[galaxy-commits] commit/galaxy-central: 4 new changesets

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bbdf4a2c3f56/ Changeset: bbdf4a2c3f56 User: dannon Date: 2015-02-09 22:37:16+00:00 Summary: Update objectstore sample to supply better defaults (and not host/port, which are unnecessary for s3). Affected #: 1 file diff -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e -r bbdf4a2c3f56e1e2fe6142803e170b8868883c33 config/object_store_conf.xml.sample --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -24,9 +24,8 @@ <object_store type="s3"><auth access_key="...." secret_key="....." /> - <bucket name="unique_bucket_name" use_reduced_redundancy="False" /> - <connection host="" port="" is_secure="" conn_path="" /> - <cache path="database/files/" size="100" /> + <bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" /> + <cache path="database/files/" size="1000" /></object_store> --> https://bitbucket.org/galaxy/galaxy-central/commits/cf105e43d141/ Changeset: cf105e43d141 User: dannon Date: 2015-02-10 14:48:46+00:00 Summary: Actually use reduced redundancy only when specified. Affected #: 1 file diff -r bbdf4a2c3f56e1e2fe6142803e170b8868883c33 -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -13,7 +13,7 @@ from datetime import datetime from galaxy.exceptions import ObjectNotFound -from galaxy.util import umask_fix_perms +from galaxy.util import umask_fix_perms, 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 @@ -76,7 +76,7 @@ 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 = string_as_bool(b_xml.get('use_reduced_redundancy', "False")) cn_xml = config_xml.findall('connection') if not cn_xml: cn_xml = {} https://bitbucket.org/galaxy/galaxy-central/commits/487461afaba5/ Changeset: 487461afaba5 User: dannon Date: 2015-02-10 14:51:33+00:00 Summary: Merge. Affected #: 10 files diff -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -150,6 +150,9 @@ /** 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? */ @@ -873,7 +876,7 @@ filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '</div>' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', @@ -1025,7 +1028,6 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ - console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1305,8 +1307,10 @@ /** 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; @@ -1314,7 +1318,7 @@ // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1322,7 +1326,7 @@ _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 ] ); @@ -1340,27 +1344,41 @@ //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 = $( '<div class="paired-drop-placeholder"></div>') + var $placeholder = $( '<div class="paired-drop-placeholder"></div>' ); if( !$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<lis.length; i++ ){ var $li = $( lis[i] ), top = $li.offset().top, diff -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 client/galaxy/scripts/utils/LazyDataLoader.js --- 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 -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -14,6 +14,7 @@ from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms, string_as_bool +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 @@ -77,6 +78,7 @@ b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') 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: cn_xml = {} @@ -84,11 +86,24 @@ 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.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)) 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") @@ -328,14 +343,14 @@ 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 -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -34,13 +34,23 @@ 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 @@ @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 diff -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -150,6 +150,9 @@ /** 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? */ @@ -873,7 +876,7 @@ filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '</div>' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', @@ -1025,7 +1028,6 @@ /** 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() @@ -1305,8 +1307,10 @@ /** 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; @@ -1314,7 +1318,7 @@ // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1322,7 +1326,7 @@ _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 ] ); @@ -1340,27 +1344,41 @@ //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 = $( '<div class="paired-drop-placeholder"></div>') + var $placeholder = $( '<div class="paired-drop-placeholder"></div>' ); if( !$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<lis.length; i++ ){ var $li = $( lis[i] ), top = $li.offset().top, diff -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$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<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=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(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){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<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);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.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$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 $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').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.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var 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 input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){console.debug("alert:",i,h);h=h||"alert-danger";this.$(".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 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 .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var 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"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expres..."',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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+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(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].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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o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=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 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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.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$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 $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').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.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].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.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file diff -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 static/scripts/packed/utils/LazyDataLoader.js --- a/static/scripts/packed/utils/LazyDataLoader.js +++ /dev/null @@ -1,1 +0,0 @@ -function LazyDataLoader(c){var a=this,d="loaded.new",b="complete";ERROR_EVENT="error";jQuery.extend(a,LoggableMixin);jQuery.extend(a,{total:undefined,url:undefined,currentIntervalId:undefined,data:[],delay:4000,start:0,size:4000,initialize:function(e){jQuery.extend(a,e);if(e.hasOwnProperty("initialize")){e.initialize.call(a,e)}this.log(this+" initialized:",a)},buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})},ajaxErrorFn:function(g,e,f){console.error("ERROR fetching data:",f)},converters:{"* text":window.String,"text html":true,"text xml":jQuery.parseXML,"text json":jQuery.parseJSON},load:function(h){this.log(this+".load");if(!a.url){throw (a+" requires a url")}if(this.total===null){this.log("\t total is null (will load all)")}else{this.log("\t total:",this.total)}var g=a.size;if((a.total!==null)&&(a.total<a.size)){g=a.total}a.log(a+"\t beginning recursion");f(a.start,g);function f(k,j){a.log(a+".loadHelper, start:",k,"size:",j);var i=a.buildUrl(k,j);a.log("\t url:",i);jQuery.ajax({url:a.buildUrl(k,j),converters:a.converters,dataType:"json",error:function(n,l,m){a.log("\t ajax error, status:",l,"error:",m);if(a.currentIntervalId){clearInterval(a.currentIntervalId)}$(a).trigger(ERROR_EVENT,[l,m]);a.ajaxErrorFn(n,l,m)},success:function(l){a.log("\t ajax success, response:",l,"next:",m,"remainder:",n);if(l!==null){a.data.push(l);$(a).trigger(d,[l,k,j]);var m=k+j,n=a.size;if(a.total!==null){n=Math.min(a.total-m,a.size)}a.log("\t next recursion, start:",m,"size:",n);if(a.total===null||n>0){a.currentIntervalId=setTimeout(function(){f(m,n)},a.delay);a.log("\t currentIntervalId:",a.currentIntervalId)}else{e()}}else{e()}}})}function e(){a.log(a+".loadHelper, has finished:",a.data);$(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 -r cf105e43d141b258dbf200d49bd3cce5f4d7dddc -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 static/scripts/utils/LazyDataLoader.js --- 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; -} - -//============================================================================== https://bitbucket.org/galaxy/galaxy-central/commits/23df5eac97f7/ Changeset: 23df5eac97f7 User: dannon Date: 2015-02-10 14:55:03+00:00 Summary: Add more accurate sample for specifying a swift object store in object_store_conf.sample Affected #: 1 file diff -r 487461afaba5cc7f0f6bb38397be3773cf46ce45 -r 23df5eac97f7c05da1e06fb63a0385b1c416d535 config/object_store_conf.xml.sample --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -20,15 +20,24 @@ <extra_dir type="temp" path="database/tmp3"/><extra_dir type="job_work" path="database/job_working_directory3"/></object_store> + <!-- Sample S3 Object Store - <object_store type="s3"><auth access_key="...." secret_key="....." /><bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" /><cache path="database/files/" size="1000" /></object_store> + --> - --> + <!-- Sample Swift Object Store + <object_store type="swift"> + <auth access_key="...." secret_key="....." /> + <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/> + <connection host="" port="" is_secure="" conn_path="" multipart="True"/> + <cache path="database/files/" size="1000" /> + </object_store> + --> + </backends></object_store> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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