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commit/galaxy-central: dannon: Branch prune.
by commits-noreply＠bitbucket.org 12 Sep '14

12 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65206cc6586c/ Changeset: 65206cc6586c Branch: igv-local-dbkey User: dannon Date: 2014-09-12 19:14:24 Summary: Branch prune. 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: dannon: Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488)
by commits-noreply＠bitbucket.org 12 Sep '14

12 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8465681a19d/ Changeset: f8465681a19d User: dannon Date: 2014-09-12 19:10:52 Summary: Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488) Allow local IGV users to visualize custom genomes Affected #: 2 files diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> 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 12 Sep '14

12 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4456e0cf7721/ Changeset: 4456e0cf7721 Branch: igv-local-dbkey User: lance_parsons Date: 2014-09-04 21:22:10 Summary: Allow local IGV users to visualize custom genomes Affected #: 2 files diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 4456e0cf7721386a728e9cb05ef7463bbd477d5b display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 4456e0cf7721386a728e9cb05ef7463bbd477d5b display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> https://bitbucket.org/galaxy/galaxy-central/commits/f8465681a19d/ Changeset: f8465681a19d User: dannon Date: 2014-09-12 19:10:52 Summary: Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488) Allow local IGV users to visualize custom genomes Affected #: 2 files diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 12 Sep '14

12 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa8d4381785e/ Changeset: aa8d4381785e User: jmchilton Date: 2014-09-12 15:32:22 Summary: More workflow module documentation improvements. I nearly understand workflow modules... Affected #: 2 files diff -r b8520d9c8269c4c7deca6418d54f2e722886073e -r aa8d4381785ee94746dbdcfd35c9b0798a10be30 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -79,10 +79,16 @@ def get_state( self ): """ Return a serializable representation of the persistable state of the step - for tools it DefaultToolState.encode returns a string and - for inputs a json description is dumped out. + for simpler module types a json description is dumped out. """ return None + def update_state( self, incoming ): + """ Update the current state of the module against the user supplied + parameters in the dict-like object `incoming`. + """ + pass + def get_errors( self ): """ It seems like this is effectively just used as boolean - some places in the tool shed self.errors is set to boolean, other places 'unavailable', @@ -97,9 +103,6 @@ def get_data_outputs( self ): return [] - def update_state( self ): - pass - def get_config_form( self ): """ Render form that is embedded in workflow editor for modifying the step state of a node. @@ -120,33 +123,38 @@ ## ---- Run time --------------------------------------------------------- def get_runtime_inputs( self ): - """ Used internally to modules and when displaying inputs in display - and run workflow templates. The ToolModule doesn't implement this and - these templates contain specialized logic for dealing with the tool and - state directly in these cases. + """ Used internally by modules and when displaying inputs in workflow + editor and run workflow templates. + + Note: The ToolModule doesn't implement this and these templates contain + specialized logic for dealing with the tool and state directly in the + case of ToolModules. """ raise TypeError( "Abstract method" ) def encode_runtime_state( self, trans, state ): - """ Encode the runtime state (loaded from the stored step and - populated via the WorkflowModuleInjector below) for use in a hidden - parameter on the webpage. + """ Encode the default runtime state at return as a simple `str` for + use in a hidden parameter on the workflow run submission form. - This will combined with runtime parameters supplied by user running - the workflow to create the final state to pass along to execute during - workflow invocation. + This default runtime state will be combined with user supplied + parameters in `compute_runtime_state` below at workflow invocation time to + actually describe how each step will be executed. """ raise TypeError( "Abstract method" ) - def compute_state( self, trans, step_updates=None ): - """ Recover the transient "state" attribute to populate corresponding - step with (currently this is always a DefaultToolState instance, - though I am not sure this is strictly nessecary). + def compute_runtime_state( self, trans, step_updates=None ): + """ Determine the runtime state (potentially different from self.state + which describes configuration state). This (again unlike self.state) is + currently always a `DefaultToolState` object. If `step_updates` is `None`, this is likely for rendering the run form for instance and no runtime properties are available and state must be - solely determined by step. If `step_updates` are available they describe - the runtime properties supplied by the workflow runner. + solely determined by the default runtime state described by the step. + + If `step_updates` are available they describe the runtime properties + supplied by the workflow runner (potentially including a `tool_state` + parameter which is the serialized default encoding state created with + encode_runtime_state above). """ raise TypeError( "Abstract method" ) @@ -232,7 +240,7 @@ errors[ name ] = error return errors - def compute_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None ): if step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -559,7 +567,7 @@ def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True ) - def compute_state( self, trans, step_updates=None ): + def compute_runtime_state( self, trans, step_updates=None ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -788,7 +796,7 @@ # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections ) - state, step_errors = module.compute_state( trans, step_args ) + state, step_errors = module.compute_runtime_state( trans, step_args ) step.state = state return step_errors diff -r b8520d9c8269c4c7deca6418d54f2e722886073e -r aa8d4381785ee94746dbdcfd35c9b0798a10be30 test/unit/workflows/test_modules.py --- a/test/unit/workflows/test_modules.py +++ b/test/unit/workflows/test_modules.py @@ -7,7 +7,6 @@ from galaxy import model from galaxy.workflow import modules -from galaxy.tools import parameters from .workflow_support import MockTrans @@ -49,17 +48,17 @@ __assert_has_runtime_input( module, label="Cool Input" ) -def test_data_input_compute_state_default(): +def test_data_input_compute_runtime_state_default(): module = __from_step( type="data_input", ) - state, errors = module.compute_state( module.trans ) + state, errors = module.compute_runtime_state( module.trans ) assert not errors assert 'input' in state.inputs assert state.inputs[ 'input' ] is None -def test_data_input_compute_state_args(): +def test_data_input_compute_runtime_state_args(): module = __from_step( type="data_input", ) @@ -68,7 +67,7 @@ hda = model.HistoryDatasetAssociation() with mock.patch('galaxy.workflow.modules.check_param') as check_method: check_method.return_value = ( hda, None ) - state, errors = module.compute_state( module.trans, { 'input': 4, 'tool_state': tool_state } ) + state, errors = module.compute_runtime_state( module.trans, { 'input': 4, 'tool_state': tool_state } ) assert not errors assert 'input' in state.inputs https://bitbucket.org/galaxy/galaxy-central/commits/945ebcd32f33/ Changeset: 945ebcd32f33 User: jmchilton Date: 2014-09-12 15:32:22 Summary: Rework workflow modules to reduce duplication and add more consistency.. Adding a recover_state method that to both implementations (though meant to be part of the module interface) that recovers the configuration state (module.state) from a dictionary. This turns out to reduce a lot of duplication between data and data collection input modules. Affected #: 1 file diff -r aa8d4381785ee94746dbdcfd35c9b0798a10be30 -r 945ebcd32f336a5b3b97c4c66aa1274a49d8e07b lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -171,24 +171,41 @@ @classmethod def new( Class, trans, tool_id=None ): module = Class( trans ) - module.state = dict( name=Class.default_name ) + module.state = Class.default_state() return module @classmethod def from_dict( Class, trans, d, secure=True ): module = Class( trans ) state = loads( d["tool_state"] ) - module.state = dict( name=state.get( "name", Class.default_name ) ) + module.recover_state( state ) return module @classmethod def from_workflow_step( Class, trans, step ): module = Class( trans ) - module.state = dict( name="Input Dataset" ) - if step.tool_inputs and "name" in step.tool_inputs: - module.state['name'] = step.tool_inputs[ 'name' ] + module.recover_state( step.tool_inputs ) return module + @classmethod + def default_state( Class ): + """ This method should return a dictionary describing each + configuration property and its default value. + """ + raise