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[hg] galaxy 3115: update bx_python egg
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e24c2590f8af changeset: 3115:e24c2590f8af user: Kanwei Li <kanwei(a)gmail.com> date: Fri Nov 20 12:07:06 2009 -0500 description: update bx_python egg diffstat: eggs.ini | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (20 lines): diff -r f4654abcec1e -r e24c2590f8af eggs.ini --- a/eggs.ini Fri Nov 20 11:03:41 2009 -0500 +++ b/eggs.ini Fri Nov 20 12:07:06 2009 -0500 @@ -60,14 +60,14 @@ pysqlite = _static MySQL_python = _5.0.67_static python_lzo = _static -bx_python = _dev_r4bf1f32e6b76 +bx_python = _dev_3b9d30e47619 GeneTrack = _dev_e380f21c704218622155b9d230a44b3c9c452524 SQLAlchemy = _dev_r6498 ; nose = .dev_r7156749efc58 ; source location, necessary for scrambling [source] -bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 +bx_python = http://bitbucket.org/james_taylor/bx-python/get/3b9d30e47619.bz2 Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 3110: Only fix OS X platform name on 2.5, the only v...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/53de6aea6445 changeset: 3110:53de6aea6445 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 18 16:18:09 2009 -0500 description: Only fix OS X platform name on 2.5, the only version on which it's broken diffstat: lib/galaxy/__init__.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (15 lines): diff -r c507bad7e373 -r 53de6aea6445 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Wed Nov 18 13:45:53 2009 -0500 +++ b/lib/galaxy/__init__.py Wed Nov 18 16:18:09 2009 -0500 @@ -12,8 +12,9 @@ import os, sys from distutils.sysconfig import get_config_vars -if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ - ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ): +if sys.version_info[:2] == ( 2, 5 ) and \ + ( ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ + ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): # Has to be before anything imports pkg_resources def _get_platform_monkeypatch(): plat = distutils.util._get_platform()

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[hg] galaxy 3109: revert to sqlite default in universe.sample
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c507bad7e373 changeset: 3109:c507bad7e373 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Nov 18 13:45:53 2009 -0500 description: revert to sqlite default in universe.sample diffstat: lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | 6 +- lib/galaxy/visualization/tracks/data/array_tree.py | 30 +- lib/galaxy/visualization/tracks/data/interval_index.py | 26 +- static/scripts/trackster.js | 116 +++++++++-- universe_wsgi.ini.sample | 12 +- 5 files changed, 131 insertions(+), 59 deletions(-) diffs (352 lines): diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Wed Nov 18 13:45:53 2009 -0500 @@ -8,7 +8,7 @@ from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader -BLOCK_SIZE = 1000 +BLOCK_SIZE = 100 def main(): @@ -20,8 +20,8 @@ # Fill array from wiggle d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE ) - for value in d.itervalues(): - value.root.build_summary() + for array_tree in d.itervalues(): + array_tree.root.build_summary() f = open( out_fname, "w" ) FileArrayTreeDict.dict_to_file( d, f ) diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Wed Nov 18 13:45:53 2009 -0500 @@ -12,9 +12,6 @@ # Maybe this should be included in the datatype itself, so users can add their # own types to the browser as long as they return the right format of data? -# FIXME: Assuming block size is always 1000 for the moment -BLOCK_SIZE = 1000 - class ArrayTreeDataProvider( object ): def __init__( self, dataset, original_dataset ): self.dataset = dataset @@ -32,32 +29,33 @@ return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } def get_data( self, chrom, start, end, **kwargs ): - start = int( start ) - end = int( end ) - resolution = max(1, ceil(float(kwargs['resolution']))) - - level = int( floor( log( resolution, BLOCK_SIZE ) ) ) - level = max( level, 0 ) - stepsize = BLOCK_SIZE ** level - step1 = stepsize * BLOCK_SIZE - - # Open the file f = open( self.dataset.file_name ) d = FileArrayTreeDict( f ) + # Get the right chromosome try: chrom_array_tree = d[chrom] except KeyError: return None + + block_size = chrom_array_tree.block_size + start = int( start ) + end = int( end ) + resolution = max(1, ceil(float(kwargs['resolution']))) + + level = int( floor( log( resolution, block_size ) ) ) + level = max( level, 0 ) + stepsize = block_size ** level + step1 = stepsize * block_size + # Is the requested level valid? assert 0 <= level <= chrom_array_tree.levels - # Calculate the actual start/range/step of the block we're getting results = [] - for block_start in range( start, end, stepsize * BLOCK_SIZE ): + for block_start in range( start, end, stepsize * block_size ): # print block_start # Return either data point or a summary depending on the level - indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize ) + indexes = range( block_start, block_start + stepsize * block_size, stepsize ) if level > 0: s = chrom_array_tree.get_summary( block_start, level ) if s is not None: diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Wed Nov 18 13:45:53 2009 -0500 @@ -27,19 +27,21 @@ payload['strand'] = feature[5] except IndexError: pass - try: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip(block_sizes, block_starts) - payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] - except IndexError: - pass + + if 'include_blocks' in kwargs: + try: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip(block_sizes, block_starts) + payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] + except IndexError: + pass - try: - payload['thick_start'] = int(feature[6]) - payload['thick_end'] = int(feature[7]) - except IndexError: - pass + try: + payload['thick_start'] = int(feature[6]) + payload['thick_end'] = int(feature[7]) + except IndexError: + pass results.append(payload) uid += 1 diff -r bcb3c0eeb72f -r c507bad7e373 static/scripts/trackster.js --- a/static/scripts/trackster.js Wed Nov 18 13:37:41 2009 -0500 +++ b/static/scripts/trackster.js Wed Nov 18 13:45:53 2009 -0500 @@ -1,9 +1,10 @@ /* Trackster 2009, James Taylor, Kanwei Li */ -var DEBUG = false; +var DEBUG = true; var DENSITY = 1000, + FEATURE_LEVELS = 100, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -108,6 +109,7 @@ // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + this.zoom_res = Math.max(1,Math.ceil( Math.log( (this.high - this.low) / FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); // Overview $("#overview-box").css( { @@ -171,7 +173,7 @@ resolution = this.view.resolution; - if (DEBUG) { $("#debug").text(resolution); } + if (DEBUG) { $("#debug").text(resolution + " " + this.view.zoom_res); } var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -279,7 +281,7 @@ max_label.css({ position: "relative", top: "35px" }); max_label.prependTo(track.container_div) - min_label.css({ position: "relative", top: track.height_px + 32 + "px", }); + min_label.css({ position: "relative", top: track.height_px + 32 + "px" }); min_label.prependTo(track.container_div); track.draw(); @@ -297,7 +299,7 @@ $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id, resolution: this.view.resolution }, function ( data ) { - track.cache[key] = data; + track.cache.set(key, data); delete track.data_queue[key]; track.draw(); }); @@ -313,12 +315,12 @@ canvas = $("<canvas class='tile'></canvas>"), key = resolution + "_" + tile_index; - if (!this.cache[key]) { + if (!this.cache.get(key)) { this.get_data( resolution, tile_index ); return; } - var data = this.cache[key]; + var data = this.cache.get(key); canvas.css( { position: "absolute", top: 0, @@ -368,7 +370,11 @@ this.showing_labels = false; this.vertical_gap = 10; this.base_color = "#2C3143"; + this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; + this.inc_slots = {}; + this.data_queue = {}; + this.data_cache = new Cache(20); }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -397,6 +403,23 @@ } }); }, + get_data: function( low, high ) { + console.log("getting: ", low, high); + var track = this, + key = low + '_' + high; + + if (!track.data_queue[key]) { + track.data_queue[key] = true; + $.getJSON( data_url, { track_type: track.track_type, chrom: track.view.chrom, + low: low, high: high, dataset_id: track.dataset_id, + include_blocks: true }, function ( data ) { + track.data_cache.set(key, data); + // console.log("datacache", track.data_cache.get(key)); + delete track.data_queue[key]; + track.draw(); + }); + } + }, calc_slots: function( include_labels ) { // console.log("num vals: " + this.values.length); var end_ary = [], @@ -438,27 +461,76 @@ this.height_px = end_ary.length * this.vertical_gap + 15; this.content_div.css( "height", this.height_px + "px" ); }, + incremental_slots: function( level, features ) { + if (!this.inc_slots[level]) { + this.inc_slots[level] = {}; + this.inc_slots[level].w_scale = 1000 / Math.pow(FEATURE_LEVELS, level); + } + var slots = this.inc_slots[level]; + if (slots[uid]) { + return slots[uid]; + } + var end_ary = [], + undone = [], + max_high = this.view.max_high, + max_low = this.view.max_low; + + for (var i = 0, len = features.length; i < len; i++) { + var feature = features[i]; + if (slots[feature.uid]) { + end_ary[ slots[feature.uid] ] = Math.ceil( (feature.end - max_low) * slots.w_scale ); + } else { + undone.push(feature); + } + } + for (var i = 0, len = undone.length; i < len; i++) { + var feature = undone[i]; + f_start = Math.floor( (feature.start - max_low) * slots.w_scale ); + f_start -= dummy_canvas.measureText(feature.name).width; + f_end = Math.ceil( (feature.end - max_low) * slots.w_scale ); + + }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - if (!this.values) { // Still loading - return null; + if (!this.values) { + return; } + var tile_low = tile_index * DENSITY * resolution, + tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_span = DENSITY * resolution; // console.log("drawing " + tile_index); // Once we zoom in enough, show name labels - if (w_scale > this.show_labels_scale && !this.showing_labels) { - this.showing_labels = true; - if (!this.zi_slots) { - this.calc_slots(true); + var data; + if (w_scale > this.show_labels_scale) { + if (!this.showing_labels) { + this.showing_labels = true; + if (!this.zi_slots) { + this.calc_slots(true); + } + this.slots = this.zi_slots; } - this.slots = this.zi_slots; - } else if (w_scale <= this.show_labels_scale && this.showing_labels) { - this.showing_labels = false; - this.slots = this.zo_slots; + for (var k in this.data_cache.obj_cache) { + var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; + if (k_low <= tile_low && k_high >= tile_high) { + data = this.data_cache.get(k); + break; + } + } + if (!data) { + this.data_queue[ [tile_low, tile_high] ] = true; + this.get_data(tile_low, tile_high); + return; + } + + } else { + if (this.showing_labels) { + this.showing_labels = false; + this.slots = this.zo_slots; + } + data = this.values; } // console.log(this.slots); - var tile_low = tile_index * DENSITY * resolution, - tile_high = ( tile_index + 1 ) * DENSITY * resolution, - tile_span = DENSITY * resolution; + // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), height = this.height_px, @@ -474,12 +546,12 @@ // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); ctx.fillStyle = this.base_color; - ctx.font = "10px monospace"; + ctx.font = this.default_font; ctx.textAlign = "right"; var j = 0; - for (var i = 0, len = this.values.length; i < len; i++) { - var feature = this.values[i]; + for (var i = 0, len = data.length; i < len; i++) { + var feature = data[i]; if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), diff -r bcb3c0eeb72f -r c507bad7e373 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed Nov 18 13:37:41 2009 -0500 +++ b/universe_wsgi.ini.sample Wed Nov 18 13:45:53 2009 -0500 @@ -31,15 +31,15 @@ paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here -#database_file = database/universe.sqlite +database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. -database_connection = postgres:///galaxy -database_engine_option_echo = true -database_engine_option_echo_pool = true -database_engine_option_pool_size = 10 -database_engine_option_max_overflow = 20 +#database_connection = postgres:///galaxy +#database_engine_option_echo = true +#database_engine_option_echo_pool = true +#database_engine_option_pool_size = 10 +#database_engine_option_max_overflow = 20 # If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-2…

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[hg] galaxy 3111: Fixed a bug in cloud store update. Also, added...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b70e23d80a75 changeset: 3111:b70e23d80a75 user: Enis Afgan <afgane(a)gmail.com> date: Thu Nov 19 12:56:24 2009 -0500 description: Fixed a bug in cloud store update. Also, added method comments to EC2 cloud provider implementation class. diffstat: lib/galaxy/cloud/providers/ec2.py | 90 ++++++++++++++++++++--------- lib/galaxy/cloud/providers/eucalyptus.py | 32 +++++----- templates/cloud/list_images.mako | 2 + 3 files changed, 81 insertions(+), 43 deletions(-) diffs (316 lines): diff -r 53de6aea6445 -r b70e23d80a75 lib/galaxy/cloud/providers/ec2.py --- a/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 16:18:09 2009 -0500 +++ b/lib/galaxy/cloud/providers/ec2.py Thu Nov 19 12:56:24 2009 -0500 @@ -94,13 +94,16 @@ log.info( "EC2 cloud manager stopped" ) def put( self, uci_wrapper ): - # Get rid of UCI from state description + """ + Add uci_wrapper object to the end of the request queue to be handled by + this cloud provider. + """ state = uci_wrapper.get_uci_state() uci_wrapper.change_state( state.split('U')[0] ) # remove 'UCI' from end of state description (i.e., mark as accepted and ready for processing) self.queue.put( uci_wrapper ) def run_next( self ): - """Run the next job, waiting until one is available if necessary""" + """Process next request, waiting until one is available if necessary.""" cnt = 0 while 1: @@ -125,7 +128,7 @@ def get_connection( self, uci_wrapper ): """ - Establishes EC2 cloud connection using user's credentials associated with given UCI + Establishes cloud connection using user's credentials associated with given UCI """ log.debug( 'Establishing %s cloud connection.' % self.type ) provider = uci_wrapper.get_provider() @@ -152,7 +155,10 @@ def check_key_pair( self, uci_wrapper, conn ): """ - Generate key pair using user's credentials + Check if a key pair associated with this UCI exists on cloud provider. + If yes, return key pair name; otherwise, generate a key pair with the cloud + provider and, again, return key pair name. + Key pair name for given UCI is generated from UCI's name and suffix '_kp' """ kp = None kp_name = uci_wrapper.get_name().replace(' ','_') + "_kp" @@ -200,6 +206,7 @@ return None def create_key_pair( self, conn, kp_name ): + """ Initiate creation of key pair under kp_name by current cloud provider. """ try: return conn.create_key_pair( kp_name ) except boto.exception.EC2ResponseError, e: @@ -226,8 +233,8 @@ def create_uci( self, uci_wrapper ): """ - Creates User Configured Instance (UCI). Essentially, creates storage volume on cloud provider - and registers relevant information in Galaxy database. + Create User Configured Instance (UCI) - i.e., create storage volume on cloud provider + and register relevant information in local Galaxy database. """ conn = self.get_connection( uci_wrapper ) if uci_wrapper.get_uci_availability_zone()=='': @@ -279,8 +286,11 @@ def delete_uci( self, uci_wrapper ): """ - Deletes UCI. NOTE that this implies deletion of any and all data associated + Delete UCI - i.e., delete all storage volumes associated with this UCI. + NOTE that this implies deletion of any and all data associated with this