diff --git a/lib/galaxy/web/controllers/library.py b/lib/galaxy/web/controllers/library.py index 50d3e2863e2..93a9ef9a320 100644 --- a/lib/galaxy/web/controllers/library.py +++ b/lib/galaxy/web/controllers/library.py @@ -6,7 +6,7 @@ from galaxy.model.orm import * from galaxy.datatypes import sniff from galaxy import model, util from galaxy.util.odict import odict -from library_common import lucene_search, whoosh_search +from library_common import get_comptypes, lucene_search, whoosh_search log = logging.getLogger( __name__ ) @@ -25,17 +25,17 @@ class LibraryListGrid( grids.Grid ): template='/library/grid.mako' default_sort_key = "name" columns = [ - NameColumn( "Name", + NameColumn( "Data library name", key="name", link=( lambda library: dict( operation="browse", id=library.id ) ), attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", + DescriptionColumn( "Data library description", key="description", attach_popup=False, filterable="advanced" ), ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "search library dataset name, info, message, dbkey", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, @@ -74,8 +74,9 @@ class Library( BaseController ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + default_action = params.get( 'default_action', None ) return trans.fill_template( "/library/index.mako", - default_action=params.get( 'default_action', None ), + default_action=default_action, message=message, status=status ) @web.expose @@ -91,8 +92,9 @@ class Library( BaseController ): search_term = kwd[ "f-free-text-search" ] if trans.app.config.enable_lucene_library_search: indexed_search_enabled = True - search_url = trans.app.config.config_dict.get( "fulltext_find_url", "" ) + search_url = trans.app.config.config_dict.get( "fulltext_url", "" ) if search_url: + indexed_search_enabled = True status, message, lddas = lucene_search( trans, 'library', search_term, search_url, **kwd ) elif trans.app.config.enable_whoosh_library_search: indexed_search_enabled = True @@ -100,11 +102,15 @@ class Library( BaseController ): else: indexed_search_enabled = False if indexed_search_enabled: + comptypes = get_comptypes( trans ) + show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) return trans.fill_template( '/library/common/library_dataset_search_results.mako', cntrller='library', search_term=search_term, + comptypes=comptypes, lddas=lddas, + show_deleted=show_deleted, use_panels=use_panels, message=message, status=status ) diff --git a/lib/galaxy/web/controllers/library_admin.py b/lib/galaxy/web/controllers/library_admin.py index 3daab155771..8012c12e796 100644 --- a/lib/galaxy/web/controllers/library_admin.py +++ b/lib/galaxy/web/controllers/library_admin.py @@ -3,7 +3,7 @@ from galaxy import model, util from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * -from library_common import lucene_search, whoosh_search +from library_common import get_comptypes, lucene_search, whoosh_search # Older py compatibility try: set() @@ -35,12 +35,12 @@ class LibraryListGrid( grids.Grid ): template='/admin/library/grid.mako' default_sort_key = "name" columns = [ - NameColumn( "Name", + NameColumn( "Data library name", key="name", link=( lambda library: dict( operation="browse", id=library.id ) ), attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", + DescriptionColumn( "Data library description", key="description", attach_popup=False, filterable="advanced" ), @@ -50,7 +50,7 @@ class LibraryListGrid( grids.Grid ): # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "search library dataset name, info, message, dbkey", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, @@ -133,11 +133,15 @@ class LibraryAdmin( BaseController ): else: indexed_search_enabled = False if indexed_search_enabled: + comptypes = get_comptypes( trans ) + show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) return trans.fill_template( '/library/common/library_dataset_search_results.mako', cntrller='library_admin', search_term=search_term, + comptypes=comptypes, lddas=lddas, + show_deleted=show_deleted, use_panels=use_panels, message=message, status=status ) diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py index 7469fa73eab..211241a5900 100644 --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1,4 +1,4 @@ -import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob, string +import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob, string, urllib2 from galaxy.web.base.controller import * from galaxy import util, jobs from galaxy.datatypes import sniff @@ -7,6 +7,7 @@ from galaxy.util.json import to_json_string from galaxy.tools.actions import upload_common from galaxy.model.orm import * from galaxy.util.streamball import StreamBall +from galaxy.util import inflector from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField import logging, tempfile, zipfile, tarfile, os, sys, operator from galaxy.eggs import require @@ -20,7 +21,7 @@ try: whoosh_search_enabled = True # The following must be defined exactly like the # schema in ~/scripts/data_libraries/build_whoosh_index.py - schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT, state=TEXT ) + schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT ) except ImportError, e: whoosh_search_enabled = False schema = None @@ -125,16 +126,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the " message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." status = "info" - comptypes_t = comptypes - if trans.app.config.nginx_x_archive_files_base: - comptypes_t = ['ngxzip'] - for comptype in trans.app.config.disable_library_comptypes: - # TODO: do this once, not every time (we're gonna raise an - # exception every time after the first time) - try: - comptypes_t.remove( comptype ) - except: - pass + comptypes = get_comptypes( trans ) try: return trans.fill_template( '/library/common/browse_library.mako', cntrller=cntrller, @@ -143,17 +135,18 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): created_ldda_ids=created_ldda_ids, hidden_folder_ids=hidden_folder_ids, show_deleted=show_deleted, - comptypes=comptypes_t, + comptypes=comptypes, current_user_roles=current_user_roles, message=message, status=status ) except Exception, e: message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) ) status = 'error' + default_action = params.get( 'default_action', None ) return trans.response.send_redirect( web.url_for( use_panels=use_panels, controller=cntrller, action='browse_libraries', - default_action=params.get( 'default_action', None ), + default_action=default_action, message=util.sanitize_text( message ), status=status ) ) @web.expose @@ -871,7 +864,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: - default_action = 'add' + default_action = 'import_to_histories' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1247,7 +1240,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: - default_action = 'add' + default_action = 'import_to_histories' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1512,7 +1505,12 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): message=util.sanitize_text( message ), status=status ) ) @web.expose - def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ): + def act_on_multiple_datasets( self, trans, cntrller, library_id=None, ldda_ids='', **kwd ): + # This method is called from 1 of 3 places: + # - this controller's download_dataset_from_folder() method + # - he browse_library.mako template + # - the library_dataset_search_results.mako template + # In the last case above, we will not have a library_id class NgxZip( object ): def __init__( self, url_base ): self.files = {} @@ -1534,6 +1532,16 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) action = params.get( 'do_action', None ) + if action == 'import_to_histories': + return trans.response.send_redirect( web.url_for( controller='library_common', + action='import_datasets_to_histories', + cntrller=cntrller, + library_id=library_id, + ldda_ids=ldda_ids, + use_panels=use_panels, + show_deleted=show_deleted, + message=message, + status=status ) ) lddas = [] error = False is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -1557,27 +1565,177 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): message = "Invalid library dataset id ( %s ) specified." % str( ldda_id ) break lddas.append( ldda ) - if action == 'import_to_history' or action == 'add': - if trans.get_history() is None: - # Must be a bot sending a request without having a history. - error = True - message = "You do not have a current history" - elif action == 'manage_permissions': - if not is_admin: + if not is_admin: + if action == 'manage_permissions': for ldda in lddas: if not ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \ trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ): error = True message = "You are not authorized to manage permissions on library dataset '%s'." % ldda.name break - elif action == 'delete': - if not is_admin: + elif action == 'delete': for ldda in lddas: if not trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): error = True message = "You are not authorized to modify library dataset '%s'." % ldda.name break - if error: + if not error: + if action == 'manage_permissions': + trans.response.send_redirect( web.url_for( controller='library_common', + action='ldda_permissions', + cntrller=cntrller, + use_panels=use_panels, + library_id=library_id, + folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ), + id=",".join( ldda_ids ), + show_deleted=show_deleted, + message=util.sanitize_text( message ), + status=status ) ) + elif action == 'delete': + for ldda in lddas: + # Do not delete the association, just delete the library_dataset. The + # cleanup_datasets.py script handles everything else. + ld = ldda.library_dataset + ld.deleted = True + trans.sa_session.add( ld ) + trans.sa_session.flush() + message = "The selected datasets have been deleted." + elif action in ['zip','tgz','tbz','ngxzip']: + error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if action == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + tmpf = os.path.join( tmpd, 'library_download.' + action ) + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif action == 'tgz': + if trans.app.config.upstream_gzip: + archive = util.streamball.StreamBall( 'w|' ) + outext = 'tar' + else: + archive = util.streamball.StreamBall( 'w|gz' ) + outext = 'tgz' + elif action == 'tbz': + archive = util.streamball.StreamBall( 'w|bz2' ) + outext = 'tbz2' + elif action == 'ngxzip': + archive = NgxZip( trans.app.config.nginx_x_archive_files_base ) + except ( OSError, zipfile.BadZipfile ): + error = True + log.exception( "Unable to create archive for download" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' + if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + continue + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: + # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + else: # simple case + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + error = True + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + if library_id: + lname = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ).name + else: + # Request must have coe from the library_dataset_search_results page. + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if action == 'zip': + archive.close() + tmpfh = open( tmpf ) + # clean up now + try: + os.unlink( tmpf ) + os.rmdir( tmpd ) + except OSError: + error = True + log.exception( "Unable to remove temporary library download archive and directory" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + trans.response.set_content_type( "application/x-zip-compressed" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) + return tmpfh + elif action == 