Source code for pudl.helpers

"""General utility functions that are used in a variety of contexts.

The functions in this module are used in various stages of the ETL and post-etl
processes. They are usually not dataset specific, but not always. If a function is
designed to be used as a general purpose tool, applicable in multiple scenarios, it
should probably live here. There are lost of transform type functions in here that help
with cleaning and restructing dataframes.
"""
import itertools
import pathlib
import re
import shutil
from collections import defaultdict
from collections.abc import Generator, Iterable
from functools import partial
from importlib import resources
from io import BytesIO
from typing import Any, Literal

import addfips
import numpy as np
import pandas as pd
import requests
import sqlalchemy as sa
from pandas._libs.missing import NAType

import pudl.logging_helpers
from pudl.metadata.fields import get_pudl_dtypes

[docs]sum_na = partial(pd.Series.sum, skipna=False)
"""A sum function that returns NA if the Series includes any NA values. In many of our aggregations we need to override the default behavior of treating NA values as if they were zero. E.g. when calculating the heat rates of generation units, if there are some months where fuel consumption is reported as NA, but electricity generation is reported normally, then the fuel consumption for the year needs to be NA, otherwise we'll get unrealistic heat rates. """
[docs]logger = pudl.logging_helpers.get_logger(__name__)
[docs]def label_map( df: pd.DataFrame, from_col: str = "code", to_col: str = "label", null_value: str | NAType = pd.NA, ) -> defaultdict[str, str | NAType]: """Build a mapping dictionary from two columns of a labeling / coding dataframe. These dataframes document the meanings of the codes that show up in much of the originally reported data. They're defined in :mod:`pudl.metadata.codes`. This function is mostly used to build maps that can translate the hard to understand short codes into longer human-readable codes. Args: df: The coding / labeling dataframe. Must contain columns ``from_col`` and ``to_col``. from_col: Label of column containing the existing codes to be replaced. to_col: Label of column containing the new codes to be swapped in. null_value: Defualt (Null) value to map to when a value which doesn't appear in ``from_col`` is encountered. Returns: A mapping dictionary suitable for use with :meth:`pandas.Series.map`. """ return defaultdict( lambda: null_value, df.loc[:, [from_col, to_col]] .drop_duplicates(subset=[from_col]) .to_records(index=False), )
[docs]def find_new_ferc1_strings( table: str, field: str, strdict: dict[str, list[str]], ferc1_engine: sa.engine.Engine, ) -> set[str]: """Identify as-of-yet uncategorized freeform strings in FERC Form 1. Args: table: Name of the FERC Form 1 DB to search. field: Name of the column in that table to search. strdict: A string cleaning dictionary. See e.g. `pudl.transform.ferc1.FUEL_UNIT_STRINGS` ferc1_engine: SQL Alchemy DB connection engine for the FERC Form 1 DB. Returns: Any string found in the searched table + field that was not part of any of categories enumerated in strdict. """ all_strings = set( pd.read_sql(f"SELECT {field} FROM {table};", ferc1_engine).pipe( # nosec simplify_strings, columns=[field] )[field] ) old_strings = set.union(*[set(strings) for strings in strdict.values()]) return all_strings.difference(old_strings)
