[2] | 1 | import sys |
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| 2 | from galaxy import model, util |
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| 3 | from galaxy.web.base.controller import * |
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| 4 | from galaxy.web.framework.helpers import time_ago, iff, grids |
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| 5 | from galaxy.model.orm import * |
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| 6 | # Older py compatibility |
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| 7 | try: |
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| 8 | set() |
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| 9 | except: |
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| 10 | from sets import Set as set |
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| 11 | |
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| 12 | import logging |
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| 13 | log = logging.getLogger( __name__ ) |
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| 14 | |
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| 15 | class LibraryListGrid( grids.Grid ): |
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| 16 | class NameColumn( grids.TextColumn ): |
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| 17 | def get_value( self, trans, grid, library ): |
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| 18 | return library.name |
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| 19 | class DescriptionColumn( grids.TextColumn ): |
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| 20 | def get_value( self, trans, grid, library ): |
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| 21 | if library.description: |
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| 22 | return library.description |
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| 23 | return '' |
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| 24 | class StatusColumn( grids.GridColumn ): |
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| 25 | def get_value( self, trans, grid, library ): |
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| 26 | if library.purged: |
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| 27 | return "purged" |
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| 28 | elif library.deleted: |
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| 29 | return "deleted" |
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| 30 | return "" |
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| 31 | # Grid definition |
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| 32 | title = "Data Libraries" |
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| 33 | model_class = model.Library |
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| 34 | template='/admin/library/grid.mako' |
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| 35 | default_sort_key = "name" |
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| 36 | columns = [ |
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| 37 | NameColumn( "Name", |
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| 38 | key="name", |
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| 39 | model_class=model.Library, |
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| 40 | link=( lambda library: dict( operation="browse", id=library.id ) ), |
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| 41 | attach_popup=False, |
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| 42 | filterable="advanced" ), |
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| 43 | DescriptionColumn( "Description", |
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| 44 | key="description", |
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| 45 | model_class=model.Library, |
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| 46 | attach_popup=False, |
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| 47 | filterable="advanced" ), |
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| 48 | grids.GridColumn( "Created", key="create_time", format=time_ago ), |
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| 49 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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| 50 | StatusColumn( "Status", attach_popup=False ), |
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| 51 | # Columns that are valid for filtering but are not visible. |
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| 52 | grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) |
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| 53 | ] |
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| 54 | columns.append( grids.MulticolFilterColumn( "Search", |
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| 55 | cols_to_filter=[ columns[0], columns[1] ], |
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| 56 | key="free-text-search", |
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| 57 | visible=False, |
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| 58 | filterable="standard" ) ) |
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| 59 | global_actions = [ |
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| 60 | grids.GridAction( "Create new data library", dict( controller='library_admin', action='create_library' ) ) |
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| 61 | ] |
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| 62 | standard_filters = [ |
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| 63 | grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), |
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| 64 | grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), |
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| 65 | grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), |
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| 66 | grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) |
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| 67 | ] |
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| 68 | default_filter = dict( name="All", description="All", deleted="False", purged="False" ) |
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| 69 | num_rows_per_page = 50 |
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| 70 | preserve_state = False |
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| 71 | use_paging = True |
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| 72 | |
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| 73 | class LibraryAdmin( BaseController ): |
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| 74 | |
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| 75 | library_list_grid = LibraryListGrid() |
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| 76 | |
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| 77 | @web.expose |
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| 78 | @web.require_admin |
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| 79 | def browse_libraries( self, trans, **kwd ): |
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| 80 | if 'operation' in kwd: |
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| 81 | operation = kwd['operation'].lower() |
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| 82 | if operation == "browse": |
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| 83 | return trans.response.send_redirect( web.url_for( controller='library_common', |
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| 84 | action='browse_library', |
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| 85 | cntrller='library_admin', |
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| 86 | **kwd ) ) |
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| 87 | # Render the list view |
