# HG changeset patch
# User sanbi-uwc
# Date 1463580182 14400
# Node ID de002a093129b58b97fa574866d77c49c8242029
# Parent ec3016ba76f277b4a80ecb0527b2a2567b28e921
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 7a82ce5ab053e4b6fd00c3d9702e13609fa9a6bb
diff -r ec3016ba76f2 -r de002a093129 neo4j.py
--- a/neo4j.py Wed May 18 09:43:44 2016 -0400
+++ b/neo4j.py Wed May 18 10:03:02 2016 -0400
@@ -7,7 +7,8 @@
from galaxy.datatypes.images import Html
from galaxy.datatypes.data import Data, Text
-#from galaxy.datatypes.metadata import MetadataElement
+
+# from galaxy.datatypes.metadata import MetadataElement
gal_Log = logging.getLogger(__name__)
verbose = True
@@ -19,54 +20,6 @@
derived from html - composite datatype elements
stored in extra files path
"""
- """
- MetadataElement( name='neostore', default=None, desc='Neo4j NeoStore File', readonly=True, visible=True, set_in_upload=True, no_value=None )
- MetadataElement( name='neostore_count_file', default=None, desc='Neo4j Count File', readonly=True, visible=True, set_in_upload=True, no_value=None )
- MetadataElement( name="neostore_labeltokenstore_db_file", default=None, desc="Neostore LabelTokenStore File", readonly=True, visible=True, no_value=None )
- MetadataElement( name="neostore_nodestore_file", default=None, desc="Neostore NodeStore File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_propertystore_file", default=None, desc="Neostore Property Store File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_relationship_group_file", default=None, desc="Neostore Relationship Group File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_relationship_file", default=None, desc="Neostore Relationship File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_relationship_type_file", default=None, desc="Neostore Relationship Type File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_schema_store_file", default=None, desc="Neostore Schema Store File", readonly=True, visible=True, no_value=None)
- MetadataElement( name="neostore_transaction_db_file", default=None, desc="Neostore Transaction File", readonly=True, visible=True, no_value=None)
-
- composite_type = 'auto_primary_file'
- allow_datatype_change = False
- file_ext = 'neo4j'
-
- def generate_primary_file( self, dataset=None ):
- rval = ['
Neo4j Galaxy Composite Dataset ']
- rval.append('This composite dataset is composed of the following files:
')
- for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
- fn = composite_name
- opt_text = ''
- if composite_file.optional:
- opt_text = ' (optional)'
- if composite_file.get('description'):
- rval.append( '- %s (%s)%s
' % ( fn, fn, composite_file.get('description'), opt_text ) )
- else:
- rval.append( '- %s%s
' % ( fn, fn, opt_text ) )
- rval.append( '
' )
- return "\n".join( rval )
-
- def regenerate_primary_file(self, dataset):
-
- cannot do this until we are setting metadata
-
- efp = dataset.extra_files_path
- flist = os.listdir(efp)
- rval = ['Files for Composite Dataset %sComposite %s contains:' % (dataset.name, dataset.name)]
- for i, fname in enumerate(flist):
- sfname = os.path.split(fname)[-1]
- f, e = os.path.splitext(fname)
- rval.append( '- %s
' % ( sfname, sfname) )
- rval.append( '
' )
- f = file(dataset.file_name, 'w')
- f.write("\n".join( rval ))
- f.write('\n')
- f.close()
- """
def get_mime(self):
"""Returns the mime type of the datatype"""
@@ -119,44 +72,73 @@
composite_type = 'basic'
allow_datatype_change = False
-
def __init__(self, **kwd):
Data.__init__(self, **kwd)
self.add_composite_file('neostore', substitute_name_with_metadata='neostore', is_binary=True)
self.add_composite_file('neostore.id', substitute_name_with_metadata='neostore', is_binary=True)
- self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file', is_binary=True)
- self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file', is_binary=True)
- self.add_composite_file('neostore.labeltokenstore.db', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
- self.add_composite_file('neostore.labeltokenstore.db.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
- self.add_composite_file('neostore.labeltokenstore.db.names', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
- self.add_composite_file('neostore.labeltokenstore.db.names.id', substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
- self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
- self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
- self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
- self.add_composite_file('neostore.nodestore.db.labels.id', substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
+ self.add_composite_file('neostore.counts.db.a', substitute_name_with_metadata='neostore_count_file',