'ngxzip': + trans.response.set_content_type( "application/zip" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) + trans.response.headers[ "X-Archive-Files" ] = "zip" + return archive + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + else: + status = 'error' + message = 'Invalid action ( %s ) specified.' % action + if library_id: + # If we have a library_id, browse the associated library return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1585,181 +1743,129 @@ class LibraryCommon( BaseController, UsesFormDefinitions ): id=library_id, show_deleted=show_deleted, message=util.sanitize_text( message ), - status='error' ) ) - if action == 'import_to_history' or action == 'add': - history = trans.get_history() - total_imported_lddas = 0 - message = '' - status = 'done' - for ldda in lddas: - if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - message += "Cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) - status = 'error' - elif ldda.dataset.state in [ 'ok', 'error' ]: - hda = ldda.to_history_dataset_association( target_history=history, add_to_history=True ) - total_imported_lddas += 1 - if total_imported_lddas: - trans.sa_session.add( history ) - trans.sa_session.flush() - message += "%i dataset(s) have been imported into your history. " % total_imported_lddas - elif action == 'manage_permissions': - trans.response.send_redirect( web.url_for( controller='library_common', - action='ldda_permissions', - cntrller=cntrller, - use_panels=use_panels, - library_id=library_id, - folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ), - id=",".join( ldda_ids ), - show_deleted=show_deleted, - message=util.sanitize_text( message ), - status=status ) ) - elif action == 'delete': - for ldda in lddas: - # Do not delete the association, just delete the library_dataset. The - # cleanup_datasets.py script handles everything else. - ld = ldda.library_dataset - ld.deleted = True - trans.sa_session.add( ld ) - trans.sa_session.flush() - message = "The selected datasets have been removed from this data library" - elif action in ['zip','tgz','tbz','ngxzip']: - error = False - killme = string.punctuation + string.whitespace - trantab = string.maketrans(killme,'_'*len(killme)) - try: - outext = 'zip' - if action == 'zip': - # Can't use mkstemp - the file must not exist first - tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + action ) - if ziptype == '64' and trans.app.config.upstream_gzip: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) - elif ziptype == '64': - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) - elif trans.app.config.upstream_gzip: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) - else: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) - archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) - elif action == 'tgz': - if trans.app.config.upstream_gzip: - archive = util.streamball.StreamBall( 'w|' ) - outext = 'tar' - else: - archive = util.streamball.StreamBall( 'w|gz' ) - outext = 'tgz' - elif action == 'tbz': - archive = util.streamball.StreamBall( 'w|bz2' ) - outext = 'tbz2' - elif action == 'ngxzip': - archive = NgxZip( trans.app.config.nginx_x_archive_files_base ) - except (OSError, zipfile.BadZipfile): - error = True - log.exception( "Unable to create archive for download" ) - message = "Unable to create archive for download, please report this error" - status = 'error' - except: - error = True - log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0]) - message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - status = 'error' - if not error: - composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) - seen = [] - for ldda in lddas: - if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - continue - ext = ldda.extension - is_composite = ext in composite_extensions - path = "" - parent_folder = ldda.library_dataset.folder - while parent_folder is not None: - # Exclude the now-hidden "root folder" - if parent_folder.parent is None: - path = os.path.join( parent_folder.library_root[0].name, path ) - break - path = os.path.join( parent_folder.name, path ) - parent_folder = parent_folder.parent - path += ldda.name - while path in seen: - path += '_' - seen.append( path ) - zpath = os.path.split(path)[-1] # comes as base_name/fname - outfname,zpathext = os.path.splitext(zpath) - if is_composite: - # need to add all the components from the extra_files_path to the zip - if zpathext == '': - zpath = '%s.html' % zpath # fake the real nature of the html file - try: - archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set - except IOError: - error = True - log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) - message = "Unable to create archive for download, please report this error" - status = 'error' - continue - flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths - for fpath in flist: - efp,fname = os.path.split(fpath) - if fname > '': - fname = fname.translate(trantab) - try: - archive.add( fpath,fname ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) - message = "Unable to create archive for download, please report this error" - status = 'error' - continue - else: # simple case - try: - archive.add( ldda.dataset.file_name, path ) - except IOError: - error = True - log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) - message = "Unable to create archive for download, please report this error" - status = 'error' - if not error: - lname = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ).name - fname = lname.replace( ' ', '_' ) + '_files' - if action == 'zip': - archive.close() - tmpfh = open( tmpf ) - # clean up now - try: - os.unlink( tmpf ) - os.rmdir( tmpd ) - except OSError: - error = True - log.exception( "Unable to remove temporary library download archive and directory" ) - message = "Unable to create archive for download, please report this error" - status = 