[docs]def find_foreign_key_errors(dfs: dict[str, pd.DataFrame]) -> list[dict[str, Any]]: """Report foreign key violations from a dictionary of dataframes. The database schema to check against is generated based on the names of the dataframes (keys of the dictionary) and the PUDL metadata structures. Args: dfs: Keys are table names, and values are dataframes ready for loading into the SQLite database. Returns: A list of dictionaries, each one pertains to a single database table in which a foreign key constraint violation was found, and it includes the table name, foreign key definition, and the elements of the dataframe that violated the foreign key constraint. """ import pudl.metadata.classes package = pudl.metadata.classes.Package.from_resource_ids( resource_ids=tuple(sorted(dfs)) ) errors = [] for resource in package.resources: for foreign_key in resource.schema.foreign_keys: x = dfs[resource.name][foreign_key.fields] y = dfs[foreign_key.reference.resource][foreign_key.reference.fields] ncols = x.shape[1] idx = range(ncols) xx, yy = x.set_axis(idx, axis=1), y.set_axis(idx, axis=1) if ncols == 1: # Faster check for single-field foreign key invalid = ~(xx[0].isin(yy[0]) | xx[0].isna()) else: invalid = ~( pd.concat([yy, xx]).duplicated().iloc[len(yy) :] | xx.isna().any(axis=1) ) if invalid.any(): errors.append( { "resource": resource.name, "foreign_key": foreign_key, "invalid": x[invalid], } ) return errors
[docs]def download_zip_url(url, save_path, chunk_size=128): """Download and save a Zipfile locally. Useful for acquiring and storing non-PUDL data locally. Args: url (str): The URL from which to download the Zipfile save_path (pathlib.Path): The location to save the file. chunk_size (int): Data chunk in bytes to use while downloading. Returns: None """ # This is a temporary hack to avoid being filtered as a bot: headers = { "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:77.0) Gecko/20100101 Firefox/77.0", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8", "Accept-Language": "en-US,en;q=0.5", "DNT": "1", "Connection": "keep-alive", "Upgrade-Insecure-Requests": "1", } r = requests.get(url, stream=True, headers=headers) with save_path.open(mode="wb") as fd: for chunk in r.iter_content(chunk_size=chunk_size): fd.write(chunk)
[docs]def add_fips_ids(df, state_col="state", county_col="county", vintage=2015): """Add State and County FIPS IDs to a dataframe. To just add State FIPS IDs, make county_col = None. """ # force the columns to be the nullable string types so we have a consistent # null value to filter out before feeding to addfips df = df.astype({state_col: pd.StringDtype()}) if county_col: df = df.astype({county_col: pd.StringDtype()}) af = addfips.AddFIPS(vintage=vintage) # Lookup the state and county FIPS IDs and add them to the dataframe: df["state_id_fips"] = df.apply( lambda x: ( af.get_state_fips(state=x[state_col]) if pd.notnull(x[state_col]) else pd.NA ), axis=1, ) # force the code columns to be nullable strings - the leading zeros are # important df = df.astype({"state_id_fips": pd.StringDtype()}) logger.info( f"Assigned state FIPS codes for " f"{len(df[df.state_id_fips.notnull()])/len(df):.2%} of records." ) if county_col: df["county_id_fips"] = df.apply( lambda x: ( af.get_county_fips(state=x[state_col], county=x[county_col]) if pd.notnull(x[county_col]) and pd.notnull(x[state_col]) else pd.NA ), axis=1, ) # force the code columns to be nullable strings - the leading zeros are # important df = df.astype({"county_id_fips": pd.StringDtype()}) logger.info( f"Assigned county FIPS codes for " f"{len(df[df.county_id_fips.notnull()])/len(df):.2%} of records." ) return df
[docs]def clean_eia_counties(df, fixes, state_col="state", county_col="county"): """Replace non-standard county names with county nmes from US Census.""" df = df.copy() df[county_col] = ( df[county_col] .str.strip() # Condense multiple whitespace chars. .str.replace(r"\s+", " ", regex=True) .str.replace(r"^St ", "St. ", regex=True) # Standardize abbreviation. # Standardize abbreviation. .str.replace(r"^Ste ", "Ste. ", regex=True) .str.replace("Kent & New Castle", "Kent, New Castle") # Two counties # Fix ordering, remove comma .str.replace("Borough, Kodiak Island", "Kodiak Island Borough") # Turn comma-separated counties into lists .str.replace(r",$", "", regex=True) .str.split(",") ) # Create new records for each county in a multi-valued record df = df.explode(county_col) df[county_col] = df[county_col].str.strip() # Yellowstone county is in MT, not WY df.loc[ (df[state_col] == "WY") & (df[county_col] == "Yellowstone"), state_col ] = "MT" # Replace individual bad county names with identified correct names in fixes: for fix in fixes.itertuples(): state_mask = df[state_col] == fix.state county_mask = df[county_col] == fix.eia_county df.loc[state_mask & county_mask, county_col] = fix.fips_county return df
