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Source code for galaxy.datatypes.neo4j

"""
Neo4j Composite Dataset
"""
import logging
import sys

from galaxy.datatypes.data import Data
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement

gal_Log = logging.getLogger(__name__)
verbose = True


[docs]class Neo4j(Html): """ base class to use for neostore datatypes derived from html - composite datatype elements stored in extra files path """
[docs] def generate_primary_file(self, dataset=None): """ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately """ # self.regenerate_primary_file(dataset) rval = [ '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\ This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext)] for composite_name, composite_file in self.get_composite_files(dataset=dataset).items(): opt_text = '' if composite_file.optional: opt_text = ' (optional)' rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text)) rval.append('</ul></html>') return "\n".join(rval)
[docs] def get_mime(self): """Returns the mime type of the datatype""" return 'text/html'
[docs] def set_peek(self, dataset, is_multi_byte=False): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'Neo4j database (multiple files)' dataset.blurb = 'Neo4j database (multiple files)' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def display_peek(self, dataset): """Create HTML content, used for displaying peek.""" try: return dataset.peek except Exception: return "NEO4J database (multiple files)"
[docs]class Neo4jDB(Neo4j, Data): """Class for neo4jDB database files.""" file_ext = 'neostore' composite_type = 'auto_primary_file'
[docs] def __init__(self, **kwd): Data.__init__(self, **kwd) self.add_composite_file('neostore', is_binary=True) self.add_composite_file('neostore.id', is_binary=True) self.add_composite_file('neostore.counts.db.a', optional=True, is_binary=True) self.add_composite_file('neostore.counts.db.b', optional=True, is_binary=True) self.add_composite_file('neostore.labeltokenstore.db', is_binary=True) self.add_composite_file( 'neostore.labeltokenstore.db.id', is_binary=True) self.add_composite_file( 'neostore.labeltokenstore.db.names', is_binary=True) self.add_composite_file( 'neostore.labeltokenstore.db.names.id', is_binary=True) self.add_composite_file('neostore.nodestore.db', is_binary=True) self.add_composite_file('neostore.nodestore.db.id', is_binary=True) self.add_composite_file('neostore.nodestore.db.labels', is_binary=True) self.add_composite_file( 'neostore.nodestore.db.labels.id', is_binary=True) self.add_composite_file('neostore.propertystore.db', is_binary=True) self.add_composite_file('neostore.propertystore.db.id', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.arrays', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.arrays.id', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.index', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.index.id', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.index.keys', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.index.keys.id', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.strings', is_binary=True) self.add_composite_file( 'neostore.propertystore.db.strings.id', is_binary=True) self.add_composite_file( 'neostore.relationshipgroupstore.db', is_binary=True) self.add_composite_file( 'neostore.relationshipgroupstore.db.id', is_binary=True) self.add_composite_file( 'neostore.relationshipstore.db', is_binary=True) self.add_composite_file( 'neostore.relationshipstore.db.id', is_binary=True) self.add_composite_file( 'neostore.relationshiptypestore.db.names', is_binary=True) self.add_composite_file( 'neostore.relationshiptypestore.db.names.id', is_binary=True) self.add_composite_file('neostore.schemastore.db', is_binary=True) self.add_composite_file('neostore.schemastore.db.id', is_binary=True) self.add_composite_file('neostore.transaction.db.0', is_binary=True)
[docs]class Neo4jDBzip(Neo4j, Data): """Class for neo4jDB database files.""" MetadataElement(name='reference_name', default='neostore_file', desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='neostore') MetadataElement(name="neostore_zip", default=None, desc="Neostore zip", readonly=True, visible=True, set_in_upload=True, no_value=None, optional=True) file_ext = "neostore.zip" composite_type = 'auto_primary_file'
[docs] def __init__(self, **kwd): Data.__init__(self, **kwd) self.add_composite_file('%s.zip', description='neostore zip', substitute_name_with_metadata='reference_name', is_binary=True)
if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__])