Mercurial > repos > sanbi-uwc > neo4j_datatypes
changeset 17:969c57578047 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 249c86259729c03d2be69b1e74d8257a43eb8e18
author | sanbi-uwc |
---|---|
date | Wed, 18 May 2016 10:11:25 -0400 |
parents | de002a093129 |
children | 3472a853df10 |
files | neo4j.py |
diffstat | 1 files changed, 80 insertions(+), 62 deletions(-) [+] |
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line diff
--- a/neo4j.py Wed May 18 10:03:02 2016 -0400 +++ b/neo4j.py Wed May 18 10:11:25 2016 -0400 @@ -7,8 +7,7 @@ from galaxy.datatypes.images import Html from galaxy.datatypes.data import Data, Text - -# from galaxy.datatypes.metadata import MetadataElement +#from galaxy.datatypes.metadata import MetadataElement gal_Log = logging.getLogger(__name__) verbose = True @@ -20,6 +19,54 @@ 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' + 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""" @@ -72,73 +119,44 @@ composite_type = 'basic' allow_datatype_change = False + 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.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.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) + 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__]) + doctest.testmod(sys.modules[__name__]) \ No newline at end of file