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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #389)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param 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 15 May '14

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/707b69b09eb4/ Changeset: 707b69b09eb4 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Unit test case for tool column parameters. Ever more duplication in these parameters tests, I need to find some time to refactor... Affected #: 1 file diff -r 8e2135ee278aa44eb5a8da04a392bfa44efc0279 -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,89 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param https://bitbucket.org/galaxy/galaxy-central/commits/6171bcdb7333/ Changeset: 6171bcdb7333 User: jmchilton Date: 2014-05-12 19:01:14 Summary: Allow c to appear in default value for Column parameters, allow specification with value attribute. Ideas purposed by Peter Cock here - http://dev.list.galaxyproject.org/Default-value-for-data-column-not-working…. Affected #: 2 files diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 707b69b09eb4be515be228a8fb2bf7a771a1bbac -r 6171bcdb7333fd7a1bfa3986768ad425e28cf8f6 test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -38,6 +38,14 @@ self.other_attributes = "default_value='2'" self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + def setUp( self ): self.setup_app( mock_model=False ) self.mock_tool = bunch.Bunch( https://bitbucket.org/galaxy/galaxy-central/commits/a50b64b9d707/ Changeset: a50b64b9d707 User: jmchilton Date: 2014-05-15 20:49:44 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #389) Small Column Parameter Enhancements Affected #: 2 files diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1096,7 +1096,13 @@ self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None + # Legacy style default value specification... self.default_value = elem.get( "default_value", None ) + if self.default_value is None: + # Newer style... more in line with other parameters. + self.default_value = elem.get( "value", None ) + if self.default_value is not None: + self.default_value = ColumnListParameter._strip_c( self.default_value ) self.is_dynamic = True self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) @@ -1105,10 +1111,6 @@ Label convention prepends column number with a 'c', but tool uses the integer. This removes the 'c' when entered into a workflow. """ - def _strip_c( column ): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] - return column if self.multiple: #split on newline and , if value: @@ -1120,16 +1122,22 @@ column2 = column2.strip() if column2: column_list.append( column2 ) - value = map( _strip_c, column_list ) + value = map( ColumnListParameter._strip_c, column_list ) else: value = [] else: if value: - value = _strip_c( value ) + value = ColumnListParameter._strip_c( value ) else: value = None return super( ColumnListParameter, self ).from_html( value, trans, context ) + @staticmethod + def _strip_c(column): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] + return column + def get_column_list( self, trans, other_values ): """ Generate a select list containing the columns of the associated diff -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b -r a50b64b9d70704542eba7dd69410c2a25c54e2a3 test/unit/tools/test_column_parameters.py --- /dev/null +++ b/test/unit/tools/test_column_parameters.py @@ -0,0 +1,97 @@ +""" Tests for tool parameters, more tests exist in test_data_parameters.py and +test_select_parameters.py. +""" + +from unittest import TestCase +from galaxy.tools.parameters import basic +from galaxy.util import bunch +from galaxy import model +from elementtree.ElementTree import XML + +import tools_support + + +class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + + def test_from_html(self): + value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "3" + + def test_from_html_strips_c(self): + value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == "1" + + def test_multiple_from_html(self): + self.multiple = True + value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_multiple_from_html_with_c(self): + self.multiple = True + value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda() } ) + assert value == ["1", "2", "3"] + + def test_get_initial_value_default(self): + self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_legacy(self): + self.other_attributes = "default_value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle(self): + self.other_attributes = "value='2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def test_get_initial_value_override_newstyle_strips_c(self): + self.other_attributes = "value='c2'" + self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) ) + + def setUp( self ): + self.setup_app( mock_model=False ) + self.mock_tool = bunch.Bunch( + app=self.app, + tool_type="default", + ) + self.test_history = model.History() + self.app.model.context.add( self.test_history ) + self.app.model.context.flush() + self.trans = bunch.Bunch( + app=self.app, + get_history=lambda: self.test_history, + get_current_user_roles=lambda: [], + workflow_building_mode=False, + webapp=bunch.Bunch( name="galaxy" ), + ) + + self.type = "data_column" + self.other_attributes = "" + self.set_data_ref = "input_tsv" + self.multiple = False + self.optional = False + self._param = None + + def build_ready_hda(self): + hist = model.History() + self.app.model.context.add( hist ) + ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) ) + ready_hda.set_dataset_state( 'ok' ) + return ready_hda + + @property + def param( self ): + if not self._param: + multi_text = "" + if self.multiple: + multi_text = 'multiple="True"' + optional_text = "" + if self.optional: + optional_text = 'optional="True"' + data_ref_text = "" + if self.set_data_ref: + data_ref_text = 'data_ref="input_tsv"' + template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>''' + self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) ) + self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml ) + self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")]) + + return self._param Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #387)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73b85f86a9d5/ Changeset: 73b85f86a9d5 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Repeat tool parameters. Expand out nested parameters and more information about the repeat itself. Affected #: 2 files diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,23 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/b411c3c86936/ Changeset: b411c3c86936 User: jmchilton Date: 2014-05-09 00:55:00 Summary: Improvements to to_dict for Conditional tool parameters. Expand out nested test_param parameter and cases. Affected #: 2 files diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -530,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r 73b85f86a9d5231fbccb8d442d819365cc33b6e9 -r b411c3c8693660a3291f0f537c61ba0b978e1813 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -27,10 +27,7 @@ @skip_without_tool( "cat1" ) def test_show_repeat( self ): - tool_show_response = self._get( "tools/cat1", data=dict( io_details=True ) ) - self._assert_status_code_is( tool_show_response, 200 ) - tool_info = tool_show_response.json() - self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + tool_info = self._show_valid_tool( "cat1" ) parameters = tool_info[ "inputs" ] assert len( parameters ) == 2 assert parameters[ 0 ][ "name" ] == "input1" @@ -42,6 +39,35 @@ assert len( repeat_params ) == 1 assert repeat_params[ 0 ][ "name" ] == "input2" + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) https://bitbucket.org/galaxy/galaxy-central/commits/44ac8fc8f7b6/ Changeset: 44ac8fc8f7b6 User: jmchilton Date: 2014-05-15 20:43:43 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #387) Recursive Tool Parameter Dictification Affected #: 2 files diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -53,6 +53,9 @@ return group_dict class Repeat( Group ): + + dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'default', 'min', 'max' ) + type = "repeat" def __init__( self ): Group.__init__( self ) @@ -117,6 +120,16 @@ rval.append( rval_dict ) return rval + def to_dict( self, trans, view='collection', value_mapper=None ): + repeat_dict = super( Repeat, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return repeat_dict + + class UploadDataset( Group ): type = "upload_dataset" def __init__( self ): @@ -517,7 +530,29 @@ rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history ) return rval -class ConditionalWhen( object ): + def to_dict( self, trans, view='collection', value_mapper=None ): + cond_dict = super( Conditional, self ).to_dict( trans, view=view, value_mapper=value_mapper ) + + def nested_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + cond_dict[ "cases" ] = map( nested_to_dict, self.cases ) + cond_dict[ "test_param" ] = nested_to_dict( self.test_param ) + return cond_dict + + +class ConditionalWhen( object, Dictifiable ): + dict_collection_visible_keys = ( 'value', ) + def __init__( self ): self.value = None self.inputs = None + + def to_dict( self, trans, view='collection', value_mapper=None ): + when_dict = super( ConditionalWhen, self ).to_dict( view=view, value_mapper=value_mapper ) + + def input_to_dict( input ): + return input.to_dict( trans, view=view, value_mapper=value_mapper ) + + when_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() ) + return when_dict diff -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 -r 44ac8fc8f7b6789cff1302a15d53f6181a54118b test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -25,6 +25,49 @@ tool_ids = map( itemgetter( "id" ), tools_index ) assert "upload1" in tool_ids + @skip_without_tool( "cat1" ) + def test_show_repeat( self ): + tool_info = self._show_valid_tool( "cat1" ) + parameters = tool_info[ "inputs" ] + assert len( parameters ) == 2 + assert parameters[ 0 ][ "name" ] == "input1" + assert parameters[ 1 ][ "name" ] == "queries" + + repeat_info = parameters[ 1 ] + self._assert_has_keys( repeat_info, "min", "max", "title", "help" ) + repeat_params = repeat_info[ "inputs" ] + assert len( repeat_params ) == 1 + assert repeat_params[ 0 ][ "name" ] == "input2" + + @skip_without_tool( "random_lines1" ) + def test_show_conditional( self ): + tool_info = self._show_valid_tool( "random_lines1" ) + + cond_info = tool_info[ "inputs" ][ 2 ] + self._assert_has_keys( cond_info, "cases", "test_param" ) + self._assert_has_keys( cond_info[ "test_param" ], 'name', 'type', 'label', 'help' ) + + cases = cond_info[ "cases" ] + assert len( cases ) == 2 + case1 = cases[ 0 ] + self._assert_has_keys( case1, "value", "inputs" ) + assert case1[ "value" ] == "no_seed" + assert len( case1[ "inputs" ] ) == 0 + + case2 = cases[ 1 ] + self._assert_has_keys( case2, "value", "inputs" ) + case2_inputs = case2[ "inputs" ] + assert len( case2_inputs ) == 1 + self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' ) + assert case2_inputs[ 0 ][ "name" ] == "seed" + + def _show_valid_tool( self, tool_id ): + tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) + self._assert_status_code_is( tool_show_response, 200 ) + tool_info = tool_show_response.json() + self._assert_has_keys( tool_info, "inputs", "outputs", "panel_section_id" ) + return tool_info + def test_upload1_paste( self ): history_id = self.dataset_populator.new_history() payload = self.dataset_populator.upload_payload( history_id, 'Hello World' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Change paired collections terminology from left/right to forward/reverse.