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Merge PR #1156 into dev and fix #1818.

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This commit is contained in:
John Chilton
2016-03-21 14:05:54 +00:00
parent b8cb5432a2 67e6ced211
commit 5eb96a5fcf
225 changed files with 4806 additions and 1491 deletions
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Makefile
+17 -12
View File
@@ -1,5 +1,5 @@
RELEASE_CURR:=16.01
RELEASE_CURR_MINOR_NEXT:=$(shell expr `awk '$$1 == "VERSION_MINOR" {print $$NF}' lib/galaxy/version.py | tr -d \" | sed 's/None/0/' ` + 1)
RELEASE_CURR_MINOR_NEXT:=$(shell expr `awk '$$1 == "VERSION_MINOR" {print $$NF}' lib/galaxy/version.py | tr -d \" | sed 's/None/0/;s/dev/0/;' ` + 1)
RELEASE_NEXT:=16.04
# TODO: This needs to be updated with create_release_rc
#RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
@@ -7,35 +7,35 @@ RELEASE_NEXT_BRANCH:=dev
RELEASE_UPSTREAM:=upstream
GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
all:
all: help
@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
npm-deps:
cd client && npm install
grunt: npm-deps
grunt: npm-deps ## Calls out to Grunt to build client
cd client && node_modules/grunt-cli/bin/grunt
style: npm-deps
style: npm-deps ## Calls the style task of Grunt
cd client && node_modules/grunt-cli/bin/grunt style
webpack: npm-deps
webpack: npm-deps ## Pack javascript
cd client && node_modules/webpack/bin/webpack.js -p
client: grunt style webpack
client: grunt style webpack ## Process all client-side tasks
grunt-docker-image:
grunt-docker-image: ## Build docker image for running grunt
docker build -t ${GRUNT_DOCKER_NAME} client
grunt-docker: grunt-docker-image
grunt-docker: grunt-docker-image ## Run grunt inside docker
docker run -it -v `pwd`:/data ${GRUNT_DOCKER_NAME}
clean-grunt-docker-image:
clean-grunt-docker-image: ## Remove grunt docker image
docker rmi ${GRUNT_DOCKER_NAME}
# Release Targets
create_release_rc:
create_release_rc: ## Create a release-candidate branch
git checkout dev
git pull --ff-only ${RELEASE_UPSTREAM} dev
git push origin dev
@@ -63,7 +63,7 @@ create_release_rc:
git branch -d version-$(RELEASE_CURR)
git branch -d version-$(RELEASE_NEXT).dev
create_release:
create_release: ## Create a release branch
git pull --ff-only $(RELEASE_UPSTREAM) master
git push origin master
git checkout release_$(RELEASE_CURR)
@@ -92,7 +92,7 @@ create_release:
#git push origin master:master
#git push origin --tags
create_point_release:
create_point_release: ## Create a point release
git pull --ff-only $(RELEASE_UPSTREAM) master
git push origin master
git checkout release_$(RELEASE_CURR)
@@ -119,3 +119,8 @@ create_point_release:
#git push origin master:master
#git push origin --tags
git checkout release_$(RELEASE_CURR)
.PHONY: help
help:
@egrep '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
client/galaxy/scripts/apps/analysis.js
+8 -4
View File
@@ -100,7 +100,7 @@ window.app = function app( options, bootstrapped ){
'(/)' : 'home',
// TODO: remove annoying 'root' from root urls
'(/)root*' : 'home',
'(/)tours(/:tour_id)' : 'show_tours',
'(/)tours(/)(:tour_id)' : 'show_tours',
},
show_tours : function( tour_id ){
@@ -116,9 +116,13 @@ window.app = function app( options, bootstrapped ){
home : function( params ){
// TODO: to router, remove Globals
// load a tool by id (tool_id) or rerun a previous tool execution (job_id)
if( ( params.tool_id || params.job_id ) && params.tool_id !== 'upload1' ){
this._loadToolForm( params );
if( params.tool_id || params.job_id ) {
if ( params.tool_id === 'upload1' ) {
Galaxy.upload.show();
this._loadCenterIframe( 'welcome' );
} else {
this._loadToolForm( params );
}
} else {
// show the workflow run form
if( params.workflow_id ){
client/galaxy/scripts/layout/menu.js
+5 -5
View File
@@ -144,15 +144,15 @@ var Collection = Backbone.Collection.extend({
target : '_blank'
},{
title : 'Interactive Tours',
url : 'tours',
onclick : function(){
if (Galaxy.app){
Galaxy.app.display(new Tours.ToursView());
} else {
// Redirect and use clientside routing to go to tour index
window.location = Galaxy.root + "#/tours";
window.location = Galaxy.root + "tours";
}
},
target : 'galaxy_main'
}
}]
};
options.terms_url && helpTab.menu.push({
@@ -274,7 +274,7 @@ var Tab = Backbone.View.extend({
this.$toggle.html( this.model.get( 'title' ) || '' )
.removeClass().addClass( 'dropdown-toggle' )
.addClass( this.model.get( 'cls' ) )
.addClass( this.model.get( 'icon' ) && 'fa fa-2x ' + this.model.get( 'icon' ) )
.addClass( this.model.get( 'icon' ) && 'dropdown-icon fa ' + this.model.get( 'icon' ) )
.addClass( this.model.get( 'toggle' ) && 'toggle' )
.attr( 'target', this.model.get( 'target' ) )
.attr( 'href', this.model.get( 'url' ) )
@@ -383,4 +383,4 @@ return {
Tab : Tab
};
});
});
client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
-1
View File
@@ -132,7 +132,6 @@ var DatasetListItemEdit = _super.extend(
var actions = _super.prototype._renderSecondaryActions.call( this );
switch( this.model.get( 'state' ) ){
case STATES.UPLOAD:
case STATES.NEW:
case STATES.NOT_VIEWABLE:
return actions;
case STATES.ERROR:
client/galaxy/scripts/mvc/history/history-contents.js
+45 -11
View File
@@ -2,9 +2,10 @@ define([
"mvc/history/history-content-model",
"mvc/history/hda-model",
"mvc/history/hdca-model",
"mvc/dataset/states",
"mvc/base-mvc",
"utils/localization"
], function( HISTORY_CONTENT, HDA_MODEL, HDCA_MODEL, BASE_MVC, _l ){
], function( HISTORY_CONTENT, HDA_MODEL, HDCA_MODEL, STATES, BASE_MVC, _l ){
'use strict';
@@ -102,15 +103,8 @@ var HistoryContents = Backbone.Collection
* @see HistoryDatasetAssociation#inReadyState
*/
running : function(){
var idList = [];
this.each( function( item ){
var isRunning = !item.inReadyState();
if( isRunning ){
//TODO: is this still correct since type_id
idList.push( item.get( 'id' ) );
}
});
return idList;
function filterFn( c ){ return !c.inReadyState(); }
return new HistoryContents( this.filter( filterFn ) );
},
/** Get the model with the given hid
@@ -156,12 +150,53 @@ var HistoryContents = Backbone.Collection
return new HistoryContents( this.filter( filterFn ) );
},
/** return a new contents collection of only hidden items */
visibleAndUndeleted : function(){
function filterFn( c ){ return c.get( 'visible' ) && !c.get( 'deleted' ); }
return new HistoryContents( this.filter( filterFn ) );
},
/** return true if any contents don't have details */
haveDetails : function(){
return this.all( function( content ){ return content.hasDetails(); });
},
// ........................................................................ ajax
/** override to use newest (versioned) api */
fetch : function( options ){
options = options || {};
options.data = _.defaults( options.data || {}, {
v : 'dev'
});
return Backbone.Collection.prototype.fetch.call( this, options );
},
/** override to use newest (versioned) api */
fetchUpdated : function( since, options ){
options = options || {};
options.traditional = true;
// TODO: this is painful - simplify here or move q/qv to named/mappable params
options.data = [{ name: 'v', value: 'dev' }];
if( since ){
options.data = options.data.concat( this._filtersFromMap({
'update_time-ge' : since.toISOString(),
}));
}
options.merge = true;
options.remove = false;
return this.fetch( options );
},
_filtersFromMap : function( filterMap ){
var filters = [];
// TODO: this seems unnecessary
_.each( filterMap, function( val, key ){
filters.push({ name: 'q', value: key });
filters.push({ name: 'qv', value: val });
});
return filters;
},
/** fetch detailed model data for all contents in this collection */
fetchAllDetails : function( options ){
options = options || {};
@@ -293,7 +328,6 @@ var HistoryContents = Backbone.Collection
});
},
/** In this override, copy the historyId to the clone */
clone : function(){
var clone = Backbone.Collection.prototype.clone.call( this );
client/galaxy/scripts/mvc/history/history-model.js
+63 -63
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@@ -137,6 +137,18 @@ var History = Backbone.Model
return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 );
},
/** Return the number of running jobs assoc with this history (note: unknown === 0) */
numOfUnfinishedJobs : function(){
var unfinishedJobIds = this.get( 'non_ready_jobs' );
return unfinishedJobIds? unfinishedJobIds.length : 0;
},
/** Return the number of running hda/hdcas in this history (note: unknown === 0) */
numOfUnfinishedShownContents : function(){
var contents = this.contents.running().visibleAndUndeleted();
return contents? contents.length : 0;
},
// ........................................................................ search
/** What model fields to search with */
searchAttributes : [
@@ -150,39 +162,56 @@ var History = Backbone.Model
},
// ........................................................................ updates
/** does the contents collection indicate they're still running and need to be updated later?
* delay + update if needed
* @param {Function} onReadyCallback function to run when all contents are in the ready state
* events: ready
*/
checkForUpdates : function( onReadyCallback ){
//this.info( 'checkForUpdates' )
// get overall History state from collection, run updater if History has running/queued contents
// boiling it down on the client to running/not
if( this.contents.running().length ){
this.setUpdateTimeout();
} else {
this.trigger( 'ready' );
if( _.isFunction( onReadyCallback ) ){
onReadyCallback.call( this );
}
}
return this;
_getSizeAndRunning : function(){
return this.fetch({ data : $.param({ keys : 'size,non_ready_jobs' }) });
},
/** create a timeout (after UPDATE_DELAY or delay ms) to refetch the contents. Clear any prev. timeout */
setUpdateTimeout : function( delay ){
delay = delay || History.UPDATE_DELAY;
var history = this;
/** */
refresh : function( options ){
options = options || {};
var self = this;
// prevent buildup of updater timeouts by clearing previous if any, then set new and cache id
this.clearUpdateTimeout();
this.updateTimeoutId = setTimeout( function(){
history.refresh();
}, delay );
return this.updateTimeoutId;
var lastUpdateTime = self.lastUpdateTime;
self.lastUpdateTime = new Date();
// note if there was no previous update time, all summary contents will be fetched
return self.contents.fetchUpdated( lastUpdateTime )
.done( _.bind( self.checkForUpdates, self ) );
},
/** */
checkForUpdates : function( options ){
options = options || {};
var delay = History.UPDATE_DELAY;
var self = this;
function _delayThenUpdate(){
// prevent buildup of updater timeouts by clearing previous if any, then set new and cache id
self.clearUpdateTimeout();
self.updateTimeoutId = setTimeout( function(){
self.refresh( options );
}, delay );
}
// if there are still datasets in the non-ready state, recurse into this function with the new time
if( this.numOfUnfinishedShownContents() > 0 ){
_delayThenUpdate();
} else {
// no datasets are running, but currently runnning jobs may still produce new datasets
// see if the history has any running jobs and continue to update if so
// (also update the size for the user in either case)
self._getSizeAndRunning()
.done( function( historyData ){
if( self.numOfUnfinishedJobs() > 0 ){
_delayThenUpdate();
} else {
// otherwise, let listeners know that all updates have stopped
self.trigger( 'ready' );
// self.lastUpdateTime = null;
}
});
}
},
/** clear the timeout and the cached timeout id */
@@ -193,32 +222,6 @@ var History = Backbone.Model
}
},
/* update the contents, getting full detailed model data for any whose id is in detailIds
* set up to run this again in some interval of time
* @param {String[]} detailIds list of content ids to get detailed model data for
* @param {Object} options std. backbone fetch options map
*/
refresh : function( detailIds, options ){
//this.info( 'refresh:', detailIds, this.contents );
detailIds = detailIds || [];
options = options || {};
var history = this;
// add detailIds to options as CSV string
options.data = options.data || {};
if( detailIds.length ){
options.data.details = detailIds.join( ',' );
}
var xhr = this.contents.fetch( options );
xhr.done( function( models ){
history.checkForUpdates( function(){
// fetch the history inside onReadyCallback in order to recalc history size
this.fetch();
});
});
return xhr;
},
// ........................................................................ ajax
/** save this history, _Mark_ing it as deleted (just a flag) */
_delete : function( options ){
@@ -330,14 +333,11 @@ History.getHistoryData = function getHistoryData( historyId, options ){
if( _.isFunction( hdcaDetailIds ) ){
hdcaDetailIds = hdcaDetailIds( historyData );
}
var data = {};
var data = {
v : 'dev'
};
if( detailIdsFn.length ) {
data.dataset_details = detailIdsFn.join( ',' );
}
if( hdcaDetailIds.length ) {
// for symmetry, not actually used by backend of consumed
// by frontend.
data.dataset_collection_details = hdcaDetailIds.join( ',' );
data.details = detailIdsFn.join( ',' );
}
return jQuery.ajax( Galaxy.root + 'api/histories/' + historyData.id + '/contents', { data: data });
}
client/galaxy/scripts/mvc/history/history-view.js
+3 -3
View File
@@ -131,8 +131,8 @@ var HistoryView = _super.extend(
/** In this override, clear the update timer on the model */
freeModel : function(){
_super.prototype.freeModel.call( this );
//TODO: move to History.free()
if( this.model ){
//TODO: move to History.free()
this.model.clearUpdateTimeout();
}
return this;
@@ -221,9 +221,9 @@ var HistoryView = _super.extend(
},
/** convenience alias to the model. Updates the item list only (not the history) */
refreshContents : function( detailIds, options ){
refreshContents : function( options ){
if( this.model ){
return this.model.refresh( detailIds, options );
return this.model.refresh( options );
}
// may have callbacks - so return an empty promise
return $.when();
client/galaxy/scripts/mvc/history/multi-panel.js
+2 -2
View File
@@ -453,7 +453,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
handleDeletedHistory : function handleDeletedHistory( history ){
if( history.get( 'deleted' ) || history.get( 'purged' ) ){
this.log( 'handleDeletedHistory', this.collection.includeDeleted, history );
var multipanel = this;
var multipanel = this,
column = multipanel.columnMap[ history.id ];
if( !column ){ return; }
@@ -723,7 +723,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
var xhrData = {},
ids = _.values( column.panel.storage.get( 'expandedIds' ) ).join();
if( ids ){
xhrData.dataset_details = ids;
xhrData.details = ids;
}
// this uses a 'named' queue so that duplicate requests are ignored
this.hdaQueue.add({
client/galaxy/scripts/mvc/library/library-folder-view.js
-7
View File
@@ -220,29 +220,22 @@ var FolderView = Backbone.View.extend({
tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');
tmpl_array.push(' </div>');
// tmpl_array.push('<% if (item.get("is_unrestricted")) { %>');
tmpl_array.push(' <p>');
tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page. ');
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');
tmpl_array.push(' </p>');
// tmpl_array.push('<% } %>');
tmpl_array.push('<div class="dataset_table">');
tmpl_array.push(' <table class="grid table table-striped table-condensed">');
tmpl_array.push(' <tr>');
tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' <% if (item.get("file_ext")) { %>');
tmpl_array.push(' <tr>');
tmpl_array.push(' <th scope="row">Data type</th>');
tmpl_array.push(' <td><%= _.escape(item.get("file_ext")) %></td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' <% } %>');
tmpl_array.push(' </table>');
tmpl_array.push('</div>');
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+4 -2
View File
@@ -99,7 +99,7 @@ var FolderToolbarView = Backbone.View.extend({
renderPaginator: function( options ){
this.options = _.extend( this.options, options );
var paginator_template = this.templatePaginator();
this.$el.find( '#folder_paginator' ).html( paginator_template({
$("body").find( '.folder-paginator' ).html( paginator_template({
id: this.options.id,
show_page: parseInt( this.options.show_page ),
page_count: parseInt( this.options.page_count ),
@@ -1059,7 +1059,7 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <div id="library_toolbar">');
tmpl_array.push('<form class="form-inline" role="form">');
tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>');
tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');
tmpl_array.push(' <span class="library-paginator folder-paginator">');
// paginator will append here
tmpl_array.push(' </span>');
tmpl_array.push('<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">');
@@ -1119,6 +1119,8 @@ var FolderToolbarView = Backbone.View.extend({
tmpl_array.push(' <div id="folder_items_element">');
tmpl_array.push(' </div>');
tmpl_array.push('</div>');
tmpl_array.push('<div class="folder-paginator paginator-bottom"></div>');
// CONTAINER END
return _.template(tmpl_array.join(''));
client/galaxy/scripts/mvc/tool/tool-form-workflow.js
+1 -1
View File
@@ -98,7 +98,7 @@ define(['utils/utils', 'mvc/tool/tool-form-base'],
type : 'boolean',
value : String(Boolean(this.post_job_actions['EmailAction' + output_id])),
ignore : 'false',
help : 'An email notification will be send when the job has completed.',
help : 'An email notification will be sent when the job has completed.',
payload : {
'host' : window.location.host
}
client/galaxy/scripts/mvc/tool/tool-form.js
+1 -1
View File
@@ -14,7 +14,7 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to
icon : 'fa-check',
tooltip : 'Execute: ' + options.name + ' (' + options.version + ')',
title : 'Execute',
cls : 'btn btn-primary',
cls : 'ui-button btn btn-primary',
floating : 'clear',
onclick : function() {
execute_btn.wait();
client/galaxy/scripts/mvc/tours.js
+3 -2
View File
@@ -101,14 +101,15 @@ define(['libs/bootstrap-tour'],function(BootstrapTour) {
"<ul>",
'<% _.each(tours, function(tour) { %>',
'<li>',
'<a href="#/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',
'<a href="/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>',
'<%- tour.attributes.name || tour.id %>',
'</a>',
' - <%- tour.attributes.description || "No description given." %>',
'</li>',
'<% }); %>',
"</ul>"].join(''));
this.$el.html(tpl({tours: this.model.models})).on("click", ".tourItem", function(){
this.$el.html(tpl({tours: this.model.models})).on("click", ".tourItem", function(e){
e.preventDefault();
giveTour($(this).data("tour.id"));
});
}
client/galaxy/scripts/mvc/workflow/workflow-canvas.js
+25 -8
View File
@@ -3,6 +3,7 @@ define([], function() {
this.app = app;
this.cv = canvas_viewport;
this.cc = this.cv.find( "#canvas-container" );
this.overview = overview;
this.oc = overview.find( "#overview-canvas" );
this.ov = overview.find( "#overview-viewport" );
// Make overview box draggable
@@ -41,18 +42,34 @@ define([], function() {
self.app.workflow.fit_canvas_to_nodes();
self.draw_overview();
});
this.overview.click( function( e ) {
if (self.overview.hasClass('blockaclick')){
self.overview.removeClass('blockaclick');
} else {
var in_w = self.cc.width(),
in_h = self.cc.height(),
o_w = self.oc.width(),
o_h = self.oc.height(),
new_x_offset = e.pageX - self.oc.offset().left - self.ov.width() / 2,
new_y_offset = e.pageY - self.oc.offset().top - self.ov.height() / 2;
move( - ( new_x_offset / o_w * in_w ),
- ( new_y_offset / o_h * in_h ) );
self.app.workflow.fit_canvas_to_nodes();
self.draw_overview();
}
});
// Dragging for overview pane
this.ov.bind( "drag", function( e, d ) {
var in_w = self.cc.width(),
in_h = self.cc.height(),
o_w = self.oc.width(),
o_h = self.oc.height(),
p = $(this).offsetParent().offset(),
new_x_offset = d.offsetX - p.left,
new_y_offset = d.offsetY - p.top;
new_x_offset = d.offsetX - self.overview.offset().left,
new_y_offset = d.offsetY - self.overview.offset().top;
move( - ( new_x_offset / o_w * in_w ),
- ( new_y_offset / o_h * in_h ) );
}).bind( "dragend", function() {
self.overview.addClass('blockaclick');
self.app.workflow.fit_canvas_to_nodes();
self.draw_overview();
});
@@ -68,11 +85,11 @@ define([], function() {
});
self.draw_overview();
});
/* Disable dragging for child element of the panel so that resizing can
only be done by dragging the borders */
$("#overview-border div").bind("drag", function() { });
},
update_viewport_overlay: function() {
var cc = this.cc,
@@ -83,7 +100,7 @@ define([], function() {
in_h = cc.height(),
o_w = oc.width(),
o_h = oc.height(),
cc_pos = cc.position();
cc_pos = cc.position();
ov.css( {
left: - ( cc_pos.left / in_w * o_w ),
top: - ( cc_pos.top / in_h * o_h ),
@@ -143,7 +160,7 @@ define([], function() {
if (node.tool_errors){
c.fillStyle = "#FFCCCC";
c.strokeStyle = "#AA6666";
} else if (node.workflow_outputs != undefined && node.workflow_outputs.length > 0){
} else if (node.workflow_outputs !== undefined && node.workflow_outputs.length > 0){
c.fillStyle = "#E8A92D";
c.strokeStyle = "#E8A92D";
}
@@ -225,4 +242,4 @@ define([], function() {
}
});
return CanvasManager;
});
});
client/galaxy/scripts/mvc/workflow/workflow-view.js
+3 -5
View File
@@ -361,12 +361,10 @@ EditorFormView = Backbone.View.extend({
self.canvas_manager.draw_overview();
// Determine if any parameters were 'upgraded' and provide message
upgrade_message = "";
$.each( data.upgrade_messages, function( step_id, messages ) {
_.each( data.upgrade_messages, function( messages, step_id ) {
var details = "";
Utils.deepeach( [ messages ], function( d ) {
$.each( d, function( i, v ) {
details += typeof v === "string" ? "<li>" + v + "</li>" : "";
});
_.each( messages, function( m ) {
details += "<li>" + m + "</li>";
});
if ( details ) {
upgrade_message += "<li>Step " + ( parseInt( step_id, 10 ) + 1 ) + ": " + self.workflow.nodes[ step_id ].name + "<ul>" + details + "</ul></li>";
client/galaxy/scripts/onload.js
+11 -5
View File
@@ -170,11 +170,17 @@ $(document).ready( function() {
if (et){
et = TOURS.hooked_tour_from_data(et);
if (et && et.steps){
var tour = new Tour(_.extend({
steps: et.steps,
}, TOURS.tour_opts));
tour.init();
tour.restart();
if (window && window.self === window.top){
// Only kick off a new tour if this is the toplevel window (non-iframe). This
// functionality actually *could* be useful, but we'd need to handle it better and
// come up with some design guidelines for tours jumping between windows.
