# HG changeset patch # User sanbi-uwc # Date 1463561439 14400 # Node ID 4b1d16644ec2e7c06e31f5e32eca59307a71fe17 # Parent b4f02c3742f1882f219b03b5ba0216ec4a867d16 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 63871d62b7acd851ff2d50dc08520c17bdf834f6 diff -r b4f02c3742f1 -r 4b1d16644ec2 neo4j.py --- a/neo4j.py Tue May 17 07:35:07 2016 -0400 +++ b/neo4j.py Wed May 18 04:50:39 2016 -0400 @@ -2,70 +2,23 @@ Neo4j Composite Dataset """ import logging +import os import sys -import os -from galaxy.datatypes.data import Data from galaxy.datatypes.images import Html from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes.data import get_file_peek +from galaxy.datatypes.data import Data, Text gal_Log = logging.getLogger(__name__) verbose = True -class Neo4j(Html): +class Neo4j(object): """ base class to use for neostore datatypes 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' - #composite_type = 'basic' - 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""" return 'text/html' @@ -114,6 +67,8 @@ class Neo4jDB(Neo4j, Data): """Class for neo4jDB database files.""" file_ext = 'neostore' + allow_datatype_change = False + composite_type = 'basic' def __init__(self, **kwd): Data.__init__(self, **kwd) @@ -153,6 +108,4 @@ if __name__ == '__main__': import doctest - doctest.testmod(sys.modules[__name__]) - - + doctest.testmod(sys.modules[__name__]) \ No newline at end of file