Source code for hyperstream.workflow.meta_data_manager

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# Copyright (c) 2014-2017 University of Bristol
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from ..utils import Printable, MetaDataTree
from ..models import MetaDataModel

import logging
from mongoengine.context_managers import switch_db
from treelib.tree import NodeIDAbsentError


[docs]class MetaDataManager(Printable):
    def __init__(self):
        self.global_plate_definitions = MetaDataTree()
        self.global_plate_definitions.create_node(identifier="root")

        to_be_added = dict((i, d) for i, d, in enumerate(self.global_meta_data))
        passes = 0

        # Populate the global plate definitions from dict given in the database
        while len(to_be_added) > 0:
            passes += 1
            if passes > 1000:
                raise NodeIDAbsentError("Nodes absent for ids {}"
                                        .format(", ".join(map(lambda x: x['identifier'], to_be_added.values()))))
            for i, item in to_be_added.items():
                try:
                    self.global_plate_definitions.create_node(**item)
                    del to_be_added[i]
                except NodeIDAbsentError:
                    pass

        logging.info("Global plate definitions: ")
        logging.info(self.global_plate_definitions)

    @property
    def global_meta_data(self):
        """
        Get the global meta data, which will be stored in a tree structure

        :return: The global meta data
        """
        with switch_db(MetaDataModel, 'hyperstream'):
            return sorted(map(lambda x: x.to_dict(), MetaDataModel.objects),
                          key=lambda x: len(x['identifier'].split('.')),
                          reverse=True)

[docs]    def contains(self, identifier):
        """
        Determines if the meta data with the given identifier is in the database

        :param identifier: The identifier
        :return: Whether the identifier is present
        """
        return self.global_plate_definitions.contains(identifier)

[docs]    def insert(self, tag, identifier, parent, data):
        """
        Insert the given meta data into the database

        :param tag: The tag (equates to meta_data_id)
        :param identifier: The identifier (a combination of the meta_data_id and the plate value)
        :param parent: The parent plate identifier
        :param data: The data (plate value)
        :return: None
        """
        # First try to add it into the tree
        if self.global_plate_definitions.contains(identifier):
            raise KeyError("Identifier {} already exists in tree".format(identifier))

        self.global_plate_definitions.create_node(tag=tag, identifier=identifier, parent=parent, data=data)

        # Now try to add it into the database
        with switch_db(MetaDataModel, 'hyperstream'):
            meta_data = MetaDataModel(tag=tag, parent=parent, data=data)
            meta_data.save()

        logging.info("Meta data {} inserted".format(identifier))

[docs]    def delete(self, identifier):
        """
        Delete the meta data with the given identifier from the database

        :param identifier: The identifier
        :return: None
        """

        node = self.global_plate_definitions[identifier]
        self.global_plate_definitions.remove_node(identifier)

        with switch_db(MetaDataModel, 'hyperstream'):
            meta_data = MetaDataModel.objects(tag=node.tag, data=node.data, parent=node.parent).first()
            meta_data.delete()