March 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3520: remove bogus string.translate
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/262b16c8e277 changeset: 3520:262b16c8e277 user: fubar: ross Lazarus at gmail period com date: Thu Mar 11 13:51:53 2010 -0500 description: remove bogus string.translate diffstat: lib/galaxy/web/controllers/library_common.py | 2 -- 1 files changed, 0 insertions(+), 2 deletions(-) diffs (12 lines): diff -r 39e4b119bdf4 -r 262b16c8e277 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Mar 11 13:41:40 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Thu Mar 11 13:51:53 2010 -0500 @@ -1357,8 +1357,6 @@ path = os.path.join( parent_folder.name, path ) parent_folder = parent_folder.parent path += ldda.name - if path > '': - path = path.translate(trantab) while path in seen: path += '_' seen.append( path )

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[hg] galaxy 3519: merge with 3518:0c9e154e9176
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/39e4b119bdf4 changeset: 3519:39e4b119bdf4 user: fubar: ross Lazarus at gmail period com date: Thu Mar 11 13:41:40 2010 -0500 description: merge with 3518:0c9e154e9176 diffstat: lib/galaxy/datatypes/sniff.py | 39 ++++++++++++++++++++++++--------------- tools/data_source/upload.py | 24 +++++++++++++++++++----- 2 files changed, 43 insertions(+), 20 deletions(-) diffs (140 lines): diff -r e98117dd6054 -r 39e4b119bdf4 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Thu Mar 11 13:37:49 2010 -0500 +++ b/lib/galaxy/datatypes/sniff.py Thu Mar 11 13:41:40 2010 -0500 @@ -70,7 +70,7 @@ f.close() return False -def convert_newlines( fname ): +def convert_newlines( fname, in_place=True ): """ Converts in place a file from universal line endings to Posix line endings. @@ -78,7 +78,7 @@ >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines(fname) - 2 + (2, None) >>> file(fname).read() '1 2\\n3 4\\n' """ @@ -87,18 +87,21 @@ for i, line in enumerate( file( fname, "U" ) ): fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) -def sep2tabs(fname, patt="\\s+"): +def sep2tabs( fname, in_place=True, patt="\\s+" ): """ Transforms in place a 'sep' separated file to a tab separated one >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\n3 4\\n") >>> sep2tabs(fname) - 2 + (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ @@ -110,11 +113,14 @@ elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) -def convert_newlines_sep2tabs( fname, patt="\\s+" ): +def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ): """ Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice @@ -122,7 +128,7 @@ >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines_sep2tabs(fname) - 2 + (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ @@ -134,9 +140,12 @@ elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) def get_headers( fname, sep, count=60, is_multi_byte=False ): """ diff -r e98117dd6054 -r 39e4b119bdf4 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Mar 11 13:37:49 2010 -0500 +++ b/tools/data_source/upload.py Thu Mar 11 13:41:40 2010 -0500 @@ -138,6 +138,7 @@ def add_file( dataset, json_file, output_path ): data_type = None line_count = None + converted_path = None if dataset.type == 'url': try: @@ -239,10 +240,15 @@ file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) return if data_type != 'binary' and data_type != 'zip': - if dataset.space_to_tab: - line_count = sniff.convert_newlines_sep2tabs( dataset.path ) - else: - line_count = sniff.convert_newlines( dataset.path ) + # don't convert newlines on data we're only going to symlink + if not dataset.get( 'link_data_only', False ): + in_place = True + if dataset.type in ( 'server_dir', 'path_paste' ): + in_place = False + if dataset.space_to_tab: + line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) + else: + line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) if dataset.file_type == 'auto': ext = sniff.guess_ext( dataset.path ) else: @@ -257,7 +263,15 @@ if dataset.get( 'link_data_only', False ): pass # data will remain in place elif dataset.type in ( 'server_dir', 'path_paste' ): - shutil.copy( dataset.path, output_path ) + if converted_path is not None: + shutil.copy( converted_path, output_path ) + try: + os.remove( converted_path ) + except: + pass + else: + # this should not happen, but it's here just in case + shutil.copy( dataset.path, output_path ) else: shutil.move( dataset.path, output_path ) # Write the job info