// Disabling for now.
var tour = new Tour(_.extend({
steps: et.steps,
}, TOURS.tour_opts));
tour.init();
tour.restart();
}
}
}
});
client/galaxy/style/less/base.less
+4
View File
@@ -430,6 +430,10 @@ div.unified-panel-body-background {
.toggle {
color : gold;
}
.dropdown-icon {
top : 1px;
font-size : 1.8em;
}
.dropdown-note {
font-weight : bold;
font-size : 10px;
client/galaxy/style/less/library.less
+5
View File
@@ -229,3 +229,8 @@ span.expandLink {
.library-paginator {
margin-left: 2em;
}
.paginator-bottom{
width: 27em;
margin-left: auto;
margin-right: auto;
}
client/galaxy/style/less/ui.less
+3 -2
View File
@@ -111,7 +111,7 @@
// buttons
.ui-button {
i {
font-size: 1.2em;
font-size: 1.1em;
}
}
.ui-button-icon {
@@ -579,6 +579,7 @@
i {
padding-right: @ui-margin-horizontal;
font-size: 1.1em;
}
}
@@ -670,7 +671,7 @@
position: relative;
.icon-dropdown {
position: absolute;
top: 8px;
top: 7px;
right: 8px;
cursor: pointer;
}
client/galaxy/style/less/upload.less
+1
View File
@@ -63,6 +63,7 @@
color: @btn-default-border;
i {
margin-right: 10px;
font-size: inherit;
}
}
.upload-row {
client/grunt-tasks/style.js
+3
View File
@@ -67,6 +67,9 @@ module.exports = function( grunt ){
// remove tmp files
grunt.config( 'clean', {
options : {
force: true
},
clean : [
fmt( '%s/tmp-site-config.less', lessPath )
]
client/package.json
+4
View File
@@ -5,6 +5,10 @@
"keywords": [
"galaxy"
],
"repository": { "type": "git",
"url": "https://github.com/galaxyproject/galaxy.git"
},
"license": "AFL-3.0",
"dependencies": {
"amdi18n-loader": "^0.2.0",
"grunt": "^0.4.5",
config/datatypes_conf.xml.sample
+56
View File
@@ -15,6 +15,7 @@
<display file="ensembl/ensembl_bam.xml" />
<display file="igv/bam.xml" />
<display file="igb/bam.xml" />
<display file="iobio/bam.xml" />
</datatype>
<datatype extension="cram" type="galaxy.datatypes.binary:CRAM" mimetype="application/octet-stream" display_in_upload="true" description="CRAM is a file format for highly efficient and tunable reference-based compression of alignment data." description_url="http://www.ebi.ac.uk/ena/software/cram-usage"/>
<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed">
@@ -246,6 +247,7 @@
<display file="ucsc/vcf.xml" />
<display file="igv/vcf.xml" />
<display file="rviewer/vcf.xml" inherit="True"/>
<display file="iobio/vcf.xml" />
</datatype>
<datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True">
<converter file="bcf_to_bcf_bgzip_converter.xml" target_datatype="bcf_bgzip"/>
@@ -440,6 +442,53 @@
<datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
<!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
<datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
<!--Cheminformatics Datatypes -->
<datatype extension="smi" type="galaxy.datatypes.molecules:SMILES" display_in_upload="True">
<!-- The ordering is important. The first one is considered as default converter in the build-in conversion function -> (as sdf)-->
<converter file="smi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="smi_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="smi_to_cml_converter.xml" target_datatype="cml"/>
<converter file="smi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="smi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="smi_to_smi_converter.xml" target_datatype="smi"/>
</datatype>
<datatype extension="sdf" type="galaxy.datatypes.molecules:SDF" display_in_upload="True">
<converter file="sdf_to_smi_converter.xml" target_datatype="smi"/>
<converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="True">
<converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
<converter file="inchi_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="inchi_to_mol_converter.xml" target_datatype="mol"/>
<converter file="inchi_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="inchi_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol" type="galaxy.datatypes.molecules:MOL" display_in_upload="True">
<converter file="mol_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol_to_mol2_converter.xml" target_datatype="mol2"/>
<converter file="mol_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="mol2" type="galaxy.datatypes.molecules:MOL2" display_in_upload="False">
<converter file="mol2_to_smi_converter.xml" target_datatype="smi"/>
<converter file="mol2_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
<converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
</datatype>
<datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="True">
<converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
<converter file="cml_to_inchi_converter.xml" target_datatype="inchi"/>
<converter file="cml_to_sdf_converter.xml" target_datatype="sdf"/>
<converter file="cml_to_mol2_converter.xml" target_datatype="mol2"/>
</datatype>
<datatype extension="fps" type="galaxy.datatypes.molecules:FPS" mimetype="text/html" display_in_upload="True" />
<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="False" />
<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="False" />
<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="True" />
</registration>
<sniffers>
<!--
@@ -481,6 +530,7 @@
<sniffer type="galaxy.datatypes.proteomics:Msp"/>
<sniffer type="galaxy.datatypes.proteomics:SPLib"/>
<sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
<sniffer type="galaxy.datatypes.molecules:CML"/>
<sniffer type="galaxy.datatypes.xml:GenericXml"/>
<sniffer type="galaxy.datatypes.triples:Turtle"/>
<sniffer type="galaxy.datatypes.triples:NTriples"/>
@@ -490,6 +540,12 @@
<sniffer type="galaxy.datatypes.sequence:csFasta"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
<sniffer type="galaxy.datatypes.molecules:SDF"/>
<sniffer type="galaxy.datatypes.molecules:PDB"/>
<sniffer type="galaxy.datatypes.molecules:MOL2"/>
<sniffer type="galaxy.datatypes.molecules:InChI"/>
<sniffer type="galaxy.datatypes.molecules:FPS"/>
<!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
<sniffer type="galaxy.datatypes.sequence:Fasta"/>
<sniffer type="galaxy.datatypes.sequence:Fastq"/>
<sniffer type="galaxy.datatypes.interval:Wiggle"/>
config/galaxy.ini.sample
+7
View File
@@ -656,6 +656,13 @@ nglims_config_file = tool-data/nglims.yaml
# log_events and log_actions functionality will eventually be merged.
#log_actions = True
# Fluentd configuration. Various events can be logged to the fluentd instance
# configured below by enabling fluent_log.
#fluent_log = False
#fluent_host = localhost
#fluent_port = 24224
# Sanitize all HTML tool output. By default, all tool output served as
# 'text/html' will be sanitized thoroughly. This can be disabled if you have
# special tools that require unaltered output. WARNING: disabling this does
config/tool_conf.xml.main
+4 -4
View File
@@ -28,18 +28,18 @@
</section>
<section id="textutil" name="Text Manipulation">
<tool file="filters/fixedValueColumn.xml" />
<tool file="filters/catWrapper.xml" />
<tool file="filters/catWrapper.xml" hidden="True" />
<tool file="filters/condense_characters.xml" />
<tool file="filters/convert_characters.xml" />
<tool file="filters/mergeCols.xml" />
<tool file="filters/CreateInterval.xml" />
<tool file="filters/cutWrapper.xml" />
<tool file="filters/cutWrapper.xml" hidden="True" />
<tool file="filters/changeCase.xml" />
<tool file="filters/pasteWrapper.xml" />
<tool file="filters/remove_beginning.xml" />
<tool file="filters/randomlines.xml" />
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
<tool file="filters/headWrapper.xml" hidden="True" />
<tool file="filters/tailWrapper.xml" hidden="True" />
<tool file="filters/trimmer.xml" />
<tool file="filters/wc_gnu.xml" />
<tool file="filters/secure_hash_message_digest.xml" />
config/tool_data_table_conf.xml.sample
+10
View File
@@ -75,4 +75,14 @@
<columns>dbkey, name, value</columns>
<file path="tool-data/liftOver.loc" />
</table>
<!-- iobio bam servers -->
<table name="bam_iobio" comment_char="#">
<columns>value, name, url</columns>
<file path="tool-data/bam_iobio.loc" />
</table>
<!-- iobio vcf servers -->
<table name="vcf_iobio" comment_char="#">
<columns>value, name, url</columns>
<file path="tool-data/vcf_iobio.loc" />
</table>
</tables>
contrib/galaxy.fedora-init
+14 -12
View File
@@ -8,6 +8,8 @@
# chkconfig: 2345 98 20
# description: Galaxy http://galaxyproject.org/
#--- loading functions
. /etc/init.d/functions
#--- config
SERVICE_NAME="galaxy"
@@ -53,17 +55,17 @@ stop() {
echo "done."
}
status() {
echo -n "$SERVICE_NAME status: "
while read pid; do
if [ "$(readlink -m /proc/$pid/cwd)" = "$(readlink -m $RUN_IN)" ]; then
echo "started"
return 0
fi
done < <(ps ax -o 'pid cmd' | grep -P '^\s*\d+ python ./scripts/paster.py serve' | awk '{print $1}')
echo "stopped"
return 3
galaxy_status() {
if [[ $(grep '\[server:' $RUN_IN/config/galaxy.ini|awk -F'(:)|(])' '{ print $2 }') == 'main' ]]
then
echo -n "$SERVICE_NAME status: "
status -p $RUN_IN/paster.pid galaxy
else
for proc in $(grep '\[server:' $RUN_IN/config/galaxy.ini|awk -F'(:)|(])' '{ print $2 }')
do
status -p $RUN_IN/${proc}.pid ${proc}
done
fi
}
notsupported() {
@@ -90,7 +92,7 @@ case "$1" in
;;
status)
set +e
status
galaxy_status
exit $?
;;
'')
contrib/galaxy_reports.fedora-init
+95
View File
@@ -0,0 +1,95 @@
#!/bin/bash
#
# Init file for Galaxy (http://galaxyproject.org/)
# Suitable for use on Fedora and derivatives (RedHat Enterprise Linux, Scientific Linux, CentOS)
#
# Contributed by Brad Chapman
#
# chkconfig: 2345 98 20
# description: Galaxy http://galaxyproject.org/
#--- loading functions
. /etc/init.d/functions
#--- config
SERVICE_NAME="galaxy-reports"
RUN_AS="galaxy"
RUN_IN="/path/to/galaxy-dist"
#--- main actions
start() {
echo "Starting $SERVICE_NAME... "
cmd="cd $RUN_IN && sh run_reports.sh --daemon"
case "$(id -un)" in
$RUN_AS)
eval "$cmd"
;;
root)
su - $RUN_AS -c "$cmd"
;;
*)
echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2
exit 1
esac
echo "...done."
}
stop() {
echo -n "Stopping $SERVICE_NAME... "
cmd="cd $RUN_IN && sh run_reports.sh --stop-daemon"
case "$(id -un)" in
$RUN_AS)
eval "$cmd"
;;
root)
su - $RUN_AS -c "$cmd"
;;
*)
echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2
exit 1
esac
echo "done."
}
notsupported() {
echo "*** ERROR*** $SERVICE_NAME: operation [$1] not supported"
}
usage() {
echo "Usage: $SERVICE_NAME start|stop|restart|status"
}
#---
case "$1" in
start)
start "$@"
;;
stop)
stop
;;
restart|reload)
stop
start
;;
status)
set +e
echo -n "$SERVICE_NAME status: "
status -p $RUN_IN/reports_webapp.pid $SERVICE_NAME
exit $?
;;
'')
usage >&2
exit 1
;;
*)
notsupported "$1" >&2
usage >&2
exit 1
;;
esac
create_db.sh
+5 -3
View File
@@ -1,9 +1,11 @@
#!/bin/sh
if [ -d .venv ];
: ${GALAXY_VIRTUAL_ENV:=.venv}
if [ -d "$GALAXY_VIRTUAL_ENV" ];
then
printf "Activating virtualenv at %s/.venv\n" $(pwd)
. .venv/bin/activate
printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
. "$GALAXY_VIRTUAL_ENV/bin/activate"
fi
cd `dirname $0`
display_applications/iobio/bam.xml
+8
View File
@@ -0,0 +1,8 @@
<?xml version="1.0"?>
<display id="iobio_bam" version="1.0.0" name="display at bam.iobio">
<dynamic_links from_data_table="bam_iobio" skip_startswith="#" id="value" name="name">
<url>${url}?bam=${bam_file.qp}</url>
<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
</dynamic_links>
</display>
display_applications/iobio/vcf.xml
+8
View File
@@ -0,0 +1,8 @@
<?xml version="1.0"?>
<display id="iobio_vcf" version="1.0.0" name="display at vcf.iobio">
<dynamic_links from_data_table="vcf_iobio" skip_startswith="#" id="value" name="name">
<url>${url}?vcf=${bgzip_file.qp}</url>
<param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
<param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
</dynamic_links>
</display>
doc/source/admin/framework_dependencies.rst
+4 -6
View File
@@ -125,10 +125,10 @@ virtualenv using the ``--no-create-venv`` option:
repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker,
Markdown, Cheetah, requests, requests-toolbelt, boto, bioblend, amqp,
anyjson, kombu, pbr, sqlparse, decorator, Tempita, sqlalchemy-migrate,
Parsley, nose, SVGFig, ecdsa, paramiko, Fabric, Whoosh, pysam
Parsley, nose, svgwrite, ecdsa, paramiko, Fabric, Whoosh, pysam
Successfully installed Babel-2.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.10.2
Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2
PasteDeploy-1.5.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.8 SVGFig-1.1.6
PasteDeploy-1.5.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.8 svgwrite-1.1.6
Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.4.1+gx1 amqp-1.4.8
anyjson-0.3.3 bioblend-0.6.1 boto-2.38.0 bx-python-0.7.3 decorator-4.0.2
docutils-0.12 ecdsa-0.13 kombu-3.0.30 mercurial-3.4.2 nose-1.3.7
@@ -178,10 +178,8 @@ Galaxy to start without attempting to fetch wheels:
$ sh run.sh --no-create-venv --skip-wheels
Including ``--index-url=https://wheels.galaxyproject.org/simple/`` is important
- at least one current Galaxy dependency (SVGFig) is not available in PyPI but
is available (in both source and wheel form) on `wheels.galaxyproject.org`_,
and two (pysam, Whoosh) include modifications specific to Galaxy which are only
available on `wheels.galaxyproject.org`_.
as two dependencies (pysam, Whoosh) include modifications specific to Galaxy
which are only available on `wheels.galaxyproject.org`_.
.. _unpinned requirements file: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
lib/galaxy/app.py
+11 -1
View File
@@ -41,6 +41,11 @@ app = None
class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
"""Encapsulates the state of a Universe application"""
def __init__( self, **kwargs ):
if not log.handlers:
# Paste didn't handle it, so we need a temporary basic log
# configured. The handler added here gets dumped and replaced with
# an appropriately configured logger in configure_logging below.
logging.basicConfig(level=logging.DEBUG)
log.debug( "python path is: %s", ", ".join( sys.path ) )
self.name = 'galaxy'
self.new_installation = False
@@ -49,7 +54,7 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
self.config.check()
config.configure_logging( self.config )
self.configure_fluent_log()
self.config.reload_sanitize_whitelist(explicit='sanitize_whitelist_file' in kwargs)
self.amqp_internal_connection_obj = galaxy.queues.connection_from_config(self.config)
