Source code for galaxy.datatypes.neo4j

"""
Neo4j Composite Dataset
"""
import logging
import os
import shutil
import sys

from galaxy.datatypes.data import Data
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement
from galaxy.util import FILENAME_VALID_CHARS

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('<li><a href="%s">%s</a>%s' %
                        (composite_name, composite_name, 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, 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'

[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]    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 not preview:
            trans.response.set_content_type(data.get_mime())
            trans.log_event("Display dataset id: %s" % str(data.id))

            # the target directory name
            neo4j_dir_name = '/dataset_{}_files'.format(
                data.dataset.id)
            dir_name = str(os.path.dirname(
                trans.app.object_store.get_filename(data.dataset))) + neo4j_dir_name

            # generate unique filename for this dataset
            fname = ''.join(
                c in FILENAME_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)
            # force octet-stream so Safari doesn't append mime extensions to filename
            trans.response.set_content_type("application/octet-stream")
            trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % \
                                                            (data.hid,
                                                             download_zip, "zip")
            return open(download_zip)


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

[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, no_value=None, optional=True)

    file_ext = "neostore.zip"
    composite_type = 'auto_primary_file'
    allow_datatype_change = False

[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__])