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Merge pull request #38 from bgruening/converter_resorting

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resort the converters so that the accepted_formats are infront
This commit is contained in:
Björn Grüning
2018-01-07 23:30:22 +01:00
committed by GitHub
parent 43dd7910f4 b139726ed3
commit ea34bdc34d
1 changed files with 24 additions and 6 deletions
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lib/galaxy/datatypes/registry.py
+24 -6
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@@ -798,19 +798,34 @@ class Registry(object):
tabular.CSV()
]
def get_converters_by_datatype(self, ext):
"""Returns available converters by source type"""
def get_converters_by_datatype(self, ext, priority_formats=None):
"""
Returns available converters by source type.
`priority_formats` will contain a list of format extensions that should
be handled with priority. This means they will end up infront of the
returned ordered dictionary.
"""
if ext not in self._converters_by_datatype:
converters = odict()
prio_converters = odict()
source_datatype = type(self.get_datatype_by_extension(ext))
for ext2, converters_dict in self.datatype_converters.items():
converter_datatype = type(self.get_datatype_by_extension(ext2))
if issubclass(source_datatype, converter_datatype):
converters.update(converters_dict)
for k, v in converters_dict.items():
if k in priority_formats:
prio_converters[k] = v
else:
converters[k] = v
# Ensure ext-level converters are present
if ext in self.datatype_converters.keys():
converters.update(self.datatype_converters[ext])
self._converters_by_datatype[ext] = converters
for k, v in self.datatype_converters[ext].items():
if k in priority_formats:
prio_converters[k] = v
else:
converters[k] = v
prio_converters.update(converters)
self._converters_by_datatype[ext] = prio_converters
return self._converters_by_datatype[ext]
def get_converter_by_target_type(self, source_ext, target_ext):
@@ -822,7 +837,10 @@ class Registry(object):
def find_conversion_destination_for_dataset_by_extensions(self, dataset, accepted_formats, converter_safe=True):
"""Returns ( target_ext, existing converted dataset )"""
for convert_ext in self.get_converters_by_datatype(dataset.ext):
converters = self.get_converters_by_datatype(dataset.ext, [k.file_ext for k in accepted_formats])
for convert_ext in converters:
convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
if convert_ext_datatype is None:
self.log.warning("Datatype class not found for extension '%s', which is used as target for conversion from datatype '%s'" % (convert_ext, dataset.ext))