TypeError( "Abstract method" ) + + def recover_state( self, state, **kwds ): + """ Recover state `dict` from simple dictionary describing configuration + state (potentially from persisted step state). + + Sub-classes should supply `default_state` method and `state_fields` + attribute which are used to build up the state `dict`. + """ + self.state = self.default_state() + for key in self.state_fields: + if state and key in state: + self.state[ key ] = state[ key ] + def save_to_step( self, step ): step.type = self.type step.tool_id = None @@ -277,6 +294,11 @@ type = "data_input" name = "Input dataset" default_name = "Input Dataset" + state_fields = [ "name" ] + + @classmethod + def default_state( Class ): + return dict( name=Class.default_name ) class InputDataCollectionModule( InputModule ): @@ -285,34 +307,11 @@ type = "data_collection_input" name = "Input dataset collection" collection_type = default_collection_type + state_fields = [ "name", "collection_type" ] @classmethod - def new( Class, trans, tool_id=None ): - module = Class( trans ) - module.state = dict( name=Class.default_name, collection_type=Class.default_collection_type ) - return module - - @classmethod - def from_dict( Class, trans, d, secure=True ): - module = Class( trans ) - state = loads( d["tool_state"] ) - module.state = dict( - name=state.get( "name", Class.default_name ), - collection_type=state.get( "collection_type", Class.default_collection_type ) - ) - return module - - @classmethod - def from_workflow_step( Class, trans, step ): - module = Class( trans ) - module.state = dict( - name=Class.default_name, - collection_type=Class.default_collection_type - ) - for key in [ "name", "collection_type" ]: - if step.tool_inputs and key in step.tool_inputs: - module.state[ key ] = step.tool_inputs[ key ] - return module + def default_state( Class ): + return dict( name=Class.default_name, collection_type=Class.default_collection_type ) def get_runtime_inputs( self, filter_set=['data'] ): label = self.state.get( "name", self.default_name ) @@ -408,10 +407,9 @@ # tool being previously unavailable. return module_factory.from_dict(trans, loads(step.config), secure=False) module = Class( trans, tool_id ) - module.state = galaxy.tools.DefaultToolState() if step.tool_version and (step.tool_version != module.tool.version): module.version_changes.append("%s: using version '%s' instead of version '%s' indicated in this workflow." % (tool_id, module.tool.version, step.tool_version)) - module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + module.recover_state( step.tool_inputs ) module.errors = step.tool_errors module.workflow_outputs = step.workflow_outputs pjadict = {} @@ -421,6 +419,17 @@ return module return None + def recover_state( self, state, **kwds ): + """ Recover module configuration state property (a `DefaultToolState` + object) using the tool's `params_from_strings` method. + """ + app = self.trans.app + self.state = galaxy.tools.DefaultToolState() + params_from_kwds = dict( + ignore_errors=kwds.get( "ignore_errors", True ) + ) + self.state.inputs = self.tool.params_from_strings( state, app, **params_from_kwds ) + @classmethod def __get_tool_version( cls, trans, tool_id ): # Return a ToolVersion if one exists for tool_id. https://bitbucket.org/galaxy/galaxy-central/commits/2346e098b27e/ Changeset: 2346e098b27e User: jmchilton Date: 2014-09-12 15:32:22 Summary: Better OOP design for separation between input and input collection modules. (Lot easier now that I understand what all of the module methods are doing and have an example of a 4th module downstream.) Now with even more unit tests. Affected #: 2 files diff -r 945ebcd32f336a5b3b97c4c66aa1274a49d8e07b -r 2346e098b27e0141fdd3e9821895413e27bc2c2f lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -214,12 +214,8 @@ def get_data_inputs( self ): return [] - def get_data_outputs( self ): - return [ dict( name='output', extensions=['input'] ) ] - def get_config_form( self ): - form = formbuilder.FormBuilder( title=self.name ) \ - .add_text( "name", "Name", value=self.state['name'] ) + form = self._abstract_config_form( ) return self.trans.fill_template( "workflow/editor_generic_form.mako", module=self, form=form ) @@ -227,11 +223,7 @@ return dumps( self.state ) def update_state( self, incoming ): - self.state['name'] = incoming.get( 'name', 'Input Dataset' ) - - def get_runtime_inputs( self, filter_set=['data'] ): - label = self.state.get( "name", "Input Dataset" ) - return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) ) + self.recover_state( incoming ) def get_runtime_state( self ): state = galaxy.tools.DefaultToolState() @@ -300,6 +292,18 @@ def default_state( Class ): return dict( name=Class.default_name ) + def _abstract_config_form( self ): + form = formbuilder.FormBuilder( title=self.name ) \ + .add_text( "name", "Name", value=self.state['name'] ) + return form + + def get_data_outputs( self ): + return [ dict( name='output', extensions=['input'] ) ] + + def get_runtime_inputs( self, filter_set=['data'] ): + label = self.state.get( "name", "Input Dataset" ) + return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) ) + class InputDataCollectionModule( InputModule ): default_name = "Input Dataset Collection" @@ -319,7 +323,7 @@ input_element = Element( "param", name="input", label=label, type="data_collection", collection_type=collection_type ) return dict( input=DataCollectionToolParameter( None, input_element, self.trans ) ) - def get_config_form( self ): + def _abstract_config_form( self ): type_hints = odict.odict() type_hints[ "list" ] = "List of Datasets" type_hints[ "paired" ] = "Dataset Pair" @@ -338,12 +342,7 @@ "name", "Name", value=self.state['name'] ) form.inputs.append( type_input ) - return self.trans.fill_template( "workflow/editor_generic_form.mako", - module=self, form=form ) - - def update_state( self, incoming ): - self.state[ 'name' ] = incoming.get( 'name', self.default_name ) - self.state[ 'collection_type' ] = incoming.get( 'collection_type', self.collection_type ) + return form def get_data_outputs( self ): return [ dict( name='output', extensions=['input_collection'], collection_type=self.state[ 'collection_type' ] ) ] diff -r 945ebcd32f336a5b3b97c4c66aa1274a49d8e07b -r 2346e098b27e0141fdd3e9821895413e27bc2c2f test/unit/workflows/test_modules.py --- a/test/unit/workflows/test_modules.py +++ b/test/unit/workflows/test_modules.py @@ -74,6 +74,49 @@ assert state.inputs[ 'input' ] is hda +def test_data_input_connections(): + module = __from_step( + type="data_input", + ) + assert len( module.get_data_inputs() ) == 0 + + outputs = module.get_data_outputs() + assert len( outputs ) == 1 + output = outputs[ 0 ] + assert output[ 'name' ] == 'output' + assert output[ 'extensions' ] == [ 'input' ] + + +def test_data_input_update(): + module = __from_step( + type="data_input", + tool_inputs={ + "name": "Cool Input", + }, + ) + module.update_state( dict( name="Awesome New Name" ) ) + assert module.state[ 'name' ] == "Awesome New Name" + + +def test_data_input_get_form(): + module = __from_step( + type="data_input", + tool_inputs={ + "name": "Cool Input", + }, + ) + + def test_form(template, **kwds ): + assert template == "workflow/editor_generic_form.mako" + assert "form" in kwds + assert len( kwds[ "form" ].inputs ) == 1 + return "TEMPLATE" + + fill_mock = mock.Mock( side_effect=test_form ) + module.trans.fill_template = fill_mock + assert module.get_config_form() == "TEMPLATE" + + def test_data_collection_input_default_state(): trans = MockTrans() module = modules.module_factory.new( trans, "data_collection_input" ) @@ -99,6 +142,55 @@ __assert_has_runtime_input( module, label="Cool Input Collection", collection_type="list:paired" ) +def test_data_collection_input_connections(): + module = __from_step( + type="data_collection_input", + tool_inputs={ + 'collection_type': 'list:paired' + } + ) + assert len( module.get_data_inputs() ) == 0 + + outputs = module.get_data_outputs() + assert len( outputs ) == 1 + output = outputs[ 0 ] + assert output[ 'name' ] == 'output' + assert output[ 'extensions' ] == [ 'input_collection' ] + assert output[ 'collection_type' ] == 'list:paired' + + +def test_data_collection_input_update(): + module = __from_step( + type="data_collection_input", + tool_inputs={ + 'name': 'Cool Collection', + 'collection_type': 'list:paired', + } + ) + module.update_state( dict( name="New Collection", collection_type="list" ) ) + assert module.state[ 'name' ] == "New Collection" + + +def test_data_collection_input_config_form(): + module = __from_step( + type="data_collection_input", + tool_inputs={ + 'name': 'Cool Collection', + 'collection_type': 'list:paired', + } + ) + + def test_form(template, **kwds ): + assert template == "workflow/editor_generic_form.mako" + assert "form" in kwds + assert len( kwds[ "form" ].inputs ) == 2 + return "TEMPLATE" + + fill_mock = mock.Mock( side_effect=test_form ) + module.trans.fill_template = fill_mock + assert module.get_config_form() == "TEMPLATE" + + def test_cannot_create_tool_modules_for_missing_tools(): trans = MockTrans() exception = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

