Mercurial > repos > sanbi-uwc > neo4j_datatypes

annotate neo4j.py @ 19:2287178087eb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
author sanbi-uwc
date Thu, 09 Jun 2016 05:52:56 -0400
parents 3472a853df10
children 45b969e6ff9a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
1 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
2 Neo4j Composite Dataset
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
3 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
4 import logging
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
5 import sys
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
6
13
7f63bb1dd162 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit c70e817056b8b40ca30339792cc8457670bbf9eb
sanbi-uwc
parents: 11
diff changeset
7 from galaxy.datatypes.images import Html
7f63bb1dd162 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit c70e817056b8b40ca30339792cc8457670bbf9eb
sanbi-uwc
parents: 11
diff changeset
8 from galaxy.datatypes.data import Data, Text
19
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
9 from galaxy.datatypes.metadata import MetadataElement
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
10 import shutil
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
11 import os
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
12
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
13 gal_Log = logging.getLogger(__name__)
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
14 verbose = True
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
15
5
7f262236d352 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit ebd884bad7609048e02d1ef04985cf812ab142a3
sanbi-uwc
parents: 4
diff changeset
16
15
ec3016ba76f2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 002030d20f30ca916e883b64e332dcbdfa0d10a0
sanbi-uwc
parents: 14
diff changeset
17 class Neo4j(Html):
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
18 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
19 base class to use for neostore datatypes
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
20 derived from html - composite datatype elements
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
21 stored in extra files path
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
22 """
19
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
23 MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
24 MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
25 MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
26 MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
27 MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
28 MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
29 MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
30 MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
31 MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
32 MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
11
6a177f046b73 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 2de149508da75c935142db2fcba5e62c3faf2070
sanbi-uwc
parents: 10
diff changeset
33
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
34 def get_mime(self):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
35 """Returns the mime type of the datatype"""
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
36 return 'text/html'
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
37
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
38 def set_peek(self, dataset, is_multi_byte=False):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
39 """Set the peek and blurb text"""
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
40 if not dataset.dataset.purged:
1
9f8e04bd6fa9 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 3f5361a7226127ec8b8d6cb5591b5bb4f52bb6fe
sanbi-uwc
parents: 0
diff changeset
41 dataset.peek = 'Neo4j database (multiple files)'
9f8e04bd6fa9 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 3f5361a7226127ec8b8d6cb5591b5bb4f52bb6fe
sanbi-uwc
parents: 0
diff changeset
42 dataset.blurb = 'Neo4j database (multiple files)'
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
43 else:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
44 dataset.peek = 'file does not exist'
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
45 dataset.blurb = 'file purged from disk'
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
46
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
47 def display_peek(self, dataset):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
48 """Create HTML content, used for displaying peek."""
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
49 try:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
50 return dataset.peek
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
51 except Exception:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
52 return "NEO4J database (multiple files)"
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
53
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
54 def display_data(self, trans, data, preview=False, filename=None,
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
55 to_ext=None, size=None, offset=None, **kwd):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
56 """Documented as an old display method, but still gets called via tests etc
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
57 This allows us to format the data shown in the central pane via the "eye" icon.
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
58 """
19
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
59 trans.response.set_content_type(data.get_mime())
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
60 trans.log_event( "Display dataset id: %s" % str( data.id ) )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
61
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
62 # the target directory name
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
63 dir_name = str(os.path.dirname( trans.app.object_store.get_filename(data.dataset) )) + '/dataset_{}_files/neo4jdb'.format( data.dataset.id )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
64
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
65 # generate unique filename for this dataset
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
66 valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
67 fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
68
19
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
69 # zip the target directory (dir_name) using the fname
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
70 shutil.make_archive(fname, 'zip', dir_name)
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
71 download_zip = fname + '.zip'
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
72
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
73 # setup headers for the download
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
74 trans.response.headers['Content-Length'] = int( os.stat( download_zip ).st_size )
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
75 trans.response.set_content_type( "application/octet-stream" ) # force octet-stream so Safari doesn't append mime extensions to filename
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
76 trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, download_zip , "zip")
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
77
2287178087eb planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 0f90b9e2eae026ccea40bcc164f142313af7d397
sanbi-uwc
parents: 18
diff changeset
78 return open( download_zip )
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
79
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
80 class Neo4jDB(Neo4j, Data):
1
9f8e04bd6fa9 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 3f5361a7226127ec8b8d6cb5591b5bb4f52bb6fe
sanbi-uwc
parents: 0
diff changeset
81 """Class for neo4jDB database files."""
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
82 file_ext = 'neostore'
15
ec3016ba76f2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 002030d20f30ca916e883b64e332dcbdfa0d10a0
sanbi-uwc
parents: 14
diff changeset
83 composite_type = 'basic'
ec3016ba76f2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 002030d20f30ca916e883b64e332dcbdfa0d10a0
sanbi-uwc
parents: 14
diff changeset
84 allow_datatype_change = False
ec3016ba76f2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 002030d20f30ca916e883b64e332dcbdfa0d10a0
sanbi-uwc
parents: 14
diff changeset
85
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
86
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
87 def __init__(self, **kwd):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
88 Data.__init__(self, **kwd)
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
89 self.add_composite_file('neostore', substitute_name_with_metadata='neostore', is_binary=True)
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
90 self.add_composite_file('neostore.id', substitute_name_with_metadata='neostore', is_binary=True)
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
91 self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
92 self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
93 self.add_composite_file('neostore.labeltokenstore.db', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
94 self.add_composite_file('neostore.labeltokenstore.db.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
95 self.add_composite_file('neostore.labeltokenstore.db.names', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
96 self.add_composite_file('neostore.labeltokenstore.db.names.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
97 self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
98 self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
99 self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
100 self.add_composite_file('neostore.nodestore.db.labels.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
101
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
102 self.add_composite_file('neostore.propertystore.db', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
103 self.add_composite_file('neostore.propertystore.db.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
104 self.add_composite_file('neostore.propertystore.db.arrays', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
105 self.add_composite_file('neostore.propertystore.db.arrays.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
106 self.add_composite_file('neostore.propertystore.db.index', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
107 self.add_composite_file('neostore.propertystore.db.index.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
108 self.add_composite_file('neostore.propertystore.db.index.keys', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
109 self.add_composite_file('neostore.propertystore.db.index.keys.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
110 self.add_composite_file('neostore.propertystore.db.strings', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
111 self.add_composite_file('neostore.propertystore.db.strings.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
112
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
113 self.add_composite_file('neostore.relationshipgroupstore.db', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
114 self.add_composite_file('neostore.relationshipgroupstore.db.id', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
115 self.add_composite_file('neostore.relationshipstore.db', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
116 self.add_composite_file('neostore.relationshipstore.db.id', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
117 self.add_composite_file('neostore.relationshiptypestore.db.names', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
118 self.add_composite_file('neostore.relationshiptypestore.db.names.id', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
119 self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
120 self.add_composite_file('neostore.schemastore.db.id', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
121 self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file', is_binary=True)
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
122
5
7f262236d352 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit ebd884bad7609048e02d1ef04985cf812ab142a3
sanbi-uwc
parents: 4
diff changeset
123
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
124 if __name__ == '__main__':
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
diff changeset
125 import doctest
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
parents: 16
diff changeset
126 doctest.testmod(sys.modules[__name__])