galaxy-commits August 2013

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commit/galaxy-central: jgoecks: UI and Trackster: (a) restore trackster tool save functionality; (b) add toggle functionality to visibility mixin; (c) extend tool class to create trackster tool rather than create new class.
by commits-noreply＠bitbucket.org 28 Aug '13

28 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/533fb8fcc330/ Changeset: 533fb8fcc330 User: jgoecks Date: 2013-08-28 23:46:03 Summary: UI and Trackster: (a) restore trackster tool save functionality; (b) add toggle functionality to visibility mixin; (c) extend tool class to create trackster tool rather than create new class. Affected #: 2 files diff -r fc4e1a162195e45f69573724adec564ffe1ea9ee -r 533fb8fcc330c52646529659a246e1c50dc18e6a static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -18,6 +18,10 @@ hide: function() { this.set("hidden", true); }, + + toggle: function() { + this.set("hidden", !this.get("hidden")); + }, is_visible: function() { return !this.attributes.hidden; @@ -600,8 +604,8 @@ query_changed: function( evData ) { // check for the 'clear key' (ESC) first - if( ( this.model.attributes.clear_key ) - && ( this.model.attributes.clear_key === evData.which ) ){ + if( ( this.model.attributes.clear_key ) && + ( this.model.attributes.clear_key === evData.which ) ){ this.clear(); return false; } diff -r fc4e1a162195e45f69573724adec564ffe1ea9ee -r 533fb8fcc330c52646529659a246e1c50dc18e6a static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1622,25 +1622,25 @@ /** * Encapsulation of a tool that users can apply to tracks/datasets. */ -var TracksterTool = Backbone.RelationalModel.extend({ +var TracksterTool = tools_mod.Tool.extend({ defaults: { - track: null, - tool: null, + track: null }, - relations: [ - { - type: Backbone.HasOne, - key: 'tool', - relatedModel: tools_mod.Tool + initialize: function(options) { + // Restore tool visibility from state. + if (options.tool_state !== undefined) { + this.set('hidden', options.tool_state.hidden) } - ], - - initialize: function(options) { + + // FIXME: need to restore tool values from options.tool_state + // HACK: remove some inputs because Trackster does yet not work with them. - this.get('tool').remove_inputs( [ 'data', 'hidden_data', 'conditional' ] ); - - // FIXME: need to restore tool values/visibility. + this.remove_inputs( [ 'data', 'hidden_data', 'conditional' ] ); + }, + + state_dict: function(options) { + return _.extend( this.get_inputs_dict(), { hidden: !this.is_visible() } ); } }); @@ -1678,12 +1678,16 @@ */ var TracksterToolView = Backbone.View.extend({ + initialize: function(options) { + this.model.on('change:hidden', this.set_visible, this); + }, + /** * Render tool UI. */ render: function() { var self = this; - tool = this.model.get('tool'), + tool = this.model, parent_div = this.$el.addClass("dynamic-tool").hide(); // Prevent div events from propogating to other elements. @@ -1719,11 +1723,21 @@ self.run_on_dataset(); }); - /* - if ('visible' in tool_state_dict && tool_state_dict.visible) { - this.parent_div.show(); + if (tool.is_visible()) { + this.$el.show(); } - */ + }, + + /** + * Show or hide tool depending on tool visibility state. + */ + set_visible: function() { + if (this.model.is_visible()) { + this.$el.show(); + } + else { + this.$el.hide(); + } }, /** @@ -1736,23 +1750,10 @@ }, /** - * Returns a dict with tool state information. - */ - state_dict: function() { - // Save parameter values. - var tool_state = this.model.get('tool').get_param_values_dict(); - - // Save visibility. - tool_state.visible = this.parent_div.is(":visible"); - - return tool_state; - }, - - /** * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made. */ run_on_dataset: function() { - var tool = this.model.get('tool'); + var tool = this.model; this.run( // URL params. { @@ -1779,7 +1780,7 @@ // Create track for tool's output immediately to provide user feedback. // var track = this.model.get('track'), - tool = this.model.get('tool'), + tool = this.model, region = new visualization.GenomeRegion({ chrom: track.view.chrom, start: track.view.low, @@ -1850,7 +1851,7 @@ */ run: function(url_params, new_track, success_callback) { // Run tool. - url_params.inputs = this.model.get('tool').get_inputs_dict(); + url_params.inputs = this.model.get_inputs_dict(); var ss_deferred = new util.ServerStateDeferred({ ajax_settings: { url: galaxy_config.root + "api/tools", @@ -2405,10 +2406,10 @@ on_click_fn: function(track) { // TODO: update tipsy text. - track.dynamic_tool_div.toggle(); + track.tool.toggle(); // Update track name. - if (track.dynamic_tool_div.is(":visible")) { + if (track.tool.is_visible()) { track.set_name(track.name + track.tool_region_and_parameters_str()); } else { @@ -2790,11 +2791,10 @@ // FIXME: prolly need function to set filters and update data_manager reference. this.data_manager.set('filters_manager', this.filters_manager); this.filters_available = false; - this.tool = (obj_dict.tool ? new TracksterTool({ - 'track': this, - 'tool': obj_dict.tool, + this.tool = (obj_dict.tool ? new TracksterTool( _.extend( obj_dict.tool, { + 'track': this, 'tool_state': obj_dict.tool_state - }) + } ) ) : null); this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE); this.left_offset = 0; @@ -3333,9 +3333,7 @@ * @param w_scale pixels per base * @param ref_seq reference sequence data */ - draw_tile: function(result, ctx, mode, resolution, region, w_scale, ref_seq) { - console.log("Warning: TiledTrack.draw_tile() not implemented."); - }, + draw_tile: function(result, ctx, mode, resolution, region, w_scale, ref_seq) {}, /** * Show track tile and perform associated actions. Showing tile may actually move @@ -3406,7 +3404,7 @@ tool_region_and_parameters_str: function(region) { var track = this, region_str = (region !== undefined ? region.toString() : "all"), - param_str = _.values( track.tool.get('tool').get_inputs_dict()).join(', '); + param_str = _.values( track.tool.get_inputs_dict()).join(', '); return " - region=[" + region_str + "], parameters=[" + param_str + "]"; }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 28 Aug '13