# control_worker *can* be initialized with a queue, but here we don't
# want to and we'll allow postfork to bind and start it.
@@ -155,6 +160,11 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
self.heartbeat.start()
if not config.process_is_uwsgi:
_start()
if self.config.sentry_dsn:
import raven
self.sentry_client = raven.Client(self.config.sentry_dsn)
else:
self.sentry_client = None
# Transfer manager client
if self.config.get_bool( 'enable_beta_job_managers', False ):
from galaxy.jobs import transfer_manager
lib/galaxy/config.py
+3 -3
View File
@@ -267,7 +267,6 @@ class Configuration( object ):
self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root )
self.reload_sanitize_whitelist()
self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames( kwargs )
self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) )
@@ -484,7 +483,7 @@ class Configuration( object ):
else:
return None
def reload_sanitize_whitelist( self ):
def reload_sanitize_whitelist( self, explicit=True ):
self.sanitize_whitelist = []
try:
with open(self.sanitize_whitelist_file, 'rt') as f:
@@ -492,7 +491,8 @@ class Configuration( object ):
if not line.startswith("#"):
self.sanitize_whitelist.append(line.strip())
except IOError:
log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
if explicit:
log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
def __parse_config_file_options( self, kwargs ):
"""
lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_cml_to_inchi" name="CML to InChI" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -icml "${input}" -oinchi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
</inputs>
<outputs>
<data name="output" format="inchi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_cml_to_mol2" name="CML to mol2" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -icml "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_cml_to_sdf" name="CML to SDF" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -icml "${input}" -osdf "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
</inputs>
<outputs>
<data name="output" format="sdf"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
+48
View File
@@ -0,0 +1,48 @@
<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command >
<![CDATA[
obabel
-icml "${input}"
#if $can:
-ocan
#else:
-osmi
#end if
-O "${output}"
-e
$remove_h
#if $iso_chi or $can or $exp_h:
-x$iso_chi$exp_h$can
#end if
#if $dative_bonds:
-b
#end if
#if int($ph) >= 0:
-p $ph
#end if
2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="cml" label="Molecules in CML-format"/>
<param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
<param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
<param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
<param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
<param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
<param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_inchi_to_cml" name="InChI to CML" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -iinchi "${input}" -ocml -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
</inputs>
<outputs>
<data name="output" format="cml"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_inchi_to_mol2" name="InChI to MOL2" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -iinchi "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_inchi_to_mol" name="InChI to MOL" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -iinchi "${input}" -omol -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="inchi" label="Molecules in InChI-format"/>
</inputs>
<outputs>
<data name="output" format="mol"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_inchi_to_sdf" name="InChI to SDF" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -iinchi "${input}" -osdf -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
</inputs>
<outputs>
<data name="output" format="sdf"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_inchi_to_smi" name="InChI to SMILES" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -iinchi "${input}" -osmi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_mol2_to_cml" name="MOL2 to CML" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol2 "${input}" -ocml -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
</inputs>
<outputs>
<data name="output" format="cml"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_mol2_to_inchi" name="MOL2 to InChI" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol2 "${input}" -oinchi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
</inputs>
<outputs>
<data name="output" format="inchi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_mol2_to_mol" name="MOL2 to MOL" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol2 "${input}" -omol -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
</inputs>
<outputs>
<data name="output" format="mol"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_mol2_to_sdf" name="MOL2 to SDF" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol2 "${input}" -osdf "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
</inputs>
<outputs>
<data name="output" format="sdf"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_mol2_to_smi" name="MOL2 to SMILES" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol2 "${input}" -omol "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
+21
View File
@@ -0,0 +1,21 @@
<tool id="CONVERTER_mol_to_cml" name="MOL to CML" version="1.0.0">
<description></description>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol "${input}" -ocml -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
</inputs>
<outputs>
<data name="output" format="cml"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
+21
View File
@@ -0,0 +1,21 @@
<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
<description></description>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
+21
View File
@@ -0,0 +1,21 @@
<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
<description></description>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
+21
View File
@@ -0,0 +1,21 @@
<tool id="CONVERTER_mol_to_smi" name="MOL to SMILES" version="1.0.0">
<description></description>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -imol "${input}" -osmi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_sdf_to_cml" name="SDF to CML" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -isdf "${input}" -ocml -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
</inputs>
<outputs>
<data name="output" format="cml"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_sdf_to_inchi" name="SDF to InChI" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -isdf "${input}" -oinchi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
</inputs>
<outputs>
<data name="output" format="inchi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_sdf_to_mol2" name="SDF to mol2" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -isdf "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
+27
View File
@@ -0,0 +1,27 @@
<tool id="CONVERTER_sdf_to_smiles" name="SDF to SMILES" version="1.0.1">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command >
<![CDATA[
obabel
-isdf "${input}"
-ocan
-O "${output}"
-e
2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_SMILES_to_cml" name="SMILES to CML" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -ismi "${input}" -ocml -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
</inputs>
<outputs>
<data name="output" format="cml"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_SMILES_to_inchi" name="SMILES to InChI" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -ismi "${input}" -oinchi -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
</inputs>
<outputs>
<data name="output" format="inchi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_SMILES_to_MOL2" name="SMILES to MOL2" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -ismi "${input}" -omol2 -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
</inputs>
<outputs>
<data name="output" format="mol2"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_SMILES_to_MOL" name="SMILES to MOL" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -ismi "${input}" -omol -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
</inputs>
<outputs>
<data name="output" format="mol"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
+22
View File
@@ -0,0 +1,22 @@
<tool id="CONVERTER_SMILES_to_sdf" name="SMILES to SDF" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command>
<![CDATA[
obabel -ismi "${input}" -osdf -O "${output}" -e 2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
</inputs>
<outputs>
<data name="output" format="sdf"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
+48
View File
@@ -0,0 +1,48 @@
<tool id="CONVERTER_smiles_to_smiles" name="SMILES to SMILES" version="1.0.0">
<description></description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
<requirements>
<requirement type="package" version="2.3.2">openbabel</requirement>
</requirements>
<command >
<![CDATA[
obabel
-ismi "${input}"
#if $can:
-ocan
#else:
-osmi
#end if
-O "${output}"
-e
$remove_h
#if $iso_chi or $can or $exp_h:
-x$iso_chi$exp_h$can
#end if
#if $dative_bonds:
-b
#end if
#if int($ph) >= 0:
-p $ph
#end if
2>&1
]]>
</command>
<inputs>
<param name="input" type="data" format="smi" label="Molecules in SD-format"/>
<param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
<param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
<param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
<param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
<param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
<param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
</inputs>
<outputs>
<data name="output" format="smi"/>
</outputs>
<help>
<![CDATA[
]]>
</help>
</tool>
lib/galaxy/datatypes/display_applications/application.py
+1 -1
View File
@@ -142,7 +142,7 @@ class DynamicDisplayApplicationBuilder( object ):
max_col = max( id_col, name_col )
dynamic_params = {}
if data_table is not None:
max_col = max( [ max_col ] + data_table.columns.values() )
max_col = max( [ max_col ] + data_table.columns.values() )
for key, value in data_table.columns.items():
dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
for dynamic_param in elem.findall( 'dynamic_param' ):
lib/galaxy/datatypes/molecules.py
+769
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@@ -0,0 +1,769 @@
# -*- coding: utf-8 -*-
from galaxy.datatypes import data
import logging
from galaxy.datatypes.sniff import get_headers
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.xml import GenericXml
import subprocess
import os
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes import metadata
log = logging.getLogger(__name__)
def count_special_lines(word, filename, invert=False):
"""
searching for special 'words' using the grep tool
grep is used to speed up the searching and counting
The number of hits is returned.
"""
try:
cmd = ["grep", "-c"]
if invert:
cmd.append('-v')
cmd.extend([word, filename])
out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
except:
pass
return 0
def count_lines(filename, non_empty=False):
"""
counting the number of lines from the 'filename' file
"""
try:
if non_empty:
out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
else:
out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
except:
pass
return 0
class GenericMolFile(data.Text):
"""
abstract class for most of the molecule files
"""
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
if (dataset.metadata.number_of_molecules == 1):
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def get_mime(self):
return 'text/plain'
class MOL(GenericMolFile):
file_ext = "mol"
def set_meta(self, dataset, **kwd):
"""
Set the number molecules, in the case of MOL its always one.
"""
dataset.metadata.number_of_molecules = 1
class SDF(GenericMolFile):
file_ext = "sdf"
def sniff(self, filename):
"""
Try to guess if the file is a SDF2 file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.sdf')
>>> SDF().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> SDF().sniff(fname)
False
"""
counter = count_special_lines("^M\s*END", filename) + count_special_lines("^\$\$\$\$", filename)
if counter > 0 and counter % 2 == 0:
return True
else:
return False
def set_meta(self, dataset, **kwd):
"""
Set the number of molecules in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)
def split(cls, input_datasets, subdir_generator_function, split_params):
"""
Split the input files by molecule records.
"""
if split_params is None:
return None
if len(input_datasets) > 1:
raise Exception("SD-file splitting does not support multiple files")
input_files = [ds.file_name for ds in input_datasets]
chunk_size = None
if split_params['split_mode'] == 'number_of_parts':
raise Exception('Split mode "%s" is currently not implemented for SD-files.' % split_params['split_mode'])
elif split_params['split_mode'] == 'to_size':
chunk_size = int(split_params['split_size'])
else:
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
def _read_sdf_records(filename):
lines = []
with open(filename) as handle:
for line in handle:
lines.append(line)
if line.startswith("$$$$"):
yield lines
lines = []
def _write_part_sdf_file(accumulated_lines):
part_dir = subdir_generator_function()
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
part_file = open(part_path, 'w')
part_file.writelines(accumulated_lines)
part_file.close()
try:
sdf_records = _read_sdf_records(input_files[0])
sdf_lines_accumulated = []
for counter, sdf_record in enumerate(sdf_records, start=1):
sdf_lines_accumulated.extend(sdf_record)
if counter % chunk_size == 0:
_write_part_sdf_file(sdf_lines_accumulated)
sdf_lines_accumulated = []
if sdf_lines_accumulated:
_write_part_sdf_file(sdf_lines_accumulated)
except Exception, e:
log.error('Unable to split files: %s' % str(e))
raise
split = classmethod(split)
class MOL2(GenericMolFile):
file_ext = "mol2"
def sniff(self, filename):
"""
Try to guess if the file is a MOL2 file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.mol2')
>>> MOL2().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> MOL2().sniff(fname)
False
"""
if count_special_lines("@<TRIPOS>MOLECULE", filename) > 0:
return True
else:
return False
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines("@<TRIPOS>MOLECULE", dataset.file_name)
def split(cls, input_datasets, subdir_generator_function, split_params):
"""
Split the input files by molecule records.
"""
if split_params is None:
return None
if len(input_datasets) > 1:
raise Exception("MOL2-file splitting does not support multiple files")
input_files = [ds.file_name for ds in input_datasets]
chunk_size = None
if split_params['split_mode'] == 'number_of_parts':
raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
elif split_params['split_mode'] == 'to_size':
chunk_size = int(split_params['split_size'])
else:
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
def _read_mol2_records(filename):
lines = []
start = True
with open(filename) as handle:
for line in handle:
if line.startswith("@<TRIPOS>MOLECULE"):
if start:
start = False
else:
yield lines
lines = []
lines.append(line)
def _write_part_mol2_file(accumulated_lines):
part_dir = subdir_generator_function()
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
part_file = open(part_path, 'w')
part_file.writelines(accumulated_lines)
part_file.close()
try:
mol2_records = _read_mol2_records(input_files[0])
mol2_lines_accumulated = []
for counter, mol2_record in enumerate(mol2_records, start=1):
mol2_lines_accumulated.extend(mol2_record)
if counter % chunk_size == 0:
_write_part_mol2_file(mol2_lines_accumulated)
mol2_lines_accumulated = []
if mol2_lines_accumulated:
_write_part_mol2_file(mol2_lines_accumulated)
except Exception, e:
log.error('Unable to split files: %s' % str(e))
raise
split = classmethod(split)
class FPS(GenericMolFile):
"""
chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
"""
file_ext = "fps"
def sniff(self, filename):
"""
Try to guess if the file is a FPS file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('q.fps')
>>> FPS().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> FPS().sniff(fname)
False
"""
header = get_headers(filename, sep='\t', count=1)
if header[0][0].strip() == '#FPS1':
return True
else:
return False
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines('^#', dataset.file_name, invert=True)
def split(cls, input_datasets, subdir_generator_function, split_params):
"""
Split the input files by fingerprint records.
"""
if split_params is None:
return None
if len(input_datasets) > 1:
raise Exception("FPS-file splitting does not support multiple files")
input_files = [ds.file_name for ds in input_datasets]
chunk_size = None
if split_params['split_mode'] == 'number_of_parts':
raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
elif split_params['split_mode'] == 'to_size':
chunk_size = int(split_params['split_size'])
else:
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
def _write_part_fingerprint_file(accumulated_lines):
part_dir = subdir_generator_function()
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
part_file = open(part_path, 'w')
part_file.writelines(accumulated_lines)
part_file.close()
try:
header_lines = []
lines_accumulated = []
fingerprint_counter = 0
for line in open(input_files[0]):
if not line.strip():
continue
if line.startswith('#'):
header_lines.append(line)
else:
fingerprint_counter += 1
lines_accumulated.append(line)
if fingerprint_counter != 0 and fingerprint_counter % chunk_size == 0:
_write_part_fingerprint_file(header_lines + lines_accumulated)
lines_accumulated = []
if lines_accumulated:
_write_part_fingerprint_file(header_lines + lines_accumulated)
except Exception, e:
log.error('Unable to split files: %s' % str(e))
raise
split = classmethod(split)
def merge(split_files, output_file):
"""
Merging fps files requires merging the header manually.
We take the header from the first file.
"""
if len(split_files) == 1:
# For one file only, use base class method (move/copy)
return data.Text.merge(split_files, output_file)
if not split_files:
raise ValueError("No fps files given, %r, to merge into %s"
% (split_files, output_file))
out = open(output_file, "w")
first = True
for filename in split_files:
with open(filename) as handle:
for line in handle:
if line.startswith('#'):
if first:
out.write(line)
else:
# line is no header and not a comment, we assume the first header is written to out and we set 'first' to False
first = False
out.write(line)
out.close()
merge = staticmethod(merge)
class OBFS(Binary):
"""OpenBabel Fastsearch format (fs)."""
file_ext = 'fs'
composite_type = 'basic'
allow_datatype_change = False
MetadataElement(name="base_name", default='OpenBabel Fastsearch Index',
readonly=True, visible=True, optional=True,)
def __init__(self, **kwd):
"""
A Fastsearch Index consists of a binary file with the fingerprints
and a pointer the actual molecule file.
"""
Binary.__init__(self, **kwd)
self.add_composite_file('molecule.fs', is_binary=True,
description='OpenBabel Fastsearch Index')
self.add_composite_file('molecule.sdf', optional=True,
is_binary=False, description='Molecule File')
self.add_composite_file('molecule.smi', optional=True,
is_binary=False, description='Molecule File')
self.add_composite_file('molecule.inchi', optional=True,
is_binary=False, description='Molecule File')
self.add_composite_file('molecule.mol2', optional=True,
is_binary=False, description='Molecule File')
self.add_composite_file('molecule.cml', optional=True,
is_binary=False, description='Molecule File')
def set_peek(self, dataset, is_multi_byte=False):
"""Set the peek and blurb text."""
if not dataset.dataset.purged:
dataset.peek = "OpenBabel Fastsearch Index"
dataset.blurb = "OpenBabel Fastsearch Index"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
def display_peek(self, dataset):
"""Create HTML content, used for displaying peek."""
try:
return dataset.peek
except:
return "OpenBabel Fastsearch Index"
def display_data(self, trans, data, preview=False, filename=None,
to_ext=None, size=None, offset=None, **kwd):
"""Apparently an old display method, but still gets called.
This allows us to format the data shown in the central pane via the "eye" icon.
"""
return "This is a OpenBabel Fastsearch format. You can speed up your similarity and substructure search with it."
def get_mime(self):
"""Returns the mime type of the datatype (pretend it is text for peek)"""
return 'text/plain'
def merge(split_files, output_file, extra_merge_args):
"""Merging Fastsearch indices is not supported."""
raise NotImplementedError("Merging Fastsearch indices is not supported.")
def split(cls, input_datasets, subdir_generator_function, split_params):
"""Splitting Fastsearch indices is not supported."""
if split_params is None:
return None
raise NotImplementedError("Splitting Fastsearch indices is not possible.")
class DRF(GenericMolFile):
file_ext = "drf"
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines('\"ligand id\"', dataset.file_name, invert=True)
class PHAR(GenericMolFile):
"""
Pharmacophore database format from silicos-it.
"""
file_ext = "phar"
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
dataset.blurb = "pharmacophore"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
class PDB(GenericMolFile):
"""
Protein Databank format.
http://www.wwpdb.org/documentation/format33/v3.3.html
"""
file_ext = "pdb"
def sniff(self, filename):
"""
Try to guess if the file is a PDB file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('5e5z.pdb')
>>> PDB().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> PDB().sniff(fname)
False
"""
headers = get_headers(filename, sep=' ', count=300)
h = t = c = s = k = e = False
for line in headers:
section_name = line[0].strip()
if section_name == 'HEADER':
h = True
elif section_name == 'TITLE':
t = True
elif section_name == 'COMPND':
c = True
elif section_name == 'SOURCE':
s = True
elif section_name == 'KEYWDS':
k = True
elif section_name == 'EXPDTA':
e = True
if h * t * c * s * k * e:
return True
else:
return False
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
atom_numbers = count_special_lines("^ATOM", dataset.file_name)
hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
class grd(data.Text):
file_ext = "grd"
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
dataset.blurb = "grids for docking"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
class grdtgz(Binary):
file_ext = "grd.tgz"
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = 'binary data'
dataset.blurb = "compressed grids for docking"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
class InChI(Tabular):
file_ext = "inchi"
column_names = ['InChI']
MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
MetadataElement(name="column_types", default=['str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
if (dataset.metadata.number_of_molecules == 1):
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def sniff(self, filename):
"""
Try to guess if the file is a InChI file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.inchi')
>>> InChI().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> InChI().sniff(fname)
False
"""
inchi_lines = get_headers(filename, sep=' ', count=10)
for inchi in inchi_lines:
if not inchi[0].startswith('InChI='):
return False
return True
class SMILES(Tabular):
file_ext = "smi"
column_names = ['SMILES', 'TITLE']
MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
MetadataElement(name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
if dataset.metadata.number_of_molecules == 1:
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
'''
def sniff(self, filename):
"""
Its hard or impossible to sniff a SMILES File. We can
try to import the first SMILES and check if it is a molecule, but
currently its not possible to use external libraries in datatype definition files.
Moreover it seems mpossible to inlcude OpenBabel as python library because OpenBabel
is GPL licensed.
"""
self.molecule_number = count_lines(filename, non_empty = True)
word_count = count_lines(filename)
if self.molecule_number != word_count:
return False
if self.molecule_number > 0:
# test first 3 SMILES
smiles_lines = get_headers(filename, sep='\t', count=3)
for smiles_line in smiles_lines:
if len(smiles_line) > 2:
return False
smiles = smiles_line[0]
try:
# if we have atoms, we have a molecule
if not len(pybel.readstring('smi', smiles).atoms) > 0:
return False
except:
# if convert fails its not a smiles string
return False
return True
else:
return False
'''
class CML(GenericXml):
"""
Chemical Markup Language
http://cml.sourceforge.net/
"""
file_ext = "cml"
MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
def set_meta(self, dataset, **kwd):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines('^\s*<molecule', dataset.file_name)
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
if (dataset.metadata.number_of_molecules == 1):
dataset.blurb = "1 molecule"
else:
dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def sniff(self, filename):
"""
Try to guess if the file is a CML file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('interval.interval')
>>> CML().sniff(fname)
False
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> CML().sniff(fname)
True
"""
handle = open(filename)
line = handle.readline()
if line.strip() != '<?xml version="1.0"?>':
handle.close()
return False
line = handle.readline()
if line.strip().find('http://www.xml-cml.org/schema') == -1:
handle.close()
return False
handle.close()
return True
def split(cls, input_datasets, subdir_generator_function, split_params):
"""
Split the input files by molecule records.
"""
if split_params is None:
return None
if len(input_datasets) > 1:
raise Exception("CML-file splitting does not support multiple files")
input_files = [ds.file_name for ds in input_datasets]
chunk_size = None
if split_params['split_mode'] == 'number_of_parts':
raise Exception('Split mode "%s" is currently not implemented for CML-files.' % split_params['split_mode'])
elif split_params['split_mode'] == 'to_size':
chunk_size = int(split_params['split_size'])
else:
raise Exception('Unsupported split mode %s' % split_params['split_mode'])
def _read_cml_records(filename):
lines = []
with open(filename) as handle:
for line in handle:
if line.lstrip().startswith('<?xml version="1.0"?>') or \
line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
line.lstrip().startswith('</cml>'):
continue
lines.append(line)
if line.lstrip().startswith('</molecule>'):
yield lines
lines = []
header_lines = ['<?xml version="1.0"?>\n', '<cml xmlns="http://www.xml-cml.org/schema">\n']
footer_line = ['</cml>\n']
def _write_part_cml_file(accumulated_lines):
part_dir = subdir_generator_function()
part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
part_file = open(part_path, 'w')
part_file.writelines(header_lines)
part_file.writelines(accumulated_lines)
part_file.writelines(footer_line)
part_file.close()
try:
cml_records = _read_cml_records(input_files[0])
cml_lines_accumulated = []
for counter, cml_record in enumerate(cml_records, start=1):
cml_lines_accumulated.extend(cml_record)
if counter % chunk_size == 0:
_write_part_cml_file(cml_lines_accumulated)
cml_lines_accumulated = []
if cml_lines_accumulated:
_write_part_cml_file(cml_lines_accumulated)
except Exception, e:
log.error('Unable to split files: %s' % str(e))
raise
split = classmethod(split)
def merge(split_files, output_file):
"""
Merging CML files.