[galaxyproject/usegalaxy-playbook] 14926e: Update pulsar vars for new job_managers.ini templa...
by GitHub 12 Sep '14

12 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 14926e345bc4f9e1426398508abf1f1886b175c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/14926e345bc4f9e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-11 (Thu, 11 Sep 2014) Changed paths: M stage/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Update pulsar vars for new job_managers.ini template style.

1 0

[galaxyproject/usegalaxy-playbook] 87f275: Update galaxyprojectdotorg.pulsar to v0.3
by GitHub 12 Sep '14

12 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 87f2751c7c727d57146f436dcf0f10d3f089dbad https://github.com/galaxyproject/usegalaxy-playbook/commit/87f2751c7c727d57… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-11 (Thu, 11 Sep 2014) Changed paths: M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml M roles/galaxyprojectdotorg.pulsar/templates/job_managers.ini.j2 Log Message: ----------- Update galaxyprojectdotorg.pulsar to v0.3

1 0

commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 12 Sep '14

12 Sep '14

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9278a44330b7/ Changeset: 9278a44330b7 User: jmchilton Date: 2014-09-11 22:01:08 Summary: Initial work on a tags manager. Rest of UsesTagsMixin needs to be copied over similarly and deprecated, following that I guess all references need to be updated and then the mixin eliminated all together I guess (exhausting :)). Affected #: 3 files diff -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 -r 9278a44330b7343a7f414057669fc1e047cfc1b6 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -10,9 +10,9 @@ from galaxy.web.base.controller import ( UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems, - UsesTagsMixin, ) from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. +from galaxy.managers import tags from galaxy.managers.collections_util import validate_input_element_identifiers from galaxy.util import validation from galaxy.util import odict @@ -27,8 +27,7 @@ class DatasetCollectionsService( UsesHistoryDatasetAssociationMixin, - UsesLibraryMixinItems, - UsesTagsMixin, + UsesLibraryMixinItems ): """ Abstraction for interfacing with dataset collections instance - ideally abstarcts @@ -41,6 +40,7 @@ self.model = app.model self.security = app.security self.hda_manager = hdas.HDAManager() + self.tag_manager = tags.TagsManager( app ) def create( self, @@ -166,7 +166,7 @@ dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] ) changed[ 'annotation' ] = new_data[ 'annotation' ] if 'tags' in new_data.keys() and trans.get_user(): - self.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) + self.tag_manager.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) if changed.keys(): trans.sa_session.flush() diff -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 -r 9278a44330b7343a7f414057669fc1e047cfc1b6 lib/galaxy/managers/tags.py --- /dev/null +++ b/lib/galaxy/managers/tags.py @@ -0,0 +1,20 @@ + + +class TagsManager( object ): + """ Manages CRUD operations related to tagging objects. + """ + + def __init__( self, app ): + self.app = app + self.tag_handler = app.tag_handler + + def set_tags_from_list( self, trans, item, new_tags_list, user=None ): + #precondition: item is already security checked against user + #precondition: incoming tags is a list of sanitized/formatted strings + user = user or trans.user + + self.tag_handler.delete_item_tags( trans, user, item ) + new_tags_str = ','.join( new_tags_list ) + self.tag_handler.apply_item_tags( trans, user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) ) + trans.sa_session.flush() + return item.tags diff -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 -r 9278a44330b7343a7f414057669fc1e047cfc1b6 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -38,6 +38,7 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation from galaxy.managers import api_keys +from galaxy.managers import tags from galaxy.datatypes.metadata import FileParameter from galaxy.tools.parameters import RuntimeValue, visit_input_values from galaxy.tools.parameters.basic import DataToolParameter @@ -2808,16 +2809,9 @@ return self.get_tag_handler( trans )._get_item_tag_assoc( user, tagged_item, tag_name ) def set_tags_from_list( self, trans, item, new_tags_list, user=None ): - #precondition: item is already security checked against user - #precondition: incoming tags is a list of sanitized/formatted strings - user = user or trans.user - - # based on controllers/tag retag_async: delete all old, reset to entire new - trans.app.tag_handler.delete_item_tags( trans, user, item ) - new_tags_str = ','.join( new_tags_list ) - trans.app.tag_handler.apply_item_tags( trans, user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) ) - trans.sa_session.flush() - return item.tags + # Method deprecated - try to use TagsHandler instead. + tags_manager = tags.TagsManager( trans.app ) + return tags_manager.set_tags_from_list( trans, item, new_tags_list, user=user ) def get_user_tags_used( self, trans, user=None ): """ https://bitbucket.org/galaxy/galaxy-central/commits/6f5195e15d09/ Changeset: 6f5195e15d09 User: jmchilton Date: 2014-09-11 22:01:08 Summary: Refactor generic controller mixin code for security out for reuse in managers. Affected #: 2 files diff -r 9278a44330b7343a7f414057669fc1e047cfc1b6 -r 6f5195e15d0919790db68865dba5e365d67d14c1 lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -1,7 +1,41 @@ +from galaxy import exceptions class ModelManager( object ): pass + class ModelSerializer( object ): pass + + +def security_check( trans, item, check_ownership=False, check_accessible=False ): + """ Security checks for an item: checks if (a) user owns item or (b) item + is accessible to user. This is a generic method for dealing with objects + uniformly from the older controller mixin code - however whenever possible + the managers for a particular model should be used to perform security + checks. + """ + + # all items are accessible to an admin + if trans.user_is_admin(): + return item + + # Verify ownership: there is a current user and that user is the same as the item's + if check_ownership: + if not trans.user: + raise exceptions.ItemOwnershipException( "Must be logged in to manage Galaxy items", type='error' ) + if item.user != trans.user: + raise exceptions.ItemOwnershipException( "%s is not owned by the current user" % item.__class__.__name__, type='error' ) + + # Verify accessible: + # if it's part of a lib - can they access via security + # if it's something else (sharable) have they been added to the item's users_shared_with_dot_users + if check_accessible: + if type( item ) in ( trans.app.model.LibraryFolder, trans.app.model.LibraryDatasetDatasetAssociation, trans.app.model.LibraryDataset ): + if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), item, trans.user ): + raise exceptions.ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) + else: + if ( item.user != trans.user ) and ( not item.importable ) and ( trans.user not in item.users_shared_with_dot_users ): + raise exceptions.ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) + return item diff -r 9278a44330b7343a7f414057669fc1e047cfc1b6 -r 6f5195e15d0919790db68865dba5e365d67d14c1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -39,6 +39,7 @@ from galaxy.managers import api_keys from galaxy.managers import tags +from galaxy.managers import base as managers_base from galaxy.datatypes.metadata import FileParameter from galaxy.tools.parameters import RuntimeValue, visit_input_values from galaxy.tools.parameters.basic import DataToolParameter @@ -301,28 +302,7 @@ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ - # all items are accessible to an admin - if trans.user_is_admin(): - return item - - # Verify ownership: there is a current user and that user is the same as the item's - if check_ownership: - if not trans.user: - raise ItemOwnershipException( "Must be logged in to manage Galaxy items", type='error' ) - if item.user != trans.user: - raise ItemOwnershipException( "%s is not owned by the current user" % item.__class__.__name__, type='error' ) - - # Verify accessible: - # if it's part of a lib - can they access via security - # if it's something else (sharable) have they been added to the item's users_shared_with_dot_users - if check_accessible: - if type( item ) in ( trans.app.model.LibraryFolder, trans.app.model.LibraryDatasetDatasetAssociation, trans.app.model.LibraryDataset ): - if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), item, trans.user ): - raise ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) - else: - if ( item.user != trans.user ) and ( not item.importable ) and ( trans.user not in item.users_shared_with_dot_users ): - raise ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) - return item + return managers_base.security_check( trans, item, check_ownership=check_ownership, check_accessible=check_accessible ) class UsesHistoryMixin( SharableItemSecurityMixin ): https://bitbucket.org/galaxy/galaxy-central/commits/83016af21151/ Changeset: 83016af21151 User: jmchilton Date: 2014-09-11 22:01:08 Summary: Refactor generic controller mixin code for loading objects into managers. Affected #: 2 files diff -r 6f5195e15d0919790db68865dba5e365d67d14c1 -r 83016af2115156f4ebb640ea231824f23aeecad3 lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -1,5 +1,12 @@ from galaxy import exceptions +from galaxy import model +from galaxy.model import tool_shed_install + + +import logging +log = logging.getLogger( __name__ ) + class ModelManager( object ): pass @@ -39,3 +46,75 @@ if ( item.user != trans.user ) and ( not item.importable ) and ( trans.user not in item.users_shared_with_dot_users ): raise exceptions.ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) return item + + +def get_class( class_name ): + """ Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """ + if class_name == 'History': + item_class = model.History + elif class_name == 'HistoryDatasetAssociation': + item_class = model.HistoryDatasetAssociation + elif class_name == 'Page': + item_class = model.Page + elif class_name == 'StoredWorkflow': + item_class = model.StoredWorkflow + elif class_name == 'Visualization': + item_class = model.Visualization + elif class_name == 'Tool': + item_class = model.Tool + elif class_name == 'Job': + item_class = model.Job + elif class_name == 'User': + item_class = model.User + elif class_name == 'Group': + item_class = model.Group + elif class_name == 'Role': + item_class = model.Role + elif class_name == 'Quota': + item_class = model.Quota + elif class_name == 'Library': + item_class = model.Library + elif class_name == 'LibraryFolder': + item_class = model.LibraryFolder + elif class_name == 'LibraryDatasetDatasetAssociation': + item_class = model.LibraryDatasetDatasetAssociation + elif class_name == 'LibraryDataset': + item_class = model.LibraryDataset + elif class_name == 'ToolShedRepository': + item_class = tool_shed_install.ToolShedRepository + else: + item_class = None + return item_class + + +def get_object( trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ): + """ + Convenience method to get a model object with the specified checks. This is + a generic method for dealing with objects uniformly from the older + controller mixin code - however whenever possible the managers for a + particular model should be used to load objects. + """ + try: + decoded_id = trans.security.decode_id( id ) + except: + raise exceptions.MessageException( "Malformed %s id ( %s ) specified, unable to decode" + % ( class_name, str( id ) ), type='error' ) + try: + item_class = get_class( class_name ) + assert item_class is not None + item = trans.sa_session.query( item_class ).get( decoded_id ) + assert item is not None + except Exception: + log.exception( "Invalid %s id ( %s ) specified." % ( class_name, id ) ) + raise exceptions.MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" ) + + if check_ownership or check_accessible: + security_check( trans, item, check_ownership, check_accessible ) + if deleted is True and not item.deleted: + raise exceptions.ItemDeletionException( '%s "%s" is not deleted' + % ( class_name, getattr( item, 'name', id ) ), type="warning" ) + elif deleted is False and item.deleted: + raise exceptions.ItemDeletionException( '%s "%s" is deleted' + % ( class_name, getattr( item, 'name', id ) ), type="warning" ) + return item + diff -r 6f5195e15d0919790db68865dba5e365d67d14c1 -r 83016af2115156f4ebb640ea231824f23aeecad3 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -78,70 +78,14 @@ def get_class( self, class_name ): """ Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """ - if class_name == 'History': - item_class = self.app.model.History - elif class_name == 'HistoryDatasetAssociation': - item_class = self.app.model.HistoryDatasetAssociation - elif class_name == 'Page': - item_class = self.app.model.Page - elif class_name == 'StoredWorkflow': - item_class = self.app.model.StoredWorkflow - elif class_name == 'Visualization': - item_class = self.app.model.Visualization - elif class_name == 'Tool': - item_class = self.app.model.Tool - elif class_name == 'Job': - item_class = self.app.model.Job - elif class_name == 'User': - item_class = self.app.model.User - elif class_name == 'Group': - item_class = self.app.model.Group - elif class_name == 'Role': - item_class = self.app.model.Role - elif class_name == 'Quota': - item_class = self.app.model.Quota - elif class_name == 'Library': - item_class = self.app.model.Library - elif class_name == 'LibraryFolder': - item_class = self.app.model.LibraryFolder - elif class_name == 'LibraryDatasetDatasetAssociation': - item_class = self.app.model.LibraryDatasetDatasetAssociation - elif class_name == 'LibraryDataset': - item_class = self.app.model.LibraryDataset - elif class_name == 'ToolShedRepository': - item_class = self.app.install_model.ToolShedRepository - else: - item_class = None - return item_class + return managers_base.get_class( class_name ) def get_object( self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ): """ Convenience method to get a model object with the specified checks. """ - try: - decoded_id = trans.security.decode_id( id ) - except: - raise MessageException( "Malformed %s id ( %s ) specified, unable to decode" - % ( class_name, str( id ) ), type='error' ) - try: - item_class = self.get_class( class_name ) - assert item_class is not None - item = trans.sa_session.query( item_class ).get( decoded_id ) - assert item is not None - except Exception: - log.exception( "Invalid %s id ( %s ) specified." % ( class_name, id ) ) - raise MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" ) - - if check_ownership or check_accessible: - self.security_check( trans, item, check_ownership, check_accessible ) - if deleted == True and not item.deleted: - raise ItemDeletionException( '%s "%s" is not deleted' - % ( class_name, getattr( item, 'name', id ) ), type="warning" ) - elif deleted == False and item.deleted: - raise ItemDeletionException( '%s "%s" is deleted' - % ( class_name, getattr( item, 'name', id ) ), type="warning" ) - return item - + return managers_base.get_object( trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) + # this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin # but *don't* then becomes difficult #def security_check( self, trans, item, check_ownership=False, check_accessible=False ): https://bitbucket.org/galaxy/galaxy-central/commits/355aee34a371/ Changeset: 355aee34a371 User: jmchilton Date: 2014-09-11 22:01:08 Summary: Introduce LDDA manager stub. Use it to eliminate awful controller dependencies (and associated circular dependency errors when controllers are not loaded before everything else) in galaxy.dataset_collections. Affected #: 3 files diff -r 83016af2115156f4ebb640ea231824f23aeecad3 -r 355aee34a371c99f9251b965ea625066a80419ea lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -7,11 +7,9 @@ from galaxy.exceptions import MessageException from galaxy.exceptions import ItemAccessibilityException from galaxy.exceptions import RequestParameterInvalidException -from galaxy.web.base.controller import ( - UsesHistoryDatasetAssociationMixin, - UsesLibraryMixinItems, -) from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. +from galaxy.managers import histories +from galaxy.managers import lddas from galaxy.managers import tags from galaxy.managers.collections_util import validate_input_element_identifiers from galaxy.util import validation @@ -25,10 +23,7 @@ ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type." -class DatasetCollectionsService( - UsesHistoryDatasetAssociationMixin, - UsesLibraryMixinItems -): +class DatasetCollectionsService( object ): """ Abstraction for interfacing with dataset collections instance - ideally abstarcts out model and plugin details. @@ -40,7 +35,9 @@ self.model = app.model self.security = app.security self.hda_manager = hdas.HDAManager() + self.history_manager = histories.HistoryManager() self.tag_manager = tags.TagsManager( app ) + self.ldda_manager = lddas.LDDAManager( ) def create( self, @@ -249,7 +246,7 @@ decoded_id = int( trans.app.security.decode_id( encoded_id ) ) element = self.hda_manager.get( trans, decoded_id, check_ownership=False ) elif src_type == 'ldda': - element = self.get_library_dataset_dataset_association( trans, encoded_id ) + element = self.ldda_manager.get( trans, encoded_id ) elif src_type == 'hdca': # TODO: Option to copy? Force copy? Copy or allow if not owned? element = self.__get_history_collection_instance( trans, encoded_id ).collection @@ -281,7 +278,7 @@ def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): instance_id = int( trans.app.security.decode_id( id ) ) collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id ) - self.security_check( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible ) + self.history_manager.secure( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible ) return collection_instance def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): diff -r 83016af2115156f4ebb640ea231824f23aeecad3 -r 355aee34a371c99f9251b965ea625066a80419ea lib/galaxy/managers/lddas.py --- /dev/null +++ b/lib/galaxy/managers/lddas.py @@ -0,0 +1,16 @@ +from galaxy.managers import base as manager_base + + +class LDDAManager( manager_base.ModelManager ): + """ A fairly sparse manager for LDDAs. + """ + + def __init__( self ): + """ + Set up and initialize other managers needed by lddas. + """ + pass + + def get( self, trans, id, check_accessible=True ): + return manager_base.get_object( trans, id, 'LibraryDatasetDatasetAssociation', + check_ownership=False, check_accessible=check_accessible ) diff -r 83016af2115156f4ebb640ea231824f23aeecad3 -r 355aee34a371c99f9251b965ea625066a80419ea lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -875,6 +875,9 @@ check_ownership=False, check_accessible=check_accessible ) def get_library_dataset_dataset_association( self, trans, id, check_ownership=False, check_accessible=True ): + # Deprecated in lieu to galaxy.managers.lddas.LDDAManager.get() but not + # reusing that exactly because of subtle differences in exception handling + # logic (API controller override get_object to be slightly different). return self.get_object( trans, id, 'LibraryDatasetDatasetAssociation', check_ownership=False, check_accessible=check_accessible ) https://bitbucket.org/galaxy/galaxy-central/commits/dd31ab49162d/ Changeset: dd31ab49162d User: jmchilton Date: 2014-09-11 22:01:08 Summary: Make dataset collections service a manager. It would hve been arcitected this way from the beginning but my initial work on it predated Carl's managers work and it had those pesky controller dependencies. Affected #: 3 files diff -r 355aee34a371c99f9251b965ea625066a80419ea -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -5,7 +5,7 @@ from galaxy import config, jobs import galaxy.model import galaxy.security -from galaxy import dataset_collections +from galaxy.managers.collections import DatasetCollectionManager import galaxy.quota from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.visualization.genomes import Genomes @@ -57,7 +57,7 @@ # Tag handler self.tag_handler = GalaxyTagHandler() # Dataset Collection Plugins - self.dataset_collections_service = dataset_collections.DatasetCollectionsService(self) + self.dataset_collections_service = DatasetCollectionManager(self) # Tool Data Tables self._configure_tool_data_tables( from_shed_config=False ) diff -r 355aee34a371c99f9251b965ea625066a80419ea -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -1,292 +0,0 @@ -from .registry import DatasetCollectionTypesRegistry -from .matching import MatchingCollections -from .type_description import CollectionTypeDescriptionFactory - - -from galaxy import model -from galaxy.exceptions import MessageException -from galaxy.exceptions import ItemAccessibilityException -from galaxy.exceptions import RequestParameterInvalidException -from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. -from galaxy.managers import histories -from galaxy.managers import lddas -from galaxy.managers import tags -from galaxy.managers.collections_util import validate_input_element_identifiers -from galaxy.util import validation -from galaxy.util import odict - -import logging -log = logging.getLogger( __name__ ) - - -ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers." -ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type." - - -class DatasetCollectionsService( object ): - """ - Abstraction for interfacing with dataset collections instance - ideally abstarcts - out model and plugin details. - """ - - def __init__( self, app ): - self.type_registry = DatasetCollectionTypesRegistry( app ) - self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry ) - self.model = app.model - self.security = app.security - self.hda_manager = hdas.HDAManager() - self.history_manager = histories.HistoryManager() - self.tag_manager = tags.TagsManager( app ) - self.ldda_manager = lddas.LDDAManager( ) - - def create( - self, - trans, - parent, # PRECONDITION: security checks on ability to add to parent occurred during load. - name, - collection_type, - element_identifiers=None, - elements=None, - implicit_collection_info=None, - ): - """ - """ - # Trust embedded, newly created objects created by tool subsystem. - trusted_identifiers = implicit_collection_info is not None - - if element_identifiers and not trusted_identifiers: - validate_input_element_identifiers( element_identifiers ) - - dataset_collection = self.__create_dataset_collection( - trans=trans, - collection_type=collection_type, - element_identifiers=element_identifiers, - elements=elements, - ) - if isinstance( parent, model.History ): - dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation( - collection=dataset_collection, - name=name, - ) - if implicit_collection_info: - for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]: - dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) - for output_dataset in implicit_collection_info.get( "outputs" ): - output_dataset.hidden_beneath_collection_instance = dataset_collection_instance - trans.sa_session.add( output_dataset ) - - dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ] - log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) ) - # Handle setting hid - parent.add_dataset_collection( dataset_collection_instance ) - elif isinstance( parent, model.LibraryFolder ): - dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation( - collection=dataset_collection, - folder=parent, - name=name, - ) - else: - message = "Internal logic error - create called with unknown parent type %s" % type( parent ) - log.exception( message ) - raise MessageException( message ) - - return self.__persist( dataset_collection_instance ) - - def __create_dataset_collection( - self, - trans, - collection_type, - element_identifiers=None, - elements=None, - ): - if element_identifiers is None and elements is None: - raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION ) - if not collection_type: - raise RequestParameterInvalidException( ERROR_NO_COLLECTION_TYPE ) - collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type ) - # If we have elements, this is an internal request, don't need to load - # objects from identifiers. - if elements is None: - if collection_type_description.has_subcollections( ): - # Nested collection - recursively create collections and update identifiers. - self.__recursively_create_collections( trans, element_identifiers ) - elements = self.__load_elements( trans, element_identifiers ) - # else if elements is set, it better be an ordered dict! - - type_plugin = collection_type_description.rank_type_plugin() - dataset_collection = type_plugin.build_collection( elements ) - dataset_collection.collection_type = collection_type - return dataset_collection - - def delete( self, trans, instance_type, id ): - dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True ) - dataset_collection_instance.deleted = True - trans.sa_session.add( dataset_collection_instance ) - trans.sa_session.flush( ) - - def update( self, trans, instance_type, id, payload ): - dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True ) - if trans.user is None: - anon_allowed_payload = {} - if 'deleted' in payload: - anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ] - if 'visible' in payload: - anon_allowed_payload[ 'visible' ] = payload[ 'visible' ] - payload = self._validate_and_parse_update_payload( anon_allowed_payload ) - else: - payload = self._validate_and_parse_update_payload( payload ) - changed = self._set_from_dict( trans, dataset_collection_instance, payload ) - return changed - - def copy( - self, - trans, - parent, # PRECONDITION: security checks on ability to add to parent occurred during load. - source, - encoded_source_id, - ): - assert source == "hdca" # for now - source_hdca = self.__get_history_collection_instance( trans, encoded_source_id ) - new_hdca = source_hdca.copy() - parent.add_dataset_collection( new_hdca ) - trans.sa_session.add( new_hdca ) - trans.sa_session.flush() - return source_hdca - - def _set_from_dict( self, trans, dataset_collection_instance, new_data ): - # Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict. - - # send what we can down into the model - changed = dataset_collection_instance.set_from_dict( new_data ) - # the rest (often involving the trans) - do here - if 'annotation' in new_data.keys() and trans.get_user(): - dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] ) - changed[ 'annotation' ] = new_data[ 'annotation' ] - if 'tags' in new_data.keys() and trans.get_user(): - self.tag_manager.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) - - if changed.keys(): - trans.sa_session.flush() - - return changed - - def _validate_and_parse_update_payload( self, payload ): - validated_payload = {} - for key, val in payload.items(): - if val is None: - continue - if key in ( 'name' ): - val = validation.validate_and_sanitize_basestring( key, val ) - validated_payload[ key ] = val - if key in ( 'deleted', 'visible' ): - validated_payload[ key ] = validation.validate_boolean( key, val ) - elif key == 'tags': - validated_payload[ key ] = validation.validate_and_sanitize_basestring_list( key, val ) - return validated_payload - - def history_dataset_collections(self, history, query): - collections = history.active_dataset_collections - collections = filter( query.direct_match, collections ) - return collections - - def __persist( self, dataset_collection_instance ): - context = self.model.context - context.add( dataset_collection_instance ) - context.flush() - return dataset_collection_instance - - def __recursively_create_collections( self, trans, element_identifiers ): - for index, element_identifier in enumerate( element_identifiers ): - try: - if not element_identifier[ "src" ] == "new_collection": - # not a new collection, keep moving... - continue - except KeyError: - # Not a dictionary, just an id of an HDA - move along. - continue - - # element identifier is a dict with src new_collection... - collection_type = element_identifier.get( "collection_type", None ) - collection = self.__create_dataset_collection( - trans=trans, - collection_type=collection_type, - element_identifiers=element_identifier[ "element_identifiers" ], - ) - element_identifier[ "__object__" ] = collection - - return element_identifiers - - def __load_elements( self, trans, element_identifiers ): - elements = odict.odict() - for element_identifier in element_identifiers: - elements[ element_identifier[ "name" ] ] = self.__load_element( trans, element_identifier ) - return elements - - def __load_element( self, trans, element_identifier ): - #if not isinstance( element_identifier, dict ): - # # Is allowing this to just be the id of an hda too clever? Somewhat - # # consistent with other API methods though. - # element_identifier = dict( src='hda', id=str( element_identifier ) ) - - # Previously created collection already found in request, just pass - # through as is. - if "__object__" in element_identifier: - return element_identifier[ "__object__" ] - - # dateset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>} - try: - src_type = element_identifier.get( 'src', 'hda' ) - except AttributeError: - raise MessageException( "Dataset collection element definition (%s) not dictionary-like." % element_identifier ) - encoded_id = element_identifier.get( 'id', None ) - if not src_type or not encoded_id: - raise RequestParameterInvalidException( "Problem decoding element identifier %s" % element_identifier ) - - if src_type == 'hda': - decoded_id = int( trans.app.security.decode_id( encoded_id ) ) - element = self.hda_manager.get( trans, decoded_id, check_ownership=False ) - elif src_type == 'ldda': - element = self.ldda_manager.get( trans, encoded_id ) - elif src_type == 'hdca': - # TODO: Option to copy? Force copy? Copy or allow if not owned? - element = self.__get_history_collection_instance( trans, encoded_id ).collection - # TODO: ldca. - else: - raise RequestParameterInvalidException( "Unknown src_type parameter supplied '%s'." % src_type ) - return element - - def match_collections( self, collections_to_match ): - """ - May seem odd to place it here, but planning to grow sophistication and - get plugin types involved so it will likely make sense in the future. - """ - return MatchingCollections.for_collections( collections_to_match, self.collection_type_descriptions ) - - def get_dataset_collection_instance( self, trans, instance_type, id, **kwds ): - """ - """ - if instance_type == "history": - return self.