galaxy-commits October 2013

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226 discussions

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Oct '13

25 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/edab395a78b1/ Changeset: edab395a78b1 Branch: tool_api User: Kyle Ellrott Date: 2013-10-25 01:34:30 Summary: Adding output_name to /api/tool submit output. So files created by a tool can be mapped to the possible multiple output declaration it could have Affected #: 1 file diff -r bf0057b13f58f5c5438f1a6477b27bfceb14a2ce -r edab395a78b1f9d27bc2f2d233b2ded002b3080a lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -119,14 +119,18 @@ return { "message": { "type": "error", "data" : vars[ 'errors' ] } } # TODO: check for errors and ensure that output dataset(s) are available. - output_datasets = vars.get( 'out_data', {} ).values() + output_datasets = vars.get( 'out_data', {} ).iteritems() rval = { "outputs": [] } outputs = rval[ "outputs" ] #TODO:?? poss. only return ids? - for output in output_datasets: + for output_name, output in output_datasets: output_dict = output.to_dict() + #add the output name back into the output data structure + #so it's possible to figure out which newly created elements + #correspond with which tool file outputs + output_dict['output_name'] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) return rval https://bitbucket.org/galaxy/galaxy-central/commits/115a6924dc4c/ Changeset: 115a6924dc4c User: jmchilton Date: 2013-10-25 04:08:11 Summary: Merged in kellrott/galaxy-central/tool_api (pull request #243) Adding output_name to /api/tool submit output Matching client code added to blend4j: https://github.com/jmchilton/blend4j/commit/991ec2b30fd538c0b8e97aa55e681aa…. Thanks for the contribution Kyle! Affected #: 1 file diff -r 97cb7306dc345ce5e81861e421c5277701161802 -r 115a6924dc4c459467ca162e10ee24ba04001a1e lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -119,14 +119,18 @@ return { "message": { "type": "error", "data" : vars[ 'errors' ] } } # TODO: check for errors and ensure that output dataset(s) are available. - output_datasets = vars.get( 'out_data', {} ).values() + output_datasets = vars.get( 'out_data', {} ).iteritems() rval = { "outputs": [] } outputs = rval[ "outputs" ] #TODO:?? poss. only return ids? - for output in output_datasets: + for output_name, output in output_datasets: output_dict = output.to_dict() + #add the output name back into the output data structure + #so it's possible to figure out which newly created elements + #correspond with which tool file outputs + output_dict['output_name'] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) return rval 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: dannon: Re-close search feature branch.
by commits-noreply＠bitbucket.org 25 Oct '13

25 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e19d39296919/ Changeset: e19d39296919 Branch: search User: dannon Date: 2013-10-25 00:12:50 Summary: Re-close search feature branch. Affected #: 0 files 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 25 Oct '13

25 Oct '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9da06a2f3db4/ Changeset: 9da06a2f3db4 Branch: search User: Kyle Ellrott Date: 2013-10-24 21:50:53 Summary: Default merge Affected #: 45 files diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -42,11 +42,20 @@ Binary.unsniffable_binary_formats.append(ext) @staticmethod - def is_sniffable_binary(filename): + def is_sniffable_binary( filename ): + format_information = None for format in Binary.sniffable_binary_formats: - if format["class"]().sniff(filename): - return (format["type"], format["ext"]) - return None + format_instance = format[ "class" ]() + try: + if format_instance.sniff(filename): + format_information = ( format["type"], format[ "ext" ] ) + break + except Exception: + # Sniffer raised exception, could be any number of + # reasons for this so there is not much to do besides + # trying next sniffer. + pass + return format_information @staticmethod def is_ext_unsniffable(ext): diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/datatypes/checkers.py --- a/lib/galaxy/datatypes/checkers.py +++ b/lib/galaxy/datatypes/checkers.py @@ -1,5 +1,6 @@ import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr from galaxy import util +from StringIO import StringIO try: import Image as PIL @@ -53,20 +54,15 @@ if file_path: temp = open( name, "U" ) else: - temp = name + temp = StringIO( name ) chars_read = 0 - for chars in temp: - for char in chars: - chars_read += 1 + try: + for char in temp.read( 100 ): if util.is_binary( char ): is_binary = True break - if chars_read > 100: - break - if chars_read > 100: - break - if file_path: - temp.close() + finally: + temp.close( ) return is_binary def check_gzip( file_path ): diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -5,7 +5,6 @@ from galaxy import eggs eggs.require("simplejson") - import copy import cPickle import logging @@ -37,10 +36,12 @@ """ def __init__( self, target ): self.target = target + def __call__( self, *args, **kwargs ): class_locals = sys._getframe( 1 ).f_locals #get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement) statements = class_locals.setdefault( STATEMENTS, [] ) #get and set '__galaxy_statments__' to an empty list if not in locals dict statements.append( ( self, args, kwargs ) ) #add Statement containing info to populate a MetadataElementSpec + @classmethod def process( cls, element ): for statement, args, kwargs in getattr( element, STATEMENTS, [] ): @@ -59,29 +60,38 @@ #initialize dict if needed if self.parent._metadata is None: self.parent._metadata = {} + def get_parent( self ): if "_parent" in self.__dict__: return self.__dict__["_parent"]() return None + def set_parent( self, parent ): self.__dict__["_parent"] = weakref.ref( parent ) # use weakref to prevent a circular reference interfering with garbage collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be hashable, so cannot use proxy. parent = property( get_parent, set_parent ) + @property def spec( self ): return self.parent.datatype.metadata_spec + def __iter__( self ): return self.parent._metadata.__iter__() + def get( self, key, default=None ): try: return self.__getattr__( key ) or default except: return default + def items(self): return iter( [ ( k, self.get( k ) ) for k in self.spec.iterkeys() ] ) + def __str__(self): return dict( self.items() ).__str__() + def __nonzero__( self ): return bool( self.parent._metadata ) + def __getattr__( self, name ): if name in self.spec: if name in self.parent._metadata: @@ -89,6 +99,7 @@ return self.spec[name].wrap( self.spec[name].default, object_session( self.parent ) ) if name in self.parent._metadata: return self.parent._metadata[name] + def __setattr__( self, name, value ): if name == "parent": return self.set_parent( value ) @@ -97,14 +108,17 @@ self.parent._metadata[name] = self.spec[name].unwrap( value ) else: self.parent._metadata[name] = value + def element_is_set( self, name ): return bool( self.parent._metadata.get( name, False ) ) + def get_html_by_name( self, name, **kwd ): if name in self.spec: rval = self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd ) if rval is None: return self.spec[name].no_value return rval + def make_dict_copy( self, to_copy ): """Makes a deep copy of input iterable to_copy according to self.spec""" rval = {} @@ -112,6 +126,7 @@ if key in self.spec: rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy ) return rval + def from_JSON_dict( self, filename ): dataset = self.parent log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) ) @@ -123,6 +138,7 @@ #if the metadata value is not found in our externally set metadata but it has a value in the 'old' #metadata associated with our dataset, we'll delete it from our dataset's metadata dict del dataset._metadata[ name ] + def to_JSON_dict( self, filename ): #galaxy.model.customtypes.json_encoder.encode() meta_dict = {} @@ -131,6 +147,7 @@ if name in dataset_meta_dict: meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] ) simplejson.dump( meta_dict, open( filename, 'wb+' ) ) + def __getstate__( self ): return None #cannot pickle a weakref item (self._parent), when data._metadata_collection is None, it will be recreated on demand @@ -163,10 +180,12 @@ def __init__( self, spec ): self.spec = spec - def get_html_field( self, value=None, context={}, other_values={}, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, **kwd ): + context = context or {} + other_values = other_values or {} return form_builder.TextField( self.spec.name, value=value ) - def get_html( self, value, context={}, other_values={}, **kwd ): + def get_html( self, value, context=None, other_values=None, **kwd ): """ The "context" is simply the metadata collection/bunch holding this piece of metadata. This is passed in to allow for @@ -175,6 +194,9 @@ example, a column assignment should validate against the number of columns in the dataset. """ + context = context or {} + other_values = other_values or {} + if self.spec.get("readonly"): return value if self.spec.get("optional"): @@ -296,7 +318,10 @@ value = [value] return ",".join( map( str, value ) ) - def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + field = form_builder.SelectField( self.spec.name, multiple=self.multiple, display=self.spec.get("display") ) if self.values: value_list = self.values @@ -316,7 +341,10 @@ field.add_option( val, label, selected=False ) return field - def get_html( self, value, context={}, other_values={}, values=None, **kwd ): + def get_html( self, value, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + if self.spec.get("readonly"): if value in [ None, [] ]: return str( self.spec.no_value ) @@ -338,21 +366,30 @@ if not isinstance( value, list ): return [value] return value + class DBKeyParameter( SelectParameter ): - def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd): + + def get_html_field( self, value=None, context=None, other_values=None, values=None, **kwd): + context = context or {} + other_values = other_values or {} try: values = kwd['trans'].db_builds except KeyError: pass return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd) - def get_html( self, value=None, context={}, other_values={}, values=None, **kwd): + + def get_html( self, value=None, context=None, other_values=None, values=None, **kwd): + context = context or {} + other_values = other_values or {} try: values = kwd['trans'].db_builds except KeyError: pass return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd) + class RangeParameter( SelectParameter ): + def __init__( self, spec ): SelectParameter.