'error' - if not error: - trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) - return tmpfh - elif action == 'ngxzip': - trans.response.set_content_type( "application/zip" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) - trans.response.headers[ "X-Archive-Files" ] = "zip" - return archive - else: - trans.response.set_content_type( "application/x-tar" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (fname,outext) - archive.wsgi_status = trans.response.wsgi_status() - archive.wsgi_headeritems = trans.response.wsgi_headeritems() - return archive.stream + status=status ) ) else: - status = 'error' - message = 'Invalid action ( %s ) specified.' % action - return trans.response.send_redirect( web.url_for( controller='library_common', - action='browse_library', - cntrller=cntrller, - use_panels=use_panels, - id=library_id, - show_deleted=show_deleted, - message=util.sanitize_text( message ), - status=status ) ) + # We must have arrived here from the library_dataset_search_results page, so reddirect there. + search_term = params.get( 'search_term', '' ) + comptypes = get_comptypes( trans ) + return trans.fill_template( '/library/common/library_dataset_search_results.mako', + cntrller=cntrller, + search_term=search_term, + comptypes=comptypes, + lddas=lddas, + show_deleted=show_deleted, + use_panels=use_panels, + message=message, + status=status ) + + @web.expose + def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_ids='', new_history_name='', **kwd ): + # This method is called from one of the following places: + # - a menu option for a library dataset ( ldda_ids will be a singel dataset id ) + # - a menu option for a library folder ( folder_id will have a value ) + # - a menu option for a library dataset search result set ( ldda_ids will be a comma separated string of dataset ids ) + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) + user = trans.get_user() + current_history = trans.get_history() + if library_id: + library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) + else: + library = None + if folder_id: + folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) + else: + folder = None + ldda_ids = util.listify( ldda_ids ) + if ldda_ids: + # Check boxes cause 2 copies of each id to be included in the request + ldda_ids = map( trans.security.decode_id, ldda_ids ) + unique_ldda_ids = [] + for ldda_id in ldda_ids: + if ldda_id not in unique_ldda_ids: + unique_ldda_ids.append( ldda_id ) + ldda_ids = unique_ldda_ids + target_history_ids = util.listify( target_history_ids ) + if target_history_ids: + target_history_ids = [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ] + if params.get( 'import_datasets_to_histories_button', False ): + invalid_datasets = 0 + if not ldda_ids or not ( target_history_ids or new_history_name ): + message = "You must provide one or more source library datasets and one or more target histories." + status = 'error' + else: + if new_history_name: + new_history = trans.app.model.History() + new_history.name = new_history_name + new_history.user = user + trans.sa_session.add( new_history ) + trans.sa_session.flush() + target_history_ids.append( new_history.id ) + if user: + target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if ( hist is not None and hist.user == user )] + else: + target_histories = [ current_history ] + if len( target_histories ) != len( target_history_ids ): + message += "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) + status = 'error' + for ldda in map( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get, ldda_ids ): + if ldda is None: + message += "You tried to import a library dataset that does not exist. " + status = 'error' + invalid_datasets += 1 + elif ldda.dataset.state not in [ trans.model.Dataset.states.OK, trans.model.Dataset.states.ERROR ]: + message += "Cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) + status = 'error' + invalid_datasets += 1 + elif not ldda.has_data(): + message += "Cannot import empty dataset '%s'. " % ldda.name + status = 'error' + invalid_datasets += 1 + else: + for target_history in target_histories: + hda = ldda.to_history_dataset_association( target_history=target_history, add_to_history=True ) + trans.sa_session.flush() + hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] ) + num_source = len( ldda_ids ) - invalid_datasets + num_target = len( target_histories ) + message = "%i %s have been imported into %i %s: %s" % ( num_source, + inflector.cond_plural( num_source, "dataset" ), + num_target, + inflector.cond_plural( num_target, "history" ), + hist_names_str ) + trans.sa_session.refresh( current_history ) + current_user_roles = trans.get_current_user_roles() + source_lddas = [] + if folder: + for library_dataset in folder.datasets: + ldda = library_dataset.library_dataset_dataset_association + if not ldda.deleted and trans.app.security_agent.can_access_library_item( current_user_roles, ldda, trans.user ): + source_lddas.append( ldda ) + elif ldda_ids: + for ldda_id in ldda_ids: + # Secuirty access permiision chcck is not needed here since the current user had access + # to the lddas in order for the menu optin to be available. + ldda = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) + source_lddas.append( ldda ) + target_histories = [ current_history ] + if user: + target_histories = user.active_histories + return trans.fill_template( "/library/common/import_datasets_to_histories.mako", + cntrller=cntrller, + library=library, + current_history=trans.get_history(), + ldda_ids=ldda_ids, + target_history_ids=target_history_ids, + source_lddas=source_lddas, + target_histories=target_histories, + new_history_name=new_history_name, + show_deleted=show_deleted, + use_panels=use_panels, + message=message, + status=status ) @web.expose def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): params = util.Params( kwd ) @@ -2064,6 +2170,31 @@ def get_containing_library_from_library_dataset( trans, library_dataset ): if library.root_folder == folder: return library return None +def get_comptypes( trans ): + comptypes_t = comptypes + if trans.app.config.nginx_x_archive_files_base: + comptypes_t = ['ngxzip'] + for comptype in trans.app.config.disable_library_comptypes: + # TODO: do this once, not every time (we're gonna raise an + # exception every time after the first time) + try: + comptypes_t.remove( comptype ) + except: + pass + return comptypes_t +def get_sorted_accessible_library_items( trans, cntrller, items, sort_attr ): + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + if is_admin: + accessible_items = items + else: + # Enforce access permission settings + current_user_roles = trans.get_current_user_roles() + accessible_items = [] + for item in items: + if trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ): + accessible_items.append( item ) + # Sort by name + return sort_by_attr( [ item for item in accessible_items ], sort_attr ) def sort_by_attr( seq, attr ): """ Sort the sequence of objects by object's attribute @@ -2079,25 +2210,12 @@ def sort_by_attr( seq, attr ): intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) intermed.sort() return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) -def get_sorted_accessible_library_items( trans, cntrller, items, sort_attr ): - is_admin = trans.user_is_admin() and cntrller == 'library_admin' - if is_admin: - accessible_items = items - else: - # Enforce access permission settings - current_user_roles = trans.get_current_user_roles() - accessible_items = [] - for item in items: - if trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ): - accessible_items.append( item ) - # Sort by name - return sort_by_attr( [ item for item in accessible_items ], sort_attr ) def lucene_search( trans, cntrller, search_term, search_url, **kwd ): """Return display of results from a full-text lucene search of data libraries.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - full_url = "%s?%s" % ( search_url, urllib.urlencode( { "kwd" : search_term } ) ) + full_url = "%s/find?%s" % ( search_url, urllib.urlencode( { "kwd" : search_term } ) ) response = urllib2.urlopen( full_url ) ldda_ids = util.json.from_json_string( response.read() )[ "ids" ] response.close() @@ -2115,17 +2233,20 @@ def whoosh_search( trans, cntrller, search_term, **kwd ): if index_exists: index = whoosh.index.open_dir( whoosh_index_dir ) # Set field boosts for searcher to place equal weight on all search fields. - searcher = index.searcher( weighting=BM25F( field_B={ 'name_B' : 3.5, - 'info_B' : 2.3, - 'dbkey_B' : 3.1, - 'message_B' : 2.1, - 'state_B' : 1.2 } ) ) + searcher = index.searcher( weighting=BM25F( field_B={ 'name_B' : 3.4, + 'info_B' : 3.2, + 'dbkey_B' : 3.3, + 'message_B' : 3.5 } ) ) # Perform search - parser = MultifieldParser( [ 'name', 'info', 'dbkey', 'message', 'state' ], schema=schema ) + parser = MultifieldParser( [ 'name', 'info', 'dbkey', 'message' ], schema=schema ) # Search term with wildcards may be slow... - results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=1.0 ) + results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=0.1 ) ldda_ids = [ result[ 'id' ] for result in results ] - lddas = [ trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) for ldda_id in ldda_ids ] + lddas = [] + for ldda_id in ldda_ids: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) + if ldda: + lddas.append( ldda ) lddas = get_sorted_accessible_library_items( trans, cntrller, lddas, 'name' ) else: message = "Tell your Galaxy administrator that the directory %s does not contain valid whoosh indexes" % str( whoosh_index_dir ) diff --git a/scripts/data_libraries/build_lucene_index.py b/scripts/data_libraries/build_lucene_index.py index 10f503be8a3..5489c18bf93 100644 --- a/scripts/data_libraries/build_lucene_index.py +++ b/scripts/data_libraries/build_lucene_index.py @@ -30,7 +30,7 @@ def main( ini_file ): sa_session, gconfig = get_sa_session( ini_file ) max_size = float( gconfig.get( "fulltext_max_size", 100 ) ) * 1048576 ignore_exts = gconfig.get( "fulltext_noindex_filetypes", "" ).split( "," ) - search_url = gconfig.get( "fulltext_index_url", None ) + search_url = gconfig.get( "fulltext_url", None ) if not search_url: raise ValueError( "Need to specify search functionality in universe_wsgi.ini" ) dataset_file = create_dataset_file( get_lddas( sa_session, max_size, ignore_exts ) ) @@ -41,7 +41,7 @@ def main( ini_file ): os.remove( dataset_file ) def build_index( search_url, dataset_file ): - url = "%s?%s" % ( search_url, urllib.urlencode( { "docfile" : dataset_file } ) ) + url = "%s/index?%s" % ( search_url, urllib.urlencode( { "docfile" : dataset_file } ) ) request = urllib2.Request( url ) request.get_method = lambda: "PUT" response = urllib2.urlopen( request ) @@ -57,21 +57,35 @@ def create_dataset_file( dataset_iter ): def get_lddas( sa_session, max_size, ignore_exts ): for ldda in sa_session.query( model.LibraryDatasetDatasetAssociation ).filter_by( deleted=False ): - id = ldda.id - name = ldda.name - info = ldda.library_dataset.get_info() - if info and not info.startswith( 'upload' ): - info = info.replace( 'no info', '' ) - else: - info = '' - dbkey = ldda.metadata.dbkey - state = ldda.state - message = ldda.message if ( float( ldda.dataset.get_size() ) > max_size or ldda.extension in ignore_exts ): fname = "" else: fname = ldda.dataset.get_file_name() - yield id, name, info, dbkey, state, message, fname + yield ldda.id, fname, _get_dataset_metadata(ldda) + +def _get_dataset_metadata(ldda): + """Retrieve descriptions and information associated with a dataset. + """ + lds = ldda.library_dataset + folder_info = _get_folder_info(lds.folder) + lds_info = lds.get_info() + if lds_info and not lds_info.startswith("upload"): + lds_info = lds_info.replace("no info", "") + else: + lds_info = "" + return "%s %s %s %s %s" % (lds.name or "", lds_info, ldda.metadata.dbkey, + ldda.message, folder_info) + +def _get_folder_info(folder): + """Get names and descriptions for all parent folders except top level. + """ + folder_info = "" + if folder and folder.parent: + folder_info = _get_folder_info(folder.parent) + folder_info += " %s %s" % ( + folder.name.replace("Unnamed folder", ""), + folder.description or "") + return folder_info def get_sa_session( ini_file ): conf_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } ) diff --git a/scripts/data_libraries/build_whoosh_index.py b/scripts/data_libraries/build_whoosh_index.py index dc17f1bb08c..32f54e62678 100644 --- a/scripts/data_libraries/build_whoosh_index.py +++ b/scripts/data_libraries/build_whoosh_index.py @@ -24,7 +24,7 @@ try: from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT from whoosh.index import Index whoosh_search_enabled = True - schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT, state=TEXT ) + schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT ) import galaxy.model.mapping from galaxy import config, model import pkg_resources @@ -43,13 +43,12 @@ def build_index( sa_session, whoosh_index_dir ): else: return a_basestr lddas_indexed = 0 - for id, name, info, dbkey, state, message in get_lddas( sa_session ): + for id, name, info, dbkey, message in get_lddas( sa_session ): writer.add_document( id=id, name=to_unicode( name ), info=to_unicode( info ), dbkey=to_unicode( dbkey ), - message=to_unicode( message ), - state=to_unicode( state ) ) + message=to_unicode( message ) ) lddas_indexed += 1 writer.commit() print "Number of active library datasets indexed: ", lddas_indexed @@ -64,9 +63,8 @@ def get_lddas( sa_session ): else: info = '' dbkey = ldda.metadata.dbkey - state = ldda.state message = ldda.message - yield id, name, info, dbkey, state, message + yield id, name, info, dbkey, message def get_sa_session_and_needed_config_settings( ini_file ): conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } ) diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako index d598f7dad9f..f72fc831ad6 100644 --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -1,6 +1,7 @@ <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/library/common/library_item_info.mako" import="render_library_item_info" /> <%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> <%! def inherit(context): @@ -46,6 +47,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("class", "jquery.jstore")} + ${common_javascripts()} ${self.grid_javascripts()} @@ -152,15 +154,6 @@ }); }); - function checkForm() { - if ( $("select#action_on_datasets_select option:selected").text() == "delete" ) { - if ( confirm( "Click OK to delete these datasets?" ) ) { - return true; - } else { - return false; - } - } - } // Looks for changes in dataset state using an async request. Keeps // calling itself (via setTimeout) until all datasets are in a terminal // state. @@ -212,7 +205,7 @@ -<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False, render_checkboxes=True )"> +<%def name="render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, parent, row_counter, tracked_datasets, show_deleted=False )"> <% ## The received ldda must always be a LibraryDatasetDatasetAssociation object. The object id passed to methods ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying @@ -248,13 +241,11 @@ %endif id="libraryItem-${ldda.id}"> - %if render_checkboxes: - + %if ldda.library_dataset.deleted: %endif @@ -288,7 +279,7 @@ Upload a new version of this dataset %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - Import this dataset into your current history + Import this dataset into selected histories Download this dataset %endif %if can_modify: @@ -379,6 +370,7 @@ Add sub-folder %endif %if not branch_deleted( folder ): + Select folder datasets for import into selected histories %if can_modify: Edit information %else: @@ -515,6 +507,7 @@ %endif Edit permissions %endif + Select datasets for import into selected histories %elif can_modify and not library.purged: Undelete this data library %elif library.purged: @@ -539,7 +532,10 @@ - + diff --git a/templates/library/common/common.mako b/templates/library/common/common.mako index a51cf5d37db..29c3abb70e0 100644 --- a/templates/library/common/common.mako +++ b/templates/library/common/common.mako @@ -1,5 +1,48 @@ <%namespace file="/common/template_common.mako" import="render_template_field" /> +<%def name="common_javascripts()"> + + + <%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, space_to_tab, link_data_only, widgets, roles_select_list, history, show_deleted )"> <% import os, os.path @@ -319,26 +362,34 @@ %endif -<%def name="render_actions_on_multiple_items()"> +<%def name="render_actions_on_multiple_items( actions_to_exclude=[] )"> + <% + is_admin = trans.user_is_admin() and cntrller=='library_admin' + can_delete = 'delete' not in actions_to_exclude and is_admin + can_download = 'download' not in actions_to_exclude + can_import_to_histories = 'import_to_histories' not in actions_to_exclude + can_manage_permissions = 'manage_permissions' not in actions_to_exclude + %> diff --git a/templates/library/common/import_datasets_to_histories.mako b/templates/library/common/import_datasets_to_histories.mako new file mode 100644 index 00000000000..ad7522b7bf8 --- /dev/null +++ b/templates/library/common/import_datasets_to_histories.mako @@ -0,0 +1,101 @@ +<%namespace file="/message.mako" import="render_msg" /> +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="javascripts" /> +<%def name="title()">Import library datasets to histories + +<%def name="javascripts()"> + +${parent.javascripts()} +${h.js( "jquery", "galaxy.base" )} + + + + +%if message: + ${render_msg( message, status )} +%endif + +

