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December 2011

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commit/galaxy-central: jgoecks: When exporting a history archive, use user dataset names rather than Galaxy dataset names. Fixes #680
by Bitbucket 01 Dec '11

01 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/effb888d61e1/ changeset: effb888d61e1 user: jgoecks date: 2011-12-01 16:22:46 summary: When exporting a history archive, use user dataset names rather than Galaxy dataset names. Fixes #680 affected #: 1 file diff -r a2ae1bb435378eefc659941b790ec15f3a0a8584 -r effb888d61e1214ac57222bee419ac378fed606f lib/galaxy/tools/imp_exp/export_history.py --- a/lib/galaxy/tools/imp_exp/export_history.py +++ b/lib/galaxy/tools/imp_exp/export_history.py @@ -10,6 +10,14 @@ from galaxy.util.json import * import optparse, sys, os, tempfile, tarfile +def get_dataset_filename( name, ext ): + """ + Builds a filename for a dataset using its name an extension. + """ + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + base = ''.join( c in valid_chars and c or '_' for c in name ) + return base + ".%s" % ext + def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ): """ Create archive from the given attribute/metadata files and save it to out_file. """ tarfile_mode = "w" @@ -37,7 +45,8 @@ # TODO: security check to ensure that files added are in Galaxy dataset directory? for dataset_attrs in datasets_attrs: dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name. - dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] ) + dataset_archive_name = os.path.join( 'datasets', + get_dataset_filename( dataset_attrs[ 'name' ], dataset_attrs[ 'extension' ] ) ) history_archive.add( dataset_file_name, arcname=dataset_archive_name ) # Update dataset filename to be archive name. dataset_attrs[ 'file_name' ] = dataset_archive_name Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Apply HTML escaping when editing dataset name.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a2ae1bb43537/ changeset: a2ae1bb43537 user: jgoecks date: 2011-12-01 04:50:12 summary: Apply HTML escaping when editing dataset name. affected #: 1 file diff -r 1638bc41454922e24dfa5e01d840fbf5ea505782 -r a2ae1bb435378eefc659941b790ec15f3a0a8584 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -39,7 +39,7 @@ Name: </label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${data.get_display_name()}" size="40"/> + <input type="text" name="name" value="${data.get_display_name() | h}" size="40"/></div><div style="clear: both"></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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