mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'dev' into ui_pref_routing
This commit is contained in:
guerler
@@ -43,6 +43,12 @@ HDAListItemView.prototype.templates = (function(){
|
||||
'<span class="hid"><%- dataset.hid %></span> ',
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||||
'<span class="name"><%- dataset.name %></span>',
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||||
'</div>',
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||||
'</br>',
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||||
'<span class="nametags">',
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||||
'<% _.each(dataset.nametags, function(tag){ %>',
|
||||
'<span class="label label-info"><%- tag %></span>',
|
||||
'<% }); %>',
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||||
'</span>',
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||||
'</div>'
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||||
], 'dataset' );
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||||
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||||
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||||
@@ -221,7 +221,8 @@ var View = Backbone.View.extend({
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||||
hid : item.hid,
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keep : item.keep,
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||||
label: item.hid + ': ' + item.name,
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value: item.id
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value: item.id,
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||||
tags : item.tags
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||||
});
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||||
self.history[ item.id + '_' + src ] = item;
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||||
});
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||||
|
||||
@@ -109,6 +109,11 @@ var View = Backbone.View.extend({
|
||||
}
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||||
},
|
||||
|
||||
/** Matches a search term with a given text */
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||||
_match: function( term, text ) {
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||||
return !term || term == '' || String( text ).toUpperCase().indexOf( term.toUpperCase() ) >= 0
|
||||
},
|
||||
|
||||
/** Updates the selection options */
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||||
_changeData: function() {
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||||
var self = this;
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||||
@@ -125,22 +130,44 @@ var View = Backbone.View.extend({
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||||
if ( this.model.get( 'searchable' ) ) {
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||||
this.data2 = [];
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||||
_.each( this.data, function( option, index ) {
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self.data2.push( { order: index, id: option.value, text: option.label } );
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self.data2.push( { order: index, id: option.value, text: option.label, tags: option.tags } );
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});
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this.$select.data( 'select2' ) && this.$select.select2( 'destroy' );
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this.matched_tags = {};
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||||
this.$select.select2({
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data : self.data2,
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closeOnSelect : !this.model.get( 'multiple' ),
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||||
multiple : this.model.get( 'multiple' ),
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||||
query : function( q ) {
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||||
self.matched_tags = {};
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||||
var pagesize = self.model.get( 'pagesize' );
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var results = _.filter( self.data2, function ( e ) {
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||||
return !q.term || q.term == '' || e.text.toUpperCase().indexOf( q.term.toUpperCase() ) >= 0;
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var found = false;
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_.each( e.tags, function( tag ) {
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||||
if ( self._match( q.term, tag ) ) {
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found = self.matched_tags[ tag ] = true;
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||||
}
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||||
});
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||||
return found || self._match( q.term, e.text );
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||||
});
|
||||
q.callback({
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||||
results: results.slice( ( q.page - 1 ) * pagesize, q.page * pagesize ),
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more : results.length >= q.page * pagesize
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||||
});
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||||
},
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||||
formatResult : function( result ) {
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||||
return _.escape( result.text ) +
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'<div class="ui-tags">' +
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_.reduce( result.tags, function( memo, tag ) {
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if ( self.matched_tags[ tag ] ) {
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||||
return memo + ' ' +
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||||
'<div class="label label-info">' +
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||||
_.escape( tag ) +
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||||
'</div>'
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||||
}
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||||
return memo;
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||||
}, '' ) +
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'</div>';
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}
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||||
});
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this.$( '.select2-container .select2-search input' ).off( 'blur' );
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@@ -106,7 +106,7 @@ define( [ 'utils/utils' ], function( Utils ) {
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_templateRow: function( options ) {
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||||
return '<tr class="upload-ftp-row">' +
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'<td class="_has_collection" style="display: none;"><div class="icon"/></td>' +
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||||
'<td class="ftp-name">' + options.path + '</td>' +
|
||||
'<td class="ftp-name">' + _.escape(options.path) + '</td>' +
|
||||
'<td class="ftp-size">' + Utils.bytesToString( options.size ) + '</td>' +
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||||
'<td class="ftp-time">' + options.ctime + '</td>' +
|
||||
'</tr>';
|
||||
|
||||
@@ -18,6 +18,7 @@ window.async_save_text = require( 'utils/async-save-text' );
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||||
var POPUPMENU = require( 'ui/popupmenu' );
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||||
window.make_popupmenu = POPUPMENU.make_popupmenu;
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||||
window.make_popup_menus = POPUPMENU.make_popup_menus;
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||||
window.toolform = require( 'mvc/tool/tool-form' );
|
||||
window.init_tag_click_function = require( 'ui/autocom_tagging' );
|
||||
var TOURS = require( 'mvc/tours' );
|
||||
var QUERY_STRING = require( 'utils/query-string-parsing' );
|
||||
|
||||
@@ -221,6 +221,13 @@
|
||||
}
|
||||
}
|
||||
}
|
||||
span.nametags {
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||||
span.label {
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||||
display: inline-block;
|
||||
margin-right: 2px;
|
||||
text-decoration: none;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -68,6 +68,11 @@
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||||
font-weight: bold;
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||||
}
|
||||
|
||||
.ui-tags {
|
||||
word-wrap: break-word;
|
||||
padding-right: 25px;
|
||||
}
|
||||
|
||||
.ui-message {
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||||
padding: 2px 10px 2px 10px;
|
||||
margin-top: @ui-margin-vertical-large;
|
||||
|
||||
@@ -598,6 +598,10 @@
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||||
<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
|
||||
<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
|
||||
<!-- PlantTribes datatypes -->
|
||||
<datatype extension="ptalign" type="galaxy.datatypes.text:PlantTribesMultipleSequenceAlignment" />
|
||||
<datatype extension="ptortho" type="galaxy.datatypes.text:PlantTribesOrtho" />
|
||||
<datatype extension="ptorthocs" type="galaxy.datatypes.text:PlantTribesOrthoCodingSequence" />
|
||||
<datatype extension="pttree" type="galaxy.datatypes.text:PlantTribesPhylogeneticTree" />
|
||||
<datatype extension="smat" type="galaxy.datatypes.text:Smat" display_in_upload="true" />
|
||||
</registration>
|
||||
<sniffers>
|
||||
|
||||
@@ -355,6 +355,16 @@ paste.app_factory = galaxy.web.buildapp:app_factory
|
||||
# separated list.
|
||||
#interactive_environment_plugins_directory =
|
||||
|
||||
# To run interactive environment containers in Docker Swarm mode (on an
|
||||
# existing swarm), set this option to True and set `docker_connect_port` in the
|
||||
# IE plugin config (ini) file(s) of any IE plugins you have enabled and ensure
|
||||
# that you are not using any `docker run`-specific options in your plugins'
|
||||
# `command_inject` options (swarm mode services run using `docker service
|
||||
# create`, which has a different and more limited set of options). This option
|
||||
# can be overridden on a per-plugin basis by using the `swarm_mode` option in
|
||||
# the plugin's ini config file.
|
||||
#interactive_environment_swarm_mode = False
|
||||
|
||||
# Interactive tour directory: where to store interactive tour definition files.
|
||||
# Galaxy ships with several basic interface tours enabled, though a different
|
||||
# directory with custom tours can be specified here. The path is relative to the
|
||||
@@ -1191,7 +1201,7 @@ use_interactive = True
|
||||
# walltime limits but did fail quickly (either while queueing or running). The
|
||||
# commented out default below results in no default job resubmission condition,
|
||||
# failing jobs are just failed outright.
|
||||
#default_job_resubmission_condition =
|
||||
#default_job_resubmission_condition =
|
||||
|
||||
# In multiprocess configurations, notification between processes about new jobs
|
||||
# must be done via the database. In single process configurations, this can be
|
||||
|
||||
@@ -41,3 +41,15 @@ image = qiaoy/iobio-bundle.bam-iobio:1.0-ondemand
|
||||
# share data between the IE and Galaxy.
|
||||
#docker_galaxy_temp_dir = None
|
||||
|
||||
# If your Docker container exposes more then one port, Galaxy needs to know to
|
||||
# which ports it needs to connect. With this option you can specify the port number
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For qiaoy/iobio-bundle.bam-iobio the port
|
||||
# should most likely be 8000.
|
||||
# - If command_inject is uncommented and includes `--sig-proxy`, that option should
|
||||
# be removed.
|
||||
#swarm_mode = False
|
||||
|
||||
@@ -18,7 +18,7 @@
|
||||
# The image argument was moved to "allowed_images.yml.sample"
|
||||
|
||||
# Additional arguments that are passed to the `docker run` command.
|
||||
command_inject = --sig-proxy=true -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120
|
||||
#command_inject = --sig-proxy=true -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120
|
||||
|
||||
# URL to access the Galaxy API with from the spawn Docker containter, if empty
|
||||
# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
|
||||
@@ -43,4 +43,12 @@ command_inject = --sig-proxy=true -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=12
|
||||
# If your Docker container exposes more then one port, Galaxy needs to know to
|
||||
# which ports it needs to connect. With this option you can specify the port number
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
# docker_connect_port = None
|
||||
#docker_connect_port = None
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For Jupyter the # port should most likely be
|
||||
# 8888.
|
||||
# - If command_inject is uncommented and includes `--sig-proxy`, that option should
|
||||
# be removed.
|
||||
#swarm_mode = False
|
||||
|
||||
@@ -40,3 +40,16 @@ command_inject = --sig-proxy=true -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=12
|
||||
# you can have a shared sshfs share which you can use as temporary directory to
|
||||
# share data between the IE and Galaxy.
|
||||
#docker_galaxy_temp_dir = None
|
||||
|
||||
# If your Docker container exposes more then one port, Galaxy needs to know to
|
||||
# which ports it needs to connect. With this option you can specify the port number
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For thoba/neo4j_galaxy_ie the port
|
||||
# should most likely be 7474.
|
||||
# - If command_inject is uncommented and includes `--sig-proxy`, that option should
|
||||
# be removed.
|
||||
#swarm_mode = False
|
||||
|
||||
@@ -19,3 +19,16 @@ image = shiltemann/docker-phinch-galaxy:16.04
|
||||
# The Docker hostname. It can be useful to run the Docker daemon on a different
|
||||
# host than Galaxy.
|
||||
#docker_hostname = localhost
|
||||
|
||||
# If your Docker container exposes more then one port, Galaxy needs to know to
|
||||
# which ports it needs to connect. With this option you can specify the port number
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For shiltemann/docker-phinch-galaxy the port
|
||||
# should most likely be 80.
|
||||
# - If command_inject is uncommented and includes `--sig-proxy`, that option should
|
||||
# be removed.
|
||||
#swarm_mode = False
|
||||
|
||||
@@ -41,3 +41,16 @@ password_auth = True
|
||||
# you can have a shared sshfs share which you can use as temporary directory to
|
||||
# share data between the IE and Galaxy.
|
||||
#docker_galaxy_temp_dir = None
|
||||
|
||||
# If your Docker container exposes more then one port, Galaxy needs to know to
|
||||
# which ports it needs to connect. With this option you can specify the port number
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For erasche/docker-rstudio-notebook the port
