From 71a4e31262319f8a6c2754d1fa99f3be05aeb3fa Mon Sep 17 00:00:00 2001 From: charz Date: Tue, 27 Jan 2015 06:17:30 +0000 Subject: [PATCH 1/8] Fix type of in_secure(should be boolean, not string). --- lib/galaxy/objectstore/s3.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) --- lib/galaxy/objectstore/s3.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index a6b97ab4668..dcbded50d3a 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -84,7 +84,8 @@ class S3ObjectStore(ObjectStore): cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.is_secure = cn_xml.get('is_secure', True) + self.is_secure = {'true': True, + 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) From 63939a72db04e2c1075aa1c70d43eda1ada74554 Mon Sep 17 00:00:00 2001 From: charz Date: Tue, 27 Jan 2015 06:17:45 +0000 Subject: [PATCH 2/8] Fixed cannot use multipart-upload for 'swift' backend with swift3 middleware. Add two options('multipart' and 'max_chunk_size'). --- config/object_store_conf.xml.sample | 4 +-- lib/galaxy/objectstore/s3.py | 22 ++++++++++++++--- lib/galaxy/objectstore/s3_multipart_upload.py | 33 +++++++++++++++++-------- 3 files changed, 44 insertions(+), 15 deletions(-) --- config/object_store_conf.xml.sample | 4 +-- lib/galaxy/objectstore/s3.py | 22 +++++++++++-- lib/galaxy/objectstore/s3_multipart_upload.py | 33 +++++++++++++------ 3 files changed, 44 insertions(+), 15 deletions(-) diff --git a/config/object_store_conf.xml.sample b/config/object_store_conf.xml.sample index b0964e1d4d7..fc8025109b2 100644 --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -24,8 +24,8 @@ - - + + diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index dcbded50d3a..6a894c036c5 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -76,7 +76,9 @@ class S3ObjectStore(ObjectStore): self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr = b_xml.get('use_reduced_redundancy', False) + self.use_rr= {'true': True, + 'false': False}.get(b_xml.get('use_reduced_redundancy', 'False').lower()) + self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: cn_xml = {} @@ -84,12 +86,26 @@ class S3ObjectStore(ObjectStore): cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) + self.multipart = {'true': True, + 'false': False}.get(cn_xml.get('multipart', 'True').lower()) self.is_secure = {'true': True, 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) self.cache_path = c_xml.get('path') + + # for multipart upload + self.s3server = {'access_key': self.access_key, + 'secret_key': self.secret_key, + 'is_secure': self.is_secure, + 'max_chunk_size': self.max_chunk_size, + 'host': self.host, + 'port': self.port, + 'use_rr': self.use_rr, + 'conn_path': self.conn_path} + + except Exception: # Toss it back up after logging, we can't continue loading at this point. log.exception("Malformed ObjectStore Configuration XML -- unable to continue") @@ -329,14 +345,14 @@ class S3ObjectStore(ObjectStore): start_time = datetime.now() log.debug("Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)) mb_size = os.path.getsize(source_file) / 1e6 - if mb_size < 10 or type(self) == SwiftObjectStore: + if mb_size < 10 or (not self.multipart): self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: - multipart_upload(self.bucket, key.name, source_file, mb_size, self.access_key, self.secret_key, use_rr=self.use_rr) + multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size) end_time = datetime.now() log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py index 236996cfcb9..623fdc8e439 100644 --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -34,13 +34,23 @@ def map_wrap(f): return wrapper -def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key): +def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): """Get the multipart upload from the bucket and multipart IDs. This allows us to reconstitute a connection to the upload from within multiprocessing functions. """ - conn = S3Connection(aws_access_key_id, aws_secret_access_key) + if s3server['host']: + conn = boto.connect_s3(aws_access_key_id=s3server['access_key'], + aws_secret_access_key=s3server['secret_key'], + is_secure=s3server['is_secure'], + host=s3server['host'], + port=s3server['port'], + calling_format=boto.s3.connection.OrdinaryCallingFormat(), + path=s3server['conn_path']) + else: + conn = S3Connection(s3server['access_key'], s3server['secret_key']) + bucket = conn.lookup(mp_bucketname) mp = boto.s3.multipart.MultiPartUpload(bucket) mp.key_name = mp_keyname @@ -49,33 +59,36 @@ def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_ @map_wrap -def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, aws_access_key_id, aws_secret_access_key): +def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): """Transfer a part of a multipart upload. Designed to be run in parallel. """ - mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key) + mp = mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname) with open(part) as t_handle: mp.upload_part_from_file(t_handle, i + 1) os.remove(part) -def multipart_upload(bucket, s3_key_name, tarball, mb_size, aws_access_key_id, aws_secret_access_key, use_rr=True): +def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() def split_file(in_file, mb_size, split_num=5): prefix = os.path.join(os.path.dirname(in_file), - "%sS3PART" % (os.path.basename(s3_key_name))) - # Split chunks so they are 5MB < chunk < 250MB - split_size = int(max(min(mb_size / (split_num * 2.0), 250), 5)) + "%sS3PART" % (os.path.basename(s3_key_name))) + max_chunk = s3server['max_chunk_size'] + # Split chunks so they are 5MB < chunk < 250MB(max_chunk_size) + split_size = int(max(min(mb_size / (split_num * 2.0), max_chunk), 5)) if not os.path.exists("%saa" % prefix): cl = ["split", "-b%sm" % split_size, in_file, prefix] subprocess.check_call(cl) return sorted(glob.glob("%s*" % prefix)) - mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr) + mp = bucket.initiate_multipart_upload(s3_key_name, + reduced_redundancy=s3server['use_rr']) + with multimap(cores) as pmap: - for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part, aws_access_key_id, aws_secret_access_key) + for _ in pmap(transfer_part, ((s3server, mp.id, mp.key_name, mp.bucket_name, i, part) for (i, part) in enumerate(split_file(tarball, mb_size, cores)))): pass From b9f24a7ec08c70b1fa018d07665daee46808cc50 Mon Sep 17 00:00:00 2001 From: charz Date: Tue, 27 Jan 2015 15:13:55 +0000 Subject: [PATCH 3/8] Use string_as_bool(). --- lib/galaxy/objectstore/s3.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) --- lib/galaxy/objectstore/s3.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py index 6a894c036c5..9ed1d6874da 100644 --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -14,6 +14,7 @@ from datetime import datetime from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms +from galaxy.util import string_as_bool from galaxy.util.directory_hash import directory_hash_id from galaxy.util.sleeper import Sleeper from .s3_multipart_upload import multipart_upload @@ -76,8 +77,7 @@ class S3ObjectStore(ObjectStore): self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr= {'true': True, - 'false': False}.get(b_xml.get('use_reduced_redundancy', 'False').lower()) + self.use_rr= string_as_bool(b_xml.get('use_reduced_redundancy', 'False')) self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: @@ -86,10 +86,8 @@ class S3ObjectStore(ObjectStore): cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.multipart = {'true': True, - 'false': False}.get(cn_xml.get('multipart', 'True').lower()) - self.is_secure = {'true': True, - 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) + self.multipart = string_as_bool(cn_xml.get('multipart', 'True')) + self.is_secure = string_as_bool(cn_xml.get('is_secure', 'True')) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) From eed33430d7121a4843358a965c2991e19787a68c Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Mon, 9 Feb 2015 17:40:53 -0500 Subject: [PATCH 4/8] UI, Paired collection creator: when dragging within the paired section autoscroll the list when the mouse is within 'autoscrollDist' pixels of the top or bottom --- .../collection/paired-collection-creator.js | 28 +++++++++++++++---- .../collection/paired-collection-creator.js | 28 +++++++++++++++---- .../collection/paired-collection-creator.js | 2 +- templates/webapps/galaxy/root/index.mako | 6 ++++ 4 files changed, 51 insertions(+), 13 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js index 7835974882d..e1db7dba787 100644 --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -150,6 +150,9 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** fn to call when the collection is created (scoped to this) */ this.oncreate = attributes.oncreate; + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ + this.autoscrollDist = attributes.autoscrollDist || 24; + /** is the unpaired panel shown? */ this.unpairedPanelHidden = false; /** is the paired panel shown? */ @@ -1025,7 +1028,6 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ - console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1340,27 +1342,41 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte //console.