__get_history_collection_instance( trans, id, **kwds ) - elif instance_type == "library": - return self.__get_library_collection_instance( trans, id, **kwds ) - - def get_dataset_collection( self, trans, encoded_id ): - collection_id = int( trans.app.security.decode_id( encoded_id ) ) - collection = trans.sa_session.query( trans.app.model.DatasetCollection ).get( collection_id ) - return collection - - def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): - instance_id = int( trans.app.security.decode_id( id ) ) - collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id ) - self.history_manager.secure( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible ) - return collection_instance - - def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): - if check_ownership: - raise NotImplemented( "Functionality (getting library dataset collection with ownership check) unimplemented." ) - instance_id = int( trans.security.decode_id( id ) ) - collection_instance = trans.sa_session.query( trans.app.model.LibraryDatasetCollectionAssociation ).get( instance_id ) - if check_accessible: - if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), collection_instance, trans.user ): - raise ItemAccessibilityException( "LibraryDatasetCollectionAssociation is not accessible to the current user", type='error' ) - return collection_instance diff -r 355aee34a371c99f9251b965ea625066a80419ea -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 lib/galaxy/managers/collections.py --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -1,1 +1,291 @@ -""" Future home of dataset collections managers. """ +from galaxy.dataset_collections.registry import DatasetCollectionTypesRegistry +from galaxy.dataset_collections.matching import MatchingCollections +from galaxy.dataset_collections.type_description import CollectionTypeDescriptionFactory + +from galaxy import model +from galaxy.exceptions import MessageException +from galaxy.exceptions import ItemAccessibilityException +from galaxy.exceptions import RequestParameterInvalidException +from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. +from galaxy.managers import histories +from galaxy.managers import lddas +from galaxy.managers import tags +from galaxy.managers.collections_util import validate_input_element_identifiers +from galaxy.util import validation +from galaxy.util import odict + +import logging +log = logging.getLogger( __name__ ) + + +ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers." +ERROR_NO_COLLECTION_TYPE = "Create called without specifing a collection type." + + +class DatasetCollectionManager( object ): + """ + Abstraction for interfacing with dataset collections instance - ideally abstarcts + out model and plugin details. + """ + + def __init__( self, app ): + self.type_registry = DatasetCollectionTypesRegistry( app ) + self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry ) + self.model = app.model + self.security = app.security + self.hda_manager = hdas.HDAManager() + self.history_manager = histories.HistoryManager() + self.tag_manager = tags.TagsManager( app ) + self.ldda_manager = lddas.LDDAManager( ) + + def create( + self, + trans, + parent, # PRECONDITION: security checks on ability to add to parent occurred during load. + name, + collection_type, + element_identifiers=None, + elements=None, + implicit_collection_info=None, + ): + """ + """ + # Trust embedded, newly created objects created by tool subsystem. + trusted_identifiers = implicit_collection_info is not None + + if element_identifiers and not trusted_identifiers: + validate_input_element_identifiers( element_identifiers ) + + dataset_collection = self.__create_dataset_collection( + trans=trans, + collection_type=collection_type, + element_identifiers=element_identifiers, + elements=elements, + ) + if isinstance( parent, model.History ): + dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation( + collection=dataset_collection, + name=name, + ) + if implicit_collection_info: + for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]: + dataset_collection_instance.add_implicit_input_collection( input_name, input_collection ) + for output_dataset in implicit_collection_info.get( "outputs" ): + output_dataset.hidden_beneath_collection_instance = dataset_collection_instance + trans.sa_session.add( output_dataset ) + + dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ] + log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) ) + # Handle setting hid + parent.add_dataset_collection( dataset_collection_instance ) + elif isinstance( parent, model.LibraryFolder ): + dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation( + collection=dataset_collection, + folder=parent, + name=name, + ) + else: + message = "Internal logic error - create called with unknown parent type %s" % type( parent ) + log.exception( message ) + raise MessageException( message ) + + return self.__persist( dataset_collection_instance ) + + def __create_dataset_collection( + self, + trans, + collection_type, + element_identifiers=None, + elements=None, + ): + if element_identifiers is None and elements is None: + raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION ) + if not collection_type: + raise RequestParameterInvalidException( ERROR_NO_COLLECTION_TYPE ) + collection_type_description = self.collection_type_descriptions.for_collection_type( collection_type ) + # If we have elements, this is an internal request, don't need to load + # objects from identifiers. + if elements is None: + if collection_type_description.has_subcollections( ): + # Nested collection - recursively create collections and update identifiers. + self.__recursively_create_collections( trans, element_identifiers ) + elements = self.__load_elements( trans, element_identifiers ) + # else if elements is set, it better be an ordered dict! + + type_plugin = collection_type_description.rank_type_plugin() + dataset_collection = type_plugin.build_collection( elements ) + dataset_collection.collection_type = collection_type + return dataset_collection + + def delete( self, trans, instance_type, id ): + dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True ) + dataset_collection_instance.deleted = True + trans.sa_session.add( dataset_collection_instance ) + trans.sa_session.flush( ) + + def update( self, trans, instance_type, id, payload ): + dataset_collection_instance = self.get_dataset_collection_instance( trans, instance_type, id, check_ownership=True ) + if trans.user is None: + anon_allowed_payload = {} + if 'deleted' in payload: + anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ] + if 'visible' in payload: + anon_allowed_payload[ 'visible' ] = payload[ 'visible' ] + payload = self._validate_and_parse_update_payload( anon_allowed_payload ) + else: + payload = self._validate_and_parse_update_payload( payload ) + changed = self._set_from_dict( trans, dataset_collection_instance, payload ) + return changed + + def copy( + self, + trans, + parent, # PRECONDITION: security checks on ability to add to parent occurred during load. + source, + encoded_source_id, + ): + assert source == "hdca" # for now + source_hdca = self.__get_history_collection_instance( trans, encoded_source_id ) + new_hdca = source_hdca.copy() + parent.add_dataset_collection( new_hdca ) + trans.sa_session.add( new_hdca ) + trans.sa_session.flush() + return source_hdca + + def _set_from_dict( self, trans, dataset_collection_instance, new_data ): + # Blatantly stolen from UsesHistoryDatasetAssociationMixin.set_hda_from_dict. + + # send what we can down into the model + changed = dataset_collection_instance.set_from_dict( new_data ) + # the rest (often involving the trans) - do here + if 'annotation' in new_data.keys() and trans.get_user(): + dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] ) + changed[ 'annotation' ] = new_data[ 'annotation' ] + if 'tags' in new_data.keys() and trans.get_user(): + self.tag_manager.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) + + if changed.keys(): + trans.sa_session.flush() + + return changed + + def _validate_and_parse_update_payload( self, payload ): + validated_payload = {} + for key, val in payload.items(): + if val is None: + continue + if key in ( 'name' ): + val = validation.validate_and_sanitize_basestring( key, val ) + validated_payload[ key ] = val + if key in ( 'deleted', 'visible' ): + validated_payload[ key ] = validation.validate_boolean( key, val ) + elif key == 'tags': + validated_payload[ key ] = validation.validate_and_sanitize_basestring_list( key, val ) + return validated_payload + + def history_dataset_collections(self, history, query): + collections = history.active_dataset_collections + collections = filter( query.direct_match, collections ) + return collections + + def __persist( self, dataset_collection_instance ): + context = self.model.context + context.add( dataset_collection_instance ) + context.flush() + return dataset_collection_instance + + def __recursively_create_collections( self, trans, element_identifiers ): + for index, element_identifier in enumerate( element_identifiers ): + try: + if not element_identifier[ "src" ] == "new_collection": + # not a new collection, keep moving... + continue + except KeyError: + # Not a dictionary, just an id of an HDA - move along. + continue + + # element identifier is a dict with src new_collection... + collection_type = element_identifier.get( "collection_type", None ) + collection = self.__create_dataset_collection( + trans=trans, + collection_type=collection_type, + element_identifiers=element_identifier[ "element_identifiers" ], + ) + element_identifier[ "__object__" ] = collection + + return element_identifiers + + def __load_elements( self, trans, element_identifiers ): + elements = odict.odict() + for element_identifier in element_identifiers: + elements[ element_identifier[ "name" ] ] = self.