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annotate neo4j.py @ 0:ba6fe46519e4 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
author sanbi-uwc
date Fri, 13 May 2016 08:36:48 -0400
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children 9f8e04bd6fa9
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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
parents:
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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 os
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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6 import sys
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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7
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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8 from galaxy.datatypes.text import Html
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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9 from galaxy.datatypes.metadata import MetadataElement
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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10 from galaxy.datatypes.data import get_file_peek
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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11 from galaxy.datatypes.data import Data, Text
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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12
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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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
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14 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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15
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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16 class Neo4j(Html):
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 """
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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22 MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
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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23 MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
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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24 MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
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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25 MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
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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26 MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
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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27 MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
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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28 MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
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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29 MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
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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30 MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
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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31 MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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32
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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33 composite_type = 'auto_primary_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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34 allow_datatype_change = False
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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35 file_ext = 'neo4j'
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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36
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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37 def generate_primary_file( self, dataset=None ):
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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38 rval = ['<html><head><title>Neo4j Galaxy Composite Dataset </title></head><p/>']
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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39 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
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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40 for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
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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41 fn = composite_name
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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42 opt_text = ''
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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43 if composite_file.optional:
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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44 opt_text = ' (optional)'
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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45 if composite_file.get('description'):
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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46 rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
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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47 else:
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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48 rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
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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49 rval.append( '</ul></div></html>' )
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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50 return "\n".join( rval )
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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51
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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52 def regenerate_primary_file(self, 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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53 """
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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54 cannot do this until we are setting metadata
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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55 """
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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56 efp = dataset.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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57 flist = os.listdir(efp)
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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58 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name, dataset.name)]
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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59 for i, fname in enumerate(flist):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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60 sfname = os.path.split(fname)[-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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61 f, e = os.path.splitext(fname)
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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62 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
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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63 rval.append( '</ul></body></html>' )
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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64 f = file(dataset.file_name, 'w')
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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65 f.write("\n".join( rval ))
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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66 f.write('\n')
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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67 f.close()
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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68
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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69 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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70 """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
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71 return 'text/html'
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
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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73 def set_meta( self, dataset, **kwd ):
ba6fe46519e4 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 6f0defa160a42559d15bc47768b845f24227dc03
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74 """
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
75 for lped/pbed eg
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 """
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
77 Html.set_meta( self, dataset, **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
78 if not kwd.get('overwrite'):
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 if verbose:
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 gal_Log.debug('@@@ neostore set_meta called with overwrite = 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
81 return 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
82 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
83 efp = dataset.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
84 except:
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 if verbose:
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 gal_Log.debug('@@@neostore set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.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
87 return 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
88 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
89 flist = os.listdir(efp)
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 except:
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 if verbose:
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 gal_Log.debug('@@@neostore set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.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
93 return 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
94 if len(flist) == 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
95 if verbose:
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
96 gal_Log.debug('@@@neostore set_meta failed - %s efp %s is empty?' % (dataset.name, efp))
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
97 return 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
98 self.regenerate_primary_file(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
99 if not dataset.info:
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
100 dataset.info = 'Galaxy genotype datatype object'
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 if not dataset.blurb:
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 dataset.blurb = 'Composite file - Neo4j Galaxy toolkit'
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 return 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
104
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
105 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
106 """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
107 if not dataset.dataset.purged:
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 dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
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 dataset.blurb = 'Neo4j database data'
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 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
111 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
112 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
113
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 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
115 """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
116 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
117 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
118 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
119 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
120
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
121 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
122 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
123 """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
124 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
125 """
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 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
parents:
diff changeset
127 # 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
parents:
diff changeset
128 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
129 to_ext, size, offset, **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
130 if self.file_ext == "neo4j":
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
131 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
132 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
133 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
134 # 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
parents:
diff changeset
135 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
136 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
137 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
138 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
139 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
140 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
141 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
142 # 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
143 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
144
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
145
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
146 class Neo4jDB(Neo4j, Data):
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
147 """Class for nucleotide BLAST database 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
148 file_ext = 'neostore'
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
149
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
150 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
151 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
152 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
153 self.add_composite_file('neostore.id', 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:
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154 self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file', 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:
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155 self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file', 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
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156 self.add_composite_file('neostore.labeltokenstore.db', substitute_name_with_metadata='neostore_labeltokenstore_db_file', 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:
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157 self.add_composite_file('neostore.labeltokenstore.db.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', 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:
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158 self.add_composite_file('neostore.labeltokenstore.db.names', substitute_name_with_metadata='neostore_labeltokenstore_db_file', 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:
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159 self.add_composite_file('neostore.labeltokenstore.db.names.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', 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
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160 self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file', 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:
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161 self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file', 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
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162 self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file', 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:
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163 self.add_composite_file('neostore.nodestore.db.labels.id', substitute_name_with_metadata='neostore_nodestore_file', 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:
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164
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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165 self.add_composite_file('neostore.propertystore.db', substitute_name_with_metadata='neostore_propertystore_file', 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:
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166 self.add_composite_file('neostore.propertystore.db.id', substitute_name_with_metadata='neostore_propertystore_file', 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:
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167 self.add_composite_file('neostore.propertystore.db.arrays', substitute_name_with_metadata='neostore_propertystore_file', 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:
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168 self.add_composite_file('neostore.propertystore.db.arrays.id', substitute_name_with_metadata='neostore_propertystore_file', 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:
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169 self.add_composite_file('neostore.propertystore.db.index', substitute_name_with_metadata='neostore_propertystore_file', 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:
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170 self.add_composite_file('neostore.propertystore.db.index.id',substitute_name_with_metadata='neostore_propertystore_file', 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:
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171 self.add_composite_file('neostore.propertystore.db.index.keys', substitute_name_with_metadata='neostore_propertystore_file', 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:
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172 self.add_composite_file('neostore.propertystore.db.index.keys.id', substitute_name_with_metadata='neostore_propertystore_file', 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:
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173 self.add_composite_file('neostore.propertystore.db.strings', substitute_name_with_metadata='neostore_propertystore_file', 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:
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174 self.add_composite_file('neostore.propertystore.db.strings.id', substitute_name_with_metadata='neostore_propertystore_file', 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:
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175
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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176 self.add_composite_file('neostore.relationshipgroupstore.db', substitute_name_with_metadata='neostore_relationship_group_file', 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:
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177 self.add_composite_file('neostore.relationshipgroupstore.db.id', substitute_name_with_metadata='neostore_relationship_group_file', 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:
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178 self.add_composite_file('neostore.relationshipstore.db', substitute_name_with_metadata='neostore_relationship_file', 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:
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179 self.add_composite_file('neostore.relationshipstore.db.id', substitute_name_with_metadata='neostore_relationship_file', 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:
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180 self.add_composite_file('neostore.relationshiptypestore.db', substitute_name_with_metadata='neostore_relationship_type_file', 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:
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181 self.add_composite_file('neostore.relationshiptypestore.db.id', substitute_name_with_metadata='neostore_relationship_type_file', 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:
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182 self.add_composite_file('neostore.relationshiptypestore.db.names', substitute_name_with_metadata='neostore_relationship_type_file', 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:
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183 self.add_composite_file('neostore.relationshiptypestore.db.names.id', substitute_name_with_metadata='neostore_relationship_type_file', 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:
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184 self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file', 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:
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185 self.add_composite_file('neostore.schemastore.db.id', substitute_name_with_metadata='neostore_schema_store_file', 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:
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186 self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file', 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:
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187
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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188 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:
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189 import doctest
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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190 doctest.testmod(sys.modules[__name__])