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Bug fix in biomart - metadata will now be correctly set for biomart data.

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This commit is contained in:
Greg Von Kuster
2007-12-11 18:40:30 +00:00
parent 4eeecaea63
commit d61ae1181e
2 changed files with 10 additions and 22 deletions
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lib/galaxy/datatypes/registry.py
+1 -1
View File
@@ -151,8 +151,8 @@ class Registry( object ):
# call init_meta and copy metadata from itself. The datatype
# being converted *to* will handle any metadata copying and
# initialization.
data.init_meta( copy_from=data )
if data.has_data():
data.init_meta( copy_from=data )
data.set_peek()
return data
tools/data_source/biomart_filter.py
+9 -21
View File
@@ -1,7 +1,6 @@
# Greg Von Kuster
import urllib
from galaxy.datatypes import sniff
from galaxy import datatypes, config
import tempfile, shutil
@@ -18,27 +17,21 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
"""Verifies the data after the run"""
URL = param_dict.get( 'URL', None )
if not URL:
raise Exception('Datasource has not sent back a URL parameter')
URL = URL + '&_export=1&GALAXY_URL=0'
CHUNK_SIZE = 2**20 # 1Mb
MAX_SIZE = CHUNK_SIZE * 100
try:
# damn you stupid sanitizer! - URL is now in the NEVER_SANITIZE list in util.py
#URL = URL.replace('martX', 'mart&')
#URL = URL.replace('0X_', '0&_')
page = urllib.urlopen(URL)
except Exception, exc:
raise Exception('Problems connecting to %s (%s)' % (URL, exc) )
name, data = out_data.items()[0]
fp = open(data.file_name, 'wb')
size = 0
max_size_exceeded = False
while 1:
chunk = page.read(CHUNK_SIZE)
if not chunk:
@@ -48,15 +41,15 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
max_size_exceeded = True
break
fp.write(chunk)
fp.close()
if max_size_exceeded:
data.info = 'Maximum data size of 100 MB exceeded, incomplete data retrieval.'
else:
data.info = data.name
#Set meta data, format file to be valid interval type
if isinstance(data.datatype, datatypes.interval.Interval):
if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval):
#Set meta data, format file to be valid interval type
data.set_meta(first_line_is_header=True)
#check for missing meta data, if all there, comment first line and process file
if not data.missing_meta():
@@ -69,17 +62,13 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
startCol = int(data.metadata.startCol) - 1
strandCol = int(data.metadata.strandCol) - 1
for line in open(data.file_name, 'r'):
line_ctr += 1
#First line is a non-commented header line, lets comment it out here
if line_ctr == 0:
temp.write("#%s" % line)
continue
fields = line.strip().split('\t')
#If chrom col is an int, make it chrInt
try:
int(fields[chromCol])
@@ -89,14 +78,12 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
if fields[chromCol].upper()== "X" or fields[chromCol].upper()== "Y":
fields[chromCol] = "chr%s" % fields[chromCol].upper()
except:
pass
pass
#change to BED coordinate system
try:
fields[startCol] = str(int(fields[startCol]) - 1)
except:
pass
#set strand to +/-, instead of +1/-1
try:
if strandCol > 0:
@@ -106,17 +93,18 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
fields[strandCol] = "-"
except:
pass
temp.write("%s\n" % '\t'.join(fields))
temp.close()
shutil.move(temp_filename,data.file_name)
else:
data_type = sniff.guess_ext(data.file_name)
data = app.datatypes_registry.change_datatype(data, data_type)
if data.missing_meta():
data.set_meta()
else:
data_type = sniff.guess_ext(data.file_name)
data = app.datatypes_registry.change_datatype(data, data_type)
if data.missing_meta():
data.set_meta()
data.set_peek()
data.flush()