28 Aug '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1593c067833/ Changeset: d1593c067833 User: natefoo Date: 2013-08-28 22:08:21 Summary: Reorganize object store options in sample config file. Affected #: 1 file diff -r 4fea98291cbce9a0e8d580bfd9c4ef4a5184c680 -r d1593c067833c8dc4c85bdcc7b4d90b79d8ab01c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -203,6 +203,41 @@ # breaking existing tools. #collect_outputs_from = new_file_path,job_working_directory +# -- Data Storage (Object Store) + +# Object store backend module (valid options are: disk, s3, swift, irods, +# distributed, hierarchical) +#object_store = disk + +# Credentials used by certain (s3, swift) object store backends +#os_access_key = <your cloud object store access key> +#os_secret_key = <your cloud object store secret key> +#os_bucket_name = <name of an existing object store bucket or container> + +# If using 'swift' object store, you must specify the following connection +# properties +#os_host = swift.rc.nectar.org.au +#os_port = 8888 +#os_is_secure = False +#os_conn_path = / + +# Reduced redundancy can be used only with the 's3' object store +#os_use_reduced_redundancy = False + +# Path to cache directory for object store backends that utilize a cache (s3, +# swift, irods) +#object_store_cache_path = database/files/ + +# Size (in GB) that the cache used by object store should be limited to. +# If the value is not specified, the cache size will be limited only by the +# file system size. +#object_store_cache_size = 100 + +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + + # -- Mail and notification # Galaxy sends mail for various things: Subscribing users to the mailing list @@ -524,28 +559,6 @@ # -- Beta features -# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) -#object_store = disk -#os_access_key = <your cloud object store access key> -#os_secret_key = <your cloud object store secret key> -#os_bucket_name = <name of an existing object store bucket or container> -# If using 'swift' object store, you must specify the following connection properties -#os_host = swift.rc.nectar.org.au -#os_port = 8888 -#os_is_secure = False -#os_conn_path = / -# Reduced redundancy can be used only with the 's3' object store -#os_use_reduced_redundancy = False -# Size (in GB) that the cache used by object store should be limited to. -# If the value is not specified, the cache size will be limited only by the -# file system size. The file system location of the cache is considered the -# configuration of the ``file_path`` directive defined above. -#object_store_cache_size = 100 - -# Configuration file for the distributed object store, if object_store = -# distributed. See the sample at distributed_object_store_conf.xml.sample -#distributed_object_store_config_file = None - # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False https://bitbucket.org/galaxy/galaxy-central/commits/75bcfb029e8c/ Changeset: 75bcfb029e8c User: natefoo Date: 2013-08-28 22:11:29 Summary: Implement a local_extra_dirs decorator in the object store that object store plugins (e.g. cloud object stores) can use to cause things like the job_working_directory to be stored on local disk. Affected #: 1 file diff -r d1593c067833c8dc4c85bdcc7b4d90b79d8ab01c -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -25,7 +25,7 @@ """ ObjectStore abstract interface """ - def __init__(self): + def __init__(self, config, **kwargs): self.running = True self.extra_dirs = {} @@ -195,7 +195,7 @@ >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat' """ def __init__(self, config, file_path=None, extra_dirs=None): - super(DiskObjectStore, self).__init__() + super(DiskObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs) self.file_path = file_path or config.file_path self.config = config self.extra_dirs['job_work'] = config.job_working_directory @@ -213,6 +213,7 @@ if not os.path.exists(path): return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) + # TODO: rename to _disk_path or something like that to avoid conflicts with children that'll use the local_extra_dirs decorator, e.g. S3 def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): """ Construct the expected absolute path for accessing the object identified by `obj`.id. @@ -544,6 +545,19 @@ else: log.error("Unrecognized object store definition: {0}".format(store)) +def local_extra_dirs( func ): + """ A decorator for non-local plugins to utilize local directories for their extra_dirs (job_working_directory and temp). + """ + def wraps( self, *args, **kwargs ): + if kwargs.get( 'base_dir', None ) is None: + return func( self, *args, **kwargs ) + else: + for c in self.__class__.__mro__: + if c.__name__ == 'DiskObjectStore': + return getattr( c, func.__name__ )( self, *args, **kwargs ) + raise Exception( "Could not call DiskObjectStore's %s method, does your Object Store plugin inherit from DiskObjectStore?" % func.