|
||||
# should most likely be 80.
|
||||
# - If command_inject is uncommented and includes `--sig-proxy`, that option should
|
||||
# be removed.
|
||||
#swarm_mode = False
|
||||
|
||||
@@ -0,0 +1,22 @@
|
||||
name: searchover
|
||||
type:
|
||||
- masthead
|
||||
activate: true
|
||||
|
||||
icon: fa-search
|
||||
tooltip: Click to activate search and press Ctrl + Alt + q to open the overlay
|
||||
|
||||
function: >
|
||||
$.getJSON("/api/webhooks", function( data ) {
|
||||
for( var item in data ) {
|
||||
var webhook = data[item];
|
||||
if( webhook.name === "searchover" ) {
|
||||
if( webhook.script && !window.static_search ) {
|
||||
$( '<script/>', { type: 'text/javascript' } ).text( webhook.script ).appendTo( 'head' );
|
||||
$( '<style/>', { type: 'text/css' } ).text( webhook.styles ).appendTo( 'head' );
|
||||
window.static_search = true;
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
});
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,177 @@
|
||||
.overlay-wrapper {
|
||||
margin-top: -5%;
|
||||
}
|
||||
|
||||
.search-screen {
|
||||
position: fixed;
|
||||
z-index: 202;
|
||||
width:100%;
|
||||
height:100%;
|
||||
display:none;
|
||||
}
|
||||
|
||||
.search-screen-overlay {
|
||||
position: fixed;
|
||||
top:0;
|
||||
left:0;
|
||||
background: rgba(224, 224, 224, 0.75);
|
||||
z-index: 201;
|
||||
width:100%;
|
||||
height:100%;
|
||||
display:none;
|
||||
opacity: 2;
|
||||
}
|
||||
|
||||
.overlay-filters {
|
||||
display: table;
|
||||
margin: 0 auto 5px;
|
||||
}
|
||||
|
||||
.overlay-filters ul {
|
||||
list-style-type: none;
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
overflow: hidden;
|
||||
}
|
||||
|
||||
.overlay-filters li {
|
||||
float: left;
|
||||
}
|
||||
|
||||
.overlay-filters li a {
|
||||
display: block;
|
||||
text-decoration: none;
|
||||
cursor: pointer;
|
||||
font-weight: bold;
|
||||
padding: 5px 5px;
|
||||
}
|
||||
|
||||
.overlay-filters li a:hover i {
|
||||
color: #212121;
|
||||
}
|
||||
|
||||
.overlay-filters li a i {
|
||||
font-size: 1.5em;
|
||||
}
|
||||
|
||||
.search-header {
|
||||
background-color: #e1e1e1;
|
||||
background: -moz-linear-gradient(top, rgba(225, 225, 225, 1) 0%, rgba(238, 238, 238, 1) 37%, rgba(225, 225, 225, 1) 100%);
|
||||
background: linear-gradient(to bottom, rgba(225, 225, 225, 1) 0%, rgba(238, 238, 238, 1) 37%, rgba(225, 225, 225, 1) 100%);
|
||||
-moz-box-shadow: 0px 2px 5px 0px rgba(158, 158, 158, 0.75);
|
||||
box-shadow: 0px 2px 5px 0px rgba(158, 158, 158, 0.75);
|
||||
|
||||
position: fixed;
|
||||
top: 34px;
|
||||
width: 100%;
|
||||
z-index: 203;
|
||||
}
|
||||
|
||||
.txtbx-search-data {
|
||||
font-size: 12px;
|
||||
text-align: center;
|
||||
border-radius: 14px;
|
||||
border: 1px solid #2c3143;
|
||||
margin: 20px auto 10px;
|
||||
width: 300px;
|
||||
padding: 11px;
|
||||
}
|
||||
|
||||
.search-section {
|
||||
color: #007AB5;
|
||||
margin-top: 20px;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.search-section .section-title {
|
||||
margin-left: 7px;
|
||||
}
|
||||
|
||||
.link-tile {
|
||||
background-color: #0070A8;
|
||||
border: 1px solid #005A85;
|
||||
border-radius: 5px;
|
||||
font-size: 12px;
|
||||
width: 19%;
|
||||
height: 75px;
|
||||
margin: 0.5%;
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
.link-tile.btn-primary:hover,
|
||||
.link-tile.btn-primary:hover {
|
||||
background-color: #005A85;
|
||||
border-color: #005A85;
|
||||
}
|
||||
|
||||
.link-tile.btn-primary:active,
|
||||
.link-tile.btn-primary:focus {
|
||||
background-color: #005A85;
|
||||
border-color: #005A85;
|
||||
}
|
||||
|
||||
.search-results,
|
||||
.removed-items {
|
||||
position: fixed;
|
||||
top: 125px;
|
||||
overflow-x: hidden;
|
||||
overflow-y: auto;
|
||||
padding: 0 15px;
|
||||
width: 100%;
|
||||
height: 83%;
|
||||
display: none;
|
||||
}
|
||||
|
||||
.item-actions {
|
||||
padding: 5px;
|
||||
}
|
||||
|
||||
.item-actions:hover {
|
||||
color: gold;
|
||||
}
|
||||
|
||||
.pin-item {
|
||||
float: left;
|
||||
}
|
||||
|
||||
.restore-item,
|
||||
.remove-fav,
|
||||
.remove-item {
|
||||
float: right;
|
||||
}
|
||||
|
||||
.filter-active i {
|
||||
/*color: gold;*/
|
||||
color: #616161;
|
||||
}
|
||||
|
||||
.filter-active i:hover {
|
||||
color: #212121;
|
||||
}
|
||||
|
||||
.filter-inactive i {
|
||||
font-size: 0.875em;
|
||||
color: #9e9e9e;
|
||||
}
|
||||
|
||||
.rotate {
|
||||
transform: rotate(90deg);
|
||||
}
|
||||
|
||||
.pinned-item {
|
||||
color: gold;
|
||||
transform: rotate(60deg);
|
||||
}
|
||||
|
||||
.hide {
|
||||
display: none;
|
||||
}
|
||||
|
||||
.show {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.no-results {
|
||||
color: white;
|
||||
margin-top: 0.8%;
|
||||
}
|
||||
@@ -0,0 +1,24 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
# When running Galaxy Interactive Environments on a swarm (using Docker Engine
|
||||
# swarm mode), GIE sessions that have ended will leave behind "shut down"
|
||||
# Docker services. These must be removed, which you can do with this script.
|
||||
#
|
||||
# Note that this is dependent on the specific ordering and output format of
|
||||
# `docker service ls` and `docker service ps`. As of the time of writing
|
||||
# (Docker version 1.13.1) these formats cannot be controlled as can be done
|
||||
# with `docker ps` and the `--format` option, so be careful when upgrading
|
||||
# Docker releases.
|
||||
|
||||
|
||||
CONTAINER_NAME_PREFIX='galaxy_gie_'
|
||||
LOG_PATH=${1:-'/tmp/galaxy_gie_service_clean.log'}
|
||||
|
||||
|
||||
{
|
||||
echo "Running cleanup at $(date)"
|
||||
for service_name in $(docker service ls | awk "\$2 ~ /^$CONTAINER_NAME_PREFIX/ {print \$2}"); do
|
||||
docker service ps --no-trunc $service_name | tail -1 | awk '{print $6}' | grep -q '^Shutdown$' && docker service rm $service_name;
|
||||
done
|
||||
echo "Done"
|
||||
} >>$LOG_PATH
|
||||
@@ -201,7 +201,8 @@ You might want to run your IEs on a host different to the one that hosts your
|
||||
Galaxy webserver, since IEs on the same host as the webserver compete for
|
||||
resources with that webserver and introduce some security considerations which
|
||||
could be mitigated by moving containers to a separate host. This feature has
|
||||
been available since 15.07 and is used in production at the University of Freiburg.
|
||||
been available since 15.07 and is used in production at the University of
|
||||
Freiburg and on usegalaxy.org.
|
||||
|
||||
First you need to configure a second host to be Docker enabled. In the
|
||||
following we call this host ``gx-docker`` You need to start the Docker daemon
|
||||
@@ -213,9 +214,9 @@ you can start the daemon with
|
||||
$ docker -H 0.0.0.0:4243 -d
|
||||
|
||||
On your client, the Galaxy webserver, you can now install a Docker client. This
|
||||
can also be done on older Systems like Scientific-Linux, CentOS 6, which does
|
||||
not have Docker support by default. The client just talks to the Docker daemon
|
||||
on host ``gx-docker``, and does not run anything itself, locally. You can test
|
||||
can also be done on older systems like Scientific-Linux, CentOS 6, which do not
|
||||
have Docker support by default. The client just talks to the Docker daemon on
|
||||
host ``gx-docker``, and does not run anything itself, locally. You can test
|
||||
your configuration for example by starting busybox from your client on the
|
||||
Docker host with
|
||||
|
||||
@@ -223,7 +224,13 @@ Docker host with
|
||||
|
||||
$ docker -H tcp://gx-docker:4243 run -it busybox sh
|
||||
|
||||
So far so good! Now we need to configure Galaxy to use our new Docker host
|
||||
So far so good! Note, however, that unless restricted by a firewall, this mode
|
||||
of operation is insecure, as any client could connect and run containers on
|
||||
``gx-docker``. If this is a concern at your site, follow the instructions in
|
||||
the Docker documentation to `Protect the Docker daemon socket
|
||||
<https://docs.docker.com/engine/security/https/>`__.
|
||||
|
||||
Now we need to configure Galaxy to use our new Docker host
|
||||
to start the Interactive Environments. For that we need to edit the Jupyter GIE
|
||||
configuration, ``jupyter.ini`` to use our custom docker host
|
||||
|
||||
@@ -233,14 +240,18 @@ configuration, ``jupyter.ini`` to use our custom docker host
|
||||
|
||||
[docker]
|
||||
command = docker -H tcp://gx-docker:4243 {docker_args}
|
||||
image = bgruening/docker-ipython-notebook:dev
|
||||
docker_hostname = gx-docker
|
||||
|
||||
Please adapt your ``command`` and the ``image`` as needed.
|
||||
Please adapt your ``command`` as needed.
|
||||
|
||||
As next step we need to configure a share mount point between the Docker host
|
||||
and Galaxy. Unfortunately, this can not be a NFS mount. Docker does not like
|
||||
NFS yet. You could for example use a sshfs mount with the following script
|
||||
The Jupyter GIE supports getting and fetching Galaxy history datasets entirely
|
||||
through the Galaxy API so it is not necessary to share a filesystem with
|
||||
``gx-docker``. However, other GIE plugins may still require this.
|
||||
|
||||
For those GIE plugins, we need to configure a share mount point between the
|
||||
Docker host and Galaxy. Unfortunately, this can not be a NFS mount. Docker does
|
||||
not like NFS yet. You could for example use a sshfs mount with the following
|
||||
script
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@@ -252,3 +263,58 @@ NFS yet. You could for example use a sshfs mount with the following script
|
||||
fi
|
||||
|
||||
This will let Galaxy and the Docker host share temporary files.
|
||||
|
||||
Docker Engine Swarm Mode
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
As of Docker Engine version 1.12, Docker Engine can be configured to provide a
|
||||
cluster of Docker Engines in a configuration known as *Docker Engine swarm
|
||||
mode*. This replaces the previous and similarly named *Docker Swarm*
|
||||
clustering solution, which is not compatible with swarm mode.
|
||||
|
||||
`The Docker Engine swarm mode documentation
|
||||
<https://docs.docker.com/engine/swarm/>`__ fully explains the differences, but
|
||||
the major difference is that whereas under Docker Swarm one could run commands
|
||||
on the swarm with ``docker run``, Docker Engine swarm mode requires one to
|
||||
create persistent services with ``docker service create`` and to remove those
|
||||
services once no longer in use with ``docker service rm``.
|
||||
|
||||
Galaxy supports both Docker Engine swarm mode and the legacy Docker Swarm
|
||||
system. Legacy Docker Swarm is supported without any special configuration,
|
||||
because the containers are still run with ``docker run`` as before. To support
|
||||
Docker Engine swarm mode, additional configuration is required. Begin by
|
||||
editing your GIE config plugin's ini configuration file (e.g. ``jupyter.ini``)
|
||||
and set the ``docker_connect_port`` and ``swarm_mode options`` in addition to
|
||||
any other relevant options. Unless you are using a non-standard Docker image,
|
||||
the correct value for ``docker_connect_port`` should be suggested to you in the
|
||||
sample configuration file:
|
||||
|
||||
.. code-block:: ini
|
||||
|
||||
[docker]
|
||||
docker_connect_port = 8888
|
||||
swarm_mode = True
|
||||
|
||||
Note that your Galaxy server does not need to be a member of the swarm itself.
|
||||
It can use the method outlined above in the `Docker on Another Host`_ section
|
||||
to connect as a client to a Docker daemon acting as a swarm mode manager.
|
||||
|
||||
Once configured, you should see that your GIE containers are started and run as
|
||||
services, which you can inspect using the ``docker service ls`` command and
|
||||
other ``docker service`` subcommands.
|
||||
|
||||
**Docker services are not cleaned up by Galaxy**. To clean them up, we have
|
||||
provided a script that can be run from cron which will locate "shut down"
|
||||
services (GIE containers which have stopped themselves) at
|
||||
`cron/clean_docker_swarm_mode_services.sh
|
||||
<https://github.com/galaxyproject/galaxy/blob/dev/cron/clean_docker_swarm_mode_services.sh>`__
|
||||
in the Galaxy source. This script can be run from cron with a crontab entry
|
||||
like this example which runs every 15 minutes:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
*/15 * * * * bash /path/to/clean_docker_swarm_mode_services.sh /path/to/galaxy/log/dir/clean_docker_swarm_mode_services.log
|
||||
|
||||
This entry would be suitable to be run as ``root`` on a swarm mode manager. You
|
||||
could also run it as the Galaxy user on the Galaxy server (with modifications
|
||||
to set the correct daemon socket, if running remotely).
|
||||
|
||||
+12
-19
@@ -577,6 +577,8 @@ class Configuration( object ):
|
||||
elif ie_dirs:
|
||||
self.visualization_plugins_directory += ",%s" % ie_dirs
|
||||
|
||||
self.gie_swarm_mode = string_as_bool( kwargs.get( 'interactive_environment_swarm_mode', False ) )
|
||||
|
||||
self.proxy_session_map = self.resolve_path( kwargs.get( "dynamic_proxy_session_map", "database/session_map.sqlite" ) )
|
||||
self.manage_dynamic_proxy = string_as_bool( kwargs.get( "dynamic_proxy_manage", "True" ) ) # Set to false if being launched externally
|
||||
self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) )
|
||||
@@ -901,34 +903,25 @@ class ConfiguresGalaxyMixin:
|
||||
|
||||
time.sleep(1)
|
||||
|
||||
def reload_toolbox(self):
|
||||
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
|
||||
|
||||
tool_configs = self.config.tool_configs
|
||||
if self.config.migrated_tools_config not in tool_configs:
|
||||
tool_configs.append( self.config.migrated_tools_config )
|
||||
|
||||
from galaxy import tools
|
||||
old_toolbox = self.toolbox
|
||||
self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
|
||||
self.reindex_tool_search()
|
||||
if old_toolbox:
|
||||
old_toolbox.shutdown()
|
||||
|
||||
def _configure_toolbox( self ):
|
||||
from galaxy import tools
|
||||
from galaxy.managers.citations import CitationsManager
|
||||
self.citations_manager = CitationsManager( self )
|
||||
|
||||
from galaxy.tools.deps import containers
|
||||
from galaxy.tools.toolbox.cache import ToolCache
|
||||
from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
|
||||
|
||||
self.citations_manager = CitationsManager( self )
|
||||
self.tool_cache = ToolCache()
|
||||
self.tool_version_cache = ToolVersionCache(self)
|
||||
|
||||
self._toolbox_lock = threading.RLock()
|
||||
self.toolbox = None
|
||||
self.reload_toolbox()
|
||||
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
|
||||
tool_configs = self.config.tool_configs
|
||||
if self.config.migrated_tools_config not in tool_configs:
|
||||
tool_configs.append( self.config.migrated_tools_config )
|
||||
self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
|
||||
self.reindex_tool_search()
|
||||
|
||||
from galaxy.tools.deps import containers
|
||||
galaxy_root_dir = os.path.abspath(self.config.root)
|
||||
file_path = os.path.abspath(getattr(self.config, "file_path"))
|
||||
app_info = containers.AppInfo(
|
||||
|
||||
@@ -270,7 +270,8 @@ class AlignCheck(Tabular):
|
||||
dataset.metadata.column_names = self.column_names
|
||||
dataset.metadata.column_types = self.column_types
|
||||
dataset.metadata.comment_lines = self.comment_lines
|
||||
dataset.metadata.data_lines -= self.comment_lines
|
||||
if isinstance(dataset.metadata.data_lines, int):
|
||||
dataset.metadata.data_lines -= self.comment_lines
|
||||
|
||||
|
||||
class AlignReport(Tabular):
|
||||
@@ -735,7 +736,8 @@ class CountTable(Tabular):
|
||||
dataset.metadata.groups = colnames[2:]
|
||||
|
||||
dataset.metadata.comment_lines = 1
|
||||
dataset.metadata.data_lines -= 1
|
||||
if isinstance(dataset.metadata.data_lines, int):
|
||||
dataset.metadata.data_lines -= 1
|
||||
|
||||
|
||||
class RefTaxonomy(Tabular):
|
||||
|
||||
@@ -605,3 +605,50 @@ class Smat(Text):
|
||||
if re.match(r"[-+]?\d+$", item) is None:
|
||||
return False
|
||||
return True
|
||||
|
||||
|
||||
class PlantTribesOrtho(Html):
|
||||
"""
|
||||
PlantTribes sequences classified into precomputed, orthologous gene family
|
||||
clusters.