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f24bb5dde1f5/ Changeset: f24bb5dde1f5 User: jmchilton Date: 2014-05-15 20:01:36 Summary: Change paired collections terminology from left/right to forward/reverse. If you have paired datasets in your database they will no longer work - send me an e-mail and I can give you an SQL update statement. Affected #: 5 files diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 lib/galaxy/dataset_collections/types/paired.py --- a/lib/galaxy/dataset_collections/types/paired.py +++ b/lib/galaxy/dataset_collections/types/paired.py @@ -2,8 +2,10 @@ from galaxy.model import DatasetCollectionElement -LEFT_IDENTIFIER = "left" -RIGHT_IDENTIFIER = "right" +FORWARD_IDENTIFIER = "forward" +REVERSE_IDENTIFIER = "reverse" + +INVALID_IDENTIFIERS_MESSAGE = "Paired instance must define '%s' and '%s' datasets ." % ( FORWARD_IDENTIFIER, REVERSE_IDENTIFIER ) class PairedDatasetCollectionType( BaseDatasetCollectionType ): @@ -16,16 +18,16 @@ pass def build_collection( self, elements ): - left_dataset = elements.get("left", None) - right_dataset = elements.get("right", None) - if not left_dataset or not right_dataset: - self._validation_failed("Paired instance must define 'left' and 'right' datasets .") + forward_dataset = elements.get( FORWARD_IDENTIFIER, None ) + reverse_dataset = elements.get( REVERSE_IDENTIFIER, None ) + if not forward_dataset or not reverse_dataset: + self._validation_failed( INVALID_IDENTIFIERS_MESSAGE ) left_association = DatasetCollectionElement( - element=left_dataset, - element_identifier=LEFT_IDENTIFIER, + element=forward_dataset, + element_identifier=FORWARD_IDENTIFIER, ) right_association = DatasetCollectionElement( - element=right_dataset, - element_identifier=RIGHT_IDENTIFIER, + element=reverse_dataset, + element_identifier=REVERSE_IDENTIFIER, ) return self._new_collection_for_elements([left_association, right_association]) diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -292,8 +292,8 @@ hda1, hda2 = self.__datasets( history_id, count=2, contents=contents ) element_identifiers = [ - dict( name="left", src="hda", id=hda1[ "id" ] ), - dict( name="right", src="hda", id=hda2[ "id" ] ), + dict( name="forward", src="hda", id=hda1[ "id" ] ), + dict( name="reverse", src="hda", id=hda2[ "id" ] ), ] return element_identifiers diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -204,8 +204,8 @@ first_object = first_element[ "object" ] assert first_object[ "collection_type" ] == "paired" assert len( first_object[ "elements" ] ) == 2 - first_object_left_element = first_object[ "elements" ][ 0 ] - self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] ) + first_object_forward_element = first_object[ "elements" ][ 0 ] + self.assertEquals( outputs[ 0 ][ "id" ], first_object_forward_element[ "object" ][ "id" ] ) @skip_without_tool( "cat1" ) def test_map_over_two_collections( self ): diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_mixed_param.xml --- a/test/functional/tools/collection_mixed_param.xml +++ b/test/functional/tools/collection_mixed_param.xml @@ -13,8 +13,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><param name="f2" value="simple_lines_both.txt" /> diff -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 -r f24bb5dde1f5f23353bd410001bf2b2ce82a9653 test/functional/tools/collection_paired_test.xml --- a/test/functional/tools/collection_paired_test.xml +++ b/test/functional/tools/collection_paired_test.xml @@ -1,6 +1,6 @@ <tool id="collection_paired_test" name="paired_test" version="0.1.0"><command> - cat #for $f in $f1# ${f} #end for# >> $out1; + cat $f1.forward $f1.reverse >> $out1; </command><inputs><param name="f1" type="data_collection" collection_type="paired" /> @@ -12,8 +12,8 @@ <test><param name="f1"><collection type="paired"> - <element name="left" value="simple_line.txt" /> - <element name="right" value="simple_line_alternative.txt" /> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /></collection></param><output name="out1"> 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: 4 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ef71c8b55a5/ Changeset: 6ef71c8b55a5 User: jmchilton Date: 2014-05-15 19:04:58 Summary: Bugfix: Copying datasets to existing and new history at same time. Previously would give error about set not having an append method. Affected #: 1 file diff -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1000,7 +1000,7 @@ elif target_history_ids: if not isinstance( target_history_ids, list ): target_history_ids = target_history_ids.split(",") - target_history_ids = set([ trans.security.decode_id(h) for h in target_history_ids if h ]) + target_history_ids = list(set([ trans.security.decode_id(h) for h in target_history_ids if h ])) else: target_history_ids = [] done_msg = error_msg = "" https://bitbucket.org/galaxy/galaxy-central/commits/e1a1ffe4bfaf/ Changeset: e1a1ffe4bfaf User: jmchilton Date: 2014-05-15 19:04:58 Summary: Allow 'Copy Datasets' page to copy collections as well. Affected #: 2 files diff -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -981,7 +981,7 @@ return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors ) @web.expose - def copy_datasets( self, trans, source_history=None, source_dataset_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): + def