__init__( self, spec ) # The spec must be set with min and max values @@ -360,12 +397,18 @@ self.max = spec.get( "max" ) or 1 self.step = self.spec.get( "step" ) or 1 - def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + if values is None: values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) return SelectParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) - def get_html( self, value, context={}, other_values={}, values=None, **kwd ): + def get_html( self, value, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + if values is None: values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) return SelectParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) @@ -376,35 +419,46 @@ values = [ int(x) for x in value ] return values + class ColumnParameter( RangeParameter ): - def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + if values is None and context: column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) - def get_html( self, value, context={}, other_values={}, values=None, **kwd ): + def get_html( self, value, context=None, other_values=None, values=None, **kwd ): + context = context or {} + other_values = other_values or {} + if values is None and context: column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) + class ColumnTypesParameter( MetadataParameter ): def to_string( self, value ): return ",".join( map( str, value ) ) + class ListParameter( MetadataParameter ): def to_string( self, value ): return ",".join( [str(x) for x in value] ) + class DictParameter( MetadataParameter ): def to_string( self, value ): return simplejson.dumps( value ) + class PythonObjectParameter( MetadataParameter ): def to_string( self, value ): @@ -412,16 +466,21 @@ return self.spec._to_string( self.spec.no_value ) return self.spec._to_string( value ) - def get_html_field( self, value=None, context={}, other_values={}, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, **kwd ): + context = context or {} + other_values = other_values or {} return form_builder.TextField( self.spec.name, value=self._to_string( value ) ) - def get_html( self, value=None, context={}, other_values={}, **kwd ): + def get_html( self, value=None, context=None, other_values=None, **kwd ): + context = context or {} + other_values = other_values or {} return str( self ) @classmethod def marshal( cls, value ): return value + class FileParameter( MetadataParameter ): def to_string( self, value ): @@ -429,10 +488,14 @@ return str( self.spec.no_value ) return value.file_name - def get_html_field( self, value=None, context={}, other_values={}, **kwd ): + def get_html_field( self, value=None, context=None, other_values=None, **kwd ): + context = context or {} + other_values = other_values or {} return form_builder.TextField( self.spec.name, value=str( value.id ) ) - def get_html( self, value=None, context={}, other_values={}, **kwd ): + def get_html( self, value=None, context=None, other_values=None, **kwd ): + context = context or {} + other_values = other_values or {} return "<div>No display available for Metadata Files</div>" def wrap( self, value, session ): @@ -497,12 +560,15 @@ #we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us return MetadataTempFile( **kwds ) + #This class is used when a database file connection is not available class MetadataTempFile( object ): tmp_dir = 'database/tmp' #this should be overwritten as necessary in calling scripts + def __init__( self, **kwds ): self.kwds = kwds self._filename = None + @property def file_name( self ): if self._filename is None: @@ -510,17 +576,21 @@ self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) open( self._filename, 'wb+' ) #create an empty file, so it can't be reused using tempfile return self._filename + def to_JSON( self ): return { '__class__':self.__class__.__name__, 'filename':self.file_name, 'kwds':self.kwds } + @classmethod def from_JSON( cls, json_dict ): #need to ensure our keywords are not unicode rval = cls( **stringify_dictionary_keys( json_dict['kwds'] ) ) rval._filename = json_dict['filename'] return rval + @classmethod def is_JSONified_value( cls, value ): return ( isinstance( value, dict ) and value.get( '__class__', None ) == cls.__name__ ) + @classmethod def cleanup_from_JSON_dict_filename( cls, filename ): try: @@ -533,12 +603,15 @@ except Exception, e: log.debug( 'Failed to cleanup MetadataTempFile temp files from %s: %s' % ( filename, e ) ) + #Class with methods allowing set_meta() to be called externally to the Galaxy head class JobExternalOutputMetadataWrapper( object ): #this class allows access to external metadata filenames for all outputs associated with a job #We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well) + def __init__( self, job ): self.job_id = job.id + def get_output_filenames_by_dataset( self, dataset, sa_session ): if isinstance( dataset, galaxy.model.HistoryDatasetAssociation ): return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \ @@ -549,12 +622,15 @@ .filter_by( job_id = self.job_id, library_dataset_dataset_association_id = dataset.id ) \ .first() #there should only be one or None return None + def get_dataset_metadata_key( self, dataset ): # Set meta can be called on library items and history items, # need to make different keys for them, since ids can overlap return "%s_%d" % ( dataset.__class__.__name__, dataset.id ) + def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, - output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, kwds={} ): + output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, kwds=None ): + kwds = kwds or {} #fill in metadata_files_dict and return the command with args required to set metadata def __metadata_files_list_to_cmd_line( metadata_files ): def __get_filename_override(): @@ -652,6 +728,7 @@ os.remove( fname ) except Exception, e: log.debug( 'Failed to cleanup external metadata file (%s) for %s: %s' % ( key, dataset_key, e ) ) + def set_job_runner_external_pid( self, pid, sa_session ): for metadata_files in sa_session.query( galaxy.model.Job ).get( self.job_id ).external_output_metadata: metadata_files.job_runner_external_pid = pid diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -547,8 +547,11 @@ display_app.id = tool_dict[ 'guid' ] break if deactivate: - del self.display_applications[ display_app.id ] - del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] + if display_app.id in self.display_applications: + del self.display_applications[ display_app.id ] + if extension in self.datatypes_by_extension: + if display_app.id in self.datatypes_by_extension[ extension ].display_applications: + del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] if inherit and ( self.datatypes_by_extension[ extension ], display_app ) in self.inherit_display_application_by_class: self.inherit_display_application_by_class.remove( ( self.datatypes_by_extension[ extension ], display_app ) ) self.log.debug( "Deactivated display application '%s' for datatype '%s'." % ( display_app.id, extension ) ) diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -311,8 +311,9 @@ payload = self._validate_and_parse_update_payload( payload ) hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=True ) - # additional checks here (security, etc.) - changed = self.set_hda_from_dict( trans, hda, payload ) + # get_dataset can return a string during an error + if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): + changed = self.set_hda_from_dict( trans, hda, payload ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -4,7 +4,7 @@ import logging from paste.httpexceptions import HTTPBadRequest, HTTPNotImplemented from galaxy import util, web -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController log = logging.getLogger( __name__ ) @@ -22,27 +22,19 @@ query = trans.sa_session.query( trans.app.model.User ) deleted = util.string_as_bool( deleted ) if deleted: - route = 'deleted_user' query = query.filter( trans.app.model.User.table.c.deleted == True ) # only admins can see deleted users if not trans.user_is_admin(): return [] - else: - route = 'user' query = query.filter( trans.app.model.User.table.c.deleted == False ) # special case: user can see only their own user if not trans.user_is_admin(): item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for( route, id=item['id'] ) - item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) return [item] - for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) #TODO: move into api_values - item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) - item['url'] = url_for( route, id=item['id'] ) rval.append( item ) return rval diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 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 @@ -2741,6 +2741,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if repository: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} @@ -2751,21 +2754,24 @@ tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' else: next_installable_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - if next_installable_revision: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + if repository_metadata is None: + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' else: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' # Handle revision updates. if changeset_revision == repository.tip( trans.app ): tool_shed_status_dict[ 'revision_update' ] = 'False' else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: + if repository_metadata is None: + tool_shed_status_dict[ 'revision_update' ] = 'True' + else: tool_shed_status_dict[ 'revision_update' ] = 'False' - else: - tool_shed_status_dict[ 'revision_update' ] = 'True' # Handle revision