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comparison neo4j.py @ 18:3472a853df10 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 8e48c62981e1e81254b777ebd5df2436d53a7f10
author sanbi-uwc
date Wed, 18 May 2016 10:13:46 -0400
parents 969c57578047
children 2287178087eb
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17:969c57578047 18:3472a853df10
16 class Neo4j(Html): 16 class Neo4j(Html):
17 """ 17 """
18 base class to use for neostore datatypes 18 base class to use for neostore datatypes
19 derived from html - composite datatype elements 19 derived from html - composite datatype elements
20 stored in extra files path 20 stored in extra files path
21 """
22 """
23 MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
24 MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
25 MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
26 MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
27 MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
28 MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
29 MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
30 MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
31 MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
32 MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
33
34 composite_type = 'auto_primary_file'
35 allow_datatype_change = False
36 file_ext = 'neo4j'
37
38 def generate_primary_file( self, dataset=None ):
39 rval = ['<html><head><title>Neo4j Galaxy Composite Dataset </title></head><p/>']
40 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
41 for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
42 fn = composite_name
43 opt_text = ''
44 if composite_file.optional:
45 opt_text = ' (optional)'
46 if composite_file.get('description'):
47 rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
48 else:
49 rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
50 rval.append( '</ul></div></html>' )
51 return "\n".join( rval )
52
53 def regenerate_primary_file(self, dataset):
54
55 cannot do this until we are setting metadata
56
57 efp = dataset.extra_files_path
58 flist = os.listdir(efp)
59 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name, dataset.name)]
60 for i, fname in enumerate(flist):
61 sfname = os.path.split(fname)[-1]
62 f, e = os.path.splitext(fname)
63 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
64 rval.append( '</ul></body></html>' )
65 f = file(dataset.file_name, 'w')
66 f.write("\n".join( rval ))
67 f.write('\n')
68 f.close()
69 """ 21 """
70 22
71 def get_mime(self): 23 def get_mime(self):
72 """Returns the mime type of the datatype""" 24 """Returns the mime type of the datatype"""
73 return 'text/html' 25 return 'text/html'