Add Tests

merge.py

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+import pandas as pd
+import os
+import glob
+import numpy as np
+import datetime
+import itertools as it
+import argparse
+import re
+from urllib.parse import urlparse
+import pysftp
+
+#NOTE for now, each of the arrays should be all lowercase
+#TODO eventually make them case agnostic
+# all of the columns we want to extract from the csv file
+# excluding the question ids (they are found using regex)
+final_columns_student = {
+    'Start Date': ['startdate', 'start date'],
+    'End Date': ['enddate', 'end date'],
+    'Status': ['status'],
+    'Ip Address': ['ip address', 'ipaddress'],
+    'Progress': ['progress'],
+    'Duration': ['duration', 'duration..in.seconds', 'duration (in seconds)'],
+    'District': ['district', 'please select your school district.'],
+    'LASID': ['lasid', 'please enter your locally assigned student id number (lasid, or student lunch number).'],
+    'Grade': ['grade', 'what grade are you in?'],
+    'Gender': ['gender', 'what is your gender?', 'what is your gender? - selected choice'],
+    'Race': ['race'],
+    'Recorded Date': ['recorded date', 'recordeddate'],
+    'Response Id': ['responseid', 'response id'],
+    'Dese Id': ['deseid', 'dese id', 'school'],
+}
+
+final_columns_teacher = {
+    'Start Date': ['startdate', 'start date'],
+    'End Date': ['enddate', 'end date'],
+    'Status': ['status'],
+    'Ip Address': ['ip address', 'ipaddress'],
+    'Progress': ['progress'],
+    'Duration': ['duration', 'duration..in.seconds', 'duration (in seconds)'],
+    'District': ['district', 'please select your school district.'],
+    'Recorded Date': ['recorded date', 'recordeddate'],
+    'Response Id': ['responseid', 'response id'],
+    'Dese Id': ['deseid', 'dese id', 'school'],
+}
+
+argVerbose = False
+argQuiet = True
+
+
+class Sftp:
+    def __init__(self, hostname, username, password, cnopts, port=22):
+        """Constructor Method"""
+        # Set connection object to None (initial value)
+        self.connection = None
+        self.hostname = hostname
+        self.username = username
+        self.password = password
+        self.cnopts = cnopts
+        self.port = port
+
+    def connect(self):
+        """Connects to the sftp server and returns the sftp connection object"""
+
+        try:
+            # Get the sftp connection object
+            self.connection = pysftp.Connection(
+                host=self.hostname,
+                username=self.username,
+                password=self.password,
+                cnopts=self.cnopts,
+                port=self.port,
+            )
+        except Exception as err:
+            raise Exception(err)
+        finally:
+            if not argQuiet: print(f"Connected to {self.hostname} as {self.username}.")
+
+    def disconnect(self):
+        """Closes the sftp connection"""
+        self.connection.close()
+        if not argQuiet: print(f"Disconnected from host {self.hostname}")
+
+    def listdir(self, remote_path):
+        """lists all the files and directories in the specified path and returns them"""
+        for obj in self.connection.listdir(remote_path):
+            yield obj
+
+    def listdir_attr(self, remote_path):
+        """lists all the files and directories (with their attributes) in the specified path and returns them"""
+        for attr in self.connection.listdir_attr(remote_path):
+            yield attr
+
+    def download(self, remote_path, target_local_path):
+        """
+        Downloads the file from remote sftp server to local.
+        Also, by default extracts the file to the specified target_local_path
+        """
+
+        try:
+            if not argQuiet: print(
+                f"downloading from {self.hostname} as {self.username} [(remote path : {remote_path});(local path: {target_local_path})]"
+            )
+
+            # Create the target directory if it does not exist
+            path, _ = os.path.split(target_local_path)
+            if not os.path.isdir(path):
+                try:
+                    os.makedirs(path)
+                except Exception as err:
+                    raise Exception(err)
+
+            # Download from remote sftp server to local
+            self.connection.get(remote_path, target_local_path)
+            if not argQuiet: print("download completed")
+
+        except Exception as err:
+            raise Exception(err)
+
+    def upload(self, source_local_path, remote_path):
+        """
+        Uploads the source files from local to the sftp server.
+        """
+
+        try:
+            if not argQuiet: print(
+                f"uploading to {self.hostname} as {self.username} [(remote path: {remote_path});(source local path: {source_local_path})]"
+            )
+
+            # Download file from SFTP
+            self.connection.put(source_local_path, remote_path)
+            if not argQuiet: print("upload completed")
+
+        except Exception as err:
+            raise Exception(err)
+
+
+# prepare csv and merged csv directories
+def prep_dir(folder=''):
+    # prepare directories
+    cwd = os.path.join(os.getcwd(), folder)
+    mwd = os.path.join(cwd, 'merged')
+    if not os.path.exists(mwd):
+        if argVerbose: print(f'Creating directory {mwd}')
+        os.mkdir(mwd)
+    if argVerbose: print('Source data directory: ' + cwd)
+    if argVerbose: print('Merged data directory: ' + mwd)
+    return cwd, mwd
+
+
+# get current date in Month-XX-YYYY format
+def get_date():
+    return datetime.date.today().strftime("%B-%d-%Y")
+
+
+# in dataframe df, merges any column in possibilities into the final column col
+def combine_cols(df, col, possibilities):
+    # if final column doesn't exist, create it
+    if col not in df.columns:
+        tmpdf = pd.DataFrame([np.nan], columns=[col])
+        df = pd.concat((df, tmpdf), axis=1)
+    # list to store replaced columns
+    drops = []
+    # for every column possibility that does exist...