"""
if len(split_files) == 1:
# For one file only, use base class method (move/copy)
return data.Text.merge(split_files, output_file)
if not split_files:
raise ValueError("Given no CML files, %r, to merge into %s"
% (split_files, output_file))
with open(output_file, "w") as out:
for filename in split_files:
with open(filename) as handle:
header = handle.readline()
if not header:
raise ValueError("CML file %s was empty" % filename)
if not header.lstrip().startswith('<?xml version="1.0"?>'):
out.write(header)
raise ValueError("%s is not a valid XML file!" % filename)
line = handle.readline()
header += line
if not line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema'):
out.write(header)
raise ValueError("%s is not a CML file!" % filename)
molecule_found = False
for line in handle.readlines():
# We found two required header lines, the next line should start with <molecule >
if line.lstrip().startswith('</cml>'):
continue
if line.lstrip().startswith('<molecule'):
molecule_found = True
if molecule_found:
out.write(line)
out.write("</cml>\n")
merge = staticmethod(merge)
lib/galaxy/datatypes/registry.py
+71 -71
View File
@@ -647,81 +647,81 @@ class Registry( object ):
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'db3' : binary.SQlite(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'db3' : binary.SQlite(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'gemini.sqlite' : binary.GeminiSQLite(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'h5' : binary.H5(),
'idpdb' : binary.IdpDB(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'mz.sqlite' : binary.MzSQlite(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'csv' : tabular.CSV(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'h5' : binary.H5(),
'idpdb' : binary.IdpDB(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'mz.sqlite' : binary.MzSQlite(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'csv' : tabular.CSV(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
}
self.mimetypes_by_extension = {
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'db3' : 'application/octet-stream',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'db3' : 'application/octet-stream',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'gemini.sqlite' : 'application/octet-stream',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'h5' : 'application/octet-stream',
'idpdb' : 'application/octet-stream',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'mz.sqlite' : 'application/octet-stream',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'csv' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'h5' : 'application/octet-stream',
'idpdb' : 'application/octet-stream',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'mz.sqlite' : 'application/octet-stream',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'csv' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
}
# super supertype fix for input steps in workflows.
if 'data' not in self.datatypes_by_extension:
lib/galaxy/datatypes/sniff.py
+32 -2
View File
@@ -263,8 +263,9 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
>>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
>>> from galaxy.datatypes import registry
>>> sample_conf = os.path.join(util.galaxy_directory(), "config", "datatypes_conf.xml.sample")
>>> datatypes_registry = registry.Registry()
>>> datatypes_registry.load_datatypes()
>>> datatypes_registry.load_datatypes(root_dir=util.galaxy_directory(), config=sample_conf)
>>> sniff_order = datatypes_registry.sniff_order
>>> guess_ext(fname, sniff_order)
'xml'
@@ -327,7 +328,26 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
>>> fname = get_test_fname('issue1818.tabular')
>>> guess_ext(fname, sniff_order)
'tabular'
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> guess_ext(fname, sniff_order)
'cml'
>>> fname = get_test_fname('q.fps')
>>> guess_ext(fname, sniff_order)
'fps'
>>> fname = get_test_fname('drugbank_drugs.inchi')
>>> guess_ext(fname, sniff_order)
'inchi'
>>> fname = get_test_fname('drugbank_drugs.mol2')
>>> guess_ext(fname, sniff_order)
'mol2'
>>> fname = get_test_fname('drugbank_drugs.sdf')
>>> guess_ext(fname, sniff_order)
'sdf'
>>> fname = get_test_fname('5e5z.pdb')
>>> guess_ext(fname, sniff_order)
'pdb'
"""
file_ext = None
for datatype in sniff_order:
"""
Some classes may not have a sniff function, which is ok. In fact, the
@@ -339,9 +359,19 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
"""
try:
if datatype.sniff( fname ):
return datatype.file_ext
file_ext = datatype.file_ext
break
except:
pass
# Ugly hack for tsv vs tabular sniffing, we want to prefer tabular
# to tsv but it doesn't have a sniffer - is TSV was sniffed just check
# if it is an okay tabular and use that instead.
if file_ext == 'tsv':
if is_column_based( fname, '\t', 1, is_multi_byte=is_multi_byte ):
file_ext = 'tabular'
if file_ext is not None:
return file_ext
headers = get_headers( fname, None )
is_binary = False
if is_multi_byte:
lib/galaxy/datatypes/tabular.py
+3 -4
View File
@@ -8,17 +8,16 @@ import gzip
import logging
import os
import re
import tempfile
import subprocess
import tempfile
from cgi import escape
from json import dumps
from galaxy import util
from galaxy.datatypes import data, metadata
from galaxy.util.checkers import is_gzip
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import get_headers
from galaxy.util.json import dumps
from galaxy.util.checkers import is_gzip
from . import dataproviders
lib/galaxy/datatypes/test/5e5z.pdb
+357
View File
@@ -0,0 +1,357 @@
HEADER DE NOVO PROTEIN, MEMBRANE PROTEIN 09-OCT-15 5E5Z
TITLE STRUCTURE OF THE AMYLOID FORMING PEPTIDE LVHSSN (RESIDUES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LVHSSN (RESIDUES 16-21) FROM ISLET AMYLOID POLYPEPTIDE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS AMYLOID-LIKE PROTOFIBRIL, DE NOVO PROTEIN, MEMBRANE PROTEIN, PROTEIN
KEYWDS 2 FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR A.B.SORIAGA,D.EISENBERG
REVDAT 2 20-JAN-16 5E5Z 1 JRNL
REVDAT 1 16-DEC-15 5E5Z 0
JRNL AUTH A.B.SORIAGA,S.SANGWAN,R.MACDONALD,M.R.SAWAYA,D.EISENBERG
JRNL TITL CRYSTAL STRUCTURES OF IAPP AMYLOIDOGENIC SEGMENTS REVEAL A
JRNL TITL 2 NOVEL PACKING MOTIF OF OUT-OF-REGISTER BETA SHEETS.
JRNL REF J.PHYS.CHEM.B 2016
JRNL REFN ISSN 1089-5647
JRNL PMID 26629790
JRNL DOI 10.1021/ACS.JPCB.5B09981
REMARK 2
REMARK 2 RESOLUTION. 1.66 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.6.4_486
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : LS_WUNIT_K1
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.46
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1
REMARK 3 NUMBER OF REFLECTIONS : 391
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.170
REMARK 3 R VALUE (WORKING SET) : 0.167
REMARK 3 FREE R VALUE : 0.198
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600
REMARK 3 FREE R VALUE TEST SET COUNT : 18
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 9.4587 - 1.6644 0.89 373 18 0.1673 0.1983
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 0.00
REMARK 3 SHRINKAGE RADIUS : 0.00
REMARK 3 K_SOL : 0.60
REMARK 3 B_SOL : 251.4
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.270
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.51090
REMARK 3 B22 (A**2) : -3.44720
REMARK 3 B33 (A**2) : -8.26450
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.77970
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.004 46
REMARK 3 ANGLE : 0.975 62
REMARK 3 CHIRALITY : 0.056 8
REMARK 3 PLANARITY : 0.004 8
REMARK 3 DIHEDRAL : 10.740 15
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 4.5323 0.1096 3.9760
REMARK 3 T TENSOR
REMARK 3 T11: -0.1260 T22: -0.0788
REMARK 3 T33: -0.0487 T12: 0.0821
REMARK 3 T13: -0.0518 T23: 0.0723
REMARK 3 L TENSOR
REMARK 3 L11: 0.1003 L22: 0.0184
REMARK 3 L33: 0.0647 L12: -0.0319
REMARK 3 L13: 0.0506 L23: -0.0233
REMARK 3 S TENSOR
REMARK 3 S11: 0.0084 S12: -0.0300 S13: -0.0565
REMARK 3 S21: 0.0231 S22: 0.0090 S23: 0.0127
REMARK 3 S31: -0.0046 S32: -0.0049 S33: -0.0009
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5E5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15.
REMARK 100 THE DEPOSITION ID IS D_1000214421.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10
REMARK 200 TEMPERATURE (KELVIN) : 291
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-E
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1136
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : 0.07600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 6.59
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML IN WATER AND MIXED WITH 0.09
REMARK 280 M HEPES PH 7.5, 1.26M TRI-SODIUM CITRATE, AND 10% GLYCEROL,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 4.80450
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -9.60900
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.60900
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 9.64300
REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 9.64300
REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.60900
REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 9.64300
REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 9.60900
REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 9.64300
REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 -4.80450
REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 9.64300
REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 4.80450
REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 19.28600
REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -4.80450
REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 19.28600
REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 4.80450
REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5E5V RELATED DB: PDB
REMARK 900 RELATED ID: 5E5X RELATED DB: PDB
REMARK 900 RELATED ID: 5E61 RELATED DB: PDB
DBREF 5E5Z A 1 6 PDB 5E5Z 5E5Z 1 6
SEQRES 1 A 6 LEU VAL HIS SER SER ASN
FORMUL 2 HOH *(H2 O)
CRYST1 9.643 9.609 19.029 90.00 101.22 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.103702 0.000000 0.020579 0.00000
SCALE2 0.000000 0.104069 0.000000 0.00000
SCALE3 0.000000 0.000000 0.053576 0.00000
ATOM 1 N LEU A 1 6.078 -0.306 -5.753 1.00 0.00 N
ANISOU 1 N LEU A 1 0 0 0 0 0 0 N
ATOM 2 CA LEU A 1 5.166 -0.026 -4.647 1.00 2.42 C
ANISOU 2 CA LEU A 1 307 307 307 0 0 0 C
ATOM 3 C LEU A 1 5.682 -0.642 -3.356 1.00 3.48 C
ANISOU 3 C LEU A 1 435 443 445 1 1 9 C
ATOM 4 O LEU A 1 6.056 -1.814 -3.322 1.00 3.52 O
ANISOU 4 O LEU A 1 436 449 454 2 2 16 O
ATOM 5 CB LEU A 1 3.755 -0.555 -4.967 1.00 1.86 C
ANISOU 5 CB LEU A 1 232 237 238 1 1 5 C
ATOM 6 CG LEU A 1 2.596 -0.354 -3.975 1.00 6.87 C
ANISOU 6 CG LEU A 1 861 873 877 2 2 14 C
ATOM 7 CD1 LEU A 1 2.753 -1.182 -2.704 1.00 11.83 C
ANISOU 7 CD1 LEU A 1 1481 1504 1512 4 4 27 C
ATOM 8 CD2 LEU A 1 2.404 1.122 -3.638 1.00 4.27 C
ANISOU 8 CD2 LEU A 1 537 543 544 1 2 7 C
ATOM 9 N VAL A 2 5.715 0.161 -2.297 1.00 0.61 N
ANISOU 9 N VAL A 2 71 80 82 2 2 11 N
ATOM 10 CA VAL A 2 5.968 -0.352 -0.960 1.00 0.12 C
ANISOU 10 CA VAL A 2 1 20 24 4 4 22 C
ATOM 11 C VAL A 2 4.976 0.281 0.000 1.00 3.40 C
ANISOU 11 C VAL A 2 413 437 440 5 5 27 C
ATOM 12 O VAL A 2 4.746 1.489 -0.046 1.00 3.22 O
ANISOU 12 O VAL A 2 395 414 414 4 5 20 O
ATOM 13 CB VAL A 2 7.400 -0.027 -0.475 1.00 3.56 C
ANISOU 13 CB VAL A 2 440 456 458 3 3 18 C
ATOM 14 CG1 VAL A 2 7.566 -0.421 0.993 1.00 7.93 C
ANISOU 14 CG1 VAL A 2 986 1012 1016 5 5 30 C
ATOM 15 CG2 VAL A 2 8.429 -0.722 -1.342 1.00 6.71 C
ANISOU 15 CG2 VAL A 2 841 853 856 2 2 14 C
ATOM 16 N HIS A 3 4.367 -0.537 0.850 1.00 0.22 N
ANISOU 16 N HIS A 3 1 38 44 7 8 41 N
ATOM 17 CA HIS A 3 3.603 -0.011 1.971 1.00 1.73 C
ANISOU 17 CA HIS A 3 189 233 237 10 10 48 C
ATOM 18 C HIS A 3 4.003 -0.675 3.280 1.00 1.84 C
ANISOU 18 C HIS A 3 194 250 255 12 12 61 C
ATOM 19 O HIS A 3 4.208 -1.889 3.338 1.00 0.73 O
ANISOU 19 O HIS A 3 47 109 120 11 12 69 O
ATOM 20 CB HIS A 3 2.095 -0.177 1.781 1.00 2.62 C
ANISOU 20 CB HIS A 3 296 346 351 11 11 54 C
ATOM 21 CG HIS A 3 1.324 0.074 3.040 1.00 2.97 C
ANISOU 21 CG HIS A 3 335 396 399 14 14 66 C
ATOM 22 ND1 HIS A 3 0.950 -0.937 3.900 1.00 4.29 N
ANISOU 22 ND1 HIS A 3 491 566 573 16 17 82 N
ATOM 23 CD2 HIS A 3 0.921 1.230 3.620 1.00 4.90 C
ANISOU 23 CD2 HIS A 3 581 642 639 16 16 64 C
ATOM 24 CE1 HIS A 3 0.321 -0.417 4.940 1.00 5.53 C
ANISOU 24 CE1 HIS A 3 644 727 729 20 20 89 C
ATOM 25 NE2 HIS A 3 0.290 0.896 4.794 1.00 6.02 N
ANISOU 25 NE2 HIS A 3 714 790 785 20 19 78 N
ATOM 26 N SER A 4 4.099 0.141 4.326 1.00 0.34 N
ANISOU 26 N SER A 4 3 63 63 14 14 62 N
ATOM 27 CA SER A 4 4.357 -0.330 5.683 1.00 1.49 C
ANISOU 27 CA SER A 4 141 213 213 16 16 75 C
ATOM 28 C SER A 4 3.814 0.686 6.681 1.00 2.14 C
ANISOU 28 C SER A 4 222 299 292 20 19 78 C
ATOM 29 O SER A 4 4.008 1.889 6.507 1.00 3.47 O
ANISOU 29 O SER A 4 397 465 454 19 18 68 O
ATOM 30 CB SER A 4 5.858 -0.513 5.905 1.00 5.61 C
ANISOU 30 CB SER A 4 665 734 734 15 15 72 C
ATOM 31 OG SER A 4 6.132 -0.771 7.272 1.00 9.89 O
ANISOU 31 OG SER A 4 1200 1280 1278 18 18 83 O
ATOM 32 N SER A 5 3.138 0.213 7.725 1.00 2.34 N
ANISOU 32 N SER A 5 239 330 322 24 23 93 N
ATOM 33 CA SER A 5 2.651 1.119 8.765 1.00 0.66 C
ANISOU 33 CA SER A 5 24 123 106 28 26 97 C
ATOM 34 C SER A 5 3.677 1.311 9.885 1.00 2.66 C
ANISOU 34 C SER A 5 275 378 356 30 27 100 C
ATOM 35 O SER A 5 3.411 2.024 10.851 1.00 2.02 O
ANISOU 35 O SER A 5 193 303 273 35 30 104 O
ATOM 36 CB SER A 5 1.318 0.639 9.350 1.00 2.68 C
ANISOU 36 CB SER A 5 269 383 365 32 29 113 C
ATOM 37 OG SER A 5 1.478 -0.544 10.117 1.00 2.49 O
ANISOU 37 OG SER A 5 236 363 349 33 31 128 O
ATOM 38 N ASN A 6 4.838 0.672 9.758 1.00 2.94 N
ANISOU 38 N ASN A 6 311 412 394 28 25 98 N
ATOM 39 CA ASN A 6 5.912 0.838 10.741 1.00 4.68 C
ANISOU 39 CA ASN A 6 530 634 613 29 26 100 C
ATOM 40 C ASN A 6 6.574 2.203 10.638 1.00 10.84 C
ANISOU 40 C ASN A 6 1320 1413 1387 28 24 87 C
ATOM 41 O ASN A 6 7.335 2.594 11.519 1.00 13.68 O
ANISOU 41 O ASN A 6 1680 1775 1745 30 26 88 O
ATOM 42 CB ASN A 6 6.986 -0.243 10.589 1.00 5.08 C
ANISOU 42 CB ASN A 6 579 682 668 27 25 102 C
ATOM 43 CG ASN A 6 6.592 -1.558 11.236 1.00 8.08 C
ANISOU 43 CG ASN A 6 948 1067 1057 28 27 120 C
ATOM 44 OD1 ASN A 6 5.576 -1.644 11.923 1.00 8.72 O
ANISOU 44 OD1 ASN A 6 1022 1152 1139 32 30 131 O
ATOM 45 ND2 ASN A 6 7.409 -2.588 11.030 1.00 9.89 N
ANISOU 45 ND2 ASN A 6 1174 1293 1290 25 25 122 N
ATOM 46 OXT ASN A 6 6.383 2.933 9.667 1.00 14.02 O
ANISOU 46 OXT ASN A 6 1730 1811 1787 25 22 75 O
TER 47 ASN A 6
HETATM 48 O HOH A 101 8.203 1.052 -4.564 1.00 12.67 O
ANISOU 48 O HOH A 101 1605 1605 1605 0 0 0 O
MASTER 227 0 0 0 0 0 0 6 47 1 0 1
END
lib/galaxy/datatypes/test/drugbank_drugs.cml
+385
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@@ -0,0 +1,385 @@
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<atomParity atomRefs4="a48 a47 a61 a49">1</atomParity>
</atom>
<atom id="a49" elementType="C" x2="9.886900" y2="-3.730000"/>
<atom id="a50" elementType="C" x2="12.763100" y2="-2.876200"/>
<atom id="a51" elementType="C" x2="12.763100" y2="-3.730000"/>
<atom id="a52" elementType="C" x2="12.044100" y2="-2.471700"/>
<atom id="a53" elementType="C" x2="12.044100" y2="-4.134500"/>
<atom id="a54" elementType="N" x2="7.055700" y2="-2.876200"/>
<atom id="a55" elementType="C" x2="6.336600" y2="-2.471700"/>
<atom id="a56" elementType="C" x2="5.617600" y2="-2.876200"/>
<atom id="a57" elementType="C" x2="5.617600" y2="-3.730000"/>
<atom id="a58" elementType="C" x2="8.448800" y2="-2.876200"/>
<atom id="a59" elementType="O" x2="8.448800" y2="-3.730000"/>
<atom id="a60" elementType="C" x2="7.774700" y2="-2.471700">
<atomParity atomRefs4="a60 a63 a54 a58">1</atomParity>
</atom>
<atom id="a61" elementType="N" x2="9.167800" y2="-2.471700"/>
<atom id="a62" elementType="O" x2="9.167800" y2="-4.134500"/>
<atom id="a63" elementType="C" x2="7.774700" y2="-1.662800"/>
<atom id="a64" elementType="C" x2="9.167800" y2="-1.662800"/>
<atom id="a65" elementType="C" x2="8.448800" y2="-1.258300"/>
<atom id="a66" elementType="C" x2="9.886900" y2="-1.258300"/>
<atom id="a67" elementType="C" x2="9.886900" y2="-0.404500"/>
<atom id="a68" elementType="C" x2="8.448800" y2="-0.404500"/>
<atom id="a69" elementType="C" x2="9.167800" y2="0.000000"/>
<atom id="a70" elementType="O" x2="6.336600" y2="-1.662800"/>
<atom id="a71" elementType="O" x2="10.606000" y2="0.000000"/>
<atom id="a72" elementType="C" x2="1.393200" y2="-5.437800"/>
<atom id="a73" elementType="N" x2="1.393200" y2="-6.246700"/>
<atom id="a74" elementType="N" x2="0.674100" y2="-5.033300"/>
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<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a2 a10" order="2"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a5 a6" order="1"/>
<bond atomRefs2="a5 a11" order="2"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a6 a12" order="1"/>
<bond atomRefs2="a7 a8" order="1"/>
<bond atomRefs2="a8 a9" order="2"/>
<bond atomRefs2="a16 a8" order="1"/>
<bond atomRefs2="a12 a13" order="1"/>
<bond atomRefs2="a13 a14" order="1"/>
<bond atomRefs2="a14 a15" order="1"/>
<bond atomRefs2="a15 a72" order="1"/>
<bond atomRefs2="a16 a17" order="1"/>
<bond atomRefs2="a16 a18" order="1"/>
<bond atomRefs2="a17 a19" order="1"/>
<bond atomRefs2="a18 a20" order="1"/>
<bond atomRefs2="a18 a21" order="1"/>
<bond atomRefs2="a19 a20" order="1"/>
<bond atomRefs2="a22 a21" order="1"/>
<bond atomRefs2="a21 a27" order="2"/>
<bond atomRefs2="a22 a23" order="1"/>
<bond atomRefs2="a22 a28" order="1"/>
<bond atomRefs2="a23 a24" order="1"/>
<bond atomRefs2="a24 a25" order="1"/>
<bond atomRefs2="a24 a31" order="2"/>
<bond atomRefs2="a25 a26" order="1"/>
<bond atomRefs2="a25 a32" order="1"/>
<bond atomRefs2="a26 a36" order="1"/>
<bond atomRefs2="a28 a29" order="1"/>
<bond atomRefs2="a29 a30" order="1"/>
<bond atomRefs2="a30 a57" order="1"/>
<bond atomRefs2="a32 a33" order="1"/>
<bond atomRefs2="a33 a34" order="2"/>
<bond atomRefs2="a33 a35" order="1"/>
<bond atomRefs2="a36 a37" order="1"/>
<bond atomRefs2="a36 a38" order="2"/>
<bond atomRefs2="a37 a39" order="1"/>
<bond atomRefs2="a37 a44" order="1"/>
<bond atomRefs2="a39 a40" order="1"/>
<bond atomRefs2="a40 a41" order="1"/>
<bond atomRefs2="a41 a42" order="1"/>
<bond atomRefs2="a41 a43" order="2"/>
<bond atomRefs2="a44 a49" order="1"/>
<bond atomRefs2="a45 a47" order="1"/>
<bond atomRefs2="a45 a52" order="1"/>