copy_datasets( self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): user = trans.get_user() if source_history is not None: history = self.get_history(trans, source_history) @@ -989,12 +989,16 @@ else: history = current_history = trans.get_history() refresh_frames = [] - if source_dataset_ids: - if not isinstance( source_dataset_ids, list ): - source_dataset_ids = source_dataset_ids.split(",") - source_dataset_ids = set(map( trans.security.decode_id, source_dataset_ids )) + if source_content_ids: + if not isinstance( source_content_ids, list ): + source_content_ids = source_content_ids.split(",") + encoded_dataset_collection_ids = [ s[ len("dataset_collection|"): ] for s in source_content_ids if s.startswith("dataset_collection|") ] + encoded_dataset_ids = [ s[ len("dataset|"): ] for s in source_content_ids if s.startswith("dataset|") ] + decoded_dataset_collection_ids = set(map( trans.security.decode_id, encoded_dataset_collection_ids )) + decoded_dataset_ids = set(map( trans.security.decode_id, encoded_dataset_ids )) else: - source_dataset_ids = [] + decoded_dataset_collection_ids = [] + decoded_dataset_ids = [] if target_history_id: target_history_ids = [ trans.security.decode_id(target_history_id) ] elif target_history_ids: @@ -1006,8 +1010,8 @@ done_msg = error_msg = "" new_history = None if do_copy: - invalid_datasets = 0 - if not source_dataset_ids or not ( target_history_ids or new_history_name ): + invalid_contents = 0 + if not ( decoded_dataset_ids or decoded_dataset_collection_ids ) or not ( target_history_ids or new_history_name ): error_msg = "You must provide both source datasets and target histories. " else: if new_history_name: @@ -1023,18 +1027,22 @@ target_histories = [ history ] if len( target_histories ) != len( target_history_ids ): error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) - source_hdas = map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ) - source_hdas.sort(key=lambda hda: hda.hid) - for hda in source_hdas: - if hda is None: + source_contents = map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, decoded_dataset_ids ) + source_contents.extend( map( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get, decoded_dataset_collection_ids ) ) + source_contents.sort(key=lambda content: content.hid) + for content in source_contents: + if content is None: error_msg = error_msg + "You tried to copy a dataset that does not exist. " - invalid_datasets += 1 - elif hda.history != history: + invalid_contents += 1 + elif content.history != history: error_msg = error_msg + "You tried to copy a dataset which is not in your current history. " - invalid_datasets += 1 + invalid_contents += 1 else: for hist in target_histories: - hist.add_dataset( hda.copy( copy_children = True ) ) + if content.history_content_type == "dataset": + hist.add_dataset( content.copy( copy_children=True ) ) + else: + hist.add_dataset_collection( content.copy( ) ) if current_history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() @@ -1042,21 +1050,21 @@ ( url_for( controller="history", action="switch_to_history", \ hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ for hist in target_histories ] ) - num_source = len( source_dataset_ids ) - invalid_datasets + num_source = len( source_content_ids ) - invalid_contents num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) trans.sa_session.refresh( history ) - source_datasets = history.visible_datasets + source_contents = history.active_contents target_histories = [history] if user: target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", source_history = history, current_history = current_history, - source_dataset_ids = source_dataset_ids, + source_content_ids = source_content_ids, target_history_id = target_history_id, target_history_ids = target_history_ids, - source_datasets = source_datasets, + source_contents = source_contents, target_histories = target_histories, new_history_name = new_history_name, done_msg = done_msg, diff -r 6ef71c8b55a56be844a5a57aad9fe91a4222663e -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 templates/webapps/galaxy/dataset/copy_view.mako --- a/templates/webapps/galaxy/dataset/copy_view.mako +++ b/templates/webapps/galaxy/dataset/copy_view.mako @@ -59,17 +59,18 @@ </select></div><div class="toolFormBody"> - %if len(source_datasets) > 0: - %for data in source_datasets: + %if source_contents: + %for data in source_contents: <% checked = "" encoded_id = trans.security.encode_id(data.id) - if data.id in source_dataset_ids: + input_id = "%s|%s" % ( data.history_content_type, encoded_id ) + if input_id in source_content_ids: checked = " checked='checked'" %><div class="form-row"> - <input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> + <input type="checkbox" name="source_content_ids" id="${input_id}" value="${input_id}"${checked}/> + <label for="${input_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label></div> %endfor %else: https://bitbucket.org/galaxy/galaxy-central/commits/1f35c462c606/ Changeset: 1f35c462c606 User: jmchilton Date: 2014-05-15 19:04:58 Summary: PEP-8 fixes for DatasetInterface.copy_datasets. Affected #: 1 file diff -r e1a1ffe4bfaf06b1c0ab293d0057c6e793fee493 -r 1f35c462c606dca541e5f5f16d2c3f4e33334cfe lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1047,9 +1047,9 @@ refresh_frames = ['history'] trans.sa_session.flush() hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % - ( url_for( controller="history", action="switch_to_history", \ - hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ - for hist in target_histories ] ) + ( url_for( controller="history", action="switch_to_history", + hist_id=trans.security.encode_id( hist.id ) ), hist.name ) + for hist in target_histories ] ) num_source = len( source_content_ids ) - invalid_contents num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) @@ -1057,19 +1057,19 @@ source_contents = history.active_contents target_histories = [history] if user: - target_histories = user.active_histories + target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", - source_history = history, - current_history = current_history, - source_content_ids = source_content_ids, - target_history_id = target_history_id, - target_history_ids = target_history_ids, - source_contents = source_contents, - target_histories = target_histories, - new_history_name = new_history_name, - done_msg = done_msg, - error_msg = error_msg, - refresh_frames = refresh_frames ) + source_history=history, + current_history=current_history, + source_content_ids=source_content_ids, + target_history_id=target_history_id, + target_history_ids=target_history_ids, + source_contents=source_contents, + target_histories=target_histories, + new_history_name=new_history_name, + done_msg=done_msg, + error_msg=error_msg, + refresh_frames=refresh_frames ) def _copy_datasets( self, trans, dataset_ids, target_histories, imported=False ): """ Helper method for copying datasets. """ https://bitbucket.org/galaxy/galaxy-central/commits/b5a1cd130f71/ Changeset: b5a1cd130f71 User: jmchilton Date: 2014-05-15 19:04:58 Summary: Order history.{active,visible}_dataset_collections by hid instead of id. Affected #: 1 file diff -r 1f35c462c606dca541e5f5f16d2c3f4e33334cfe -r b5a1cd130f71b20a25f1bf110b0e1e24843df4b7 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1461,9 +1461,9 @@ model.HistoryDatasetCollectionAssociation, primaryjoin=( ( model.HistoryDatasetCollectionAssociation.table.c.history_id ) == model.History.table.c.id ) & not_( model.HistoryDatasetCollectionAssociation.table.c.deleted ), - order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.id ), + order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.hid ), viewonly=True, - ), # TODO:orderbyhid + ), visible_datasets=relation( model.HistoryDatasetAssociation, primaryjoin=( ( model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id ) & not_( model.HistoryDatasetAssociation.table.c.deleted ) & model.HistoryDatasetAssociation.table.c.visible ), @@ -1473,7 +1473,7 @@ visible_dataset_collections=relation( model.HistoryDatasetCollectionAssociation, primaryjoin=( ( model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id ) & not_( model.HistoryDatasetCollectionAssociation.table.c.deleted ) & model.HistoryDatasetCollectionAssociation.table.c.visible ), - order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.id ), + order_by=asc( model.HistoryDatasetCollectionAssociation.table.c.hid ), viewonly=True, ), tags=relation( model.HistoryTagAssociation, order_by=model.HistoryTagAssociation.table.c.id, backref="histories" ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Fix multipanels in heatmap
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2300bcd6008/ Changeset: d2300bcd6008 User: guerler Date: 2014-05-15 17:57:43 Summary: Charts: Fix multipanels in heatmap Affected #: 3 files diff -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw 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u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for 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Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file +define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams"})}),define("plugin/charts/nvd3_bar_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_bar_horizontal_stacked/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_tick:{init:".2"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others"})}),define("plugin/charts/nvd3_line_focus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others"})}),define("plugin/charts/nvd3_pie/config",[],function(){return{title:"Pie chart",library:"nvd3.js",category:"Area charts",tag:"svg",use_panels:!0,columns:{label:{title:"Labels",is_label:!0},y:{title:"Values"}},settings:{show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"select",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_scatter/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_full/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",category:"Area charts"})}),define("plugin/charts/nvd3_stackedarea_stream/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"highcharts.js",tag:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/heatmap/config",[],function(){return{title:"Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",library:"",tag:"div",use_panels:!0,execute:"heatmap",columns:{row_label:{title:"Row labels",is_label:!0},col_label:{title:"Column labels",is_label:!0},value:{title:"Observations"}},settings:{color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"ocean",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gebco",value:"gebco"},{label:"Globe",value:"globe"},{label:"Gray scale",value:"gray"},{label:"Haxby",value:"haxby"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Rainbow",value:"rainbow"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Topo",value:"topo"},{label:"Wysiwyg",value:"wysiwyg"}]},sorting:{title:"Sorting",info:"How should the columns be clustered?",type:"select",init:"hclust",data:[{label:"Read from dataset",value:"hclust"},{label:"Sort column and row labels",value:"byboth"},{label:"Sort column labels",value:"bycolumns"},{label:"Sort by