Download 17/replication_package/code/lib/data_helpers/pull_events.py from chuxuan/REPRO-Bench: direct link, hf CLI and curl.
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https://huggingface.co/datasets/chuxuan/REPRO-Bench/resolve/main/17/replication_package/code/lib/data_helpers/pull_events.py
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17.3 kB
| import os | |
| import sys | |
| import shutil | |
| import zipfile | |
| import multiprocessing | |
| import pandas as pd | |
| from datetime import datetime,timedelta | |
| from lib.data_helpers import data_utils | |
| from lib.experiment_specs import study_config | |
| from lib.data_helpers import test | |
| from lib.data_helpers.builder_utils import BuilderUtils | |
| from lib.data_helpers.gaming import Gaming | |
| from lib.utilities import serialize | |
| class PullEvents(): | |
| port_dir = {"PCDashboard": os.path.join("data","external","dropbox","..","PCPort"), | |
| "PhoneDashboard":os.path.join("data","external","dropbox","..","PhoneDashboardPort")} | |
| #identifying_cols are a list of columns in the dataframe that identify a row. none of them can be empty | |
| def __init__(self,source: str, keyword: str, scratch: bool, test: bool, | |
| time_cols: list, raw_timezone: str, appcode_col: str, identifying_cols: list, sort_cols: list, | |
| drop_cols: list, cat_cols: list, | |
| compress_type: str, processing_func = BuilderUtils.default_puller_process, file_reader = None): | |
| """ | |
| Purpose | |
| ------- | |
| This class appends the raw data files housed in self.zipped_directory, cleans them a bit with the self.processing func, | |
| and saves the merged data file in self.raw_file. Unless self.scratch == True, the puller will only process new raw data files | |
| and appends them to the dataframe saved in self.raw_file. The puller documents which files have been processed in the config located in self.config_file_path | |
| WARNING: if self.scratch==TRUE, it may take hours or days to reprocess all the data. Call Michael to discuss if this needs to happen. | |
| Parameters | |
| ---------- | |
| source - source the app data source (either PC or PD) | |
| keyword - the kind of data coming in (e.g. Snooze, Use etc) | |
| scratch - whether or not to start data processing from scratch | |
| test - whether or not to test the pulling pipeline (it will reprocess that latest three zipfiles) (I wouldn't play with this) | |
| time_cols - list of columns that contain datetimes | |
| raw_timezone - the timezone of the raw data | |
| appcode_col - the raw column name containing the appcodes | |
| identifying_cols - list of columns that should identify a unique row | |
| sort_cols - list of columns that describes how the df should be ordered. The df will be sorted from smallest to largest value of the sort_cols | |
| drop_cols - list of columns that appear in the raw zipfile or after zipfile processing that should be dropped | |
| cat_cols - list of columns that can be converted into the categorical data type | |
| compress_type - how the zipfiles are compressed (either "folder", "csv", or "txt") | |
| processing_func - the function used to process the raw data (e.g. clean_master dates) | |
| file_reader - function that reads in the raw file into memory. only required for file stored in zip folders. | |
| """ | |
| self.source = source | |
| self.keyword = keyword | |
| self.scratch = scratch | |
| self.pull_test = test | |
| self.time_cols = time_cols | |
| self.raw_timezone = raw_timezone | |
| self.appcode_col = appcode_col | |
| self.identifying_cols = identifying_cols | |
| self.sort_cols = sort_cols | |
| self.drop_cols = drop_cols | |
| self.cat_cols = cat_cols | |
| self.compress_type = compress_type | |
| self.processing_func = processing_func | |
| self.file_reader = file_reader | |
| self.zipped_directory = os.path.join("data","external", "input", source, f"Raw{self.keyword}Zipped") | |
| self.buggy_dir = os.path.join("data","external", "input", source, "BuggyFiles") | |
