1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
# Author: Martin D. Smith
from __future__ import absolute_import
import os
import logging
log = logging.getLogger(__name__)
def fileType(fname):
"""Get the extension of fname (with h5 type)"""
remainder, ftype = os.path.splitext(fname)
if ftype == '.h5':
_, prefix = os.path.splitext(remainder)
ftype = prefix + ftype
elif ftype == '.index':
_, prefix = os.path.splitext(remainder)
if prefix == '.contig':
ftype = prefix + ftype
ftype = ftype.strip('.')
return ftype
def getDataSetUuid(xmlfile):
"""
Quickly retrieve the uuid from the root element of a dataset XML file,
using a streaming parser to avoid loading the entire dataset into memory.
Returns None if the parsing fails.
"""
try:
import xml.etree.cElementTree as ET
for event, element in ET.iterparse(xmlfile, events=("start",)):
return element.get("UniqueId")
except Exception:
return None
def getDataSetMetaType(xmlfile):
"""
Quickly retrieve the MetaType from the root element of a dataset XML file,
using a streaming parser to avoid loading the entire dataset into memory.
Returns None if the parsing fails.
"""
try:
import xml.etree.cElementTree as ET
for event, element in ET.iterparse(xmlfile, events=("start",)):
return element.get("MetaType")
except Exception:
return None
def loadMockCollectionMetadata():
"""
Load CollectionMetadata template from pbcore.data.datasets
"""
from pbcore.data.datasets import getMockCollectionMetadata
from pbcore.io.dataset.DataSetReader import parseCollectionMetadata
return parseCollectionMetadata(getMockCollectionMetadata())
|
