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commit/galaxy-central: jmchilton: PEP-8 fixes for tools/actions/__init__.py
by commits-noreply＠bitbucket.org 11 Jan '14

11 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9f55b4b37d35/ Changeset: 9f55b4b37d35 User: jmchilton Date: 2014-01-11 04:17:39 Summary: PEP-8 fixes for tools/actions/__init__.py Affected #: 1 file diff -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d -r 9f55b4b37d35b8366f42ab430ac4213554d83311 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -3,7 +3,8 @@ from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation -from galaxy.tools.parameters import DataToolParameter, SelectToolParameter +from galaxy.tools.parameters import DataToolParameter +from galaxy.tools.parameters import SelectToolParameter from galaxy.tools.parameters.grouping import Conditional, Repeat from galaxy.util.json import from_json_string from galaxy.util.json import to_json_string @@ -15,6 +16,7 @@ import logging log = logging.getLogger( __name__ ) + class ToolAction( object ): """ The actions to be taken when a tool is run (after parameters have @@ -23,6 +25,7 @@ def execute( self, tool, trans, incoming={}, set_output_hid=True ): raise TypeError("Abstract method") + class DefaultToolAction( object ): """Default tool action is to run an external command""" @@ -33,8 +36,10 @@ of the DataToolParameter type. """ input_datasets = dict() - def visitor( prefix, input, value, parent = None ): - def process_dataset( data, formats = None ): + + def visitor( prefix, input, value, parent=None ): + + def process_dataset( data, formats=None ): if not data: return data if formats is None: @@ -48,11 +53,11 @@ data = converted_dataset else: #run converter here - new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] + new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False ) trans.sa_session.add( assoc ) trans.sa_session.flush() data = new_data @@ -77,17 +82,17 @@ input_datasets[ prefix + conversion_name + str( i + 1 ) ] = new_data conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) + raise Exception('A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) ) if parent: parent[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - parent[ conversion_name ][i] = conversion_data.id #a more robust way to determine JSONable value is desired + parent[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired else: param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - param_values[ conversion_name ][i] = conversion_data.id #a more robust way to determine JSONable value is desired + param_values[ conversion_name ][i] = conversion_data.id # a more robust way to determine JSONable value is desired else: input_datasets[ prefix + input.name ] = process_dataset( value ) conversions = [] @@ -97,14 +102,14 @@ input_datasets[ prefix + conversion_name ] = new_data conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, conversion_extensions ) + raise Exception( 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, conversion_extensions ) ) target_dict = parent if not target_dict: target_dict = param_values target_dict[ input.name ] = input_datasets[ prefix + input.name ] for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - target_dict[ conversion_name ] = conversion_data.id #a more robust way to determine JSONable value is desired + target_dict[ conversion_name ] = conversion_data.id # a more robust way to determine JSONable value is desired tool.visit_inputs( param_values, visitor ) return input_datasets @@ -130,6 +135,7 @@ else: copy_from_dict[ key ] = value return copy_from_dict + def make_list_copy( from_list ): new_list = [] for value in from_list: @@ -140,32 +146,33 @@ else: new_list.append( value ) return new_list - def wrap_values( inputs, input_values, skip_missing_values = False ): + + def wrap_values( inputs, input_values, skip_missing_values=False ): # Wrap tool inputs as necessary for input in inputs.itervalues(): if input.name not in input_values and skip_missing_values: continue if isinstance( input, Repeat ): for d in input_values[ input.name ]: - wrap_values( input.inputs, d, skip_missing_values = skip_missing_values ) + wrap_values( input.inputs, d, skip_missing_values=skip_missing_values ) elif isinstance( input, Conditional ): values = input_values[ input.name ] current = values[ "__current_case__" ] - wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values ) + wrap_values( input.cases[current].inputs, values, skip_missing_values=skip_missing_values ) elif isinstance( input, DataToolParameter ) and input.multiple: input_values[ input.name ] = \ galaxy.tools.DatasetListWrapper( input_values[ input.name ], - datatypes_registry = trans.app.datatypes_registry, - tool = tool, - name = input.name ) + datatypes_registry=trans.app.datatypes_registry, + tool=tool, + name=input.name ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], - datatypes_registry = trans.app.datatypes_registry, - tool = tool, - name = input.name ) + datatypes_registry=trans.app.datatypes_registry, + tool=tool, + name=input.name ) elif isinstance( input, SelectToolParameter ): - input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) + input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values=incoming ) else: input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) @@ -183,7 +190,7 @@ input_dbkey = incoming.get( "dbkey", "?" ) for name, data in inp_data.items(): if not data: - data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) + data = NoneDataset( datatypes_registry=trans.app.datatypes_registry ) continue # Convert LDDA to an HDA. @@ -191,7 +198,7 @@ data = data.to_history_dataset_association( None ) inp_data[name] = data - else: # HDA + else: # HDA if data.hid: input_names.append( 'data %s' % data.hid ) input_ext = data.ext @@ -212,9 +219,9 @@ if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - # HACK: the attempt to get chrom_info below will trigger the + # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, - # which will in turn create a recursive loop when + # which will in turn create a recursive loop when # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. @@ -248,7 +255,7 @@ on_text = "" # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey - params = None #wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed + params = None # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] @@ -258,10 +265,10 @@ for filter in output.filters: try: if not eval( filter.text.strip(), globals(), incoming ): - break #do not create this dataset + break # do not create this dataset except Exception, e: log.debug( 'Dataset output filter failed: %s' % e ) - else: #all filters passed + else: # all filters passed if output.parent: parent_to_child_pairs.append( ( output.parent, name ) ) child_dataset_names.add( name ) @@ -291,7 +298,7 @@ if output.change_format: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): check = when_elem.get( 'input', None ) @@ -300,9 +307,9 @@ if '$' not in check: #allow a simple name or more complex