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commit/galaxy-central: natefoo: Library datasets can now be job inputs - needed to be able to use the deferred job runner and transfer manager with set_metadata_externally = True.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e04154ed4639/ changeset: e04154ed4639 user: natefoo date: 2011-06-17 22:06:17 summary: Library datasets can now be job inputs - needed to be able to use the deferred job runner and transfer manager with set_metadata_externally = True. affected #: 7 files (2.6 KB) --- a/lib/galaxy/jobs/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -229,7 +229,7 @@ return JOB_DELETED elif job.state == model.Job.states.ERROR: return JOB_ADMIN_DELETED - for dataset_assoc in job.input_datasets: + for dataset_assoc in job.input_datasets + job.input_library_datasets: idata = dataset_assoc.dataset if not idata: continue @@ -330,6 +330,7 @@ # Restore input / output data lists inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # Set up output dataset association for export history jobs. Because job @@ -614,6 +615,7 @@ # custom post process setup inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows param_dict = self.tool.params_from_strings( param_dict, self.app ) @@ -665,7 +667,7 @@ def get_input_fnames( self ): job = self.get_job() filenames = [] - for da in job.input_datasets: #da is JobToInputDatasetAssociation object + for da in job.input_datasets + job.input_library_datasets: #da is JobToInputDatasetAssociation object if da.dataset: filenames.append( da.dataset.file_name ) #we will need to stage in metadata file names also @@ -861,9 +863,10 @@ self.tool.handle_unvalidated_param_values( incoming, self.app ) # Restore input / output data lists inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) + out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) + out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # DBTODO New method for generating command line for a task? - out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) - out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) # These can be passed on the command line if wanted as $userId $userEmail if job.history and job.history.user: # check for anonymous user! userId = '%d' % job.history.user.id --- a/lib/galaxy/jobs/deferred/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/deferred/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -98,14 +98,14 @@ job_state = self.plugins[job.plugin].check_job( job ) except Exception, e: self.__fail_job( job ) - log.error( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) ) + log.exception( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) ) continue if job_state == self.job_states.READY: try: self.plugins[job.plugin].run_job( job ) except Exception, e: self.__fail_job( job ) - log.error( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) ) + log.exception( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) ) continue elif job_state == self.job_states.INVALID: self.__fail_job( job ) @@ -160,8 +160,14 @@ self.app = app self.sa_session = app.model.context.current self.dummy = Dummy() - self.history = history - self.user = user + if not history: + self.history = Dummy() + else: + self.history = history + if not user: + self.user = Dummy() + else: + self.user = user self.model = app.model def get_galaxy_session( self ): return self.dummy --- a/lib/galaxy/jobs/deferred/data_transfer.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/deferred/data_transfer.py Fri Jun 17 16:06:17 2011 -0400 @@ -93,12 +93,18 @@ # In this case, job.params will be a dictionary that contains a key named 'result'. The value # of the result key is a dictionary that looks something like: # {'sample_dataset_id': '8', 'status': 'Not started', 'protocol': 'scp', 'name': '3.bed', - # 'file_path': '/tmp/library/3.bed', 'host': '127.0.0.1', 'sample_id': 8, 'external_service_id': 2, - # 'password': 'galaxy', 'user_name': 'gvk', 'error_msg': '', 'size': '8.0K'} - result_dict = job.params[ 'result' ] + # 'file_path': '/data/library/3.bed', 'host': '127.0.0.1', 'sample_id': 8, 'external_service_id': 2, + # 'local_path': '/tmp/kjl2Ss4', 'password': 'galaxy', 'user_name': 'gvk', 'error_msg': '', 'size': '8.0K'} + try: + tj = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params['transfer_job_id'] ) ) + result_dict = tj.params + result_dict['local_path'] = tj.path + except Exception, e: + log.error( "Updated transfer result unavailable, using old result. Error was: %s" % str( e ) ) + result_dict = job.params[ 'result' ] library_dataset_name = result_dict[ 'name' ] # Determine the data format (see the relevant TODO item in the manual_data_transfer plugin).. - extension = sniff.guess_ext( result_dict[ 'file_path' ], sniff_order=self.app.datatypes_registry.sniff_order ) + extension = sniff.guess_ext( result_dict[ 'local_path' ], sniff_order=self.app.datatypes_registry.sniff_order ) self._update_sample_dataset_status( protocol=job.params[ 'protocol' ], sample_id=int( job.params[ 'sample_id' ] ), result_dict=result_dict, @@ -132,7 +138,9 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) if self.app.config.set_metadata_externally: self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( self.app.datatypes_registry.set_external_metadata_tool, - FakeTrans( self.app ), + FakeTrans( self.app, + history=sample.history, + user=sample.request.user ), incoming = { 'input1':ldda } ) else: ldda.set_meta() --- a/lib/galaxy/jobs/transfer_manager.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/jobs/transfer_manager.py Fri Jun 17 16:06:17 2011 -0400 @@ -106,6 +106,7 @@ error = dict( code=256, message='Error connecting to transfer daemon', data=str( e ) ) rval.append( dict( transfer_job_id=tj.id, state=tj.state, error=error ) ) else: + self.sa_session.refresh( tj ) rval.append( dict( transfer_job_id=tj.id, state=tj.state ) ) for tj_state in rval: if tj_state['state'] in self.app.model.TransferJob.terminal_states: --- a/lib/galaxy/model/__init__.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/model/__init__.py Fri Jun 17 16:06:17 2011 -0400 @@ -95,6 +95,7 @@ self.parameters = [] self.input_datasets = [] self.output_datasets = [] + self.input_library_datasets = [] self.output_library_datasets = [] self.state = Job.states.NEW self.info = None @@ -109,6 +110,8 @@ self.input_datasets.append( JobToInputDatasetAssociation( name, dataset ) ) def add_output_dataset( self, name, dataset ): self.output_datasets.append( JobToOutputDatasetAssociation( name, dataset ) ) + def add_input_library_dataset( self, name, dataset ): + self.input_library_datasets.append( JobToInputLibraryDatasetAssociation( name, dataset ) ) def add_output_library_dataset( self, name, dataset ): self.output_library_datasets.append( JobToOutputLibraryDatasetAssociation( name, dataset ) ) def add_post_job_action(self, pja): @@ -215,6 +218,11 @@ self.name = name self.dataset = dataset +class JobToInputLibraryDatasetAssociation( object ): + def __init__( self, name, dataset ): + self.name = name + self.dataset = dataset + class JobToOutputLibraryDatasetAssociation( object ): def __init__( self, name, dataset ): self.name = name --- a/lib/galaxy/model/mapping.