17/replication_package/code/lib/data_helpers/data_utils.py

import pandas as pd
import os
import sys
import re
import pickle
import yaml
from datetime import datetime, timedelta, timezone
import dateutil.parser
import pytz


from lib.experiment_specs import study_config
from lib.utilities import codebook

""" Purpose: cleans the iso datetimes in a dataframe column
        -Input: 
            - DataFrame: data - raw input data that contains the time column
            - col_name - the name of the column
            - keep_nan : keep rows with empty value for df[col_name]
            - orig_tz: when you remove the timezone adjustment, what is the timezone. if "local", then removing the timezone
            yields the local time for the participant.

        - Output: 
            -dataframe with the following new columns:
                - {col_name}Datetime - in the phone's local time
                - {col_name}DatetimeHour
                - {col_name}Date

                - {col_name}EasternDatetime - in eastern time
                - {col_name}EasternDatetimeHour
         """

def clean_iso_dates(data_raw: pd.DataFrame, col_name: str, keep_nan: bool = False, orig_tz: str  = "Local"):

    data = data_raw.loc[data_raw[col_name].notnull()]
    data[col_name + 'DatetimeTZ'] = data[col_name].apply(lambda x: dateutil.parser.parse(x).replace(microsecond=0))

    # if the datetime without the timezone adjustment brings the time to local
    if orig_tz == "Local":
        data[col_name + 'Datetime'] = data[col_name + 'DatetimeTZ'].apply(lambda x: x.replace(tzinfo=None))
        data[col_name + 'DatetimeUTC'] = data[col_name + 'DatetimeTZ'].apply(
            lambda x: x.replace(tzinfo=timezone.utc) - x.utcoffset())

    # if the datetime without the timezone adjustment brings the time UTC
    else:
        data[col_name + 'Datetime'] = data[col_name + 'DatetimeTZ'].apply(
            lambda x: x.replace(tzinfo=timezone.utc) + x.utcoffset())
        data[col_name + 'Datetime'] = data[col_name + 'Datetime'].apply( lambda x: x.replace(tzinfo=None))
        data[col_name + 'DatetimeUTC'] = data[col_name + 'DatetimeTZ'].apply(lambda x: x.replace(tzinfo=timezone.utc))

    data[col_name + 'DatetimeHour'] = data[col_name + 'Datetime'].apply(lambda x: x.replace(minute=0, second=0))
    data[col_name + 'Date'] = data[col_name + 'DatetimeHour'].apply(lambda x: x.date())

    # Create Col in Eastern Time
    eastern = pytz.timezone('US/Eastern')
    data[col_name + 'EasternDatetime'] = data[col_name + 'DatetimeUTC'].apply(
        lambda x: x.astimezone(eastern).replace(tzinfo=None))
    data[col_name + 'EasternDatetimeHour'] = data[col_name + 'EasternDatetime'].apply(
        lambda x: x.replace(minute=0, second=0))
    data = data.drop(columns=[col_name, col_name + 'DatetimeTZ', col_name + 'DatetimeUTC'])

    if keep_nan:
        missing = data_raw.loc[data_raw[col_name].isnull()]
        data = data.append(missing)
    return data


"""remove data files from directory"""
def remove_files(directory):
    for file in os.listdir(directory):
        file_path = os.path.join(directory, file)
        try:
            if os.path.isfile(file_path):
                os.unlink(file_path)
        except Exception as e:
            print(e)


""" This method inputs missing start and enddatetime for survey incompletes. This helps determine what to count as use in phase, 
for people that have not completed their surveys"""
def inpute_missing_survey_datetimes(df, phase):
    specs = study_config.phases[phase]
    old_code = specs["StartSurvey"]["Code"]
    new_code = specs["EndSurvey"]["Code"]

    # the missing end date will be today if the survey hasn't ended yet
    missing_end_date = min(datetime.now().replace(microsecond=0), study_config.phases[phase]["EndSurvey"]["End"])

    # if the end survey hasn't even been distributed yet, add end survey completion col artificially to df
    if datetime.now() < study_config.phases[phase]["EndSurvey"]["Start"]:
        df.loc[(df[f"{old_code}_Complete"] == "Complete") , f"{new_code}_SurveyStartDatetime"] = missing_end_date

    else:
        # we inpute the completion of the end survey, if they completed the start survey:
        df.loc[(df[f"{old_code}_Complete"] == "Complete") &
               (df[f"{new_code}_SurveyStartDatetime"].isnull()), f"{new_code}_SurveyStartDatetime"] = missing_end_date

    return df

""" Adds survey code prefix to each column in the df"""
def add_survey_code(df, code):
    for col in df.columns.values:
        no_prefix_cols = study_config.main_cols + study_config.embedded_main_cols
        if col not in no_prefix_cols:
            new_name = code + "_" + col
            df = df.rename(columns={col: new_name})
    return df


