# 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
#             experiment = os.path.basename(dirname)
#             description = experiment + ' ' + filename
#             ctime = os.stat(fname).st_ctime
#             run = LcmsRun(name=filename, description=description,
#                           created_by=user,
#                           modified_by=user,
#                           created=ctime, last_modified=ctime,
#                           mzml_file=fname, hdf5_file=hdf_file)
#             runs.append(run)
#         except Exception as e:
#             print(e)
#     store(runs)
#     return runs


@set_docstring
class LcmsRun(MetatlasObject):
    """An LCMS run is the reference to a file prepared with liquid
    chromatography and mass spectrometry.

    The msconvert program is used to convert raw data (centroided is prefered)
    to mzML.

    Note: These objects are not intented to be created directly, but by putting
    the files in /project/projectdirs/metatlas/raw_data/<username> or by
    running `load_lcms_files()`.
    """
    method = MetInstance(Method)
    experiment = MetUnicode(help='The name of the experiment')
    hdf5_file = MetUnicode(help='Path to the HDF5 file at NERSC')

# 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

#             experiment = os.path.basename(dirname)
#             description = experiment + ' ' + filename
#             ctime = os.stat(fname).st_ctime
#             run = LcmsRun(name=filename, description=description,
#                           created_by=user,
#                           modified_by=user,
#                           created=ctime, last_modified=ctime,
#                           mzml_file=fname, hdf5_file=hdf_file)
#             runs.append(run)
#         except Exception as e:
#             print(e)
#     store(runs)
#     return runs


@set_docstring
class LcmsRun(MetatlasObject):
    """An LCMS run is the reference to a file prepared with liquid
    chromatography and mass spectrometry.

    The msconvert program is used to convert raw data (centroided is prefered)
    to mzML.

    Note: These objects are not intented to be created directly, but by putting
    the files in /project/projectdirs/metatlas/raw_data/<username> or by
    running `load_lcms_files()`.
    """
    method = MetInstance(Method)
    experiment = MetUnicode(help='The name of the experiment')
    hdf5_file = MetUnicode(help='Path to the HDF5 file at NERSC')

    mzml_file = MetUnicode(help='Path to the MZML file at NERSC')