[docs]def oob_to_nan(df, cols, lb=None, ub=None): """Set non-numeric values and those outside of a given rage to NaN. Args: df (pandas.DataFrame): The dataframe containing values to be altered. cols (iterable): Labels of the columns whose values are to be changed. lb: (number): Lower bound, below which values are set to NaN. If None, don't use a lower bound. ub: (number): Upper bound, below which values are set to NaN. If None, don't use an upper bound. Returns: pandas.DataFrame: The altered DataFrame. """ out_df = df.copy() for col in cols: # Force column to be numeric if possible, NaN otherwise: out_df.loc[:, col] = pd.to_numeric(out_df[col], errors="coerce") if lb is not None: out_df.loc[out_df[col] < lb, col] = np.nan if ub is not None: out_df.loc[out_df[col] > ub, col] = np.nan return out_df
[docs]def prep_dir(dir_path, clobber=False): """Create (or delete and recreate) a directory. Args: dir_path (path-like): path to the directory that you are trying to clean and prepare. clobber (bool): If True and dir_path exists, it will be removed and replaced with a new, empty directory. Raises: FileExistsError: if a file or directory already exists at dir_path. Returns: pathlib.Path: Path to the created directory. """ dir_path = pathlib.Path(dir_path) if dir_path.exists(): if clobber: shutil.rmtree(dir_path) else: raise FileExistsError(f"{dir_path} exists and clobber is {clobber}") dir_path.mkdir(parents=True) return dir_path
[docs]def is_doi(doi): """Determine if a string is a valid digital object identifier (DOI). Function simply checks whether the offered string matches a regular expresssion -- it doesn't check whether the DOI is actually registered with the relevant authority. Args: doi (str): String to validate. Returns: bool: True if doi matches the regex for valid DOIs, False otherwise. """ doi_regex = re.compile( r"(doi:\s*|(?:https?://)?(?:dx\.)?doi\.org/)?(10\.\d+(.\d+)*/.+)$", re.IGNORECASE | re.UNICODE, ) return bool(re.match(doi_regex, doi))
[docs]def convert_col_to_datetime(df, date_col_name): """Convert a column in a dataframe to a datetime. If the column isn't a datetime, it needs to be converted to a string type first so that integer years are formatted correctly. Args: df (pandas.DataFrame): Dataframe with column to convert. date_col_name (string): name of the column to convert. Returns: Dataframe with the converted datetime column. """ if pd.api.types.is_datetime64_ns_dtype(df[date_col_name]) is False: logger.warning( f"{date_col_name} is {df[date_col_name].dtype} column. Converting to datetime." ) df[date_col_name] = pd.to_datetime(df[date_col_name].astype("string")) return df
[docs]def full_timeseries_date_merge( left: pd.DataFrame, right: pd.DataFrame, on: list[str], left_date_col: str = "report_date", right_date_col: str = "report_date", new_date_col: str = "report_date", date_on: list[str] = ["year"], how: Literal["inner", "outer", "left", "right", "cross"] = "inner", report_at_start: bool = True, freq: str = "MS", **kwargs, ): """Merge dataframes with different date frequencies and expand to a full timeseries. Arguments: see arguments for ``date_merge`` and ``expand_timeseries`` """ out = date_merge( left=left, right=right, left_date_col=left_date_col, right_date_col=right_date_col, new_date_col=new_date_col, on=on, date_on=date_on, how=how, report_at_start=report_at_start, **kwargs, ) out = expand_timeseries( df=out, date_col=new_date_col, freq=freq, key_cols=on, ) return out
