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(f'<li><a href="{composite_name}">{composite_name}</a>{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): """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, 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__])