rows",value:"byrow"}]}},menu:function(){return{color_set:this.settings.color_set}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bar/config","plugin/charts/nvd3_bar_stacked/config","plugin/charts/nvd3_bar_horizontal/config","plugin/charts/nvd3_bar_horizontal_stacked/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_line_focus/config","plugin/charts/nvd3_pie/config","plugin/charts/nvd3_scatter/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/nvd3_stackedarea_full/config","plugin/charts/nvd3_stackedarea_stream/config","plugin/charts/highcharts_boxplot/config","plugin/charts/heatmap/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_stackedarea:f,nvd3_stackedarea_full:l,nvd3_stackedarea_stream:c,nvd3_line:s,nvd3_line_focus:o,nvd3_scatter:a,nvd3_pie:u,nvd3_histogram:i,highcharts_boxplot:h,heatmap:p}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js @@ -20,51 +20,66 @@ // loop through data groups var index = 0; for (var group_index in request_dictionary.groups) { + + // configure request + var tmp_dict = { + id : request_dictionary.id, + groups : [{ + key : request_dictionary.groups[group_index].key, + columns : { + row_label: { + index : index++, + is_label : true + }, + col_label: { + index : index++, + is_label : true + }, + value: { + index : index++ + } + } + }] + }; - // configure request - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - } - - // request data - this.app.datasets.request(request_dictionary, function() { + // target div + var group_div = self.options.canvas[group_index]; - // get group - var group = request_dictionary.groups[group_index]; - var div = self.options.canvas[group_index]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // check if done + // draw group + this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { if (group_index == request_dictionary.groups.length - 1) { // set chart state chart.state('ok', 'Heat map drawn.'); - + // unregister process chart.deferred.done(process_id); } }); } + }, + + // draw group + _draw_group: function(group_index, div, chart, request_dictionary, callback) { + // link this + var self = this; + + // request data + this.app.datasets.request(request_dictionary, function() { + + // get group + var group = request_dictionary.groups[0]; + + // draw plot + var heatmap = new HeatmapPlugin({ + 'title' : group.key, + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : div + }); + + // callback on completion + callback (group_index); + }); } }); diff -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 -r d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -198,8 +198,12 @@ var group_index = 0; var self = this; chart.groups.each(function(group) { + // increase group counter + group_index++; + + // add selected columns to column string for (var key in self.chart_settings.columns) { - request_string += key + '_' + (++group_index) + ':' + (parseInt(group.get(key)) + 1) + ', '; + request_string += key + '_' + group_index + ':' + (parseInt(group.get(key)) + 1) + ', '; } }); @@ -244,13 +248,13 @@ // add columns var columns = {}; - for (var key in self.chart_settings.columns) { + for (var column_key in self.chart_settings.columns) { // get settings for column - var column_settings = self.chart_settings.columns[key]; + var column_settings = self.chart_settings.columns[column_key]; // add to columns - columns[key] = { - index : group.get(key), + columns[column_key] = { + index : group.get(column_key), is_label : column_settings.is_label } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Merged in erasche2/galaxy-central (pull request #393)
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f6110335f4e/ Changeset: 5f6110335f4e User: natefoo Date: 2014-05-15 17:33:20 Summary: Merged in erasche2/galaxy-central (pull request #393) Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r 0d2c45f321ed234115a15d46c255818192ba41a2 -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + 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: 6 new changesets
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2892895e566/ Changeset: a2892895e566 User: erasche2 Date: 2014-05-14 21:48:26 Summary: Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r b483d9df129c00480fc72253a277de18ab67b27d -r a2892895e566ebad6edc1401519c72b83138a2a9 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep 'Starting server in PID [0-9]+' $1 -o | sed 's/Starting server in PID //g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ & + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + https://bitbucket.org/galaxy/galaxy-central/commits/8bd0ea03bc28/ Changeset: 8bd0ea03bc28 User: erasche2 Date: 2014-05-14 22:23:26 Summary: Removed detach as --daemon flag will detach process Affected #: 1 file diff -r a2892895e566ebad6edc1401519c72b83138a2a9 -r 8bd0ea03bc2877bc7a9fc6880337c3a07706e655 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -31,7 +31,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ & + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ # Wait for the server to start sleep 1 # Grab the new pid https://bitbucket.org/galaxy/galaxy-central/commits/b189178db4ae/ Changeset: b189178db4ae User: erasche2 Date: 2014-05-14 22:33:44 Summary: Added --daemon flag so user doesn't have to Affected #: 1 file diff -r 8bd0ea03bc2877bc7a9fc6880337c3a07706e655 -r b189178db4aef2a3dbe9fbfbe2be4582911f8597 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -31,7 +31,7 @@ echo "$server not running" fi # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ # Wait for the server to start sleep 1 # Grab the new pid https://bitbucket.org/galaxy/galaxy-central/commits/a3530f2474fc/ Changeset: a3530f2474fc User: erasche2 Date: 2014-05-15 16:43:04 Summary: Added line anchors for performance Affected #: 1 file diff -r b189178db4aef2a3dbe9fbfbe2be4582911f8597 -r a3530f2474fc2ccc0529e35cf154615de4474365 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -3,7 +3,7 @@ check_if_not_started(){ # Search for all pids in the logs and tail for the last one - latest_pid=`egrep 'Starting server in PID [0-9]+' $1 -o | sed 's/Starting server in PID //g' | tail -n 1` + latest_pid=`egrep '^Starting server in PID [0-9]+.