opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Determine dynamically if an extension corresponds to an unsniffable binary datatype

Browse Source 
Remove the need to call `Binary.register_unsniffable_binary_ext()` for
each unsniffable binary datatype.

Fix https://github.com/galaxyproject/galaxy/issues/3441 , where the upload
of files of a datatype defined in datatypes_conf.xml as subclass of an
unsniffable binary datatype ended up with "The uploaded binary file
contains inappropriate content" because it was not possible to register the
subclassed datatype as unsniffable.

Also remove unused `stop_err()` function in upload.py .
This commit is contained in:
Nicola Soranzo
2017-12-01 10:30:24 +00:00
parent dcd7e7809e
commit 0dfe73a54c
5 changed files with 12 additions and 40 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/data_source/upload.py
+5 -14
View File
@@ -36,11 +36,6 @@ else:
assert sys.version_info[:2] >= (2, 7)
def stop_err(msg, ret=1):
sys.stderr.write(msg)
sys.exit(ret)
def file_err(msg, dataset, json_file):
json_file.write(dumps(dict(type='dataset',
ext='data',
@@ -249,22 +244,18 @@ def add_file(dataset, registry, json_file, output_path):
dataset.name = uncompressed_name
data_type = 'zip'
if not data_type:
# 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):
if check_binary(dataset.path) or registry.is_extension_unsniffable_binary(dataset.file_type):
# We have a binary dataset, but it is not Bam, Sff or Pdf
data_type = 'binary'
# binary_ok = False
parts = dataset.name.split(".")
if len(parts) > 1:
ext = parts[-1].strip().lower()
if check_content and not Binary.is_ext_unsniffable(ext):
is_ext_unsniffable_binary = registry.is_extension_unsniffable_binary(ext)
if check_content and not is_ext_unsniffable_binary:
file_err('The uploaded binary file contains inappropriate content', dataset, json_file)
return
elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext:
err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % (ext.capitalize(), ext)
elif is_ext_unsniffable_binary and dataset.file_type != ext:
err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % (ext, ext)
file_err(err_msg, dataset, json_file)
return
if not data_type: