# Path: metatlas/datastructures/object_helpers.py
# ON_NERSC = 'METATLAS_LOCAL' not in os.environ
# def callback_method(func):
#     def notify(self, *args, **kwargs):
#     def __getitem__(self, item):
#     def __init__(self, *args):
#     def register_callback(self, cb):
#     def unregister_callback(self, cbid):
# def set_docstring(cls):
# def _get_subclasses(cls):
#     def __init__(self):
#     def get_instance(cls):
#     def get_connection(self):
#     def close_connection(self):
#     def convert_to_double(self, table, entry):
#     def save_objects(self, objects, _override=False):
#     def create_link_tables(self, klass):
#     def _get_save_data(self, obj, override=False):
#     def fix_table(self, table_name):
#     def retrieve(self, object_type, **kwargs):
#     def remove(self, object_type, **kwargs):
#     def remove_objects(self, objects, all_versions=True, **kwargs):
# def format_timestamp(tstamp):
#     def validate(self, obj, value):
#     def retrieve(self):
#     def __repr__(self):
#     def __str__(self):
#     def validate(self, obj, value):
# def get_from_nersc(user, relative_path):
# def rollback_and_log(db_connection, err):
# class NotifyList(list):
# class Workspace(object):
# class MetList(List):
# class MetUnicode(CUnicode):
# class MetFloat(CFloat):
# class MetInt(CInt):
# class MetBool(CBool):
# class Stub(HasTraits):
# class MetInstance(Instance):
# class MetEnum(Enum):


import getpass
import logging
import os
import pprint
import time
import uuid
import pandas as pd
from typing import Dict
from pwd import getpwuid
from tabulate import tabulate
from .object_helpers import (
    set_docstring, Workspace, format_timestamp, MetList,
    MetUnicode, MetFloat, MetInstance, MetInt, MetEnum, MetBool, HasTraits,
    Stub
)
from six.moves import zip
    adduct = MetEnum(ADDUCTS,'',help='Adduct')
    #add when needed: charge = MetFloat(help='the charge on the m/z feature')
    modification = MetUnicode(help='Optional modification')
    observed_formula = MetUnicode(help='Optional observed formula')

@set_docstring
class IntensityReference(Reference):
    """Source of the assertion that a compound has a given m/z and
    other properties directly tied to m/z.
    """
    peak_height = MetFloat()
    peak_area = MetFloat()
    amount = MetFloat()
    amount_units = MetEnum(('nmol', 'mol'), 'nmol')

@set_docstring
class CompoundIdentification(MetatlasObject):
    """A CompoundIdentification links multiple sources of evidence about a
    compound's identity to an Atlas."""
    compound = MetList(MetInstance(Compound))
    identification_grade = _IdGradeTrait(
        help='Identification grade of the id (can be specified by a letter A-H'
    )
    identification_notes = MetUnicode('',
                             help='notes about this identifiation')
    ms1_notes = MetUnicode('',
                             help='notes about ms1 peaks')
    ms2_notes = MetUnicode('',
                             help='notes about ms2 matches')
    mz_references = MetList(MetInstance(MzReference))

# Path: metatlas/datastructures/object_helpers.py
# ON_NERSC = 'METATLAS_LOCAL' not in os.environ
# def callback_method(func):
#     def notify(self, *args, **kwargs):
#     def __getitem__(self, item):
#     def __init__(self, *args):
#     def register_callback(self, cb):
#     def unregister_callback(self, cbid):
# def set_docstring(cls):
# def _get_subclasses(cls):
#     def __init__(self):
#     def get_instance(cls):
#     def get_connection(self):
#     def close_connection(self):
#     def convert_to_double(self, table, entry):
#     def save_objects(self, objects, _override=False):
#     def create_link_tables(self, klass):
#     def _get_save_data(self, obj, override=False):
#     def fix_table(self, table_name):
#     def retrieve(self, object_type, **kwargs):
#     def remove(self, object_type, **kwargs):
#     def remove_objects(self, objects, all_versions=True, **kwargs):
# def format_timestamp(tstamp):
#     def validate(self, obj, value):
#     def retrieve(self):
#     def __repr__(self):
#     def __str__(self):
#     def validate(self, obj, value):
# def get_from_nersc(user, relative_path):
# def rollback_and_log(db_connection, err):
# class NotifyList(list):
# class Workspace(object):
# class MetList(List):
# class MetUnicode(CUnicode):
# class MetFloat(CFloat):
# class MetInt(CInt):
# class MetBool(CBool):
# class Stub(HasTraits):
# class MetInstance(Instance):
# class MetEnum(Enum):


# Path: metatlas/datastructures/metatlas_objects.py
import getpass
import logging
import os
import pprint
import time
import uuid
import pandas as pd
from typing import Dict
from pwd import getpwuid
from tabulate import tabulate
from .object_helpers import (
    set_docstring, Workspace, format_timestamp, MetList,
    MetUnicode, MetFloat, MetInstance, MetInt, MetEnum, MetBool, HasTraits,
    Stub
)
from six.moves import zip

    adduct = MetEnum(ADDUCTS,'',help='Adduct')
    #add when needed: charge = MetFloat(help='the charge on the m/z feature')
    modification = MetUnicode(help='Optional modification')
    observed_formula = MetUnicode(help='Optional observed formula')

@set_docstring
class IntensityReference(Reference):
    """Source of the assertion that a compound has a given m/z and
    other properties directly tied to m/z.
    """
    peak_height = MetFloat()
    peak_area = MetFloat()
    amount = MetFloat()
    amount_units = MetEnum(('nmol', 'mol'), 'nmol')

@set_docstring
class CompoundIdentification(MetatlasObject):
    """A CompoundIdentification links multiple sources of evidence about a
    compound's identity to an Atlas."""
    compound = MetList(MetInstance(Compound))
    identification_grade = _IdGradeTrait(
        help='Identification grade of the id (can be specified by a letter A-H'
    )
    identification_notes = MetUnicode('',
                             help='notes about this identifiation')
    ms1_notes = MetUnicode('',
                             help='notes about ms1 peaks')
    ms2_notes = MetUnicode('',
                             help='notes about ms2 matches')
    mz_references = MetList(MetInstance(MzReference))

    rt_references = MetList(MetInstance(RtReference))