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/model/mapping.py Fri Jun 17 16:06:17 2011 -0400 @@ -370,6 +370,12 @@ Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), Column( "name", String(255) ) ) +JobToInputLibraryDatasetAssociation.table = Table( "job_to_input_library_dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), + Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), + Column( "name", String(255) ) ) + JobToOutputLibraryDatasetAssociation.table = Table( "job_to_output_library_dataset", metadata, Column( "id", Integer, primary_key=True ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), @@ -1376,6 +1382,9 @@ assign_mapper( context, JobToOutputDatasetAssociation, JobToOutputDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation, lazy=False ) ) ) +assign_mapper( context, JobToInputLibraryDatasetAssociation, JobToInputLibraryDatasetAssociation.table, + properties=dict( job=relation( Job ), dataset=relation( LibraryDatasetDatasetAssociation, lazy=False ) ) ) + assign_mapper( context, JobToOutputLibraryDatasetAssociation, JobToOutputLibraryDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( LibraryDatasetDatasetAssociation, lazy=False ) ) ) @@ -1410,6 +1419,7 @@ input_datasets=relation( JobToInputDatasetAssociation ), output_datasets=relation( JobToOutputDatasetAssociation ), post_job_actions=relation( PostJobActionAssociation, lazy=False ), + input_library_datasets=relation( JobToInputLibraryDatasetAssociation ), output_library_datasets=relation( JobToOutputLibraryDatasetAssociation ), external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) ) --- a/lib/galaxy/tools/actions/metadata.py Fri Oct 22 14:30:58 2010 +0100 +++ b/lib/galaxy/tools/actions/metadata.py Fri Jun 17 16:06:17 2011 -0400 @@ -13,6 +13,12 @@ if isinstance( value, trans.app.model.HistoryDatasetAssociation ): dataset = value dataset_name = name + type = 'hda' + break + elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ): + dataset = value + dataset_name = name + type = 'ldda' break else: raise Exception( 'The dataset to set metadata on could not be determined.' ) @@ -22,6 +28,8 @@ job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id + if trans.user: + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW try: # For backward compatibility, some tools may not have versions yet. @@ -50,7 +58,10 @@ for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) #add the dataset to job_to_input_dataset table - job.add_input_dataset( dataset_name, dataset ) + if type == 'hda': + job.add_input_dataset( dataset_name, dataset ) + elif type == 'ldda': + job.add_input_library_dataset( dataset_name, dataset ) #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset._state = dataset.states.SETTING_METADATA Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: peterjc: Support optional integer/float arguments (Fixes #403)
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/adcc600effa4/ changeset: adcc600effa4 user: peterjc date: 2010-10-22 15:30:58 summary: Support optional integer/float arguments (Fixes #403) affected #: 1 file (1.0 KB) --- a/lib/galaxy/tools/parameters/basic.py Fri Jun 17 15:31:07 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Oct 22 14:30:58 2010 +0100 @@ -36,6 +36,8 @@ self.html = "no html set" self.repeat = param.get("repeat", None) self.condition = param.get( "condition", None ) + # Optional DataToolParameters are used in tools like GMAJ and LAJ + self.optional = string_as_bool( param.get( 'optional', False ) ) self.validators = [] for elem in param.findall("validator"): self.validators.append( validation.Validator.from_element( self, elem ) ) @@ -131,7 +133,11 @@ return value def to_param_dict_string( self, value, other_values={} ): - value = str( value ) + """Called via __str__ when used in the Cheetah template""" + if value is None: + value = "" + else: + value = str( value ) if self.tool is None or self.tool.options.sanitize: if self.sanitizer: value = self.sanitizer.sanitize_param( value ) @@ -140,6 +146,8 @@ return value def validate( self, value, history=None ): + if value=="" and self.optional: + return for validator in self.validators: validator.validate( value, history ) @@ -226,9 +234,22 @@ try: return int( value ) except: + if not value and self.optional: + return "" raise ValueError( "An integer is required" ) + def to_string( self, value, app ): + """Convert a value to a string representation suitable for persisting""" + if value is None: + return "" + else: + return str( value ) def to_python( self, value, app ): - return int( value ) + try: + return int( value ) + except Exception, err: + if not value and self.optional: + return None + raise err def get_initial_value( self, trans, context ): if self.value: return int( self.value ) @@ -281,10 +302,23 @@ def from_html( self, value, trans=None, other_values={} ): try: return float( value ) - except: + except: + if not value and self.optional: + return "" raise ValueError( "A real number is required" ) + def to_string( self, value, app ): + """Convert a value to a string representation suitable for persisting""" + if value is None: + return "" + else: + return str( value ) def to_python( self, value, app ): - return float( value ) + try: + return float( value ) + except Exception, err: + if not value and self.optional: + return None + raise err def get_initial_value( self, trans, context ): try: return float( self.value ) @@ -1259,8 +1293,6 @@ formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) - # Optional DataToolParameters are used in tools like GMAJ and LAJ - self.optional = string_as_bool( elem.get( 'optional', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, # only the special case key='build' of type='data_meta' is # a valid filter 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: kanwei: typo
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4a722839e77a/ changeset: 4a722839e77a user: kanwei date: 2011-06-17 21:31:07 summary: typo affected #: 1 file (1 byte) --- a/templates/workflow/list.mako Fri Jun 17 15:30:01 2011 -0400 +++ b/templates/workflow/list.mako Fri Jun 17 15:31:07 2011 -0400 @@ -121,5 +121,5 @@ <span>Configure your workflow menu</span></a></div> - </div + </div></%def> \ No newline at end of file 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: kanwei: Cleanup
