details: http://www.bx.psu.edu/hg/galaxy/rev/8d9c8cf65dee changeset: 3386:8d9c8cf65dee user: rerla@localhost date: Fri Feb 12 17:10:05 2010 -0500 description: fixes to allow downloading of composite files from a library. if a single file is chosen, act_on_multiple_datasets is used and zip is always the format. if act_on_multiple_datasets encounters any composite files, it adds the html file and all the files in extra_files_path to the archive

diffstat:

lib/galaxy/web/controllers/library_common.py | 80 ++++++++++++++++++++------- 1 files changed, 59 insertions(+), 21 deletions(-)

diffs (117 lines):

diff -r c1f22feda926 -r 8d9c8cf65dee lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Fri Feb 12 15:17:36 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Feb 12 17:10:05 2010 -0500 @@ -1,4 +1,4 @@ -import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy +import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob from galaxy.web.base.controller import * from galaxy import util, jobs from galaxy.datatypes import sniff @@ -1048,21 +1048,30 @@ show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id ) + msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) messagetype = 'error' else: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) - fStat = os.stat( ldda.file_name ) - trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ldda.name - fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) - try: - return open( ldda.file_name ) - except: - msg = 'This dataset contains no content' + composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) + ext = ldda.extension + if ext in composite_extensions: + # is composite - must return a zip of contents and the html file itself - ugh - should be reversible at upload! + # use act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ) since it does what we need + kwd['do_action'] = 'zip' + return self.act_on_multiple_datasets( trans, cntrller, library_id, ldda_ids=id, **kwd ) + + else: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) + trans.response.set_content_type( mime ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) + try: + return open( ldda.file_name ) + except: + msg = 'This dataset contains no content' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1246,6 +1255,7 @@ msg = "Unable to create archive for download, please report this error" messagetype = 'error' if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) seen = [] current_user_roles = trans.get_current_user_roles() for ldda_id in ldda_ids: @@ -1254,6 +1264,9 @@ or not trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset ) \ or ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: continue + ext = ldda.extension + if ext in composite_extensions: + is_composite = True path = "" parent_folder = ldda.library_dataset.folder while parent_folder is not None: @@ -1267,13 +1280,38 @@ while path in seen: path += '_' seen.append( path ) - try: - archive.add( ldda.dataset.file_name, path ) - except IOError: - error = True - log.exception( "Unable to write to temporary library download archive" ) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + if is_composite: # need to add all the components from the extra_files_path to the zip + zpath = os.path.split(path)[-1] # comes as base_name/fname + zpathext = os.path.splitext(zpath)[-1] + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + msg = "Unable to create archive for download, please report this error" + messagetype = '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) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % fname) + msg = "Unable to create archive for download, please report this error" + messagetype = '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) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' if not error: if params.do_action == 'zip': archive.close()