__name__ ) + return wraps + def convert_bytes(bytes): """ A helper function used for pretty printing disk usage """ if bytes is None: https://bitbucket.org/galaxy/galaxy-central/commits/fc4e1a162195/ Changeset: fc4e1a162195 User: natefoo Date: 2013-08-28 22:20:19 Summary: Experimental/alpha/in-development/incomplete object store plugin for iRODS. This plugin will probably set your iRODS instance on fire: do not use except in development/testing. Affected #: 6 files diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -18,6 +18,7 @@ MarkupSafe = 0.12 mercurial = 2.2.3 MySQL_python = 1.2.3c1 +PyRods = 3.2.4 numpy = 1.6.0 pbs_python = 4.3.5 psycopg2 = 2.0.13 diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -209,6 +209,7 @@ if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) self.object_store = kwargs.get( 'object_store', 'disk' ) + self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root ) # Handle AWS-specific config options for backward compatibility if kwargs.get( 'aws_access_key', None) is not None: self.os_access_key= kwargs.get( 'aws_access_key', None ) @@ -228,6 +229,8 @@ self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) if self.distributed_object_store_config_file is not None: self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) + self.irods_root_collection_path = kwargs.get( 'irods_root_collection_path', None ) + self.irods_default_resource = kwargs.get( 'irods_default_resource', None ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() @@ -369,6 +372,7 @@ self.nginx_upload_store, \ './static/genetrack/plots', \ self.whoosh_index_dir, \ + self.object_store_cache_path, \ os.path.join( self.tool_data_path, 'shared', 'jars' ): if path not in [ None, False ] and not os.path.isdir( path ): try: diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -387,7 +387,8 @@ "guppy": lambda: self.config.get( "app:main", "use_memdump" ), "python_openid": lambda: self.config.get( "app:main", "enable_openid" ), "python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ), - "pysam": lambda: check_pysam() + "pysam": lambda: check_pysam(), + "PyRods": lambda: self.config.get( "app:main", "object_store" ) == "irods" }.get( egg_name, lambda: True )() except: return False diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -542,6 +542,9 @@ return DistributedObjectStore(config=config, fsmon=fsmon) elif store == 'hierarchical': return HierarchicalObjectStore() + elif store == 'irods': + from galaxy.objectstore.rods import IRODSObjectStore + return IRODSObjectStore(config=config) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee lib/galaxy/objectstore/rods.py --- /dev/null +++ b/lib/galaxy/objectstore/rods.py @@ -0,0 +1,332 @@ +""" +Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS) + +The module is named rods to avoid conflicting with the PyRods module, irods +""" + +import os +import time +import errno +import logging +#import traceback + +from posixpath import join as path_join +from posixpath import basename as path_basename +from posixpath import dirname as path_dirname + +from galaxy.objectstore import DiskObjectStore, ObjectStore, local_extra_dirs +from galaxy.exceptions import ObjectNotFound, ObjectInvalid + +import galaxy.eggs +galaxy.eggs.require( 'PyRods' ) +import irods + +log = logging.getLogger( __name__ ) + + +class IRODSObjectStore( DiskObjectStore, ObjectStore ): + """ + Galaxy object store based on iRODS + """ + def __init__( self, config, file_path=None, extra_dirs=None ): + super( IRODSObjectStore, self ).__init__( config, file_path=file_path, extra_dirs=extra_dirs ) + self.cache_path = config.object_store_cache_path + self.default_resource = config.irods_default_resource or None + + # Connect to iRODS (AssertionErrors will be raised if anything goes wrong) + self.rods_env, self.rods_conn = rods_connect() + + # if the root collection path in the config is unset or relative, try to use a sensible default + if config.irods_root_collection_path is None or ( config.irods_root_collection_path is not None and not config.irods_root_collection_path.startswith( '/' ) ): + rods_home = self.rods_env.rodsHome + assert rods_home != '', "Unable to initialize iRODS Object Store: rodsHome cannot be determined and irods_root_collection_path in Galaxy config is unset or not absolute." + if config.irods_root_collection_path is None: + self.root_collection_path = path_join( rods_home, 'galaxy_data' ) + else: + self.root_collection_path = path_join( rods_home, config.irods_root_collection_path ) + else: + self.root_collection_path = config.irods_root_collection_path + + # will return a collection object regardless of whether it exists + self.root_collection = irods.irodsCollection( self.rods_conn, self.root_collection_path ) + + if self.root_collection.getId() == -1: + log.warning( "iRODS root collection does not exist, will attempt to create: %s", self.root_collection_path ) + self.root_collection.upCollection() + assert self.root_collection.createCollection( os.path.basename( self.root_collection_path ) ) == 0, "iRODS root collection creation failed: %s" % self.root_collection_path + self.root_collection = irods.irodsCollection( self.rods_conn, self.root_collection_path ) + assert self.root_collection.getId() != -1, "iRODS root collection creation claimed success but still does not exist" + + if self.default_resource is None: + self.default_resource = self.rods_env.rodsDefResource + + log.info( "iRODS data for this instance will be stored in collection: %s, resource: %s", self.root_collection_path, self.default_resource ) + + def __get_rods_path( self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, strip_dat=True, **kwargs ): + path = "" + if extra_dir is not None: + path = extra_dir + + # extra_dir_at_root is ignored - since the iRODS plugin does not use + # the directory hash, there is only one level of subdirectory. + + if not dir_only: + # the .dat extension is stripped when stored in iRODS + # TODO: is the strip_dat kwarg the best way to implement this? + if strip_dat and alt_name and alt_name.endswith( '.dat' ): + alt_name = os.path.splitext( alt_name )[0] + default_name = 'dataset_%s' % obj.id + if not strip_dat: + default_name += '.dat' + path = path_join( path, alt_name if alt_name else default_name ) + + path = path_join( self.root_collection_path, path ) + + #log.debug( 'iRODS path for %s %s is %s', obj.__class__.__name__, obj.id, path ) + + return path + + def __get_cache_path( self, obj, **kwargs ): + # FIXME: does not handle collections + # FIXME: collisions could occur here + return os.path.join( self.cache_path, path_basename( self.__get_rods_path( obj, strip_dat=False, **kwargs ) ) ) + + def __clean_cache_entry( self, obj, **kwargs ): + # FIXME: does not handle collections + try: + os.unlink( self.