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7030dfb18ef9/ changeset: 7030dfb18ef9 user: kanwei date: 2011-06-17 21:30:01 summary: Cleanup affected #: 2 files (361 bytes) --- a/templates/visualization/list.mako Fri Jun 17 15:23:28 2011 -0400 +++ b/templates/visualization/list.mako Fri Jun 17 15:30:01 2011 -0400 @@ -14,51 +14,51 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> %if message: - <% - try: - status - except: - status = "done" - %> - <p /> - <div class="${status}message"> - ${h.to_unicode( message )} - </div> + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> %endif - + ${h.to_unicode( grid )} - <br><br> - <h2>Visualizations shared with you by others</h2> + <br><br> + <h2>Visualizations shared with you by others</h2> - %if shared_by_others: - <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr class="header"> - <th>Title</th> - <th>Owner</th> - <th></th> - </tr> - %for i, association in enumerate( shared_by_others ): - <% visualization = association.visualization %> - <tr> - <td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a> - </td> - <td>${visualization.user.username}</td> - <td> - <div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a> - </div> - </td> - </tr> - %endfor - </table> - %else: + %if shared_by_others: + <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr class="header"> + <th>Title</th> + <th>Owner</th> + <th></th> + </tr> + %for i, association in enumerate( shared_by_others ): + <% visualization = association.visualization %> + <tr> + <td> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a> + </td> + <td>${visualization.user.username}</td> + <td> + <div popupmenu="shared-${i}-popup"> + <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a> + </div> + </td> + </tr> + %endfor + </table> + %else: - No visualizations have been shared with you. + No visualizations have been shared with you. - %endif + %endif </div></div> --- a/templates/workflow/list.mako Fri Jun 17 15:23:28 2011 -0400 +++ b/templates/workflow/list.mako Fri Jun 17 15:30:01 2011 -0400 @@ -15,16 +15,16 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> %if message: - <% - try: - status - except: - status = "done" - %> - <p /> - <div class="${status}message"> - ${h.to_unicode( message )} - </div> + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> %endif <h2>Your workflows</h2> @@ -43,7 +43,7 @@ </a></li></ul> - + %if workflows: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" style="width:100%;"><tr class="header"> @@ -72,7 +72,7 @@ <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( action='delete', id=trans.security.encode_id(workflow.id) )}">Delete</a></div></td> - </tr> + </tr> %endfor </table> %else: @@ -101,12 +101,12 @@ <td>${len(workflow.latest_workflow.steps)}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> + <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a></div></td> - </tr> + </tr> %endfor </table> %else: @@ -121,5 +121,5 @@ <span>Configure your workflow menu</span></a></div> - </div> + </div </%def> \ 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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commit/galaxy-central: kanwei: Upgrade to Mako 0.4.1 and fix failing tests due to entity escaping. Improve error message for checking strings in history.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5b9fe1d9b4fa/ changeset: 5b9fe1d9b4fa user: kanwei date: 2011-06-17 21:23:28 summary: Upgrade to Mako 0.4.1 and fix failing tests due to entity escaping. Improve error message for checking strings in history. affected #: 4 files (501 bytes) --- a/eggs.ini Fri Jun 17 15:00:22 2011 -0400 +++ b/eggs.ini Fri Jun 17 15:23:28 2011 -0400 @@ -38,7 +38,7 @@ elementtree = 1.2.6_20050316 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 -Mako = 0.2.5 +Mako = 0.4.1 nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 --- a/templates/sharing_base.mako Fri Jun 17 15:00:22 2011 -0400 +++ b/templates/sharing_base.mako Fri Jun 17 15:23:28 2011 -0400 @@ -41,13 +41,11 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> - $(document).ready( function() - { + $(document).ready( function() { // // Set up slug-editing functionality. // - var on_start = function( text_elt ) - { + var on_start = function( text_elt ) { // Replace URL with URL text. $('#item-url').hide(); $('#item-url-text').show(); @@ -58,8 +56,7 @@ }); }; - var on_finish = function( text_elt ) - { + var on_finish = function( text_elt ) { // Replace URL text with URL. $('#item-url-text').hide(); $('#item-url').show(); @@ -81,20 +78,17 @@ ${parent.stylesheets()} <style> ## Put some whitespace before each section header. - h3 - { + h3 { margin-top: 2em; } - input.action-button - { + input.action-button { margin-left: 0; } ## If page is displayed in panels, pad from edges for readability. %if context.get('use_panels'): - div#center - { - padding: 10px; - } + div#center { + padding: 10px; + } %endif </style></%def> @@ -131,8 +125,8 @@ ## Require that user have a public username before sharing or publishing an item. %if trans.get_user().username is None or trans.get_user().username is "": - To make a ${item_class_name_lc} accessible via link or publish it, you must create a public username: - <p> + <p>To make a ${item_class_name_lc} accessible via link or publish it, you must create a public username:</p> + <form action="${h.url_for( action='set_public_username', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"> @@ -181,38 +175,36 @@ <p>You can: <div> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" - method="POST"> - %if not item.published: - ## Item is importable but not published. User can disable importable or publish. - <input class="action-button" type="submit" name="disable_link_access" value="Disable Access to ${item_class_name} Link"> - <div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div> - <br> - <input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST"> - <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> + <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" method="POST"> + %if not item.published: + ## Item is importable but not published. User can disable importable or publish. + <input class="action-button" type="submit" name="disable_link_access" value="Disable Access to ${item_class_name} Link"> + <div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div> + <br /> + <input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST"> + <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> - <br> - %else: ## item.published == True - ## Item is importable and published. User can unpublish or disable import and unpublish. - <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}"> - <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> - <br> - <input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish"> - <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> - %endif - + <br /> + %else: ## item.published == True + ## Item is importable and published. User can unpublish or disable import and unpublish. + <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}"> + <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + <br /> + <input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish"> + <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + %endif </form></div> %else: - This ${item_class_name_lc} is currently restricted so that only you and the users listed below can access it. You can: - <p> + <p>This ${item_class_name_lc} is currently restricted so that only you and the users listed below can access it. You can:</p> + <form action="${h.url_for( action='sharing', id=trans.security.encode_id(item.id) )}" method="POST"><input class="action-button" type="submit" name="make_accessible_via_link" value="Make ${item_class_name} Accessible via Link"><div class="toolParamHelp">Generates a web link that you can share with other people so that they can view and import the ${item_class_name_lc}.