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[hg] galaxy 3517: Modify the newline conversion methods in sniff...
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0c9e154e9176 changeset: 3517:0c9e154e9176 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Mar 11 11:56:20 2010 -0500 description: Modify the newline conversion methods in sniff so converting in place is optional. This is necessary to fix a bug that occurs if using the 'server_dir' or 'path_paste' library upload methods: previously, they would modify the file to be imported in-place if permissions allowed (probably not what the admin wanted) or fail if permissions did not allow. New functionality is to return the converted tempfile if 'server_dir' or 'path_paste' methods are used. Also, no newline conversion will be done if the administrator uses the symlink checkbox. diffstat: lib/galaxy/datatypes/sniff.py | 39 ++++++++++++++++++++++++--------------- tools/data_source/upload.py | 24 +++++++++++++++++++----- 2 files changed, 43 insertions(+), 20 deletions(-) diffs (140 lines): diff -r 2e97ae04856d -r 0c9e154e9176 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Thu Mar 11 11:17:11 2010 -0500 +++ b/lib/galaxy/datatypes/sniff.py Thu Mar 11 11:56:20 2010 -0500 @@ -70,7 +70,7 @@ f.close() return False -def convert_newlines( fname ): +def convert_newlines( fname, in_place=True ): """ Converts in place a file from universal line endings to Posix line endings. @@ -78,7 +78,7 @@ >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines(fname) - 2 + (2, None) >>> file(fname).read() '1 2\\n3 4\\n' """ @@ -87,18 +87,21 @@ for i, line in enumerate( file( fname, "U" ) ): fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) -def sep2tabs(fname, patt="\\s+"): +def sep2tabs( fname, in_place=True, patt="\\s+" ): """ Transforms in place a 'sep' separated file to a tab separated one >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\n3 4\\n") >>> sep2tabs(fname) - 2 + (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ @@ -110,11 +113,14 @@ elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) -def convert_newlines_sep2tabs( fname, patt="\\s+" ): +def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ): """ Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice @@ -122,7 +128,7 @@ >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines_sep2tabs(fname) - 2 + (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ @@ -134,9 +140,12 @@ elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() - shutil.move( temp_name, fname ) - # Return number of lines in file. - return i + 1 + if in_place: + shutil.move( temp_name, fname ) + # Return number of lines in file. + return ( i + 1, None ) + else: + return ( i + 1, temp_name ) def get_headers( fname, sep, count=60, is_multi_byte=False ): """ diff -r 2e97ae04856d -r 0c9e154e9176 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Mar 11 11:17:11 2010 -0500 +++ b/tools/data_source/upload.py Thu Mar 11 11:56:20 2010 -0500 @@ -138,6 +138,7 @@ def add_file( dataset, json_file, output_path ): data_type = None line_count = None + converted_path = None if dataset.type == 'url': try: @@ -239,10 +240,15 @@ file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) return if data_type != 'binary' and data_type != 'zip': - if dataset.space_to_tab: - line_count = sniff.convert_newlines_sep2tabs( dataset.path ) - else: - line_count = sniff.convert_newlines( dataset.path ) + # don't convert newlines on data we're only going to symlink + if not dataset.get( 'link_data_only', False ): + in_place = True + if dataset.type in ( 'server_dir', 'path_paste' ): + in_place = False + if dataset.space_to_tab: + line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) + else: + line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) if dataset.file_type == 'auto': ext = sniff.guess_ext( dataset.path ) else: @@ -257,7 +263,15 @@ if dataset.get( 'link_data_only', False ): pass # data will remain in place elif dataset.type in ( 'server_dir', 'path_paste' ): - shutil.copy( dataset.path, output_path ) + if converted_path is not None: + shutil.copy( converted_path, output_path ) + try: + os.remove( converted_path ) + except: + pass + else: + # this should not happen, but it's here just in case + shutil.copy( dataset.path, output_path ) else: shutil.move( dataset.path, output_path ) # Write the job info

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[hg] galaxy 3518: fix for string.translate on empty path in crea...
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e98117dd6054 changeset: 3518:e98117dd6054 user: fubar: ross Lazarus at gmail period com date: Thu Mar 11 13:37:49 2010 -0500 description: fix for string.translate on empty path in creating an archive of library composite datatypes diffstat: lib/galaxy/web/controllers/library_common.py | 6 ++++-- 1 files changed, 4 insertions(+), 2 deletions(-) diffs (23 lines): diff -r 2e97ae04856d -r e98117dd6054 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Mar 11 11:17:11 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Thu Mar 11 13:37:49 2010 -0500 @@ -1357,7 +1357,8 @@ path = os.path.join( parent_folder.name, path ) parent_folder = parent_folder.parent path += ldda.name - path = path.translate(trantab) + if path > '': + path = path.translate(trantab) while path in seen: path += '_' seen.append( path ) @@ -1377,7 +1378,8 @@ 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) - fname = fname.translate(trantab) + if fname > '': + fname = fname.translate(trantab) try: archive.add( fpath,fname ) except IOError:

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[hg] galaxy 3516: Fix for implicit datatype conversion.
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2e97ae04856d changeset: 3516:2e97ae04856d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Mar 11 11:17:11 2010 -0500 description: Fix for implicit datatype conversion. diffstat: lib/galaxy/datatypes/data.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 6fa986527398 -r 2e97ae04856d lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Wed Mar 10 23:59:25 2010 -0500 +++ b/lib/galaxy/datatypes/data.py Thu Mar 11 11:17:11 2010 -0500 @@ -257,7 +257,7 @@ break params[input_name] = original_dataset #Run converter, job is dispatched through Queue - converted_dataset = converter.execute( trans, incoming = params, set_output_hid = visible ) + converted_dataset = converter.execute( trans, incoming = params, set_output_hid = visible )[1] if len(params) > 0: trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id ) if not visible:

