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No need to iterate

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This commit is contained in:
Nicola Soranzo
2019-03-07 12:47:25 +00:00
parent 5f738d9503
commit cf2f192d1b
1 changed files with 21 additions and 49 deletions
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lib/galaxy/datatypes/microarrays.py
+21 -49
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@@ -5,7 +5,7 @@ from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
iter_headers
get_headers
)
log = logging.getLogger(__name__)
@@ -70,39 +70,24 @@ class Gal(GenericMicroarrayFile):
>>> Gal().sniff(fname)
False
"""
headers = iter_headers(file_prefix, sep="\t", count=3)
found_gal = False
found_atf = False
for count, line in enumerate(headers):
if count == 0:
if "ATF" in line[0]:
found_atf = True
elif count == 2:
if "GenePix ArrayList" in line[0]:
found_gal = True
return found_gal and found_atf
headers = get_headers(file_prefix, sep="\t", count=3)
return "ATF" in headers[0][0] and "GenePix ArrayList" in headers[2][0]
def set_meta(self, dataset, **kwd):
"""
Set metadata for Gal file.
"""
super(Gal, self).set_meta(dataset, **kwd)
headers = iter_headers(dataset.file_name, sep="\t", count=5)
for count, line in enumerate(headers):
if count == 0:
dataset.metadata.file_format = line[0]
dataset.metadata.version_number = line[1]
elif count == 1:
dataset.metadata.number_of_optional_header_records = int(line[0])
dataset.metadata.number_of_data_columns = int(line[1])
elif count == 2:
dataset.metadata.file_type = line[0].strip().replace('"', '').split("=")[1]
elif count == 3:
if "BlockCount" in line[0]:
dataset.metadata.block_count = int(line[0].strip().replace('"', '').split("=")[1])
elif count == 4:
if "BlockType" in line[0]:
dataset.metadata.block_type = int(line[0].strip().replace('"', '').split("=")[1])
headers = get_headers(dataset.file_name, sep="\t", count=5)
dataset.metadata.file_format = headers[0][0]
dataset.metadata.version_number = headers[0][1]
dataset.metadata.number_of_optional_header_records = int(headers[1][0])
dataset.metadata.number_of_data_columns = int(headers[1][1])
dataset.metadata.file_type = headers[2][0].strip().strip('"').split("=")[1]
if "BlockCount" in headers[3][0]:
dataset.metadata.block_count = int(headers[3][0].strip().strip('"').split("=")[1])
if "BlockType" in headers[4][0]:
dataset.metadata.block_type = int(headers[4][0].strip().strip('"').split("=")[1])
@build_sniff_from_prefix
@@ -126,30 +111,17 @@ class Gpr(GenericMicroarrayFile):
>>> Gpr().sniff(fname)
False
"""
headers = iter_headers(file_prefix, sep="\t", count=3)
found_gpr = False
found_atf = False
for count, line in enumerate(headers):
if count == 0:
if "ATF" in line[0]:
found_atf = True
elif count == 2:
if "GenePix Results" in line[0]:
found_gpr = True
return found_atf and found_gpr
headers = get_headers(file_prefix, sep="\t", count=3)
return "ATF" in headers[0][0] and "GenePix Results" in headers[2][0]
def set_meta(self, dataset, **kwd):
"""
Set metadata for Gpr file.
"""
super(Gpr, self).set_meta(dataset, **kwd)
headers = iter_headers(dataset.file_name, sep="\t", count=5)
for count, line in enumerate(headers):
if count == 0:
dataset.metadata.file_format = line[0]
dataset.metadata.version_number = line[1]
elif count == 1:
dataset.metadata.number_of_optional_header_records = int(line[0])
dataset.metadata.number_of_data_columns = int(line[1])
elif count == 2:
dataset.metadata.file_type = line[0].strip().replace('"', '').split("=")[1]
headers = get_headers(dataset.file_name, sep="\t", count=5)
dataset.metadata.file_format = headers[0][0]
dataset.metadata.version_number = headers[0][1]
dataset.metadata.number_of_optional_header_records = int(headers[1][0])
dataset.metadata.number_of_data_columns = int(headers[1][1])
dataset.metadata.file_type = headers[2][0].strip().strip('"').split("=")[1]