</div> - <br> + <br /><input class="action-button" type="submit" name="make_accessible_and_publish" value="Make ${item_class_name} Accessible and Publish" method="POST"><div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div></form> @@ -266,13 +258,13 @@ href="${h.url_for( action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"><span>Share with a user</span></a> - <br> + <br /> %endif </div></div> %endif - <p><br><br> + <br /><br /><a href="${h.url_for( action="list" )}">Back to ${item_class_plural_name} List</a></%def> \ No newline at end of file --- a/test/base/twilltestcase.py Fri Jun 17 15:00:22 2011 -0400 +++ b/test/base/twilltestcase.py Fri Jun 17 15:23:28 2011 -0400 @@ -8,6 +8,8 @@ import twill.commands as tc from twill.other_packages._mechanize_dist import ClientForm pkg_resources.require( "elementtree" ) +pkg_resources.require( "MarkupSafe" ) +from markupsafe import escape from elementtree import ElementTree from galaxy.web import security from galaxy.web.framework.helpers import iff @@ -239,7 +241,12 @@ else: self.visit_page( "history" ) for subpatt in patt.split(): - tc.find(subpatt) + try: + tc.find( escape(subpatt) ) + except: + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( escape(subpatt), fname ) + raise AssertionError( errmsg ) self.home() def clear_history( self ): """Empties a history of all datasets""" @@ -611,13 +618,10 @@ return hids def makeTfname(self, fname=None): - """ - safe temp name - preserve the file extension for tools that interpret it - """ + """safe temp name - preserve the file extension for tools that interpret it""" suffix = os.path.split(fname)[-1] # ignore full path - fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix) - return temp_prefix - + fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix) + return temp_prefix def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ): """Verifies that the attributes and contents of a history item meet expectations""" @@ -673,12 +677,12 @@ self.files_re_match( local_name, temp_name, attributes=attributes ) elif compare == 're_match_multiline': self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) - elif compare == 'sim_size': - delta = attributes.get('delta','100') - s1 = len(data) - s2 = os.path.getsize(local_name) - if abs(s1-s2) > int(delta): - raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) + elif compare == 'sim_size': + delta = attributes.get('delta','100') + s1 = len(data) + s2 = os.path.getsize(local_name) + if abs(s1-s2) > int(delta): + raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) elif compare == "contains": self.files_contains( local_name, temp_name, attributes=attributes ) else: @@ -749,7 +753,7 @@ errmsg += str( err ) raise AssertionError( errmsg ) finally: - os.remove( temp_name ) + os.remove( temp_name ) def is_zipped( self, filename ): if not zipfile.is_zipfile( filename ): --- a/test/functional/test_history_functions.py Fri Jun 17 15:00:22 2011 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 17 15:23:28 2011 -0400 @@ -282,9 +282,9 @@ .first() assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" # Make sure the deleted datasets are included in the cloned history - check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_2_bed.id + check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_2_bed.id self.check_history_for_string( check_str, show_deleted=True ) - check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_3_bed.id + check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_3_bed.id self.check_history_for_string( check_str, show_deleted=True ) # Test cloning only active datasets self.clone_history( self.security.encode_id( history3.id ), @@ -353,7 +353,7 @@ .first() assert history5 is not None, "Problem retrieving history5 from database" self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name=urllib.quote( 'history 5' ) ) - # Current history is hostory5 + # Current history is history5 sa_session.refresh( history5 ) # Due to the limitations of twill ( not functional with the permissions forms ), we're forced # to do this manually. At this point, we just want to restrict the access permission on history5 @@ -514,7 +514,7 @@ self.visit_page( "root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) - raise AssertionError, "history5 still shared with regular_user2 after unshaing it with that user." + raise AssertionError, "history5 still shared with regular_user2 after unsharing it with that user." except: pass self.logout() 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 support for uncompressing a gz or bz2 compressed file upon upload to the galaxy tool shed. Fixes issue # 586.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a746bfc39b17/ changeset: a746bfc39b17 user: greg date: 2011-06-17 21:00:22 summary: Add support for uncompressing a gz or bz2 compressed file upon upload to the galaxy tool shed. Fixes issue # 586. affected #: 2 files (5.1 KB) --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Jun 17 14:27:47 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Jun 17 15:00:22 2011 -0400 @@ -1,6 +1,7 @@ import sys, os, shutil, logging, tarfile, tempfile from galaxy.web.base.controller import * from galaxy.model.orm import * +from galaxy.datatypes.checkers import * from common import get_categories, get_repository from mercurial import hg, ui @@ -8,6 +9,7 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +CHUNK_SIZE = 2**20 # 1Mb class UploadError( Exception ): pass @@ -26,6 +28,7 @@ repository = get_repository( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) + uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) ) uploaded_file = None upload_point = params.get( 'upload_point', None ) if upload_point is not None: @@ -59,25 +62,37 @@ uploaded_file = None elif file_data not in ( '', None ): uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = file_data.filename if uploaded_file: # Our current support for browsing repo contents requires a copy of the - # repository files in the repo root directory. To produce these copies, - # we update without passing the "-r null" flag. + # repository files in the repo root directory. To eliminate these copies, + # we update the repo, passing the "-r null" flag. os.chdir( repo_dir ) os.system( 'hg update -r null > /dev/null 2>&1' ) os.chdir( current_working_dir ) + isgzip = False + isbz2 = False + if uncompress_file: + isgzip = is_gzip( uploaded_file_name ) + if not isgzip: + isbz2 = is_bz2( uploaded_file_name ) ok = True files_to_commit = [] # Determine what we have - a single file or an archive try: - tar = tarfile.open( uploaded_file.name ) + if uncompress_file: + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) istar = True except tarfile.ReadError, e: tar = None istar = False if repository.is_new: if istar: - # We have an archive ( a tarball ) + # We have an archive ( a tarball ) in a new repository. ok, message = self.