|
||||
"""
|
||||
file_ext = "ptortho"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "PlantTribes gene family clusters: %d files" % dataset.metadata.data_lines
|
||||
|
||||
|
||||
class PlantTribesOrthoCodingSequence(Html):
|
||||
"""
|
||||
PlantTribes sequences classified into precomputed, orthologous gene family
|
||||
clusters and corresponding coding sequences.
|
||||
"""
|
||||
file_ext = "ptorthocs"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "PlantTribes gene family clusters with corresponding coding sequences: %d files" % dataset.metadata.data_lines
|
||||
|
||||
|
||||
class PlantTribesPhylogeneticTree(Html):
|
||||
"""
|
||||
PlantTribes multiple sequence alignments and inferred maximum likelihood
|
||||
phylogenies for orthogroups.
|
||||
"""
|
||||
file_ext = "pttree"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "PlantTribes phylogenetic trees: %d files" % dataset.metadata.data_lines
|
||||
|
||||
|
||||
class PlantTribesMultipleSequenceAlignment(Html):
|
||||
"""
|
||||
PlantTribes multiple sequence alignments for orthogroups.
|
||||
"""
|
||||
file_ext = "ptalign"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
|
||||
dataset.blurb = "PlantTribes multiple sequence alignments: %d files" % dataset.metadata.data_lines
|
||||
|
||||
@@ -254,13 +254,18 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
|
||||
'id',
|
||||
'type_id',
|
||||
'name',
|
||||
'history_id', 'hid',
|
||||
'history_id',
|
||||
'hid',
|
||||
'history_content_type',
|
||||
'dataset_id',
|
||||
'state', 'extension',
|
||||
'state',
|
||||
'extension',
|
||||
'deleted', 'purged', 'visible',
|
||||
'type', 'url',
|
||||
'create_time', 'update_time',
|
||||
'nametags',
|
||||
'type',
|
||||
'url',
|
||||
'create_time',
|
||||
'update_time',
|
||||
])
|
||||
self.add_view( 'detailed', [
|
||||
'model_class',
|
||||
@@ -281,6 +286,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
|
||||
'creating_job',
|
||||
'rerunnable',
|
||||
|
||||
'tags',
|
||||
'uuid',
|
||||
'permissions',
|
||||
'file_name',
|
||||
@@ -292,7 +298,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
|
||||
# 'url',
|
||||
'download_url',
|
||||
|
||||
'annotation', 'tags',
|
||||
'annotation',
|
||||
|
||||
'api_type'
|
||||
], include_keys_from='summary' )
|
||||
@@ -326,7 +332,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
|
||||
'misc_blurb' : self._remap_from( 'blurb' ),
|
||||
'file_ext' : self._remap_from( 'extension' ),
|
||||
'file_path' : self._remap_from( 'file_name' ),
|
||||
|
||||
'nametags' : self.serialize_nametags,
|
||||
'resubmitted' : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ),
|
||||
'display_apps' : self.serialize_display_apps,
|
||||
'display_types' : self.serialize_old_display_applications,
|
||||
@@ -380,6 +386,17 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize
|
||||
|
||||
return display_apps
|
||||
|
||||
def serialize_nametags( self, hda, key, trans=None, **context ):
|
||||
"""
|
||||
Return list of 'name' child tags attached to this dataset.
|
||||
TODO: investigate faster ways to fetch 'name' tags and values
|
||||
"""
|
||||
nametags = []
|
||||
for tag in hda.tags:
|
||||
if tag.tag.name == 'name':
|
||||
nametags.append(tag.value)
|
||||
return nametags
|
||||
|
||||
def serialize_old_display_applications( self, hda, key, trans=None, **context ):
|
||||
"""
|
||||
Return dictionary containing old-style display app urls.
|
||||
|
||||
@@ -745,9 +745,7 @@ class WorkflowContentsManager(UsesAnnotations):
|
||||
del step_dict['tool_id']
|
||||
del step_dict['tool_version']
|
||||
del step_dict['tool_inputs']
|
||||
workflow = step.subworkflow
|
||||
step_dict['stored_workflow_id'] = encode(workflow.stored_workflow.id)
|
||||
step_dict['workflow_id'] = encode(workflow.id)
|
||||
step_dict['workflow_id'] = encode(step.subworkflow.id)
|
||||
|
||||
for conn in step.input_connections:
|
||||
step_id = step.id if legacy else step.order_index
|
||||
|
||||
@@ -1416,6 +1416,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
|
||||
.options( joinedload("dataset"),
|
||||
joinedload("dataset.actions"),
|
||||
joinedload("dataset.actions.role"),
|
||||
joinedload("tags"),
|
||||
))
|
||||
self._active_datasets_and_roles = query.all()
|
||||
return self._active_datasets_and_roles
|
||||
|
||||
@@ -226,13 +226,13 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
|
||||
if body.get('noop', None) != self.app.config.server_name:
|
||||
try:
|
||||
f = self.task_mapping[body['task']]
|
||||
log.info("Instance '%s' recieved '%s' task, executing now.", self.app.config.server_name, body['task'])
|
||||
log.info("Instance '%s' received '%s' task, executing now.", self.app.config.server_name, body['task'])
|
||||
f(self.app, **body['kwargs'])
|
||||
except Exception:
|
||||
# this shouldn't ever throw an exception, but...
|
||||
log.exception("Error running control task type: %s" % body['task'])
|
||||
else:
|
||||
log.warning("Recieved a malformed task message:\n%s" % body)
|
||||
log.warning("Received a malformed task message:\n%s" % body)
|
||||
message.ack()
|
||||
|
||||
def shutdown(self):
|
||||
|
||||
@@ -214,6 +214,7 @@ class DefaultToolAction( object ):
|
||||
# format.
|
||||
input_ext = 'data' if tool.profile < 16.04 else "input"
|
||||
input_dbkey = incoming.get( "dbkey", "?" )
|
||||
preserved_tags = []
|
||||
for name, data in reversed(inp_data.items()):
|
||||
if not data:
|
||||
data = NoneDataset( datatypes_registry=app.datatypes_registry )
|
||||
@@ -234,6 +235,9 @@ class DefaultToolAction( object ):
|
||||
if identifier is not None:
|
||||
incoming[ "%s|__identifier__" % name ] = identifier
|
||||
|
||||
for tag in data.tags:
|
||||
preserved_tags.append(tag)
|
||||
|
||||
# Collect chromInfo dataset and add as parameters to incoming
|
||||
( chrom_info, db_dataset ) = app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id != 'CONVERTER_fasta_to_len' )
|
||||
if db_dataset:
|
||||
@@ -303,6 +307,9 @@ class DefaultToolAction( object ):
|
||||
trans.sa_session.add( data )
|
||||
trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions, new=True )
|
||||
|
||||
for tag in preserved_tags:
|
||||
data.tags.append(tag.copy())
|
||||
|
||||
# Must flush before setting object store id currently.
|
||||
# TODO: optimize this.
|
||||
trans.sa_session.flush()
|
||||
|
||||
@@ -215,16 +215,19 @@ class CondaContext(installable.InstallableContext):
|
||||
|
||||
def exec_command(self, operation, args):
|
||||
command = self.command(operation, args)
|
||||
env = {'HOME': self.conda_prefix} # We don't want to pollute ~/.conda, which may not even be writable
|
||||
env = {}
|
||||
condarc_override = self.condarc_override
|
||||
if condarc_override:
|
||||
env["CONDARC"] = condarc_override
|
||||
log.debug("Executing command: %s", command)
|
||||
env['HOME'] = tempfile.mkdtemp(prefix='conda_exec_home_') # We don't want to pollute ~/.conda, which may not even be writable
|
||||
try:
|
||||
return self.shell_exec(command, env=env)
|
||||
except commands.CommandLineException as e:
|
||||
log.warning(e)
|
||||
return e.returncode
|
||||
finally:
|
||||
shutil.rmtree(env['HOME'], ignore_errors=True)
|
||||
|
||||
def exec_create(self, args):
|
||||
create_base_args = [
|
||||
|
||||
@@ -232,7 +232,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li
|
||||
if job_directory:
|
||||
conda_environment = os.path.join(job_directory, conda_env)
|
||||
else:
|
||||
conda_environment = None
|
||||
conda_environment = self.conda_context.env_path(conda_target.install_environment)
|
||||
|
||||
return CondaDependency(
|
||||
self.conda_context,
|
||||
|
||||
@@ -2,7 +2,6 @@
|
||||
Basic tool parameters.
|
||||
"""
|
||||
import logging
|
||||
import numbers
|
||||
import os
|
||||
import os.path
|
||||
import re
|
||||
@@ -131,8 +130,6 @@ class ToolParameter( object, Dictifiable ):
|
||||
|
||||
def to_python( self, value, app ):
|
||||
"""Convert a value created with to_json back to an object representation"""
|
||||
if isinstance( value, numbers.Number ):
|
||||
return unicodify( value )
|
||||
return value
|
||||
|
||||
def value_to_basic( self, value, app, use_security=False ):
|
||||
@@ -1767,8 +1764,13 @@ class DataToolParameter( BaseDataToolParameter ):
|
||||
multiple = self.multiple
|
||||
|
||||
# build and append a new select option
|
||||
def append( list, id, hid, name, src, keep=False ):
|
||||
return list.append( { 'id' : trans.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src, 'keep': keep } )
|
||||
def append( list, hda, name, src, keep=False ):
|
||||
return list.append( { 'id' : trans.security.encode_id( hda.id ),
|
||||
'hid' : hda.hid,
|
||||
'name' : name,
|
||||
'tags' : [ t.user_tname if not t.value else "%s:%s" % (t.user_tname, t.value) for t in hda.tags ],
|
||||
'src' : src,
|
||||
'keep' : keep } )
|
||||
|
||||
# add datasets
|
||||
visible_hda = other_values.get( self.name )
|
||||
@@ -1779,7 +1781,7 @@ class DataToolParameter( BaseDataToolParameter ):
|
||||
m = match.hda
|
||||
has_matched = has_matched or visible_hda == m or visible_hda == hda
|
||||
m_name = '%s (as %s)' % ( match.original_hda.name, match.target_ext ) if match.implicit_conversion else m.name
|
||||
append( d[ 'options' ][ 'hda' ], m.id, m.hid, m_name, 'hda' )
|
||||
append( d[ 'options' ][ 'hda' ], m, m_name, 'hda' )
|
||||
if not has_matched and hasattr( visible_hda, 'hid' ):
|
||||
if visible_hda.deleted:
|
||||
hda_state = 'deleted'
|
||||
@@ -1787,13 +1789,13 @@ class DataToolParameter( BaseDataToolParameter ):
|
||||
hda_state = 'hidden'
|
||||
else:
|
||||
hda_state = 'unavailable'
|
||||
append( d[ 'options' ][ 'hda' ], visible_hda.id, visible_hda.hid, '(%s) %s' % ( hda_state, visible_hda.name ), 'hda', True )
|
||||
append( d[ 'options' ][ 'hda' ], visible_hda, '(%s) %s' % ( hda_state, visible_hda.name ), 'hda', True )
|
||||
|
||||
# add dataset collections
|
||||
dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
|
||||
for hdca in history.active_dataset_collections:
|
||||
if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ):
|
||||
append( d[ 'options' ][ 'hdca' ], hdca.id, hdca.hid, hdca.name, 'hdca' )
|
||||
append( d[ 'options' ][ 'hdca' ], hdca, hdca.name, 'hdca' )
|
||||
|
||||
# sort both lists
|
||||
d['options']['hda'] = sorted(d['options']['hda'], key=lambda k: k['hid'], reverse=True)
|
||||
@@ -1920,20 +1922,22 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
|
||||
# append directly matched collections
|
||||
for hdca in self.match_collections( trans, history, dataset_matcher ):
|
||||
d['options']['hdca'].append({
|
||||
'id': trans.security.encode_id( hdca.id ),
|
||||
'hid': hdca.hid,
|
||||
'name': hdca.name,
|
||||
'src': 'hdca'
|
||||
'id' : trans.security.encode_id( hdca.id ),
|
||||
'hid' : hdca.hid,
|
||||
'name' : hdca.name,
|
||||
'src' : 'hdca',
|
||||
'tags' : [ t.user_tname if not t.value else "%s:%s" % (t.user_tname, t.value) for t in hdca.tags ]
|
||||
})
|
||||
|
||||
# append matching subcollections
|
||||
for hdca in self.match_multirun_collections( trans, history, dataset_matcher ):
|
||||
subcollection_type = self._history_query( trans ).can_map_over( hdca ).collection_type
|
||||
d['options']['hdca'].append({
|
||||
'id': trans.security.encode_id( hdca.id ),
|
||||
'hid': hdca.hid,
|
||||
'name': hdca.name,
|
||||
'src': 'hdca',
|
||||
'id' : trans.security.encode_id( hdca.id ),
|
||||
'hid' : hdca.hid,
|
||||
'name' : hdca.name,
|
||||
'src' : 'hdca',
|
||||
'tags' : [ t.user_tname if not t.value else "%s:%s" % (t.user_tname, t.value) for t in hdca.tags ],
|
||||
'map_over_type': subcollection_type
|
||||
})
|
||||
|
||||
|
||||
@@ -56,10 +56,13 @@ def swap_inf_nan( val ):
|
||||
def safe_loads( arg ):
|
||||
"""
|
||||
This is a wrapper around loads that returns the parsed value instead of
|
||||
raising a value error.
