# HG changeset patch # User sanbi-uwc # Date 1463577431 14400 # Node ID ce5df18856ee22720f5a61ddbae2349346c4bd26 # Parent f4714c838f2790cbad292bed2049b7931cee4234 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 31097469911a6200b265a1a8dcea285b3a65b6a9 diff -r f4714c838f27 -r ce5df18856ee datatypes_conf.xml --- a/datatypes_conf.xml Wed May 18 09:10:51 2016 -0400 +++ b/datatypes_conf.xml Wed May 18 09:17:11 2016 -0400 @@ -4,8 +4,8 @@ - - + + diff -r f4714c838f27 -r ce5df18856ee neo4j.py --- a/neo4j.py Wed May 18 09:10:51 2016 -0400 +++ b/neo4j.py Wed May 18 09:17:11 2016 -0400 @@ -5,68 +5,20 @@ import sys import os -from galaxy.datatypes.images import Html +#from galaxy.datatypes.images import Html from galaxy.datatypes.data import Data, Text, Html -from galaxy.datatypes.metadata import MetadataElement +#from galaxy.datatypes.metadata import MetadataElement 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:

    ') - 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 %s

Composite %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""" return 'text/html' @@ -115,6 +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) @@ -155,6 +109,4 @@ if __name__ == '__main__': import doctest - - - doctest.testmod(sys.modules[__name__]) + doctest.testmod(sys.modules[__name__]) \ No newline at end of file