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1 """
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2 PRIMS proteomics classes for types defined in datatypes_conf.xml
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3 """
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4 import logging
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5 import re
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6 from galaxy.datatypes.data import *
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7 from galaxy.datatypes.xml import *
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8 from galaxy.datatypes.sniff import *
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9 from galaxy.datatypes.binary import *
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10 from galaxy.datatypes.interval import *
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11
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12 log = logging.getLogger(__name__)
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13
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14
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15 class ProteomicsXml(GenericXml):
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16 """ An enhanced XML datatype used to reuse code across several
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17 proteomic/mass-spec datatypes. (this part of the code is taken from protk proteomics datatypes package) """
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18
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19 def sniff(self, filename):
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20 """ Determines whether the file is the correct XML type. """
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21 with open(filename, 'r') as contents:
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22 while True:
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23 line = contents.readline()
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24 if line == None or not line.startswith('<?'):
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25 break
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26 pattern = '^<(\w*:)?%s' % self.root # pattern match <root or <ns:root for any ns string
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27 return line != None and re.match(pattern, line) != None
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28
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29 def set_peek( self, dataset, is_multi_byte=False ):
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30 """Set the peek and blurb text"""
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31 if not dataset.dataset.purged:
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32 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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33 dataset.blurb = self.blurb
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34 else:
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35 dataset.peek = 'file does not exist'
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36 dataset.blurb = 'file purged from disk'
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37
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38 class Apml( ProteomicsXml ):
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39 """APML data"""
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40 file_ext = "apml"
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41 blurb = 'PRIMS APML proteomics data'
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42 root = "apml" |