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[hg] galaxy 3515: merge
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6fa986527398 changeset: 3515:6fa986527398 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 23:59:25 2010 -0500 description: merge

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[hg] galaxy 3513: Remove old Lmap from datatypes_conf.xml.sample...
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/87da8cd1f091 changeset: 3513:87da8cd1f091 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 20:59:11 2010 -0500 description: Remove old Lmap from datatypes_conf.xml.sample - now deprecated from genetics.py Causing buildbot to barf. diffstat: datatypes_conf.xml.sample | 1 - lib/galaxy/web/controllers/library_common.py | 3 ++- run_functional_tests.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diffs (43 lines): diff -r 53ddb4b728f7 -r 87da8cd1f091 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Wed Mar 10 19:48:28 2010 -0500 +++ b/datatypes_conf.xml.sample Wed Mar 10 20:59:11 2010 -0500 @@ -194,7 +194,6 @@  <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>  - <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/> <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>  <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> diff -r 53ddb4b728f7 -r 87da8cd1f091 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 10 19:48:28 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 20:59:11 2010 -0500 @@ -1111,7 +1111,7 @@ # 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 ) + 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 ) @@ -1258,6 +1258,7 @@ messagetype = 'error' else: ldda_ids = util.listify( ldda_ids ) + log.debug('## act on multiple got %s' % ldda_ids) if action == 'import_to_history': history = trans.get_history() if history is None: diff -r 53ddb4b728f7 -r 87da8cd1f091 run_functional_tests.sh --- a/run_functional_tests.sh Wed Mar 10 19:48:28 2010 -0500 +++ b/run_functional_tests.sh Wed Mar 10 20:59:11 2010 -0500 @@ -1,7 +1,7 @@ #!/bin/sh # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ - +export PATH=/usr/local/bin:$PATH rm -f run_functional_tests.log if [ ! $1 ]; then

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[hg] galaxy 3514: Fixes for downloading library archives - corre...
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/06dcf56688ea changeset: 3514:06dcf56688ea user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 23:58:35 2010 -0500 description: Fixes for downloading library archives - correct extensions help a lot and removing spaces from ldda.name helps too. diffstat: lib/galaxy/web/controllers/library_common.py | 15 +++++++++------ 1 files changed, 9 insertions(+), 6 deletions(-) diffs (63 lines): diff -r 87da8cd1f091 -r 06dcf56688ea lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 10 20:59:11 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 23:58:35 2010 -0500 @@ -1,4 +1,4 @@ -import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob +import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile, copy, glob, string from galaxy.web.base.controller import * from galaxy import util, jobs from galaxy.datatypes import sniff @@ -1258,7 +1258,6 @@ messagetype = 'error' else: ldda_ids = util.listify( ldda_ids ) - log.debug('## act on multiple got %s' % ldda_ids) if action == 'import_to_history': history = trans.get_history() if history is None: @@ -1312,6 +1311,8 @@ msg = "The selected datasets have been removed from this data library" else: error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) try: outext = 'zip' if action == 'zip': @@ -1325,10 +1326,10 @@ archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif action == 'tgz': archive = util.streamball.StreamBall( 'w|gz' ) - outext = 'gz' + outext = 'tgz' elif action == 'tbz': archive = util.streamball.StreamBall( 'w|bz2' ) - outext = 'bz2' + outext = 'tbz2' except (OSError, zipfile.BadZipFile): error = True log.exception( "Unable to create archive for download" ) @@ -1356,12 +1357,13 @@ path = os.path.join( parent_folder.name, path ) parent_folder = parent_folder.parent path += ldda.name + path = path.translate(trantab) 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 - zpath = os.path.split(path)[-1] # comes as base_name/fname - outfname,zpathext = os.path.splitext(zpath) if zpathext == '': zpath = '%s.html' % zpath # fake the real nature of the html file try: @@ -1375,6 +1377,7 @@ 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) + fname = fname.translate(trantab) try: archive.add( fpath,fname ) except IOError:

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[hg] galaxy 3512: Reverted missing python version check for zipf...
by Greg Von Kuster 18 Mar '10

