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