| self.config_file_path = os.path.join("data","external", "input", source, f"{self.source}{self.keyword}Config.csv") | |
| self.raw_file = os.path.join("data","external", "input", source, f"Raw{self.keyword}") | |
| self.test_file = os.path.join("data","external", "input_test", source, f"Raw{self.keyword}") | |
| self.config_user_dict = serialize.open_yaml("config_user.yaml") | |
| self.builder_utils = BuilderUtils() | |
| self.added_config = self.builder_utils.get_config(self.config_file_path) #dictionary of zipfiles in the raw_file | |
| self.new_config = {} | |
| def update_data(self): | |
| print(f"\n Updating {self.keyword} data! {datetime.now()}") | |
| if self.config_user_dict["local"]["test"]==True: | |
| df = serialize.soft_df_open(self.test_file) | |
| df = self._memory_redux(df) | |
| print(df.memory_usage(deep=True) / 1024 ** 2) | |
| return df | |
| else: | |
| self.builder_utils.transport_new_zip_files(PullEvents.port_dir[self.source], self.keyword, self.zipped_directory) | |
| new_zip_files = [x for x in os.listdir(self.zipped_directory) if (x.replace(".zip", "") not in self.added_config) & (".zip" in x)] | |
| print(f"new zip files {len(new_zip_files)}") | |
| # if no new data or scratch run, just load old data | |
| if ((self.scratch == False) & | |
| (len(new_zip_files) == 0) & | |
| (self.pull_test == False)): | |
| print("\t No New Data! Loading pickled raw data into memory") | |
| if(os.path.getsize(self.raw_file+".pickle") > 0) : | |
| df = serialize.soft_df_open(self.raw_file) | |
| else: | |
| print("Raw file is empty. Reading Backup Compression Zip") | |
| df = serialize.read_gz(self.raw_file+".gz") | |
| df = self._memory_redux(df) | |
| # Archiving Recruitment Data IF Use Data | |
| if (self.keyword == "Alternative") or (self.keyword == "Use"): | |
| #self._archive_recruitment(df) | |
| df = df.loc[df["CreatedDatetimeHour"] >= study_config.surveys["Baseline"]["Start"]-timedelta(1)] | |
| return df | |
| else: | |
| print(f"Length of new zip files {len(new_zip_files)}") | |
| df = self.aggregate_data(new_zip_files) | |
| self.builder_utils.update_config(self.added_config, | |
| self.new_config, | |
| self.config_file_path) | |
| return df | |
| def aggregate_data(self,new_zip_files): | |
| old_df, new_zip_files = self._configure_data(new_zip_files) | |
| print(f"\t Going to add {len(new_zip_files)} files:") | |
| if self.config_user_dict['local']["parallel"] == False: | |
| df_dic = self._process_zips(new_zip_files) | |
| #if the number of files > # of cores, then multiprocess | |
| elif multiprocessing.cpu_count() < len(new_zip_files): | |
| df_dic = self._process_zips_mp(new_zip_files) | |
| else: | |
| print(f"not multiprocessing b/c number of cores {multiprocessing.cpu_count()} < {len(new_zip_files)}") | |
| df_dic = self._process_zips(new_zip_files) | |
| #get appcodes to keep | |
| print("\t get data survey") | |
| cl_file = os.path.join(os.path.join("data","external","dropbox_confidential","ContactLists","Used"), | |
| study_config.kept_appcode_cl) | |
| a_df = pd.read_csv(cl_file) | |
| a_df = data_utils.add_A_to_appcode(a_df,"AppCode") | |
| appcodes = list(a_df["AppCode"]) | |
| print(len(appcodes)) | |
| assert len(appcodes) == study_config.number_of_kept_appcodes | |
| # combine new with old and keep relevant appcodes | |
| if len(df_dic)>0: | |
| print("\t adding new data to master") | |
| new_df = pd.concat(list(df_dic.values()), sort=True) | |
| new_df = new_df.loc[new_df["AppCode"].isin(appcodes)] | |
| parent_df = pd.concat([old_df,new_df], sort=True) | |
| else: | |
| print("\t no new data!") | |
| parent_df = old_df | |
| # minimal cleaning and save to disk: sort from smallest to largest values of sort_cols | |
| print(f"\t Len before duplicate drop {len(parent_df)}") | |
| parent_df = parent_df.sort_values(by = self.sort_cols) | |
| parent_df = parent_df.drop_duplicates(subset = self.identifying_cols, keep = 'last') | |
| print(f"\t Len after duplicate drop {len(parent_df)}") | |