__check_archive( tar ) if ok: tar.extractall( path=repo_dir ) @@ -108,23 +123,28 @@ else: tar.close() else: - # We have a single file + # We have a single file in a new repository. + if uncompress_file and ( isgzip or isbz2 ): + uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) if upload_point is not None: - full_path = os.path.abspath( os.path.join( upload_point, file_data.filename ) ) - file_path = os.path.join( upload_point, file_data.filename ) + full_path = os.path.abspath( os.path.join( upload_point, uploaded_file_filename ) ) + file_path = os.path.join( upload_point, uploaded_file_filename ) else: - full_path = os.path.abspath( os.path.join( repo_dir, file_data.filename ) ) - file_path = os.path.join( file_data.filename ) - shutil.move( uploaded_file.name, full_path ) + full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) + file_path = os.path.join( uploaded_file_filename ) + shutil.move( uploaded_file_name, full_path ) repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: + # We have a repository that is not new (it contains files). + if uncompress_file and ( isgzip or isbz2 ): + uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) # Clone the repository to a temporary location. tmp_dir, cloned_repo_dir = self.__hg_clone( trans, repository, repo_dir, current_working_dir ) # Move the uploaded files to the upload_point within the cloned repository. - self.__move_to_upload_point( upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ) + self.__move_to_upload_point( upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ) # Commit and push the changes from the cloned repo to the master repo. - self.__hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) + self.__hg_push( trans, repository, file_data.filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() @@ -132,7 +152,11 @@ os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + if uncompress_file: + uncompress_str = ' uncompressed and ' + else: + uncompress_str = ' ' + message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', message=message, @@ -146,8 +170,50 @@ return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, commit_message=commit_message, + uncompress_file=uncompress_file, message=message, status=status ) + def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): + if isgzip: + self.__handle_gzip( repository, uploaded_file_name ) + return uploaded_file_filename.rstrip( '.gz' ) + if isbz2: + self.__handle_bz2( repository, uploaded_file_name ) + return uploaded_file_filename.rstrip( '.bz2' ) + def __handle_gzip( self, repository, uploaded_file_name ): + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) + while 1: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError, e: + os.close( fd ) + os.remove( uncompressed ) + log.exception( 'Problem uncompressing gz data "%s": %s' % ( uploaded_file_name, str( e ) ) ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + shutil.move( uncompressed, uploaded_file_name ) + def __handle_bz2( self, repository, uploaded_file_name ): + fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) + bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) + while 1: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + log.exception( 'Problem uncompressing bz2 data "%s": %s' % ( uploaded_file_name, str( e ) ) ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + shutil.move( uncompressed, uploaded_file_name ) def __hg_clone( self, trans, repository, repo_dir, current_working_dir ): tmp_dir = tempfile.mkdtemp() tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) @@ -160,9 +226,9 @@ os.chdir( current_working_dir ) cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) return tmp_dir, cloned_repo_dir - def __hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + def __hg_push( self, trans, repository, filename, uncompress_file, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): repo = hg.repository( ui.ui(), repo_dir ) - tip = repo.changectx( "tip" ) + tip = repo[ 'tip' ] # We want these change sets to be associated with the owner of the repository, so we'll # set the HGUSER environment variable accordingly. os.environ[ 'HGUSER' ] = trans.user.username @@ -184,19 +250,30 @@ os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) shutil.rmtree( tmp_dir ) - if tip != repo.changectx( "tip" ): - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + repo = hg.repository( ui.ui(), repo_dir ) + if tip != repo[ 'tip' ]: + if uncompress_file: + uncompress_str = ' uncompressed and ' + else: + uncompress_str = ' ' + message = "The file '%s' has been successfully%suploaded to the repository." % ( filename, uncompress_str ) else: message = 'No changes in uploaded files.' trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - def __move_to_upload_point( self, upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ): + def __move_to_upload_point( self, upload_point, uploaded_file, uploaded_file_name, uploaded_file_filename, cloned_repo_dir, istar, tar ): if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + if istar: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, uploaded_file_filename ) ) else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + full_path = os.path.abspath( os.path.join( cloned_repo_dir ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, uploaded_file_filename ) ) if istar: # Extract the uploaded tarball to the load_point within the cloned repository hierarchy tar.extractall( path=full_path ) @@ -204,7 +281,7 @@ uploaded_file.close() else: # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) + shutil.move( uploaded_file_name, full_path ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/repository/upload.mako Fri Jun 17 14:27:47 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Fri Jun 17 15:00:22 2011 -0400 @@ -72,6 +72,30 @@ </div><div style="clear: both"></div></div> + + <div class="form-row"> + <% + if uncompress_file: + yes_selected = 'selected' + no_selected = '' + else: + yes_selected = '' + no_selected = 'selected' + %> + <label>Uncompress files?</label> + <div class="form-row-input"> + <select name="uncompress_file"> + <option value="true" ${yes_selected}>Yes + <option value="false" ${no_selected}>No + </select> + </div> + <div class="toolParamHelp" style="clear: both;"> + Supported compression types are gz and bz2. If <b>Yes</b> is selected, the uploaded file will be uncompressed. However, + if the uploaded file is an archive that contains compressed files, the contained files will not be uncompressed. For + example, if the uploaded compressed file is some_file.tar.gz, some_file.tar will be uncompressed and extracted, but if + some_file.tar contains 4.bed.gz, the contained file 4.bed.gz will not be uncompressed. + </div> + </div><div class="form-row"><label>Message:</label><div class="form-row-input"> 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: (1) Create generic methods for copying visualizations and visualization configurations; (2) use generic visualization copying to support importing and cloning visualizations.