__load_element( trans, element_identifier ) + return elements + + def __load_element( self, trans, element_identifier ): + #if not isinstance( element_identifier, dict ): + # # Is allowing this to just be the id of an hda too clever? Somewhat + # # consistent with other API methods though. + # element_identifier = dict( src='hda', id=str( element_identifier ) ) + + # Previously created collection already found in request, just pass + # through as is. + if "__object__" in element_identifier: + return element_identifier[ "__object__" ] + + # dateset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>} + try: + src_type = element_identifier.get( 'src', 'hda' ) + except AttributeError: + raise MessageException( "Dataset collection element definition (%s) not dictionary-like." % element_identifier ) + encoded_id = element_identifier.get( 'id', None ) + if not src_type or not encoded_id: + raise RequestParameterInvalidException( "Problem decoding element identifier %s" % element_identifier ) + + if src_type == 'hda': + decoded_id = int( trans.app.security.decode_id( encoded_id ) ) + element = self.hda_manager.get( trans, decoded_id, check_ownership=False ) + elif src_type == 'ldda': + element = self.ldda_manager.get( trans, encoded_id ) + elif src_type == 'hdca': + # TODO: Option to copy? Force copy? Copy or allow if not owned? + element = self.__get_history_collection_instance( trans, encoded_id ).collection + # TODO: ldca. + else: + raise RequestParameterInvalidException( "Unknown src_type parameter supplied '%s'." % src_type ) + return element + + def match_collections( self, collections_to_match ): + """ + May seem odd to place it here, but planning to grow sophistication and + get plugin types involved so it will likely make sense in the future. + """ + return MatchingCollections.for_collections( collections_to_match, self.collection_type_descriptions ) + + def get_dataset_collection_instance( self, trans, instance_type, id, **kwds ): + """ + """ + if instance_type == "history": + return self.__get_history_collection_instance( trans, id, **kwds ) + elif instance_type == "library": + return self.__get_library_collection_instance( trans, id, **kwds ) + + def get_dataset_collection( self, trans, encoded_id ): + collection_id = int( trans.app.security.decode_id( encoded_id ) ) + collection = trans.sa_session.query( trans.app.model.DatasetCollection ).get( collection_id ) + return collection + + def __get_history_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): + instance_id = int( trans.app.security.decode_id( id ) ) + collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id ) + self.history_manager.secure( trans, collection_instance.history, check_ownership=check_ownership, check_accessible=check_accessible ) + return collection_instance + + def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ): + if check_ownership: + raise NotImplemented( "Functionality (getting library dataset collection with ownership check) unimplemented." ) + instance_id = int( trans.security.decode_id( id ) ) + collection_instance = trans.sa_session.query( trans.app.model.LibraryDatasetCollectionAssociation ).get( instance_id ) + if check_accessible: + if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), collection_instance, trans.user ): + raise ItemAccessibilityException( "LibraryDatasetCollectionAssociation is not accessible to the current user", type='error' ) + return collection_instance https://bitbucket.org/galaxy/galaxy-central/commits/d2ec0f230bda/ Changeset: d2ec0f230bda User: jmchilton Date: 2014-09-11 22:01:08 Summary: Work on workflow module testing. Affected #: 3 files diff -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 -r d2ec0f230bdaed4ce52607b6ac1b6d5348dc1834 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -120,6 +120,11 @@ ## ---- Run time --------------------------------------------------------- def get_runtime_inputs( self ): + """ Used internally to modules and when displaying inputs in display + and run workflow templates. The ToolModule doesn't implement this and + these templates contain specialized logic for dealing with the tool and + state directly in these cases. + """ raise TypeError( "Abstract method" ) def encode_runtime_state( self, trans, state ): diff -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 -r d2ec0f230bdaed4ce52607b6ac1b6d5348dc1834 test/unit/workflows/test_modules.py --- a/test/unit/workflows/test_modules.py +++ b/test/unit/workflows/test_modules.py @@ -1,16 +1,19 @@ from galaxy import eggs eggs.require( "mock" ) - +import json import mock +from galaxy import model + from galaxy.workflow import modules +from galaxy.tools import parameters from .workflow_support import MockTrans def test_input_has_no_errors(): trans = MockTrans() - input_step_module = modules.module_factory.new( trans, 'data_input' ) + input_step_module = modules.module_factory.new( trans, "data_input" ) assert not input_step_module.get_errors() @@ -18,15 +21,129 @@ trans = MockTrans() mock_tool = mock.Mock() trans.app.toolbox.tools[ "cat1" ] = mock_tool - tool_module = modules.module_factory.new( trans, 'tool', tool_id="cat1" ) + tool_module = modules.module_factory.new( trans, "tool", tool_id="cat1" ) assert not tool_module.get_errors() +def test_data_input_default_state(): + trans = MockTrans() + module = modules.module_factory.new( trans, "data_input" ) + __assert_has_runtime_input( module, label="Input Dataset" ) + + +def test_data_input_modified_state(): + module = __from_state( { + "type": "data_input", + "tool_state": json.dumps({ "name": "Cool Input" }), + } ) + __assert_has_runtime_input( module, label="Cool Input" ) + + +def test_data_input_step_modified_state(): + module = __from_step( + type="data_input", + tool_inputs={ + "name": "Cool Input", + }, + ) + __assert_has_runtime_input( module, label="Cool Input" ) + + +def test_data_input_compute_state_default(): + module = __from_step( + type="data_input", + ) + state, errors = module.compute_state( module.trans ) + assert not errors + assert 'input' in state.inputs + assert state.inputs[ 'input' ] is None + + +def test_data_input_compute_state_args(): + module = __from_step( + type="data_input", + ) + tool_state = module.encode_runtime_state( module.trans, module.test_step.state ) + + hda = model.HistoryDatasetAssociation() + with mock.patch('galaxy.workflow.modules.check_param') as check_method: + check_method.return_value = ( hda, None ) + state, errors = module.compute_state( module.trans, { 'input': 4, 'tool_state': tool_state } ) + + assert not errors + assert 'input' in state.inputs + assert state.inputs[ 'input' ] is hda + + +def test_data_collection_input_default_state(): + trans = MockTrans() + module = modules.module_factory.new( trans, "data_collection_input" ) + __assert_has_runtime_input( module, label="Input Dataset Collection", collection_type="list" ) + + +def test_data_input_collection_modified_state(): + module = __from_state( { + "type": "data_collection_input", + "tool_state": json.dumps({ "name": "Cool Input Collection", "collection_type": "list:paired" }), + } ) + __assert_has_runtime_input( module, label="Cool Input Collection", collection_type="list:paired" ) + + +def test_data_input_collection_step_modified_state(): + module = __from_step( + type="data_collection_input", + tool_inputs={ + "name": "Cool Input Collection", + "collection_type": "list:paired", + }, + ) + __assert_has_runtime_input( module, label="Cool Input Collection", collection_type="list:paired" ) + + def test_cannot_create_tool_modules_for_missing_tools(): trans = MockTrans() exception = False try: - modules.module_factory.new( trans, 'tool', tool_id="cat1" ) + modules.module_factory.new( trans, "tool", tool_id="cat1" ) except Exception: exception = True assert exception + + +def __assert_has_runtime_input( module, label=None, collection_type=None ): + inputs = module.get_runtime_inputs() + assert len( inputs ) == 1 + assert "input" in inputs + + input_param = inputs[ "input" ] + if label is not None: + assert input_param.get_label() == label, input_param.get_label() + if collection_type is not None: + assert input_param.collection_type == collection_type + return input_param + + +def __from_state( state ): + trans = MockTrans() + module = modules.module_factory.from_dict( trans, state ) + return module + + +def __from_step( **kwds ): + trans = MockTrans() + step = __step( + **kwds + ) + injector = modules.WorkflowModuleInjector( trans ) + injector.inject( step ) + module = step.module + module.test_step = step + return module + + +def __step( **kwds ): + step = model.WorkflowStep() + for key, value in kwds.iteritems(): + setattr( step, key, value ) + + return step diff -r dd31ab49162d3faa30818947a80a6165c2f0b4c7 -r d2ec0f230bdaed4ce52607b6ac1b6d5348dc1834 test/unit/workflows/workflow_support.py --- a/test/unit/workflows/workflow_support.py +++ b/test/unit/workflows/workflow_support.py @@ -11,13 +11,25 @@ class TestApp( object ): def __init__( self ): - self.config = bunch.Bunch( ) + self.config = bunch.Bunch( + tool_secret="awesome_secret", + ) self.model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True ) self.toolbox = TestToolbox() + self.datatypes_registry = TestDatatypesRegistry() + + +class TestDatatypesRegistry( object ): + + def __init__( self ): + pass + + def get_datatype_by_extension( self, ext ): + return ext class TestToolbox( object ): https://bitbucket.org/galaxy/galaxy-central/commits/b8520d9c8269/ Changeset: b8520d9c8269 User: jmchilton Date: 2014-09-11 22:01:08 Summary: Allow uuid values in to_dict. Affected #: 1 file diff -r d2ec0f230bdaed4ce52607b6ac1b6d5348dc1834 -r b8520d9c8269c4c7deca6418d54f2e722886073e lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -4,6 +4,7 @@ import galaxy import logging import datetime +import uuid log = logging.getLogger( __name__ ) @@ -186,6 +187,8 @@ return value_mapper.get( key )( item ) if type(item) == datetime.datetime: return item.isoformat() + elif type(item) == uuid.UUID: + return str(item) # Leaving this for future reference, though we may want a more # generic way to handle special type mappings going forward. # If the item is of a class that needs to be 'stringified' before being put into a JSON data structure Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/ansible-pulsar]
by GitHub 12 Sep '14