<bond atomRefs2="a45 a46" order="2"/>
<bond atomRefs2="a46 a53" order="1"/>
<bond atomRefs2="a48 a47" order="1"/>
<bond atomRefs2="a48 a61" order="1"/>
<bond atomRefs2="a48 a49" order="1"/>
<bond atomRefs2="a49 a62" order="2"/>
<bond atomRefs2="a50 a51" order="1"/>
<bond atomRefs2="a50 a52" order="2"/>
<bond atomRefs2="a51 a53" order="2"/>
<bond atomRefs2="a54 a55" order="1"/>
<bond atomRefs2="a54 a60" order="1"/>
<bond atomRefs2="a55 a56" order="1"/>
<bond atomRefs2="a55 a70" order="2"/>
<bond atomRefs2="a56 a57" order="1"/>
<bond atomRefs2="a58 a59" order="2"/>
<bond atomRefs2="a58 a60" order="1"/>
<bond atomRefs2="a58 a61" order="1"/>
<bond atomRefs2="a60 a63" order="1"/>
<bond atomRefs2="a63 a65" order="1"/>
<bond atomRefs2="a64 a66" order="2"/>
<bond atomRefs2="a64 a65" order="1"/>
<bond atomRefs2="a65 a68" order="2"/>
<bond atomRefs2="a66 a67" order="1"/>
<bond atomRefs2="a67 a69" order="2"/>
<bond atomRefs2="a67 a71" order="1"/>
<bond atomRefs2="a68 a69" order="1"/>
<bond atomRefs2="a72 a73" order="2"/>
<bond atomRefs2="a72 a74" order="1"/>
</bondArray>
</molecule>
</cml>
lib/galaxy/datatypes/test/drugbank_drugs.inchi
+2
View File
@@ -0,0 +1,2 @@
InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1
lib/galaxy/datatypes/test/drugbank_drugs.mol2
+354
View File
@@ -0,0 +1,354 @@
@<TRIPOS>MOLECULE
Goserelin
91 96 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 12.8548 -2.6382 0.0000 O.2 4 UNK4 -0.2730
2 O 13.9726 -2.5226 0.0000 O.2 4 UNK4 -0.2699
3 O 10.1766 -3.9327 0.0000 O.2 4 UNK4 -0.2715
4 O 11.2019 -0.7961 0.0000 O.3 4 UNK4 -0.3562
5 O 8.7800 -1.3064 0.0000 O.2 4 UNK4 -0.2714
6 O 16.8589 -3.2421 0.0000 O.2 4 UNK4 -0.2457
7 O 10.3562 1.2163 0.0000 O.2 4 UNK4 -0.2715
8 O 3.2702 4.8341 0.0000 O.2 1 UNK1 -0.2715
9 O 2.3500 8.2734 0.0000 O.2 1 UNK1 -0.2733
10 O 3.8213 4.2201 0.0000 O.2 2 HIS2 -0.2715
11 O 5.2178 1.5938 0.0000 O.2 3 TRP3 -0.2715
12 O 7.8960 2.8883 0.0000 O.2 4 UNK4 -0.2714
13 O 7.1271 0.5358 0.0000 O.3 4 UNK4 -0.2179
14 O 12.4834 3.1249 0.0000 O.3 4 UNK4 -0.2866
15 N 13.1495 -4.0364 0.0000 N.am 4 UNK4 -0.2715
16 N 11.2402 -2.9784 0.0000 N.am 4 UNK4 -0.1964
17 N 15.2089 -3.2393 0.0000 N.am 4 UNK4 -0.0850
18 N 10.1383 -1.7503 0.0000 N.am 4 UNK4 -0.1963
19 N 15.6226 -2.5255 0.0000 N.am 4 UNK4 -0.0678
20 N 12.3806 -6.3890 0.0000 N.pl3 4 UNK4 -0.0865
21 N 9.2926 0.2619 0.0000 N.am 4 UNK4 -0.1937
22 N 3.1485 7.0391 0.0000 N.am 1 UNK1 -0.1978
23 N 4.3338 5.7884 0.0000 N.am 2 HIS2 -0.1959
24 N 16.8613 -1.8132 0.0000 N.am 4 UNK4 -0.0665
25 N 8.1907 1.4900 0.0000 N.am 4 UNK4 -0.1959
26 N 5.1795 3.7761 0.0000 N.am 3 TRP3 -0.1960
27 N 6.2814 2.5480 0.0000 N.am 4 UNK4 -0.1936
28 N 11.3170 -7.3433 0.0000 N.pl3 4 UNK4 0.1354
29 N 12.6753 -7.7873 0.0000 N.pl3 4 UNK4 0.1354
30 NE1 3.8596 0.7098 0.0000 N.ar 3 TRP3 -0.2442
31 ND1 6.7335 6.3823 0.0000 N.ar 2 HIS2 -0.2267
32 NE2 5.9507 7.4636 0.0000 N.ar 2 HIS2 -0.2212
33 C 13.9701 -3.9516 0.0000 C.3 4 UNK4 0.1552
34 C 14.3043 -4.7058 0.0000 C.3 4 UNK4 0.0311
35 C 13.6903 -5.2569 0.0000 C.3 4 UNK4 0.0237
36 C 12.9766 -4.8431 0.0000 C.3 4 UNK4 0.0939
37 C 12.5984 -3.4224 0.0000 C.2 4 UNK4 0.2458
38 C 11.7912 -3.5925 0.0000 C.3 4 UNK4 0.1714
39 C 14.3838 -3.2378 0.0000 C.2 4 UNK4 0.2788
40 C 11.5349 -4.3767 0.0000 C.3 4 UNK4 0.0347
41 C 12.0859 -4.9907 0.0000 C.3 4 UNK4 0.0492
42 C 9.8819 -2.5345 0.0000 C.3 4 UNK4 0.1728
43 C 10.4330 -3.1486 0.0000 C.2 4 UNK4 0.2616
44 C 9.0747 -2.7046 0.0000 C.3 4 UNK4 0.0311
45 C 8.8184 -3.4889 0.0000 C.3 4 UNK4 0.0022
46 C 11.8295 -5.7750 0.0000 C.3 4 UNK4 0.2205
47 C 8.0112 -3.6590 0.0000 C.3 4 UNK4 0.0001
48 C 9.3694 -4.1029 0.0000 C.3 4 UNK4 0.0001
49 C 9.5873 -1.1363 0.0000 C.2 4 UNK4 0.2642
50 C 9.8436 -0.3521 0.0000 C.3 4 UNK4 0.2021
51 C 10.6509 -0.1820 0.0000 C.3 4 UNK4 0.1729
52 C 16.4476 -2.5269 0.0000 C.2 4 UNK4 0.3786
53 C 2.9756 6.2324 0.0000 C.3 1 UNK1 0.1732
54 C 12.0091 -0.6259 0.0000 C.3 4 UNK4 0.0931
55 C 8.9979 1.6602 0.0000 C.3 4 UNK4 0.1771
56 C 9.5489 1.0461 0.0000 C.2 4 UNK4 0.2620
57 C 12.1242 -7.1732 0.0000 C.cat 4 UNK4 0.5346
58 C 2.1549 6.1475 0.0000 C.3 1 UNK1 0.0407
59 CA 4.8848 5.1744 0.0000 C.3 2 HIS2 0.1787
60 CA 4.9232 2.9920 0.0000 C.3 3 TRP3 0.1771
61 C 1.8207 6.9019 0.0000 C.3 1 UNK1 0.0891
62 C 9.2542 2.4444 0.0000 C.3 4 UNK4 0.0574
63 CB 4.1159 2.8219 0.0000 C.3 3 TRP3 0.0590
64 C 3.5266 5.6183 0.0000 C.2 1 UNK1 0.2616
65 C 2.4348 7.4528 0.0000 C.2 1 UNK1 0.2418
66 CB 5.6921 5.3445 0.0000 C.3 2 HIS2 0.0785
67 C 6.8324 1.9340 0.0000 C.3 4 UNK4 0.2055
68 C 4.6285 4.3902 0.0000 C.2 2 HIS2 0.2620
69 C 12.1793 -1.4332 0.0000 C.3 4 UNK4 0.0296
70 C 12.8164 -0.4557 0.0000 C.3 4 UNK4 0.0296
71 C 11.8389 0.1814 0.0000 C.3 4 UNK4 0.0296
72 CG 3.8596 2.0376 0.0000 C.ar 3 TRP3 0.0006
73 C 5.4742 2.3779 0.0000 C.2 3 TRP3 0.2620
74 C 7.6397 2.1041 0.0000 C.2 4 UNK4 0.2643
75 C 10.0615 2.6145 0.0000 C.ar 4 UNK4 -0.0198
76 CD2 3.0790 1.7862 0.0000 C.ar 3 TRP3 0.0152
77 CG 5.9484 6.1287 0.0000 C.ar 2 HIS2 0.0821
78 CD1 4.3411 1.3737 0.0000 C.ar 3 TRP3 0.0946
79 CE2 3.0790 0.9612 0.0000 C.ar 3 TRP3 0.0810
80 C 6.5761 1.1498 0.0000 C.3 4 UNK4 0.2130
81 CE3 2.3645 2.1987 0.0000 C.ar 3 TRP3 0.0012
82 C 10.3178 3.3987 0.0000 C.ar 4 UNK4 -0.0009
83 C 10.6125 2.0005 0.0000 C.ar 4 UNK4 -0.0009
84 CZ2 2.3645 0.5487 0.0000 C.ar 3 TRP3 0.0191
85 CD2 5.4646 6.7970 0.0000 C.ar 2 HIS2 0.1154
86 CZ3 1.6500 1.7862 0.0000 C.ar 3 TRP3 0.0001
87 CH2 1.6500 0.9612 0.0000 C.ar 3 TRP3 0.0015
88 C 11.1251 3.5688 0.0000 C.ar 4 UNK4 0.0417
89 C 11.4198 2.1706 0.0000 C.ar 4 UNK4 0.0417
90 CE1 6.7349 7.2073 0.0000 C.ar 2 HIS2 0.1986
91 C 11.6761 2.9548 0.0000 C.ar 4 UNK4 0.1957
@<TRIPOS>BOND
1 1 37 2
2 2 39 2
3 3 43 2
4 4 51 1
5 4 54 1
6 5 49 2
7 6 52 2
8 7 56 2
9 8 64 2
10 9 65 2
11 10 68 2
12 11 73 2
13 12 74 2
14 13 80 1
15 14 91 1
16 15 33 1
17 15 36 1
18 15 37 am
19 38 16 1
20 16 43 am
21 17 19 1
22 17 39 am
23 42 18 1
24 18 49 am
25 19 52 am
26 20 46 1
27 20 57 2
28 50 21 1
29 21 56 am
30 22 53 1
31 22 65 am
32 59 23 1
33 23 64 am
34 24 52 am
35 55 25 1
36 25 74 am
37 60 26 1
38 26 68 am
39 67 27 1
40 27 73 am
41 28 57 1
42 29 57 1
43 30 78 ar
44 30 79 ar
45 31 77 ar
46 31 90 ar
47 32 85 ar
48 32 90 ar
49 33 34 1
50 33 39 1
51 34 35 1
52 35 36 1
53 37 38 1
54 38 40 1
55 40 41 1
56 41 46 1
57 42 43 1
58 42 44 1
59 44 45 1
60 45 47 1
61 45 48 1
62 49 50 1
63 50 51 1
64 53 58 1
65 53 64 1
66 54 69 1
67 54 70 1
68 54 71 1
69 55 56 1
70 55 62 1
71 58 61 1
72 59 66 1
73 59 68 1
74 60 63 1
75 60 73 1
76 61 65 1
77 62 75 1
78 63 72 1
79 66 77 1
80 67 74 1
81 67 80 1
82 72 76 ar
83 72 78 ar
84 75 82 ar
85 75 83 ar
86 76 79 ar
87 76 81 ar
88 77 85 ar
89 79 84 ar
90 81 86 ar
91 82 88 ar
92 83 89 ar
93 84 87 ar
94 86 87 ar
95 88 91 ar
96 89 91 ar
@<TRIPOS>MOLECULE
Desmopressin
74 77 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 N 0.0000 -7.8646 0.0000 N.am 1 LIG1 -0.0862
2 C 0.6741 -7.4601 0.0000 C.2 1 LIG1 0.2828
3 C 1.3932 -7.8646 0.0000 C.3 1 LIG1 0.2031
4 N 2.1122 -7.4601 0.0000 N.am 1 LIG1 -0.1939
5 C 2.8313 -7.8646 0.0000 C.2 1 LIG1 0.2617
6 C 3.5503 -7.4601 0.0000 C.3 1 LIG1 0.1729
7 N 4.2693 -7.8646 0.0000 N.am 1 LIG1 -0.1964
8 C 4.9435 -7.4601 0.0000 C.2 1 LIG1 0.2598
9 O 5.6625 -7.8646 0.0000 O.2 1 LIG1 -0.2715
10 O 0.6741 -6.6512 0.0000 O.2 1 LIG1 -0.2697
11 O 2.8313 -8.7184 0.0000 O.2 1 LIG1 -0.2715
12 C 3.5503 -6.6512 0.0000 C.3 1 LIG1 0.0348
13 C 2.8313 -6.2467 0.0000 C.3 1 LIG1 0.0492
14 C 2.8313 -5.4378 0.0000 C.3 1 LIG1 0.2205
15 N 2.1122 -5.0333 0.0000 N.pl3 1 LIG1 -0.0865
16 C 4.9435 -6.6512 0.0000 C.3 1 LIG1 0.1536
17 C 4.3143 -6.1568 0.0000 C.3 1 LIG1 0.0310
18 N 5.6176 -6.1568 0.0000 N.am 1 LIG1 -0.2715
19 C 4.5390 -5.3929 0.0000 C.3 1 LIG1 0.0237
20 C 5.3479 -5.3929 0.0000 C.3 1 LIG1 0.0939
21 C 6.3366 -6.5613 0.0000 C.2 1 LIG1 0.2467
22 C 7.0557 -6.1568 0.0000 C.3 1 LIG1 0.1828
23 N 7.7747 -6.5613 0.0000 N.am 1 LIG1 -0.1954
24 C 8.4488 -6.1568 0.0000 C.2 1 LIG1 0.2621
25 C 9.1678 -6.5613 0.0000 C.3 1 LIG1 0.1819
26 N 9.8869 -6.1568 0.0000 N.am 1 LIG1 -0.1958
27 O 6.3366 -7.4152 0.0000 O.2 1 LIG1 -0.2730
28 C 7.0557 -5.3479 0.0000 C.3 1 LIG1 0.0996
29 S 6.3366 -4.9435 0.0000 S.3 1 LIG1 -0.0798
30 S 6.3366 -4.1345 0.0000 S.3 1 LIG1 -0.0816
31 O 8.4488 -5.3479 0.0000 O.2 1 LIG1 -0.2715
32 C 9.1678 -7.4152 0.0000 C.3 1 LIG1 0.1195
33 C 9.8869 -7.8197 0.0000 C.2 1 LIG1 0.2630
34 O 9.8869 -8.6286 0.0000 O.2 1 LIG1 -0.2716
35 N 10.6060 -7.4152 0.0000 N.am 1 LIG1 -0.0877
36 C 9.8869 -5.3479 0.0000 C.2 1 LIG1 0.2616
37 C 10.6060 -4.9435 0.0000 C.3 1 LIG1 0.1733
38 O 9.1678 -4.9435 0.0000 O.2 1 LIG1 -0.2715
39 C 11.3250 -5.3479 0.0000 C.3 1 LIG1 0.0408
40 C 12.0441 -4.9435 0.0000 C.3 1 LIG1 0.0908
41 C 12.7631 -5.3479 0.0000 C.2 1 LIG1 0.2608
42 N 13.4822 -4.9435 0.0000 N.am 1 LIG1 -0.0878
43 O 12.7631 -6.2018 0.0000 O.2 1 LIG1 -0.2717
44 N 10.6060 -4.1345 0.0000 N.am 1 LIG1 -0.1963
45 C 11.3250 -2.8762 0.0000 C.ar 1 LIG1 -0.0200
46 C 11.3250 -3.7300 0.0000 C.ar 1 LIG1 -0.0042
47 C 10.6060 -2.4717 0.0000 C.3 1 LIG1 0.0574
48 C 9.8869 -2.8762 0.0000 C.3 1 LIG1 0.1771
49 C 9.8869 -3.7300 0.0000 C.2 1 LIG1 0.2619
50 C 12.7631 -2.8762 0.0000 C.ar 1 LIG1 -0.0003
51 C 12.7631 -3.7300 0.0000 C.ar 1 LIG1 -0.0000
52 C 12.0441 -2.4717 0.0000 C.ar 1 LIG1 -0.0042
53 C 12.0441 -4.1345 0.0000 C.ar 1 LIG1 -0.0003
54 N 7.0557 -2.8762 0.0000 N.am 1 LIG1 -0.1974
55 C 6.3366 -2.4717 0.0000 C.2 1 LIG1 0.2427
56 C 5.6176 -2.8762 0.0000 C.3 1 LIG1 0.0993
57 C 5.6176 -3.7300 0.0000 C.3 1 LIG1 0.0783
58 C 8.4488 -2.8762 0.0000 C.2 1 LIG1 0.2620
59 O 8.4488 -3.7300 0.0000 O.2 1 LIG1 -0.2715
60 C 7.7747 -2.4717 0.0000 C.3 1 LIG1 0.1770
61 N 9.1678 -2.4717 0.0000 N.am 1 LIG1 -0.1960
62 O 9.1678 -4.1345 0.0000 O.2 1 LIG1 -0.2715
63 C 7.7747 -1.6628 0.0000 C.3 1 LIG1 0.0574
64 C 9.1678 -1.6628 0.0000 C.ar 1 LIG1 -0.0009
65 C 8.4488 -1.2583 0.0000 C.ar 1 LIG1 -0.0198
66 C 9.8869 -1.2583 0.0000 C.ar 1 LIG1 0.0417
67 C 9.8869 -0.4045 0.0000 C.ar 1 LIG1 0.1957
68 C 8.4488 -0.4045 0.0000 C.ar 1 LIG1 -0.0009
69 C 9.1678 0.0000 0.0000 C.ar 1 LIG1 0.0417
70 O 6.3366 -1.6628 0.0000 O.2 1 LIG1 -0.2733
71 O 10.6060 0.0000 0.0000 O.3 1 LIG1 -0.2866
72 C 1.3932 -5.4378 0.0000 C.cat 1 LIG1 0.5346
73 N 1.3932 -6.2467 0.0000 N.pl3 1 LIG1 0.1354
74 N 0.6741 -5.0333 0.0000 N.pl3 1 LIG1 0.1354
@<TRIPOS>BOND
1 1 2 am
2 2 3 1
3 2 10 2
4 3 4 1
5 4 5 am
6 5 6 1
7 5 11 2
8 6 7 1
9 6 12 1
10 7 8 am
11 8 9 2
12 16 8 1
13 12 13 1
14 13 14 1
15 14 15 1
16 15 72 1
17 16 17 1
18 16 18 1
19 17 19 1
20 18 20 1
21 18 21 am
22 19 20 1
23 22 21 1
24 21 27 2
25 22 23 1
26 22 28 1
27 23 24 am
28 24 25 1
29 24 31 2
30 25 26 1
31 25 32 1
32 26 36 am
33 28 29 1
34 29 30 1
35 30 57 1
36 32 33 1
37 33 34 2
38 33 35 am
39 36 37 1
40 36 38 2
41 37 39 1
42 37 44 1
43 39 40 1
44 40 41 1
45 41 42 am
46 41 43 2
47 44 49 am
48 45 47 1
49 45 52 ar
50 45 46 ar
51 46 53 ar
52 48 47 1
53 48 61 1
54 48 49 1
55 49 62 2
56 50 51 ar
57 50 52 ar
58 51 53 ar
59 54 55 am
60 54 60 1
61 55 56 1
62 55 70 2
63 56 57 1
64 58 59 2
65 58 60 1
66 58 61 am
67 60 63 1
68 63 65 1
69 64 66 ar
70 64 65 ar
71 65 68 ar
72 66 67 ar
73 67 69 ar
74 67 71 1
75 68 69 ar
76 72 73 2
77 72 74 1
lib/galaxy/datatypes/test/drugbank_drugs.sdf
+491
View File
@@ -0,0 +1,491 @@
Goserelin
Mrv0541 04221219462D
91 96 0 0 1 0 999 V2000
12.8548 -2.6382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
13.9726 -2.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.1766 -3.9327 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.2019 -0.7961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7800 -1.3064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
16.8589 -3.2421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.3562 1.2163 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2702 4.8341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.3500 8.2734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8213 4.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.2178 1.5938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8960 2.8883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1271 0.5358 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12.4834 3.1249 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
13.1495 -4.0364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.2402 -2.9784 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
15.2089 -3.2393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
10.1383 -1.7503 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
15.6226 -2.5255 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.3806 -6.3890 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.2926 0.2619 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.1485 7.0391 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.3338 5.7884 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.8613 -1.8132 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.1907 1.4900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.1795 3.7761 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.2814 2.5480 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.3170 -7.3433 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.6753 -7.7873 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.8596 0.7098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.7335 6.3823 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.9507 7.4636 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
13.9701 -3.9516 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
14.3043 -4.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.6903 -5.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.9766 -4.8431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5984 -3.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.7912 -3.5925 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
14.3838 -3.2378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.5349 -4.3767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0859 -4.9907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8819 -2.5345 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
10.4330 -3.1486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0747 -2.7046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.8184 -3.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8295 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0112 -3.6590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3694 -4.1029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.5873 -1.1363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8436 -0.3521 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
10.6509 -0.1820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.4476 -2.5269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9756 6.2324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
12.0091 -0.6259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9979 1.6602 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.5489 1.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1242 -7.1732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1549 6.1475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8848 5.1744 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.9232 2.9920 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
1.8207 6.9019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2542 2.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1159 2.8219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5266 5.6183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4348 7.4528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6921 5.3445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8324 1.9340 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.6285 4.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1793 -1.4332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8164 -0.4557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8389 0.1814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8596 2.0376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4742 2.3779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6397 2.1041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0615 2.6145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0790 1.7862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9484 6.1287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3411 1.3737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0790 0.9612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5761 1.1498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3645 2.1987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.3178 3.3987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6125 2.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3645 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4646 6.7970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6500 1.7862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6500 0.9612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.1251 3.5688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.4198 2.1706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7349 7.2073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6761 2.9548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 37 2 0 0 0 0
2 39 2 0 0 0 0
3 43 2 0 0 0 0
4 51 1 0 0 0 0
4 54 1 0 0 0 0
5 49 2 0 0 0 0
6 52 2 0 0 0 0
7 56 2 0 0 0 0
8 64 2 0 0 0 0
9 65 2 0 0 0 0
10 68 2 0 0 0 0
11 73 2 0 0 0 0
12 74 2 0 0 0 0
13 80 1 0 0 0 0
14 91 1 0 0 0 0
15 33 1 0 0 0 0
15 36 1 0 0 0 0
15 37 1 0 0 0 0
38 16 1 6 0 0 0
16 43 1 0 0 0 0
17 19 1 0 0 0 0
17 39 1 0 0 0 0
42 18 1 6 0 0 0
18 49 1 0 0 0 0
19 52 1 0 0 0 0
20 46 1 0 0 0 0
20 57 2 0 0 0 0
50 21 1 6 0 0 0
21 56 1 0 0 0 0
22 53 1 0 0 0 0
22 65 1 0 0 0 0
59 23 1 1 0 0 0
23 64 1 0 0 0 0
24 52 1 0 0 0 0
55 25 1 1 0 0 0
25 74 1 0 0 0 0
60 26 1 6 0 0 0
26 68 1 0 0 0 0
67 27 1 6 0 0 0
27 73 1 0 0 0 0
28 57 1 0 0 0 0
29 57 1 0 0 0 0
30 78 1 0 0 0 0
30 79 1 0 0 0 0
31 77 1 0 0 0 0
31 90 1 0 0 0 0
32 85 1 0 0 0 0
32 90 2 0 0 0 0
33 34 1 0 0 0 0
33 39 1 6 0 0 0
34 35 1 0 0 0 0
35 36 1 0 0 0 0
37 38 1 0 0 0 0
38 40 1 0 0 0 0
40 41 1 0 0 0 0
41 46 1 0 0 0 0
42 43 1 0 0 0 0
42 44 1 0 0 0 0
44 45 1 0 0 0 0
45 47 1 0 0 0 0
45 48 1 0 0 0 0
49 50 1 0 0 0 0
50 51 1 0 0 0 0
53 58 1 0 0 0 0
53 64 1 6 0 0 0
54 69 1 0 0 0 0
54 70 1 0 0 0 0
54 71 1 0 0 0 0
55 56 1 0 0 0 0
55 62 1 0 0 0 0
58 61 1 0 0 0 0
59 66 1 0 0 0 0
59 68 1 0 0 0 0
60 63 1 0 0 0 0
60 73 1 0 0 0 0
61 65 1 0 0 0 0
62 75 1 0 0 0 0
63 72 1 0 0 0 0