|
||||
raising a value error. It also avoids autoconversion of non-iterables
|
||||
i.e numeric and boolean values.
|
||||
"""
|
||||
try:
|
||||
loaded = json.loads( arg )
|
||||
if loaded is not None and not isinstance( loaded, collections.Iterable ):
|
||||
loaded = arg
|
||||
except ( TypeError, ValueError ):
|
||||
loaded = arg
|
||||
return loaded
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
import logging
|
||||
import os
|
||||
from datetime import datetime, timedelta
|
||||
from six import string_types
|
||||
import six
|
||||
from string import punctuation as PUNCTUATION
|
||||
|
||||
from sqlalchemy import and_, false, func, or_
|
||||
@@ -1120,6 +1120,30 @@ class Admin( object ):
|
||||
job=job,
|
||||
message="<a href='jobs'>Back</a>" )
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def manage_tool_dependencies( self, trans, install_dependencies=False, build_cache=False, install_for_tools=[], viewkey='View tool-centric dependencies'):
|
||||
tools_by_id = trans.app.toolbox.tools_by_id
|
||||
if install_dependencies:
|
||||
# install the dependencies for the tools in the install_for_tools list
|
||||
if not isinstance(install_for_tools, list):
|
||||
install_for_tools = [install_for_tools]
|
||||
requirements = set([tools_by_id[tid].tool_requirements for tid in install_for_tools])
|
||||
[trans.app.toolbox.tools_by_id[install_for_tools[0]]._view.install_dependencies(r) for r in requirements]
|
||||
view = six.next(six.itervalues(trans.app.toolbox.tools_by_id))._view
|
||||
tool_ids_by_requirements = {}
|
||||
for tid, tool in trans.app.toolbox.tools_by_id.items():
|
||||
if tool.tool_requirements not in tool_ids_by_requirements:
|
||||
tool_ids_by_requirements[tool.tool_requirements] = [tid]
|
||||
else:
|
||||
tool_ids_by_requirements[tool.tool_requirements].append(tid)
|
||||
requirements_status = {r: view.get_requirements_status({tid: r}, tools_by_id[tids[0]].installed_tool_dependencies) for r, tids in tool_ids_by_requirements.items()}
|
||||
return trans.fill_template( '/webapps/galaxy/admin/manage_dependencies.mako',
|
||||
tools=tools_by_id,
|
||||
requirements_status=requirements_status,
|
||||
tool_ids_by_requirements=tool_ids_by_requirements,
|
||||
viewkey=viewkey )
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def sanitize_whitelist( self, trans, submit_whitelist=False, tools_to_whitelist=[]):
|
||||
@@ -1127,7 +1151,7 @@ class Admin( object ):
|
||||
# write the configured sanitize_whitelist_file with new whitelist
|
||||
# and update in-memory list.
|
||||
with open(trans.app.config.sanitize_whitelist_file, 'wt') as f:
|
||||
if isinstance(tools_to_whitelist, string_types):
|
||||
if isinstance(tools_to_whitelist, six.string_types):
|
||||
tools_to_whitelist = [tools_to_whitelist]
|
||||
new_whitelist = sorted([tid for tid in tools_to_whitelist if tid in trans.app.toolbox.tools_by_id])
|
||||
f.write("\n".join(new_whitelist))
|
||||
|
||||
@@ -6,8 +6,10 @@ import yaml
|
||||
import stat
|
||||
import random
|
||||
import tempfile
|
||||
import uuid
|
||||
from subprocess import Popen, PIPE
|
||||
|
||||
from galaxy.util import string_as_bool_or_none
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy import web, model
|
||||
from galaxy.managers import api_keys
|
||||
@@ -17,6 +19,9 @@ import logging
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
CONTAINER_NAME_PREFIX = 'galaxy_gie_'
|
||||
|
||||
|
||||
class InteractiveEnvironmentRequest(object):
|
||||
|
||||
def __init__(self, trans, plugin):
|
||||
@@ -44,6 +49,11 @@ class InteractiveEnvironmentRequest(object):
|
||||
self.attr.docker_hostname = self.attr.viz_config.get("docker", "docker_hostname")
|
||||
self.attr.docker_connect_port = self.attr.viz_config.get("docker", "docker_connect_port") or None
|
||||
|
||||
if string_as_bool_or_none(self.attr.viz_config.get("docker", "swarm_mode")) is not None:
|
||||
self.attr.swarm_mode = string_as_bool_or_none(self.attr.viz_config.get("docker", "swarm_mode"))
|
||||
else:
|
||||
self.attr.swarm_mode = trans.app.config.gie_swarm_mode
|
||||
|
||||
# Generate per-request passwords the IE plugin can use to configure
|
||||
# the destination container.
|
||||
self.notebook_pw_salt = self.generate_password(length=12)
|
||||
@@ -78,6 +88,10 @@ class InteractiveEnvironmentRequest(object):
|
||||
if self.attr.proxy_prefix.startswith('/'):
|
||||
self.attr.proxy_prefix = '/' + self.attr.proxy_prefix.lstrip('/')
|
||||
|
||||
assert not self.attr.swarm_mode or (self.attr.swarm_mode and
|
||||
self.attr.docker_connect_port is not None), \
|
||||
"Error: Docker swarm mode enabled but docker_connect_port is not set"
|
||||
|
||||
def load_allowed_images(self):
|
||||
if os.path.exists(os.path.join(self.attr.our_config_dir, 'allowed_images.yml')):
|
||||
fn = os.path.join(self.attr.our_config_dir, 'allowed_images.yml')
|
||||
@@ -108,11 +122,12 @@ class InteractiveEnvironmentRequest(object):
|
||||
# their defaults dictionary instead.
|
||||
default_dict = {
|
||||
'command': 'docker {docker_args}',
|
||||
'command_inject': '--sig-proxy=true -e DEBUG=false',
|
||||
'command_inject': '-e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120',
|
||||
'docker_hostname': 'localhost',
|
||||
'wx_tempdir': 'False',
|
||||
'docker_galaxy_temp_dir': None,
|
||||
'docker_connect_port': None
|
||||
'docker_connect_port': None,
|
||||
'swarm_mode': None,
|
||||
}
|
||||
viz_config = ConfigParser.SafeConfigParser(default_dict)
|
||||
conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
|
||||
@@ -211,33 +226,73 @@ class InteractiveEnvironmentRequest(object):
|
||||
def volume(self, host_path, container_path, **kwds):
|
||||
return DockerVolume(host_path, container_path, **kwds)
|
||||
|
||||
def docker_cmd(self, image, env_override={}, volumes=[]):
|
||||
def docker_cmd(self, image, env_override=None, volumes=None):
|
||||
"""
|
||||
Generate and return the docker command to execute
|
||||
"""
|
||||
if env_override is None:
|
||||
env_override = {}
|
||||
if volumes is None:
|
||||
volumes = []
|
||||
temp_dir = self.temp_dir
|
||||
conf = self.get_conf_dict()
|
||||
conf.update(env_override)
|
||||
env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()])
|
||||
volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
|
||||
import_volume_str = '-v "{temp_dir}:/import/"'.format(temp_dir=temp_dir) if self.attr.import_volume else ''
|
||||
name = None
|
||||
# This is the basic docker command such as "sudo -u docker docker {docker_args}"
|
||||
# or just "docker {docker_args}"
|
||||
command = self.attr.viz_config.get("docker", "command")
|
||||
# Then we format in the entire docker command in place of
|
||||
# {docker_args}, so as to let the admin not worry about which args are
|
||||
# getting passed
|
||||
command = command.format(docker_args='run {command_inject} {environment} -d -P {import_volume_str} {volume_str} {image}')
|
||||
command_inject = self.attr.viz_config.get("docker", "command_inject")
|
||||
# --name should really not be set, but we'll try to honor it anyway
|
||||
if '--name' not in command_inject:
|
||||
name = CONTAINER_NAME_PREFIX + uuid.uuid4().hex
|
||||
if not self.attr.swarm_mode:
|
||||
command = command.format(docker_args='run {command_inject} {name} {environment} -d -P {import_volume_str} {volume_str} {image}')
|
||||
# --sig-proxy is not valid in the swarm mode context
|
||||
if '--sig-proxy=' not in command_inject:
|
||||
command_inject = '--sig-proxy=true ' + command_inject
|
||||
else:
|
||||
command = command.format(docker_args='service create --replicas 1 --restart-condition none {command_inject} {name} -p {docker_connect_port} {environment} {image}')
|
||||
|
||||
# Once that's available, we format again with all of our arguments
|
||||
command = command.format(
|
||||
command_inject=self.attr.viz_config.get("docker", "command_inject"),
|
||||
command_inject=command_inject,
|
||||
name='--name=%s' % name if name is not None else '',
|
||||
environment=env_str,
|
||||
import_volume_str=import_volume_str,
|
||||
volume_str=volume_str,
|
||||
image=image,
|
||||
docker_connect_port=self.attr.docker_connect_port,
|
||||
)
|
||||
return command
|
||||
|
||||
def get_digest_image(self, image):
|
||||
"""Get the digest image string for an image.
|
||||
|
||||
:type image: str
|
||||
:param image: image name and optionally, tag
|
||||
|
||||
:returns: digest string, having the format `<name>@<hash_alg>:<digest>`, e.g.:
|
||||
`'bgruening/docker-jupyter-notebook@sha256:3ec0bc9abc9d511aa602ee4fff2534d80dd9b1564482de52cb5de36cce6debae'`
|
||||
"""
|
||||
command = self.attr.viz_config.get("docker", "command")
|
||||
command = command.format(docker_args="image inspect --format '{{{{(index .RepoDigests 0)}}}}' {image}".format(image=image))
|
||||
p = Popen(command, stdout=PIPE, stderr=PIPE, close_fds=True, shell=True)
|
||||
stdout, stderr = p.communicate()
|
||||
digest = None
|
||||
if p.returncode == 0:
|
||||
digest = stdout.strip()
|
||||
elif p.returncode == 1 and stderr.strip() == 'Error: No such image: {image}'.format(image=image):
|
||||
log.warning("%s not pulled, cannot get digest", image)
|
||||
else:
|
||||
log.error( "%s\n%s" % (stdout, stderr) )
|
||||
return digest or image
|
||||
|
||||
def _idsToVolumes(self, ids):
|
||||
if len(ids.strip()) == 0:
|
||||
return []
|
||||
@@ -286,6 +341,11 @@ class InteractiveEnvironmentRequest(object):
|
||||
raise Exception("Attempting to launch disallowed image! %s not in list of allowed images [%s]"
|
||||
% (image, ', '.join(self.allowed_images)))
|
||||
|
||||
# The digest image is necessary if using swarm mode and the image's
|
||||
# registry (e.g. docker hub, quay.io) is down. See:
|
||||
# https://github.com/docker/docker/issues/31427
|
||||
image = self.get_digest_image(image)
|
||||
|
||||
if additional_ids is not None:
|
||||
volumes += self._idsToVolumes(additional_ids)
|
||||
|
||||
@@ -355,7 +415,10 @@ class InteractiveEnvironmentRequest(object):
|
||||
:returns: inspect_data, a dict of docker inspect output
|
||||
"""
|
||||
command = self.attr.viz_config.get("docker", "command")
|
||||
command = command.format(docker_args="inspect %s" % container_id)
|
||||
if not self.attr.swarm_mode:
|
||||
command = command.format(docker_args="inspect %s" % container_id)
|
||||
else:
|
||||
command = command.format(docker_args="service inspect %s" % container_id)
|
||||
log.info("Inspecting docker container {0} with command [{1}]".format(
|
||||
container_id,
|
||||
command
|
||||
@@ -368,15 +431,6 @@ class InteractiveEnvironmentRequest(object):
|
||||
return None
|
||||
|
||||
inspect_data = json.loads(stdout)
|
||||
# [{
|
||||
# "NetworkSettings" : {
|
||||
# "Ports" : {
|
||||
# "3306/tcp" : [
|
||||
# {
|
||||
# "HostIp" : "127.0.0.1",
|
||||
# "HostPort" : "3306"
|
||||
# }
|
||||
# ]
|
||||
return inspect_data
|
||||
|
||||
def get_container_host(self, inspect_data):
|
||||
@@ -410,13 +464,43 @@ class InteractiveEnvironmentRequest(object):
|
||||
Someday code that calls this should be refactored whenever we get
|
||||
containers with multiple ports working.