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8a3730093edc/ changeset: 8a3730093edc user: jgoecks date: 2011-06-17 20:27:47 summary: (1) Create generic methods for copying visualizations and visualization configurations; (2) use generic visualization copying to support importing and cloning visualizations. affected #: 3 files (3.4 KB) --- a/lib/galaxy/model/__init__.py Fri Jun 17 13:16:53 2011 -0400 +++ b/lib/galaxy/model/__init__.py Fri Jun 17 14:27:47 2011 -0400 @@ -2244,20 +2244,59 @@ self.user = None class Visualization( object ): - def __init__( self ): + def __init__( self, user=None, type=None, title=None, dbkey=None, latest_revision=None ): self.id = None - self.user = None - self.type = None - self.title = None - self.latest_revision = None + self.user = user + self.type = type + self.title = title + self.dbkey = dbkey + self.latest_revision = latest_revision self.revisions = [] + if self.latest_revision: + self.revisions.append( latest_revision ) + + def copy( self, user=None, title=None ): + """ + Provide copy of visualization with only its latest revision. + """ + # NOTE: a shallow copy is done: the config is copied as is but datasets + # are not copied nor are the dataset ids changed. This means that the + # user does not have a copy of the data in his/her history and the + # user who owns the datasets may delete them, making them inaccessible + # for the current user. + # TODO: a deep copy option is needed. + + if not user: + user = self.user + if not title: + title = self.title + + copy_viz = Visualization( user=user, type=self.type, title=title, dbkey=self.dbkey ) + copy_revision = self.latest_revision.copy( visualization=copy_viz ) + copy_viz.latest_revision = copy_revision + return copy_viz class VisualizationRevision( object ): - def __init__( self ): + def __init__( self, visualization=None, title=None, dbkey=None, config=None ): self.id = None - self.visualization = None - self.title = None - self.config = None + self.visualization = visualization + self.title = title + self.dbkey = dbkey + self.config = config + + def copy( self, visualization=None ): + """ + Returns a copy of this object. + """ + if not visualization: + visualization = self.visualization + + return VisualizationRevision( + visualization=visualization, + title=self.title, + dbkey=self.dbkey, + config=self.config + ) class VisualizationUserShareAssociation( object ): def __init__( self ): --- a/lib/galaxy/web/controllers/visualization.py Fri Jun 17 13:16:53 2011 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Fri Jun 17 14:27:47 2011 -0400 @@ -92,29 +92,21 @@ @web.expose @web.require_login() def clone(self, trans, id, *args, **kwargs): - viz = self.get_visualization( trans, id, check_ownership=False ) + visualization = self.get_visualization( trans, id, check_ownership=False ) user = trans.get_user() - if viz.user == user: - owner = True - else: - if trans.sa_session.query( model.VisualizationUserShareAssociation ) \ - .filter_by( user=user, visualization=viz ).count() == 0: - error( "Visualization is not owned by or shared with current user" ) - owner = False - new_viz = model.Visualization() - new_viz.title = "Clone of '%s'" % viz.title - new_viz.dbkey = viz.dbkey - new_viz.type = viz.type - new_viz.latest_revision = viz.latest_revision - if not owner: - new_viz.title += " shared by '%s'" % viz.user.email - new_viz.user = user + if trans.sa_session.query( model.VisualizationUserShareAssociation ) \ + .filter_by( user=user, visualization=visualization ).count() == 0: + error( "Visualization is not owned by or shared with current user" ) + + cloned_visualization = visualization.copy( user=trans.user, title="Copy of '%s'" % visualization.title ) + # Persist session = trans.sa_session - session.add( new_viz ) + session.add( cloned_visualization ) session.flush() + # Display the management page - trans.set_message( 'Clone created with name "%s"' % new_viz.title ) + trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) return self.list( trans ) @web.expose @@ -205,36 +197,14 @@ elif visualization.deleted: return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) else: - # # Create imported visualization via copy. - # NOTE: a shallow copy is done: the config is copied as is but datasets - # are not copied nor are the dataset ids changed. This means that the - # user does not have a copy of the data in his/her history and the - # user who owns the datasets may delete them, making them inaccessible - # for the current user. - # TODO: - # -a deep copy is needed; - # -need to handle custom db keys. - # + # TODO: need to handle custom db keys. - imported_visualization = model.Visualization() - imported_visualization.title = visualization.title - imported_visualization.dbkey = visualization.dbkey - imported_visualization.type = visualization.type - imported_visualization.user = trans.user + imported_visualization = visualization.copy( user=trans.user, title="imported: " + visualization.title ) - # And the first visualization revision - imported_visualization_revision = model.VisualizationRevision() - imported_visualization_revision.title = visualization.title - imported_visualization_revision.config = visualization.latest_revision.config - imported_visualization_revision.dbkey = visualization.dbkey - imported_visualization_revision.visualization = imported_visualization - imported_visualization.latest_revision = imported_visualization_revision - # Persist session = trans.sa_session session.add( imported_visualization ) - session.add( imported_visualization_revision ) session.flush() # Redirect to load galaxy frames. --- a/templates/visualization/list.mako Fri Jun 17 13:16:53 2011 -0400 +++ b/templates/visualization/list.mako Fri Jun 17 14:27:47 2011 -0400 @@ -13,6 +13,19 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> + %if message: + <% + try: + status + except: + status = "done" + %> + <p /> + <div class="${status}message"> + ${h.to_unicode( message )} + </div> + %endif + ${h.to_unicode( grid )} <br><br> @@ -35,6 +48,7 @@ <td><div popupmenu="shared-${i}-popup"><a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(visualization.id) )}">Copy</a></div></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Jun '11

