# 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
    how the sample was prepared and LCMS data was collected.
    """
    protocol_ref = MetUnicode(help='Reference to a published protocol: ' +
        'identical to the protocol used.')
    quenching_method = MetUnicode(help='Description of the method used to ' +
        'stop metabolism.')
    extraction_solvent = MetUnicode(help='Solvent or solvent mixture used to ' +
        'extract metabolites.')
    reconstitution_method = MetUnicode(help='Solvent or solvent mixture ' +
        'the extract is reconstituted in prior to injection for an LCMS Run.')
    mobile_phase_a = MetUnicode(help='Solvent or solvent mixture.')
    mobile_phase_b = MetUnicode(help='Solvent or solvent mixture.')
    temporal_parameters = MetUnicode('List of temporal changes to the' +
        'mixing of mobile_phase_a and mobile_phase_b.')
    #Time = MetList()
    #Flow = MetList()
    #A_percent = MetList()
    #B_percent = MetList()
    #Chromatography Stack
    #Model
    #Serial Number
    #Modules
    column_model = MetUnicode(help='Brand and catalog number of the column')
    column_type = MetUnicode(help='Class of column used.')
    scan_mz_range = MetUnicode(help='Minimum and ' +
        'maximum mz recorded for a run.')
    instrument = MetUnicode(help='Brand and catalog number for the ' +
        'mass spectrometer.')
    ion_source = MetUnicode(help='Method for ionization.')
    mass_analyzer = MetUnicode(help='Method for detection.')

# 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

    how the sample was prepared and LCMS data was collected.
    """
    protocol_ref = MetUnicode(help='Reference to a published protocol: ' +
        'identical to the protocol used.')
    quenching_method = MetUnicode(help='Description of the method used to ' +
        'stop metabolism.')
    extraction_solvent = MetUnicode(help='Solvent or solvent mixture used to ' +
        'extract metabolites.')
    reconstitution_method = MetUnicode(help='Solvent or solvent mixture ' +
        'the extract is reconstituted in prior to injection for an LCMS Run.')
    mobile_phase_a = MetUnicode(help='Solvent or solvent mixture.')
    mobile_phase_b = MetUnicode(help='Solvent or solvent mixture.')
    temporal_parameters = MetUnicode('List of temporal changes to the' +
        'mixing of mobile_phase_a and mobile_phase_b.')
    #Time = MetList()
    #Flow = MetList()
    #A_percent = MetList()
    #B_percent = MetList()
    #Chromatography Stack
    #Model
    #Serial Number
    #Modules
    column_model = MetUnicode(help='Brand and catalog number of the column')
    column_type = MetUnicode(help='Class of column used.')
    scan_mz_range = MetUnicode(help='Minimum and ' +
        'maximum mz recorded for a run.')
    instrument = MetUnicode(help='Brand and catalog number for the ' +
        'mass spectrometer.')
    ion_source = MetUnicode(help='Method for ionization.')
    mass_analyzer = MetUnicode(help='Method for detection.')

    polarity = MetEnum(POLARITY, 'positive', help='polarity for the run')