specifications check = '${%s}' % check - if str( fill_template( check, context = params ) ) == when_elem.get( 'value', None ): + if str( fill_template( check, context=params ) ) == when_elem.get( 'value', None ): ext = when_elem.get( 'format', ext ) - except: #bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct + except: # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct continue else: check = when_elem.get( 'input_dataset', None ) @@ -348,7 +355,7 @@ # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> # </outputs> - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined params['tool'] = tool params['on_string'] = on_text @@ -356,7 +363,7 @@ else: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + wrap_values( tool.inputs, params, skip_missing_values=not tool.check_values ) data.name = self._get_default_data_name( data, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) # Store output out_data[ name ] = data @@ -369,10 +376,10 @@ trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history unless otherwise specified for name in out_data.keys(): - if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created + if name not in child_dataset_names and name not in incoming: # don't add children; or already existing datasets, i.e. async created data = out_data[ name ] if set_output_history: - history.add_dataset( data, set_hid = set_output_hid ) + history.add_dataset( data, set_hid=set_output_hid ) trans.sa_session.add( data ) trans.sa_session.flush() # Add all the children to their parents Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix message rendering for repositories with multiple heads.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/582d1e318dd3/ Changeset: 582d1e318dd3 User: greg Date: 2014-01-10 22:36:45 Summary: Fix message rendering for repositories with multiple heads. Affected #: 2 files diff -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -125,7 +125,7 @@ from tool_shed.util.shed_util_common import get_revision_label_from_ctx heads_str = '' for ctx in heads: - heads_str += get_revision_label_from_ctx( ctx ) + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx ) %> Contact the administrator of this Tool Shed as soon as possible and let them know that this repository has the following multiple heads which must be merged.<br/> diff -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 -r 582d1e318dd3b604f2371a861f35c6fae1a2d36d templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -72,7 +72,7 @@ from tool_shed.util.shed_util_common import get_revision_label_from_ctx heads_str = '' for ctx in heads: - heads_str += get_revision_label_from_ctx( ctx ) + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx ) %> Contact the administrator of this Tool Shed as soon as possible and let them know that this repository has the following multiple heads which must be merged.<br/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add tool shed features for displaying repository heads and alerting users if a repository has multiple heads that require merging.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56b61e7d5bbc/ Changeset: 56b61e7d5bbc User: greg Date: 2014-01-10 22:30:45 Summary: Add tool shed features for displaying repository heads and alerting users if a repository has multiple heads that require merging. Affected #: 6 files diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2255,6 +2255,7 @@ categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + heads = suc.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -2262,6 +2263,7 @@ current_allow_push_list=current_allow_push_list, allow_push_select_field=allow_push_select_field, repo=repo, + heads=heads, repository=repository, containers_dict=containers_dict, repository_metadata=repository_metadata, @@ -3043,8 +3045,10 @@ status = 'error' containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) + heads = suc.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, + heads=heads, repository=repository, repository_metadata=repository_metadata, metadata=metadata, diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -365,6 +365,7 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), + RepositoryGrid.HeadsColumn( "Heads" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -89,6 +89,29 @@ return escape_html( type_class.label ) + class HeadsColumn( grids.GridColumn ): + + def __init__( self, col_name ): + grids.GridColumn.__init__( self, col_name ) + + def get_value( self, trans, grid, repository ): + """Display the current repository heads.""" + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + heads = suc.get_repository_heads( repo ) + multiple_heads = len( heads ) > 1 + if multiple_heads: + heads_str = '<font color="red">' + else: + heads_str = '' + for ctx in heads: + heads_str += '%s<br/>' % suc.get_revision_label_from_ctx( ctx ) + heads_str.rstrip( '<br/>' ) + if multiple_heads: + heads_str += '</font>' + return heads_str + + class MetadataRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1108,6 +1108,11 @@ # This should never be reached - raise an exception? return v, None +def get_repository_heads( repo ): + """Return current repository heads, which are changesets with no child changesets.""" + heads = [ repo[ h ] for h in repo.heads( None ) ] + return heads + def get_repository_ids_requiring_prior_import_or_install( trans, tsr_ids, repository_dependencies ): """ This method is used in the Tool Shed when exporting a repository and it's dependencies, and in Galaxy when a repository and it's dependencies @@ -1213,18 +1218,20 @@ repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: - return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) + return get_revision_label_from_ctx( ctx ) else: return "-1:%s" % changeset_revision +def get_revision_label_from_ctx( ctx ): + return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), str( ctx ), str( get_readable_ctx_date( ctx ) ) ) + def get_rev_label_from_changeset_revision( repo, changeset_revision ): """Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash.""" ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() - label = '%s:%s <i><font color="#666666">(%s)</font></i>' % \ - ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) + label = get_revision_label_from_ctx( ctx ) else: rev = '-1' label = "-1:%s" % changeset_revision diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -83,6 +83,10 @@ can_render_skip_tool_test_section = True else: can_render_skip_tool_test_section = False + if heads: + multiple_heads = len( heads ) > 1 + else: + multiple_heads = False %><%! @@ -115,6 +119,18 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> +%elif multiple_heads: + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += get_revision_label_from_ctx( ctx ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> %endif %if len( changeset_revision_select_field.options ) > 1: diff -r 4ab2017348e25958bcd8babd8e110f574dff24df -r 56b61e7d5bbcea1dff823cf78229289480ee15e7 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -25,6 +25,11 @@ tip_str = '' sharable_link_label = 'Sharable link to this repository revision:' sharable_link_changeset_revision = changeset_revision + + if heads: + multiple_heads = len( heads ) > 1 + else: + multiple_heads = False %><%! @@ -61,6 +66,18 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> +%elif multiple_heads: + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += get_revision_label_from_ctx( ctx ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> %endif %if len( changeset_revision_select_field.options ) > 1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: PEP-8 fixes for pages API.