Buttons.ButtonLink,
Input : Input,
Label : Label,
Message : Message,
Modal : Modal,
RadioButton : Options.RadioButton,
Checkbox : Options.Checkbox,
Radio : Options.Radio,
Select : Select,
Hidden : Hidden,
Slider : Slider,
Drilldown : Drilldown
Button : Buttons.ButtonDefault,
ButtonIcon : Buttons.ButtonIcon,
ButtonCheck : Buttons.ButtonCheck,
ButtonMenu : Buttons.ButtonMenu,
ButtonLink : Buttons.ButtonLink,
Input : Input,
Label : Label,
Message : Message,
UnescapedMessage : UnescapedMessage,
Modal : Modal,
RadioButton : Options.RadioButton,
Checkbox : Options.Checkbox,
Radio : Options.Radio,
Select : Select,
Hidden : Hidden,
Slider : Slider,
Drilldown : Drilldown
}
});
});
2 changes: 1 addition & 1 deletion client/galaxy/scripts/mvc/workflow/workflow-canvas.js
View file
Expand Up @@ -157,7 +157,7 @@ define([], function() {
y = position.top / in_h * o_h,
w = node_element.width() / in_w * o_w,
h = node_element.height() / in_h * o_h;
if (node.tool_errors){
if (node.errors){
c.fillStyle = "#FFCCCC";
c.strokeStyle = "#AA6666";
} else if (node.workflow_outputs !== undefined && node.workflow_outputs.length > 0){
Expand Down
9 changes: 9 additions & 0 deletions client/galaxy/scripts/mvc/workflow/workflow-icons.js
View file
@@ -0,0 +1,9 @@
define([], function() {
return {
'tool': 'fa-wrench',
'data_input': 'fa-file-o',
'data_collection_input': 'fa-folder-o',
'subworkflow': 'fa-sitemap fa-rotate-270',
'pause': 'fa-pause'
};
});
23 changes: 13 additions & 10 deletions client/galaxy/scripts/mvc/workflow/workflow-manager.js
View file
Expand Up @@ -189,13 +189,15 @@ function( Connector, Toastr ) {
// really a sneaky if statement
var cons = []
$.each( t.connectors, function ( i, c ) {
var con_dict = { id: c.handle1.node.id, output_name: c.handle1.name };
var input_subworkflow_step_id = t.attributes.input.input_subworkflow_step_id;
if( input_subworkflow_step_id !== undefined ) {
con_dict["input_subworkflow_step_id"] = input_subworkflow_step_id;
if ( c.handle1 ) {
var con_dict = { id: c.handle1.node.id, output_name: c.handle1.name };
var input_subworkflow_step_id = t.attributes.input.input_subworkflow_step_id;
if( input_subworkflow_step_id !== undefined ) {
con_dict["input_subworkflow_step_id"] = input_subworkflow_step_id;
}
cons[i] = con_dict;
input_connections[ t.name ] = cons;
}
cons[i] = con_dict;
input_connections[ t.name ] = cons;
});
});
var post_job_actions = {};
Expand All @@ -219,7 +221,7 @@ function( Connector, Toastr ) {
type : node.type,
content_id : node.content_id,
tool_state : node.tool_state,
tool_errors : node.tool_errors,
errors : node.errors,
input_connections : input_connections,
position : $(node.element).position(),
annotation: node.annotation,
Expand Down Expand Up @@ -328,13 +330,13 @@ function( Connector, Toastr ) {
this.active_node.make_inactive();
this.active_node = null;
}
this.app.showToolForm( "<div>No node selected</div>", {id: 'no-node'} );
this.app.showAttributes();
},
activate_node : function( node ) {
if ( this.active_node != node ) {
this.check_changes_in_active_form();
this.clear_active_node();
this.app.showToolForm( node.form_html, node );
this.app.showForm( node.config_form, node );
node.make_active();
this.active_node = node;
}
Expand All @@ -344,8 +346,9 @@ function( Connector, Toastr ) {
if ( this.active_node == node && force ) {
// Force changes to be saved even on new connection (previously dumped)
this.check_changes_in_active_form();
this.app.showToolForm( node.form_html, node );
this.app.showForm( node.config_form, node );
}
this.app.showWorkflowParameters();
},
layout : function () {
this.check_changes_in_active_form();
Expand Down

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