__get_cache_path( obj, **kwargs ) ) + except OSError: + # it is expected that we'll call this method a lot regardless of + # whether we think the cached file exists + pass + + def __get_rods_handle( self, obj, mode='r', **kwargs ): + if kwargs.get( 'dir_only', False ): + return irods.irodsCollection( self.rods_conn, self.__get_rods_path( obj, **kwargs ) ) + else: + return irods.irodsOpen( self.rods_conn, self.__get_rods_path( obj, **kwargs ), mode ) + + def __mkcolls( self, rods_path ): + """ + An os.makedirs() for iRODS collections. `rods_path` is the desired collection to create. + """ + assert rods_path.startswith( self.root_collection_path + '/' ), '__mkcolls(): Creating collections outside the root collection is not allowed (requested path was: %s)' % rods_path + mkcolls = [] + c = irods.irodsCollection( self.rods_conn, rods_path ) + while c.getId() == -1: + assert c.getCollName().startswith( self.root_collection_path + '/' ), '__mkcolls(): Attempted to move above the root collection: %s' % c.getCollName() + mkcolls.append( c.getCollName() ) + c.upCollection() + for collname in reversed( mkcolls ): + log.debug( 'Creating collection %s' % collname ) + ci = irods.collInp_t() + ci.collName = collname + status = rcCollCreate( self.rods_conn, ci ) + assert status == 0, '__mkcolls(): Failed to create collection: %s' % collname + + @local_extra_dirs + def exists( self, obj, **kwargs ): + doi = irods.dataObjInp_t() + doi.objPath = self.__get_rods_path( obj, **kwargs ) + log.debug( 'exists(): checking: %s', doi.objPath ) + return irods.rcObjStat( self.rods_conn, doi ) is not None + + @local_extra_dirs + def create(self, obj, **kwargs): + if not self.exists( obj, **kwargs ): + rods_path = self.__get_rods_path( obj, **kwargs ) + log.debug( 'create(): %s', rods_path ) + dir_only = kwargs.get( 'dir_only', False ) + # short circuit collection creation since most of the time it will + # be the root collection which already exists + collection_path = rods_path if dir_only else path_dirname( rods_path ) + if collection_path != self.root_collection_path: + self.__mkcolls( collection_path ) + if not dir_only: + # rcDataObjCreate is used instead of the irodsOpen wrapper so + # that we can prevent overwriting + doi = irods.dataObjInp_t() + doi.objPath = rods_path + doi.createMode = 0640 + doi.dataSize = 0 # 0 actually means "unknown", although literally 0 would be preferable + irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource ) + status = irods.rcDataObjCreate( self.rods_conn, doi ) + assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % ( rods_path, status, irods.strerror( status ) ) + + @local_extra_dirs + def empty( self, obj, **kwargs ): + assert 'dir_only' not in kwargs, 'empty(): `dir_only` parameter is invalid here' + h = self.__get_rods_handle( obj, **kwargs ) + try: + return h.getSize() == 0 + except AttributeError: + # h is None + raise ObjectNotFound() + + def size( self, obj, **kwargs ): + assert 'dir_only' not in kwargs, 'size(): `dir_only` parameter is invalid here' + h = self.__get_rods_handle( obj, **kwargs ) + try: + return h.getSize() + except AttributeError: + # h is None + return 0 + + @local_extra_dirs + def delete( self, obj, entire_dir=False, **kwargs ): + assert 'dir_only' not in kwargs, 'delete(): `dir_only` parameter is invalid here' + rods_path = self.__get_rods_path( obj, **kwargs ) + # __get_rods_path prepends self.root_collection_path but we are going + # to ensure that it's valid anyway for safety's sake + assert rods_path.startswith( self.root_collection_path + '/' ), 'ERROR: attempt to delete object outside root collection (path was: %s)' % rods_path + if entire_dir: + # TODO + raise NotImplementedError() + h = self.__get_rods_handle( obj, **kwargs ) + try: + # note: PyRods' irodsFile.delete() does not set force + status = h.delete() + assert status == 0, '%d: %s' % ( status, irods.strerror( status ) ) + return True + except AttributeError: + log.warning( 'delete(): operation failed: object does not exist: %s', rods_path ) + except AssertionError, e: + # delete() does not raise on deletion failure + log.error( 'delete(): operation failed: %s', e ) + finally: + # remove the cached entry (finally is executed even when the try + # contains a return) + self.__clean_cache_entry( self, obj, **kwargs ) + return False + + @local_extra_dirs + def get_data( self, obj, start=0, count=-1, **kwargs ): + log.debug( 'get_data(): %s' ) + h = self.__get_rods_handle( obj, **kwargs ) + try: + h.seek( start ) + except AttributeError: + raise ObjectNotFound() + if count == -1: + return h.read() + else: + return f.read( count ) + # TODO: make sure implicit close is okay, DiskObjectStore actually + # reads data into a var, closes, and returns the var + + @local_extra_dirs + def get_filename( self, obj, **kwargs ): + log.debug( "get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id ) + + # For finding all places where get_filename is called... + #log.debug( ''.join( traceback.format_stack() ) ) + + cached_path = self.__get_cache_path( obj, **kwargs ) + + if not self.exists( obj, **kwargs ): + raise ObjectNotFound() + + # TODO: implement or define whether dir_only is valid + if 'dir_only' in kwargs: + raise NotImplementedError() + + # cache hit + if os.path.exists( cached_path ): + return os.path.abspath( cached_path ) + + # cache miss + # TODO: thread this + incoming_path = os.path.join( os.path.dirname( cached_path ), "__incoming_%s" % os.path.basename( cached_path ) ) + doi = irods.dataObjInp_t() + doi.objPath = self.