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); - var $list = this.$( '.paired-columns .column-datasets' ), - offset = $list.offset(); + var $list = this.$( '.paired-columns .column-datasets' ); + this._checkForAutoscroll( $list, ev.originalEvent.clientY ); //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX - offset.left, ev.originalEvent.clientY - offset.top ); $( '.paired-drop-placeholder' ).remove(); - var $placeholder = $( '
') + var $placeholder = $( '
' ); if( !$nearest.size() ){ $list.append( $placeholder ); } else { $nearest.before( $placeholder ); } }, + + /** If the mouse is near enough to the list's top or bottom, scroll the list */ + _checkForAutoscroll : function( $element, y ){ + var AUTOSCROLL_SPEED = 2; + var offset = $element.offset(), + scrollTop = $element.scrollTop(), + upperDist = y - offset.top, + lowerDist = ( offset.top + $element.outerHeight() ) - y; + //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + if( upperDist >= 0 && upperDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); + } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop + AUTOSCROLL_SPEED ); + } + }, + /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate. * If the y is at the end of the list, return an empty jQuery object. */ _getNearestPairedDatasetLi : function( y ){ var WIGGLE = 4, lis = this.$( '.paired-columns .column-datasets li' ).toArray(); -//TODO: better way? for( var i=0; i') + var $placeholder = $( '
' ); if( !$nearest.size() ){ $list.append( $placeholder ); } else { $nearest.before( $placeholder ); } }, + + /** If the mouse is near enough to the list's top or bottom, scroll the list */ + _checkForAutoscroll : function( $element, y ){ + var AUTOSCROLL_SPEED = 2; + var offset = $element.offset(), + scrollTop = $element.scrollTop(), + upperDist = y - offset.top, + lowerDist = ( offset.top + $element.outerHeight() ) - y; + //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + if( upperDist >= 0 && upperDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); + } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop + AUTOSCROLL_SPEED ); + } + }, + /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate. * If the y is at the end of the list, return an empty jQuery object. */ _getNearestPairedDatasetLi : function( y ){ var WIGGLE = 4, lis = this.$( '.paired-columns .column-datasets li' ).toArray(); -//TODO: better way? for( var i=0; i<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(np){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="
"+JSON.stringify(k.responseJSON)+"
"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("
  • ").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("
  • ").addClass("dataset unpaired").append($("").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('
    ').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('
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h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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.remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter 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h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(i,k.originalEvent.clientY);var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('
            ');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i=0&&jo&&m-h",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['
            ','
            ','
            '].join("")),header:_.template(['
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            ','',d("Less"),"","
            ","
            ",'
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                    ",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"