UCI from the cloud. All data will be deleted. + Information in local Galaxy database is marked as deleted but not actually removed + from the database. """ conn = self.get_connection( uci_wrapper ) vl = [] # volume list @@ -318,7 +328,8 @@ def snapshot_uci( self, uci_wrapper ): """ - Creates snapshot of all storage volumes associated with this UCI. + Initiate creation of a snapshot by cloud provider for all storage volumes + associated with this UCI. """ if uci_wrapper.get_uci_state() != uci_states.ERROR: conn = self.get_connection( uci_wrapper ) @@ -362,7 +373,7 @@ def start_uci( self, uci_wrapper ): """ - Starts instance(s) of given UCI on the cloud. + Start instance(s) of given UCI on the cloud. """ if uci_wrapper.get_uci_state() != uci_states.ERROR: conn = self.get_connection( uci_wrapper ) @@ -461,7 +472,7 @@ def stop_uci( self, uci_wrapper): """ - Stops all of cloud instances associated with given UCI. + Stop all of cloud instances associated with given UCI. """ conn = self.get_connection( uci_wrapper ) @@ -543,11 +554,15 @@ def update( self ): """ - Runs a global status update on all instances that are in 'running', 'pending', or 'shutting-down' state. - Also, runs update on all storage volumes that are in 'in-use', 'creating', or 'None' state. + Run status update on all instances that are in 'running', 'pending', or 'shutting-down' state. + Run status update on all storage volumes whose status is 'in-use', 'creating', or 'None'. + Run status update on all snapshots whose status is 'pending' or 'delete' + Run status update on any zombie UCIs, i.e., UCI's that is in 'submitted' state for an + extended period of time. + Reason behind this method is to sync state of local DB and real-world resources """ - log.debug( "Running general status update for EC2 UCIs..." ) + log.debug( "Running general status update for %s UCIs..." % self.type ) # Update instances instances = self.sa_session.query( model.CloudInstance ) \ .filter( or_( model.CloudInstance.table.c.state==instance_states.RUNNING, @@ -610,7 +625,11 @@ self.process_zombie( z_inst ) def update_instance( self, inst ): - + """ + Update information in local database for given instance as it is obtained from cloud provider. + Along with updating information about given instance, information about the UCI controlling + this instance is also updated. + """ # Get credentials associated wit this instance uci_id = inst.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -683,6 +702,11 @@ return None def update_store( self, store ): + """ + Update information in local database for given storage volume as it is obtained from cloud provider. + Along with updating information about given storage volume, information about the UCI controlling + this storage volume is also updated. + """ # Get credentials associated wit this store uci_id = store.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -705,6 +729,7 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: + log.debug( "Storage volume '%s' current status: '%s'" % (store.volume_id, vl[0].status ) ) if store.status != vl[0].status: # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here @@ -721,18 +746,19 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.inst.instance_id != vl[0].instance_id: - store.inst.instance_id = vl[0].instance_id - self.sa_session.add( store ) - self.sa_session.flush() - if store.attach_time != vl[0].attach_time: - store.attach_time = vl[0].attach_time - self.sa_session.add( store ) - self.sa_session.flush() - if store.device != vl[0].device: - store.device = vl[0].device - self.sa_session.add( store ) - self.sa_session.flush() + if store.inst != None: + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id + self.sa_session.add( store ) + self.sa_session.flush() + if store.attach_time != vl[0].attach_time: + store.attach_time = vl[0].attach_time + self.sa_session.add( store ) + self.sa_session.flush() + if store.device != vl[0].device: + store.device = vl[0].device + self.sa_session.add( store ) + self.sa_session.flush() except boto.exception.EC2ResponseError, e: err = "Updating status of volume(s) from cloud failed for UCI '"+ uci.name + "' during general status update: " + str( e ) log.error( err ) @@ -753,6 +779,11 @@ self.sa_session.flush() def update_snapshot( self, snapshot ): + """ + Update information in local database for given snapshot as it is obtained from cloud provider. + Along with updating information about given snapshot, information about the UCI controlling + this snapshot is also updated. + """ # Get credentials associated wit this store uci_id = snapshot.