__get_rods_path( obj, **kwargs ) + doi.dataSize = 0 # TODO: does this affect performance? should we get size? + doi.numThreads = 0 + # TODO: might want to VERIFY_CHKSUM_KW + log.debug( 'get_filename(): caching %s to %s', doi.objPath, incoming_path ) + + # do the iget + status = irods.rcDataObjGet( self.rods_conn, doi, incoming_path ) + + # if incoming already exists, we'll wait for another process or thread + # to finish caching + if status != irods.OVERWRITE_WITHOUT_FORCE_FLAG: + assert status == 0, 'get_filename(): iget %s failed (%s): %s' % ( doi.objPath, status, irods.strerror( status ) ) + # POSIX rename is atomic + # TODO: rename without clobbering + os.rename( incoming_path, cached_path ) + log.debug( 'get_filename(): cached %s to %s', doi.objPath, cached_path ) + + # another process or thread is caching, wait for it + while not os.path.exists( cached_path ): + # TODO: force restart after mod time > some configurable, or + # otherwise deal with this potential deadlock and interrupted + # transfers + time.sleep( 5 ) + log.debug( "get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id ) + + return os.path.abspath( cached_path ) + + @local_extra_dirs + def update_from_file(self, obj, file_name=None, create=False, **kwargs): + assert 'dir_only' not in kwargs, 'update_from_file(): `dir_only` parameter is invalid here' + + # do not create if not requested + if create and not self.exists( obj, **kwargs ): + raise ObjectNotFound() + + if file_name is None: + file_name = self.__get_cache_path( obj, **kwargs ) + + # put will create if necessary + doi = irods.dataObjInp_t() + doi.objPath = self.__get_rods_path( obj, **kwargs ) + doi.createMode = 0640 + doi.dataSize = os.stat( file_name ).st_size + doi.numThreads = 0 + irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource ) + irods.addKeyVal( doi.condInput, irods.FORCE_FLAG_KW, '' ) + # TODO: might want to VERIFY_CHKSUM_KW + log.debug( 'update_from_file(): updating %s to %s', file_name, doi.objPath ) + + # do the iput + status = irods.rcDataObjPut( self.rods_conn, doi, file_name ) + assert status == 0, 'update_from_file(): iput %s failed (%s): %s' % ( doi.objPath, status, irods.strerror( status ) ) + + def get_object_url(self, obj, **kwargs): + return None + + def get_store_usage_percent(self): + return 0.0 + +# monkeypatch an strerror method into the irods module +def _rods_strerror( errno ): + """ + The missing `strerror` for iRODS error codes + """ + if not hasattr( irods, '__rods_strerror_map' ): + irods.__rods_strerror_map = {} + for name in dir( irods ): + v = getattr( irods, name ) + if type( v ) == int and v < 0: + irods.__rods_strerror_map[ v ] = name + return irods.__rods_strerror_map.get( errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND' ) + +irods.strerror = _rods_strerror + +def rods_connect(): + """ + A basic iRODS connection mechanism that connects using the current iRODS + environment + """ + status, env = irods.getRodsEnv() + assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % ( status, irods.strerror( status ) ) + conn, err = irods.rcConnect( env.rodsHost, + env.rodsPort, + env.rodsUserName, + env.rodsZone ) + assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % ( err.status, err.msg ) + status, pw = irods.obfGetPw() + assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % ( status, irods.strerror( status ) ) + status = irods.clientLoginWithObfPassword( conn, pw ) + assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % ( status, irods.strerror( status ) ) + return env, conn diff -r 75bcfb029e8c5dd8e3d78829469a8583c73055ae -r fc4e1a162195e45f69573724adec564ffe1ea9ee scripts/scramble/scripts/PyRods.py --- /dev/null +++ b/scripts/scramble/scripts/PyRods.py @@ -0,0 +1,33 @@ +import os, sys +import subprocess + +# change back to the build dir +if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + +# find setuptools +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * + +tag = get_tag() # get the tag +get_deps() # require any dependent eggs +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) + +subprocess.check_call( "./scripts/configure", shell=True ) +subprocess.check_call( "CFLAGS='-fPIC' make clients", shell=True ) + +# reset args for distutils +me = sys.argv[0] +sys.argv = [ me ] +sys.argv.append( "egg_info" ) +if tag is not None: + sys.argv.append( "--tag-build=%s" %tag ) +# svn revision (if any) is handled directly in tag-build +sys.argv.append( "--no-svn-revision" ) +sys.argv.append( "bdist_egg" ) + +# apply patches (if any) +apply_patches() + +# do it +execfile( "setup.py", globals(), locals() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 28 Aug '13

28 Aug '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee6d553f7847/ Changeset: ee6d553f7847 Branch: stable User: natefoo Date: 2013-08-28 22:02:16 Summary: Logic on DiskObjectStore's empty() method was reversed (previously returned True when non-empty). Affected #: 1 file diff -r de04c251c6cae5760fd13c83030a6aab78ae0c4e -r ee6d553f7847ec47cca0cf205c767d1407eccbab lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -297,7 +297,7 @@ util.umask_fix_perms(path, self.config.umask, 0666) def empty(self, obj, **kwargs): - return os.path.getsize(self.get_filename(obj, **kwargs)) > 0 + return os.path.getsize(self.get_filename(obj, **kwargs)) == 0 def size(self, obj, **kwargs): if self.exists(obj, **kwargs): https://bitbucket.org/galaxy/galaxy-central/commits/f2677acb7d77/ Changeset: f2677acb7d77 User: natefoo Date: 2013-08-28 22:02:35 Summary: merge stable. Affected #: 2 files diff -r a60d756aeb5d40c62854fda8a5f5be274762cd86 -r f2677acb7d775a4d9ca26fc78a003dab060a0e8b lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -286,7 +286,7 @@ util.umask_fix_perms(path, self.config.umask, 0666) def empty(self, obj, **kwargs): - return os.path.getsize(self.get_filename(obj, **kwargs)) > 0 + return os.path.getsize(self.get_filename(obj, **kwargs)) == 0 def size(self, obj, **kwargs): if self.exists(obj, **kwargs): https://bitbucket.org/galaxy/galaxy-central/commits/4fea98291cbc/ Changeset: 4fea98291cbc User: natefoo Date: 2013-08-28 22:04:59 Summary: Remove S3 connection method from objectstore, missed when S3 was moved to its own module. Affected #: 1 file diff -r f2677acb7d775a4d9ca26fc78a003dab060a0e8b -r 4fea98291cbce9a0e8d580bfd9c4ef4a5184c680 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -565,25 +565,3 @@ else: size = '%.2fb' % bytes return size - -def get_OS_connection(config): - """ - Get a connection object for a cloud Object Store specified in the config. - Currently, this is a ``boto`` connection object. - """ - log.debug("Getting a connection object for '{0}' object store".format(config.object_store)) - a_key = config.os_access_key - s_key = config.os_secret_key - if config.object_store == 's3': - return S3Connection(a_key, s_key) - else: - # Establish the connection now - calling_format = boto.s3.connection.OrdinaryCallingFormat() - s3_conn = boto.connect_s3(aws_access_key_id=a_key, - aws_secret_access_key=s_key, - is_secure=config.os_is_secure, - host=config.os_host, - port=int(config.os_port), - calling_format=calling_format, - path=config.os_conn_path) - return s3_conn Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Datatypes: temporarily remove graph datatype sniffers (f3a985005267) until they can be made more discriminating
by commits-noreply＠bitbucket.org 28 Aug '13

28 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a60d756aeb5d/ Changeset: a60d756aeb5d User: carlfeberhard Date: 2013-08-28 20:22:27 Summary: Datatypes: temporarily remove graph datatype sniffers (f3a985005267) until they can be made more discriminating Affected #: 1 file diff -r 22a4f03c1fe40dedcb7e6f11510d58ada8e9c458 -r a60d756aeb5d40c62854fda8a5f5be274762cd86 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -285,9 +285,6 @@ <sniffer type="galaxy.datatypes.tabular:Sam"/><sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/> - <sniffer type="galaxy.datatypes.graph:Xgmml"/> - <sniffer type="galaxy.datatypes.graph:Sif"/> - <sniffer type="galaxy.datatypes.graph:Rdf"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Handle the case where the repository being installed has a newer downloadable changeset revision available. (Generally restricted to the new tool_dependency_definition repository type)
by commits-noreply＠bitbucket.org 28 Aug '13

28 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/22a4f03c1fe4/ Changeset: 22a4f03c1fe4 User: Dave Bouvier Date: 2013-08-28 15:54:45 Summary: Handle the case where the repository being installed has a newer downloadable changeset revision available. (Generally restricted to the new tool_dependency_definition repository type) Affected #: 1 file diff -r 29110e49c311339c521525f0b0884ce8eb172129 -r 22a4f03c1fe40dedcb7e6f11510d58ada8e9c458 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -214,24 +214,39 @@ def get_repo_info_dict( trans, repository_id, changeset_revision ): repository = suc.get_repository_in_tool_shed( trans, repository_id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - metadata = repository_metadata.metadata - if 'tools' in metadata: - includes_tools = True + if not repository_metadata: + # The received changeset_revision is no longer installable, so get the next changeset_revision in the repository's changelog. + # This generally occurs only with repositories of type tool_dependency_definition. + next_downloadable_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + if next_downloadable_changeset_revision: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision ) + if repository_metadata: + # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption is not valid we'll have to + # enhance the callers to handle repository_metadata values of None in the returned repo_info_dict. + metadata = repository_metadata.metadata + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel + if 'repository_dependencies' in metadata: + has_repository_dependencies = True + else: + has_repository_dependencies = False + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True + else: + includes_tool_dependencies = False else: + # Here's where we may have to handle enhancements to the callers. See above comment. includes_tools = False - includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel - if 'repository_dependencies' in metadata: - has_repository_dependencies = True - else: has_repository_dependencies = False - if 'tool_dependencies' in metadata: - includes_tool_dependencies = True - else: includes_tool_dependencies = False - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_dir ) + includes_tools_for_display_in_tool_panel = False ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add pipe (|) to the set of VALID_CHARS in shed_util_common.py. Fixes an issue with e.g. ReST display. TODO: Revisit this method and its usage throughout the toolshed and the toolshed interaction with Galaxy: e.g. is it still needed everywhere it is being used, and is it still doing what it is supposed to be doing?
by commits-noreply＠bitbucket.org 27 Aug '13

27 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/29110e49c311/ Changeset: 29110e49c311 User: dan Date: 2013-08-27 22:21:16 Summary: Add pipe (|) to the set of VALID_CHARS in shed_util_common.py. Fixes an issue with e.g. ReST display. TODO: Revisit this method and its usage throughout the toolshed and the toolshed interaction with Galaxy: e.g. is it still needed everywhere it is being used, and is it still doing what it is supposed to be doing? Affected #: 1 file diff -r f8b3dbe32435516af63e449cedb2e2fc9eb5bf26 -r 29110e49c311339c521525f0b0884ce8eb172129 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -37,7 +37,7 @@ INITIAL_CHANGELOG_HASH = '000000000000' MAX_CONTENT_SIZE = 1048576 MAX_DISPLAY_SIZE = 32768 -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>|" ) DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml' REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the installed repositories container on the Manage repository page in Galaxy to properly display mising repositroy and tool dependencies for an installed repository.