| for col in parent_df.columns: | |
| if "Unnamed" in col: | |
| parent_df = parent_df.drop(columns= [col]) | |
| parent_df = parent_df.reset_index(drop=True) | |
| print(parent_df.memory_usage(deep=True) / 1024 ** 2) | |
| try: | |
| os.rename(self.raw_file+".pickle",self.raw_file+"PrevRun.pickle") | |
| except: | |
| print('could not find old pickle file') | |
| try: | |
| serialize.save_pickle(parent_df, self.raw_file) | |
| except: | |
| print("Failed to save pickle!") | |
| try: | |
| test.save_test_df(parent_df, self.test_file) | |
| except: | |
| print("Failed to save testfile") | |
| # DONT PUT IN TRY BECAUSE IF BACKUP FAILS, WE WANT TO RE PROCESS THE NEW FILES | |
| try: | |
| os.rename(self.raw_file + ".gz", self.raw_file + "PrevRun.gz") | |
| except: | |
| print("no old gz file") | |
| parent_df.to_csv(self.raw_file + '.gz', index=False, compression='gzip') | |
| print(f"\t Done Saving {datetime.now()}") | |
| # add new guys to config in memory, now that everything has saved | |
| for zip_file, df in df_dic.items(): | |
| try: | |
| latest_hour = str(df[self.time_cols[0]].max()) | |
| earliest_hour = str(df[self.time_cols[0]].min()) | |
| except: | |
| latest_hour = "NAN" | |
| earliest_hour = "NAN" | |
| self.new_config[zip_file.replace(".zip", "")] = {"EarliestHour": earliest_hour, | |
| "LatestHour": latest_hour, | |
| "ZipFile": zip_file} | |
| return parent_df | |
| """ modifes the reaggregation in the following way: | |
| - if self.scatch is True: all zipfiles in data dire are new, and old_df is empty | |
| - if self.test is True: reprocess the last three data files, and old_df is reloaded | |
| - else: process the new zip files with old df""" | |
| def _configure_data(self,new_zip_files): | |
| if self.scratch: | |
| all_zip_files = [x for x in os.listdir(self.zipped_directory) if ".zip" in x] | |
| new_zip_files = sorted(all_zip_files) | |
| #continue_ans = input("Warning: Do you want to reprocess all use files? Enter (Y or N) \n ") | |
| continue_ans = "Y" | |
| if continue_ans == "N": | |
| sys.exit() | |
| print(f"DELETING ADDED EVENT CONFIG, CAUSING REAGGREGATION OF ALL {self.keyword} ZIPFILES") | |
| self.added_config = {} | |
| if self.keyword == "Use": | |
| print("\t Also Deleting all Granular Gaming Files") | |
| for gran_folder in [os.path.join(Gaming.gaming_dir, "FirstLast"), | |
| os.path.join(Gaming.gaming_dir, "Granular")]: | |
| shutil.rmtree(gran_folder) | |
| os.mkdir(gran_folder) | |
| old_df = pd.DataFrame() | |
| else: | |
| if self.pull_test: | |
| try: | |
| assert len(new_zip_files) == 0 | |
| except: | |
| print("There are actual new zip files to process! First process these files, then test") | |
| sys.exit() | |
| print("TEST: Reprocessing 3 files from zipped directory") | |
| test_files = os.listdir(self.zipped_directory)[-3:] | |
| for zip_file in test_files: | |
| del self.added_config[zip_file.replace(".zip", "")] | |
| new_zip_files = test_files | |
| if not os.path.exists((self.raw_file+".pickle")): | |
| old_df = pd.DataFrame() | |
| elif os.path.getsize(self.raw_file + ".pickle") > 0: | |
| old_df = serialize.soft_df_open(self.raw_file) | |
| else: | |
| print("Raw file is empty. Reading Backup Compression Zip") | |
| old_df = serialize.read_gz(self.raw_file + ".gz") | |
| if len(old_df)>1: | |
| old_df = self._memory_redux(old_df) | |
| # Archiving Recruitment Data IF Use Data | |
| if (self.keyword == "Alternative") or (self.keyword == "Use"): | |
| #self._archive_recruitment(old_df) | |
| old_df = old_df.loc[old_df["CreatedDatetimeHour"] >= study_config.surveys["Baseline"]["Start"]-timedelta(1)] | |
| return old_df, new_zip_files | |
| def _process_zips_mp(self, new_zip_files: list): | |
| # create the pool object for multiprocessing | |
| pool = multiprocessing.Pool(processes=study_config.cores) | |
| # split the files to add into n lists where n = cores | |
| chunks = [new_zip_files[i::study_config.cores] for i in range(study_config.cores)] | |