                    ","

                    ",d(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"

                      To pair datasets, you can:","
                    • Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
                      • ",'
                    • Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
                      • ",'
                    • Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
                      • ","
                    "].join("")),"

                    ","

                    ",d(["

                      You can filter what is shown in the unpaired sections by:","
                    • Entering partial dataset names in either the ",'forward filter or ','reverse filter.',"
                      • ","
                    • Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
                      • ","
                    • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
                      • ","
                    • Clearing the filters by clicking the ",'"Clear filters" link.',"
                      • ","
                    "].join("")),"

                    ","

                    ",d(["To unpair individual dataset pairs, click the ",'unpair buttons ( ). ','Click the "Unpair all" link to unpair all pairs.'].join("")),"

                    ","

                    ",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"

                    ","

                    ",d(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

                    "].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file diff --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako index d4514e7c125..21f10d14a16 100644 --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,6 +152,12 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; + +currPanel.once( 'rendered', function(){ + currPanel.showSelectors(); + currPanel.selectAll(); + _.last( currPanel.actionsPopup.options ).func(); +}); }); }); From f3aadb7e03a0c889422f3084c9b5ada278f02b35 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Mon, 9 Feb 2015 17:42:13 -0500 Subject: [PATCH 5/8] Fix to 389f0dcc1589: remove debugging code in index.mako --- templates/webapps/galaxy/root/index.mako | 6 ------ 1 file changed, 6 deletions(-) diff --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako index 21f10d14a16..d4514e7c125 100644 --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,12 +152,6 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; - -currPanel.once( 'rendered', function(){ - currPanel.showSelectors(); - currPanel.selectAll(); - _.last( currPanel.actionsPopup.options ).func(); -}); }); }); From 89d76ae9290eb72a7b2963e699e5f5423dfab406 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Mon, 9 Feb 2015 17:47:30 -0500 Subject: [PATCH 6/8] UI: remove unused LazyDataLoader module --- client/galaxy/scripts/utils/LazyDataLoader.js | 228 ------------------ static/scripts/packed/utils/LazyDataLoader.js | 1 - static/scripts/utils/LazyDataLoader.js | 228 ------------------ 3 files changed, 457 deletions(-) delete mode 100644 client/galaxy/scripts/utils/LazyDataLoader.js delete mode 100644 static/scripts/packed/utils/LazyDataLoader.js delete mode 100644 static/scripts/utils/LazyDataLoader.js diff --git a/client/galaxy/scripts/utils/LazyDataLoader.js b/client/galaxy/scripts/utils/LazyDataLoader.js deleted file mode 100644 index fafb3062090..00000000000 --- a/client/galaxy/scripts/utils/LazyDataLoader.js +++ /dev/null @@ -1,228 +0,0 @@ -//============================================================================== -/* -TODO: - ?? superclass dataloader, subclass lazydataloader?? - -*/ -//============================================================================== -/** - * Object to progressively load JSON data from a REST url, delaying some time between loading chunks - * - * Will load size amount of data every delay ms, starting at start and ending at total. - * - * NOTE: Data from ajax loading is aggregated in a list, with one element for each ajax response. - * It's up to the calling code to combine the results in a meaningful, correct way. - * - * example: - * var loader = new scatterplot.LazyDataLoader({ - * //logger : console, - * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' - * + '&columns=[10,14]' ), - * total : hda.metadata_data_lines, - * size : 500, - * - * initialize : function( config ){ - * // ... do some stuff - * }, - * - * buildUrl : function( start, size ){ - * // change the formation of start, size in query string - * return loader.url + '&' + jQuery.param({ - * start_val: start, - * max_vals: size - * }); - * }, - * }); - * - * // you can use events - * $( loader ).bind( 'error', function( event, xhr, status, error ){ - * alert( loader + ' ERROR:' + status + '\n' + error ); - * // bail out... - * }); - * $( loader ).bind( 'loaded.new', function( event, response ){ - * console.info( 'new data available:', event, response ); - * // ... do stuff with new data - * }); - * $( loader ).bind( 'complete', function( event, allDataArray, total ){ - * console.info( 'final load complete:', event, allDataArray, total ); - * // ... do stuff with all data - * }); - * - * // ...or use a callback called when all data is loaded - * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); - */ -function LazyDataLoader( config ){ - // for now assume: - // get, async, and params sent via url query string - // we want json - // we know the size of the data on the server beforehand - var loader = this, - // events to trigger when new or all data has been loaded - // new batches of data (including last). Will be sent: the ajax response data, start value, and size - LOADED_NEW_EVENT = 'loaded.new', - // all data has been loaded: the final loader's data array and the total - LOADED_ALL_EVENT = 'complete'; - // error from ajax - ERROR_EVENT = 'error'; - - jQuery.extend( loader, LoggableMixin ); - jQuery.extend( loader, { - - //NOTE: the next two need to be sent in config (required) - // total size of data on server - total : undefined, - // url of service to get the data - url : undefined, - - // holds the interval id for the current load delay - currentIntervalId : undefined, - - // each load call will add an element to this array - // it's the responsibility of the code using this to combine them properly - data : [], - // ms btwn recursive loads - delay : 4000, - // starting line, element, whatever - start : 0, - // size to fetch per load - size : 4000, - - // loader init func: extends loader with config and calls config.init if there - //@param {object} config : object containing variables to override (or additional) - initialize : function( config ){ - jQuery.extend( loader, config ); - - // call the custom initialize function if any - // only dangerous if the user tries LazyDataLoader.prototype.init - if( config.hasOwnProperty( 'initialize' ) ){ - config.initialize.call( loader, config ); - } - this.log( this + ' initialized:', loader ); - }, - - // returns query string formatted start and size (for the next fetch) appended to the loader.url - //OVERRIDE: to change how params are passed, param names, etc. - //@param {int} start : the line/row/datum indicating where in the dataset the next load begins - //@param {int} size : the number of lines/rows/data to get on the next load - buildUrl : function( start, size ){ - // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params - return this.url + '&' + jQuery.param({ - start_val: start, - max_vals: size - }); - }, - - //OVERRIDE: to handle ajax errors differently - ajaxErrorFn : function( xhr, status, error ){ - console.error( 'ERROR fetching data:', error ); - }, - - // converters passed to the jQuery ajax call for data type parsing - //OVERRIDE: to provide custom parsing - converters : { - '* text' : window.String, - 'text html' : true, - 'text xml' : jQuery.parseXML, - 'text json' : jQuery.parseJSON - }, - - // interface to begin load (and first recursive call) - //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data - load : function( callback ){ - this.log( this + '.load' ); - - // ensure necessary stuff - if( !loader.url ){ throw( loader + ' requires a url' ); } - - if( this.total === null ){ - this.log( '\t total is null (will load all)' ); - } else { - this.log( '\t total:', this.total ); - } - //if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } - - //FIRST RECURSION: start - var startingSize = loader.size; - if( ( loader.total !== null ) && ( loader.total < loader.size ) ){ - startingSize = loader.total; - } - loader.log( loader + '\t beginning recursion' ); - loadHelper( loader.start, startingSize ); - - //FIRST, SUBSEQUENT RECURSION function - function loadHelper( start, size ){ - loader.log( loader + '.loadHelper, start:', start, 'size:', size ); - var url = loader.buildUrl( start, size ); - loader.log( '\t url:', url ); - - jQuery.ajax({ - url : loader.buildUrl( start, size ), - converters : loader.converters, - dataType : 'json', - - error : function( xhr, status, error ){ - loader.log( '\t ajax error, status:', status, 'error:', error ); - if( loader.currentIntervalId ){ - clearInterval( loader.currentIntervalId ); - } - $( loader ).trigger( ERROR_EVENT, [ status, error ] ); - loader.ajaxErrorFn( xhr, status, error ); - }, - - success : function( response ){ - loader.log( '\t ajax success, response:', response, 'next:', next, 'remainder:', remainder ); - - if( response !== null ){ - // store the response as is in a new element - //TODO:?? store start, size as well? - loader.data.push( response ); - - //TODO: these might not be the best way to split this up - // fire the first load event (if this is the first batch) AND partial - $( loader ).trigger( LOADED_NEW_EVENT, [ response, start, size ] ); - - //RECURSION: - var next = start + size, - remainder = loader.size; - - if( loader.total !== null ){ - remainder = Math.min( loader.total - next, loader.size ); - } - loader.log( '\t next recursion, start:', next, 'size:', remainder ); - - // if we haven't gotten everything yet, so set up for next recursive call and set the timer - if( loader.total === null || remainder > 0 ){ - loader.currentIntervalId = setTimeout( - function(){ loadHelper( next, remainder ); }, - loader.delay - ); - loader.log( '\t currentIntervalId:', loader.currentIntervalId ); - - // otherwise (base-case), don't do anything - } else { - loadFinished(); - } - - } else { //response === null --> base-case, server sez nuthin left - loadFinished(); - } - } - }); - } - - //HANDLE BASE-CASE, LAST RECURSION - function loadFinished(){ - loader.log( loader + '.loadHelper, has finished:', loader.data ); - $( loader ).trigger( LOADED_ALL_EVENT, [ loader.data, loader.total ] ); - if( callback ){ callback( loader.data ); } - } - }, - - toString : function(){ return 'LazyDataLoader'; } - }); - - loader.initialize( config ); - return loader; -} - -//============================================================================== diff --git