by commits-noreply＠bitbucket.org 27 Aug '13

27 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8b3dbe32435/ Changeset: f8b3dbe32435 User: greg Date: 2013-08-27 20:51:33 Summary: Enhance the installed repositories container on the Manage repository page in Galaxy to properly display mising repositroy and tool dependencies for an installed repository. Affected #: 1 file diff -r 6dfd50e1cfd1e2b9f356cb9e9319f85caf6a74f3 -r f8b3dbe32435516af63e449cedb2e2fc9eb5bf26 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1265,6 +1265,35 @@ return get_folder( sub_folder, key ) return None +def get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ): + """ + Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page. + """ + if len( repository_dependency ) == 6: + # Metadata should have been reset on this installed repository, but it wasn't. + tool_shed_repository_id = repository_dependency[ 4 ] + installation_status = repository_dependency[ 5 ] + tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ] + # Default prior_installation_required to False. + prior_installation_required = False + repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required ] + elif len( repository_dependency ) == 7: + # We have a repository dependency tuple that includes a prior_installation_required value. + tool_shed_repository_id = repository_dependency[ 5 ] + installation_status = repository_dependency[ 6 ] + repository_dependency = repository_dependency[ 0:5 ] + else: + tool_shed_repository_id = None + installation_status = 'unknown' + if tool_shed_repository_id: + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, trans.security.encode_id( tool_shed_repository_id ) ) + if tool_shed_repository: + if tool_shed_repository.missing_repository_dependencies: + installation_status = '%s, missing repository dependencies' % installation_status + elif tool_shed_repository.missing_tool_dependencies: + installation_status = '%s, missing tool dependencies' % installation_status + return tool_shed_repository_id, installation_status, repository_dependency + def get_components_from_key( key ): # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. items = key.split( STRSEP ) @@ -1315,22 +1344,8 @@ sub_folder.repository_dependencies.append( repository_dependency ) for repository_dependency in rd_value: if trans.webapp.name == 'galaxy': - if len( repository_dependency ) == 6: - # Metadata should have been reset on this installed repository, but it wasn't. - tool_shed_repository_id = repository_dependency[ 4 ] - installation_status = repository_dependency[ 5 ] - tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ] - # Default prior_installation_required to False. - prior_installation_required = False - repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required ] - elif len( repository_dependency ) == 7: - # We have a repository dependency tuple that includes a prior_installation_required value. - tool_shed_repository_id = repository_dependency[ 5 ] - installation_status = repository_dependency[ 6 ] - repository_dependency = repository_dependency[ 0:5 ] - else: - tool_shed_repository_id = None - installation_status = 'unknown' + tool_shed_repository_id, installation_status, repository_dependency = \ + get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ) else: tool_shed_repository_id = None installation_status = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Correctly handle the case where a repository installs correctly, but it depends on a repository with a tool dependency that is in an error state.
by commits-noreply＠bitbucket.org 27 Aug '13

27 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6dfd50e1cfd1/ Changeset: 6dfd50e1cfd1 User: Dave Bouvier Date: 2013-08-27 19:50:30 Summary: Correctly handle the case where a repository installs correctly, but it depends on a repository with a tool dependency that is in an error state. Affected #: 1 file diff -r 6439459c265ea7748ff9a16706fa5af5cc224269 -r 6dfd50e1cfd1e2b9f356cb9e9319f85caf6a74f3 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -269,6 +269,14 @@ url += '&%s' % params return url +def get_failed_tool_dependencies( repository ): + missing_dependencies = repository.missing_tool_dependencies + for repository_dependency in repository.repository_dependencies: + if not repository_dependency.includes_tool_dependencies: + continue + missing_dependencies.extend( get_failed_tool_dependencies( repository_dependency ) ) + return missing_dependencies + def get_latest_downloadable_changeset_revision( url, name, owner ): api_url_parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] params = urllib.urlencode( dict( name=name, owner=owner ) ) @@ -459,7 +467,7 @@ Update the repository metadata tool_test_results and appropriate flags using the API. ''' params[ 'tool_test_results' ] = test_results_dict - if '-info_only' in sys.argv: + if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: return {} else: return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) @@ -914,7 +922,7 @@ # "reason": "The Galaxy development team has determined that this repository should not be installed and tested by the automated framework." # } # } - failed_tool_dependencies = repository.includes_tool_dependencies and repository.tool_dependencies_with_installation_errors + failed_tool_dependencies = get_failed_tool_dependencies( repository ) failed_repository_dependencies = repository.repository_dependencies_with_installation_errors if 'missing_test_components' not in repository_status: repository_status[ 'missing_test_components' ] = [] @@ -958,7 +966,7 @@ log.error( 'One or more tool dependencies of this repository are marked as missing.' ) log.error( 'Updating repository and skipping functional tests.' ) # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.tool_dependencies_with_installation_errors: + for dependency in failed_tool_dependencies: test_result = dict( type=dependency.type, name=dependency.name, version=dependency.version, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Send changeset_revision to method that renders the Repository Actions pop-up menu in the tool shed to ensure the desired repository revision is used when choosing actions.
by commits-noreply＠bitbucket.org 27 Aug '13

27 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6439459c265e/ Changeset: 6439459c265e User: greg Date: 2013-08-27 19:24:37 Summary: Send changeset_revision to method that renders the Repository Actions pop-up menu in the tool shed to ensure the desired repository revision is used when choosing actions. Affected #: 5 files diff -r d7ea2536e8e370cd202f735351c37264270ddbaf -r 6439459c265ea7748ff9a16706fa5af5cc224269 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -664,10 +664,12 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. suc.update_repository( repo ) - metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + changeset_revision = repository.tip( trans.app ) + metadata = self.get_metadata( trans, id, changeset_revision ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, + changeset_revision=changeset_revision, metadata=metadata, commit_message=commit_message, repository_type_select_field=repository_type_select_field, @@ -1102,6 +1104,7 @@ repositories_archive_filename = os.path.basename( repositories_archive.name ) if error_message: message = error_message + status = 'error' else: trans.response.set_content_type( 'application/x-gzip' ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % ( repositories_archive_filename ) @@ -1109,9 +1112,7 @@ # Make sure the file is removed from disk after the contents have