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` # Grab the current pid from the file we were given current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs https://bitbucket.org/galaxy/galaxy-central/commits/65ea2c82a973/ Changeset: 65ea2c82a973 User: erasche2 Date: 2014-05-15 16:48:17 Summary: Fixed typo on regex Affected #: 1 file diff -r a3530f2474fc2ccc0529e35cf154615de4474365 -r 65ea2c82a9738f8782a3c06d2ee06d5471ba9bd0 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -3,7 +3,7 @@ check_if_not_started(){ # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` # Grab the current pid from the file we were given current_pid_in_file=$(cat $2); # If they're equivalent, then the current pid file agrees with our logs https://bitbucket.org/galaxy/galaxy-central/commits/5f6110335f4e/ Changeset: 5f6110335f4e User: natefoo Date: 2014-05-15 17:33:20 Summary: Merged in erasche2/galaxy-central (pull request #393) Added rolling restart script to kill servers sequentially Affected #: 1 file diff -r 0d2c45f321ed234115a15d46c255818192ba41a2 -r 5f6110335f4e328e6fd1a83c65a9312fcf5caeb0 rolling_restart.sh --- /dev/null +++ b/rolling_restart.sh @@ -0,0 +1,49 @@ +#!/bin/bash +cd `dirname $0` + +check_if_not_started(){ + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [[ $latest_pid -eq $current_pid_in_file ]]; + then + echo 0; + else + echo 1; + fi +} + +servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` +for server in $servers; +do + # If there's a pid + if [[ -e $server.pid ]] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [[ $result -eq 1 ]] + do + result=$(check_if_not_started $server.log $server.pid) + echo -n "." + sleep 1 + done + echo "" +done + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactoring cleanup in the Tool Shed's package installation framework.
by commits-noreply＠bitbucket.org 15 May '14

15 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d2c45f321ed/ Changeset: 0d2c45f321ed User: greg Date: 2014-05-15 15:59:55 Summary: Refactoring cleanup in the Tool Shed's package installation framework. Affected #: 4 files diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -26,8 +26,6 @@ from tool_shed.util import xml_util from tool_shed.galaxy_install import repository_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager import pkg_resources eggs.require( 'mercurial' ) @@ -458,63 +456,16 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) err_msg = '' - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - installed_tool_dependencies = [] - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ trans.app.install_model.ToolDependency.installation_status.INSTALLED, - trans.app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if trans.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -22,9 +22,6 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager - from galaxy import eggs eggs.require( 'mercurial' ) @@ -624,58 +621,12 @@ trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir ) - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - repository_tool_dependencies = util.listify( tool_shed_repository.tool_dependencies ) - # elem is a package tag set. - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in repository_tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = repository_tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=repository_tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=repository_tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ trans.app.install_model.ToolDependency.installation_status.INSTALLED, - trans.app.install_model.ToolDependency.installation_status.ERROR ]: - if trans.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies, + from_tool_migration_manager=False ) suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -916,72 +867,24 @@ for tool_dependency in repository.missing_tool_dependencies: if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR, trans.install_model.ToolDependency.installation_status.INSTALLING ]: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( trans.app, - tool_dependency=tool_dependency, - status=trans.install_model.ToolDependency.installation_status.UNINSTALLED, - error_message=None, - remove_from_disk=True ) + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( trans.app, + tool_dependency=tool_dependency, + status=trans.install_model.ToolDependency.installation_status.UNINSTALLED, + error_message=None, + remove_from_disk=True ) # Install tool dependencies. suc.update_tool_shed_repository_status( trans.app, repository, trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( trans.app ) ) - installed_tool_dependencies = [] - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if tree is None: - return installed_tool_dependencies - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependency_db_records[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( trans.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=False ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, - app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=trans.app, + tool_shed_repository=repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=repository.tool_dependencies, + from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -19,8 +19,6 @@ from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util -from tool_shed.galaxy_install.install_manager import InstallManager -from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager from galaxy.util.odict import odict log = logging.getLogger( __name__ ) @@ -447,64 +445,12 @@ self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) - installed_tool_dependencies = [] - # Parse the tool_dependencies.xml config. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - install_manager = InstallManager() - tag_manager = TagManager() - root = tree.getroot() - for elem in root: - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - # elem is a package tag set. - tool_dependency = None - for tool_dependency in tool_dependencies: - if package_name == str( tool_dependency.name ) and package_version == str( tool_dependency.version ): - break - if tool_dependency is not None: - attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] - attr_tup = ( package_name, package_version, 'package' ) - try: - index = attr_tups_of_dependencies_for_install.index( attr_tup ) - except Exception, e: - index = None - if index is not None: - tool_dependency = tool_dependencies[ index ] - tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( self.app, - tool_shed_repository, - tool_dependency, - elem, - package_name, - package_version, - from_tool_migration_manager=False, - tool_dependency_db_records=tool_dependencies ) - if proceed_with_install: - try: - tool_dependency = install_manager.install_package( self.app, - elem, - tool_shed_repository, - tool_dependencies=tool_dependencies, - from_tool_migration_manager=True ) - except Exception, e: - error_message = "Error installing tool dependency package %s version %s: %s" % \ - ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The - # remove_installation_path option must be left False here. - tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( self.app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.INSTALLED, - self.app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) - if self.app.config.manage_dependency_relationships: - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - self.app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + installed_tool_dependencies = \ + common_install_util.install_specified_packages( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' diff -r 75be6c49a65d8d52920696216ffb5af74a3fdd9c -r 0d2c45f321ed234115a15d46c255818192ba41a2 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -3,7 +3,6 @@ import os import urllib import urllib2 -from galaxy import eggs from galaxy import util from galaxy import web from galaxy.util import json @@ -18,6 +17,9 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.install_manager import InstallManager +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager + log = logging.getLogger( __name__ ) def activate_repository( trans, repository ): @@ -481,6 +483,73 @@ all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict +def install_specified_packages( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False ): + """ + Follow the recipe in the received tool_dependencies_config to install specified packages for + repository tools. The received list of tool_dependencies are the database records for those + dependencies defined in the tool_dependencies_config that are to be installed. This list may + be a subset of the set of dependencies defined in the tool_dependencies_config. This allows + for filtering out dependencies that have not been checked for installation on the 'Manage tool + dependencies' page for an installed Tool Shed repository. + """ + attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] + installed_packages = [] + install_manager = InstallManager() + tag_manager = TagManager() + # Parse the tool_dependencies.xml config. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + log.debug( "The received tool_dependencies.xml file is likely invalid: %s" % str( error_message ) ) + return installed_packages + root = tree.getroot() + for elem in root: + package_name = elem.get( 'name', None ) + package_version = elem.get( 'version', None ) + if package_name and package_version: + # elem is a package tag set. + attr_tup = ( package_name, package_version, 'package' ) + try: + index = attr_tups_of_dependencies_for_install.index( attr_tup ) + except Exception, e: + index = None + if index is not None: + tool_dependency = tool_dependencies[ index ] + tool_dependency, proceed_with_install, action_elem_tuples = \ + tag_manager.process_tag_set( app, + tool_shed_repository, + tool_dependency, + elem, + package_name, + package_version, + from_tool_migration_manager=from_tool_migration_manager, + tool_dependency_db_records=tool_dependencies ) + if proceed_with_install: + try: + tool_dependency = install_manager.install_package( app, + elem, + tool_shed_repository, + tool_dependencies=tool_dependencies, + from_tool_migration_manager=from_tool_migration_manager ) + except Exception, e: + error_message = "Error installing tool dependency package %s version %s: %s" % \ + ( str( package_name ), str( package_version ), str( e ) ) + log.exception( error_message ) + if tool_dependency: + # Since there was an installation error, update the tool dependency status to Error. The + # remove_installation_path option must be left False here. + tool_dependency = \ + tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, + app.install_model.ToolDependency.installation_status.ERROR ]: + installed_packages.append( tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + return installed_packages + def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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