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Merge pull request #1198 from blankenberg/dt-biom

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BIOM1 Datatype enhancements
This commit is contained in:
John Chilton
2015-12-10 18:30:37 -05:00
parent 7a3aa044fb 3acfa9c786
commit b455157bd6
1 changed files with 68 additions and 15 deletions
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lib/galaxy/datatypes/text.py
+68 -15
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@@ -11,7 +11,7 @@ import subprocess
import tempfile
from galaxy.datatypes.data import get_file_peek, Text
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
from galaxy.util import nice_size, string_as_bool
log = logging.getLogger(__name__)
@@ -122,45 +122,98 @@ class Ipynb( Json ):
pass
class Biom1(Json):
class Biom1( Json ):
"""
BIOM version 1.0 file format description
http://biom-format.org/documentation/format_versions/biom-1.0.html
"""
file_ext = "biom1"
def set_peek(self, dataset, is_multi_byte=False):
super(Biom1, self).set_peek(dataset, is_multi_byte)
MetadataElement( name="table_rows", default=[], desc="table_rows", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
MetadataElement( name="table_matrix_element_type", default="", desc="table_matrix_element_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
MetadataElement( name="table_format", default="", desc="table_format", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
MetadataElement( name="table_generated_by", default="", desc="table_generated_by", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
MetadataElement( name="table_matrix_type", default="", desc="table_matrix_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
MetadataElement( name="table_shape", default=[], desc="table_shape", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
MetadataElement( name="table_format_url", default="", desc="table_format_url", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
MetadataElement( name="table_date", default="", desc="table_date", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
MetadataElement( name="table_type", default="", desc="table_type", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
MetadataElement( name="table_id", default=None, desc="table_id", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value=None )
MetadataElement( name="table_columns", default=[], desc="table_columns", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
def set_peek( self, dataset, is_multi_byte=False ):
super( Biom1, self ).set_peek( dataset, is_multi_byte )
if not dataset.dataset.purged:
dataset.blurb = "Biological Observation Matrix v1"
def sniff(self, filename):
def sniff( self, filename ):
is_biom = False
if self._looks_like_json( filename ):
is_biom = self._looks_like_biom(filename)
is_biom = self._looks_like_biom( filename )
return is_biom
def _looks_like_biom(self, filepath, load_size=50000):
def _looks_like_biom( self, filepath, load_size=50000 ):
"""
@param filepath: [str] The path to the evaluated file.
@param load_size: [int] The size of the file block load in RAM (in
bytes).
"""
is_biom = False
segment_size = int(load_size / 2)
segment_size = int( load_size / 2 )
try:
with open(filepath, "r") as fh:
with open( filepath, "r" ) as fh:
prev_str = ""
segment_str = fh.read(segment_size)
if segment_str.strip().startswith('{'):
while segment_str and not is_biom:
segment_str = fh.read( segment_size )
if segment_str.strip().startswith( '{' ):
while segment_str:
current_str = prev_str + segment_str
if '"format"' in current_str:
current_str = re.sub(r'\s', '', current_str)
current_str = re.sub( r'\s', '', current_str )
if '"format":"BiologicalObservationMatrix' in current_str:
is_biom = True
break
prev_str = segment_str
segment_str = fh.read(segment_size)
except:
segment_str = fh.read( segment_size )
except Exception:
pass
return is_biom
def set_meta( self, dataset, **kwd ):
"""
Store metadata information from the BIOM file.
"""
if dataset.has_data():
with open( dataset.file_name ) as fh:
try:
json_dict = json.load( fh )
except Exception:
return
def _transform_dict_list_ids( dict_list ):
if dict_list:
return [ x.get( 'id', None ) for x in dict_list ]
return []
b_transform = { 'rows': _transform_dict_list_ids, 'columns': _transform_dict_list_ids }
for ( m_name, b_name ) in [ ('table_rows', 'rows'),
('table_matrix_element_type', 'matrix_element_type'),
('table_format', 'format'),
('table_generated_by', 'generated_by'),
('table_matrix_type', 'matrix_type'),
('table_shape', 'shape'),
('table_format_url', 'format_url'),
('table_date', 'date'),
('table_type', 'type'),
('table_id', 'id'),
('table_columns', 'columns') ]:
try:
metadata_value = json_dict.get( b_name, None )
if b_name in b_transform:
metadata_value = b_transform[ b_name ]( metadata_value )
setattr( dataset.metadata, m_name, metadata_value )
except Exception:
pass
class Obo( Text ):
"""