2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b6e1ffaa053/ Changeset: 8b6e1ffaa053 Branch: next-stable User: dannon Date: 2014-06-02 19:16:15 Summary: Fix for when check_binary fails against an actual binary datatype. The logic in upload needs to be revisited per the comments. Affected #: 1 file diff -r f11149134d6dfafcaf7245f543381e60a937578b -r 8b6e1ffaa053f87c944290f3a84e5f73633cd901 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -241,7 +241,11 @@ dataset.name = uncompressed_name data_type = 'zip' if not data_type: - if check_binary( dataset.path ): + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): # We have a binary dataset, but it is not Bam, Sff or Pdf data_type = 'binary' #binary_ok = False https://bitbucket.org/galaxy/galaxy-central/commits/5273e0bf9ae5/ Changeset: 5273e0bf9ae5 User: dannon Date: 2014-06-02 19:16:51 Summary: merge next-stable Affected #: 1 file diff -r 15d426f19dcccb5ee3c06158898f1102c62d365d -r 5273e0bf9ae54599f1dadbce9d943dcac828d0f0 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -241,7 +241,11 @@ dataset.name = uncompressed_name data_type = 'zip' if not data_type: - if check_binary( dataset.path ): + # TODO refactor this logic. check_binary isn't guaranteed to be + # correct since it only looks at whether the first 100 chars are + # printable or not. If someone specifies a known unsniffable + # binary datatype and check_binary fails, the file gets mangled. + if check_binary( dataset.path ) or Binary.is_ext_unsniffable(dataset.file_type): # We have a binary dataset, but it is not Bam, Sff or Pdf data_type = 'binary' #binary_ok = False 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.