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -799,6 +830,9 @@ self.sa_session.flush() def delete_snapshot( self, snapshot ): + """ + Initiate deletion of given snapshot from cloud provider. + """ if snapshot.status == snapshot_status.DELETE: # Get credentials associated wit this store uci_id = snapshot.uci_id @@ -845,7 +879,7 @@ def process_zombie( self, inst ): """ - Attempt at discovering if starting an instance was successful but local database was not updated + Attempt at discovering if starting a cloud instance was successful but local database was not updated accordingly or if something else failed and instance was never started. Currently, no automatic repairs are being attempted; instead, appropriate error messages are set. """ @@ -921,7 +955,7 @@ def get_connection_from_uci( self, uci ): """ - Establishes and returns connection to cloud provider. Information needed to do so is obtained + Establish and return connection to cloud provider. Information needed to do so is obtained directly from uci database object. """ log.debug( 'Establishing %s cloud connection' % self.type ) diff -r 53de6aea6445 -r b70e23d80a75 lib/galaxy/cloud/providers/eucalyptus.py --- a/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 16:18:09 2009 -0500 +++ b/lib/galaxy/cloud/providers/eucalyptus.py Thu Nov 19 12:56:24 2009 -0500 @@ -94,7 +94,7 @@ def put( self, uci_wrapper ): """ - Adds uci_wrapper object to the end of the request queue to be handled by + Add uci_wrapper object to the end of the request queue to be handled by this cloud provider. """ state = uci_wrapper.get_uci_state() @@ -536,7 +536,7 @@ Reason behind this method is to sync state of local DB and real-world resources """ - log.debug( "Running general status update for EPC UCIs..." ) + log.debug( "Running general status update for %s UCIs..." % self.type ) # Update instances instances = self.sa_session.query( model.CloudInstance ) \ .filter( or_( model.CloudInstance.table.c.state==instance_states.RUNNING, @@ -695,7 +695,8 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: - if store.status != vl[0].status and store.availability_zone != 'epc': + log.debug( "Storage volume '%s' current status: '%s'" % (store.volume_id, vl[0].status ) ) + if store.status != vl[0].status: # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here if ( store.status == None ) and ( store.volume_id != None ): @@ -718,10 +719,11 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.inst.instance_id != vl[0].instance_id: - store.inst.instance_id = vl[0].instance_id - self.sa_session.add( store ) - self.sa_session.flush() + if store.inst != None: + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id + self.sa_session.add( store ) + self.sa_session.flush() if store.attach_time != vl[0].attach_time: store.attach_time = vl[0].attach_time self.sa_session.add( store ) @@ -937,7 +939,7 @@ def get_connection_from_uci( self, uci ): """ - Establishes and returns connection to cloud provider. Information needed to do so is obtained + Establish and return connection to cloud provider. Information needed to do so is obtained directly from uci database object. """ log.debug( 'Establishing %s cloud connection' % self.type ) @@ -946,13 +948,13 @@ # Get connection try: region = RegionInfo( None, uci.credentials.provider.region_name, uci.credentials.provider.region_endpoint ) - log.debug( "[%s] Using following command to connect to cloud provider: " - "conn = EC2Connection( aws_access_key_id=%s, " - "aws_secret_access_key=%s, " - "port=%s, " - "is_secure=%s, " - "region=region, " - "path=%s )" % ( self.type, a_key, s_key, uci.credentials.provider.is_secure, uci.credentials.provider.port, uci.credentials.provider.path ) ) +# log.debug( "[%s] Using following command to connect to cloud provider: " +# "conn = EC2Connection( aws_access_key_id=%s, " +# "aws_secret_access_key=%s, " +# "port=%s, " +# "is_secure=%s, " +# "region=region, " +# "path=%s )" % ( self.type, a_key, s_key, uci.credentials.provider.is_secure, uci.credentials.provider.port, uci.credentials.provider.path ) ) conn = EC2Connection( aws_access_key_id=a_key, aws_secret_access_key=s_key, is_secure=uci.credentials.provider.is_secure, diff -r 53de6aea6445 -r b70e23d80a75 templates/cloud/list_images.mako --- a/templates/cloud/list_images.mako Wed Nov 18 16:18:09 2009 -0500 +++ b/templates/cloud/list_images.mako Thu Nov 19 12:56:24 2009 -0500 @@ -78,6 +78,8 @@ </tr> %endfor </table> + + <p /></p><a href="${h.url_for( controller='cloud', action='add_new_image' )}" target="galaxy_main">Add another machine image</a> %else: <h3>There are no registered machine images.</h3><br /> <a href="${h.url_for( controller='cloud', action='add_new_image' )}" target="galaxy_main">Add machine image now?</a>

1 0

[hg] galaxy 3108: merge
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bcb3c0eeb72f changeset: 3108:bcb3c0eeb72f user: Enis Afgan <afgane(a)gmail.com> date: Wed Nov 18 13:37:41 2009 -0500 description: merge diffstat: lib/galaxy/web/framework/helpers/grids.py | 3 +++ static/images/mag_glass.png | templates/grid_base.mako | 35 +++++++++++++++++++++++++++++++++++ templates/grid_common.mako | 13 ++++++++----- 4 files changed, 46 insertions(+), 5 deletions(-) diffs (97 lines): diff -r 5fbda2fdb3ca -r bcb3c0eeb72f lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 13:36:37 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 13:37:41 2009 -0500 @@ -120,6 +120,9 @@ column_filter = from_json_string_recurse( column_filter ) if len( column_filter ) == 1: column_filter = column_filter[0] + # If filter criterion is empty, do nothing. + if column_filter == '': + continue # Update query. query = column.filter( trans.sa_session, query, column_filter ) # Upate current filter dict. diff -r 5fbda2fdb3ca -r bcb3c0eeb72f static/images/mag_glass.png Binary file static/images/mag_glass.png has changed diff -r 5fbda2fdb3ca -r bcb3c0eeb72f templates/grid_base.mako --- a/templates/grid_base.mako Wed Nov 18 13:36:37 2009 -0500 +++ b/templates/grid_base.mako