Mercurial > repos > sanbi-uwc > neo4j_datatypes

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

from galaxy.datatypes.images import Html
from galaxy.datatypes.data import Data, Text

import shutil
import os

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
    """
    def __init__(self):
         Html.__init__( self, **kwd )

    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
        """
        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).iteritems():
            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)

    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 preview == False:
            trans.response.set_content_type(data.get_mime())
            trans.log_event( "Display dataset id: %s" % str( data.id ) )

            # the target directory name
            dir_name = str(os.path.dirname( trans.app.object_store.get_filename(data.dataset) )) + '/dataset_{}_files/neo4jdb'.format( data.dataset.id )

            # generate unique filename for this dataset
            valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
            fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]

            # zip the target directory (dir_name) using the fname
            shutil.make_archive(fname, 'zip', dir_name)
            download_zip = fname + '.zip'

            # setup headers for the download
            trans.response.headers['Content-Length'] = int( os.stat( download_zip ).st_size )
            trans.response.set_content_type( "application/octet-stream" )  # force octet-stream so Safari doesn't append mime extensions to filename
            trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, download_zip , "zip")

            return open( download_zip )

class Neo4jDB(Neo4j, Data):
    """Class for neo4jDB database files."""
    file_ext = 'neostore'
    composite_type = 'basic'
    allow_datatype_change = False


    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', is_binary=True)
        self.add_composite_file('neostore.counts.db.b', 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)


if __name__ == '__main__':
    import doctest
    doctest.testmod(sys.modules[__name__])
author	sanbi-uwc
date	Sat, 25 Jun 2016 20:56:23 -0400
parents	c48ea98bd3b2
children	1c926de292e1