a/static/scripts/packed/utils/LazyDataLoader.js b/static/scripts/packed/utils/LazyDataLoader.js deleted file mode 100644 index 64d16ab9c0f..00000000000 --- a/static/scripts/packed/utils/LazyDataLoader.js +++ /dev/null @@ -1 +0,0 @@ -function LazyDataLoader(c){var a=this,d="loaded.new",b="complete";ERROR_EVENT="error";jQuery.extend(a,LoggableMixin);jQuery.extend(a,{total:undefined,url:undefined,currentIntervalId:undefined,data:[],delay:4000,start:0,size:4000,initialize:function(e){jQuery.extend(a,e);if(e.hasOwnProperty("initialize")){e.initialize.call(a,e)}this.log(this+" initialized:",a)},buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})},ajaxErrorFn:function(g,e,f){console.error("ERROR fetching data:",f)},converters:{"* text":window.String,"text html":true,"text xml":jQuery.parseXML,"text json":jQuery.parseJSON},load:function(h){this.log(this+".load");if(!a.url){throw (a+" requires a url")}if(this.total===null){this.log("\t total is null (will load all)")}else{this.log("\t total:",this.total)}var g=a.size;if((a.total!==null)&&(a.total0){a.currentIntervalId=setTimeout(function(){f(m,n)},a.delay);a.log("\t currentIntervalId:",a.currentIntervalId)}else{e()}}else{e()}}})}function e(){a.log(a+".loadHelper, has finished:",a.data);$(a).trigger(b,[a.data,a.total]);if(h){h(a.data)}}},toString:function(){return"LazyDataLoader"}});a.initialize(c);return a}; \ No newline at end of file diff --git a/static/scripts/utils/LazyDataLoader.js b/static/scripts/utils/LazyDataLoader.js deleted file mode 100644 index fafb3062090..00000000000 --- a/static/scripts/utils/LazyDataLoader.js +++ /dev/null @@ -1,228 +0,0 @@ -//============================================================================== -/* -TODO: - ?? superclass dataloader, subclass lazydataloader?? - -*/ -//============================================================================== -/** - * Object to progressively load JSON data from a REST url, delaying some time between loading chunks - * - * Will load size amount of data every delay ms, starting at start and ending at total. - * - * NOTE: Data from ajax loading is aggregated in a list, with one element for each ajax response. - * It's up to the calling code to combine the results in a meaningful, correct way. - * - * example: - * var loader = new scatterplot.LazyDataLoader({ - * //logger : console, - * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' - * + '&columns=[10,14]' ), - * total : hda.metadata_data_lines, - * size : 500, - * - * initialize : function( config ){ - * // ... do some stuff - * }, - * - * buildUrl : function( start, size ){ - * // change the formation of start, size in query string - * return loader.url + '&' + jQuery.param({ - * start_val: start, - * max_vals: size - * }); - * }, - * }); - * - * // you can use events - * $( loader ).bind( 'error', function( event, xhr, status, error ){ - * alert( loader + ' ERROR:' + status + '\n' + error ); - * // bail out... - * }); - * $( loader ).bind( 'loaded.new', function( event, response ){ - * console.info( 'new data available:', event, response ); - * // ... do stuff with new data - * }); - * $( loader ).bind( 'complete', function( event, allDataArray, total ){ - * console.info( 'final load complete:', event, allDataArray, total ); - * // ... do stuff with all data - * }); - * - * // ...or use a callback called when all data is loaded - * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); - */ -function LazyDataLoader( config ){ - // for now assume: - // get, async, and params sent via url query string - // we want json - // we know the size of the data on the server beforehand - var loader = this, - // events to trigger when new or all data has been loaded - // new batches of data (including last). Will be sent: the ajax response data, start value, and size - LOADED_NEW_EVENT = 'loaded.new', - // all data has been loaded: the final loader's data array and the total - LOADED_ALL_EVENT = 'complete'; - // error from ajax - ERROR_EVENT = 'error'; - - jQuery.extend( loader, LoggableMixin ); - jQuery.extend( loader, { - - //NOTE: the next two need to be sent in config (required) - // total size of data on server - total : undefined, - // url of service to get the data - url : undefined, - - // holds the interval id for the current load delay - currentIntervalId : undefined, - - // each load call will add an element to this array - // it's the responsibility of the code using this to combine them properly - data : [], - // ms btwn recursive loads - delay : 4000, - // starting line, element, whatever - start : 0, - // size to fetch per load - size : 4000, - - // loader init func: extends loader with config and calls config.init if there - //@param {object} config : object containing variables to override (or additional) - initialize : function( config ){ - jQuery.extend( loader, config ); - - // call the custom initialize function if any - // only dangerous if the user tries LazyDataLoader.prototype.init - if( config.hasOwnProperty( 'initialize' ) ){ - config.initialize.call( loader, config ); - } - this.log( this + ' initialized:', loader ); - }, - - // returns query string formatted start and size (for the next fetch) appended to the loader.url - //OVERRIDE: to change how params are passed, param names, etc. - //@param {int} start : the line/row/datum indicating where in the dataset the next load begins - //@param {int} size : the number of lines/rows/data to get on the next load - buildUrl : function( start, size ){ - // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params - return this.url + '&' + jQuery.param({ - start_val: start, - max_vals: size - }); - }, - - //OVERRIDE: to handle ajax errors differently - ajaxErrorFn : function( xhr, status, error ){ - console.error( 'ERROR fetching data:', error ); - }, - - // converters passed to the jQuery ajax call for data type parsing - //OVERRIDE: to provide custom parsing - converters : { - '* text' : window.String, - 'text html' : true, - 'text xml' : jQuery.parseXML, - 'text json' : jQuery.parseJSON - }, - - // interface to begin load (and first recursive call) - //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data - load : function( callback ){ - this.log( this + '.load' ); - - // ensure necessary stuff - if( !loader.url ){ throw( loader + ' requires a url' ); } - - if( this.total === null ){ - this.log( '\t total is null (will load all)' ); - } else { - this.log( '\t total:', this.total ); - } - //if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } - - //FIRST RECURSION: start - var startingSize = loader.size; - if( ( loader.total !== null ) && ( loader.total < loader.size ) ){ - startingSize = loader.total; - } - loader.log( loader + '\t beginning recursion' ); - loadHelper( loader.start, startingSize ); - - //FIRST, SUBSEQUENT RECURSION function - function loadHelper( start, size ){ - loader.log( loader + '.loadHelper, start:', start, 'size:', size ); - var url = loader.buildUrl( start, size ); - loader.log( '\t url:', url ); - - jQuery.ajax({ - url : loader.buildUrl( start, size ), - converters : loader.converters, - dataType : 'json', - - error : function( xhr, status, error ){ - loader.log( '\t ajax error, status:', status, 'error:', error ); - if( loader.currentIntervalId ){ - clearInterval( loader.currentIntervalId ); - } - $( loader ).trigger( ERROR_EVENT, [ status, error ] ); - loader.ajaxErrorFn( xhr, status, error ); - }, - - success : function( response ){ - loader.log( '\t ajax success, response:', response, 'next:', next, 'remainder:', remainder ); - - if( response !== null ){ - // store the response as is in a new element - //TODO:?? store start, size as well? - loader.data.push( response ); - - //TODO: these might not be the best way to split this up - // fire the first load event (if this is the first batch) AND partial - $( loader ).trigger( LOADED_NEW_EVENT, [ response, start, size ] ); - - //RECURSION: - var next = start + size, - remainder = loader.size; - - if( loader.total !== null ){ - remainder = Math.min( loader.total - next, loader.size ); - } - loader.log( '\t next recursion, start:', next, 'size:', remainder ); - - // if we haven't gotten everything yet, so set up for next recursive call and set the timer - if( loader.total === null || remainder > 0 ){ - loader.currentIntervalId = setTimeout( - function(){ loadHelper( next, remainder ); }, - loader.delay - ); - loader.log( '\t currentIntervalId:', loader.currentIntervalId ); - - // otherwise (base-case), don't do anything - } else { - loadFinished(); - } - - } else { //response === null --> base-case, server sez nuthin left - loadFinished(); - } - } - }); - } - - //HANDLE BASE-CASE, LAST RECURSION - function loadFinished(){ - loader.log( loader + '.loadHelper, has finished:', loader.data ); - $( loader ).trigger( LOADED_ALL_EVENT, [ loader.data, loader.total ] ); - if( callback ){ callback( loader.data ); } - } - }, - - toString : function(){ return 'LazyDataLoader'; } - }); - - loader.initialize( config ); - return loader; -} - -//============================================================================== From ed32b63e50411bc26d27edc775d7ebbb28473942 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Mon, 9 Feb 2015 17:54:17 -0500 Subject: [PATCH 7/8] UI, Paired collection creator: fix template function for 'Choose Filters' --- .../galaxy/scripts/mvc/collection/paired-collection-creator.js | 2 +- static/scripts/mvc/collection/paired-collection-creator.js | 2 +- .../scripts/packed/mvc/collection/paired-collection-creator.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js index e1db7dba787..67ff4108bae 100644 --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -876,7 +876,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '
                    ' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', diff --git a/static/scripts/mvc/collection/paired-collection-creator.js b/static/scripts/mvc/collection/paired-collection-creator.js index e1db7dba787..67ff4108bae 100644 --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -876,7 +876,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', diff --git a/static/scripts/packed/mvc/collection/paired-collection-creator.js b/static/scripts/packed/mvc/collection/paired-collection-creator.js index b6fa2189e42..9d79d899363 100644 --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1 +1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(np){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="
                    "+JSON.stringify(k.responseJSON)+"
                    "}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("
                  1. ").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("
                  2. ").addClass("dataset unpaired").append($("").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('
                    ').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('
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                            ",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"