"""A function which takes the clean_master master and outputs all the variables from a phase, without the prefixes"""
def keep_relevant_variables(df_raw, phase):
    start_code = study_config.phases[phase]["StartSurvey"]["Code"]
    end_code = study_config.phases[phase]["EndSurvey"]["Code"]

    """Keep participants that completed the relevant survey in the phase"""
    df = df_raw.loc[df_raw[f"{start_code}_Complete"] == "Complete"].copy()

    #"""LIMIT INDEX CONSTRUCTION TO FOLKS WITH CONSISTENT USE"""
    #codebook_dic = pd.read_csv(codebook.main_codebook_path, index_col="VariableName").to_dict(orient='index')

    ## get all columns in the given phase that are also in the df
    #keep_cols = [codebook.add_prefix_var(x, phase, codebook_dic) for x in codebook_dic.keys()]
    #keep_cols_in_df = [x for x in keep_cols if x in df.columns]

    keep_cols = [x for x in df.columns if f"{start_code}_" in x or x in study_config.main_cols+study_config.embedded_main_cols]
    df = df[keep_cols]

    # drop prefixes on these columns
    df.columns = [x.replace(f"{start_code}_","") for x in df.columns]
    return df

def add_A_to_appcode(df,appcode_col):
    df[appcode_col] = df[appcode_col].astype(str).fillna("nan")

    #convert weird float appcodes to integers
    df[appcode_col] = df[appcode_col].apply(lambda x: int(float(x)) if (x != "nan") and (x[0] != "A") else x)

    # add to those who need it
    df[appcode_col] = df[appcode_col].astype(str).apply(lambda x: "A" + x if len(x) == 8 else x)

    # assert we only have nans and proper appcodes
    df["Check"] = df[appcode_col].apply(lambda x: True if (len(x) == 9) or (len(x) == 3) else False)
    l = df["Check"].value_counts()
    l_s = df.loc[df["Check"]==False]
    assert df["Check"].all() == True
    return df

"returns the latest main survey that has already ended"
def get_last_survey():
    last_complete_time = datetime(2018, 1, 1, 0, 0)
    last_survey = ""
    surveys = study_config.main_surveys
    for survey in surveys:
        chars = study_config.surveys[survey]
        if chars["End"] < datetime.now():
            if chars["End"] > last_complete_time:
                last_survey = survey
                last_complete_time = chars["End"]
    return last_survey


# asserts two dfs that share common appcodes and columns, within a col_list
def assert_common_appcode_values(df1, df2, col_list):
    common_appcodes = set(df1["AppCode"]).intersection(set(df2["AppCode"]))
    common_columns = list(set(df1.columns).intersection(set(df2.columns)).intersection(col_list))
    compare_list = []
    for df in [df1, df2]:
        df = df.loc[df["AppCode"].isin(common_appcodes)]
        df = df[common_columns]
        df = df.sort_values(by="AppCode").reset_index(drop=True).astype(str)
        compare_list.append(df)
    assert len(compare_list[0]) == len(compare_list[1])

    c = compare_list[0].merge(compare_list[1], how='outer', on='AppCode', )
    for col in compare_list[0].columns:
        if col == "AppCode":
            continue
        try:
            c[col + "_x"].equals(c[col + "_y"]) == True
        except:
            print(f"no match on{col}")
            print(c[col + "_x"].dtype)
            print(c[col + "_y"].dtype)
            print("First five rows that don't match:")
            print(c.loc[c[col + "_x"] != c[col + "_y"]].head())
            sys.exit()

def merge_back_master(df_master, df_phase, phase):
    """ add prefixes to a phase specific df, and merge it to master"""
    codebook_dic = pd.read_csv(codebook.codebook_path, index_col="VariableName").to_dict(orient='index')
    df_phase.columns = [codebook.add_prefix_var(x, phase, codebook_dic) for x in df_phase.columns]
    new_cols = ["AppCode"] + list(set(df_phase.columns) - set(df_master.columns))
    df_master = df_master.merge(df_phase[new_cols], how='outer', left_on="AppCode", right_on="AppCode")
    return df_master