+    for cl in df.columns:
+        if cl.lower() in possibilities:
+            # we don't want to merge and drop our final column
+            if cl == col:
+                continue
+            # replace the column...
+            if argVerbose: print(f'Replacing column {cl}')
+            df[col] = df[col].replace(r'^\s*$', np.nan, regex=True).fillna(df[cl])
+            # and add it to the drop list
+            drops.append(cl)
+    # drop spent columns
+    df = df.drop(columns=drops)
+    if argVerbose: print(f'Dropped columns: {drops}')
+    return df
+
+
+# removes unused columns from student data
+def clean_cols_student(df):
+    keep = list(final_columns_student.keys())
+    keep = list(map(str.lower, keep))
+    drops = []
+    question_pattern = re.compile("^s-[a-zA-Z]{4}-q[0-9][0-9]?$")
+    for col in df.columns:
+        if col.lower() not in keep and not bool(question_pattern.match(col)):
+            drops.append(col)
+    df = df.drop(columns=drops)
+    if argVerbose: print(f'Dropped columns: {drops}')
+    return df
+
+
+# removes unused columns from teacher data
+def clean_cols_teacher(df):
+    keep = list(final_columns_teacher.keys())
+    keep = list(map(str.lower, keep))
+    drops = []
+    question_pattern = re.compile("^t-[a-zA-Z]{4}-q[0-9][0-9]?$")
+    for col in df.columns:
+        if col.lower() not in keep and not bool(question_pattern.match(col)):
+            drops.append(col)
+    df = df.drop(columns=drops)
+    if argVerbose: print(f'Dropped columns: {drops}')
+    return df
+
+
+# performs all merging operations for student data
+def do_merge_student(cwd, mwd):
+    # identify and merge student files
+    if not argQuiet: print('---Merging Student Data---')
+    all_files = glob.glob(os.path.join(cwd, "*student*.csv"))
+    if not argQuiet: print(f'Found {len(all_files)} Student CSV files')
+    if len(all_files) < 1:
+        if not argQuiet: print('No files found. Skipping merge...')
+        return
+    if not argQuiet: print('Merging...')
+    files = [pd.read_csv(f, low_memory=False) for f in all_files]
+    # count lines in read csv files
+    lines = 0
+    for fi in files:
+        lines += fi.shape[0]
+    # combine csv files
+    df = pd.concat(files, axis=0)
+    # combine related columns
+    if not argQuiet: print('Repairing rows...')
+    df = repair_student_columns(df)
+    # clean out unnecessary columns
+    if not argQuiet: print('Cleaning out columns...')
+    df = clean_cols_student(df)
+    # ensure line count matches what is expected
+    if df.shape[0] != lines:
+        print(f'Warning: Line count mismatch: {lines} expected, but got {df.shape[0]}')
+    # save merged file
+    date = get_date()
+    if args.project:
+        proj = '-' + args.project
+    else:
+        proj = ''
+    fn = f'{date}{proj}-student-data-merged.csv'
+    df.to_csv(os.path.join(mwd, fn), index=False)
+    if not argQuiet: print('Student data merged successfully!')
+    return fn
+
+
+# performs all merging operations for teacher data
+def do_merge_teacher(cwd, mwd):
+    # identify and merge teacher files
+    if not argQuiet: print('---Merging Teacher Data---')
+    all_files = glob.glob(os.path.join(cwd, "*teacher*.csv"))
+    if not argQuiet: print(f'Found {len(all_files)} Teacher CSV files')
+    if len(all_files) < 1:
+        if not argQuiet: print('No files found. Skipping merge...')
+        return
+    if not argQuiet: print('Merging...')
+    files = [pd.read_csv(f, low_memory=False) for f in all_files]
+    # count lines in read csv files
+    lines = 0
+    for f in files:
+        lines += f.shape[0]
+    # combine csv files
+    df = pd.concat(files, axis=0)
+    # combine related columns
+    if not argQuiet: print('Repairing columns...')
+    df = repair_teacher_columns(df)
+    # clean out unnecessary columns
+    if not argQuiet: print('Cleaning out columns...')
+    df = clean_cols_teacher(df)
+    # ensure line count matches what is expected
+    if df.shape[0] != lines:
+        print(f'Warning: Line count mismatch: {lines} expected, but got {df.shape[0]}')
+    # save merged file
+    date = get_date()
+    if args.project:
+        proj = '-' + args.project
+    else:
+        proj = ''
+    fn = f'{date}{proj}-teacher-data-merged.csv'
+    df.to_csv(os.path.join(mwd, fn), index=False)
+    if not argQuiet: print('Teacher data merged successfully!')