Wed Nov 18 13:37:41 2009 -0500 @@ -62,6 +62,21 @@ t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); } + + // Initialize submit image elements. + $('.submit-image').each( function() + { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); + + }); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -168,6 +183,26 @@ text-align: center; display: inline-block; } + .submit-image { + vertical-align: text-bottom; + margin: 0; + padding: 0; + } + .no-padding-or-margin { + margin: 0; + padding: 0; + } + .gray-background { + background-color: #DDDDDD; + } + .text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 3px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; + } </style> </%def> diff -r 5fbda2fdb3ca -r bcb3c0eeb72f templates/grid_common.mako --- a/templates/grid_common.mako Wed Nov 18 13:36:37 2009 -0500 +++ b/templates/grid_common.mako Wed Nov 18 13:37:41 2009 -0500 @@ -32,10 +32,11 @@ <% column_filter = cur_filter_dict[column.key] %> %if isinstance( column_filter, basestring ): %if column_filter != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | + <span class='text-filter-val'> + ${cur_filter_dict[column.key]} + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> %endif %elif isinstance( column_filter, list ): %for i, filter in enumerate( column_filter ): @@ -53,7 +54,9 @@ %endif %endif - <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> + <span> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span> </form> %else: %for i, filter in enumerate( column.get_accepted_filters() ):

1 0

[hg] galaxy 3107: Fixed table migration bug encountered with Pos...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5fbda2fdb3ca changeset: 3107:5fbda2fdb3ca user: Enis Afgan <afgane(a)gmail.com> date: Wed Nov 18 13:36:37 2009 -0500 description: Fixed table migration bug encountered with PostgreSQL. diffstat: lib/galaxy/cloud/__init__.py | 12 ++++++++++-- lib/galaxy/cloud/providers/ec2.py | 8 ++++++-- lib/galaxy/cloud/providers/eucalyptus.py | 14 +++++++++----- lib/galaxy/model/__init__.py | 1 - lib/galaxy/model/mapping.py | 6 +++--- lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 4 ++-- templates/cloud/view_instance.mako | 6 ++++-- universe_wsgi.ini.sample | 12 ++++++------ 8 files changed, 40 insertions(+), 23 deletions(-) diffs (258 lines): diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/__init__.py --- a/lib/galaxy/cloud/__init__.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/__init__.py Wed Nov 18 13:36:37 2009 -0500 @@ -45,6 +45,14 @@ ERROR = "error" ) +store_status = Bunch( + WAITING = "waiting", + IN_USE = "in-use", + CREATING = "creating", + DELETED = 'deleted', + ERROR = "error" +) + snapshot_status = Bunch( SUBMITTED = 'submitted', PENDING = 'pending', @@ -413,7 +421,7 @@ be given in following format: 'vol-78943248' """ vol = self.sa_session.query( model.CloudStore ).filter( model.CloudStore.table.c.volume_id == vol_id ).first() - vol.i_id = instance_id + vol.inst.instance_id = instance_id self.sa_session.add( vol ) self.sa_session.flush() @@ -559,7 +567,7 @@ def get_mi_id( self, instance_id=0 ): uci = self.sa_session.query( model.UCI ).get( self.uci_id ) self.sa_session.refresh( uci ) - return uci.instance[instance_id].mi_id + return uci.instance[instance_id].image.image_id def get_public_dns( self, instance_id=0 ): uci = self.sa_session.query( model.UCI ).get( self.uci_id ) diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/ec2.py --- a/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 13:36:37 2009 -0500 @@ -49,6 +49,7 @@ ) store_status = Bunch( + WAITING = "waiting", IN_USE = "in-use", CREATING = "creating", DELETED = 'deleted', @@ -441,6 +442,8 @@ s = reservation.instances[0].state uci_wrapper.change_state( s, i_id, s ) uci_wrapper.set_security_group_name( self.security_group, i_id=i_id ) + vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this! + uci_wrapper.set_store_status( vol_id, store_status.WAITING ) log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) ) except boto.exception.EC2ResponseError, e: err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e ) @@ -560,6 +563,7 @@ stores = self.sa_session.query( model.CloudStore ) \ .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, model.CloudStore.table.c.status==store_status.CREATING, + model.CloudStore.table.c.status==store_status.WAITING, model.CloudStore.table.c.status==None ) ) \ .all() for store in stores: @@ -717,8 +721,8 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.i_id != vl[0].instance_id: - store.i_id = vl[0].instance_id + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id self.sa_session.add( store ) self.sa_session.flush() if store.attach_time != vl[0].attach_time: diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/eucalyptus.py --- a/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 13:36:37 2009 -0500 @@ -49,6 +49,7 @@ ) store_status = Bunch( + WAITING = "waiting", IN_USE = "in-use", CREATING = "creating", DELETED = 'deleted', @@ -428,6 +429,8 @@ uci_wrapper.set_instance_id( i_index, i_id ) s = reservation.instances[0].state uci_wrapper.change_state( s, i_id, s ) + vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this! + uci_wrapper.set_store_status( vol_id, store_status.WAITING ) log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) ) except boto.exception.EC2ResponseError, e: err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e ) @@ -497,7 +500,7 @@ ## log.debug ( 'Error detaching volume; still going to try and stop instance %s.' % dbInstances.instance_id ) # store.attach_time = None # store.device = None -# store.i_id = None +# store.inst.instance_id = None # store.status = volStat # log.debug ( '***** volume status: %s' % volStat ) # @@ -549,6 +552,7 @@ stores = self.sa_session.query( model.CloudStore ) \ .