Mercurial > repos > cmonjeau > mapsembler2
comparison GSV.py @ 0:f905f982ee3d
Imported from capsule None
| author | cmonjeau |
|---|---|
| date | Fri, 05 Jun 2015 11:40:49 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:f905f982ee3d |
|---|---|
| 1 | |
| 2 """ | |
| 3 GSV visualisation datatypes | |
| 4 """ | |
| 5 | |
| 6 | |
| 7 import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re | |
| 8 | |
| 9 from galaxy.datatypes.sniff import * | |
| 10 from galaxy.datatypes import data | |
| 11 from galaxy.datatypes.metadata import MetadataElement | |
| 12 from galaxy.datatypes.xml import GenericXml | |
| 13 | |
| 14 log = logging.getLogger(__name__) | |
| 15 | |
| 16 class GenericMapJson( data.Text ): | |
| 17 """Base format class for any JSON file.""" | |
| 18 file_ext = "mapjson" | |
| 19 | |
| 20 def set_peek( self, dataset, is_multi_byte=False ): | |
| 21 """Set the peek and blurb text""" | |
| 22 if not dataset.dataset.purged: | |
| 23 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) | |
| 24 dataset.blurb = 'Mapjson data' | |
| 25 else: | |
| 26 dataset.peek = 'file does not exist' | |
| 27 dataset.blurb = 'file purged from disk' | |
| 28 | |
| 29 def sniff( self, filename ): | |
| 30 """ | |
| 31 Determines whether the file is JSON or not | |
| 32 | |
| 33 >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) | |
| 34 >>> GenericMapJson().sniff( fname ) | |
| 35 True | |
| 36 >>> fname = get_test_fname( 'interval.interval' ) | |
| 37 >>> GenericMapJson().sniff( fname ) | |
| 38 False | |
| 39 """ | |
| 40 #TODO - Use a context manager on Python 2.5+ to close handle | |
| 41 handle = open(filename) | |
| 42 line = handle.readline() | |
| 43 handle.close() | |
| 44 | |
| 45 | |
| 46 class Gjson( GenericMapJson ): | |
| 47 """ | |
| 48 Resource Description Framework format (http://www.w3.org/RDF/). | |
| 49 """ | |
| 50 file_ext = "gjson" | |
| 51 | |
| 52 def sniff( self, filename ): | |
| 53 """ | |
| 54 Returns false and the user must manually set. | |
| 55 """ | |
| 56 return False | |
| 57 | |
| 58 def set_peek( self, dataset, is_multi_byte=False ): | |
| 59 """Set the peek and blurb text""" | |
| 60 if not dataset.dataset.purged: | |
| 61 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) | |
| 62 dataset.blurb = 'GJSON data' | |
| 63 else: | |
| 64 dataset.peek = 'file does not exist' | |
| 65 dataset.blurb = 'file purged from disk' | |
| 66 |