| print(f"Multiprocessing with {study_config.cores} cpus") | |
| df_list_of_dics = pool.map(func = self._process_zips, iterable = chunks) | |
| pool.close() | |
| print("Done Multiprocessing") | |
| # flatten the list of dictionaries | |
| df_dic = {} | |
| for d in df_list_of_dics: | |
| for k, v in d.items(): | |
| df_dic[k] = v | |
| return df_dic | |
| def _process_zips(self,new_zip_files): | |
| df_dic = {} | |
| i = 1 | |
| for zip_file in new_zip_files: | |
| print(f"processing {zip_file} ({round((i * 100) / len(new_zip_files))}%)", end = "\r") | |
| df = self._process_zip(zip_file) | |
| if len(df) == 0: | |
| continue | |
| df_dic[zip_file] = df | |
| i = i + 1 | |
| return df_dic | |
| def _process_zip(self, zip_file): | |
| if ".zip" not in zip_file: | |
| return pd.DataFrame() | |
| # open zipfile | |
| if self.compress_type != "folder": | |
| df, problem = self._open_zipfile(zip_file) | |
| # open json zip folder | |
| else: | |
| df = self._open_zipfolder(zip_file) | |
| problem = "" | |
| if len(df) == 0: | |
| if problem != "Corrupt": | |
| problem = "Empty" | |
| print(f"{zip_file} is empty ...archiving in {self.buggy_dir}/{problem}") | |
| old_file = os.path.join(self.zipped_directory, zip_file) | |
| new_file = os.path.join(self.buggy_dir, problem, zip_file) | |
| os.rename(old_file, new_file) | |
| return df | |
| df.columns = df.columns.str.replace(' ', '') | |
| df = df.rename(columns={self.appcode_col: "AppCode"}) | |
| df["AppCode"] = df["AppCode"].astype(str).apply(lambda x: "A" + x if x != "nan" and x.isnumeric() else x) | |
| df = self.processing_func(df, zip_file, self) | |
| df["Zipfile"] = zip_file | |
| df = self._memory_redux(df) | |
| return df | |
| def _open_zipfile(self,zip_file): | |
| if self.compress_type == "txt": | |
| separator = '\t' | |
| elif self.compress_type == "csv": | |
| separator = ',' | |
| else: | |
| separator = "" | |
| print("Illegal seperator") | |
| sys.exit() | |
| try: | |
| df = pd.read_csv(os.path.join(self.zipped_directory, zip_file), compression='zip', header=0, | |
| sep=separator, quotechar='"') | |
| problem = "None" | |
| except: | |
| print(f"{zip_file} is corrupt. Investigate in archive") | |
| df = pd.DataFrame() | |
| problem = "Corrupt" | |
| return df, problem | |
| def _open_zipfolder(self,zip_folder): | |
| #print(zip_folder) | |
| #print(self.zipped_directory) | |
| zip_ref = zipfile.ZipFile(os.path.join(self.zipped_directory, zip_folder)) | |
| temp_folder = os.path.join(self.zipped_directory, zip_folder.replace(".zip", "FOLDER")) | |
| zip_ref.extractall(path=temp_folder) | |
| df_list = [] | |
| for file in os.listdir(temp_folder): | |
| file_path = os.path.join(temp_folder, file) | |
| clean_data = self.file_reader(file_path) | |
| df_list.append(clean_data) | |
| shutil.rmtree(temp_folder) | |
| df = pd.concat(df_list) | |
| return df | |
| def _open_zipfolders_install(self,zip_folders): | |
| """for recovering install data""" | |
| for zip_folder in zip_folders: | |
| df = self._open_zipfolder(zip_folder) | |
| def _memory_redux(self,df): | |
| # drop columns that were initially in raw data or processing byproduct | |
| for drop_col in self.drop_cols + ["Server","AsOf"]: | |
| if drop_col in df.columns.values: | |
| df = df.drop(columns = [drop_col]) | |
| # make columns categorical | |
| for cat_col in self.cat_cols + ["Zipfile"]: | |
| if cat_col in df.columns.values: | |
| try: | |
| df[cat_col] = df[cat_col].astype('category') | |
| except: | |
| print(f"\t categorizing {cat_col} failed!") | |
| return df | |
| def _archive_recruitment(self,df): | |
| if os.path.exists(self.raw_file + "RecruitmentPhase.pickle"): | |
| pass | |
| else: | |
| r_df_raw = df.loc[df["CreatedDatetimeHour"] < study_config.surveys["Baseline"]["Start"]-timedelta(1)] | |
| try: | |
| serialize.save_pickle(r_df_raw, self.raw_file + "RecruitmentPhase.pickle") | |
| except: | |
| r_df_raw.to_csv(self.raw_file + 'RecruitmentPhase.gz', index=False, compression='gzip') | |