66 77 1 0 0 0 0
67 74 1 0 0 0 0
67 80 1 0 0 0 0
72 76 1 0 0 0 0
72 78 2 0 0 0 0
75 82 2 0 0 0 0
75 83 1 0 0 0 0
76 79 1 0 0 0 0
76 81 2 0 0 0 0
77 85 2 0 0 0 0
79 84 2 0 0 0 0
81 86 1 0 0 0 0
82 88 1 0 0 0 0
83 89 2 0 0 0 0
84 87 1 0 0 0 0
86 87 2 0 0 0 0
88 91 2 0 0 0 0
89 91 1 0 0 0 0
M END
> <DRUGBANK_ID>
DB00014
> <DRUG_GROUPS>
approved
> <GENERIC_NAME>
Goserelin
> <SALTS>
Goserelin acetate
> <BRANDS>
Zoladex
> <CHEMICAL_FORMULA>
C59H84N18O14
> <MOLECULAR_WEIGHT>
1269.4105
> <EXACT_MASS>
1268.641439486
> <IUPAC_NAME>
(2S)-1-[(2S)-2-[(2S)-2-[(2R)-3-(tert-butoxy)-2-[(2S)-2-[(2S)-3-hydroxy-2-[(2S)-2-[(2S)-3-(1H-imidazol-5-yl)-2-{[(2S)-5-oxopyrrolidin-2-yl]formamido}propanamido]-3-(1H-indol-3-yl)propanamido]propanamido]-3-(4-hydroxyphenyl)propanamido]propanamido]-4-methylpentanamido]-5-[(diaminomethylidene)amino]pentanoyl]-N-(carbamoylamino)pyrrolidine-2-carboxamide
> <INCHI_IDENTIFIER>
InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
> <INCHI_KEY>
InChIKey=BLCLNMBMMGCOAS-URPVMXJPSA-N
> <SMILES>
CC(C)C[C@H](NC(=O)[C@@H](COC(C)(C)C)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)[C@H](CO)NC(=O)[C@H](CC1=CNC2=CC=CC=C12)NC(=O)[C@H](CC1=CN=CN1)NC(=O)[C@@H]1CCC(=O)N1)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N1CCC[C@H]1C(=O)NNC(N)=O
> <JCHEM_ACCEPTOR_COUNT>
18
> <JCHEM_DONOR_COUNT>
17
> <JCHEM_ACIDIC_PKA>
9.82
> <ALOGPS_LOGP>
0.3
> <JCHEM_LOGP>
-5.2
> <ALOGPS_LOGS>
-4.7
> <JCHEM_POLARIZABILITY>
131.22
> <JCHEM_POLAR_SURFACE_AREA>
495.89
> <JCHEM_REFRACTIVITY>
325.84
> <JCHEM_ROTATABLE_BOND_COUNT>
33
> <ALOGPS_SOLUBILITY>
2.83e-02 g/l
$$$$
Desmopressin
Mrv0541 04221221522D
74 77 0 0 1 0 999 V2000
0.0000 -7.8646 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.6741 -7.4601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3932 -7.8646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1122 -7.4601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8313 -7.8646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5503 -7.4601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
4.2693 -7.8646 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.9435 -7.4601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6625 -7.8646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.6741 -6.6512 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8313 -8.7184 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.5503 -6.6512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8313 -6.2467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8313 -5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1122 -5.0333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.9435 -6.6512 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
4.3143 -6.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6176 -6.1568 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.5390 -5.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3479 -5.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -6.5613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0557 -6.1568 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
7.7747 -6.5613 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -6.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1678 -6.5613 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
9.8869 -6.1568 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -7.4152 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.0557 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -4.9435 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -4.1345 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -5.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.1678 -7.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -7.8197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -8.6286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.6060 -7.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6060 -4.9435 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.1678 -4.9435 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.3250 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0441 -4.9435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7631 -5.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4822 -4.9435 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.7631 -6.2018 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.6060 -4.1345 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.3250 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3250 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6060 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -2.8762 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
9.8869 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7631 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7631 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0441 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0441 -4.1345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0557 -2.8762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -2.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6176 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6176 -3.7300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -2.8762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -3.7300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7747 -2.4717 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.1678 -2.4717 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.1678 -4.1345 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7747 -1.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1678 -1.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -1.2583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -1.2583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8869 -0.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4488 -0.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1678 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3366 -1.6628 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.6060 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3932 -5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3932 -6.2467 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.6741 -5.0333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 10 2 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
5 11 2 0 0 0 0
6 7 1 0 0 0 0
6 12 1 6 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
16 8 1 6 0 0 0
12 13 1 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
15 72 1 0 0 0 0
16 17 1 0 0 0 0
16 18 1 0 0 0 0
17 19 1 0 0 0 0
18 20 1 0 0 0 0
18 21 1 0 0 0 0
19 20 1 0 0 0 0
22 21 1 6 0 0 0
21 27 2 0 0 0 0
22 23 1 0 0 0 0
22 28 1 0 0 0 0
23 24 1 0 0 0 0
24 25 1 0 0 0 0
24 31 2 0 0 0 0
25 26 1 0 0 0 0
25 32 1 1 0 0 0
26 36 1 0 0 0 0
28 29 1 0 0 0 0
29 30 1 0 0 0 0
30 57 1 0 0 0 0
32 33 1 0 0 0 0
33 34 2 0 0 0 0
33 35 1 0 0 0 0
36 37 1 0 0 0 0
36 38 2 0 0 0 0
37 39 1 1 0 0 0
37 44 1 0 0 0 0
39 40 1 0 0 0 0
40 41 1 0 0 0 0
41 42 1 0 0 0 0
41 43 2 0 0 0 0
44 49 1 0 0 0 0
45 47 1 0 0 0 0
45 52 1 0 0 0 0
45 46 2 0 0 0 0
46 53 1 0 0 0 0
48 47 1 1 0 0 0
48 61 1 0 0 0 0
48 49 1 0 0 0 0
49 62 2 0 0 0 0
50 51 1 0 0 0 0
50 52 2 0 0 0 0
51 53 2 0 0 0 0
54 55 1 0 0 0 0
54 60 1 0 0 0 0
55 56 1 0 0 0 0
55 70 2 0 0 0 0
56 57 1 0 0 0 0
58 59 2 0 0 0 0
58 60 1 0 0 0 0
58 61 1 0 0 0 0
60 63 1 1 0 0 0
63 65 1 0 0 0 0
64 66 2 0 0 0 0
64 65 1 0 0 0 0
65 68 2 0 0 0 0
66 67 1 0 0 0 0
67 69 2 0 0 0 0
67 71 1 0 0 0 0
68 69 1 0 0 0 0
72 73 2 3 0 0 0
72 74 1 0 0 0 0
M END
> <DRUGBANK_ID>
DB00035
> <DRUG_GROUPS>
approved
> <GENERIC_NAME>
Desmopressin
> <SYNONYMS>
1-Desamino-8-D-arginine vasopressin; Desmopresina [INN-Spanish]; Desmopressine [INN-French]; Desmopressinum [INN-Latin]
> <SALTS>
Desmopressin acetate
> <BRANDS>
Adiuretin; Concentraid; DDAVP; Minirin; Stimate
> <CHEMICAL_FORMULA>
C46H64N14O12S2
> <MOLECULAR_WEIGHT>
1069.217
> <EXACT_MASS>
1068.426954962
> <IUPAC_NAME>
(2S)-2-{[(2S)-1-{[(4R,7S,10S,13S,16S)-13-benzyl-10-(2-carbamoylethyl)-7-(carbamoylmethyl)-16-[(4-hydroxyphenyl)methyl]-6,9,12,15,18-pentaoxo-1,2-dithia-5,8,11,14,17-pentaazacycloicosan-4-yl]carbonyl}pyrrolidin-2-yl]formamido}-5-carbamimidamido-N-(carbamoylmethyl)pentanamide
> <INCHI_IDENTIFIER>
InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1
> <INCHI_KEY>
InChIKey=NFLWUMRGJYTJIN-NXBWRCJVSA-N
> <SMILES>
NC(=O)CC[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=C(O)C=C2)NC(=O)CCSSC[C@H](NC(=O)[C@H](CC(N)=O)NC1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(N)=O
> <JCHEM_ACCEPTOR_COUNT>
15
> <JCHEM_DONOR_COUNT>
14
> <JCHEM_ACIDIC_PKA>
11.34
> <ALOGPS_LOGP>
-1
> <JCHEM_LOGP>
-6.1
> <ALOGPS_LOGS>
-4
> <JCHEM_POLARIZABILITY>
106.19
> <JCHEM_POLAR_SURFACE_AREA>
435.41
> <JCHEM_REFRACTIVITY>
279.78
> <JCHEM_ROTATABLE_BOND_COUNT>
19
> <ALOGPS_SOLUBILITY>
1.10e-01 g/l
$$$$
lib/galaxy/datatypes/test/drugbank_drugs.smi
+2
View File
@@ -0,0 +1,2 @@
O=C(N1[C@@H](CCC1)C(=O)NNC(=O)N)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]1NC(=O)CC1)Cc1[nH]cnc1)Cc1c2c([nH]c1)cccc2)CO)Cc1ccc(O)cc1)COC(C)(C)C)CC(C)C)CCCN=C(N)N Goserelin
NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@H]1NC(=O)[C@@H](NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](NC(=O)CCSSC1)Cc1ccc(cc1)O)CC(=O)N)CCCNC(=N)N Desmopressin
lib/galaxy/datatypes/test/q.fps
+7
View File
@@ -0,0 +1,7 @@
#FPS1
#num_bits=881
#type=CACTVS-E_SCREEN/1.0 extended=2
#software=CACTVS/unknown
#source=CID_28434379.sdf
#date=2012-02-03T13:08:39
07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000 28434379
lib/galaxy/dependencies/conda-environment.txt
+1 -1
View File
@@ -64,7 +64,7 @@ sqlparse
six
#Parsley
nose
#SVGFig
svgwrite
# Fabric and dependencies
Fabric
lib/galaxy/dependencies/requirements.txt
+2 -1
View File
@@ -46,7 +46,8 @@ sqlparse
six
Parsley
nose
SVGFig
svgwrite
# Fabric and dependencies
Fabric
lib/galaxy/external_services/result_handlers/basic.py
+1 -1
View File
@@ -1,5 +1,5 @@
from galaxy.util.json import loads
import logging
from json import loads
log = logging.getLogger( __name__ )
lib/galaxy/jobs/__init__.py
+81 -51
View File
@@ -1,13 +1,8 @@
"""
Support for running a tool in Galaxy via an internal job management system
"""
from abc import ABCMeta
from abc import abstractmethod
import time
import copy
import datetime
import galaxy
import logging
import os
import pwd
@@ -15,20 +10,23 @@ import random
import shutil
import subprocess
import sys
import time
import traceback
from abc import ABCMeta, abstractmethod
from json import loads
from xml.etree import ElementTree
import galaxy
from galaxy import model, util
from galaxy.util.xml_macros import load
from galaxy.datatypes import metadata
from galaxy.datatypes import metadata, sniff
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
from galaxy.jobs.actions.post import ActionBox
from galaxy.jobs.mapper import JobRunnerMapper
from galaxy.jobs.runners import BaseJobRunner, JobState
from galaxy.util import safe_makedirs, unicodify
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
from galaxy.util.json import loads
from galaxy.util import safe_makedirs
from galaxy.util import unicodify
from galaxy.datatypes import sniff
from galaxy.util.xml_macros import load
from .output_checker import check_output
from .datasets import TaskPathRewriter
@@ -112,6 +110,15 @@ class JobConfiguration( object ):
"""
DEFAULT_NWORKERS = 4
JOB_RESOURCE_CONDITIONAL_XML = """<conditional name="__job_resource">
<param name="__job_resource__select" type="select" label="Job Resource Parameters">
<option value="no">Use default job resource parameters</option>
<option value="yes">Specify job resource parameters</option>
</param>
<when value="no"/>
<when value="yes"/>
</conditional>"""
def __init__(self, app):
"""Parse the job configuration XML.
"""
@@ -354,53 +361,44 @@ class JobConfiguration( object ):
log.debug('Done loading job configuration')
def get_tool_resource_parameters( self, tool_id ):
def get_tool_resource_xml( self, tool_id, tool_type ):
""" Given a tool id, return XML elements describing parameters to
insert into job resources.
:tool id: A tool ID (a string)
:tool type: A tool type (a string)
:returns: List of parameter elements.
"""
fields = []
if not tool_id:
return fields
# TODO: Only works with exact matches, should handle different kinds of ids
# the way destination lookup does.
resource_group = None
if tool_id in self.tools:
resource_group = self.tools[ tool_id ][ 0 ].get_resource_group()
resource_group = resource_group or self.default_resource_group
if resource_group and resource_group in self.resource_groups:
fields_names = self.resource_groups[ resource_group ]
fields = [ self.resource_parameters[ n ] for n in fields_names ]
return fields
if tool_id and tool_type is 'default':
# TODO: Only works with exact matches, should handle different kinds of ids
# the way destination lookup does.
resource_group = None
if tool_id in self.tools:
resource_group = self.tools[ tool_id ][ 0 ].get_resource_group()
resource_group = resource_group or self.default_resource_group
if resource_group and resource_group in self.resource_groups:
fields_names = self.resource_groups[ resource_group ]
fields = [ self.resource_parameters[ n ] for n in fields_names ]
if fields:
conditional_element = ElementTree.fromstring( self.JOB_RESOURCE_CONDITIONAL_XML )
when_yes_elem = conditional_element.findall( 'when' )[ 1 ]
for parameter in fields:
when_yes_elem.append( parameter )
return conditional_element
def __parse_resource_parameters( self ):
if not os.path.exists( self.app.config.job_resource_params_file ):
return
resource_param_file = self.app.config.job_resource_params_file
try:
resource_definitions = util.parse_xml( resource_param_file )
except Exception as e:
raise config_exception(e, resource_param_file)
resource_definitions_root = resource_definitions.getroot()
# TODO: Also handling conditionals would be awesome!
for parameter_elem in resource_definitions_root.findall( "param" ):
name = parameter_elem.get( "name" )
# Considered prepending __job_resource_param__ here and then
# stripping it off when making it available to dynamic job
# destination. Not needed because resource parameters are wrapped
# in a conditional.
# # expanded_name = "__job_resource_param__%s" % name
# # parameter_elem.set( "name", expanded_name )
self.resource_parameters[ name ] = parameter_elem
if os.path.exists( self.app.config.job_resource_params_file ):
resource_param_file = self.app.config.job_resource_params_file
try:
resource_definitions = util.parse_xml( resource_param_file )
except Exception as e:
raise config_exception( e, resource_param_file )
resource_definitions_root = resource_definitions.getroot()
# TODO: Also handling conditionals would be awesome!
for parameter_elem in resource_definitions_root.findall( "param" ):
name = parameter_elem.get( "name" )
self.resource_parameters[ name ] = parameter_elem
def __get_default(self, parent, names):
"""
@@ -771,6 +769,7 @@ class JobWrapper( object ):
if use_persisted_destination:
self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job )
self.__commands_in_new_shell = self.app.config.commands_in_new_shell
self.__user_system_pwent = None
self.__galaxy_system_pwent = None
@@ -803,13 +802,19 @@ class JobWrapper( object ):
def shell(self):
return self.job_destination.shell or getattr(self.app.config, 'default_job_shell', DEFAULT_JOB_SHELL)
def disable_commands_in_new_shell(self):
"""Provide an extension point to disable this isolation,
Pulsar builds its own job script so this is not needed for
remote jobs."""
self.__commands_in_new_shell = False
@property
def strict_shell(self):
return self.tool.strict_shell
@property
def commands_in_new_shell(self):
return self.app.config.commands_in_new_shell
return self.__commands_in_new_shell
@property
def galaxy_lib_dir(self):
@@ -1024,6 +1029,7 @@ class JobWrapper( object ):
self.sa_session.add( job )
self.sa_session.flush()
self._report_error_to_sentry()
# Perform email action even on failure.
for pja in [pjaa.post_job_action for pjaa in job.post_job_actions if pjaa.post_job_action.action_type == "EmailAction"]:
ActionBox.execute(self.app, self.sa_session, pja, job)
@@ -1283,7 +1289,7 @@ class JobWrapper( object ):
dataset.extension = 'txt'
self.sa_session.add( dataset )
if job.states.ERROR == final_job_state:
log.debug( "setting dataset state to ERROR" )
log.debug( "(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id )
# TODO: This is where the state is being set to error. Change it!
dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
# Pause any dependent jobs (and those jobs' outputs)
@@ -1392,6 +1398,8 @@ class JobWrapper( object ):
self._collect_metrics( job )
self.sa_session.flush()
log.debug( 'job %d ended (finish() executed in %s)' % (self.job_id, finish_timer) )
if job.state == job.states.ERROR:
self._report_error_to_sentry()
cleanup_job = self.cleanup_job
delete_files = cleanup_job == 'always' or ( job.state == job.states.OK and cleanup_job == 'onsuccess' )
self.cleanup( delete_files=delete_files )
@@ -1741,6 +1749,28 @@ class JobWrapper( object ):
return self.tool.requires_setting_metadata
return False
def _report_error_to_sentry( self ):
job = self.get_job()
tool = self.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version) or None
if self.app.sentry_client and job.state == job.states.ERROR:
self.app.sentry_client.capture(
'raven.events.Message',
message="Galaxy Job Error: %s v.%s" % (job.tool_id, job.tool_version),
extra={
'info' : job.info,
'id' : job.id,
'command_line' : job.command_line,
'stderr' : job.stderr,
'traceback': job.traceback,
'exit_code': job.exit_code,
'stdout': job.stdout,
'handler': job.handler,
'user': self.user,
'tool_version': job.tool_version,
'tool_xml': tool.config_file if tool else None
}
)
class TaskWrapper(JobWrapper):
"""
lib/galaxy/jobs/actions/post.py
+4 -2
View File
@@ -6,10 +6,12 @@ immediate_actions listed below. Currently only used in workflows.
import datetime
import logging
import socket
from galaxy.util import send_mail
from galaxy.util.json import dumps
from json import dumps
from markupsafe import escape
from galaxy.util import send_mail
log = logging.getLogger( __name__ )
lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
+1 -1
View File
@@ -2,10 +2,10 @@
Module for managing jobs in Pacific Bioscience's SMRT Portal and automatically transferring files
produced by SMRT Portal.