upgrades. ordered_metadata_changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) num_metadata_revisions = len( ordered_metadata_changeset_revisions ) diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -502,7 +502,6 @@ pre_cmd = './configure %s && make && make install' % configure_opts else: pre_cmd = './configure prefix=$INSTALL_DIR %s && make && make install' % configure_opts - cmd = install_environment.build_command( td_common_util.evaluate_template( pre_cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -318,22 +318,23 @@ error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) return revised, elem, error_message -def handle_set_environment_for_install( trans, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): +def handle_repository_dependency_sub_elem( trans, package_altered, altered, actions_elem, action_index, action_elem, unpopulate=False ): + # This method populates the toolshed and changeset_revision attributes for each of the following. # <action type="set_environment_for_install"> - # <repository name="package_eigen_2_0" owner="test" changeset_revision="09eb05087cd0"> - # <package name="eigen" version="2.0.17" /> - # </repository> - # </action> + # <action type="setup_r_environment"> + # <action type="setup_ruby_environment"> for repo_index, repo_elem in enumerate( action_elem ): - revised, repository_elem, error_message = handle_repository_dependency_elem( trans, repo_elem, unpopulate=unpopulate ) - if error_message: - exception_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - raise Exception( exception_message ) - if revised: - action_elem[ repo_index ] = repository_elem - package_altered = True - if not altered: - altered = True + # Make sure to skip comments and tags that are not <repository>. + if repo_elem.tag == 'repository': + revised, repository_elem, error_message = handle_repository_dependency_elem( trans, repo_elem, unpopulate=unpopulate ) + if error_message: + exception_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message + raise Exception( exception_message ) + if revised: + action_elem[ repo_index ] = repository_elem + package_altered = True + if not altered: + altered = True if package_altered: actions_elem[ action_index ] = action_elem return package_altered, altered, actions_elem @@ -402,29 +403,28 @@ last_actions_elem[ last_actions_elem_package_index ] = last_actions_elem_package_elem actions_group_elem[ last_actions_index ] = last_actions_elem else: - last_actions_elem_action_type = last_actions_elem.get( 'type' ) - if last_actions_elem_action_type == 'set_environment_for_install': - last_actions_package_altered, altered, last_actions_elem = \ - handle_set_environment_for_install( trans, - last_actions_package_altered, - altered, - actions_group_elem, - last_actions_index, - last_actions_elem, - unpopulate=unpopulate ) + # Inspect the sub elements of last_actions_elem to locate all <repository> tags and + # populate them with toolshed and changeset_revision attributes if necessary. + last_actions_package_altered, altered, last_actions_elem = \ + handle_repository_dependency_sub_elem( trans, + last_actions_package_altered, + altered, + actions_group_elem, + last_actions_index, + last_actions_elem, + unpopulate=unpopulate ) elif actions_elem.tag == 'actions': # We are not in an <actions_group> tag set, so we must be in an <actions> tag set. for action_index, action_elem in enumerate( actions_elem ): - - action_type = action_elem.get( 'type' ) - if action_type == 'set_environment_for_install': - package_altered, altered, actions_elem = handle_set_environment_for_install( trans, - package_altered, - altered, - actions_elem, - action_index, - action_elem, - unpopulate=unpopulate ) + # Inspect the sub elements of last_actions_elem to locate all <repository> tags and populate them with + # toolshed and changeset_revision attributes if necessary. + package_altered, altered, actions_elem = handle_repository_dependency_sub_elem( trans, + package_altered, + altered, + actions_elem, + action_index, + action_elem, + unpopulate=unpopulate ) if package_altered: package_elem[ actions_index ] = actions_elem if package_altered: diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -483,7 +483,7 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - env_var_name = env_var_elem.get( 'name', None ) + env_var_name = elem.get( 'name', None ) if env_var_name: # Tool dependencies of type "set_environmnet" always have the version attribute set to None. attr_tup = ( env_var_name, None, 'set_environment' ) diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -278,7 +278,7 @@ sy.addClass(this.state.success); // update galaxy history - Galaxy.currHistoryPanel.refresh(); + Galaxy.currHistoryPanel.refreshHdas(); }, // error diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -5,7 +5,7 @@ //============================================================================== /** @class Read only view for HistoryDatasetAssociation. * @name HDABaseView - * + * * @augments Backbone.View * @borrows LoggableMixin#logger as #logger * @borrows LoggableMixin#log as #log @@ -23,7 +23,7 @@ fxSpeed : 'fast', - // ......................................................................... SET UP + // ......................................................................... set up /** Set up the view, cache url templates, bind listeners * @param {Object} attributes * @config {Object} urlTemplates nested object containing url templates for this view @@ -44,16 +44,28 @@ this._setUpListeners(); }, + /** event listeners */ _setUpListeners : function(){ + // re-rendering on any model changes - this.model.on( 'change', this.render, this ); + this.model.on( 'change', function( model, options ){ + + // if the model moved into the ready state and is expanded without details, fetch those details now + if( this.model.changedAttributes().state && this.model.inReadyState() + && this.expanded && !this.model.hasDetails() ){ + this.model.fetch(); // will render automatically (due to lines below) + + } else { + this.render(); + } + }, this ); //this.on( 'all', function( event ){ // this.log( event ); //}, this ); }, - // ......................................................................... RENDER MAIN + // ......................................................................... render main /** Render this HDA, set up ui. * @fires rendered:ready when rendered and NO running HDAs * @fires rendered when rendered and running HDAs @@ -114,7 +126,6 @@ _setUpBehaviors : function( $container ){ $container = $container || this.$el; // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - //TODO: we can potentially skip this step and call popupmenu directly on the download button make_popup_menus( $container ); $container.find( '[title]' ).tooltip({ placement : 'bottom' }); }, @@ -205,13 +216,10 @@ * @returns {jQuery} rendered DOM */ _render_titleLink : function(){ - return $( jQuery.trim( HDABaseView.templates.titleLink( - //TODO?? does this need urls? - _.extend( this.model.toJSON(), { urls: this.urls } ) - ))); + return $( jQuery.trim( HDABaseView.templates.titleLink( this.model.toJSON() ))); }, - // ......................................................................... RENDER BODY + // ......................................................................... body /** Render the data/metadata summary (format, size, misc info, etc.). * @returns {jQuery} rendered DOM */ @@ -275,7 +283,7 @@ /** Render links to external genome display applications (igb, gbrowse, etc.). * @param {jQuery} $parent the jq node to search for .display-apps and render into to (defaults to this.$el) */ - //TODO: not a fan of the style on these +//TODO: move into visualization button _render_displayApps : function( $parent ){ $parent = $parent || this.$el; var $displayAppsDiv = $parent.find( 'div.display-apps' ), @@ -302,7 +310,6 @@ /** Render the data peek. * @returns {jQuery} rendered DOM */ - //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible _render_peek : function(){ var peek = this.model.get( 'peek' ); if( !peek ){ return null; } @@ -318,74 +325,38 @@ /** Render the enclosing div of the hda body and, if expanded, the html in the body * @returns {jQuery} rendered DOM */ - //TODO: only render these on expansion (or already expanded) _render_body : function(){ - var body = $( '<div/>' ) + var $body = $( '<div/>' ) .attr( 'id', 'info-' + this.model.get( 'id' ) ) .addClass( 'historyItemBody' ) .attr( 'style', 'display: none' ); if( this.expanded ){ // only render the body html if it's being shown - this._render_body_html( body ); - //TODO: switch back when jq -> 1.9 - //body.show(); - body.css( 'display', 'block' ); + this._render_body_html( $body ); + $body.show(); } - return body; + return $body; }, /** Render the (expanded) body of an HDA, dispatching to other functions based on the HDA state * @param {jQuery} body the body element to append the html to */ - //TODO: only render these on expansion (or already expanded) - _render_body_html : function( body ){ + _render_body_html : function( $body ){ //this.log( this + '_render_body' ); - body.html( '' ); - //TODO: not a fan of this dispatch - switch( this.model.get( 'state' ) ){ - case hdaModel.HistoryDatasetAssociation.STATES.NEW : - this._render_body_new( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE : - this._render_body_not_viewable( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.UPLOAD : - this._render_body_uploading( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.PAUSED: - this._render_body_paused( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.QUEUED : - this._render_body_queued( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.RUNNING : - this._render_body_running( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.ERROR : - this._render_body_error( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.DISCARDED : - this._render_body_discarded( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.SETTING_METADATA : - this._render_body_setting_metadata( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.EMPTY : - this._render_body_empty( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.FAILED_METADATA : - this._render_body_failed_metadata( body ); - break; - case hdaModel.HistoryDatasetAssociation.STATES.OK : - this._render_body_ok( body ); - break; - default: - //??: no body? - body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); + $body.empty(); + + var modelState = this.model.get( 'state' ); + // cheesy get function by assumed matching name + var renderFnName = '_render_body_' + modelState, + renderFn = this[ renderFnName ]; + if( _.isFunction( renderFn ) ){ + this[ renderFnName ]( $body ); + } else { + $body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) ); } - body.append( '<div style="clear: both"></div>' ); - this._setUpBehaviors( body ); + $body.append( '<div style="clear: both"></div>' ); + this._setUpBehaviors( $body ); }, /** Render a new dataset - this should be a transient state that's never shown @@ -400,15 +371,14 @@ /** Render inaccessible, not-owned by curr user. * @param {jQuery} parent DOM to which to append this body */ - _render_body_not_viewable : function( parent ){ - //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right - parent.append( $( '<div>' + _l( 'You do not have permission to view dataset' ) + '</div>' ) ); + _render_body_noPermission : function( parent ){ + parent.append( $( '<div>' + _l( 'You do not have permission to view this dataset' ) + '</div>' ) ); }, /** Render an HDA still being uploaded. * @param {jQuery} parent DOM to which to append this body */ - _render_body_uploading : function( parent ){ + _render_body_upload : function( parent ){ parent.append( $( '<div>' + _l( 'Dataset is uploading' ) + '</div>' ) ); }, @@ -424,7 +394,8 @@ * @param {jQuery} parent DOM to which to append this body */ _render_body_paused: function( parent ){ - parent.append( $( '<div>' + _l( 'Job is paused. Use the history menu to resume' ) + '</div>' ) ); + parent.append( $( '<div>' + _l( 'Job is paused. ' + + 'Use the "Resume Paused Jobs" in the history menu to resume' ) + '</div>' ) ); parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); }, @@ -469,8 +440,6 @@ * @param {jQuery} parent DOM to which to append this body */ _render_body_empty : function( parent ){ - //TODO: replace i with dataset-misc-info class - //?? why are we showing the file size when we know it's zero?? parent.append( $( '<div>' + _l( 'No data' ) + ': <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); }, @@ -479,7 +448,6 @@ * @param {jQuery} parent DOM to which to append this body */ _render_body_failed_metadata : function( parent ){ - //TODO: the css for this box is broken (unlike the others) // add a message box about the failure at the top of the body... parent.append( $( HDABaseView.templates.failedMetadata( _.extend( this.model.toJSON(), { urls: this.urls } ) @@ -496,7 +464,6 @@ parent.append( this._render_hdaSummary() ); // return shortened form if del'd - //TODO: is this correct? maybe only on purged if( this.model.isDeletedOrPurged() ){ parent.append( this._render_primaryActionButtons([ this._render_downloadButton, @@ -517,44 +484,55 @@ parent.append( this._render_peek() ); }, - // ......................................................................... EVENTS + // ......................................................................... events /** event map */ events : { + // expand the body when the title is clicked 'click .historyItemTitle' : 'toggleBodyVisibility' }, - /** Render an HDA that's done running and where everything worked. + /** Show or hide the body/details of an HDA. + * note: if the model does not have detailed data, fetch that data before showing the body * @param {Event} event the event that triggered this (@link HDABaseView#events) * @param {Boolean} expanded if true, expand; if false, collapse * @fires body-expanded when a body has been expanded * @fires body-collapsed when a body has been collapsed */ toggleBodyVisibility : function( event, expand ){ - var hdaView = this; expand = ( expand === undefined )?( !this.body.is( ':visible' ) ):( expand ); if( expand ){ - if( this.model.inReadyState() && !this.model.hasDetails() ){ - var xhr = this.model.fetch(); - xhr.done( function( model ){ - hdaView.expandBody(); - }); - } else { - this.expandBody(); - } + this.expandBody(); } else { this.collapseBody(); } }, + /** Render and show the full, detailed body of this view including extra data and controls. + * @fires body-expanded when a body has been expanded + */ expandBody : function(){ var hdaView = this; - hdaView._render_body_html( hdaView.body ); - this.body.slideDown( hdaView.fxSpeed, function(){ - hdaView.expanded = true; - hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); - }); + + function _renderBodyAndExpand(){ + hdaView._render_body_html( hdaView.body ); + hdaView.body.slideDown( hdaView.fxSpeed, function(){ + hdaView.expanded = true; + hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); + }); + } + // fetch first if no details in the model + if( this.model.inReadyState() && !this.model.hasDetails() ){ + this.model.fetch().done( function( model ){ + _renderBodyAndExpand(); + }); + } else { + _renderBodyAndExpand(); + } }, + /** Hide the body/details of an HDA. + * @fires body-collapsed when a body has been collapsed + */ collapseBody : function(){ var hdaView = this; this.body.slideUp( hdaView.fxSpeed, function(){ @@ -563,7 +541,10 @@ }); }, - // ......................................................................... DELETION + // ......................................................................... removal + /** Remove this view's html from the DOM and remove all event listeners. + * @param {Function} callback an optional function called when removal is done + */ remove : function( callback ){ var hdaView = this; this.$el.fadeOut( hdaView.fxSpeed, function(){ @@ -573,7 +554,8 @@ }); }, - // ......................................................................... MISC + // ......................................................................... misc + /** String representation */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); return 'HDABaseView(' + modelString + ')'; @@ -594,5 +576,5 @@ //============================================================================== return { - HDABaseView : HDABaseView, + HDABaseView : HDABaseView };}); diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -14,7 +14,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( /** @lends HDAEditView.prototype */{ - // ......................................................................... SET UP + // ......................................................................... set up /** Set up the view, cache url templates, bind listeners. * Overrides HDABaseView.initialize to change default actions (adding re-run). * @param {Object} attributes @@ -43,7 +43,7 @@ //var hdaView = this; }, - // ......................................................................... RENDER WARNINGS + // ......................................................................... render warnings /** Render any hda warnings including: is deleted, is purged, is hidden. * Overrides _render_warnings to include links to further actions (undelete, etc.)). * @returns {Object} the templated urls @@ -71,13 +71,14 @@ return buttonDiv; }, +//TODO: move titleButtons into state renderers, remove state checks in the buttons + /** Render icon-button to edit the attributes (format, permissions, etc.) this hda. * @returns {jQuery} rendered DOM */ _render_editButton : function(){ // don't show edit while uploading, in-accessible // DO show if in error (ala previous history panel) - //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ) || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) @@ -114,7 +115,6 @@ */ _render_deleteButton : function(){ // don't show delete if... - //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ @@ -147,7 +147,7 @@ return this.deleteButton.render().$el; }, - // ......................................................................... RENDER BODY + // ......................................................................... render body /** Render the data/metadata summary (format, size, misc info, etc.). * Overrides _render_hdaSummary to include edit link in dbkey. * @see HDABaseView#_render_hdaSummary @@ -158,7 +158,6 @@ // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' if( this.model.get( 'metadata_dbkey' ) === '?' && !this.model.isDeletedOrPurged() ){ - //TODO: use HDABaseView and select/replace base on this switch _.extend( modelData, { dbkey_unknown_and_editable : true }); } return hdaBase.HDABaseView.templates.hdaSummary( modelData ); @@ -238,10 +237,8 @@ var $icon = this.visualizationsButton.render().$el; $icon.addClass( 'visualize-icon' ); // needed? - //TODO: make this more concise // map a function to each visualization in the icon's attributes // create a popupmenu from that map - /** @inner */ function create_viz_action( visualization ) { switch( visualization ){ @@ -269,7 +266,6 @@ // >1: Populate menu dict with visualization fns, make the popupmenu } else { _.each( visualizations, function( visualization ) { - //TODO: move to utils var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); popup_menu_dict[ _l( titleCaseVisualization ) ] = create_viz_action( visualization ); }); @@ -334,9 +330,7 @@ /** Render icon-button to load and display tagging html. * @returns {jQuery} rendered DOM */ - //TODO: these should be a sub-MV _render_tagButton : function(){ - //TODO: check for User if( !this.hasUser || !this.urls.tags.get ){ this.tagButton = null; return null; @@ -354,9 +348,7 @@ /** Render icon-button to load and display annotation html. * @returns {jQuery} rendered DOM */ - //TODO: these should be a sub-MV _render_annotateButton : function(){ - //TODO: check for User if( !this.hasUser || !this.urls.annotation.get ){ this.annotateButton = null; return null; @@ -370,33 +362,6 @@ return this.annotateButton.render().