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, model.CloudStore.table.c.status==store_status.CREATING, + model.CloudStore.table.c.status==store_status.WAITING, model.CloudStore.table.c.status==None ) ) \ .all() for store in stores: @@ -691,7 +695,7 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: - if store.status != vl[0].status: + if store.status != vl[0].status and store.availability_zone != 'epc': # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here if ( store.status == None ) and ( store.volume_id != None ): @@ -714,8 +718,8 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.i_id != vl[0].instance_id: - store.i_id = vl[0].instance_id + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id self.sa_session.add( store ) self.sa_session.flush() if store.attach_time != vl[0].attach_time: @@ -981,7 +985,7 @@ # try: # volumes = conn.get_all_volumes( vols ) # for i, v in enumerate( volumes ): -# uci.store[i].i_id = v.instance_id +# uci.store[i].inst.instance_id = v.instance_id # uci.store[i].status = v.status # uci.store[i].device = v.device # uci.store[i].flush() diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/__init__.py Wed Nov 18 13:36:37 2009 -0500 @@ -1077,7 +1077,6 @@ def __init__( self ): self.id = None self.volume_id = None - self.i_id = None self.user = None self.size = None self.availability_zone = None diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/mapping.py Wed Nov 18 13:36:37 2009 -0500 @@ -429,7 +429,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.image_id" ), index=True ), + Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -447,7 +447,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.instance_id" ) ), + Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ), @@ -1133,7 +1133,7 @@ assign_mapper( context, CloudStore, CloudStore.table, properties=dict( user=relation( User ), - i=relation( CloudInstance ), + inst=relation( CloudInstance ), snapshot=relation( CloudSnapshot, backref="store" ) ) ) diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 13:36:37 2009 -0500 @@ -56,7 +56,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.id" ), index=True ), + Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -74,7 +74,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.id" ) ), + Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ), diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca templates/cloud/view_instance.mako --- a/templates/cloud/view_instance.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/cloud/view_instance.mako Wed Nov 18 13:36:37 2009 -0500 @@ -67,7 +67,7 @@ %endif <tr> <td> AMI: </td> - <td> ${liveInstance.mi_id} </td> + <td> ${liveInstance.image.image_id} </td> </tr> <tr> <td> State:</td> @@ -81,6 +81,7 @@ <td> Storage size:</td> <td> ${liveInstance.uci.total_size} </td> </tr> + %if liveInstance.public_dns != None and liveInstance.public_dns != '': <tr> <td> Public DNS:</td> <% @@ -88,7 +89,8 @@ %> <td> <a href="${lnk}" target="_blank">${liveInstance.public_dns}</a></td> </tr> - %if liveInstance.private_dns != None: + %endif + %if liveInstance.private_dns != None and liveInstance.private_dns != '': <tr> <td> Private DNS:</td> <td> ${liveInstance.private_dns}</td> diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed Nov 18 10:57:24 2009 -0500 +++ b/universe_wsgi.ini.sample Wed Nov 18 13:36:37 2009 -0500 @@ -31,15 +31,15 @@ paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here -database_file = database/universe.sqlite +#database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. -#database_connection = postgres:///galaxy -#database_engine_option_echo = true -#database_engine_option_echo_pool = true -#database_engine_option_pool_size = 10 -#database_engine_option_max_overflow = 20 +database_connection = postgres:///galaxy +database_engine_option_echo = true +database_engine_option_echo_pool = true +database_engine_option_pool_size = 10 +database_engine_option_max_overflow = 20 # If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-2…

1 0

[hg] galaxy 3105: Change a few foreign keys, this may change beh...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f4c2bf76b2e2 changeset: 3105:f4c2bf76b2e2 user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 18 10:57:24 2009 -0500 description: Change a few foreign keys, this may change behavior of the cloud stuff, needs to be checked. diffstat: lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r 2beaa0783b69 -r f4c2bf76b2e2 lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:47:14 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:57:24 2009 -0500 @@ -56,7 +56,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.image_id" ), index=True ), + Column( "mi_id", TEXT, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -74,7 +74,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.instance_id" ) ), + Column( "i_id", TEXT, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ),