+    return fn
+
+
+# merges teacher columns that may have mismatched names
+def repair_teacher_columns(df):
+    for col in final_columns_teacher:
+        df = combine_cols(df, col, final_columns_teacher[col])
+    return df
+
+
+# merges student columns that may have mismatched names, 
+# and combines question variants
+def repair_student_columns(df):
+    for col in final_columns_student:
+        df = combine_cols(df, col, final_columns_student[col])
+    if not argQuiet: print('Combining Question Variants...')
+    df = combine_variants(df)
+    return df
+
+
+# combines question variants into non-variant columns
+def combine_variants(df):
+    drops = []
+    for col in df:
+        x = re.search(r'^s-[a-z]{4}-q[0-9][0-9]?-1$', col)
+        if x is not None:
+            # get non variant version
+            nonvar = col[:-2]
+            # combine into non variant
+            df[nonvar] = df[nonvar].replace(r'^\s*$', np.nan, regex=True).fillna(df[col])
+            # and add it to the drop list
+            drops.append(col)
+    df = df.drop(columns=drops)
+    return df
+
+
+
+if __name__ == '__main__':
+
+    # parse flags
+    parser = argparse.ArgumentParser(
+        prog='merge-csv',
+        description='Merges CSV Files containing student and teacher data',
+        epilog='Usage: python merge-csv.py (-stq) (-d directory) (-r remote) (-p project)')
+    parser.add_argument('-d', '--directory',
+                        action='store',
+                        help='directory for local csv , defaults to current directory')
+    parser.add_argument('-t', '--teacher',
+                        action='store_true',
+                        dest='teacher',
+                        help='merge teacher data')
+    parser.add_argument('-s', '--student',
+                        action='store_true',
+                        dest='student',
+                        help='merge student data')
+    parser.add_argument('-q', '--quiet',
+                        action='store_true',
+                        dest='quiet',
+                        help='run without output (besides errors and warnings)')
+    parser.add_argument('-v', '--verbose',
+                        action='store_true',
+                        dest='verbose',
+                        help='run with extra output information')
+    parser.add_argument('-p', '--project',
+                        action='store',
+                        help='add a project name to the merged csv file name')
+    parser.add_argument('-r', '--remote-url',
+                        action='store',
+                        dest='remote_url',
+                        help='sftp url for remote merging')
+    args = parser.parse_args()
+
+    argVerbose = args.verbose
+    argQuiet = args.quiet
+
+    #quiet takes precedence over verbose
+    if argQuiet:
+        argVerbose = False
+
+    # make sure -s or -t is set
+    if not (args.student or args.teacher):
+        if not argQuiet: print('Notice: Neither -s nor -t are specified. No merge will be performed.')
+
+    if args.directory and not args.remote_url:
+        c, m = prep_dir(args.directory)
+    elif not args.directory:
+        if not argQuiet: print('Notice: No directory specified. Defaulting to current directory.')
+        c, m = prep_dir()
+
+    # prepare sftp if flagged
+    if args.remote_url:
+        if not argQuiet: print(f'Remote destination set, fetching files...')
+        parsed_url = urlparse(args.remote_url)
+        cnopts = pysftp.CnOpts()
+        cnopts.hostkeys = None
+        sftp = Sftp(
+            hostname=parsed_url.hostname,
+            username=parsed_url.username,
+            password=parsed_url.password,
+            cnopts=cnopts,
+        )
+        sftp.connect()
+        # current directory is used for remote file merging
+        c, m = prep_dir()
+
+        # prepare remote path
+        path = args.directory
+        if not path:
+            path = "/"
+        # ensure trailing slash
+        if not path.endswith("/"): path += "/"
+
+        filelist = []
+        # get csv list from remote
+        for file in sftp.listdir_attr(path):
+            if file.filename.endswith(".csv"):
+                filelist.append(file.filename)
+                if not argQuiet: print(f'Fetching file {file.filename}...')
+                sftp.download(path + file.filename, c + file.filename)
+
+    # perform merges
+    if args.teacher:
+        tmd = do_merge_teacher(c, m)
+    if args.student:
+        smd = do_merge_student(c, m)
+
+    if args.remote_url:
+        # upload tmd and smd to remote
+        if not argQuiet: print('Uploading merged data...')
+        sftp.upload(m + '/' + tmd, path + 'merged/' + tmd)
+        sftp.upload(m + '/' + smd, path + 'merged/' + smd)
+        # remove merged directory
+        if not argQuiet: print('Cleaning up...')
+        os.remove(m + '/' + tmd)
+        os.remove(m + '/' + smd)
+        os.rmdir(m)
+        # remove downloaded files
+        for f in filelist:
+            if os.path.exists(f):
+                os.remove(f)
+        sftp.disconnect()
+    if not argQuiet: print('Done!')