$el; }, - // ......................................................................... other elements - /** Render area to display tags. - * @returns {jQuery} rendered DOM - */ -//TODO: into sub-MV -//TODO: check for User - _render_tagArea : function(){ - if( !this.urls.tags.set ){ return null; } - //TODO: move to mvc/tags.js - return $( HDAEditView.templates.tagArea( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ).trim() ); - }, - - /** Render area to display annotation. - * @returns {jQuery} rendered DOM - */ -//TODO: into sub-MV -//TODO: check for User - _render_annotationArea : function(){ - if( !this.urls.annotation.get ){ return null; } - //TODO: move to mvc/annotations.js - return $( HDAEditView.templates.annotationArea( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ).trim() ); - }, - // ......................................................................... state body renderers /** Render an HDA whose job has failed. * Overrides _render_body_error to prepend error report button to primary actions strip. @@ -415,7 +380,6 @@ * @see HDABaseView#_render_body_ok */ _render_body_ok : function( parent ){ - //TODO: should call super somehow and insert the needed... // most common state renderer and the most complicated parent.append( this._render_hdaSummary() ); @@ -451,7 +415,7 @@ parent.append( this._render_peek() ); }, - // ......................................................................... EVENTS + // ......................................................................... events /** event map */ events : { 'click .historyItemTitle' : 'toggleBodyVisibility', @@ -463,16 +427,28 @@ 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' }, - // ......................................................................... STATE CHANGES / MANIPULATION + /** listener for item purge */ confirmPurge : function _confirmPurge( ev ){ - //TODO: confirm dialog +//TODO: confirm dialog this.model.purge({ url: this.urls.purge }); return false; }, + // ......................................................................... tags + /** Render area to display tags. + * @returns {jQuery} rendered DOM + */ +//TODO: into sub-MV + _render_tagArea : function(){ + if( !this.hasUser || !this.urls.tags.set ){ return null; } + return $( HDAEditView.templates.tagArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ).trim() ); + }, + /** Find the tag area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ - //TODO: into sub-MV +//TODO: into sub-MV loadAndDisplayTags : function( event ){ //BUG: broken with latest //TODO: this is a drop in from history.mako - should use MV as well @@ -508,6 +484,18 @@ } return false; }, + + // ......................................................................... annotations + /** Render area to display annotation. + * @returns {jQuery} rendered DOM + */ +//TODO: into sub-MV + _render_annotationArea : function(){ + if( !this.hasUser || !this.urls.annotation.get ){ return null; } + return $( HDAEditView.templates.annotationArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ).trim() ); + }, /** Find the annotation area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ @@ -555,7 +543,7 @@ return false; }, - // ......................................................................... UTILTIY + // ......................................................................... misc /** string rep */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); @@ -678,5 +666,5 @@ //============================================================================== return { - HDAEditView : HDAEditView, + HDAEditView : HDAEditView };}); diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -53,41 +53,42 @@ misc_info : '' }, - /** fetch location of this history in the api */ + /** fetch location of this HDA's history in the api */ urlRoot: 'api/histories/', + /** full url spec. for this HDA */ url : function(){ return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); }, + /** controller urls assoc. with this HDA */ urls : function(){ var id = this.get( 'id' ); if( !id ){ return {}; } var urls = { - 'delete' : '/datasets/' + id + '/delete_async', - 'purge' : '/datasets/' + id + '/purge_async', - 'unhide' : '/datasets/' + id + '/unhide', - 'undelete' : '/datasets/' + id + '/undelete', + 'purge' : galaxy_config.root + 'datasets/' + id + '/purge_async', - 'display' : '/datasets/' + id + '/display/?preview=True', - 'download' : '/datasets/' + id + '/display?to_ext=' + this.get( 'file_ext' ), - 'edit' : '/datasets/' + id + '/edit', - 'report_error': '/dataset/errors?id=' + id, - 'rerun' : '/tool_runner/rerun?id=' + id, - 'show_params': '/datasets/' + id + '/show_params', - 'visualization': '/visualization', + 'display' : galaxy_config.root + 'datasets/' + id + '/display/?preview=True', + 'download' : galaxy_config.root + 'datasets/' + id + '/display?to_ext=' + this.get( 'file_ext' ), + 'edit' : galaxy_config.root + 'datasets/' + id + '/edit', + 'report_error' : galaxy_config.root + 'dataset/errors?id=' + id, + 'rerun' : galaxy_config.root + 'tool_runner/rerun?id=' + id, + 'show_params' : galaxy_config.root + 'datasets/' + id + '/show_params', + 'visualization' : galaxy_config.root + 'visualization', - 'annotation': { 'get': '/dataset/get_annotation_async?id=' + id, - 'set': '/dataset/annotate_async?id=' + id }, - 'tags' : { 'get': '/tag/get_tagging_elt_async?item_id=' + id + '&item_class=HistoryDatasetAssociation', - 'set': '/tag/retag?item_id=' + id + '&item_class=HistoryDatasetAssociation' } + 'annotation': { 'get': galaxy_config.root + 'dataset/get_annotation_async?id=' + id, + 'set': galaxy_config.root + 'dataset/annotate_async?id=' + id }, + 'tags' : { 'get': galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' + + id + '&item_class=HistoryDatasetAssociation', + 'set': galaxy_config.root + 'tag/retag?item_id=' + + id + '&item_class=HistoryDatasetAssociation' } }; - //'meta_download': '/dataset/get_metadata_file?hda_id=%3C%25%3D+id+%25%3E&metadata_name=%3C%25%3D+file_type+%25%3E', + // download links to assoc. metadata files (bam indeces, etc.) var meta_files = this.get( 'meta_files' ); if( meta_files ){ urls.meta_download = _.map( meta_files, function( meta_file ){ return { - //url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), - url : '/dataset/get_metadata_file?hda_id=' + id + '&metadata_name=' + meta_file.file_type, + url : galaxy_config.root + 'dataset/get_metadata_file?hda_id=' + + id + '&metadata_name=' + meta_file.file_type, file_type : meta_file.file_type }; }); @@ -110,6 +111,9 @@ this._setUpListeners(); }, + /** set up any event listeners + * event: state:ready fired when this HDA moves into a ready state + */ _setUpListeners : function(){ // if the state has changed and the new state is a ready state, fire an event this.on( 'change:state', function( currModel, newState ){ @@ -121,8 +125,7 @@ }, // ........................................................................ common queries - /** Is this hda deleted or purged? - */ + /** Is this hda deleted or purged? */ isDeletedOrPurged : function(){ return ( this.get( 'deleted' ) || this.get( 'purged' ) ); }, @@ -132,7 +135,6 @@ * @param {Boolean} show_deleted are we showing deleted hdas? * @param {Boolean} show_hidden are we showing hidden hdas? */ - //TODO: too many 'visible's isVisible : function( show_deleted, show_hidden ){ var isVisible = true; if( ( !show_deleted ) @@ -146,6 +148,7 @@ return isVisible; }, + /** the more common alias of visible */ hidden : function(){ return !this.get( 'visible' ); }, @@ -158,33 +161,37 @@ return ( this.isDeletedOrPurged() || ready ); }, + /** Does this model already contain detailed data (as opposed to just summary level data)? */ hasDetails : function(){ //?? this may not be reliable return _.has( this.attributes, 'genome_build' ); }, - /** Convenience function to match hda.has_data. - */ + /** Convenience function to match hda.has_data. */ hasData : function(){ - //TODO:?? is this equivalent to all possible hda.has_data calls? return ( this.get( 'file_size' ) > 0 ); }, // ........................................................................ ajax + /** save this HDA, _Mark_ing it as deleted (just a flag) */ 'delete' : function _delete( options ){ return this.save( { deleted: true }, options ); }, + /** save this HDA, _Mark_ing it as undeleted */ undelete : function _undelete( options ){ return this.save( { deleted: false }, options ); }, + /** save this HDA as not visible */ hide : function _hide( options ){ return this.save( { visible: false }, options ); }, + /** save this HDA as visible */ unhide : function _uhide( options ){ return this.save( { visible: true }, options ); }, + /** purge this HDA and remove the underlying dataset file from the server's fs */ purge : function _purge( options ){ //TODO: ideally this would be a DELETE call to the api // using purge async for now @@ -210,10 +217,15 @@ }, // ........................................................................ sorting/filtering + /** what attributes of an HDA will be used in a search */ searchKeys : [ 'name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags' ], + /** search this HDA for the string searchFor + * @param {String} searchFor look for this string in all attributes listed in searchKeys (above) using indexOf + * @returns {Array} an array of attribute keys where searchFor was found + */ search : function( searchFor ){ var model = this; searchFor = searchFor.toLowerCase(); @@ -223,13 +235,16 @@ }); }, + /** alias of search, but returns a boolean + * @param {String} matchesWhat look for this string in all attributes listed in searchKeys (above) using indexOf + * @returns {Boolean} was matchesWhat found in any attributes + */ matches : function( matchesWhat ){ return !!this.search( matchesWhat ).length; }, // ........................................................................ misc - /** String representation - */ + /** String representation */ toString : function(){ var nameAndId = this.get( 'id' ) || ''; if( this.get( 'name' ) ){ @@ -274,6 +289,7 @@ ERROR : 'error' }; +/** states that are in a final state (the underlying job is complete) */ HistoryDatasetAssociation.READY_STATES = [ HistoryDatasetAssociation.STATES.NEW, HistoryDatasetAssociation.STATES.OK, @@ -285,6 +301,7 @@ HistoryDatasetAssociation.STATES.ERROR ]; +/** states that will change (the underlying job is not finished) */ HistoryDatasetAssociation.NOT_READY_STATES = [ HistoryDatasetAssociation.STATES.UPLOAD, HistoryDatasetAssociation.STATES.QUEUED, @@ -306,7 +323,10 @@ ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output //logger : console, - urlRoot : '/api/histories', + + /** root api url */ + urlRoot : galaxy_config.root + 'api/histories', + /** complete api url */ url : function(){ return this.urlRoot + '/' + this.historyId + '/contents'; }, @@ -331,6 +351,9 @@ return this.map( function( hda ){ return hda.id; }); }, + /** Get hdas that are not ready + * @returns array of HDAs + */ notReady : function(){ return this.filter( function( hda ){ return !hda.inReadyState(); @@ -370,11 +393,13 @@ }, // ........................................................................ ajax + /** fetch detailed model data for all HDAs in this collection */ fetchAllDetails : function(){ return this.fetch({ data : { details : 'all' } }); }, // ........................................................................ sorting/filtering + /** return a new collection of HDAs whose attributes contain the substring matchesWhat */ matches : function( matchesWhat ){ return this.filter( function( hda ){ return hda.matches( matchesWhat ); diff -r f82bbdc5c22b24d329a6710a20ce4c049f124064 -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -13,7 +13,6 @@ */ var History = Backbone.Model.extend( LoggableMixin ).extend( /** @lends History.prototype */{ - //TODO: bind change events from items and collection to this (itemLengths, states) ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output @@ -31,29 +30,33 @@ }, // ........................................................................ urls - urlRoot: 'api/histories', + urlRoot: galaxy_config.root + 'api/histories', + /** url for changing the name of the history */ renameUrl : function(){ //TODO: just use this.save() var id = this.get( 'id' ); if( !id ){ return undefined; } - return '/history/rename_async?id=' + this.get( 'id' ); + return galaxy_config.root + 'history/rename_async?id=' + this.get( 'id' ); }, + /** url for changing the annotation of the history */ annotateUrl : function(){ var id = this.get( 'id' ); if( !id ){ return undefined; } - return '/history/annotate_async?id=' + this.get( 'id' ); + return galaxy_config.root + 'history/annotate_async?id=' + this.get( 'id' ); }, + /** url for changing the tags of the history */ tagUrl : function(){ var id = this.get( 'id' ); if( !id ){ return undefined; } - return '/tag/get_tagging_elt_async?item_id=' + this.get( 'id' ) + '&item_class=History'; + return galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' + this.get( 'id' ) + '&item_class=History'; }, // ........................................................................ set up/tear down - /** Set up the hdas collection + /** Set up the model * @param {Object} historyJSON model data for this History * @param {Object[]} hdaJSON array of model data for this History's HDAs + * @param {Object} options any extra settings including logger * @see BaseModel#initialize */ initialize : function( historyJSON, hdaJSON, options ){ @@ -69,17 +72,24 @@ } this._setUpListeners(); - this._installAjaxErrorHandler( this.ajaxErrorHandler ); + /** cached timeout id for the HDA updater */ + this.updateTimeoutId = null; // set up update timeout if needed this.checkForUpdates(); }, + /** set up any event listeners for this history including those to the contained HDAs + * events: error:hdas if an error occurred with the HDA collection + */ _setUpListeners : function(){ + this.on( 'error', function( model, xhr, options, msg, details ){ + this.errorHandler( model, xhr, options, msg, details ); + }); + // hda collection listening if( this.hdas ){ this.listenTo( this.hdas, 'error', function(){ - //this.ajaxErrorHandler.apply( this, arguments ); this.trigger.apply( this, [ 'error:hdas' ].concat( jQuery.makeArray( arguments ) ) ); }); } @@ -105,34 +115,29 @@ // } //}, + /** event listener for errors. Generally errors are handled outside this model */ + errorHandler : function( model, xhr, options, msg, details ){ + // clear update timeout on model err + this.clearUpdateTimeout(); + }, + // ........................................................................ common queries + /** is this model already associated with a user? */ hasUser : function(){ var user = this.get( 'user' ); return !!( user && user.id ); }, // ........................................................................ ajax - // override to add ajax error event - //TODO: into mixin/base - _installAjaxErrorHandler : function( handler ){ - this.sync = function _sync( method, model, options ){ - return Backbone.Model.prototype.sync.call( model, method, model, options ) - .fail( function( xhr, status, message ){ - handler.call( model, model, xhr, options, method ); - }); - }; - }, - - ajaxErrorHandler : function( model, xhr, options, method ){ - }, - - // get the history's state from it's cummulative ds states, delay + update if needed - // events: ready + /** does the HDA collection indicate they're still running and need to be updated later? delay + update if needed + * @param {Function} onReadyCallback function to run when all HDAs are in the ready state + * events: ready + */ checkForUpdates : function( onReadyCallback ){ //console.info( 'checkForUpdates' ) // get overall History state from collection, run updater if History has running/queued hdas - // boiling it down on the client to running/not + // boiling it down on the client to running/not if( this.hdas.running().length ){ this.setUpdateTimeout(); @@ -145,8 +150,8 @@ return this; }, + /** create a timeout (after UPDATE_DELAY or delay ms) to refetch the HDA collection. Clear any prev. timeout */ setUpdateTimeout : function( delay ){ - //TODO: callbacks? delay = delay || History.UPDATE_DELAY; var history = this; @@ -158,6 +163,7 @@ return this.updateTimeoutId; }, + /** clear the timeout and the cached timeout id */ clearUpdateTimeout : function(){ if( this.updateTimeoutId ){ clearTimeout( this.updateTimeoutId ); @@ -165,25 +171,26 @@ } }, - // update this history, find any hda's running/queued, update ONLY those that have changed states, - // set up to run this again in some interval of time - // events: ready + /* update the HDA collection getting full detailed model data for any hda whose id is in detailIds + * set up to run this again in some interval of time + * @param {String[]} detailIds list of HDA ids to get detailed model data for + * @param {Object} options std. backbone fetch options map + */ refresh : function( detailIds, options ){ //console.info( 'refresh:', detailIds, this.hdas ); detailIds = detailIds || []; options = options || {}; var history = this; + // add detailIds to options as CSV string options.data = options.data || {}; if( detailIds.length ){ options.data.details = detailIds.join( ',' ); } var xhr = this.hdas.fetch( options ); xhr.done( function( hdaModels ){ - //this.trigger( 'hdas-refreshed', this, hdaModels ); - history.checkForUpdates(function(){ - // fetch the history after an update in order to recalc history size - //TODO: move to event? + history.checkForUpdates( function(){ + // fetch the history inside onReadyCallback in order to recalc history size this.fetch(); }); }); @@ -214,7 +221,7 @@ function getHistory( id ){ // get the history data //return jQuery.ajax( '/generate_json_error' ); - return jQuery.ajax( '/api/histories/' + historyId ); + return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyId ); } function countHdasFromHistory( historyData ){ // get the number of hdas accrd. to the history @@ -232,7 +239,7 @@ hdaDetailIds = hdaDetailIds( historyData ); } var data = ( hdaDetailIds.length )?( { details : hdaDetailIds.join( ',' ) } ):( {} ); - return jQuery.ajax( '/api/histories/' + historyData.id + '/contents', { data: data }); + return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data }); //return jQuery.ajax( '/generate_json_error' ); } @@ -283,7 +290,7 @@ var HistoryCollection = Backbone.Collection.extend( LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - urlRoot : 'api/histories' + urlRoot : galaxy_config.root + 'api/histories' ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/35a847f0f33d/ Changeset: 35a847f0f33d Branch: search User: Kyle Ellrott Date: 2013-10-25 00:04:33 Summary: Adding missing import Affected #: 1 file diff -r 9da06a2f3db4bf535cf179af6ba66b98741e7ea1 -r 35a847f0f33d2944b8033aefeb8d5ef0c734c8c6 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -35,7 +35,7 @@ History, Library, LibraryFolder, LibraryDataset,StoredWorkflowTagAssociation, StoredWorkflow, HistoryTagAssociation,HistoryDatasetAssociationTagAssociation, ExtendedMetadata, ExtendedMetadataIndex, HistoryAnnotationAssociation, Job, JobParameter, -JobToInputDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion) +JobToInputLibraryDatasetAssociation, JobToInputDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion ) from galaxy.util.json import to_json_string from sqlalchemy import and_ https://bitbucket.org/galaxy/galaxy-central/commits/97cb7306dc34/ Changeset: 97cb7306dc34 User: dannon Date: 2013-10-25 00:10:01 Summary: Merged in kellrott/galaxy-central/search (pull request #241) Fixing missing import in search.py Affected #: 1 file diff -r bf0057b13f58f5c5438f1a6477b27bfceb14a2ce -r 97cb7306dc345ce5e81861e421c5277701161802 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -35,7 +35,7 @@ History, Library, LibraryFolder, LibraryDataset,StoredWorkflowTagAssociation, StoredWorkflow, HistoryTagAssociation,HistoryDatasetAssociationTagAssociation, ExtendedMetadata, ExtendedMetadataIndex, HistoryAnnotationAssociation, Job, JobParameter, -JobToInputDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion) +JobToInputLibraryDatasetAssociation, JobToInputDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion ) from galaxy.util.json import to_json_string from sqlalchemy import and_ 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: dannon: Strip quota information and url from primary users collection -- not useful, and a ton of extra info that can be attained other ways. Issue deprecation warning with dist.