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[hg] galaxy 3106: Tweaks to grid filter UI: (1) added search ima...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fb7dd12ea39c changeset: 3106:fb7dd12ea39c user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Nov 18 11:51:09 2009 -0500 description: Tweaks to grid filter UI: (1) added search image/submit button for initiating search and (2) styled text filter criteria. diffstat: lib/galaxy/web/framework/helpers/grids.py | 3 +++ static/images/mag_glass.png | templates/grid_base.mako | 35 +++++++++++++++++++++++++++++++++++ templates/grid_common.mako | 13 ++++++++----- 4 files changed, 46 insertions(+), 5 deletions(-) diffs (97 lines): diff -r f4c2bf76b2e2 -r fb7dd12ea39c lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 11:51:09 2009 -0500 @@ -120,6 +120,9 @@ column_filter = from_json_string_recurse( column_filter ) if len( column_filter ) == 1: column_filter = column_filter[0] + # If filter criterion is empty, do nothing. + if column_filter == '': + continue # Update query. query = column.filter( trans.sa_session, query, column_filter ) # Upate current filter dict. diff -r f4c2bf76b2e2 -r fb7dd12ea39c static/images/mag_glass.png Binary file static/images/mag_glass.png has changed diff -r f4c2bf76b2e2 -r fb7dd12ea39c templates/grid_base.mako --- a/templates/grid_base.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/grid_base.mako Wed Nov 18 11:51:09 2009 -0500 @@ -62,6 +62,21 @@ t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); } + + // Initialize submit image elements. + $('.submit-image').each( function() + { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); + + }); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -168,6 +183,26 @@ text-align: center; display: inline-block; } + .submit-image { + vertical-align: text-bottom; + margin: 0; + padding: 0; + } + .no-padding-or-margin { + margin: 0; + padding: 0; + } + .gray-background { + background-color: #DDDDDD; + } + .text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 3px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; + } </style> </%def> diff -r f4c2bf76b2e2 -r fb7dd12ea39c templates/grid_common.mako --- a/templates/grid_common.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/grid_common.mako Wed Nov 18 11:51:09 2009 -0500 @@ -32,10 +32,11 @@ <% column_filter = cur_filter_dict[column.key] %> %if isinstance( column_filter, basestring ): %if column_filter != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | + <span class='text-filter-val'> + ${cur_filter_dict[column.key]} + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> %endif %elif isinstance( column_filter, list ): %for i, filter in enumerate( column_filter ): @@ -53,7 +54,9 @@ %endif %endif - <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> + <span> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span> </form> %else: %for i, filter in enumerate( column.get_accepted_filters() ):

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[hg] galaxy 3104: Another tweak to cloud table order
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2beaa0783b69 changeset: 3104:2beaa0783b69 user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 18 10:47:14 2009 -0500 description: Another tweak to cloud table order diffstat: lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (14 lines): diff -r cffcf1cae94c -r 2beaa0783b69 lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:43:08 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:47:14 2009 -0500 @@ -138,9 +138,9 @@ CloudImage_table.create() UCI_table.create() + CloudInstance_table.create() CloudStore_table.create() CloudSnapshot_table.create() - CloudInstance_table.create() def downgrade(): metadata.reflect()

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[hg] galaxy 3103: Change cloud table creation order
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cffcf1cae94c changeset: 3103:cffcf1cae94c user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 18 10:43:08 2009 -0500 description: Change cloud table creation order diffstat: lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 18 +++++++++++------- 1 files changed, 11 insertions(+), 7 deletions(-) diffs (37 lines): diff -r b39f3d484220 -r cffcf1cae94c lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 09:52:38 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:43:08 2009 -0500 @@ -132,21 +132,25 @@ # Load existing tables metadata.reflect() + CloudProvider_table.create() + CloudUserCredentials_table.create() + CloudImage_table.create() UCI_table.create() - CloudUserCredentials_table.create() + CloudStore_table.create() CloudSnapshot_table.create() CloudInstance_table.create() - CloudProvider_table.create() def downgrade(): metadata.reflect() + CloudInstance_table.drop() + CloudSnapshot_table.drop() + CloudStore_table.drop() + + UCI_table.drop() CloudImage_table.drop() - CloudInstance_table.drop() - CloudStore_table.drop() - CloudSnapshot_table.drop() + CloudUserCredentials_table.drop() - UCI_table.drop() - CloudProvider_table.drop() \ No newline at end of file + CloudProvider_table.drop()

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