+ is_binary=True)
+ self.add_composite_file('neostore.counts.db.b', substitute_name_with_metadata='neostore_count_file',
+ is_binary=True)
+ self.add_composite_file('neostore.labeltokenstore.db',
+ substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+ self.add_composite_file('neostore.labeltokenstore.db.id',
+ substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+ self.add_composite_file('neostore.labeltokenstore.db.names',
+ substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+ self.add_composite_file('neostore.labeltokenstore.db.names.id',
+ substitute_name_with_metadata='neostore_labeltokenstore_db_file', is_binary=True)
+ self.add_composite_file('neostore.nodestore.db', substitute_name_with_metadata='neostore_nodestore_file',
+ is_binary=True)
+ self.add_composite_file('neostore.nodestore.db.id', substitute_name_with_metadata='neostore_nodestore_file',
+ is_binary=True)
+ self.add_composite_file('neostore.nodestore.db.labels', substitute_name_with_metadata='neostore_nodestore_file',
+ is_binary=True)
+ self.add_composite_file('neostore.nodestore.db.labels.id',
+ substitute_name_with_metadata='neostore_nodestore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.arrays', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.arrays.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.index', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.index.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.index.keys', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.index.keys.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.strings', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.propertystore.db.strings.id', substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.id',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.arrays',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.arrays.id',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.index',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.index.id',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.index.keys',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.index.keys.id',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.strings',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
+ self.add_composite_file('neostore.propertystore.db.strings.id',
+ substitute_name_with_metadata='neostore_propertystore_file', is_binary=True)
- self.add_composite_file('neostore.relationshipgroupstore.db', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
- self.add_composite_file('neostore.relationshipgroupstore.db.id', substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
- self.add_composite_file('neostore.relationshipstore.db', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
- self.add_composite_file('neostore.relationshipstore.db.id', substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
- self.add_composite_file('neostore.relationshiptypestore.db.names', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
- self.add_composite_file('neostore.relationshiptypestore.db.names.id', substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
- self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
- self.add_composite_file('neostore.schemastore.db.id', substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
- self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file', is_binary=True)
+ self.add_composite_file('neostore.relationshipgroupstore.db',
+ substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
+ self.add_composite_file('neostore.relationshipgroupstore.db.id',
+ substitute_name_with_metadata='neostore_relationship_group_file', is_binary=True)
+ self.add_composite_file('neostore.relationshipstore.db',
+ substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
+ self.add_composite_file('neostore.relationshipstore.db.id',
+ substitute_name_with_metadata='neostore_relationship_file', is_binary=True)
+ self.add_composite_file('neostore.relationshiptypestore.db.names',
+ substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
+ self.add_composite_file('neostore.relationshiptypestore.db.names.id',
+ substitute_name_with_metadata='neostore_relationship_type_file', is_binary=True)
+ self.add_composite_file('neostore.schemastore.db', substitute_name_with_metadata='neostore_schema_store_file',
+ is_binary=True)
+ self.add_composite_file('neostore.schemastore.db.id',
+ substitute_name_with_metadata='neostore_schema_store_file', is_binary=True)
+ self.add_composite_file('neostore.transaction.db.0', substitute_name_with_metadata='neostore_count_file',
+ is_binary=True)
if __name__ == '__main__':
import doctest
- doctest.testmod(sys.modules[__name__])
\ No newline at end of file
+
+ doctest.testmod(sys.modules[__name__])