17 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/55af252cd550/ changeset: 55af252cd550 user: jgoecks date: 2011-06-17 19:16:34 summary: Enable importing of visualizations via a shallow copy: only a viz's config is copied, not its datasets. affected #: 2 files (1.1 KB) --- a/lib/galaxy/web/controllers/visualization.py Fri Jun 17 12:16:53 2011 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Fri Jun 17 13:16:34 2011 -0400 @@ -87,7 +87,7 @@ @web.require_login( "use Galaxy visualizations", use_panels=True ) def index( self, trans, *args, **kwargs ): """ Lists user's saved visualizations. """ - return self.list( trans, args, kwargs ) + return self.list( trans, *args, **kwargs ) @web.expose @web.require_login() @@ -202,20 +202,39 @@ visualization = self.get_visualization( trans, id, check_ownership=False ) if visualization.importable == False: return trans.show_error_message( "The owner of this visualization has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) - elif visualization.user == trans.user: - return trans.show_error_message( "You can't import this visualization because you own it.<br>You can %s" % referer_message, use_panels=True ) elif visualization.deleted: return trans.show_error_message( "You can't import this visualization because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) else: - # Create imported visualization via copy. TODO: Visualizations use datasets -- do we need to check to ensure that - # datasets can be imported/viewed and/or copy datasets to user? + # + # Create imported visualization via copy. + # NOTE: a shallow copy is done: the config is copied as is but datasets + # are not copied nor are the dataset ids changed. This means that the + # user does not have a copy of the data in his/her history and the + # user who owns the datasets may delete them, making them inaccessible + # for the current user. + # TODO: + # -a deep copy is needed; + # -need to handle custom db keys. + # + imported_visualization = model.Visualization() - imported_visualization.title = "imported: " + visualization.title - imported_visualization.latest_revision = visualization.latest_revision + imported_visualization.title = visualization.title + imported_visualization.dbkey = visualization.dbkey + imported_visualization.type = visualization.type imported_visualization.user = trans.user - # Save new visualization. + + # And the first visualization revision + imported_visualization_revision = model.VisualizationRevision() + imported_visualization_revision.title = visualization.title + imported_visualization_revision.config = visualization.latest_revision.config + imported_visualization_revision.dbkey = visualization.dbkey + imported_visualization_revision.visualization = imported_visualization + imported_visualization.latest_revision = imported_visualization_revision + + # Persist session = trans.sa_session session.add( imported_visualization ) + session.add( imported_visualization_revision ) session.flush() # Redirect to load galaxy frames. --- a/templates/visualization/display.mako Fri Jun 17 12:16:53 2011 -0400 +++ b/templates/visualization/display.mako Fri Jun 17 13:16:34 2011 -0400 @@ -49,7 +49,12 @@ </%def><%def name="render_item_links( visualization )"> - + <a + href="${h.url_for( controller='/visualization', action='imp', id=trans.security.encode_id( visualization.id ) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import visualization">Import visualization</a></%def><%def name="render_item( visualization, config )"> http://bitbucket.org/galaxy/galaxy-central/changeset/dc33340cad7d/ changeset: dc33340cad7d user: jgoecks date: 2011-06-17 19:16:53 summary: Merge. affected #: 1 file (8 bytes) --- a/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:16:34 2011 -0400 +++ b/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:16:53 2011 -0400 @@ -26,7 +26,7 @@ def set_meta( self, dataset, overwrite = True, **kwd ): - Tabular.set_meta( self, dataset, overwrite=overwrite, skip=1, max_data_lines=None, **kwd ) + Tabular.set_meta( self, dataset, overwrite=overwrite, max_data_lines=None, **kwd ) # these two if statements work around a potential bug in metadata.py if dataset.metadata.labels is None or dataset.metadata.labels == dataset.metadata.spec['labels'].no_value: self._set_column_labels_metadata( dataset ) 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: richard_burhans: fixed displayed line count
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/acbd9488ba36/ changeset: acbd9488ba36 user: richard_burhans date: 2011-06-17 19:13:01 summary: fixed displayed line count affected #: 1 file (8 bytes) --- a/lib/galaxy/datatypes/wsf.py Fri Jun 17 12:16:53 2011 -0400 +++ b/lib/galaxy/datatypes/wsf.py Fri Jun 17 13:13:01 2011 -0400 @@ -26,7 +26,7 @@ def set_meta( self, dataset, overwrite = True, **kwd ): - Tabular.set_meta( self, dataset, overwrite=overwrite, skip=1, max_data_lines=None, **kwd ) + Tabular.set_meta( self, dataset, overwrite=overwrite, max_data_lines=None, **kwd ) # these two if statements work around a potential bug in metadata.py if dataset.metadata.labels is None or dataset.metadata.labels == dataset.metadata.spec['labels'].no_value: self._set_column_labels_metadata( dataset ) 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: richard_burhans: updated error handling for genome diversity select snps tool