by commits-noreply＠bitbucket.org 25 Oct '13

25 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf0057b13f58/ Changeset: bf0057b13f58 User: dannon Date: 2013-10-24 21:18:51 Summary: Strip quota information and url from primary users collection -- not useful, and a ton of extra info that can be attained other ways. Issue deprecation warning with dist. Affected #: 1 file diff -r 05fb304579771af681eb1a89de633133364c5f7d -r bf0057b13f58f5c5438f1a6477b27bfceb14a2ce lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -4,7 +4,7 @@ import logging from paste.httpexceptions import HTTPBadRequest, HTTPNotImplemented from galaxy import util, web -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController log = logging.getLogger( __name__ ) @@ -22,27 +22,19 @@ query = trans.sa_session.query( trans.app.model.User ) deleted = util.string_as_bool( deleted ) if deleted: - route = 'deleted_user' query = query.filter( trans.app.model.User.table.c.deleted == True ) # only admins can see deleted users if not trans.user_is_admin(): return [] - else: - route = 'user' query = query.filter( trans.app.model.User.table.c.deleted == False ) # special case: user can see only their own user if not trans.user_is_admin(): item = trans.user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for( route, id=item['id'] ) - item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) return [item] - for user in query: item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } ) #TODO: move into api_values - item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) - item['url'] = url_for( route, id=item['id'] ) rval.append( item ) return rval 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: Add a link to the repository from the repository dependency when displayed in the tool shed.
by commits-noreply＠bitbucket.org 25 Oct '13

25 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05fb30457977/ Changeset: 05fb30457977 User: greg Date: 2013-10-24 20:13:09 Summary: Add a link to the repository from the repository dependency when displayed in the tool shed. Affected #: 1 file diff -r 99aa4cab1812998a767e3a26ce727a1ca50e03f8 -r 05fb304579771af681eb1a89de633133364c5f7d templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -603,9 +603,9 @@ </%def><%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter, row_is_header=False )"> - <% from galaxy.util import asbool + from tool_shed.util.shed_util_common import get_repository_by_name_and_owner encoded_id = trans.security.encode_id( repository_dependency.id ) if trans.webapp.name == 'galaxy': if repository_dependency.tool_shed_repository_id: @@ -623,14 +623,15 @@ prior_installation_required_str = " <i>(prior install required)</i>" else: prior_installation_required_str = "" - if trans.webapp.name == 'galaxy': if row_is_header: cell_type = 'th' else: cell_type = 'td' else: + # We're in the tool shed. cell_type = 'td' + rd = get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) %><tr class="datasetRow" %if parent is not None: @@ -658,7 +659,11 @@ </${cell_type}> %else: <td style="padding-left: ${pad+20}px;"> - Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b>${prior_installation_required_str} + %if rd: + <a class="view-info" href="${h.url_for( controller='repository', action='view_or_manage_repository', id=trans.security.encode_id( rd.id ), changeset_revision=changeset_revision )}">Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b></a>${prior_installation_required_str} + %else: + Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b>${prior_installation_required_str} + %endif </td> %endif </tr> 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: 2 new changesets
by commits-noreply＠bitbucket.org 24 Oct '13

24 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7266b5e09cb2/ Changeset: 7266b5e09cb2 Branch: next-stable User: greg Date: 2013-10-24 16:48:48 Summary: Fix for handling set_environment when installing tool dependencies along with a tool shed repository. Affected #: 1 file diff -r 83bed9c7dbbc7fa5acfbced6491d63f8a50982b0 -r 7266b5e09cb20cac801cddef87b0466ddc32d41e lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -483,7 +483,7 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - env_var_name = env_var_elem.get( 'name', None ) + env_var_name = elem.get( 'name', None ) if env_var_name: # Tool dependencies of type "set_environmnet" always have the version attribute set to None. attr_tup = ( env_var_name, None, 'set_environment' ) https://bitbucket.org/galaxy/galaxy-central/commits/99aa4cab1812/ Changeset: 99aa4cab1812 User: greg Date: 2013-10-24 16:49:15 Summary: Merged from next-stable Affected #: 1 file diff -r 30cedd7e894eea1f4ce9fc6fc36a697a13ea5dba -r 99aa4cab1812998a767e3a26ce727a1ca50e03f8 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -483,7 +483,7 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - env_var_name = env_var_elem.get( 'name', None ) + env_var_name = elem.get( 'name', None ) if env_var_name: # Tool dependencies of type "set_environmnet" always have the version attribute set to None. attr_tup = ( env_var_name, None, 'set_environment' ) 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: jgoecks: Tool JS module: put template references into render() rather than model definition to allow for module loading when templates are not available.
