Mercurial > repos > sanbi-uwc > neo4j_datatypes

annotate neo4j.py @ 17:969c57578047 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
author sanbi-uwc
date Wed, 18 May 2016 10:11:25 -0400
parents de002a093129
children 3472a853df10
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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1 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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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
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3 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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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
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5 import sys
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666c7e606768 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 017f62614ecc913e42cdd8df79b94775968f0c2c
sanbi-uwc
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6 import os
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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7
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7f63bb1dd162 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit c70e817056b8b40ca30339792cc8457670bbf9eb
sanbi-uwc
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8 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
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9 from galaxy.datatypes.data import Data, Text
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969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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10 #from galaxy.datatypes.metadata import MetadataElement
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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12 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
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13 verbose = True
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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14
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7f262236d352 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit ebd884bad7609048e02d1ef04985cf812ab142a3
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ec3016ba76f2 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 002030d20f30ca916e883b64e332dcbdfa0d10a0
sanbi-uwc
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16 class Neo4j(Html):
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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17 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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18 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
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19 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
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20 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
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21 """
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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22 """
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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23 MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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24 MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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25 MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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26 MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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27 MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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28 MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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29 MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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30 MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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31 MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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32 MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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33
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34 composite_type = 'auto_primary_file'
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
sanbi-uwc
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35 allow_datatype_change = False
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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36 file_ext = 'neo4j'
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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37
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38 def generate_primary_file( self, dataset=None ):
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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39 rval = ['<html><head><title>Neo4j Galaxy Composite Dataset </title></head><p/>']
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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40 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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41 for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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42 fn = composite_name
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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43 opt_text = ''
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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44 if composite_file.optional:
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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45 opt_text = ' (optional)'
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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46 if composite_file.get('description'):
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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47 rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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48 else:
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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49 rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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50 rval.append( '</ul></div></html>' )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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51 return "\n".join( rval )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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52
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53 def regenerate_primary_file(self, dataset):
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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54
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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55 cannot do this until we are setting metadata
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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56
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57 efp = dataset.extra_files_path
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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58 flist = os.listdir(efp)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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59 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name, dataset.name)]
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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60 for i, fname in enumerate(flist):
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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61 sfname = os.path.split(fname)[-1]
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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62 f, e = os.path.splitext(fname)
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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63 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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64 rval.append( '</ul></body></html>' )
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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65 f = file(dataset.file_name, 'w')
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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66 f.write("\n".join( rval ))
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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67 f.write('\n')
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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68 f.close()
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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69 """
11
6a177f046b73 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 2de149508da75c935142db2fcba5e62c3faf2070
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70
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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71 def get_mime(self):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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72 """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
73 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
74
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
parents:
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75 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
76 """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:
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77 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
78 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
79 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
80 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
81 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
82 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
83
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
84 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
85 """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
86 try:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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diff changeset
87 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
88 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
89 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
90
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
91 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
92 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
93 """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
94 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
95 """
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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96 if filename is not None and filename != "index":
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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97 # Change nothing - important for the unit tests to access child files:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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98 return Data.display_data(self, trans, data, preview, filename,
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
99 to_ext, size, offset, **kwd)
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
100 if self.file_ext == "neostore":
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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diff changeset
101 title = "This is a NEO4J database"
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
102 msg = ""
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
103 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
104 # Try to use any text recorded in the dummy index file:
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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diff changeset
105 handle = open(data.file_name, "rU")
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
106 msg = handle.read().strip()
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
107 handle.close()
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
108 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
109 pass
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
110 if not msg:
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
111 msg = title
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 # Galaxy assumes HTML for the display of composite 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
113 return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)
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
114
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
115
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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diff changeset
116 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
117 """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
118 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
119 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
120 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
121
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
122
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
123 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
124 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
125 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
126 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
127 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
128 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
129 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
130 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
131 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
132 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
133 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
134 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
135 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
136 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
137
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
138 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
139 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
140 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
141 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
142 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
143 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
144 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
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145 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
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146 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
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147 self.add_composite_file('neostore.propertystore.db.strings.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
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ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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148
17
969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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149 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
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150 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
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151 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
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152 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
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153 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
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154 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
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155 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
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156 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
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157 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
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158
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
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159
0
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
sanbi-uwc
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160 if __name__ == '__main__':
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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161 import doctest
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969c57578047 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
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162 doctest.testmod(sys.modules[__name__])