+

Import library datasets into histories.
+
+

+

+
+

+
+ + %if source_lddas: + %for source_ldda in source_lddas: + <% + checked = "" + encoded_id = trans.security.encode_id( source_ldda.id ) + if source_ldda.id in ldda_ids: + checked = " checked='checked'" + %> +
+ + +
+ %endfor + %else: +
This folder has no accessible library datasets.
+ %endif +
+
+
→
+
+
Destination Histories:
+
+
+ +

+ Choose multiple histories +
+ + %if trans.get_user(): + <% + checked = "" + if "create_new_history" in target_history_ids: + checked = " checked='checked'" + %> +
+
— OR —
+
+ + +
+ %endif +
+
+
+
+ +
+ + +

diff --git a/templates/library/common/ldda_info.mako b/templates/library/common/ldda_info.mako index 4b23cddf864..82ac6107f26 100644 --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -66,7 +66,7 @@ Upload a new version of this dataset %endif %if cntrller=='library' and ldda.has_data(): - Import this dataset into your current history + Select histories to import this datasetDownload this dataset %endif %if show_associated_hdas_and_lddas: diff --git a/templates/library/common/library_dataset_search_results.mako b/templates/library/common/library_dataset_search_results.mako index 6a930471a28..b0ac151a5b7 100644 --- a/templates/library/common/library_dataset_search_results.mako +++ b/templates/library/common/library_dataset_search_results.mako @@ -1,5 +1,7 @@ <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/library/common/browse_library.mako" import="render_dataset" /> +<%namespace file="/library/common/common.mako" import="render_actions_on_multiple_items" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> <%! def inherit(context): @@ -44,6 +46,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("class", "jquery.jstore")} + ${common_javascripts()} <%def name="render_searched_components()"> @@ -52,7 +55,6 @@
  • info
  • dbkey (genome build)
  • message
    • -
  • state
    • %if trans.app.config.enable_lucene_library_search:
  • disk file content
    • %endif @@ -91,34 +93,69 @@ %if lddas:

    The string "${search_term}" was found in at least one of the following information components of the displayed library datasets.

    ${render_searched_components()} -
    Name + + Name + Message Uploaded By Date
    For selected items:
    - - - - - - - - - - <% - tracked_datasets = {} - row_counter = RowCounter() - my_row = row_counter.count - %> - %for ldda in lddas: - <% - library_dataset = ldda.library_dataset - folder = library_dataset.folder - library = folder.parent_library - %> - ${render_dataset( cntrller, ldda, library_dataset, False, library, folder, 0, my_row, row_counter, tracked_datasets, show_deleted=False, render_checkboxes=False )} + +
    NameMessageUploaded ByDateFile Size
    + + + + + + + + + <% + tracked_datasets = {} + row_counter = RowCounter() my_row = row_counter.count - row_counter.increment() %> - %endfor -
    + + Name + MessageUploaded ByDateFile Size
    + %for ldda in lddas: + <% + library_dataset = ldda.library_dataset + folder = library_dataset.folder + library = folder.parent_library + %> + ${render_dataset( cntrller, ldda, library_dataset, False, library, folder, 0, my_row, row_counter, tracked_datasets, show_deleted=False )} + <% + my_row = row_counter.count + row_counter.increment() + %> + %endfor + ${render_actions_on_multiple_items( actions_to_exclude=[ 'manage_permissions' ] )} + + + ## Help about compression types + +
    +

    + TIP: You can download individual library files by selecting "Download this dataset" from the context menu (triangle) next to the dataset's name. +

    +
    + %if len( comptypes ) > 1: +
    +

    + TIP: Multiple compression options are available for downloading library datasets: +

    + +
    + %endif %elif status != 'error':

    The string "${search_term}" was not found in any of the following information components for any library datasets that you can access.