by commits-noreply＠bitbucket.org 24 Oct '13

24 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30cedd7e894e/ Changeset: 30cedd7e894e User: jgoecks Date: 2013-10-24 16:47:36 Summary: Tool JS module: put template references into render() rather than model definition to allow for module loading when templates are not available. Affected #: 1 file diff -r 7f048ac9d878c59734a7272364e7e580a44576a5 -r 30cedd7e894eea1f4ce9fc6fc36a697a13ea5dba static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -492,10 +492,9 @@ */ var ToolLinkView = BaseView.extend({ tagName: 'div', - template: Handlebars.templates.tool_link, - + render: function() { - this.$el.append( this.template(this.model.toJSON()) ); + this.$el.append( Handlebars.templates.tool_link(this.model.toJSON()) ); return this; } }); @@ -519,14 +518,15 @@ var ToolSectionView = BaseView.extend({ tagName: 'div', className: 'toolSectionWrapper', - template: Handlebars.templates.panel_section, + initialize: function() { BaseView.prototype.initialize.call(this); this.model.on("change:open", this.update_open, this); }, + render: function() { // Build using template. - this.$el.append( this.template(this.model.toJSON()) ); + this.$el.append( Handlebars.templates.panel_section(this.model.toJSON()) ); // Add tools to section. var section_body = this.$el.find(".toolSectionBody"); @@ -574,7 +574,6 @@ tagName: 'div', id: 'tool-search', className: 'bar', - template: Handlebars.templates.tool_search, events: { 'click': 'focus_and_select', @@ -583,7 +582,7 @@ }, render: function() { - this.$el.append( this.template(this.model.toJSON()) ); + this.$el.append( Handlebars.templates.tool_search(this.model.toJSON()) ); if (!this.model.is_visible()) { this.$el.hide(); } @@ -684,11 +683,10 @@ */ var ToolFormView = Backbone.View.extend({ className: 'toolForm', - template: Handlebars.templates.tool_form, render: function() { this.$el.children().remove(); - this.$el.append( this.template(this.model.toJSON()) ); + this.$el.append( Handlebars.templates.tool_form(this.model.toJSON()) ); } }); 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: 2 new changesets
by commits-noreply＠bitbucket.org 24 Oct '13

24 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83bed9c7dbbc/ Changeset: 83bed9c7dbbc Branch: next-stable User: greg Date: 2013-10-24 15:47:04 Summary: Eliminate restriction to repository owner (make it to anyone that has write permission on the repository) for resetting metadata on the repository in the tool shed. Affected #: 1 file diff -r 71c35dbde130994265d85c34a00d9f845eda28cc -r 83bed9c7dbbc7fa5acfbced6491d63f8a50982b0 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_download = False - if ( is_admin or ( trans.user and trans.user == repository.user ) ) and not repository.deleted and not repository.deprecated and not is_new: + if ( is_admin or can_push ) and not repository.deleted and not repository.deprecated and not is_new: can_reset_all_metadata = True else: can_reset_all_metadata = False https://bitbucket.org/galaxy/galaxy-central/commits/7f048ac9d878/ Changeset: 7f048ac9d878 User: greg Date: 2013-10-24 15:47:35 Summary: Merged from next-stable Affected #: 1 file diff -r 319c21e395a32f66b783578e43a4da2daa0b375c -r 7f048ac9d878c59734a7272364e7e580a44576a5 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -54,7 +54,7 @@ else: can_download = False - if ( is_admin or ( trans.user and trans.user == repository.user ) ) and not repository.deleted and not repository.deprecated and not is_new: + if ( is_admin or can_push ) and not repository.deleted and not repository.deprecated and not is_new: can_reset_all_metadata = True else: can_reset_all_metadata = False 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 24 Oct '13

24 Oct '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/200bd6479490/ Changeset: 200bd6479490 User: Dave Bouvier Date: 2013-10-24 14:51:16 Summary: Check for the existence of a display application before attempting to delete it from the registry. Affected #: 1 file diff -r e5b91a357c909cb63b5bbb7fc922226f34255d31 -r 200bd6479490cb7c85e18e95beb5a1cb072af307 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -547,8 +547,11 @@ display_app.id = tool_dict[ 'guid' ] break if deactivate: - del self.display_applications[ display_app.id ] - del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] + if display_app.id in self.display_applications: + del self.display_applications[ display_app.id ] + if extension in self.datatypes_by_extension: + if display_app.id in self.datatypes_by_extension[ extension ].display_applications: + del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] if inherit and ( self.datatypes_by_extension[ extension ], display_app ) in self.inherit_display_application_by_class: self.inherit_display_application_by_class.remove( ( self.datatypes_by_extension[ extension ], display_app ) ) self.log.debug( "Deactivated display application '%s' for datatype '%s'." % ( display_app.id, extension ) ) https://bitbucket.org/galaxy/galaxy-central/commits/71c35dbde130/ Changeset: 71c35dbde130 Branch: next-stable User: Dave Bouvier Date: 2013-10-24 14:51:16 Summary: Check for the existence of a display application before attempting to delete it from the registry. Affected #: 1 file diff -r 434254daaa091f4b9999e015ff090da518327a13 -r 71c35dbde130994265d85c34a00d9f845eda28cc lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -547,8 +547,11 @@ display_app.id = tool_dict[ 'guid' ] break if deactivate: - del self.display_applications[ display_app.id ] - del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] + if display_app.id in self.display_applications: + del self.display_applications[ display_app.id ] + if extension in self.datatypes_by_extension: + if display_app.id in self.datatypes_by_extension[ extension ].display_applications: + del self.datatypes_by_extension[ extension ].display_applications[ display_app.id ] if inherit and ( self.datatypes_by_extension[ extension ], display_app ) in self.inherit_display_application_by_class: self.inherit_display_application_by_class.remove( ( self.datatypes_by_extension[ extension ], display_app ) ) self.log.debug( "Deactivated display application '%s' for datatype '%s'." % ( display_app.id, extension ) ) https://bitbucket.org/galaxy/galaxy-central/commits/319c21e395a3/ Changeset: 319c21e395a3 User: Dave Bouvier Date: 2013-10-24 14:55:55 Summary: Merge with next-stable. Affected #: 0 files 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: 2 new changesets
by commits-noreply＠bitbucket.org 24 Oct '13

24 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cbfae86c6def/ Changeset: cbfae86c6def User: jmchilton Date: 2013-04-23 16:57:14 Summary: Add exception handling for Binary sniffers. Image sniffers can fail for large files because signed integers are used internally, this catches that and other potential problems. Traceback (most recent call last): File "/opt/galaxy/web/tools/data_source/upload.py", line 432, in <module> __main__() File "/opt/galaxy/web/tools/data_source/upload.py", line 421, in __main__ add_file( dataset, registry, json_file, output_path ) File "/opt/galaxy/web/tools/data_source/upload.py", line 155, in add_file type_info = Binary.is_sniffable_binary( dataset.path ) File "/opt/galaxy/web/lib/galaxy/datatypes/binary.py", line 38, in is_sniffable_binary if format["class"]().sniff(filename): File "/opt/galaxy/web/lib/galaxy/datatypes/images.py", line 203, in sniff headers = get_headers(filename, None, 1) File "/opt/galaxy/web/lib/galaxy/datatypes/sniff.py", line 179, in get_headers for idx, line in enumerate(file(fname)): SystemError: Negative size passed to PyString_FromStringAndSize Affected #: 1 file diff -r 1e3d92ec22b2794bfa2294edb74695c580791406 -r cbfae86c6def520dff8d922066054ede3072ebfb lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -33,11 +33,20 @@ Binary.unsniffable_binary_formats.append(ext) @staticmethod - def is_sniffable_binary(filename): + def is_sniffable_binary( filename ): + format_information = None for format in Binary.sniffable_binary_formats: - if format["class"]().sniff(filename): - return (format["type"], format["ext"]) - return None + format_instance = format[ "class" ]() + try: + if format_instance.sniff(filename): + format_information = ( format["type"], format[ "ext" ] ) + break + except Exception: + # Sniffer raised exception, could be any number of + # reasons for this so there is not much to do besides + # trying next sniffer. + pass + return format_information @staticmethod def is_ext_unsniffable(ext): https://bitbucket.org/galaxy/galaxy-central/commits/4f400cb23860/ Changeset: 4f400cb23860 User: jmchilton Date: 2013-04-23 19:24:16 Summary: Rework checking binary files. Why read in line by line if only going to check 100 characters? This approach to just read first 100 characters is cleaner, more efficient, and hopefully less error prone. Should avoid the following exception caused when checking large files: Traceback (most recent call last): File "/opt/galaxy/web/tools/data_source/upload.py", line 432, in <module> __main__() File "/opt/galaxy/web/tools/data_source/upload.py", line 421, in __main__ add_file( dataset, registry, json_file, output_path ) File "/opt/galaxy/web/tools/data_source/upload.py", line 283, in add_file if check_binary( dataset.path ): File "/opt/galaxy/web/lib/galaxy/datatypes/checkers.py", line 58, in check_binary for chars in temp: SystemError: Negative size passed to PyString_FromStringAndSize Affected #: 1 file diff -r cbfae86c6def520dff8d922066054ede3072ebfb -r 4f400cb238607d7563a001ab0cf0d3b24bb10f17 lib/galaxy/datatypes/checkers.py --- a/lib/galaxy/datatypes/checkers.py +++ b/lib/galaxy/datatypes/checkers.py @@ -1,5 +1,6 @@ import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr from galaxy import util +from StringIO import StringIO try: import Image as PIL @@ -53,20 +54,15 @@ if file_path: temp = open( name, "U" ) else: - temp = name + temp = StringIO( name ) chars_read = 0 - for chars in temp: - for char in chars: - chars_read += 1 + try: + for char in temp.read( 100 ): if ord( char ) > 128: is_binary = True break - if chars_read > 100: - break - if chars_read > 100: - break - if file_path: - temp.close() + finally: + temp.close( ) return is_binary def check_gzip( file_path ): 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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galaxy-commits October 2013