been downloaded. os.unlink( repositories_archive.name ) return opened_archive - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ @@ -1822,6 +1823,10 @@ return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) @web.expose + def import_capsule( self, trans, **kwd ): + pass + + @web.expose def index( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -2449,9 +2454,11 @@ message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) + changeset_revision = repository.tip( trans.app ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, + changeset_revision=changeset_revision, commit_message=commit_message, repository_type_select_field=repository_type_select_field, message=message, diff -r d7ea2536e8e370cd202f735351c37264270ddbaf -r 6439459c265ea7748ff9a16706fa5af5cc224269 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -241,6 +241,7 @@ selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/tool_shed/repository/upload.mako', repository=repository, + changeset_revision=tip, url=url, commit_message=commit_message, uncompress_file=uncompress_file, diff -r d7ea2536e8e370cd202f735351c37264270ddbaf -r 6439459c265ea7748ff9a16706fa5af5cc224269 templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -147,6 +147,9 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='import_capsule' )}">Import repository capsule</a> + </div> %if can_review_repositories: <div class="toolSectionPad"></div><div class="toolSectionTitle"> diff -r d7ea2536e8e370cd202f735351c37264270ddbaf -r 6439459c265ea7748ff9a16706fa5af5cc224269 templates/webapps/tool_shed/repository/browse_repository.mako --- a/templates/webapps/tool_shed/repository/browse_repository.mako +++ b/templates/webapps/tool_shed/repository/browse_repository.mako @@ -31,7 +31,7 @@ can_browse_contents = not is_new %> -${render_tool_shed_repository_actions( repository )} +${render_tool_shed_repository_actions( repository, changeset_revision=changeset_revision )} %if message: ${render_msg( message, status )} diff -r d7ea2536e8e370cd202f735351c37264270ddbaf -r 6439459c265ea7748ff9a16706fa5af5cc224269 templates/webapps/tool_shed/repository/rate_repository.mako --- a/templates/webapps/tool_shed/repository/rate_repository.mako +++ b/templates/webapps/tool_shed/repository/rate_repository.mako @@ -33,7 +33,7 @@ ${render_msg( message, status )} %endif -${render_tool_shed_repository_actions( repository, repo=None, metadata=None, changeset_revision=None )} +${render_tool_shed_repository_actions( repository, metadata=None, changeset_revision=None )} %if repository.user != trans.user: <div class="toolForm"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Aug '13

26 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/19c4ec5b8faf/ Changeset: 19c4ec5b8faf User: jgoecks Date: 2013-08-26 23:36:50 Summary: Use Galaxy root to dynamically load CSS files. Affected #: 3 files diff -r dd8329aa8d9e84397fd226adb9e54589bd1aea2f -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -74,7 +74,7 @@ initialize : function(options) { // load required css files - css.load_file(options.root + "static/style/galaxy.frame.css"); + css.load_file("static/style/galaxy.frame.css"); // read in defaults if (options) diff -r dd8329aa8d9e84397fd226adb9e54589bd1aea2f -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 static/scripts/utils/galaxy.css.js --- a/static/scripts/utils/galaxy.css.js +++ b/static/scripts/utils/galaxy.css.js @@ -29,7 +29,7 @@ { // check if css is already available if (!$('link[href^="' + url + '"]').length) - $('<link href="' + url + '" rel="stylesheet">').appendTo('head'); + $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head'); }; // return diff -r dd8329aa8d9e84397fd226adb9e54589bd1aea2f -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -21,12 +21,12 @@ ], function(css) { // load css - css.load_file("/static/style/jquery.rating.css"); - css.load_file("/static/style/history.css"); - css.load_file("/static/style/autocomplete_tagging.css"); - css.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css"); - css.load_file("/static/style/library.css"); - css.load_file("/static/style/trackster.css"); + css.load_file("static/style/jquery.rating.css"); + css.load_file("static/style/history.css"); + css.load_file("static/style/autocomplete_tagging.css"); + css.load_file("static/style/jquery-ui/smoothness/jquery-ui.css"); + css.load_file("static/style/library.css"); + css.load_file("static/style/trackster.css"); }); // trackster viewer https://bitbucket.org/galaxy/galaxy-central/commits/d7ea2536e8e3/ Changeset: d7ea2536e8e3 User: jgoecks Date: 2013-08-26 23:38:00 Summary: Pack scripts. Affected #: 3 files diff -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 -r d7ea2536e8e370cd202f735351c37264270ddbaf static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file(d.root+"static/style/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();$(".galaxy-frame-active").tooltip({title:"Enable/Disable Scratchbook"});$(".galaxy-frame-load").tooltip({title:"Show/Hide Scratchbook"});var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".galaxy-frame").fadeOut("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;$(".galaxy-frame").fadeIn("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file +define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file("static/style/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();$(".galaxy-frame-active").tooltip({title:"Enable/Disable Scratchbook"});$(".galaxy-frame-load").tooltip({title:"Show/Hide Scratchbook"});var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".galaxy-frame").fadeOut("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;$(".galaxy-frame").fadeIn("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file diff -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 -r d7ea2536e8e370cd202f735351c37264270ddbaf static/scripts/packed/utils/galaxy.css.js --- a/static/scripts/packed/utils/galaxy.css.js +++ b/static/scripts/packed/utils/galaxy.css.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(a){function b(g,d){var e=$('<div class="'+g+'"></div>');e.appendTo(":eq(0)");var f=e.css(d);e.remove();return f}function c(d){if(!$('link[href^="'+d+'"]').length){$('<link href="'+d+'" rel="stylesheet">').appendTo("head")}}return{load_file:c,get_attribute:b}}); \ No newline at end of file +define(["libs/underscore"],function(a){function b(g,d){var e=$('<div class="'+g+'"></div>');e.appendTo(":eq(0)");var f=e.css(d);e.remove();return f}function c(d){if(!$('link[href^="'+d+'"]').length){$('<link href="'+galaxy_config.root+d+'" rel="stylesheet">').appendTo("head")}}return{load_file:c,get_attribute:b}}); \ No newline at end of file diff -r 19c4ec5b8fafbf9095b102d4c59c6a59f125a8a1 -r d7ea2536e8e370cd202f735351c37264270ddbaf static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("/static/style/jquery.rating.css");a.load_file("/static/style/history.css");a.load_file("/static/style/autocomplete_tagging.css");a.load_file("/static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("/static/style/library.css");a.load_file("/static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/jquery-ui-combobox","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("static/style/jquery.rating.css");a.load_file("static/style/history.css");a.load_file("static/style/autocomplete_tagging.css");a.load_file("static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("static/style/library.css");a.load_file("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").combobox({appendTo:$("#overlay"),size:40});$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits August 2013