|
||||
"""
|
||||
# non-swarm:
|
||||
# [{
|
||||
# "NetworkSettings" : {
|
||||
# "Ports" : {
|
||||
# "3306/tcp" : [
|
||||
# {
|
||||
# "HostIp" : "127.0.0.1",
|
||||
# "HostPort" : "3306"
|
||||
# }
|
||||
# ]
|
||||
# swarm:
|
||||
# [{
|
||||
# "Endpoint": {
|
||||
# "Ports": [
|
||||
# {
|
||||
# "Protocol": "tcp",
|
||||
# "TargetPort": 8888,
|
||||
# "PublishedPort": 30000,
|
||||
# "PublishMode": "ingress"
|
||||
# }
|
||||
# ]
|
||||
mappings = []
|
||||
port_mappings = inspect_data[0]['NetworkSettings']['Ports']
|
||||
for port_name in port_mappings:
|
||||
for binding in port_mappings[port_name]:
|
||||
if not self.attr.swarm_mode:
|
||||
port_mappings = inspect_data[0]['NetworkSettings']['Ports']
|
||||
for port_name in port_mappings:
|
||||
for binding in port_mappings[port_name]:
|
||||
mappings.append((
|
||||
port_name.replace('/tcp', '').replace('/udp', ''),
|
||||
binding['HostIp'],
|
||||
binding['HostPort']
|
||||
))
|
||||
else:
|
||||
port_mappings = inspect_data[0]['Endpoint']['Ports']
|
||||
for binding in port_mappings:
|
||||
mappings.append((
|
||||
port_name.replace('/tcp', '').replace('/udp', ''),
|
||||
binding['HostIp'],
|
||||
binding['HostPort']
|
||||
binding['TargetPort'],
|
||||
'127.0.0.1', # use the routing mesh
|
||||
binding['PublishedPort']
|
||||
))
|
||||
return mappings
|
||||
|
||||
@@ -52,7 +52,12 @@ def edgelist_for_workflow_steps( steps ):
|
||||
for step in steps:
|
||||
edges.append( ( steps_to_index[step], steps_to_index[step] ) )
|
||||
for conn in step.input_connections:
|
||||
edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
|
||||
output_index = steps_to_index[conn.output_step]
|
||||
input_index = steps_to_index[conn.input_step]
|
||||
# self connection - a cycle not detectable by topsort function.
|
||||
if output_index == input_index:
|
||||
raise CycleError([], 0, 0)
|
||||
edges.append( ( output_index, input_index ) )
|
||||
return edges
|
||||
|
||||
|
||||
|
||||
+38
-8
@@ -8,7 +8,6 @@ rm -f run_functional_tests.log
|
||||
|
||||
show_help() {
|
||||
cat <<EOF
|
||||
'${0##*/} (test_path)' for testing all the tools in functional directory
|
||||
'${0##*/} -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)
|
||||
'${0##*/} -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
|
||||
'${0##*/} -list' for listing all the tool ids
|
||||
@@ -24,14 +23,49 @@ cat <<EOF
|
||||
'${0##*/} -qunit testname' for running single JavaScript test with given name
|
||||
'${0##*/} -selenium' for running all selenium web tests (in test/selenium_tests)
|
||||
'${0##*/} -selenium (test_path)' for running specified selenium web tests (use nosetest path)
|
||||
'${0##*/} -casperjs (py_test_path)' for running casperjs JavaScript tests using a Python wrapper for consistency. py_test_path in casperjs_runner.py e.g. 'Test_04_HDAs' or 'Test_04_HDAs.test_00_HDA_states'.
|
||||
|
||||
This wrapper script largely serves as a point documentation and convenience -
|
||||
most tests shipped with Galaxy can be run with nosetests or qunit directly.
|
||||
|
||||
The main test types are as follows:
|
||||
|
||||
- API: These tests are located in test/api and test various aspects of the Galaxy
|
||||
API and test general backend aspects of Galaxy using the API.
|
||||
- Integration: These tests are located in test/integration and test special
|
||||
configurations of Galaxy. All API tests assume a particular Galaxy configuration
|
||||
defined by test/base/driver_util.py and integration tests can be used to
|
||||
launch and test Galaxy in other configurations.
|
||||
- Framework: These tests are all Galaxy tool tests and can be found in
|
||||
test/functional/tools. These are for the most part meant to test and
|
||||
demonstrate features of the tool evaluation environment and of Galaxy tool XML
|
||||
files.
|
||||
- Unit: These are Python unit tests either defined as doctests or inside of
|
||||
test/unit. These should generally not require a Galaxy instance and should
|
||||
quickly test just a component or a few components of Galaxy's backend code.
|
||||
- QUnit: These are JavaScript unit tests defined in test/qunit.
|
||||
- Selenium: These are full stack tests meant to test the Galaxy UI with real
|
||||
browsers and are located in test/selenium_tests.
|
||||
- ToolShed: These are web tests that use the older Python web testing
|
||||
framework twill to test ToolShed related functionality. These are
|
||||
located in test/shed_functional.
|
||||
|
||||
Nose tests will allow specific tests to be selected per the documentation at
|
||||
https://nose.readthedocs.org/en/latest/usage.html#selecting-tests. These are
|
||||
indicated with the optional parameter (test_path). A few examples are:
|
||||
|
||||
Run all TestUserInfo functional tests:
|
||||
./run_tests.sh test/functional/test_user_info.py:TestUserInfo
|
||||
Run all API tests:
|
||||
./run_tests.sh -api
|
||||
|
||||
The same test as above can be run using nosetests directly as follows:
|
||||
nosetests test/api
|
||||
|
||||
However when using nosetests directly output options defined in this
|
||||
file aren't respected and a new Galaxy instance will be created for each
|
||||
TestCase class (this scripts optimizes it so all tests can share a Galaxy
|
||||
instance).
|
||||
|
||||
Run a full class of API tests:
|
||||
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase
|
||||
|
||||
Run a specific API test:
|
||||
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_with_output_format_actions
|
||||
@@ -140,10 +174,6 @@ GALAXY_CONFIG_MASTER_KEY Master or admin API key to use as part of
|
||||
testing with GALAXY_TEST_EXTERNAL.
|
||||
GALAXY_TEST_USER_API_KEY User API key to use as part of testing with
|
||||
GALAXY_TEST_EXTERNAL.
|
||||
GALAXY_TEST_HISTORY_ID Point casperjs tests at specific external
|
||||
history for testing.
|
||||
GALAXY_TEST_WORKFLOW_FILE Point casperjs tests at specific workflow
|
||||
file for testing.
|
||||
GALAXY_TEST_VERBOSE_ERRORS Enable more verbose errors during API tests.
|
||||
GALAXY_TEST_UPLOAD_ASYNC Upload tool test inputs asynchronously (may
|
||||
overwhelm sqlite database).
|
||||
|
||||
@@ -0,0 +1 @@
|
||||
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|
||||
@@ -0,0 +1 @@
|
||||
{"version":3,"file":"app.js","sources":["../src/app.js"],"names":["define","Utils","Masthead","Modal","QuotaMeter","Backbone","View","extend","initialize","options","Galaxy","app","this","modal","masthead","setElement","_template","$el","append","$","render","require","Analysis","window","console","log","err","debug","initialize2","merge","params","$container","parent","attr","addClass","message_box_visible","show","show_inactivity_warning","menu","Menu","GalaxyMenu","config","quotaMeter","UserQuotaMeter","model","user","el","display","target","remove","panels","_buildPanels","Views","panel_ids","i","id","view","components","header","title","cls","buttons","body","$panel","_templatePanel","find","html","Panel","center","panel","drag","toggle","right","message_box_class","message_box_content","inactivity_box_content","root"],"mappings":"AAGAA,QAAQ,cAAe,kBAAmB,kBAAmB,kBAAmB,4BAC5E,SAAUC,EAAOC,EAAUC,EAAOC,GAClC,MAAOC,UAASC,KAAKC,QACjBC,WAAY,SAAUC,GAClBC,OAAOC,IAAMC,KACbF,OAAOG,MAAQ,GAAIV,GAAMG,KACzBI,OAAOI,SAAW,GAAIZ,GAASI,KAAMG,GAErCG,KAAKG,WAAYH,KAAKI,UAAWP,IACjCG,KAAKK,IAAIC,OAAQR,OAAOI,SAASG,KACjCE,EAAG,QAASD,OAAQN,KAAKK,KACzBL,KAAKQ,UAETA,OAAQ,WAIJC,SAAW,gBAAkB,SAAUC,GACnCC,OAAOC,QAAQC,IAAKH,IAGrB,SAAUI,GACTF,QAAQG,MAAOD,MAIvBE,YAAa,SAAUnB,GACnBG,KAAKH,QAAUR,EAAM4B,MAAOpB,MAC5BG,KAAKkB,OAAUlB,KAAKH,QAAQqB,OAC5BlB,KAAKG,WAAYH,KAAKI,UAAWP,IAGjCC,OAAOC,IAAMC,KAGbO,EAAG,QAASD,OAAQN,KAAKK,IAIzB,IAAIc,GAAaZ,EAAGP,KAAKK,IAAIe,UAAWC,KAAM,SAAU,MAAOC,SAAU,eACpEtB,MAAKH,QAAQ0B,sBACdJ,EAAWG,SAAU,mBACrBtB,KAAKO,EAAG,eAAgBiB,QAEvBxB,KAAKH,QAAQ4B,0BACdN,EAAWG,SAAU,sBACrBtB,KAAKO,EAAG,gBAAiBiB,QAIvB1B,OAAOI,WACTJ,OAAOI,SAAW,GAAIZ,GAASI,KAAMG,GACrCC,OAAOG,MAAQ,GAAIV,GAAMG,KAIzBI,OAAO4B,KAAO,GAAIC,MAAKC,YACnB1B,SAAcJ,OAAOI,SACrB2B,OAAchC,IAKlBC,OAAOgC,WAAa,GAAItC,GAAWuC,gBAC/BC,MAAclC,OAAOmC,KACrBC,GAAcpC,OAAOI,SAASK,EAAG,4BAClCC,WAQX2B,QAAS,SAAW9B,EAAK+B,GAErB7B,EAAG,8BAA+B8B,SAClCrC,KAAKsC,QAAUtC,KAAKsC,OAAQF,GAAU,UAAWD,QAAS9B,IAI9DkC,aAAc,SAAUC,EAAO3C,GAC3BG,KAAKsC,SACL,IAAIG,IAAc,OAAQ,SAAU,QACpC,KAAM,GAAIC,KAAKD,GAAY,CACvB,GAAIE,GAAKF,EAAWC,GAChBE,EAAO5C,KAAKsC,OAAQK,GAAO,GAAIH,GAAOG,GAAM9C,EAChD,IAAW,UAAN8C,EACD3C,KAAKO,EAAE,WAAWD,OAAQsC,EAAKvC,SAC5B,CACH,GAAIwC,GAAaxD,EAAM4B,MAAO2B,EAAKC,YAC/BC,QACIC,MAAU,GACVC,IAAU,GACVC,YAEJC,MACIF,IAAU,MAGdG,EAAS5C,EAAGP,KAAKoD,eAAgBT,GACrCQ,GAAOE,KAAK,sBAAsBC,KAAMT,EAAWC,OAAOC,OAC1DI,EAAOE,KAAK,+BAA+B/B,SAAUuB,EAAWC,OAAOE,IACvE,KAAM,GAAIN,KAAKG,GAAWC,OAAOG,QAC7BE,EAAOE,KAAK,yBAAyB/C,OAAQuC,EAAWC,OAAOG,QAASP,GAAIrC,IAEhF8C,GAAOE,KAAK,uBAAuB/B,SAAUuB,EAAWK,KAAKF,KAAM1C,OAAQsC,EAAKvC,IAChF,EAAY,GAAIkD,QACZC,OAAUxD,KAAKO,EAAG,WAClBkD,MAAUN,EACVO,KAAUP,EAAOE,KAAK,iCACtBM,OAAUR,EAAOE,KAAK,2CACtBO,MAAgB,SAANjB,IAEd3C,KAAKK,IAAIC,OAAQ6C,MAM7BC,eAAgB,SAAUT,GACtB,MAAQ,YAAcA,EAAK,mSASqBA,EAAK,sCAOzDvC,UAAW,WACP,MAAQ,wJAE2CN,OAAO+B,OAAOgC,kBAAoB,oCACrE/D,OAAO+B,OAAOiC,oBAClB,oFAEIhE,OAAO+B,OAAOkC,uBACV,aAAejE,OAAOkE,KAAO"}
|
||||
@@ -0,0 +1 @@
|
||||
{"version":3,"file":"analysis.js","sources":["../../src/app/analysis.js"],"names":["define","Backbone","View","extend","initialize","options","this","Utils","merge","setElement","_template","params","$","prop","Galaxy","root","tool_id","param","workflow_id","m_c","m_a","config","require_login","user","id","self","on","show","empty","hide","display","$el","scrollTop","append","tool_search","Tools","ToolSearch","spinner_url","search_url","hidden","tools","ToolCollection","toolbox","tool_panel","ToolPanel","layout","toolbox_in_panel","tool_panel_view","ToolPanelView","model","toolPanel","get","size","render","prepend","_templateTool","title","href","i","stored_workflow_menu_entries","m","stored_workflow","name","encoded_stored_workflow_id","click","parent","handle_minwidth_hint","attr","upload","Upload","components","header","buttons","buttonRefresh","Ui","ButtonLink","cls","icon","onclick","top","currHistoryPanel","loadCurrentHistory","buttonOptions","target","buttonViewMulti","body","historyOptionsMenu","optionsMenu","anonymous","purgeAllowed","allow_user_dataset_purge","HistoryPanel","CurrentHistoryPanel","el","linkTarget","$scrollContainer","connectToQuotaMeter","quotaMeter","listenToGalaxy","left"],"mappings":"AAAAA,UAAW,WAGWC,SAASC,KAAKC,QAC5BC,WAAY,SAAUC,GAClBC,KAAKD,QAAUE,MAAMC,MAAOH,MAC5BC,KAAKG,WAAYH,KAAKI,YACtB,IAAIC,GAASL,KAAKD,QAAQM,MAC1BL,MAAKM,EAAG,gBAAiBC,KAAM,MAAOC,OAAOC,MACvCJ,EAAOK,SAAa,eAAiBJ,EAAEK,MAAON,IAC9CA,EAAOO,aAAiB,mBAAqBP,EAAOO,aACpDP,EAAOQ,KAASR,EAAOQ,IAAM,IAAMR,EAAOS,KAC1CN,OAAOO,OAAOC,gBAAkBR,OAAOS,KAAKC,IAAM,cACpD,gBAEJ,IAAIC,GAAOnB,IACXA,MAAKM,EAAG,gBAAiBc,GAAI,OAAQ,WACjCd,EAAGN,MAAOqB,OACVF,EAAKb,EAAG,iBAAkBgB,QAAQC,UAG1CC,QAAS,SAAUC,GACfzB,KAAKM,EAAG,gBAAiBiB,OACzBvB,KAAKM,EAAG,iBAAkBgB,QAAQI,UAAW,GAAIC,OAAQF,GAAMJ,QAEnEjB,UAAW,WACP,MAAQ,ySAQAT,SAASC,KAAKC,QAC1BC,WAAY,SAAUC,GAIlB,GAHAC,KAAKD,QAAUE,MAAMC,MAAOH,MAC5BC,KAAKG,WAAYH,KAAKI,aAEjBI,OAAOS,KAAKC,KAAOV,OAAOO,OAAOC,cAAgB,CAClD,GAAIY,GAAc,GAAIC,OAAMC,YACxBC,YAAchC,EAAQgC,YACtBC,WAAcjC,EAAQiC,WACtBC,QAAc,IAEdC,EAAQ,GAAIL,OAAMM,eAAgBpC,EAAQqC,SAC1CC,EAAa,GAAIR,OAAMS,WACvBV,YAAcA,EACdM,MAAcA,EACdK,OAAcxC,EAAQyC,kBAE1BC,iBAAkB,GAAIZ,OAAMa,eAAgBC,MAAON,IAGnD7B,OAAOoC,UAAYP,EAGfA,EAAWQ,IAAK,UAAWC,OAAS,IACpCL,gBAAgBM,SAChB/C,KAAKM,EAAG,aAAce,QAE1BrB,KAAKyB,IAAIuB,QAASP,gBAAgBhB,KAGlCzB,KAAKM,EAAG,uBAAwBqB,OAAQ3B,KAAKiD,eACzCC,MAAU,gBACVC,KAAU,0BAEd,KAAM,GAAIC,KAAKrD,GAAQsD,6BAA+B,CAClD,GAAIC,GAAIvD,EAAQsD,6BAA8BD,EAC9CpD,MAAKM,EAAG,uBAAwBqB,OAAQ3B,KAAKiD,eACzCC,MAAQI,EAAEC,gBAAgBC,KAC1BL,KAAQ,mBAAqBG,EAAEG,8BAKvCzD,KAAKM,EAAG,kBAAmBoD,MAAO,WACzBC,OAAOC,sBACRD,OAAOC,qBAAsBtD,EAAGN,MAAO6D,KAAM,kBAKrDrD,OAAOsD,OAAS,GAAIC,QAAQhE,GAG5BC,KAAKgE,YACDC,QACIf,MAAU,QACVgB,SAAY1D,OAAOsD,YAMnCb,cAAe,SAAUlD,GACrB,MAAQ,mCACkBS,OAAOC,KAAOV,EAAQoD,KAAO,0BAA4BpD,EAAQmD,MAAQ,cAIvG9C,UAAW,WACP,MAAQ,2cAmBCT,SAASC,KAAKC,QAC3BC,WAAY,SAASC,GACjBC,KAAKD,QAAUE,MAAMC,MAAOH,MAC5BC,KAAKG,WAAYH,KAAKI,YAGtB,IAAI+D,GAAgB,GAAIC,IAAGC,YACvBnD,GAAU,yBACVgC,MAAU,kBACVoB,IAAU,sBACVC,KAAU,gBACVC,QAAU,WACFC,IAAIjE,QAAUiE,IAAIjE,OAAOkE,kBACzBD,IAAIjE,OAAOkE,iBAAiBC,wBAIpCC,EAAgB,GAAIR,IAAGC,YACvBnD,GAAU,yBACVgC,MAAU,kBACVoB,IAAU,sBACVO,OAAU,cACVN,KAAU,YACVpB,KAAU3C,OAAOC,KAAO,yBAExBqE,EAAkB,GAAIV,IAAGC,YACzBnD,GAAU,4BACVgC,MAAU,qBACVoB,IAAU,sBACVC,KAAU,gBACVpB,KAAU3C,OAAOC,KAAO,yBAI5BT,MAAKgE,YACDC,QACIf,MAAU,UACVoB,IAAU,uBACVJ,SAAYC,EAAeS,EAAeE,IAE9CC,MACIT,IAAU,kCAKlB9D,OAAOwE,mBAAqBC,YAAaL,EAAcnD,KACnDyD,UAAe1E,OAAOS,KAAKC,IAAM,QAAU,QAC3CiE,aAAe3E,OAAOO,OAAOqE,0BAA4B,QAAU,QACnE3E,KAAeD,OAAOC,OAI1BD,OAAOkE,iBAAmB,GAAIW,cAAaC,qBACvCC,GAAkBvF,KAAKyB,IACvB0D,aAAkB3E,OAAOO,OAAOqE,yBAChCI,WAAkB,cAClBC,iBAAkB,WAAY,MAAOzF,MAAKyB,IAAIkC,YAElDnD,OAAOkE,iBAAiBgB,oBAAqBlF,OAAOmF,YACpDnF,OAAOkE,iBAAiBkB,eAAgBpF,QACxCA,OAAOkE,iBAAiBC,sBAI5BvE,UAAW,WACP,MAAO,4DAIf,QACIyF,KAAUlG,SAASC,KAAKC,QAASC,WAAY"}