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| 88 | return self.library_list_grid( trans, **kwd ) |
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| 89 | @web.expose |
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| 90 | @web.require_admin |
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| 91 | def create_library( self, trans, **kwd ): |
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| 92 | params = util.Params( kwd ) |
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| 93 | message = util.restore_text( params.get( 'message', '' ) ) |
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| 94 | status = params.get( 'status', 'done' ) |
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| 95 | if params.get( 'create_library_button', False ): |
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| 96 | name = util.restore_text( params.get( 'name', 'No name' ) ) |
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| 97 | description = util.restore_text( params.get( 'description', '' ) ) |
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| 98 | synopsis = util.restore_text( params.get( 'synopsis', '' ) ) |
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| 99 | if synopsis in [ 'None', None ]: |
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| 100 | synopsis = '' |
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| 101 | library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) |
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| 102 | root_folder = trans.app.model.LibraryFolder( name=name, description='' ) |
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| 103 | library.root_folder = root_folder |
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| 104 | trans.sa_session.add_all( ( library, root_folder ) ) |
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| 105 | trans.sa_session.flush() |
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| 106 | message = "The new library named '%s' has been created" % library.name |
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| 107 | return trans.response.send_redirect( web.url_for( controller='library_common', |
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| 108 | action='browse_library', |
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| 109 | cntrller='library_admin', |
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| 110 | id=trans.security.encode_id( library.id ), |
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| 111 | message=util.sanitize_text( message ), |
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| 112 | status='done' ) ) |
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| 113 | return trans.fill_template( '/admin/library/new_library.mako', message=message, status=status ) |
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| 114 | @web.expose |
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| 115 | @web.require_admin |
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| 116 | def purge_library( self, trans, **kwd ): |
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| 117 | # TODO: change this function to purge_library_item, behaving similar to delete_library_item |
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| 118 | # assuming we want the ability to purge libraries. |
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| 119 | # This function is currently only used by the functional tests. |
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| 120 | params = util.Params( kwd ) |
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| 121 | library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( params.id ) ) |
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| 122 | def purge_folder( library_folder ): |
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| 123 | for lf in library_folder.folders: |
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| 124 | purge_folder( lf ) |
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| 125 | trans.sa_session.refresh( library_folder ) |
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| 126 | for library_dataset in library_folder.datasets: |
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| 127 | trans.sa_session.refresh( library_dataset ) |
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| 128 | ldda = library_dataset.library_dataset_dataset_association |
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| 129 | if ldda: |
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| 130 | trans.sa_session.refresh( ldda ) |
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| 131 | dataset = ldda.dataset |
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| 132 | trans.sa_session.refresh( dataset ) |
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| 133 | # If the dataset is not associated with any additional undeleted folders, then we can delete it. |
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| 134 | # We don't set dataset.purged to True here because the cleanup_datasets script will do that for |
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| 135 | # us, as well as removing the file from disk. |
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| 136 | #if not dataset.deleted and len( dataset.active_library_associations ) <= 1: # This is our current ldda |
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| 137 | dataset.deleted = True |
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| 138 | ldda.deleted = True |
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| 139 | trans.sa_session.add_all( ( dataset, ldda ) ) |
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| 140 | library_dataset.deleted = True |
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| 141 | trans.sa_session.add( library_dataset ) |
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| 142 | library_folder.deleted = True |
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| 143 | library_folder.purged = True |
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| 144 | trans.sa_session.add( library_folder ) |
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| 145 | trans.sa_session.flush() |
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| 146 | if not library.deleted: |
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| 147 | message = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) |
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| 148 | return trans.response.send_redirect( web.url_for( controller='library_admin', |
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| 149 | action='browse_libraries', |
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| 150 | message=util.sanitize_text( message ), |
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| 151 | status='error' ) ) |
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| 152 | else: |
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| 153 | purge_folder( library.root_folder ) |
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| 154 | library.purged = True |
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| 155 | trans.sa_session.add( library ) |
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| 156 | trans.sa_session.flush() |
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| 157 | message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name |
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| 158 | return trans.response.send_redirect( web.url_for( controller='library_admin', |
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| 159 | action='browse_libraries', |
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| 160 | message=util.sanitize_text( message ), |
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| 161 | status='done' ) ) |
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