"""
import json
import logging
import urllib2
from string import Template
from galaxy.util import json
from data_transfer import DataTransfer
lib/galaxy/jobs/handler.py
+1 -1
View File
@@ -186,7 +186,7 @@ class JobHandlerQueue( object ):
jobs (either from the database or from its own queue), then iterates
over all new and waiting jobs to check the state of the jobs each
depends on. If the job has dependencies that have not finished, it
it goes to the waiting queue. If the job has dependencies with errors,
goes to the waiting queue. If the job has dependencies with errors,
it is marked as having errors and removed from the queue. If the job
belongs to an inactive user it is ignored.
Otherwise, the job is dispatched.
lib/galaxy/jobs/runners/pulsar.py
+1
View File
@@ -278,6 +278,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
compute_tool_directory=remote_tool_directory,
compute_job_directory=remote_job_directory,
)
job_wrapper.disable_commands_in_new_shell()
command_line = build_command(
self,
job_wrapper=job_wrapper,
lib/galaxy/jobs/transfer_manager.py
+6 -4
View File
@@ -2,13 +2,15 @@
Manage transfers from arbitrary URLs to temporary files. Socket interface for
IPC with multiple process configurations.
"""
import json
import logging
import os
import subprocess
import socket
import subprocess
import threading
from galaxy.util import listify, json, sleeper
from galaxy.util import listify, sleeper
from galaxy.util.json import jsonrpc_request, validate_jsonrpc_response
log = logging.getLogger( __name__ )
@@ -83,13 +85,13 @@ class TransferManager( object ):
for tj in transfer_jobs:
if via_socket and tj.state not in tj.terminal_states and tj.socket:
try:
request = json.jsonrpc_request( method='get_state', id=True )
request = jsonrpc_request( method='get_state', id=True )
sock = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
sock.settimeout( 5 )
sock.connect( ( 'localhost', tj.socket ) )
sock.send( json.dumps( request ) )
response = sock.recv( 8192 )
valid, response = json.validate_jsonrpc_response( response, id=request['id'] )
valid, response = validate_jsonrpc_response( response, id=request['id'] )
if not valid:
# No valid response received, make some pseudo-json-rpc
raise Exception( dict( code=128, message='Did not receive valid response from transfer daemon for state' ) )
lib/galaxy/managers/context.py
+1 -1
View File
@@ -3,8 +3,8 @@ Mixins for transaction-like objects.
"""
import os
from json import dumps
from galaxy.util.json import dumps
from galaxy.util import bunch
lib/galaxy/managers/histories.py
+22 -2
View File
@@ -5,13 +5,16 @@ Histories are containers for datasets or dataset collections
created (or copied) by users over the course of an analysis.
"""
from sqlalchemy import desc, asc
from sqlalchemy import desc
from sqlalchemy import asc
from galaxy import model
from galaxy import exceptions as glx_exceptions
from galaxy.managers import sharable
from galaxy.managers import deletable
from galaxy.managers import hdas
# from galaxy.managers import hdcas
from galaxy.managers import history_contents
from galaxy.managers import collections_util
@@ -34,6 +37,8 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
def __init__( self, app, *args, **kwargs ):
super( HistoryManager, self ).__init__( app, *args, **kwargs )
self.hda_manager = hdas.HDAManager( app )
self.contents_manager = history_contents.HistoryContentsManager( app )
self.contents_filters = history_contents.HistoryContentsFilters( app )
def copy( self, history, user, **kwargs ):
"""
@@ -147,6 +152,19 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
raise glx_exceptions.RequestParameterInvalidException( 'Unkown order_by', order_by=order_by_string,
available=[ 'create_time', 'update_time', 'name', 'size' ])
def non_ready_jobs( self, history ):
"""Return the currently running job objects associated with this history.
Where running is defined as new, waiting, queued, running, resubmitted,
and upload.
"""
# TODO: defer to jobModelManager (if there was one)
# TODO: genericize the params to allow other filters
jobs = ( self.session().query( model.Job )
.filter( model.Job.history == history )
.filter( model.Job.state.in_( model.Job.non_ready_states ) ) )
return jobs
class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSerializerMixin ):
"""
@@ -215,7 +233,9 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
'hdas' : lambda i, k, **c: [ self.app.security.encode_id( hda.id ) for hda in i.datasets ],
'state_details' : self.serialize_state_counts,
'state_ids' : self.serialize_state_ids,
'contents' : self.serialize_contents
'contents' : self.serialize_contents,
'non_ready_jobs': lambda i, k, **c: [ self.app.security.encode_id( job.id ) for job
in self.manager.non_ready_jobs( i ) ],
})
# remove this
lib/galaxy/managers/history_contents.py
+3 -7
View File
@@ -14,7 +14,6 @@ from galaxy.managers import base
from galaxy.managers import deletable
from galaxy.managers import containers
from galaxy.managers import hdas
from galaxy.managers import collections
import logging
log = logging.getLogger( __name__ )
@@ -31,7 +30,6 @@ class HistoryContentsManager( containers.ContainerManagerMixin ):
contained_class_type_name = 'dataset'
subcontainer_class = model.HistoryDatasetCollectionAssociation
# TODO:
subcontainer_class_manager_class = None
subcontainer_class_type_name = 'dataset_collection'
@@ -59,7 +57,6 @@ class HistoryContentsManager( containers.ContainerManagerMixin ):
def __init__( self, app ):
self.app = app
self.contained_manager = self.contained_class_manager_class( app )
self.subcontainer_manager = collections.DatasetCollectionManager( app )
# ---- interface
def contained( self, container, filters=None, limit=None, offset=None, order_by=None, **kwargs ):
@@ -136,15 +133,14 @@ class HistoryContentsManager( containers.ContainerManagerMixin ):
def _get_filter_for_contained( self, container, content_class ):
return content_class.history == container
def _union_of_contents( self, container, **kwargs ):
def _union_of_contents( self, container, expand_models=True, **kwargs ):
"""
Returns a limited and offset list of both types of contents, filtered
and in some order.
"""
contents_results = self._union_of_contents_query( container, **kwargs ).all()
# import pprint
# for result in contents_results:
# pprint.pprint( result )
if not expand_models:
return contents_results
# partition ids into a map of { component_class names -> list of ids } from the above union query
id_map = dict( (( self.contained_class_type_name, [] ), ( self.subcontainer_class_type_name, [] )) )
lib/galaxy/managers/workflows.py
+6 -7
View File
@@ -272,7 +272,6 @@ class WorkflowContentsManager(UsesAnnotations):
def _workflow_from_dict(self, trans, data, name):
if isinstance(data, string_types):
# If coming from the editor...
data = json.loads(data)
# Create new workflow from source data
@@ -294,7 +293,7 @@ class WorkflowContentsManager(UsesAnnotations):
missing_tool_tups = []
for step_dict in self.__walk_step_dicts( data ):
module, step = self.__track_module_from_dict( trans, steps, steps_by_external_id, step_dict, secure=False )
module, step = self.__track_module_from_dict( trans, steps, steps_by_external_id, step_dict )
is_tool = is_tool_module_type( module.type )
if is_tool and module.tool is None:
# A required tool is not available in the local Galaxy instance.
@@ -526,7 +525,7 @@ class WorkflowContentsManager(UsesAnnotations):
# eliminate after a few years...
'tool_version': step.tool_version,
'name': module.get_name(),
'tool_state': module.get_state( secure=False ),
'tool_state': module.get_state(),
'tool_errors': module.get_errors(),
'uuid': str(step.uuid),
'label': step.label or None,
@@ -756,8 +755,8 @@ class WorkflowContentsManager(UsesAnnotations):
yield step_dict
def __track_module_from_dict( self, trans, steps, steps_by_external_id, step_dict, secure ):
module, step = self.__module_from_dict( trans, step_dict, secure=secure )
def __track_module_from_dict( self, trans, steps, steps_by_external_id, step_dict ):
module, step = self.__module_from_dict( trans, step_dict )
# Create the model class for the step
steps.append( step )
steps_by_external_id[ step_dict['id' ] ] = step
@@ -784,7 +783,7 @@ class WorkflowContentsManager(UsesAnnotations):
trans.sa_session.add(m)
return module, step
def __module_from_dict( self, trans, step_dict, secure ):
def __module_from_dict( self, trans, step_dict ):
""" Create a WorkflowStep model object and corresponding module
representing type-specific functionality from the incoming dictionary.
"""
@@ -803,7 +802,7 @@ class WorkflowContentsManager(UsesAnnotations):
)
step_dict["subworkflow"] = subworkflow
module = module_factory.from_dict( trans, step_dict, secure=secure )
module = module_factory.from_dict( trans, step_dict )
module.save_to_step( step )
annotation = step_dict[ 'annotation' ]
lib/galaxy/model/__init__.py
+20
View File
@@ -136,6 +136,16 @@ class JobLike:
log.info( "stderr for %s %d is greater than %s, only a portion will be logged to database", type(self), self.id, galaxy.util.DATABASE_MAX_STRING_SIZE_PRETTY )
self.stderr = stderr
def log_str(self):
extra = ""
safe_id = getattr(self, "id", None)
if safe_id is not None:
extra += "id=%s" % safe_id
else:
extra += "unflushed"
return "%s[%s,tool_id=%s]" % (self.__class__.__name__, extra, self.tool_id)
class User( object, Dictifiable ):
use_pbkdf2 = True
@@ -358,6 +368,15 @@ class Job( object, JobLike, Dictifiable ):
terminal_states = [ states.OK,
states.ERROR,
states.DELETED ]
#: job states where the job hasn't finished and the model may still change
non_ready_states = [
states.NEW,
states.RESUBMITTED,
states.UPLOAD,
states.WAITING,
states.QUEUED,
states.RUNNING,
]
# Please include an accessor (get/set pair) for any new columns/members.
def __init__( self ):
@@ -1612,6 +1631,7 @@ class Dataset( StorableObject ):
# failed_metadata is only valid as DatasetInstance state currently
non_ready_states = (
states.NEW,
states.UPLOAD,
states.QUEUED,
states.RUNNING,
lib/galaxy/model/custom_types.py
+1 -1
View File
@@ -272,7 +272,7 @@ class MetadataType( JSONType ):
sz = total_size(v)
if sz > app.app.config.max_metadata_value_size:
del value[k]
log.error('Refusing to bind metadata key %s due to size (%s)' % (k, sz))
log.warning('Refusing to bind metadata key %s due to size (%s)' % (k, sz))
value = json_encoder.encode(value)
return value
lib/galaxy/model/mapping.py
+7 -7
View File
@@ -2100,16 +2100,16 @@ mapper( model.Job, model.Job.table, properties=dict(
user=relation( model.User ),
galaxy_session=relation( model.GalaxySession ),
history=relation( model.History ),
library_folder=relation( model.LibraryFolder ),
parameters=relation( model.JobParameter, lazy=False ),
library_folder=relation( model.LibraryFolder, lazy=True ),
parameters=relation( model.JobParameter, lazy=True ),
input_datasets=relation( model.JobToInputDatasetAssociation ),
output_datasets=relation( model.JobToOutputDatasetAssociation ),
output_dataset_collection_instances=relation( model.JobToOutputDatasetCollectionAssociation ),
output_dataset_collections=relation( model.JobToImplicitOutputDatasetCollectionAssociation ),
output_datasets=relation( model.JobToOutputDatasetAssociation, lazy=True ),
output_dataset_collection_instances=relation( model.JobToOutputDatasetCollectionAssociation, lazy=True ),
output_dataset_collections=relation( model.JobToImplicitOutputDatasetCollectionAssociation, lazy=True ),
post_job_actions=relation( model.PostJobActionAssociation, lazy=False ),
input_library_datasets=relation( model.JobToInputLibraryDatasetAssociation ),
output_library_datasets=relation( model.JobToOutputLibraryDatasetAssociation ),
external_output_metadata=relation( model.JobExternalOutputMetadata, lazy=False ),
output_library_datasets=relation( model.JobToOutputLibraryDatasetAssociation, lazy=True ),
external_output_metadata=relation( model.JobExternalOutputMetadata, lazy=True ),
tasks=relation( model.Task )
) )
lib/galaxy/model/metadata.py
+4 -7
View File
@@ -6,28 +6,25 @@ Galaxy Metadata
import copy
import cPickle
import json
import logging
import os
import shutil
import sys
import tempfile
import weakref
from os.path import abspath
from six import string_types
from sqlalchemy.orm import object_session
import galaxy.model
from galaxy.util import listify
from galaxy.util.object_wrapper import sanitize_lists_to_string
from galaxy.util import stringify_dictionary_keys
from galaxy.util import string_as_bool
from galaxy.util import in_directory
from galaxy.util import (in_directory, listify, string_as_bool,
stringify_dictionary_keys)
from galaxy.util.json import safe_dumps
from galaxy.util.object_wrapper import sanitize_lists_to_string
from galaxy.util.odict import odict
from galaxy.web import form_builder
import logging
log = logging.getLogger(__name__)
STATEMENTS = "__galaxy_statements__" # this is the name of the property in a Datatype class where new metadata spec element Statements are stored
lib/galaxy/model/search.py
+3 -4
View File
@@ -26,8 +26,11 @@ select * from history where name='Unnamed history'
import logging
import re
from json import dumps
import parsley
from sqlalchemy import and_
from sqlalchemy.orm import aliased
from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation,
History, Library, LibraryFolder, LibraryDataset, StoredWorkflowTagAssociation,
@@ -37,10 +40,6 @@ from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssoci
Page, PageRevision)
from galaxy.model.tool_shed_install import ToolVersion
from galaxy.util.json import dumps
from sqlalchemy import and_
from sqlalchemy.orm import aliased
log = logging.getLogger( __name__ )
lib/galaxy/queue_worker.py
+1 -1
View File
@@ -90,7 +90,7 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
"""
def __init__(self, app, queue=None, task_mapping=control_message_to_task, connection=None):
super(GalaxyQueueWorker, self).__init__()
log.info("Initalizing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))
log.info("Initializing %s Galaxy Queue Worker on %s", app.config.server_name, util.mask_password_from_url(app.config.amqp_internal_connection))
self.daemon = True
if connection:
self.connection = connection
lib/galaxy/tools/__init__.py
+54 -240
View File
@@ -2,7 +2,6 @@
Classes encapsulating galaxy tools and tool configuration.
"""
import binascii
import glob
import json
import logging
@@ -33,8 +32,7 @@ from galaxy.tools.parameters import params_to_incoming, check_param, params_from
from galaxy.tools.parameters import output_collect
from galaxy.tools.parameters.basic import (BaseURLToolParameter,
DataToolParameter, DataCollectionToolParameter, HiddenToolParameter,
SelectToolParameter, ToolParameter,
contains_workflow_parameter)
SelectToolParameter, ToolParameter)
from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
from galaxy.tools.parameters.input_translation import ToolInputTranslator
from galaxy.tools.test import parse_tests
@@ -49,7 +47,6 @@ from galaxy.util import unicodify
from galaxy.tools.parameters.meta import expand_meta_parameters
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
from galaxy.util.hash_util import hmac_new
from galaxy.util.json import json_fix
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
@@ -66,17 +63,6 @@ import galaxy.jobs
log = logging.getLogger( __name__ )
JOB_RESOURCE_CONDITIONAL_XML = """<conditional name="__job_resource">
<param name="__job_resource__select" type="select" label="Job Resource Parameters">
<option value="no">Use default job resource parameters</option>
<option value="yes">Specify job resource parameters</option>
</param>
<when value="no"></when>
<when value="yes">
</when>
</conditional>"""
HELP_UNINITIALIZED = threading.Lock()
@@ -137,27 +123,8 @@ class ToolBox( BaseGalaxyToolBox ):
tool_type = tool_source.parse_tool_type()
ToolClass = tool_types.get( tool_type )
else:
# Normal tool - only insert dynamic resource parameters for these
# tools.
root = getattr( tool_source, "root", None )
# TODO: mucking with the XML directly like this is terrible,
# modify inputs directly post load if possible.
if root is not None and hasattr( self.app, "job_config" ): # toolshed may not have job_config?
tool_id = root.get( 'id' )
parameters = self.app.job_config.get_tool_resource_parameters( tool_id )
if parameters:
inputs = root.find('inputs')
# If tool has not inputs, create some so we can insert conditional
if inputs is None:
inputs = ElementTree.fromstring( "<inputs></inputs>")
root.append( inputs )
# Insert a conditional allowing user to specify resource parameters.
conditional_element = ElementTree.fromstring( JOB_RESOURCE_CONDITIONAL_XML )
when_yes_elem = conditional_element.findall( "when" )[ 1 ]
for parameter in parameters:
when_yes_elem.append( parameter )
inputs.append( conditional_element )
# Normal tool
root = getattr( tool_source, 'root', None )
ToolClass = Tool
tool = ToolClass( config_file, tool_source, self.app, guid=guid, repository_id=repository_id, **kwds )
return tool
@@ -225,15 +192,14 @@ class ToolBox( BaseGalaxyToolBox ):
class DefaultToolState( object ):
"""
Keeps track of the state of a users interaction with a tool between
requests. The default tool state keeps track of the current page (for
multipage "wizard" tools) and the values of all
requests.
"""
def __init__( self ):
self.page = 0
self.rerun_remap_job_id = None
self.inputs = None
def encode( self, tool, app, secure=True ):
def encode( self, tool, app ):
"""
Convert the data to a string
"""
@@ -242,26 +208,12 @@ class DefaultToolState( object ):
value = params_to_strings( tool.inputs, self.inputs, app )
value["__page__"] = self.page
value["__rerun_remap_job_id__"] = self.rerun_remap_job_id
value = json.dumps( value )
# Make it secure
if secure:
a = hmac_new( app.config.tool_secret, value )
b = binascii.hexlify( value )
return "%s:%s" % ( a, b )
else:
return value
return json.dumps( value )
def decode( self, value, tool, app, secure=True ):
def decode( self, value, tool, app ):
"""
Restore the state from a string
"""
if secure:
# Extract and verify hash
a, b = value.split( ":" )
value = binascii.unhexlify( b )
test = hmac_new( app.config.tool_secret, value )
assert a == test
# Restore from string
values = json_fix( json.loads( value ) )
self.page = values.pop( "__page__" )
if '__rerun_remap_job_id__' in values:
@@ -272,13 +224,11 @@ class DefaultToolState( object ):
def copy( self ):
"""
WARNING! Makes a shallow copy, *SHOULD* rework to have it make a deep
copy.