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ab2017348e2/ Changeset: 4ab2017348e2 User: jmchilton Date: 2014-01-10 22:08:30 Summary: PEP-8 fixes for pages API. Affected #: 2 files diff -r 43a964de0758ea9deffb88fd2c59441a13cae14b -r 4ab2017348e25958bcd8babd8e110f574dff24df lib/galaxy/webapps/galaxy/api/page_revisions.py --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -4,13 +4,12 @@ import logging from galaxy import web from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin -from galaxy.model.search import GalaxySearchEngine from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ItemAccessibilityException from galaxy.util.sanitize_html import sanitize_html log = logging.getLogger( __name__ ) + class PageRevisionsController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api @@ -32,7 +31,6 @@ out.append( self.encode_all_ids( trans, page.to_dict(), True) ) return out - @web.expose_api def create( self, trans, page_id, payload, **kwd ): """ @@ -46,11 +44,10 @@ 'content' = New content of the page :rtype: dictionary - :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request """ - user = trans.get_user() error_str = "" - + if not page_id: error_str = "page_id is required" elif not payload.get("content", None): @@ -61,7 +58,7 @@ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id(page_id) ) if page is None: return { "error" : "page not found"} - + if not self.security_check( trans, page, True, True ): return { "error" : "page not found"} @@ -82,6 +79,6 @@ session = trans.sa_session session.flush() - return {"success" : "revision posted"} - - return { "error" : error_str } + return { "success" : "revision posted" } + + return { "error" : error_str } diff -r 43a964de0758ea9deffb88fd2c59441a13cae14b -r 4ab2017348e25958bcd8babd8e110f574dff24df lib/galaxy/webapps/galaxy/api/pages.py --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -4,13 +4,12 @@ import logging from galaxy import web from galaxy.web.base.controller import SharableItemSecurityMixin, BaseAPIController, SharableMixin -from galaxy.model.search import GalaxySearchEngine from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ItemAccessibilityException from galaxy.util.sanitize_html import sanitize_html log = logging.getLogger( __name__ ) + class PagesController( BaseAPIController, SharableItemSecurityMixin, UsesAnnotations, SharableMixin ): @web.expose_api @@ -26,7 +25,7 @@ :returns: dictionaries containing summary or detailed Page information """ out = [] - + if trans.user_is_admin(): r = trans.sa_session.query( trans.app.model.Page ) if not deleted: @@ -48,7 +47,6 @@ return out - @web.expose_api def create( self, trans, payload, **kwd ): """ @@ -67,7 +65,7 @@ """ user = trans.get_user() error_str = "" - + if not payload.get("title", None): error_str = "Page name is required" elif not payload.get("slug", None): @@ -85,7 +83,7 @@ page = trans.app.model.Page() page.title = payload['title'] page.slug = payload['slug'] - page_annotation = sanitize_html( payload.get("annotation",""), 'utf-8', 'text/html' ) + page_annotation = sanitize_html( payload.get( "annotation", "" ), 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) page.user = user # And the first (empty) page revision @@ -99,11 +97,10 @@ session.add( page ) session.flush() - rval = self.encode_all_ids( trans, page.to_dict(), True) + rval = self.encode_all_ids( trans, page.to_dict(), True ) return rval - - return { "error" : error_str } + return { "error" : error_str } @web.expose_api def delete( self, trans, id, **kwd ): @@ -115,9 +112,9 @@ :param id: ID of page to be deleted :rtype: dict - :returns: Dictionary with 'success' or 'error' element to indicate the result of the request + :returns: Dictionary with 'success' or 'error' element to indicate the result of the request """ - page_id = id; + page_id = id try: page = trans.sa_session.query(self.app.model.Page).get(trans.security.decode_id(page_id)) except Exception, e: @@ -130,7 +127,7 @@ #Mark a workflow as deleted page.deleted = True trans.sa_session.flush() - return {"success" : "Deleted", "id" : page_id} + return { "success" : "Deleted", "id" : page_id } @web.expose_api def show( self, trans, id, **kwd ): @@ -146,6 +143,6 @@ """ page = trans.sa_session.query( trans.app.model.Page ).get( trans.security.decode_id( id ) ) self.security_check( trans, page, check_ownership=False, check_accessible=True) - rval = self.encode_all_ids( trans, page.to_dict(), True) + rval = self.encode_all_ids( trans, page.to_dict(), True ) rval['content'] = page.latest_revision.content - return rval \ No newline at end of file + return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Library_contents API: Fix permissions and dataset ref on LD delete
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43a964de0758/ Changeset: 43a964de0758 User: carlfeberhard Date: 2014-01-10 22:03:04 Summary: Library_contents API: Fix permissions and dataset ref on LD delete Affected #: 1 file diff -r ad9661041105bbffe4772ee9bedbcf174c53eac3 -r 43a964de0758ea9deffb88fd2c59441a13cae14b lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -324,8 +324,7 @@ """ delete( self, trans, library_id, id, **kwd ) * DELETE /api/libraries/{library_id}/contents/{id} - delete the HDA with the given ``id`` - + delete the LibraryDataset with the given ``id`` :type id: str :param id: the encoded id of the library dataset to delete @@ -333,7 +332,7 @@ :param kwd: (optional) dictionary structure containing: * payload: a dictionary itself containing: - * purge: if True, purge the HDA + * purge: if True, purge the LD :rtype: dict :returns: an error object if an error occurred or a dictionary containing: @@ -345,21 +344,34 @@ purge = False if kwd.get( 'payload', None ): purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) + rval = { 'id' : id } try: - hda = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) - hda.deleted = True + ld = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) + user_is_admin = trans.user_is_admin() + can_modify = trans.app.security_agent.can_modify_library_item( trans.user.all_roles(), ld ) + print 'is_admin: %s, can_modify: %s' % ( user_is_admin, can_modify ) + if not ( user_is_admin or can_modify ): + trans.response.status = 403 + rval.update({ 'error': 'Unauthorized to delete or purge this library dataset' }) + return rval + + ld.deleted = True if purge: - if not trans.app.config.allow_user_dataset_purge: - raise