Mercurial > repos > sanbi-uwc > neo4j_datatypes
view neo4j.py @ 9:f4714c838f27 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 922fd8b22de3e555592844a4413ddcad2f726896
author | sanbi-uwc |
---|---|
date | Wed, 18 May 2016 09:10:51 -0400 |
parents | 666c7e606768 |
children | ce5df18856ee |
line wrap: on
line source
""" Neo4j Composite Dataset """ import logging import sys import os from galaxy.datatypes.images import Html from galaxy.datatypes.data import Data, Text, Html from galaxy.datatypes.metadata import MetadataElement gal_Log = logging.getLogger(__name__) verbose = True class Neo4j(Html): """ 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 = ['<html><head><title>Neo4j Galaxy Composite Dataset </title></head><p/>'] rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') 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( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) else: rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) rval.append( '</ul></div></html>' ) 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 = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name, dataset.name)] for i, fname in enumerate(flist): sfname = os.path.split(fname)[-1] f, e = os.path.splitext(fname) rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) ) rval.append( '</ul></body></html>' ) 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' 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' def display_peek(self, dataset): """Create HTML content, used for displaying peek.""" try: return dataset.peek except Exception: return "NEO4J database (multiple files)" def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): """Documented as an old display method, but still gets called via tests etc This allows us to format the data shown in the central pane via the "eye" icon. """ if filename is not None and filename != "index": # Change nothing - important for the unit tests to access child files: return Data.display_data(self, trans, data, preview, filename, to_ext, size, offset, **kwd) if self.file_ext == "neostore": title = "This is a NEO4J database" msg = "" try: # Try to use any text recorded in the dummy index file: handle = open(data.file_name, "rU") msg = handle.read().strip() handle.close() except Exception: pass if not msg: msg = title # Galaxy assumes HTML for the display of composite datatypes, return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg) class Neo4jDB(Neo4j, Data): """Class for neo4jDB database files.""" file_ext = 'neostore' 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.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) if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__])