Mercurial > repos > cropgeeks > flapjack

comparison flapjack.py @ 39:c8c40cbe2945 draft

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author cropgeeks
date Thu, 02 Mar 2017 08:16:25 -0500
parents 7ae1bb322c6f
children 4a0f069c98e0
comparison
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38:7ae1bb322c6f 39:c8c40cbe2945
1 from galaxy.datatypes.data import Text 1 from galaxy.datatypes.data import Text
2 from galaxy.datatypes.tabular import Tabular 2 from galaxy.datatypes.tabular import Tabular
3 from galaxy.datatypes.binary import SQlite 3 from galaxy.datatypes.binary import Binary
4 4
5 class FlapjackFormat(SQlite): 5 class FlapjackFormat(Binary):
6 file_ext = "flapjack" 6 file_ext = "flapjack"
7 7
8 def sniff(self, filename): 8 def sniff(self, filename):
9 if super(FlapjackFormat, self).sniff(filename): 9 # The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
10 fj_table_names = ["objects", "project"] 10 # about the format, see http://www.sqlite.org/fileformat.html
11 try: 11 try:
12 header = open(filename, 'rb').read(16)
13 if header == b'SQLite format 3\0':
14 fj_table_names = ["objects", "project"]
12 conn = sqlite.connect(filename) 15 conn = sqlite.connect(filename)
13 c = conn.cursor() 16 c = conn.cursor()
14 tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name" 17 tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
15 result = c.execute(tables_query).fetchall() 18 result = c.execute(tables_query).fetchall()
16 result = [_[0] for _ in result] 19 result = [_[0] for _ in result]
17 for table_name in fj_table_names: 20 for table_name in fj_table_names:
18 if table_name not in result: 21 if table_name not in result:
19 return False 22 return False
20 return True 23 return True
21 except Exception as e: 24 return False
22 log.warning('%s, sniff Exception: %s', self, e) 25 except:
23 return False 26 return False
24 27
25 Binary.register_sniffable_binary_format( "flapjack", "flapjack", FlapjackFormat) 28 Binary.register_sniffable_binary_format( "flapjack", "flapjack", FlapjackFormat)
26 29
27 class FlapjackMapFormat(Tabular): 30 class FlapjackMapFormat(Tabular):
28 file_ext = "fjmap" 31 file_ext = "fjmap"