|
||||
@@ -1 +1 @@
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|
||||
var jQuery=require("jquery"),$=jQuery,GalaxyApp=require("galaxy").GalaxyApp,QUERY_STRING=require("utils/query-string-parsing"),PANEL=require("layout/panel"),ToolPanel=require("./tool-panel"),HistoryPanel=require("./history-panel"),PAGE=require("layout/page"),ToolForm=require("mvc/tool/tool-form"),UserPreferences=require("mvc/user/user-preferences");Tours=require("mvc/tours"),window.app=function(a,b){window.Galaxy=new GalaxyApp(a,b),Galaxy.debug("analysis app");var c=a.config,d=new ToolPanel({el:"#left",userIsAnonymous:Galaxy.user.isAnonymous(),toolbox:c.toolbox,toolbox_in_panel:c.toolbox_in_panel,stored_workflow_menu_entries:c.stored_workflow_menu_entries,nginx_upload_path:c.nginx_upload_path,ftp_upload_site:c.ftp_upload_site,default_genome:c.default_genome,default_extension:c.default_extension}),e=new PANEL.CenterPanel({el:"#center"}),f=new HistoryPanel({el:"#right",galaxyRoot:Galaxy.root,userIsAnonymous:Galaxy.user.isAnonymous(),allow_user_dataset_purge:c.allow_user_dataset_purge}),g=new PAGE.PageLayoutView(_.extend(a,{el:"body",left:d,center:e,right:f}));Galaxy.page=g,Galaxy.params=Galaxy.config.params,Galaxy.toolPanel=d.tool_panel,Galaxy.upload=d.uploadButton,Galaxy.currHistoryPanel=f.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.app={display:function(a){$(".select2-hidden-accessible").remove(),e.display(a)}},Galaxy.router=new(Backbone.Router.extend({initialize:function(a){this.options=a},execute:function(a,b,c){Galaxy.debug("router execute:",a,b,c);var d=QUERY_STRING.parse(b.pop());b.push(d),a&&a.apply(this,b)},routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)users(/)":"show_users"},show_tours:function(a){a?Tours.giveTour(a):e.display(new Tours.ToursView)},show_users:function(){e.display(new UserPreferences.View)},home:function(a){a.tool_id||a.job_id?"upload1"===a.tool_id?(Galaxy.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(a):this._loadCenterIframe(a.workflow_id?"workflow/run?id="+a.workflow_id:a.m_c?a.m_c+"/"+a.m_a:"welcome")},_loadToolForm:function(a){a.id=a.tool_id,e.display(new ToolForm.View(a))},_loadCenterIframe:function(a,b){b=b||Galaxy.root,a=b+a,e.$("#galaxy_main").prop("src",a)}}))(a),$(function(){g.render(),g.right.historyView.loadCurrentHistory(),Galaxy.listenTo(g.right.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})}),g.right.historyView.connectToQuotaMeter(g.masthead.quotaMeter),Backbone.history.start({root:Galaxy.root,pushState:!0})})};
|
||||
//# sourceMappingURL=../maps/analysis.js.map
|
||||
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|
||||
define(["utils/utils","layout/masthead","mvc/ui/ui-modal","mvc/ui/ui-modal","mvc/user/user-quotameter"],function(a,b,c,d){return Backbone.View.extend({initialize:function(a){Galaxy.app=this,Galaxy.modal=new c.View,Galaxy.masthead=new b.View(a),this.setElement(this._template(a)),this.$el.append(Galaxy.masthead.$el),$("body").append(this.$el),this.render()},render:function(){require(["app/analysis"],function(a){window.console.log(a)},function(a){console.debug(a)})},initialize2:function(e){this.options=a.merge(e,{}),this.params=this.options.params,this.setElement(this._template(e)),Galaxy.app=this,$("body").append(this.$el);var f=$(this.$el.parent()).attr("scroll","no").addClass("full-content");this.options.message_box_visible&&(f.addClass("has-message-box"),this.$("#messagebox").show()),this.options.show_inactivity_warning&&(f.addClass("has-inactivity-box"),this.$("#inactivebox").show()),Galaxy.masthead||(Galaxy.masthead=new b.View(e),Galaxy.modal=new c.View,Galaxy.menu=new Menu.GalaxyMenu({masthead:Galaxy.masthead,config:e}),Galaxy.quotaMeter=new d.UserQuotaMeter({model:Galaxy.user,el:Galaxy.masthead.$(".quota-meter-container")}).render())},display:function(a,b){$(".select2-hidden-accessible").remove(),this.panels&&this.panels[b||"center"].display(a)},_buildPanels:function(b,c){this.panels=[];var d=["left","center","right"];for(var e in d){var f=d[e],g=this.panels[f]=new b[f](c);if("center"==f)this.$("#center").append(g.$el);else{var h=a.merge(g.components,{header:{title:"",cls:"",buttons:[]},body:{cls:""}}),i=$(this._templatePanel(f));i.find(".panel-header-text").html(h.header.title),i.find(".unified-panel-header-inner").addClass(h.header.cls);for(var e in h.header.buttons)i.find(".panel-header-buttons").append(h.header.buttons[e].$el);i.find(".unified-panel-body").addClass(h.body.cls).append(g.$el);{new Panel({center:this.$("#center"),panel:i,drag:i.find(".unified-panel-footer > .drag"),toggle:i.find(".unified-panel-footer > .panel-collapse"),right:"right"==f})}this.$el.append(i)}}},_templatePanel:function(a){return'<div id="'+a+'"><div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div class="panel-header-buttons" style="float: right"/><div class="panel-header-text"/></div></div><div class="unified-panel-body"/><div class="unified-panel-footer"><div class="panel-collapse '+a+'"/><div class="drag"/></div></div>'},_template:function(){return'<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"><div id="background"/><div id="messagebox" class="panel-'+Galaxy.config.message_box_class+'-message" style="display: none;">'+Galaxy.config.message_box_content+'</div><div id="inactivebox" class="panel-warning-message" style="display: none;">'+Galaxy.config.inactivity_box_content+' <a href="'+Galaxy.root+'user/resend_verification">Resend verification.</a></div><div id="center" class="inbound"/></div>'}})});
|
||||
//# sourceMappingURL=../maps/app.js.map
|
||||
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|
||||
define([],function(){Backbone.View.extend({initialize:function(a){this.options=Utils.merge(a,{}),this.setElement(this._template());var b=this.options.params;this.$("#galaxy_main").prop("src",Galaxy.root+(b.tool_id&&"tool_runner?"+$.param(b)||b.workflow_id&&"workflow/run?id="+b.workflow_id||b.m_c&&b.m_c+"/"+b.m_a||Galaxy.config.require_login&&!Galaxy.user.id&&"user/login"||"root/welcome"));var c=this;this.$("#galaxy_main").on("load",function(){$(this).show(),c.$("#center-panel").empty().hide()})},display:function(a){this.$("#galaxy_main").hide(),this.$("#center-panel").empty().scrollTop(0).append(a).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),Backbone.View.extend({initialize:function(a){if(this.options=Utils.merge(a,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var b=new Tools.ToolSearch({spinner_url:a.spinner_url,search_url:a.search_url,hidden:!1}),c=new Tools.ToolCollection(a.toolbox),d=new Tools.ToolPanel({tool_search:b,tools:c,layout:a.toolbox_in_panel});tool_panel_view=new Tools.ToolPanelView({model:d}),Galaxy.toolPanel=d,d.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var e in a.stored_workflow_menu_entries){var f=a.stored_workflow_menu_entries[e];this.$("#internal-workflows").append(this._templateTool({title:f.stored_workflow.name,href:"workflow/run?id="+f.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new Upload(a),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),Backbone.View.extend({initialize:function(a){this.options=Utils.merge(a,{}),this.setElement(this._template());var b=new Ui.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}}),c=new Ui.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"}),d=new Ui.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});this.components={header:{title:"History",cls:"history-panel-header",buttons:[b,c,d]},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=optionsMenu(c.$el,{anonymous:Galaxy.user.id&&"true"||"false",purgeAllowed:Galaxy.config.allow_user_dataset_purge&&"true"||"false",root:Galaxy.root}),Galaxy.currHistoryPanel=new HistoryPanel.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:Backbone.View.extend({initialize:function(){}})}});
|
||||
//# sourceMappingURL=../../maps/app/analysis.js.map
|
||||
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|
||||
webpackJsonp([4],[function(e,r,n){(function(e){var r=n(1),a=r,i=n(57).GalaxyApp,o=n(10),t=n(5),l=n(59);window.app=function(n,c){window.Galaxy=new i(n,c),Galaxy.debug("login app");var d=encodeURI(n.redirect);if(!n.show_welcome_with_login){var w=r.param({use_panels:"True",redirect:d});return void(window.location.href=Galaxy.root+"user/login?"+w)}var p=new l.PageLayoutView(e.extend(n,{el:"body",center:new o.CenterPanel({el:"#center"}),right:new o.RightPanel({title:t("Login required"),el:"#right"})}));a(function(){var e=r.param({redirect:d}),a=Galaxy.root+"user/login?"+e;p.render(),p.center.$("#galaxy_main").prop("src",n.welcome_url),p.right.$(".unified-panel-body").css("overflow","hidden").html('<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>')})}}).call(r,n(2))}]);
|
||||
webpackJsonp([4],[function(e,r,n){(function(e){var r=n(1),a=r,i=n(36).GalaxyApp,o=n(9),t=n(4),l=n(38);window.app=function(n,c){window.Galaxy=new i(n,c),Galaxy.debug("login app");var d=encodeURI(n.redirect);if(!n.show_welcome_with_login){var w=r.param({use_panels:"True",redirect:d});return void(window.location.href=Galaxy.root+"user/login?"+w)}var p=new l.PageLayoutView(e.extend(n,{el:"body",center:new o.CenterPanel({el:"#center"}),right:new o.RightPanel({title:t("Login required"),el:"#right"})}));a(function(){var e=r.param({redirect:d}),a=Galaxy.root+"user/login?"+e;p.render(),p.center.$("#galaxy_main").prop("src",n.welcome_url),p.right.$(".unified-panel-body").css("overflow","hidden").html('<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>')})}}).call(r,n(2))}]);
|
||||
//# sourceMappingURL=login.bundled.js.map
|
||||
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|
||||
define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c){"use strict";var d=a.DatasetListItemView,e=d.extend({className:d.prototype.className+" history-content",initialize:function(a,b){d.prototype.initialize.call(this,a,b)},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAListItemView("+a+")"}});return e.prototype.templates=function(){var a=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- dataset.hid %></span> ','<span class="name"><%- dataset.name %></span>',"</div>","</div>"],"dataset"),e=_.extend({},d.prototype.templates.warnings,{hidden:b.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',c("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return _.extend({},d.prototype.templates,{titleBar:a,warnings:e})}(),{HDAListItemView:e}});
|
||||
define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c){"use strict";var d=a.DatasetListItemView,e=d.extend({className:d.prototype.className+" history-content",initialize:function(a,b){d.prototype.initialize.call(this,a,b)},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAListItemView("+a+")"}});return e.prototype.templates=function(){var a=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- dataset.hid %></span> ','<span class="name"><%- dataset.name %></span>',"</div>","</br>",'<span class="nametags">',"<% _.each(dataset.nametags, function(tag){ %>",'<span class="label label-info"><%- tag %></span>',"<% }); %>","</span>","</div>"],"dataset"),e=_.extend({},d.prototype.templates.warnings,{hidden:b.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',c("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return _.extend({},d.prototype.templates,{titleBar:a,warnings:e})}(),{HDAListItemView:e}});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/hda-li.js.map
|
||||
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|
||||