    ${render_searched_components()} diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index dd83dd27669..47211875421 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2106,6 +2106,13 @@ class TwillTestCase( unittest.TestCase ): % ( self.url, cntrller, library_id, ldda_ids, do_action ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) + def import_datasets_to_histories( self, cntrller, library_id, ldda_ids='', new_history_name='Unnamed history', strings_displayed=[] ): + # Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission + # by going directly to the form action + self.visit_url( '%s/library_common/import_datasets_to_histories?cntrller=%s&library_id=%s&ldda_ids=%s&new_history_name=%s&import_datasets_to_histories_button=Import+library+datasets' \ + % ( self.url, cntrller, library_id, ldda_ids, new_history_name ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) def download_archive_of_library_files( self, cntrller, library_id, ldda_ids, format ): self.home() # Here it would be ideal to have twill set form values and submit the form, but diff --git a/test/functional/test_library_security.py b/test/functional/test_library_security.py index 00cd7e997b4..09ad5b37c3b 100644 --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -296,11 +296,11 @@ class TestLibrarySecurity( TwillTestCase ): strings_displayed=[ '2.bed', 'This is the latest version of this library dataset', 'Edit attributes of 2.bed' ] ) - self.act_on_multiple_datasets( 'library', - self.security.encode_id( library1.id ), - 'import_to_history', - ldda_ids=self.security.encode_id( ldda2.id ), - strings_displayed=[ '1 dataset(s) have been imported into your history' ] ) + self.import_datasets_to_histories( cntrller='library', + library_id=self.security.encode_id( library1.id ), + ldda_ids=self.security.encode_id( ldda2.id ), + new_history_name='goodbye', + strings_displayed=[ '1 dataset have been imported into 1 history' ] ) self.logout() # regular_user2 should not be able to see ldda2 self.login( email=regular_user2.email ) @@ -382,10 +382,10 @@ class TestLibrarySecurity( TwillTestCase ): def check_edit_page( lddas, strings_displayed=[], strings_not_displayed=[] ): for ldda in lddas: # Import each library dataset into our history - self.act_on_multiple_datasets( 'library', - self.security.encode_id( library1.id ), - 'import_to_history', - ldda_ids=self.security.encode_id( ldda.id ) ) + self.import_datasets_to_histories( cntrller='library', + library_id=self.security.encode_id( library1.id ), + ldda_ids=self.security.encode_id( ldda.id ), + new_history_name='hello' ) # Determine the new HistoryDatasetAssociation id created when the library dataset was imported into our history last_hda_created = get_latest_hda() self.edit_hda_attribute_info( str( last_hda_created.id ), @@ -393,8 +393,8 @@ class TestLibrarySecurity( TwillTestCase ): # admin_user is associated with role1, so should have all permissions on imported datasets check_edit_page( latest_3_lddas, strings_displayed=[ 'Manage dataset permissions on', - 'can manage the roles associated with permissions on this dataset', - 'can import this dataset into their history for analysis' ] ) + 'can manage the roles associated with permissions on this dataset', + 'can import this dataset into their history for analysis' ] ) self.logout() # regular_user1 is associated with role1, so should have all permissions on imported datasets self.login( email=regular_user1.email ) diff --git a/tools/data_source/access_libraries.xml b/tools/data_source/access_libraries.xml index 31195582f3e..374cbe1bcd8 100644 --- a/tools/data_source/access_libraries.xml +++ b/tools/data_source/access_libraries.xml @@ -2,7 +2,7 @@ stored locally - + diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index 65b96e312b9..eba12617ea8 100644 --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -337,18 +337,17 @@ use_interactive = True #transfer_manager_port = 8163 # Search data libraries with whoosh -enable_whoosh_library_search = True +#enable_whoosh_library_search = True # Whoosh indexes are stored in this directory. -whoosh_index_dir = database/whoosh_indexes +#whoosh_index_dir = database/whoosh_indexes # Search data libraries with lucene #enable_lucene_library_search = False # maxiumum file size to index for searching, in MB #fulltext_max_size = 500 #fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger -# base URL of server providing search functionality using whoosh. -#fulltext_index_url = http://localhost:8081/index -#fulltext_find_url = http://localhost:8081/find +# base URL of server providing search functionality using lucene +#fulltext_url = http://localhost:8081 # -- Users and Security