""" Provide basic method to process data describing tables. Created by Eugeniy E. Mikhailov 2024/05/27 The basic idea that we will have an *input* table with data description and we (re)generate *output* table based on the input table with processed rows. If output table already have processed rows with entries different from NA such rows are skipped. Super handy for bulk processing data files where only a few parameters changed. """ import pandas as pd import warnings def loadInOutTables(inputFileName=None, outputFileName=None, comment=None): """Load the input and the output tables from files. The output table loaded only if the corresponding file exists. Otherwise it is a clone of the input table. Parameters ========== inputFileName : path or string Path to the input table filename. If this file does not exists, return None for both tables. outputFileName : path or string or None Path to the outpyt table filename. If such file does not exit, clone the input table to the output one. comment : string or None (default) String which indicates a comment in the input `csv` file. Usually it is either '#' or '%'. If set to None, internally changed to '#'. """ if not inputFileName: return None, None if not comment: comment = "#" tIn = pd.read_csv(inputFileName, comment=comment) tIn.columns = tIn.columns.str.removeprefix(" ") # clean up leading white space in columns names try: tOut = pd.read_csv(outputFileName, comment=comment) except Exception: tOut = tIn.copy(deep=True) return tIn, tOut def ilocRowOrAdd(tbl, row): """Find a row in a table (`tbl`) similar to a provided `row`. NA in both sets treated as a match. If similar 'row' not found in the table, insert it. """ tSub = tbl[row.keys()] res = (tSub == row) | (tSub.isna() & row.isna()) res = res.all(axis=1) # which rows coincide if res.any(): # we have a similar row i = res[res].index[0] else: # we need to create new row since tbl does not has it i = len(tbl) updateTblRowAt(tbl, i, row) return i def updateTblRowAt(tbl, i, row): """Update row with position 'i' in the table ('tbl') with values from 'row'.""" for k in row.keys(): tbl.at[i, k] = row[k] return def isRedoNeeded(row, cols2check): """Check is Redo required in a given row. Redo is required if *all* required entries in 'cols2check' are NA or we are missing columns in cols2check list Parameters ========== row: pandas row row to perform check on cols2check: list of strings List of strings with column names which considered as generated outputs. """ for c in cols2check: if c not in row.keys(): return True if row[cols2check].isna().all(): return True return False def reflowTable( tIn, tOut, process_row_func=None, postProcessedColums=None, extraInfo=None, redo=False, ): """Reflow/update table tOut in place based on the inputs specified in table tIn. Effectively maps unprocessed rows to ``process_row_func``. Parameters ========== postProcessedColums : list of strings List of column names which need to be generated extraInfo : dictionary (optional) Dictionary of additional parameter supplied to ``process_row_func`` process_row_func : function Function which will take a row from the input table and generate row with post processed entries (columns). Expected to have signature like: ``rowOut = process_row_func(rowIn, extraInfo=userInfo)`` redo : True or False (default) Flag indicating if reflow is needed unconditionally (i.e. True forces reflow of all entries). """ if not process_row_func: warnings.warn("process_row_func is not provided, exiting reflowTable") return if not postProcessedColums: warnings.warn("postProcessedColums are not provided, exiting reflowTable") return for index, rowIn in tIn.iterrows(): iOut = ilocRowOrAdd(tOut, rowIn) rowOutBefore = tOut.iloc[iOut] if not (redo or isRedoNeeded(rowOutBefore, postProcessedColums)): continue # processing data describing row rowOut = process_row_func(rowOutBefore, extraInfo=extraInfo) updateTblRowAt(tOut, iOut, rowOut)