define(["utils/utils"],function(a){return Backbone.View.extend({initialize:function(b){var c=this;this.options=a.merge(b,{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}),this.collection=this.options.collection,this.setElement(this._template()),this.rows=[],a.get({url:Galaxy.root+"api/remote_files",success:function(a){c._fill(a)},error:function(){c._fill()}})},_fill:function(b){if(b&&b.length>0){this.$(".upload-ftp-content").html($(this._templateTable()));var c=0;for(index in b)this.rows.push(this._add(b[index])),c+=b[index].size;if(this.$(".upload-ftp-number").html(b.length+" files"),this.$(".upload-ftp-disk").html(a.bytesToString(c,!0)),this.collection){var d=this;this.$("._has_collection").show(),this.$select_all=this.$(".upload-selectall").addClass(this.options.class_add),this.$select_all.on("click",function(){var a=d.$select_all.hasClass(d.options.class_add);for(index in b){var c=b[index],e=d._find(c);(!e&&a||e&&!a)&&d.rows[index].trigger("click")}}),this._refresh()}}else this.$(".upload-ftp-content").html($(this._templateInfo()));this.$(".upload-ftp-wait").hide()},_add:function(a){var b=this,c=$(this._templateRow(a)),d=c.find(".icon");return this.$("tbody").append(c),this.collection?(d.addClass(this._find(a)?this.options.class_remove:this.options.class_add),c.on("click",function(){var c=b._find(a);d.removeClass(),c?(b.options.onremove(c),d.addClass(b.options.class_add)):(b.options.onadd(a),d.addClass(b.options.class_remove)),b._refresh()})):c.on("click",function(){b.options.onchange(a)}),c},_refresh:function(){var a=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),this.$select_all.addClass(0==a.length?this.options.class_add:a.length==this.rows.length?this.options.class_remove:this.options.class_partial)},_find:function(a){var b=this.collection.findWhere({file_path:a.path,file_mode:"ftp",enabled:!0});return b&&b.get("id")},_templateRow:function(b){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+b.path+'</td><td class="ftp-size">'+a.bytesToString(b.size)+'</td><td class="ftp-time">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/> <span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody/></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div class="upload-ftp-content"/><div>'}})});
|
||||
define(["utils/utils"],function(a){return Backbone.View.extend({initialize:function(b){var c=this;this.options=a.merge(b,{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}),this.collection=this.options.collection,this.setElement(this._template()),this.rows=[],a.get({url:Galaxy.root+"api/remote_files",success:function(a){c._fill(a)},error:function(){c._fill()}})},_fill:function(b){if(b&&b.length>0){this.$(".upload-ftp-content").html($(this._templateTable()));var c=0;for(index in b)this.rows.push(this._add(b[index])),c+=b[index].size;if(this.$(".upload-ftp-number").html(b.length+" files"),this.$(".upload-ftp-disk").html(a.bytesToString(c,!0)),this.collection){var d=this;this.$("._has_collection").show(),this.$select_all=this.$(".upload-selectall").addClass(this.options.class_add),this.$select_all.on("click",function(){var a=d.$select_all.hasClass(d.options.class_add);for(index in b){var c=b[index],e=d._find(c);(!e&&a||e&&!a)&&d.rows[index].trigger("click")}}),this._refresh()}}else this.$(".upload-ftp-content").html($(this._templateInfo()));this.$(".upload-ftp-wait").hide()},_add:function(a){var b=this,c=$(this._templateRow(a)),d=c.find(".icon");return this.$("tbody").append(c),this.collection?(d.addClass(this._find(a)?this.options.class_remove:this.options.class_add),c.on("click",function(){var c=b._find(a);d.removeClass(),c?(b.options.onremove(c),d.addClass(b.options.class_add)):(b.options.onadd(a),d.addClass(b.options.class_remove)),b._refresh()})):c.on("click",function(){b.options.onchange(a)}),c},_refresh:function(){var a=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),this.$select_all.addClass(0==a.length?this.options.class_add:a.length==this.rows.length?this.options.class_remove:this.options.class_partial)},_find:function(a){var b=this.collection.findWhere({file_path:a.path,file_mode:"ftp",enabled:!0});return b&&b.get("id")},_templateRow:function(b){return'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+_.escape(b.path)+'</td><td class="ftp-size">'+a.bytesToString(b.size)+'</td><td class="ftp-time">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/> <span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody/></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div class="upload-ftp-content"/><div>'}})});
|
||||
//# sourceMappingURL=../../../maps/mvc/upload/upload-ftp.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.panels=require("layout/panel"),_.extend(window,require("layout/modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.init_tag_click_function=require("ui/autocom_tagging");var TOURS=require("mvc/tours"),QUERY_STRING=require("utils/query-string-parsing");window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a});var a=JSON.parse(sessionStorage.getItem("activeGalaxyTour"));if(a&&(a=TOURS.hooked_tour_from_data(a),a&&a.steps&&window&&window.self===window.top)){var b=new Tour(_.extend({steps:a.steps},TOURS.tour_opts));b.init(),b.restart()}});
|
||||
function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.panels=require("layout/panel"),_.extend(window,require("layout/modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.toolform=require("mvc/tool/tool-form"),window.init_tag_click_function=require("ui/autocom_tagging");var TOURS=require("mvc/tours"),QUERY_STRING=require("utils/query-string-parsing");window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a});var a=JSON.parse(sessionStorage.getItem("activeGalaxyTour"));if(a&&(a=TOURS.hooked_tour_from_data(a),a&&a.steps&&window&&window.self===window.top)){var b=new Tour(_.extend({steps:a.steps},TOURS.tour_opts));b.init(),b.restart()}});
|
||||
//# sourceMappingURL=../maps/onload.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -78,6 +78,7 @@
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='admin', action='review_tool_migration_stages' )}" target="galaxy_main">Review tool migration stages</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_errors' )}" target="galaxy_main">View Tool Error Logs</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='admin', action='sanitize_whitelist' )}" target="galaxy_main">Manage Display Whitelist</a></div>
|
||||
<div class="toolTitle"><a href="${h.url_for( controller='admin', action='manage_tool_dependencies' )}" target="galaxy_main">Manage Tool Dependencies</a></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="toolSectionPad"></div>
|
||||
|
||||
@@ -0,0 +1,114 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/webapps/tool_shed/repository/common.mako" import="render_dependency_status"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<%def name="render_tool_dependencies( requirements_status, ctr=False, ncols_extra=4, show_environment_path=False )">
|
||||
%for i, dependency in enumerate(requirements_status):
|
||||
%if i != 0:
|
||||
</tr>
|
||||
%if ctr % 2 == 1:
|
||||
<tr class="odd_row">
|
||||
%else:
|
||||
<tr class="tr">
|
||||
%endif
|
||||
%for i in range(ncols_extra-1):
|
||||
<td></td>
|
||||
%endfor
|
||||
%endif
|
||||
%if show_environment_path:
|
||||
<td>${dependency.get('environment_path', '') | h}</td>
|
||||
%endif
|
||||
${render_dependency_status(dependency)}
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_tool_centric_table( tools, requirements_status)">
|
||||
<tr>
|
||||
<th bgcolor="#D8D8D8">Install</th>
|
||||
<th bgcolor="#D8D8D8">Name</th>
|
||||
<th bgcolor="#D8D8D8">ID</th>
|
||||
<th bgcolor="#D8D8D8">Requirement</th>
|
||||
<th bgcolor="#D8D8D8">Version</th>
|
||||
<th bgcolor="#D8D8D8">Resolver</th>
|
||||
<th bgcolor="#D8D8D8">Exact</th>
|
||||
<th bgcolor="#D8D8D8"></th>
|
||||
</tr>
|
||||
<% ctr = 0 %>
|
||||
%for tool in tools.values():
|
||||
%if tool.tool_requirements:
|
||||
%if ctr % 2 == 1:
|
||||
<tr class="odd_row">
|
||||
%else:
|
||||
<tr class="tr">
|
||||
%endif
|
||||
<td>
|
||||
<input type="checkbox" name="install_for_tools" value="${tool.id}"/>
|
||||
</td>
|
||||
<td>${ tool.name | h }</td>
|
||||
<td>${ tool.id | h }</td>
|
||||
${render_tool_dependencies( requirements_status[tool.tool_requirements], ctr=ctr) }
|
||||
</tr>
|
||||
<% ctr += 1 %>
|
||||
%endif
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_dependencies_details( tools, requirements_status, tool_ids_by_requirements)">
|
||||
<tr>
|
||||
<th bgcolor="#D8D8D8">Install</th>
|
||||
<th bgcolor="#D8D8D8">Used by</th>
|
||||
<th bgcolor="#D8D8D8">Environment Path</th>
|
||||
<th bgcolor="#D8D8D8">Requirement</th>
|
||||
<th bgcolor="#D8D8D8">Version</th>
|
||||
<th bgcolor="#D8D8D8">Resolver</th>
|
||||
<th bgcolor="#D8D8D8">Exact</th>
|
||||
<th bgcolor="#D8D8D8"></th>
|
||||
</tr>
|
||||
<% ctr = 0 %>
|
||||
%for requirements, r_status in requirements_status.items():
|
||||
%if requirements:
|
||||
<% tool_ids = tool_ids_by_requirements[requirements] %>
|
||||
%if ctr % 2 == 1:
|
||||
<tr class="odd_row">
|
||||
%else:
|
||||
<tr class="tr">
|
||||
%endif
|
||||
<td>
|
||||
<input type="checkbox" name="install_for_tools" value="${tool_ids[0]}"/>
|
||||
</td>
|
||||
<td>${ ", ".join([tools[tid].name for tid in tool_ids]) | h }</td>
|
||||
${render_tool_dependencies( r_status, ctr=ctr, show_environment_path=True, ncols_extra=3) }
|
||||
</tr>
|
||||
%endif
|
||||
<% ctr += 1 %>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<h2>Manage Tool Dependencies</h2>
|
||||
<p>This page gives an overview of all tool dependencies required by all tools currently loaded, including tools not installed through the Tool Shed.</p>
|
||||
|
||||
<form name="manage_tool_dependencies" action="${h.url_for( controller='admin', action='manage_tool_dependencies' )}">
|
||||
%if viewkey == "Switch to tool-centric view":
|
||||
<input type="submit" name="viewkey" value="Switch to details view"/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Tool-centric dependencies</div>
|
||||
<div class="toolFormBody">
|
||||
<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
|
||||
${render_tool_centric_table(tools, requirements_status)}
|
||||
%else:
|
||||
<input type="submit" name="viewkey" value="Switch to tool-centric view"/>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Dependency details</div>
|
||||
<div class="toolFormBody">
|
||||
<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
|
||||
${render_dependencies_details(tools, requirements_status, tool_ids_by_requirements)}
|
||||
%endif
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<input type="submit" name="install_dependencies" value="Install checked dependencies using Conda"/>
|
||||
</form>
|
||||
@@ -1026,6 +1026,38 @@
|
||||
%>
|
||||
</%def>
|
||||
|
||||
<%def name="render_dependency_status( dependency, prepare_for_install=False)">
|
||||
<td>${dependency['name'] | h}</td>
|
||||
<td>${dependency['version'] | h}</td>
|
||||
%if not prepare_for_install:
|
||||
%if dependency['dependency_type']:
|
||||
<td>${dependency['dependency_type'].title() | h}</td>
|
||||
%else:
|
||||
<td>${dependency['dependency_type'] | h}</td>
|
||||
%endif
|
||||
<td>${dependency['exact'] | h}</td>
|
||||
%endif
|
||||
%if dependency['dependency_type'] == None:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
|
||||
%if prepare_for_install:
|
||||
Not Installed
|
||||
%endif
|
||||
</td>
|
||||
%elif not dependency['exact']:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/images/icon_warning_sml.gif" title='Dependency resolved, but version ${dependency['version']} not found'/>
|
||||
</td>
|
||||
%else:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/>
|
||||
%if prepare_for_install:
|
||||
Installed through ${dependency['dependency_type'].title() | h}
|
||||
%endif
|
||||
</td>
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_tool_dependency_resolver( requirements_status, prepare_for_install=False )">
|
||||
<tr class="datasetRow">
|
||||
<td style="padding-left: 20 px;">
|
||||
@@ -1043,37 +1075,8 @@
|
||||
</head>
|
||||
<body>
|
||||
%for dependency in requirements_status:
|
||||
${render_dependency_status(dependency, prepare_for_install)}
|
||||
<tr>
|
||||
<td>${dependency['name'] | h}</td>
|
||||
<td>${dependency['version'] | h}</td>
|
||||
%if not prepare_for_install:
|
||||
%if dependency['dependency_type']:
|
||||
<td>${dependency['dependency_type'].title() | h}</td>
|
||||
%else:
|
||||
<td>${dependency['dependency_type'] | h}</td>
|
||||
%endif
|
||||
<td>${dependency['exact'] | h}</td>
|
||||
%endif
|
||||
%if dependency['dependency_type'] == None:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Dependency not resolved'/>
|
||||
%if prepare_for_install:
|
||||
Not Installed
|
||||
%endif
|
||||
</td>
|
||||
%elif not dependency['exact']:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/images/icon_warning_sml.gif" title='Dependency resolved, but version ${dependency['version']} not found'/>
|
||||
</td>
|
||||
%else:
|
||||
<td>
|
||||
<img src="${h.url_for('/static')}/june_2007_style/blue/ok_small.png"/>
|
||||
%if prepare_for_install:
|
||||
Installed through ${dependency['dependency_type'].title() | h}
|
||||
%endif
|
||||
</td>
|
||||
%endif
|
||||
</tr>
|
||||
%endfor
|
||||
</body>
|
||||
</table>
|
||||
|
||||
+2
-3
@@ -2,6 +2,5 @@ Galaxy Testing
|
||||
==============
|
||||
|
||||
The Galaxy code base is large and contains many kinds of tests. Please
|
||||
consult the [Galaxy
|
||||
wiki](http://wiki.galaxyproject.org/Admin/Running%20Tests) for more
|
||||
information on testing Galaxy.
