# HG changeset patch # User sanbi-uwc # Date 1465308314 14400 # Node ID 86807766529bffa573b78ea709a436240285817f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/datatypes/neo4j_datatypes commit 7b6b83e2ec95601a8af9c7d9e08159f08057d776 diff -r 000000000000 -r 86807766529b ctb_report.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctb_report.py Tue Jun 07 10:05:14 2016 -0400 @@ -0,0 +1,151 @@ +""" +CtbReports Composite Dataset +""" +import logging +import sys + +from galaxy.datatypes.data import Data +from galaxy.datatypes.images import Html + +gal_Log = logging.getLogger(__name__) +verbose = True + + +class CtbReport(object): + """ + base class to use for cbtreports datatypes + derived from html - composite datatype elements + stored in extra files path + """ + + 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 = 'CtbReports (multiple files)' + dataset.blurb = 'CtbReports (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 "CtbReports (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 == "ctbreport": + title = "This is a CtbReports 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 "%s
%s
" % (title, msg) + + +class CtbReportsNeo4j(CtbReport, Data): + """Class for neo4jDB database files.""" + file_ext = 'ctbreportneo4j' + 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.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) + + +class CtbReportsJBrowse(CtbReport, Html): + """Class for ctb report jbrowse files.""" + file_ext = 'ctbreportjbrowse' + composite_type = 'basic' + allow_datatype_change = False + + def __init__(self, **kwd): + Html.__init__(self, **kwd) + + +if __name__ == '__main__': + import doctest + + doctest.testmod(sys.modules[__name__]) diff -r 000000000000 -r 86807766529b datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Tue Jun 07 10:05:14 2016 -0400 @@ -0,0 +1,14 @@ + + + + + + + + + + + + + +