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                              You can filter what is shown in the unpaired sections by:","
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                            ",d(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

                            "].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var 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e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(np){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: 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j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="
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                            ').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['"].join("")}var j=$(_.template(['
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.alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column 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                            ');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i=0&&jo&&m-h",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['
                            ','
                            ','
                            '].join("")),header:_.template(['
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                                    ",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"

                                    ","

                                    ",d(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"

                                      To pair datasets, you can:","
                                    • Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
                                      • ",'
                                    • Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
                                      • ",'
                                    • Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
                                      • ","
                                    "].join("")),"

                                    ","

                                    ",d(["

                                      You can filter what is shown in the unpaired sections by:","
                                    • Entering partial dataset names in either the ",'forward filter or ','reverse filter.',"
                                      • ","
                                    • Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
                                      • ","
                                    • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
                                      • ","
                                    • Clearing the filters by clicking the ",'"Clear filters" link.',"
                                      • ","
                                    "].join("")),"

                                    ","

                                    ",d(["To unpair individual dataset pairs, click the ",'unpair buttons ( ). ','Click the "Unpair all" link to unpair all pairs.'].join("")),"

                                    ","

                                    ",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"

                                    ","

                                    ",d(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

                                    "].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file From 456a14d9dfc34a34057c8799223ab07be73e0c68 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Mon, 9 Feb 2015 18:09:27 -0500 Subject: [PATCH 8/8] UI, Paired collection creator: use scoped version of $.index instead of clumsy calculation --- .../mvc/collection/paired-collection-creator.js | 10 ++++++---- .../mvc/collection/paired-collection-creator.js | 10 ++++++---- .../packed/mvc/collection/paired-collection-creator.js | 2 +- 3 files changed, 13 insertions(+), 9 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js index 67ff4108bae..73858c41db9 100644 --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -1307,8 +1307,10 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** rename a pair when the pair name is clicked */ _clickPairName : function( ev ){ ev.stopPropagation(); - var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().parent().index() / 2 ], + var $name = $( ev.currentTarget ), + $pair = $name.parent().parent(), + index = $pair.index( '.dataset.paired' ), + pair = this.paired[ index ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; @@ -1316,7 +1318,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1324,7 +1326,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } //TODO: this is a hack bc each paired rev now has two elems (dataset, button) - var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 ); + var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); //TODO: animate this._unpair( this.paired[ pairIndex ] ); diff --git a/static/scripts/mvc/collection/paired-collection-creator.js b/static/scripts/mvc/collection/paired-collection-creator.js index 67ff4108bae..73858c41db9 100644 --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1307,8 +1307,10 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** rename a pair when the pair name is clicked */ _clickPairName : function( ev ){ ev.stopPropagation(); - var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().parent().index() / 2 ], + var $name = $( ev.currentTarget ), + $pair = $name.parent().parent(), + index = $pair.index( '.dataset.paired' ), + pair = this.paired[ index ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; @@ -1316,7 +1318,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1324,7 +1326,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } //TODO: this is a hack bc each paired rev now has two elems (dataset, button) - var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 ); + var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); //TODO: animate this._unpair( this.paired[ pairIndex ] ); diff --git a/static/scripts/packed/mvc/collection/paired-collection-creator.js b/static/scripts/packed/mvc/collection/paired-collection-creator.js index 9d79d899363..31749738726 100644 --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1 +1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return 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j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="
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                                            ",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"

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                                            ",d(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"

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                                              You can filter what is shown in the unpaired sections by:","
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f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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                                                    ",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"

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                                                      To pair datasets, you can:","
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                                                    • Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
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                                                    • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
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