|
||||
run the command ``sh run_tests.sh --help`` from Galaxy's root for a
|
||||
description of each test type and location.
|
||||
|
||||
@@ -1005,9 +1005,7 @@ steps:
|
||||
assert invocation[ 'state' ] != 'scheduled'
|
||||
|
||||
self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=4, action=True )
|
||||
|
||||
time.sleep( 5 )
|
||||
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
||||
self.wait_for_invocation_and_jobs( history_id, uploaded_workflow_id, invocation_id )
|
||||
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
||||
assert invocation[ 'state' ] == 'scheduled'
|
||||
self.assertEqual("reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content( history_id ) )
|
||||
|
||||
@@ -6,6 +6,7 @@ attribute.
|
||||
|
||||
from selenium.webdriver.common.action_chains import ActionChains
|
||||
from selenium.webdriver.common.by import By
|
||||
from selenium.common.exceptions import TimeoutException
|
||||
from selenium.webdriver.common.keys import Keys
|
||||
from selenium.webdriver.support import expected_conditions as ec
|
||||
from selenium.webdriver.support.ui import WebDriverWait
|
||||
@@ -14,6 +15,7 @@ UNSPECIFIED_TIMEOUT = object()
|
||||
|
||||
|
||||
class HasDriver:
|
||||
TimeoutException = TimeoutException
|
||||
|
||||
def assert_xpath(self, xpath):
|
||||
assert self.driver.find_element_by_xpath(xpath)
|
||||
@@ -30,36 +32,66 @@ class HasDriver:
|
||||
assert len(self.driver.find_elements_by_css_selector(selector)) == 0
|
||||
|
||||
def wait_for_xpath(self, xpath):
|
||||
wait = self.wait()
|
||||
element = wait.until(ec.presence_of_element_located((By.XPATH, xpath)))
|
||||
element = self._wait_on(
|
||||
ec.presence_of_element_located((By.XPATH, xpath)),
|
||||
"XPATH selector [%s] to become present" % xpath,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_xpath_visible(self, xpath):
|
||||
wait = self.wait()
|
||||
element = wait.until(ec.visibility_of_element_located((By.XPATH, xpath)))
|
||||
element = self._wait_on(
|
||||
ec.visibility_of_element_located((By.XPATH, xpath)),
|
||||
"XPATH selector [%s] to become visible" % xpath,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_selector(self, selector):
|
||||
wait = self.wait()
|
||||
element = wait.until(ec.presence_of_element_located((By.CSS_SELECTOR, selector)))
|
||||
element = self._wait_on(
|
||||
ec.presence_of_element_located((By.CSS_SELECTOR, selector)),
|
||||
"CSS selector [%s] to become present" % selector,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_selector_visible(self, selector):
|
||||
wait = self.wait()
|
||||
return wait.until(ec.visibility_of_element_located((By.CSS_SELECTOR, selector)))
|
||||
element = self._wait_on(
|
||||
ec.visibility_of_element_located((By.CSS_SELECTOR, selector)),
|
||||
"CSS selector [%s] to become visible" % selector,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_selector_clickable(self, selector):
|
||||
element = self._wait_on(
|
||||
ec.element_to_be_clickable((By.CSS_SELECTOR, selector)),
|
||||
"CSS selector [%s] to become clickable" % selector,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_selector_absent_or_hidden(self, selector):
|
||||
wait = self.wait()
|
||||
return wait.until(ec.invisibility_of_element_located((By.CSS_SELECTOR, selector)))
|
||||
element = self._wait_on(
|
||||
ec.invisibility_of_element_located((By.CSS_SELECTOR, selector)),
|
||||
"CSS selector [%s] to become absent or hidden" % selector,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_selector_absent(self, selector):
|
||||
wait = self.wait()
|
||||
return wait.until(lambda driver: len(driver.find_elements_by_css_selector(selector)) == 0)
|
||||
element = self._wait_on(
|
||||
lambda driver: len(driver.find_elements_by_css_selector(selector)) == 0,
|
||||
"CSS selector [%s] to become absent" % selector,
|
||||
)
|
||||
return element
|
||||
|
||||
def wait_for_id(self, id):
|
||||
return self._wait_on(
|
||||
ec.presence_of_element_located((By.ID, id)),
|
||||
"presence of DOM ID [%s]" % id,
|
||||
)
|
||||
|
||||
def _wait_on(self, condition, on_str=None):
|
||||
if on_str is None:
|
||||
on_str = str(condition)
|
||||
message = "Timeout waiting on %s." % on_str
|
||||
wait = self.wait()
|
||||
element = wait.until(ec.presence_of_element_located((By.ID, id)))
|
||||
return element
|
||||
return wait.until(condition, message)
|
||||
|
||||
def action_chains(self):
|
||||
return ActionChains(self.driver)
|
||||
@@ -95,3 +127,10 @@ class HasDriver:
|
||||
def click_submit(self, form):
|
||||
submit_button = form.find_element_by_css_selector("input[type='submit']")
|
||||
submit_button.click()
|
||||
|
||||
def prepend_timeout_message(self, timeout_exception, message):
|
||||
return TimeoutException(
|
||||
msg=message + (timeout_exception.msg or ''),
|
||||
screen=timeout_exception.screen,
|
||||
stacktrace=timeout_exception.stacktrace,
|
||||
)
|
||||
|
||||
@@ -107,7 +107,10 @@ class NavigatesGalaxy(HasDriver):
|
||||
assert final_state == "ok", final_state
|
||||
return final_state
|
||||
|
||||
def history_panel_wait_for_hid_ok(self, hid, timeout=30):
|
||||
def history_panel_wait_for_hid_ok(self, hid, timeout=60):
|
||||
self.history_panel_wait_for_hid_state(hid, 'ok', timeout=timeout)
|
||||
|
||||
def history_panel_wait_for_hid_state(self, hid, state, timeout=60):
|
||||
current_history_id = self.current_history_id()
|
||||
|
||||
def history_has_hid(driver):
|
||||
@@ -117,8 +120,21 @@ class NavigatesGalaxy(HasDriver):
|
||||
self.wait(timeout).until(history_has_hid)
|
||||
contents = self.api_get("histories/%s/contents" % current_history_id)
|
||||
history_item = [d for d in contents if d["hid"] == hid][0]
|
||||
history_item_selector_okay = "#%s-%s.state-ok" % (history_item["history_content_type"], history_item["id"])
|
||||
self.wait_for_selector_visible(history_item_selector_okay)
|
||||
history_item_selector = "#%s-%s" % (history_item["history_content_type"], history_item["id"])
|
||||
self.wait_for_selector_visible(history_item_selector)
|
||||
history_item_selector_state = "%s.state-%s" % (history_item_selector, state)
|
||||
try:
|
||||
self.wait_for_selector_visible(history_item_selector_state)
|
||||
except self.TimeoutException as e:
|
||||
history_item = self.driver.find_element_by_css_selector(history_item_selector)
|
||||
current_state = "UNKNOWN"
|
||||
classes = history_item.get_attribute("class").split(" ")
|
||||
for clazz in classes:
|
||||
if clazz.startswith("state-"):
|
||||
current_state = clazz[len("state-"):]
|
||||
template = "Failed waiting on history item %d state to change to [%s] current state [%s]. "
|
||||
message = template % (hid, state, current_state)
|
||||
raise self.prepend_timeout_message(e, message)
|
||||
|
||||
def get_logged_in_user(self):
|
||||
return self.api_get("users/current")
|
||||
@@ -301,6 +317,31 @@ class NavigatesGalaxy(HasDriver):
|
||||
menu_selector = self.test_data["historyOptions"]["selectors"]["menu"]
|
||||
return menu_selector
|
||||
|
||||
def history_panel_multi_operations_selector(self):
|
||||
return self.test_data["historyPanel"]["selectors"]["history"]["multiOperationsIcon"]
|
||||
|
||||
def history_panel_multi_operations_show(self):
|
||||
operations_selector = self.history_panel_multi_operations_selector()
|
||||
operations_element = self.wait_for_selector_clickable(operations_selector)
|
||||
operations_element.click()
|
||||
|
||||
def history_panel_muli_operation_select_hid(self, hid):
|
||||
item_selector = self.history_panel_item_selector(hid, wait=True)
|
||||
operation_radio_selector = "%s .selector" % item_selector
|
||||
element = self.wait_for_selector_clickable(operation_radio_selector)
|
||||
element.click()
|
||||
|
||||
def history_panel_multi_operation_action_selector(self):
|
||||
return self.test_data["historyPanel"]["selectors"]["history"]["multiOperationsActionBtn"]
|
||||
|
||||
def history_panel_multi_operation_action_click(self, action):
|
||||
time.sleep(5)
|
||||
button_element = self.wait_for_selector_clickable(self.history_panel_multi_operation_action_selector())
|
||||
button_element.click()
|
||||
menu_element = self.wait_for_selector_visible(".list-action-menu.open")
|
||||
action_element = menu_element.find_element_by_link_text(action)
|
||||
action_element.click()
|
||||
|
||||
def history_panel_item_selector(self, hid, wait=False):
|
||||
current_history_id = self.current_history_id()
|
||||
contents = self.api_get("histories/%s/contents" % current_history_id)
|
||||
|
||||
@@ -107,6 +107,8 @@ historyPanel:
|
||||
nameEditableTextInput : '.name input'
|
||||
subtitle : '.subtitle'
|
||||
size : '.history-size'
|
||||
multiOperationsIcon: '.actions .show-selectors-btn'
|
||||
multiOperationsActionBtn: '.list-action-menu .list-action-menu-btn'
|
||||
tagIcon : '.actions .history-tag-btn'
|
||||
tagArea : '.controls .tags-display'
|
||||
annoIcon : '.actions .history-annotate-btn'
|
||||
|
||||
@@ -0,0 +1,39 @@
|
||||
from .framework import SeleniumTestCase
|
||||
from .framework import selenium_test
|
||||
|
||||
|
||||
class CollectionBuildersTestCase(SeleniumTestCase):
|
||||
|
||||
ensure_registered = True
|
||||
|
||||
@selenium_test
|
||||
def test_build_list_simple(self):
|
||||
self.perform_upload(self.get_filename("1.fasta"))
|
||||
self.history_panel_wait_for_hid_ok(1)
|
||||
self.history_panel_multi_operations_show()
|
||||
self.history_panel_muli_operation_select_hid(1)
|
||||
self.history_panel_multi_operation_action_click("Build Dataset List")
|
||||
|
||||
name_element = self.wait_for_selector_visible("input.collection-name")
|
||||
name_element.send_keys("my cool list")
|
||||
|
||||
create_element = self.wait_for_selector_clickable("button.create-collection")
|
||||
create_element.click()
|
||||
self.history_panel_wait_for_hid_ok(2)
|
||||
|
||||
@selenium_test
|
||||
def test_build_pair_simple(self):
|
||||
self.perform_upload(self.get_filename("1.tabular"))
|
||||
self.perform_upload(self.get_filename("2.tabular"))
|
||||
self.history_panel_wait_for_hid_ok(1)
|
||||
self.history_panel_wait_for_hid_ok(2)
|
||||
self.history_panel_multi_operations_show()
|
||||
self.history_panel_muli_operation_select_hid(1)
|
||||
self.history_panel_muli_operation_select_hid(2)
|
||||
self.history_panel_multi_operation_action_click("Build Dataset Pair")
|
||||
name_element = self.wait_for_selector_visible("input.collection-name")
|
||||
name_element.send_keys("my awesome pair")
|
||||
|
||||
create_element = self.wait_for_selector_clickable("button.create-collection")
|
||||
create_element.click()
|
||||
self.history_panel_wait_for_hid_ok(3)
|
||||
@@ -204,11 +204,11 @@ class MockHistoryDatasetAssociation( object ):
|
||||
)
|
||||
self.dbkey = "hg19"
|
||||
self.implicitly_converted_parent_datasets = False
|
||||
|
||||
self.name = name
|
||||
self.hid = id
|
||||
self.id = id
|
||||
self.children = []
|
||||
self.tags = []
|
||||
|
||||
@property
|
||||
def state( self ):
|
||||
|
||||
Reference in New Issue
Block a user