18 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/53ddb4b728f7 changeset: 3512:53ddb4b728f7 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 19:48:28 2010 -0500 description: Reverted missing python version check for zipfile setup Changed download archive names for both libraries and for history items so they're related to the content - uses data.name rather than one fixed string for all diffstat: lib/galaxy/web/controllers/dataset.py | 25 ++++++++++++++++--------- lib/galaxy/web/controllers/library_common.py | 13 ++++++++----- 2 files changed, 24 insertions(+), 14 deletions(-) diffs (153 lines): diff -r 2af472aa0844 -r 53ddb4b728f7 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Mar 10 17:10:43 2010 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Wed Mar 10 19:48:28 2010 -0500 @@ -1,4 +1,4 @@ -import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob +import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob, sys from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids @@ -11,6 +11,11 @@ pkg_resources.require( "Paste" ) import paste.httpexceptions +if sys.version_info[:2] < ( 2, 6 ): + zipfile.BadZipFile = zipfile.error +if sys.version_info[:2] < ( 2, 5 ): + zipfile.LargeZipFile = zipfile.error + tmpd = tempfile.mkdtemp() comptypes=[] ziptype = '32' @@ -204,6 +209,9 @@ def archive_composite_dataset( self, trans, data=None, **kwd ): # save a composite object into a compressed archive for downloading params = util.Params( kwd ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + outfname = data.name[0:150] + outfname = ''.join(c in valid_chars and c or '_' for c in outfname) if (params.do_action == None): params.do_action = 'zip' # default msg = util.restore_text( params.get( 'msg', '' ) ) @@ -230,7 +238,7 @@ except (OSError, zipfile.BadZipFile): error = True log.exception( "Unable to create archive for download" ) - msg = "Unable to create archive for %s for download, please report this error" % data.name + msg = "Unable to create archive for %s for download, please report this error" % outfname messagetype = 'error' if not error: current_user_roles = trans.get_current_user_roles() @@ -239,7 +247,7 @@ fname = os.path.split(path)[-1] basename = data.metadata.base_name efp = data.extra_files_path - htmlname = os.path.splitext(data.name)[0] + htmlname = os.path.splitext(outfname)[0] if not htmlname.endswith(ext): htmlname = '%s_%s' % (htmlname,ext) archname = '%s.html' % htmlname # fake the real nature of the html file @@ -276,14 +284,14 @@ messagetype = 'error' if not error: trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyCompositeObject.zip" + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.zip" % outfname return tmpfh else: trans.response.set_content_type( "application/x-tar" ) outext = 'tgz' if params.do_action == 'tbz': outext = 'tbz' - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % outext + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream @@ -294,7 +302,8 @@ @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" - + composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) + composite_extensions.append('html') # for archiving composite datatypes # DEPRECATION: We still support unencoded ids for backward compatibility try: dataset_id = int( dataset_id ) @@ -329,8 +338,6 @@ trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) if to_ext: # Saving the file - composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) - composite_extensions.append('html') if data.ext in composite_extensions: return self.archive_composite_dataset( trans, data, **kwd ) else: @@ -340,7 +347,7 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = data.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext) + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s]%s" % (data.hid, fname, to_ext) return open( data.file_name ) if os.path.exists( data.file_name ): max_peek_size = 1000000 # 1 MB diff -r 2af472aa0844 -r 53ddb4b728f7 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 10 17:10:43 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 19:48:28 2010 -0500 @@ -1312,6 +1312,7 @@ else: error = False try: + outext = 'zip' if action == 'zip': # Can't use mkstemp - the file must not exist first tmpd = tempfile.mkdtemp() @@ -1323,8 +1324,10 @@ archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif action == 'tgz': archive = util.streamball.StreamBall( 'w|gz' ) + outext = 'gz' elif action == 'tbz': archive = util.streamball.StreamBall( 'w|bz2' ) + outext = 'bz2' except (OSError, zipfile.BadZipFile): error = True log.exception( "Unable to create archive for download" ) @@ -1357,11 +1360,11 @@ seen.append( path ) 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] + outfname,zpathext = os.path.splitext(zpath) if zpathext == '': zpath = '%s.html' % zpath # fake the real nature of the html file try: - archive.add(ldda.dataset.file_name,zpath) + 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) @@ -1375,7 +1378,7 @@ archive.add( fpath,fname ) except IOError: error = True - log.exception( "Unable to add %s to temporary library download archive" % fname) + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) msg = "Unable to create archive for download, please report this error" messagetype = 'error' continue @@ -1402,11 +1405,11 @@ messagetype = 'error' if not error: trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext) return tmpfh else: trans.response.set_content_type( "application/x-tar" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream

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Balloon tooltips
by Assaf Gordon 17 Mar '10

17 Mar '10

Hi, I was wondering if there's an easy way to disable the pop-up balloon tooltips (on the save, rerun, view, delete icons) ? The new beautiful icons (or the old text-label) are informative enough - and the constantly appearing/disappearing black tooltip balloons (when you move the mouse over datasets) is a bit annoying. Alternatively, is it possible to add a short delay before showing the tooltip (like in all regular GUI client-side applications) ? Thanks, -gordon

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