exceptions.httpexceptions.HTTPForbidden( - detail='This instance does not allow user dataset purging' ) - hda.purged = True - trans.sa_session.add( hda ) + ld.purged = True + trans.sa_session.add( ld ) trans.sa_session.flush() - if hda.dataset.user_can_purge: + + #TODO: had to change this up a bit from Dataset.user_can_purge + dataset = ld.library_dataset_dataset_association.dataset + no_history_assoc = len( dataset.history_associations ) == len( dataset.purged_history_associations ) + no_library_assoc = dataset.library_associations == [ ld.library_dataset_dataset_association ] + can_purge_dataset = not dataset.purged and no_history_assoc and no_library_assoc + + if can_purge_dataset: try: - hda.dataset.full_delete() - trans.sa_session.add( hda.dataset ) + ld.library_dataset_dataset_association.dataset.full_delete() + trans.sa_session.add( ld.dataset ) except: pass # flush now to preserve deleted state in case of later interruption @@ -367,8 +379,9 @@ rval[ 'purged' ] = True trans.sa_session.flush() rval[ 'deleted' ] = True + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: - log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + log.exception( 'Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', id, str( kwd ), str( http_server_err ) ) raise except exceptions.httpexceptions.HTTPException: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix tool shed functional test I just broke.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad9661041105/ Changeset: ad9661041105 User: greg Date: 2014-01-10 21:05:57 Summary: Fix tool shed functional test I just broke. Affected #: 1 file diff -r 5f6c670dca9f42d52480f66afeb91b63710e7ffb -r ad9661041105bbffe4772ee9bedbcf174c53eac3 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -349,6 +349,6 @@ break # Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured # unicode decoding error message. - strings_displayed = [ 'Changeset %d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:', + strings_displayed = [ '%d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:', '+These characters should not' ] - self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed ) \ No newline at end of file + self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed ) 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: inithello: Use class instead of substrings to identify integrated tool panel tools, sections, workflows, and section labels when saving and updating the panel.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f6c670dca9f/ Changeset: 5f6c670dca9f User: inithello Date: 2014-01-10 21:02:20 Summary: Use class instead of substrings to identify integrated tool panel tools, sections, workflows, and section labels when saving and updating the panel. Affected #: 2 files diff -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c -r 5f6c670dca9f42d52480f66afeb91b63710e7ffb lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -62,6 +62,7 @@ from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.model.item_attrs import Dictifiable +from galaxy.model import Workflow from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params @@ -142,13 +143,13 @@ # 1) adjusting init_tools() and called methods to get this right # 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml for key, value in self.integrated_tool_panel.iteritems(): - if key.startswith( 'section_' ): + if isinstance( value, ToolSection ): for section_key, section_value in value.elems.iteritems(): if section_value is None: - if section_key.startswith( 'tool_' ): + if isinstance( section_value, Tool ): tool_id = section_key[5:] value.elems[section_key] = self.tools_by_id.get( tool_id ) - elif section_key.startswith( 'workflow_' ): + elif isinstance( section_value, Workflow ): workflow_id = section_key[9:] value.elems[section_key] = self.workflows_by_id.get( workflow_id ) @@ -252,19 +253,19 @@ def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): - if key.startswith( 'tool_' ): + if isinstance( val, Tool ): tool_id = key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: self.__add_tool_to_tool_panel( tool_id, self.tool_panel, section=False ) - elif key.startswith( 'workflow_' ): + elif isinstance( val, Workflow ): workflow_id = key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: workflow = self.workflows_by_id[ workflow_id ] self.tool_panel[ key ] = workflow log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) - elif key.startswith( 'label_' ): + elif isinstance( val, ToolSectionLabel ): self.tool_panel[ key ] = val - elif key.startswith( 'section_' ): + elif isinstance( val, ToolSection ): elem = ElementTree.Element( 'section' ) elem.attrib[ 'id' ] = val.id or '' elem.attrib[ 'name' ] = val.name or '' @@ -276,13 +277,13 @@ tool_id = section_key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: self.__add_tool_to_tool_panel( tool_id, section, section=True ) - elif section_key.startswith( 'workflow_' ): + elif isinstance( section_val, Workflow ): workflow_id = section_key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: workflow = self.workflows_by_id[ workflow_id ] section.elems[ section_key ] = workflow log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) - elif section_key.startswith( 'label_' ): + elif isinstance( val, ToolSectionLabel ): if section_val: section.elems[ section_key ] = section_val log.debug( "Loaded label: %s" % ( section_val.text ) ) @@ -315,7 +316,7 @@ elif section_elem.tag == 'label': key = 'label_%s' % section_elem.get( 'id' ) section.elems[ key ] = None - key = 'section_%s' % elem.get( 'id' ) + key = elem.get( 'id' ) self.integrated_tool_panel[ key ] = section elif elem.tag == 'label': key = 'label_%s' % elem.get( 'id' ) @@ -331,28 +332,28 @@ os.write( fd, '<toolbox>\n' ) for key, item in self.integrated_tool_panel.items(): if item: - if key.startswith( 'tool_' ): + if isinstance( item, Tool ): os.write( fd, ' <tool id="%s" />\n' % item.id ) - elif key.startswith( 'workflow_' ): + elif isinstance( item, Workflow ): os.write( fd, ' <workflow id="%s" />\n' % item.id ) - elif key.startswith( 'label_' ): + elif isinstance( item, ToolSectionLabel ): label_id = item.id or '' label_text = item.text or '' label_version = item.version or '' os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) ) - elif key.startswith( 'section_' ): + elif isinstance( item, ToolSection ): section_id = item.id or '' section_name = item.name or '' section_version = item.version or '' os.write( fd, ' <section id="%s" name="%s" version="%s">\n' % ( section_id, section_name, section_version ) ) for section_key, section_item in item.elems.items(): - if section_key.startswith( 'tool_' ): + if isinstance( section_item, Tool ): if section_item: os.write( fd, ' <tool id="%s" />\n' % section_item.id ) - elif section_key.startswith( 'workflow_' ): + elif isinstance( section_item, Workflow ): if section_item: os.write( fd, ' <workflow id="%s" />\n' % section_item.id ) - elif section_key.startswith( 'label_' ): + elif isinstance( section_item, ToolSectionLabel ): if section_item: label_id = section_item.id or '' label_text = section_item.text or '' @@ -576,7 +577,7 @@ integrated_panel_dict.insert( index, key, label ) def load_section_tag_set( self, elem, tool_path, load_panel_dict, index=None ): - key = 'section_' + elem.get( "id" ) + key = elem.get( "id" ) if key in self.tool_panel: section = self.tool_panel[ key ] elems = section.elems @@ -1078,14 +1079,14 @@ def get_panel_section( self ): for key, item in self.app.toolbox.integrated_tool_panel.items(): if item: - if key.startswith( 'tool_' ): + if isinstance( item, Tool ): if item.id == self.id: return '', '' - if key.startswith( 'section_' ): + if isinstance( item, ToolSection ): section_id = item.id or '' section_name = item.name or '' for section_key, section_item in item.elems.items(): - if section_key.startswith( 'tool_' ): + if isinstance( section_item, Tool ): if section_item: if section_item.id == self.id: return section_id, section_name diff -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c -r 5f6c670dca9f42d52480f66afeb91b63710e7ffb lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -466,11 +466,7 @@ return sample_files, deleted_sample_files def get_or_create_tool_section( trans, tool_panel_section_id, new_tool_panel_section_label=None ): - if tool_panel_section_id.startswith( 'section_' ): - tool_panel_section_key = tool_panel_section_id - tool_panel_section_id.lstrip( 'section_' ) - else: - tool_panel_section_key = 'section_%s' % str( tool_panel_section_id ) + tool_panel_section_key = str( tool_panel_section_id ) if tool_panel_section_key in trans.app.toolbox.tool_panel: # Appending a tool to an existing section in trans.app.toolbox.tool_panel tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] @@ -680,16 +676,13 @@ # received tool_panel_section_id must be the id retrieved from a tool panel config (e.g., tool_conf.xml, which # may have getext). If new_tool_panel_section_label is received, a new section will be added to the tool panel. if new_tool_panel_section_label: - section_id = 'section_%s' % str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) + section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) tool_panel_section_key, tool_section = \ get_or_create_tool_section( trans, tool_panel_section_id=section_id, new_tool_panel_section_label=new_tool_panel_section_label ) elif tool_panel_section_id: - if tool_panel_section_id.startswith( 'section_' ): - tool_panel_section_key = str( tool_panel_section_id ) - else: - tool_panel_section_key = 'section_%s' % str( tool_panel_section_id ) + tool_panel_section_key = str( tool_panel_section_id ) tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] else: return None, None @@ -1000,7 +993,7 @@ for config_elem in config_elems: if config_elem.tag == 'section': # Get the section key for the in-memory tool panel. - section_key = 'section_%s' % str( config_elem.get( "id" ) ) + section_key = str( config_elem.get( "id" ) ) # Generate the list of tool elements to remove. tool_elems_to_remove = [] for tool_elem in config_elem: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Include the changeset revision date whenever displaying the changeset revision for a repository in the tool shed per request by Ross Lazarus.
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/afa0a32a883d/ Changeset: afa0a32a883d User: greg Date: 2014-01-10 20:30:18 Summary: Include the changeset revision date whenever displaying the changeset revision for a repository in the tool shed per request by Ross Lazarus. Affected #: 18 files diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2432,6 +2432,7 @@ message='Select a repository to rate', status='error' ) ) repository = suc.get_repository_in_tool_shed( trans, id ) + changeset_revision = repository.tip( trans.app ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', @@ -2447,12 +2448,14 @@ rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, - repository.tip( trans.app ), + changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, + revision_label=revision_label, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, @@ -2862,13 +2865,10 @@ has_metadata = True else: has_metadata = False - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[:6] ) - display_date = date.strftime( "%Y-%m-%d" ) change_dict = { 'ctx' : ctx, 'rev' : str( ctx.rev() ), 'date' : date, - 'display_date' : display_date, + 'display_date' : suc.get_readable_ctx_date( ctx ), 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), @@ -2923,16 +2923,18 @@ metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: + ctx_parent_date = suc.get_readable_ctx_date( ctx_parent ) ctx_parent_rev = ctx_parent.rev() if ctx_parent_rev < 0: prev = None else: - prev = "%s:%s" % ( ctx_parent_rev, ctx_parent ) + prev = "<b>%s:%s</b><i>(%s)</i>" % ( ctx_parent_rev, ctx_parent, ctx_parent_date ) else: prev = None if ctx_child: + ctx_child_date = suc.get_readable_ctx_date( ctx_child ) ctx_child_rev = ctx_child.rev() - next = "%s:%s" % ( ctx_child_rev, ctx_child ) + next = "<b>%s:%s</b><i>(%s)</i>" % ( ctx_child_rev, ctx_child, ctx_child_date ) else: next = None return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -19,48 +19,72 @@ class UserGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class UserLoginColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): return user.email + + class UserNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): if user.username: return user.username return 'not set' + + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.groups: return len( user.groups ) return 0 + + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.roles: return len( user.roles ) return 0 + + class ExternalColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.external: return 'yes' return 'no' + + class LastLoginColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.purged: return "purged" elif user.deleted: return "deleted" return "" + + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + title = "Users" model_class = model.User template='/admin/user/grid.mako' @@ -114,37 +138,56 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def get_current_item( self, trans, **kwargs ): return trans.user + class RoleGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): return role.name + + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): if role.description: return role.description return '' + + class TypeColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): return role.type + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.deleted: return "deleted" return "" + + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.groups: return len( role.groups ) return 0 + + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.users: return len( role.users ) return 0 + title = "Roles" model_class = model.Role template='/admin/dataset_security/role/grid.mako' @@ -205,29 +248,43 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def apply_query_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) + class GroupGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, group ): return group.name + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.deleted: return "deleted" return "" + + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.roles: return len( group.roles ) return 0 + + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.members: return len( group.members ) return 0 + title = "Groups" model_class = model.Group template='/admin/dataset_security/group/grid.mako' @@ -279,6 +336,7 @@ preserve_state = False use_paging = True + class ManageCategoryGrid( CategoryGrid ): columns = [ col for col in CategoryGrid.columns ] # Override the NameColumn to include an Edit link @@ -292,12 +350,17 @@ dict( controller='admin', action='manage_categories', operation='create' ) ) ] + class AdminRepositoryGrid( RepositoryGrid ): + + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): if repository.deleted: return 'yes' return '' + columns = [ RepositoryGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -326,27 +389,43 @@ async_compatible=False ) ) standard_filters = [] default_filter = {} + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .join( model.User.table ) + class RepositoryMetadataGrid( grids.Grid ): + + class IdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.id + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.name + + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.user.username + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) + return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision ) + + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): tools_str = '0' if repository_metadata: @@ -358,7 +437,10 @@ # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) return '%d' % len( metadata[ 'tools' ] ) return tools_str + + class DatatypesColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): datatypes_str = '0' if repository_metadata: @@ -370,7 +452,10 @@ # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] return '%d' % len( metadata[ 'datatypes' ] ) return datatypes_str + + class WorkflowsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): workflows_str = '0' if repository_metadata: @@ -387,21 +472,31 @@ # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] return '%d' % len( metadata[ 'workflows' ] ) return workflows_str + + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.repository.deleted: return 'yes' return '' + + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.repository.deprecated: return 'yes' return '' + + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.malicious: return 'yes' return '' + # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata @@ -440,6 +535,7 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.RepositoryMetadata ) \ .join( model.Repository.table ) diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -101,6 +101,10 @@ if len( select_field.options ) > 1: return select_field.get_html() elif len( select_field.options ) == 1: + option_items = select_field.options[ 0 ][ 0 ] + rev_label, rev_date = option_items.split( ' ' ) + rev_date = '<i><font color="#666666">%s</font></i>' % rev_date + return '%s %s' % ( rev_label, rev_date ) return select_field.options[ 0 ][ 0 ] return '' @@ -1134,7 +1138,7 @@ repository = repository_metadata.repository changeset_revision = repository_metadata.changeset_revision changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision ) - return escape_html( changeset_revision_label ) + return changeset_revision_label class MaliciousColumn( grids.BooleanColumn ): diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -83,9 +83,10 @@ if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + rev, label, changeset_revision = \ + metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -16,7 +16,8 @@ select_field.add_option( option_tup[ 0 ], option_tup[ 1 ], selected=selected ) return select_field -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False ): +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, + downloadable=False, reviewed=False, not_reviewed=False ): """Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository.""" options = [] changeset_tups = [] @@ -46,7 +47,10 @@ # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) + rev, label, changeset_revision = \ + metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1108,16 +1108,19 @@ changeset_revision = repository_metadata.changeset_revision ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) if ctx: + changeset_revision_date = suc.get_readable_ctx_date( ctx ) rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) else: rev = '-1' label = "-1:%s" % changeset_revision return rev, label, changeset_revision -def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): +def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, + resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: - # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. + # Keep track of the location where the repository is temporarily cloned so that we can strip + # it when setting metadata. work_dir = repository_files_dir sample_file_metadata_paths = [] sample_file_copy_paths = [] diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -924,6 +924,13 @@ return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) +def get_readable_ctx_date( ctx ): + """Convert the date of the changeset (the received ctx) to a human-readable date.""" + t, tz = ctx.date() + date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) + ctx_date = date.strftime( "%Y-%m-%d" ) + return ctx_date + def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: @@ -1206,7 +1213,8 @@ repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: - return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + return '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) else: return "-1:%s" % changeset_revision @@ -1215,7 +1223,8 @@ ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + label = '%s:%s <i><font color="#666666">(%s)</font></i>' % \ + ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) else: rev = '-1' label = "-1:%s" % changeset_revision @@ -1477,9 +1486,6 @@ email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0] tip_changeset = repo.changelog.tip() ctx = repo.changectx( tip_changeset ) - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[:6] ) - display_date = date.strftime( "%Y-%m-%d" ) try: username = ctx.user().split()[0] except: @@ -1490,6 +1496,7 @@ template = new_repo_email_alert_template else: template = email_alert_template + display_date = get_readable_ctx_date( ctx ) admin_body = string.Template( template ).safe_substitute( host=trans.request.host, sharable_link=sharable_link, repository_name=repository.name, diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -174,7 +174,9 @@ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a> + %if changeset_revision is not None: + <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a> + %endif <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -181,9 +181,9 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label | h}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: - ${revision_label | h} + ${revision_label} %endif </div><div class="form-row"> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako --- a/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako @@ -51,7 +51,7 @@ %else: <div class="form-row"><label>Revision:</label> - ${revision_label | h} + ${revision_label} </div> %endif </div> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/rate_repository.mako --- a/templates/webapps/tool_shed/repository/rate_repository.mako +++ b/templates/webapps/tool_shed/repository/rate_repository.mako @@ -44,16 +44,20 @@ ${render_clone_str( repository )} </div> %endif - ${render_repository_type_select_field( repository_type_select_field, render_help=False )} <div class="toolFormBody"><div class="form-row"> + <label>Type:</label> + ${repository.type | h} + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Description:</label> ${repository.description | h} <div style="clear: both"></div></div><div class="form-row"> - <label>Version:</label> - ${repository.revision( trans.app ) | h} + <label>Revision:</label> + ${revision_label} <div style="clear: both"></div></div><div class="form-row"> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/view_changelog.mako --- a/templates/webapps/tool_shed/repository/view_changelog.mako +++ b/templates/webapps/tool_shed/repository/view_changelog.mako @@ -5,7 +5,6 @@ <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /><% - from galaxy.web.framework.helpers import time_ago is_new = repository.is_new( trans.app ) can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_download = not is_new and ( not is_malicious or can_push ) @@ -108,7 +107,7 @@ </div><div class="form-row"><label>Pushed:</label> - ${time_ago( changeset[ 'date' ] )} + ${changeset[ 'display_date' ]} </div></td></tr> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/view_changeset.mako --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -49,13 +49,15 @@ %endif <div class="toolForm"><% + from tool_shed.util.shed_util_common import get_readable_ctx_date + changeset_revision_date = get_readable_ctx_date( ctx ) if can_download: - title_str = 'Changeset %s:%s' % ( ctx.rev(), ctx ) + title_str = 'Changeset <b>%s:%s</b><i>(%s)</i>' % ( ctx.rev(), ctx, changeset_revision_date ) else: - title_str = '%s changeset %s:%s' % ( repository.name, ctx.rev(), ctx ) + title_str = '%s changeset <b>%s:%s</b><i>(%s)</i>' % ( repository.name, ctx.rev(), ctx, changeset_revision_date ) %><div class="toolFormTitle"> - ${title_str | h} + ${title_str} </div><div class="toolFormBody"><table class="grid"> @@ -63,10 +65,10 @@ <tr><td> %if prev: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_parent )}">Previous changeset ${prev | h}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_parent )}">Previous changeset ${prev}</a> %endif %if next: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_child )}">Next changeset ${next | h}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_child )}">Next changeset ${next}</a> %endif </td></tr> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -100,7 +100,11 @@ ${repository.name | h} %endif </div> - ${render_repository_type_select_field( repository_type_select_field, render_help=False )} + <div class="form-row"> + <label>Type:</label> + ${repository.type | h} + <div style="clear: both"></div> + </div><div class="form-row"><label>Synopsis:</label> ${repository.description | h} @@ -113,7 +117,7 @@ %if can_view_change_log: <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: - ${revision_label | h} + ${revision_label} %endif </div><div class="form-row"> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository_review/browse_review.mako --- a/templates/webapps/tool_shed/repository_review/browse_review.mako +++ b/templates/webapps/tool_shed/repository_review/browse_review.mako @@ -34,7 +34,7 @@ </div><div class="form-row"><label>Repository revision:</label> - <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=review.changeset_revision )}">${changeset_revision_label | h}</a> + <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=review.changeset_revision )}">${changeset_revision_label}</a><div style="clear: both"></div></div><div class="form-row"> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako --- a/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako +++ b/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako @@ -45,7 +45,7 @@ <div class="toolFormBody"><div class="form-row"><label>Revision:</label> - <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label | h}</a> + <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label}</a><div style="clear: both"></div></div><div class="form-row"> diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository_review/reviews_of_repository.mako --- a/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako +++ b/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako @@ -67,7 +67,7 @@ <tr><td><div style="float:left;" class="menubutton split popup" id="${changeset_revision}-popup"> - <a class="view-info" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label | h}</a> + <a class="view-info" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label}</a></div><div popupmenu="${changeset_revision}-popup"> %if repository_reviews: diff -r c8d2e455f0e865662028d831d20a83316f2ab33f -r afa0a32a883dde3dee88e8cfeb2f84ba16b27f1c templates/webapps/tool_shed/repository_review/select_previous_review.mako --- a/templates/webapps/tool_shed/repository_review/select_previous_review.mako +++ b/templates/webapps/tool_shed/repository_review/select_previous_review.mako @@ -30,7 +30,7 @@ %endif <div class="warningmessage"> - You have elected to create a new review for revision <b>${changeset_revision_label | h}</b>of this repository. Since previous revisions have been reviewed, + You have elected to create a new review for revision <b>${changeset_revision_label}</b>of this repository. Since previous revisions have been reviewed, you can select a previous review to copy to your new review, or click the <b>Create a review without copying</b> button. </div> @@ -39,7 +39,7 @@ <div class="toolFormBody"><div class="form-row"><label>Revision for new review:</label> - <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label | h}</a> + <a class="action-button" href="${h.url_for( controller='repository_review', action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">${changeset_revision_label}</a><div style="clear: both"></div></div><div class="form-row"> @@ -76,7 +76,7 @@ <a class="action-button" href="${h.url_for( controller='repository_review', action='create_review', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, previous_review_id=encoded_review_id )}">Copy this review</a></div></td> - <td>${previous_changeset_revision_label | h}</td> + <td>${previous_changeset_revision_label}</td><td>${render_star_rating( repository_rating_name, review.rating, disabled=True )}</td><td>${approved_str | h}</td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Temporarily add simplejson back until webhelpers is updated