Shallow copy of the state
"""
new_state = DefaultToolState()
new_state.page = self.page
new_state.rerun_remap_job_id = self.rerun_remap_job_id
# This need to be copied.
new_state.inputs = self.inputs
return new_state
@@ -339,6 +289,8 @@ class Tool( object, Dictifiable ):
self.lineage_ids = []
# populate toolshed repository info, if available
self.populate_tool_shed_info()
# add tool resource parameters
self.populate_resource_parameters( tool_source )
# Parse XML element containing configuration
try:
self.parse( tool_source, guid=guid )
@@ -547,8 +499,9 @@ class Tool( object, Dictifiable ):
# Handle toolshed guids
self_ids = [ self.id.lower(), self.id.lower().rsplit('/', 1)[0], self.old_id.lower() ]
self.all_ids = self_ids
# In the toolshed context, there is no job config.
if 'job_config' in dir(self.app):
if hasattr( self.app, 'job_config' ):
self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids)
# Is this a 'hidden' tool (hidden in tool menu)
@@ -728,7 +681,8 @@ class Tool( object, Dictifiable ):
# Parse the actual parameters
# Handle multiple page case
for page_source in pages.page_sources:
display, inputs = self.parse_input_page( page_source, enctypes )
inputs = self.parse_input_elem( page_source, enctypes )
display = page_source.parse_display()
self.inputs_by_page.append( inputs )
self.inputs.update( inputs )
self.display_by_page.append( display )
@@ -807,17 +761,6 @@ class Tool( object, Dictifiable ):
citations.append( citation )
return citations
def parse_input_page( self, page_source, enctypes ):
"""
Parse a page of inputs. This basically just calls 'parse_input_elem',
but it also deals with possible 'display' elements which are supported
only at the top/page level (not in groups).
"""
inputs = self.parse_input_elem( page_source, enctypes )
# Display
display = page_source.parse_display()
return display, inputs
def parse_input_elem( self, page_source, enctypes, context=None ):
"""
Parse a parent element whose children are inputs -- these could be
@@ -946,6 +889,17 @@ class Tool( object, Dictifiable ):
context[ name ].refresh_on_change = True
return param
def populate_resource_parameters( self, tool_source ):
root = getattr( tool_source, 'root', None )
if root is not None and hasattr( self.app, 'job_config' ) and hasattr( self.app.job_config, 'get_tool_resource_xml' ):
resource_xml = self.app.job_config.get_tool_resource_xml( root.get( 'id' ), self.tool_type )
if resource_xml is not None:
inputs = root.find( 'inputs' )
if inputs is None:
inputs = ElementTree.fromstring( '<inputs/>' )
root.append( inputs )
inputs.append( resource_xml )
def populate_tool_shed_info( self ):
if self.repository_id is not None and self.app.name == 'galaxy':
repository_id = self.app.security.decode_id( self.repository_id )
@@ -1097,7 +1051,7 @@ class Tool( object, Dictifiable ):
return self.code_namespace[name]
return None
def visit_inputs( self, value, callback ):
def visit_inputs( self, values, callback ):
"""
Call the function `callback` on each parameter of this tool. Visits
grouping parameters recursively and constructs unique prefixes for
@@ -1106,13 +1060,8 @@ class Tool( object, Dictifiable ):
`callback( level_prefix, parameter, parameter_value )`
"""
# HACK: Yet another hack around check_values -- WHY HERE?
if not self.check_values:
return
for input in self.inputs.itervalues():
if isinstance( input, ToolParameter ):
callback( "", input, value[input.name] )
else:
input.visit_inputs( "", value[input.name], callback )
if self.check_values:
visit_input_values( self.inputs, values, callback )
def handle_input( self, trans, incoming, history=None ):
"""
@@ -1280,87 +1229,24 @@ class Tool( object, Dictifiable ):
"""
messages = {}
request_context = WorkRequestContext( app=trans.app, user=trans.user, history=trans.history, workflow_building_mode=workflow_building_mode )
self.check_and_update_param_values_helper( self.inputs, values, request_context, messages, update_values=update_values )
return messages
def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True ):
"""
Recursive helper for `check_and_update_param_values_helper`
"""
context = ExpressionContext( values, context )
for input in inputs.itervalues():
# No value, insert the default
if input.name not in values:
if isinstance( input, Conditional ):
cond_messages = {}
if not input.is_job_resource_conditional:
cond_messages = { input.test_param.name: "No value found for '%s%s', using default" % ( prefix, input.test_param.label ) }
messages[ input.name ] = cond_messages
test_value = input.test_param.get_initial_value( trans, context )
current_case = input.get_current_case( test_value )
self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, cond_messages, context, prefix, update_values=update_values )
elif isinstance( input, Repeat ):
if input.min:
messages[ input.name ] = []
for i in range( input.min ):
rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 )
rep_dict = dict()
messages[ input.name ].append( rep_dict )
self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, update_values=update_values )
elif isinstance( input, Section ):
messages[ input.name ] = {}
self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix, update_values=update_values )
else:
messages[ input.name ] = "No value found for '%s%s', using default" % ( prefix, input.label )
values[ input.name ] = input.get_initial_value( trans, context )
# Value, visit recursively as usual
else:
if isinstance( input, Repeat ):
for i, d in enumerate( values[ input.name ] ):
rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 )
self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix, update_values=update_values )
elif isinstance( input, Conditional ):
group_values = values[ input.name ]
use_initial_value = False
if '__current_case__' in group_values:
if int( group_values[ '__current_case__' ] ) >= len( input.cases ):
use_initial_value = True
else:
use_initial_value = True
if input.test_param.name not in group_values or use_initial_value:
# No test param invalidates the whole conditional
values[ input.name ] = group_values = input.get_initial_value( trans, context )
messages[ input.test_param.name ] = "No value found for '%s%s', using default" % ( prefix, input.test_param.label )
current_case = group_values[ '__current_case__' ]
for child_input in input.cases[current_case].inputs.itervalues():
messages[ child_input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, child_input.label )
else:
current = group_values[ '__current_case__' ]
self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, update_values=update_values )
elif isinstance( input, Section ):
messages[ input.name ] = {}
self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix, update_values=update_values )
else:
# Regular tool parameter, no recursion needed
def validate_inputs( input, value, error, parent, context, prefixed_name, prefixed_label, **kwargs ):
if not error:
value, error = check_param( request_context, input, value, context )
if error:
if update_values:
try:
value = values[ input.name ]
if not trans.workflow_building_mode:
input.value_from_basic( input.value_to_basic( value, trans.app ), trans.app, ignore_errors=False )
input.validate( value, trans )
else:
# skip check if is workflow parameters
ck_param = True
search = input.type in [ 'text' ]
if trans.workflow_building_mode and contains_workflow_parameter( values[ input.name ], search=search ):
ck_param = False
# this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input
if ck_param:
input.value_from_basic( input.value_to_basic( value, self.app ), self.app, ignore_errors=False )
value = input.get_initial_value( request_context, context )
if not prefixed_name.startswith( '__' ):
messages[ prefixed_name ] = '%s Using default: \'%s\'.' % ( error, value )
parent[ input.name ] = value
except:
log.info( "Parameter validation failed.", exc_info=True )
messages[ input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, input.label )
if update_values:
values[ input.name ] = input.get_initial_value( trans, context )
messages[ prefixed_name ] = 'Attempt to replace invalid value for \'%s\' failed.' % ( prefixed_label )
else:
messages[ prefixed_name ] = error
visit_input_values( self.inputs, values, validate_inputs )
return messages
def build_dependency_shell_commands( self, job_directory=None ):
"""Return a list of commands to be run to populate the current environment to include this tools requirements."""
@@ -1540,7 +1426,7 @@ class Tool( object, Dictifiable ):
return output_collect.collect_dynamic_collections( self, output, **kwds )
def to_archive(self):
tool = self.tool
tool = self
tarball_files = []
temp_files = []
tool_xml = open( os.path.abspath( tool.config_file ), 'r' ).read()
@@ -1703,10 +1589,11 @@ class Tool( object, Dictifiable ):
# load job parameters into incoming
tool_message = ''
tool_warnings = ''
if job:
try:
job_params = job.get_param_values( self.app, ignore_errors=True )
self.check_and_update_param_values( job_params, request_context, update_values=False )
tool_warnings = self.check_and_update_param_values( job_params, request_context, update_values=False )
self._map_source_to_history( request_context, self.inputs, job_params )
tool_message = self._compare_tool_version( job )
params_to_incoming( kwd, self.inputs, job_params, self.app )
@@ -1716,68 +1603,6 @@ class Tool( object, Dictifiable ):
# create parameter object
params = galaxy.util.Params( kwd, sanitize=False )
# convert value to jsonifiable value
def jsonify(v):
# check if value is numeric
isnumber = False
try:
float(v)
isnumber = True
except Exception:
pass
# fix hda parsing
if isinstance(v, self.app.model.HistoryDatasetAssociation):
return {
'id' : trans.security.encode_id(v.id),
'src' : 'hda'
}
elif isinstance(v, self.app.model.HistoryDatasetCollectionAssociation):
return {
'id' : trans.security.encode_id(v.id),
'src' : 'hdca'
}
elif isinstance(v, self.app.model.LibraryDatasetDatasetAssociation):
return {
'id' : trans.security.encode_id(v.id),
'name': v.name,
'src' : 'ldda'
}
elif isinstance(v, bool):
if v is True:
return 'true'
else:
return 'false'
elif isinstance(v, string_types) or isnumber:
return v
elif isinstance(v, dict) and hasattr(v, '__class__'):
return v
else:
return None
# ensures that input dictionary is jsonifiable
def sanitize( dict, key='value' ):
# get current value
value = dict[key] if key in dict else None
# jsonify by type
if dict['type'] in ['data']:
if isinstance(value, list):
value = [ jsonify(v) for v in value ]
else:
value = [ jsonify(value) ]
if None in value:
value = None
else:
value = { 'values': value }
elif isinstance(value, list):
value = [ jsonify(v) for v in value ]
else:
value = jsonify(value)
# update and return
dict[key] = value
# populates model from state
def populate_model( inputs, state_inputs, group_inputs, other_values=None ):
other_values = ExpressionContext( state_inputs, other_values )
@@ -1794,7 +1619,7 @@ class Tool( object, Dictifiable ):
tool_dict = input.to_dict( request_context )
if 'test_param' in tool_dict:
test_param = tool_dict[ 'test_param' ]
test_param[ 'value' ] = jsonify( group_state.get( test_param[ 'name' ], input.test_param.get_initial_value( request_context, other_values ) ) )
test_param[ 'value' ] = input.test_param.value_to_basic( group_state.get( test_param[ 'name' ], input.test_param.get_initial_value( request_context, other_values ) ), self.app )
test_param[ 'text_value' ] = input.test_param.value_to_display_text( test_param[ 'value' ], self.app )
for i in range( len( tool_dict['cases'] ) ):
current_state = {}
@@ -1807,29 +1632,14 @@ class Tool( object, Dictifiable ):
else:
try:
tool_dict = input.to_dict( request_context, other_values=other_values )
tool_dict[ 'value' ] = state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) )
tool_dict[ 'value' ] = input.value_to_basic( state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) ), self.app )
tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], self.app )
except Exception as e:
tool_dict = input.to_dict( request_context )
log.exception('tools::to_json() - Skipping parameter expansion \'%s\': %s.' % ( input.name, e ) )
pass
tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], self.app )
sanitize( tool_dict, 'value' )
group_inputs[ input_index ] = tool_dict
# sanatizes tool state
def sanitize_state( state ):
keys = None
if isinstance( state, dict ):
keys = state
elif isinstance( state, list ):
keys = range( len( state ) )
if keys:
for k in keys:
if isinstance( state[ k ], dict ) or isinstance( state[ k ], list ):
sanitize_state( state[ k ] )
else:
state[ k ] = jsonify( state[ k ] )
# expand incoming parameters (parameters might trigger multiple tool executions,
# here we select the first execution only in order to resolve dynamic parameters)
expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ )
@@ -1850,7 +1660,10 @@ class Tool( object, Dictifiable ):
populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] )
# sanitize tool state
sanitize_state( state_inputs )
def value_to_basic( input, value, parent, **kwargs ):
parent[ input.name ] = input.value_to_basic( value, self.app )
visit_input_values( self.inputs, state_inputs, value_to_basic )
# create tool help
tool_help = ''
@@ -1873,6 +1686,7 @@ class Tool( object, Dictifiable ):
'biostar_url' : self.app.config.biostar_url,
'sharable_url' : self.tool_shed_repository.get_sharable_url( self.app ) if self.tool_shed_repository else None,
'message' : tool_message,
'warnings' : tool_warnings,
'versions' : tool_versions,
'requirements' : [ { 'name' : r.name, 'version' : r.version } for r in self.requirements ],
'errors' : state_errors,
lib/galaxy/tools/actions/__init__.py
+21 -15
View File
@@ -1,15 +1,16 @@
import json
import re
from json import dumps
from six import string_types
from galaxy import model
from galaxy.exceptions import ObjectInvalid
from galaxy.model import LibraryDatasetDatasetAssociation
from galaxy import model
from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter
from galaxy.tools.parameters.wrapped import WrappedParameters
from galaxy.tools.parameters import update_param
from galaxy.util import ExecutionTimer
from galaxy.util.json import dumps
from galaxy.util.none_like import NoneDataset
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
@@ -50,7 +51,7 @@ class DefaultToolAction( object ):
current_user_roles = trans.get_current_user_roles()
input_datasets = odict()
def visitor( prefix, input, value, parent=None ):
def visitor( input, value, prefix, parent=None, **kwargs ):
def process_dataset( data, formats=None ):
if not data:
@@ -98,12 +99,12 @@ class DefaultToolAction( object ):
else:
raise Exception('A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) )
if parent:
parent[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ]
parent[ input.name ][ i ] = input_datasets[ prefix + input.name + str( i + 1 ) ]
for conversion_name, conversion_data in conversions:
# allow explicit conversion to be stored in job_parameter table
parent[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired
parent[ conversion_name ][ i ] = conversion_data.id # a more robust way to determine JSONable value is desired
else:
param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ]
param_values[ input.name ][ i ] = input_datasets[ prefix + input.name + str( i + 1 ) ]
for conversion_name, conversion_data in conversions:
# allow explicit conversion to be stored in job_parameter table
param_values[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired
@@ -143,10 +144,6 @@ class DefaultToolAction( object ):
# Skipping implicit conversion stuff for now, revisit at
# some point and figure out if implicitly converting a
# dataset collection makes senese.
# if i == 0:
# # Allow copying metadata to output, first item will be source.
# input_datasets[ prefix + input.name ] = data.dataset_instance
input_datasets[ prefix + input.name + str( i + 1 ) ] = data
tool.visit_inputs( param_values, visitor )
@@ -160,7 +157,7 @@ class DefaultToolAction( object ):
input_dataset_collections = dict()
def visitor( prefix, input, value, parent=None ):
def visitor( input, value, prefix, parent=None, **kwargs ):
if isinstance( input, DataToolParameter ):
values = value
if not isinstance( values, list ):
@@ -322,7 +319,7 @@ class DefaultToolAction( object ):
metadata_source = output.metadata_source
if metadata_source:
if isinstance( metadata_source, string_types ):
metadata_source = inp_data[metadata_source]
metadata_source = inp_data.get( metadata_source )
if metadata_source is not None:
data.init_meta( copy_from=metadata_source )
@@ -440,8 +437,9 @@ class DefaultToolAction( object ):
else:
handle_output_timer = ExecutionTimer()
handle_output( name, output )
log.info("Handled output %s" % handle_output_timer)
log.info("Handled output named %s for tool %s %s" % (name, tool.id, handle_output_timer))
add_datasets_timer = ExecutionTimer()
# Add all the top-level (non-child) datasets to the history unless otherwise specified
datasets_to_persist = []
for name in out_data.keys():
@@ -464,6 +462,8 @@ class DefaultToolAction( object ):
child_dataset = out_data[ child_name ]
parent_dataset.children.append( child_dataset )
log.info("Added output datasets to history %s" % add_datasets_timer)
job_setup_timer = ExecutionTimer()
# Create the job object
job, galaxy_session = self._new_job_for_session( trans, tool, history )
self._record_inputs( trans, tool, job, incoming, inp_data, inp_dataset_collections, current_user_roles )
@@ -512,7 +512,12 @@ class DefaultToolAction( object ):
trans.sa_session.add(jtod)
except Exception:
log.exception('Cannot remap rerun dependencies.')
log.info("Setup for job %s complete, ready to flush %s" % (job.log_str(), job_setup_timer))
job_flush_timer = ExecutionTimer()
trans.sa_session.flush()
log.info("Flushed transaction for job %s %s" % (job.log_str(), job_flush_timer))
# Some tools are not really executable, but jobs are still created for them ( for record keeping ).
# Examples include tools that redirect to other applications ( epigraph ). These special tools must
# include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job
@@ -571,7 +576,7 @@ class DefaultToolAction( object ):
first_reduction = False
incoming[ name ] = []
if reduced:
incoming[ name ].append( "__collection_reduce__|%s" % dataset_collection.id )
incoming[ name ].append( dataset_collection )
# Should verify security? We check security of individual
# datasets below?
# TODO: verify can have multiple with same name, don't want to loose tracability
@@ -600,7 +605,8 @@ class DefaultToolAction( object ):
job.add_input_dataset( name, dataset_id=dataset.id )
else:
job.add_input_dataset( name, None )
log.info("Verified access to datasets %s" % access_timer)
job_str = job.log_str()
log.info("Verified access to datasets for %s %s" % (job_str, access_timer))
def get_output_name( self, output, dataset, tool, on_text, trans, incoming, history, params, job_params ):
if output.label:
lib/galaxy/tools/actions/metadata.py
+2 -2
View File
@@ -1,10 +1,10 @@
import logging
from json import dumps
from __init__ import ToolAction
from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
from galaxy.util.odict import odict
from galaxy.util.json import dumps
from galaxy.jobs.datasets import DatasetPath
from galaxy.util.odict import odict
log = logging.getLogger( __name__ )
lib/galaxy/tools/actions/upload_common.py
+4 -4
View File
@@ -1,18 +1,18 @@
import pwd
import logging
import os
import pwd
import StringIO
import subprocess
import tempfile
from cgi import FieldStorage
from json import dumps
from sqlalchemy.orm import eagerload_all
from galaxy import datatypes, util
from galaxy.util.odict import odict
from galaxy.util.json import dumps
from galaxy.exceptions import ObjectInvalid
from galaxy.util.odict import odict
import logging
log = logging.getLogger( __name__ )
lib/galaxy/tools/evaluation.py
+1 -1
View File
@@ -58,7 +58,7 @@ class ToolEvaluator( object ):
request_context = WorkRequestContext( app=self.app, user=job.history and job.history.user, history=job.history )
def validate_inputs( input, value, context, **kwargs ):
value = input.from_html( value, request_context, context )
value = input.from_json( value, request_context, context )
input.validate( value, request_context )
visit_input_values( self.tool.inputs, incoming, validate_inputs )
lib/galaxy/tools/execute.py
+3 -12
View File
@@ -34,16 +34,6 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None,
# Only workflow invocation code gets to set this, ignore user supplied
# values or rerun parameters.
del params[ '__workflow_invocation_uuid__' ]
# If this is a workflow, everything has now been connected so we should validate
# the state we about to execute one last time. Consider whether tool executions
# should run this as well.
if workflow_invocation_uuid:
messages = tool.check_and_update_param_values( params, trans, update_values=False )
if messages:
execution_tracker.record_error( messages )
return
job, result = tool.handle_single_execution( trans, rerun_remap_job_id, params, history, collection_info, execution_cache )
if job:
message = EXECUTION_SUCCESS_MESSAGE % (tool.id, job.id, job_timer)
@@ -56,7 +46,8 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None,
burst_at = getattr( config, 'tool_submission_burst_at', 10 )
burst_threads = getattr( config, 'tool_submission_burst_threads', 1 )
if len(execution_tracker.param_combinations) < burst_at or burst_threads < 2:
job_count = len(execution_tracker.param_combinations)
if job_count < burst_at or burst_threads < 2:
for params in execution_tracker.param_combinations:
execute_single_job(params)
else:
@@ -78,7 +69,7 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None,
q.join()
log.debug("Executed all jobs for tool request: %s" % all_jobs_timer)
log.debug("Executed %d job(s) for tool %s request: %s" % (job_count, tool.id, all_jobs_timer))
if collection_info:
history = history or tool.get_default_history_by_trans( trans )
execution_tracker.create_output_collections( trans, history, params )
lib/galaxy/tools/imp_exp/__init__.py
+2 -3
View File
@@ -4,17 +4,16 @@ import logging
import os
import shutil
import tempfile
from json import dumps, loads
from sqlalchemy.orm import eagerload, eagerload_all
from sqlalchemy.sql import expression
from galaxy import model
from galaxy.exceptions import MalformedContents
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.json import dumps, loads
from galaxy.web.framework.helpers import to_unicode
from sqlalchemy.sql import expression
log = logging.getLogger(__name__)

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