# 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:

' ) - 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 %s

Composite %s contains:

' ) - 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__])