12 Sep '14

Branch: refs/tags/0.3 Home: https://github.com/galaxyproject/ansible-pulsar

1 0

[galaxyproject/ansible-pulsar] 43d526: Handle install environments for dependencies that ...
by GitHub 12 Sep '14

12 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: 43d52683a342f6788a0751c4737ac376aafcb271 https://github.com/galaxyproject/ansible-pulsar/commit/43d52683a342f6788a07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-11 (Thu, 11 Sep 2014) Changed paths: M tasks/main.yml Log Message: ----------- Handle install environments for dependencies that are pinned to a specific version.

1 0

commit/galaxy-central: carlfeberhard: Fix to 618b02d13329: remove console, add documentation
by commits-noreply＠bitbucket.org 11 Sep '14

11 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da6e8248d7b4/ Changeset: da6e8248d7b4 User: carlfeberhard Date: 2014-09-11 20:11:37 Summary: Fix to 618b02d13329: remove console, add documentation Affected #: 7 files diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -47,6 +47,7 @@ }, // ......................................................................... foldout + /** override to add linktarget to sub-panel */ _getFoldoutPanelOptions : function(){ var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call( this ); return _.extend( options, { @@ -54,7 +55,7 @@ }); }, - /** override in the case of sub-panels */ + /** override to not catch sub-panel selectors */ $selector : function(){ return this.$( '> .selector' ); }, diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -93,7 +93,7 @@ return this; }, - /** */ + /** Handle drill down by hiding this panels list and controls and showing the sub-panel */ _expandDrilldownPanel : function( drilldown ){ this.panelStack.push( drilldown ); // hide this panel's controls and list, set the name for back navigation, and attach to the $el @@ -102,7 +102,7 @@ this.$el.append( drilldown.render().$el ); }, - /** */ + /** Handle drilldown close by freeing the panel and re-rendering this panel */ _collapseDrilldownPanel : function( drilldown ){ this.panelStack.pop(); this.render(); diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -301,6 +301,7 @@ return this; }, + /** Handle drill down by hiding this panels list and controls and showing the sub-panel */ _expandDrilldownPanel : function( drilldown ){ this.panelStack.push( drilldown ); // hide this panel's controls and list, set the name for back navigation, and attach to the $el @@ -309,6 +310,7 @@ this.$el.append( drilldown.render().$el ); }, + /** Handle drilldown close by freeing the panel and re-rendering this panel */ _collapseDrilldownPanel : function( drilldown ){ this.panelStack.pop(); //TODO: MEM: free the panel diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/mvc/list/list-item.js --- a/static/scripts/mvc/list/list-item.js +++ b/static/scripts/mvc/list/list-item.js @@ -355,9 +355,18 @@ */ var FoldoutListItemView = ListItemView.extend({ + /** If 'foldout': show the sub-panel inside the expanded item + * If 'drilldown': only fire events and handle by pub-sub + * (allow the panel containing this item to attach it, hide itself, etc.) + */ foldoutStyle : 'foldout', + /** Panel view class to instantiate for the sub-panel */ foldoutPanelClass : null, + /** override to: + * add attributes foldoutStyle and foldoutPanelClass for config poly + * disrespect attributes.expanded if drilldown + */ initialize : function( attributes ){ ListItemView.prototype.initialize.call( this, attributes ); //TODO: hackish @@ -367,10 +376,10 @@ }, //TODO:?? override to exclude foldout scope? - $ : function( selector ){ - var $found = ListItemView.prototype.$.call( this, selector ); - return $found; - }, + //$ : function( selector ){ + // var $found = ListItemView.prototype.$.call( this, selector ); + // return $found; + //}, /** in this override, attach the foldout panel when rendering details */ _renderDetails : function(){ @@ -391,11 +400,13 @@ return foldout; }, + /** Stub to return proper foldout panel class */ _getFoldoutPanelClass : function(){ // override return this.foldoutPanelClass; }, + /** Stub to return proper foldout panel options */ _getFoldoutPanelOptions : function(){ return { // propagate foldout style down @@ -403,7 +414,7 @@ }; }, - /** */ + /** Render the foldout panel inside the view, hiding controls */ _attachFoldout : function( foldout, $whereTo ){ $whereTo = $whereTo || this.$( '> .details' ); this.foldout = foldout.render( 0 ); @@ -412,10 +423,7 @@ return $whereTo.append( foldout.$el ); }, - /** Render and show the full, detailed body of this view including extra data and controls. - * note: if the model does not have detailed data, fetch that data before showing the body - * @fires expanded when a body has been expanded - */ + /** In this override, branch on foldoutStyle to show expanded */ expand : function(){ var view = this; return view._fetchModelDetails() @@ -428,6 +436,7 @@ }); }, + /** For foldout, call render details then slide down */ _expandByFoldout : function(){ var view = this; var $newDetails = view._renderDetails(); @@ -439,6 +448,10 @@ }); }, + /** For drilldown, set up close handler and fire expanded:drilldown + * containing views can listen to this and handle other things + * (like hiding themselves) by listening for expanded/collapsed:drilldown + */ _expandByDrilldown : function(){ var view = this; // attachment and rendering done by listener @@ -455,6 +468,7 @@ /** underscore templates */ FoldoutListItemView.prototype.templates = (function(){ +//TODO:?? unnecessary? // use element identifier var detailsTemplate = BASE_MVC.wrapTemplate([ '<div class="details">', diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -334,15 +334,15 @@ return panel.views; }, - /** - */ + /** Filter the collection to only those models that should be currently viewed */ _filterCollection : function(){ // override this var panel = this; return panel.collection.filter( _.bind( panel._filterItem, panel ) ); }, - /** + /** Should the model be viewable in the current state? + * Checks against this.filters and this.searchFor */ _filterItem : function( model ){ // override this @@ -351,8 +351,7 @@ && ( !panel.searchFor || model.matchesAll( panel.searchFor ) ); }, - /** - */ + /** Create a view for a model and set up it's listeners */ _createItemView : function( model ){ var ViewClass = this._getItemViewClass( model ), options = _.extend( this._getItemViewOptions( model ), { @@ -363,15 +362,13 @@ return view; }, - /** - */ + /** Get the bbone view class based on the model */ _getItemViewClass : function( model ){ // override this return this.viewClass; }, - /** - */ + /** Get the options passed to the new view based on the model */ _getItemViewOptions : function( model ){ // override this return { @@ -384,8 +381,7 @@ }; }, - /** - */ + /** Set up listeners for new models */ _setUpItemViewListeners : function( view ){ var panel = this; // send all events to the panel, re-namspaceing them with the view prefix @@ -404,8 +400,7 @@ return panel; }, - /** - */ + /** Attach views in this.views to the model based on $whereTo */ _attachItems : function( $whereTo ){ this.$list( $whereTo ).append( this.views.map( function( view ){ return view.$el; @@ -435,8 +430,7 @@ }, // ------------------------------------------------------------------------ collection/views syncing - /** - */ + /** Add a view (if the model should be viewable) to the panel */ addItemView : function( model, collection, options ){ this.log( this + '.addItemView:', model ); var panel = this; @@ -446,6 +440,7 @@ var view = panel._createItemView( model ); panel.views.push( view ); + // hide the empty message if only view $( view ).queue( 'fx', [ function( next ){ panel.$emptyMessage().fadeOut( panel.fxSpeed, next ); }, function( next ){ @@ -458,13 +453,14 @@ return view; }, - /** */ + /** Remove a view from the panel (if found) */ removeItemView : function( model, collection, options ){ this.log( this + '.removeItemView:', model ); var panel = this, view = panel.viewFromModel( model ); if( !view ){ return undefined; } + // potentially show the empty message if no views left // use anonymous queue here - since remove can happen multiple times $({}).queue( 'fx', [ function( next ){ view.$el.fadeOut( panel.fxSpeed, next ); }, @@ -481,18 +477,6 @@ return view; }, - /** get views based on model - */ - viewFromModel : function( model ){ - for( var i=0; i<this.views.length; i++ ){ - var view = this.views[i]; - if( view.model === model ){ - return view; - } - } - return undefined; - }, - /** get views based on model.id */ viewFromModelId : function( id ){ for( var i=0; i<this.views.length; i++ ){ @@ -503,8 +487,12 @@ return undefined; }, - /** get views based on model properties - */ + /** get views based on model */ + viewFromModel : function( model ){ + return this.viewFromModelId( model.id ); + }, + + /** get views based on model properties */ viewsWhereModel : function( properties ){ return this.views.filter( function( view ){ //return view.model.matches( properties ); @@ -523,8 +511,7 @@ }); }, - /** - */ + /** A range of views between (and including) viewA and viewB */ viewRange : function( viewA, viewB ){ if( viewA === viewB ){ return ( viewA )?( [ viewA ] ):( [] ); } @@ -562,7 +549,9 @@ return $where; }, + /** What to do on the first search entered */ _firstSearch : function( searchFor ){ + // override to load model details if necc. this.log( 'onFirstSearch', searchFor ); return this.searchItems( searchFor ); }, @@ -591,7 +580,6 @@ this.selecting = true; this.$( '.list-actions' ).slideDown( speed ); _.each( this.views, function( view ){ -console.debug( view.$el ); view.showSelector( speed ); }); //this.selected = []; @@ -749,13 +737,16 @@ '<div class="name"><%= view.title %></div>', '</div>', '<div class="subtitle"><%= view.subtitle %></div>', + // buttons, controls go here '<div class="actions"></div>', + // deleted msg, etc. '<div class="messages"></div>', '<div class="search">', '<div class="search-input"></div>', '</div>', + // show when selectors are shown '<div class="list-actions">', '<div class="btn-group">', '<button class="select-all btn btn-default"', @@ -779,7 +770,9 @@ //============================================================================= /** View for a model that has a sub-collection (e.g. History, DatasetCollection) - * + * Allows: + * the model to be reset + * auto assign panel.collection to panel.model[ panel.modelCollectionKey ] * */ var ModelListPanel = ListPanel.extend({ @@ -791,8 +784,6 @@ ListPanel.prototype.initialize.call( this, attributes ); this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : false; - // ---- instance vars - // don't render when setting the first time this.setModel( this.model, attributes ); }, @@ -862,8 +853,6 @@ var json = this.model? this.model.toJSON() : {}, $controls = $( this.templates.controls( json, this ) ); $newRender.find( '.controls' ).replaceWith( $controls ); - this.debug( '\t .controls:', this.$( '.controls' ) ); - this.debug( '\t $controls:', $controls ); return $controls; }, @@ -882,6 +871,7 @@ var controlsTemplate = BASE_MVC.wrapTemplate([ '<div class="controls">', '<div class="title">', +//TODO: this is really the only difference - consider factoring titlebar out '<div class="name"><%= model.name %></div>', '</div>', '<div class="subtitle"><%= view.subtitle %></div>', diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/packed/mvc/list/list-item.js --- a/static/scripts/packed/mvc/list/list-item.js +++ b/static/scripts/packed/mvc/list/list-item.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.fxSpeed=f.fxSpeed||this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp(f.fxSpeed,function(){f.trigger("collapsed",f)})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find(".title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();this.toggleExpanded()},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){a.prototype.initialize.call(this,f);if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass},$:function(f){var g=a.prototype.$.call(this,f);return g},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this._createFoldoutPanel(),f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expandByFoldout()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByFoldout:function(){var f=this;var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})},_expandByDrilldown:function(){var f=this;f.foldout=this._createFoldoutPanel();f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.fxSpeed=f.fxSpeed||this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp(f.fxSpeed,function(){f.trigger("collapsed",f)})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find(".title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();this.toggleExpanded()},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){a.prototype.initialize.call(this,f);if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this._createFoldoutPanel(),f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expandByFoldout()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByFoldout:function(){var f=this;var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})},_expandByDrilldown:function(){var f=this;f.foldout=this._createFoldoutPanel();f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file diff -r 618b02d13329adf2d01b72e9743a8fa00192c6fd -r da6e8248d7b402783e829f27ee1ab9e6ba4367d7 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModel:function(g){for(var h=0;h<this.views.length;h++){var f=this.views[h];if(f.model===g){return f}}return undefined},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){console.debug(g.$el);g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);this.debug("\t .controls:",this.$(".controls"));this.debug("\t $controls:",f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit 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