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comparison neo4j.py @ 19:2287178087eb draft

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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
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18:3472a853df10 19:2287178087eb
1 """ 1 """
2 Neo4j Composite Dataset 2 Neo4j Composite Dataset
3 """ 3 """
4 import logging 4 import logging
5 import sys 5 import sys
6 import os
7 6
8 from galaxy.datatypes.images import Html 7 from galaxy.datatypes.images import Html
9 from galaxy.datatypes.data import Data, Text 8 from galaxy.datatypes.data import Data, Text
10 #from galaxy.datatypes.metadata import MetadataElement 9 from galaxy.datatypes.metadata import MetadataElement
10 import shutil
11 import os
11 12
12 gal_Log = logging.getLogger(__name__) 13 gal_Log = logging.getLogger(__name__)
13 verbose = True 14 verbose = True
14 15
15 16
17 """ 18 """
18 base class to use for neostore datatypes 19 base class to use for neostore datatypes
19 derived from html - composite datatype elements 20 derived from html - composite datatype elements
20 stored in extra files path 21 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)
22 33
23 def get_mime(self): 34 def get_mime(self):
24 """Returns the mime type of the datatype""" 35 """Returns the mime type of the datatype"""
25 return 'text/html' 36 return 'text/html'
26 37
43 def display_data(self, trans, data, preview=False, filename=None, 54 def display_data(self, trans, data, preview=False, filename=None,
44 to_ext=None, size=None, offset=None, **kwd): 55 to_ext=None, size=None, offset=None, **kwd):
45 """Documented as an old display method, but still gets called via tests etc 56 """Documented as an old display method, but still gets called via tests etc
46 This allows us to format the data shown in the central pane via the "eye" icon. 57 This allows us to format the data shown in the central pane via the "eye" icon.
47 """ 58 """
48 if filename is not None and filename != "index": 59 trans.response.set_content_type(data.get_mime())
49 # Change nothing - important for the unit tests to access child files: 60 trans.log_event( "Display dataset id: %s" % str( data.id ) )
50 return Data.display_data(self, trans, data, preview, filename,
51 to_ext, size, offset, **kwd)
52 if self.file_ext == "neostore":
53 title = "This is a NEO4J database"
54 msg = ""
55 try:
56 # Try to use any text recorded in the dummy index file:
57 handle = open(data.file_name, "rU")
58 msg = handle.read().strip()
59 handle.close()
60 except Exception:
61 pass
62 if not msg:
63 msg = title
64 # Galaxy assumes HTML for the display of composite datatypes,
65 return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)
66 61
62 # the target directory name
63 dir_name = str(os.path.dirname( trans.app.object_store.get_filename(data.dataset) )) + '/dataset_{}_files/neo4jdb'.format( data.dataset.id )
64
65 # generate unique filename for this dataset
66 valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
67 fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
68
69 # zip the target directory (dir_name) using the fname
70 shutil.make_archive(fname, 'zip', dir_name)
71 download_zip = fname + '.zip'
72
73 # setup headers for the download
74 trans.response.headers['Content-Length'] = int( os.stat( download_zip ).st_size )
75 trans.response.set_content_type( "application/octet-stream" ) # force octet-stream so Safari doesn't append mime extensions to filename
76 trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, download_zip , "zip")
77
78 return open( download_zip )
67 79
68 class Neo4jDB(Neo4j, Data): 80 class Neo4jDB(Neo4j, Data):
69 """Class for neo4jDB database files.""" 81 """Class for neo4jDB database files."""
70 file_ext = 'neostore' 82 file_ext = 'neostore'
71 composite_type = 'basic' 83 composite_type = 'basic'