by commits-noreply＠bitbucket.org 10 Jan '14

10 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8d2e455f0e8/ Changeset: c8d2e455f0e8 User: dannon Date: 2014-01-10 20:22:03 Summary: Temporarily add simplejson back until webhelpers is updated Affected #: 1 file diff -r d7b4edc2d749d9835f61dccaab0e17614a9cd336 -r c8d2e455f0e865662028d831d20a83316f2ab33f eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,6 +26,7 @@ pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static +simplejson = 2.1.1 threadframe = 0.2 guppy = 0.1.8 SQLAlchemy = 0.7.9 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 10 Jan '14

10 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7a411112a661/ Changeset: 7a411112a661 User: takadonet Date: 2013-11-08 16:38:08 Summary: added API call to delete library dataset Affected #: 1 file diff -r b9e7d751cfb5a263d778786efa4e4b4e965b3992 -r 7a411112a66155050c748c667c47cf7f6dd24d7e lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -2,8 +2,7 @@ API operations on the contents of a library. """ import logging - -from galaxy import web +from galaxy import web , exceptions from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin @@ -318,3 +317,67 @@ return 'LibraryFolder', content_id[1:] else: raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) + + + @web.expose_api + def delete( self, trans, library_id, id, **kwd ): + """ + delete( self, trans, library_id, id, **kwd ) + * DELETE /api/libraries/{library_id}/contents/{id} + delete the HDA with the given ``id`` + + + :type id: str + :param id: the encoded id of the library dataset to delete + :type kwd: dict + :param kwd: (optional) dictionary structure containing: + + * payload: a dictionary itself containing: + * purge: if True, purge the HDA + + :rtype: dict + :returns: an error object if an error occurred or a dictionary containing: + * id: the encoded id of the library dataset, + * deleted: if the library dataset was marked as deleted, + * purged: if the library dataset was purged + """ + # a request body is optional here + purge = False + if kwd.get( 'payload', None ): + purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) + rval = { 'id' : id } + try: + hda = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) + hda.deleted = True + if purge: + if not trans.app.config.allow_user_dataset_purge: + raise exceptions.httpexceptions.HTTPForbidden( + detail='This instance does not allow user dataset purging' ) + hda.purged = True + trans.sa_session.add( hda ) + trans.sa_session.flush() + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + pass + # flush now to preserve deleted state in case of later interruption + trans.sa_session.flush() + rval[ 'purged' ] = True + trans.sa_session.flush() + rval[ 'deleted' ] = True + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: + log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + id, str( kwd ), str( http_server_err ) ) + raise + except exceptions.httpexceptions.HTTPException: + raise + except Exception, exc: + log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s', + id, str( kwd ), str( exc ) ) + trans.response.status = 500 + rval.update({ 'error': str( exc ) }) + return rval + + https://bitbucket.org/galaxy/galaxy-central/commits/69669b88ac78/ Changeset: 69669b88ac78 User: takadonet Date: 2013-11-08 16:38:37 Summary: Merged galaxy/galaxy-central into default Affected #: 1 file diff -r 7a411112a66155050c748c667c47cf7f6dd24d7e -r 69669b88ac784f8db470772f15bb17e13c314fa7 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -174,8 +174,12 @@ def to_dict( self, trans, view='collection', value_mapper=None ): """ to_dict tool parameter. This can be overridden by subclasses. """ tool_dict = super( ToolParameter, self ).to_dict() - #TODO: removing html as it causes a lot of errors on subclasses - needs histories, etc. - #tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + #TODO: wrapping html as it causes a lot of errors on subclasses - needs histories, etc. + try: + tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + except AssertionError, e: + pass #HACK for assert trans.history, 'requires a history' + tool_dict[ 'model_class' ] = self.__class__.__name__ if hasattr( self, 'value' ): tool_dict[ 'value' ] = self.value https://bitbucket.org/galaxy/galaxy-central/commits/d7b4edc2d749/ Changeset: d7b4edc2d749 User: carlfeberhard Date: 2014-01-10 19:59:58 Summary: Merged in takadonet/galaxy-central-takadonet (pull request #253) Add API call to allow for deletion/purge of dataset in a data library Affected #: 1 file diff -r c04e79918595e0cefe85edac156ff5a962f4a686 -r d7b4edc2d749d9835f61dccaab0e17614a9cd336 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -2,8 +2,7 @@ API operations on the contents of a library. """ import logging - -from galaxy import web +from galaxy import web , exceptions from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin @@ -318,3 +317,67 @@ return 'LibraryFolder', content_id[1:] else: raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) + + + @web.expose_api + def delete( self, trans, library_id, id, **kwd ): + """ + delete( self, trans, library_id, id, **kwd ) + * DELETE /api/libraries/{library_id}/contents/{id} + delete the HDA with the given ``id`` + + + :type id: str + :param id: the encoded id of the library dataset to delete + :type kwd: dict + :param kwd: (optional) dictionary structure containing: + + * payload: a dictionary itself containing: + * purge: if True, purge the HDA + + :rtype: dict + :returns: an error object if an error occurred or a dictionary containing: + * id: the encoded id of the library dataset, + * deleted: if the library dataset was marked as deleted, + * purged: if the library dataset was purged + """ + # a request body is optional here + purge = False + if kwd.get( 'payload', None ): + purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) ) + rval = { 'id' : id } + try: + hda = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True ) + hda.deleted = True + if purge: + if not trans.app.config.allow_user_dataset_purge: + raise exceptions.httpexceptions.HTTPForbidden( + detail='This instance does not allow user dataset purging' ) + hda.purged = True + trans.sa_session.add( hda ) + trans.sa_session.flush() + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + pass + # flush now to preserve deleted state in case of later interruption + trans.sa_session.flush() + rval[ 'purged' ] = True + trans.sa_session.flush() + rval[ 'deleted' ] = True + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: + log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', + id, str( kwd ), str( http_server_err ) ) + raise + except exceptions.httpexceptions.HTTPException: + raise + except Exception, exc: + log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s', + id, str( kwd ), str( exc ) ) + trans.response.status = 500 + rval.update({ 'error': str( exc ) }) + return rval + + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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