by Bitbucket 17 Jun '11

17 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7feab5786a19/ changeset: 7feab5786a19 user: richard_burhans date: 2011-06-17 18:16:53 summary: updated error handling for genome diversity select snps tool affected #: 2 files (3.1 KB) --- a/tools/genome_diversity/genome_diversity.py Fri Jun 17 10:53:41 2011 -0400 +++ b/tools/genome_diversity/genome_diversity.py Fri Jun 17 12:16:53 2011 -0400 @@ -1,5 +1,6 @@ #!/usr/bin/env python2.5 +import sys import cdblib def _openfile( filename=None, mode='r' ): @@ -21,7 +22,7 @@ return None -class SnpFile: +class SnpFile( object ): def __init__( self, filename=None, seq_col=1, pos_col=2, ref_seq_col=7, ref_pos_col=8 ): self.filename = filename self.fh = _openfile( filename ) @@ -63,7 +64,7 @@ return None, None -class IndexedFile: +class IndexedFile( object ): def __init__( self, data_file=None, index_file=None ): self.data_file = data_file @@ -176,3 +177,90 @@ else: return None + + +class LocationFile( object ): + def __init__(self, filename): + self.build_map(filename) + + def build_map(self, filename): + self.map = {} + self.open_file(filename) + for line in self.read_lines(): + elems = line.split('\t', 1) + if len(elems) == 2: + self.map[ elems[0].strip() ] = elems[1].strip() + self.close_file() + + def read_lines(self): + for line in self.fh: + if not line.startswith('#'): + line = line.rstrip('\r\n') + yield line + + def open_file(self, filename): + self.filename = filename + try: + self.fh = open(filename, 'r') + except IOError, err: + print >> sys.stderr, "Error opening location file '%s': %s" % (filename, str(err)) + sys.exit(1) + + def close_file(self): + self.fh.close() + + def loc_file( self, key ): + if key in self.map: + return self.map[key] + else: + print >> sys.stderr, "'%s' does not appear in location file '%s'" % (key, self.filename) + sys.exit(1) + +class ChrLens( object ): + def __init__( self, location_file, species ): + self.chrlen_loc = LocationFile( location_file ) + self.chrlen_filename = self.chrlen_loc.loc_file( species ) + self.build_map() + + def build_map(self): + self.map = {} + self.open_file(self.chrlen_filename) + for line in self.read_lines(): + elems = line.split('\t', 1) + if len(elems) == 2: + chrom = elems[0].strip() + chrom_len_text = elems[1].strip() + try: + chrom_len = int( chrom_len_text ) + except ValueError: + print >> sys.stderr, "Bad length '%s' for chromosome '%s' in '%s'" % (chrom_len_text, chrom, self.chrlen_filename) + self.map[ chrom ] = chrom_len + self.close_file() + + def read_lines(self): + for line in self.fh: + if not line.startswith('#'): + line = line.rstrip('\r\n') + yield line + + def open_file(self, filename): + self.filename = filename + try: + self.fh = open(filename, 'r') + except IOError, err: + print >> sys.stderr, "Error opening chromosome length file '%s': %s" % (filename, str(err)) + sys.exit(1) + + def close_file(self): + self.fh.close() + + def length( self, key ): + if key in self.map: + return self.map[key] + else: + return None + + def __iter__( self ): + for chrom in self.map: + yield chrom + --- a/tools/genome_diversity/select_snps.py Fri Jun 17 10:53:41 2011 -0400 +++ b/tools/genome_diversity/select_snps.py Fri Jun 17 12:16:53 2011 -0400 @@ -1,16 +1,9 @@ #!/usr/bin/env python -""" -basic version -need to add - o indexing - o better error handing -""" - import sys -import string import math from optparse import OptionParser +import genome_diversity as gd def main_function(parse_arguments=None): if parse_arguments is None: @@ -37,32 +30,19 @@ @main_function(parse_arguments) def main(options, arguments): - ref_chrom_idx = int( options.ref_chrom_col ) - 1 - ref_pos_idx = int( options.ref_pos_col ) - 1 - chrlens_fh = open( options.chrlens_loc, 'r' ) - for line in chrlens_fh: - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - elems = line.split( '\t' ) - if len(elems) >= 2 and elems[0] == options.species: - chrom_info_file = elems[1] + ref_chrom_idx = to_int( options.ref_chrom_col ) -1 + ref_pos_idx = to_int( options.ref_pos_col ) -1 - chrom_info = open( chrom_info_file, 'r' ) + if (ref_chrom_idx < 1) or (ref_pos_idx < 1) or (ref_chrom_idx == ref_pos_idx): + print >> sys.stderr, "Cannot locate reference genome sequence (ref) or reference genome position (rPos) column for this dataset." + sys.exit(1) + + chrlens = gd.ChrLens( options.chrlens_loc, options.species ) + total_len = 0 - for i, line in enumerate( chrom_info ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - elems = line.split() - if len(elems) == 2: - chrom = elems[0] - try: - chrom_len = int(elems[1]) - except ValueError: - sys.stderr.write( "bad chrom len in line %d column 2: %s\n" % ( i, elems[1] ) ) - sys.exit(1) - total_len += chrom_len; - chrom_info.close() + for chrom in chrlens: + total_len += chrlens.length(chrom) total_requested = int( options.num_snps ) lines, data, comments = get_snp_lines_data_and_comments( options.input, ref_chrom_idx, ref_pos_idx ) @@ -70,6 +50,13 @@ out_data = fix_selection_and_order_like_input(data, selected, total_requested) write_selected_snps( options.output, out_data, lines, comments ) +def to_int( value ): + try: + int_value = int( value ) + except ValueError: + int_value = 0 + return int_value + def get_snp_lines_data_and_comments( filename, chrom_idx, pos_idx ): fh = open( filename, 'r' ) if (chrom_idx >= pos_idx): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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