[docs]def _add_suffix_to_date_on(date_on): """Check date_on list is valid and add _temp_for_merge suffix.""" if date_on is None: date_on = ["year"] date_on_suffix = [] for col in date_on: if col not in ["year", "month", "quarter", "day"]: raise AssertionError( logger.error(f"{col} is not a valid string in date_on column list.") ) date_on_suffix.append(col + "_temp_for_merge") return date_on_suffix
[docs]def date_merge( left: pd.DataFrame, right: pd.DataFrame, on: list[str], left_date_col: str = "report_date", right_date_col: str = "report_date", new_date_col: str = "report_date", date_on: list[str] = None, how: Literal["inner", "outer", "left", "right", "cross"] = "inner", report_at_start: bool = True, **kwargs, ) -> pd.DataFrame: """Merge two dataframes that have different report date frequencies. We often need to bring together data that is reported at different temporal granularities e.g. monthly basis versus annual basis. This function acts as a wrapper on a pandas merge to allow merging at different temporal granularities. The date columns of both dataframes are separated into year, quarter, month, and day columns. Then, the dataframes are merged according to ``how`` on the columns specified by the ``on`` and ``date_on`` argument, which list the new temporal columns to merge on as well any additional shared columns. Finally, the datetime column is reconstructed in the output dataframe and named according to the ``new_date_col`` parameter. Args: left: The left dataframe in the merge. Typically monthly in our use cases if doing a left merge E.g. ``generation_eia923``. Must contain columns specified by ``left_date_col`` and ``on`` argument. right: The right dataframe in the merge. Typically annual in our uses cases if doing a left merge E.g. ``generators_eia860``. Must contain columns specified by ``right_date_col`` and ``on`` argument. on: The columns to merge on that are shared between both dataframes. Typically ID columns like ``plant_id_eia``, ``generator_id`` or ``boiler_id``. left_date_col: Column in ``left`` containing datetime like data. Default is ``report_date``. Must be a Datetime or convertible to a Datetime using :func:`pandas.to_datetime` right_date_col: Column in ``right`` containing datetime like data. Default is ``report_date``. Must be a Datetime or convertible to a Datetime using :func:`pandas.to_datetime`. new_date_col: Name of the reconstructed datetime column in the output dataframe. date_on: The temporal columns to merge on. Values in this list of columns must be [``year``, ``quarter``, ``month``, ``day``]. E.g. if a monthly reported dataframe is being merged onto a daily reported dataframe, then the merge would be performed on ``["year", "month"]``. If one of these temporal columns already exists in the dataframe it will not be clobbered by the merge, as the suffix "_temp_for_merge" is added when expanding the datetime column into year, quarter, month, and day. By default, `date_on` will just include year. how: How the dataframes should be merged. See :func:`pandas.DataFrame.merge`. report_at_start: Whether the data in the dataframe whose report date is not being kept in the merged output (in most cases the less frequently reported dataframe) is reported at the start or end of the time period e.g. January 1st for annual data. kwargs : Additional arguments to pass to :func:`pandas.DataFrame.merge`. Returns: Merged contents of left and right input dataframes. Raises: ValueError: if ``left_date_col`` or ``right_date_col`` columns are missing from their respective input dataframes. ValueError: if any of the labels referenced in ``on`` are missing from either the left or right dataframes. """ def separate_date_cols(df, date_col_name, date_on): out_df = df.copy() out_df.loc[:, date_col_name] = pd.to_datetime(out_df[date_col_name]) if "year_temp_for_merge" in date_on: out_df.loc[:, "year_temp_for_merge"] = out_df[date_col_name].dt.year if "quarter_temp_for_merge" in date_on: out_df.loc[:, "quarter_temp_for_merge"] = out_df[date_col_name].dt.quarter if "month_temp_for_merge" in date_on: out_df.loc[:, "month_temp_for_merge"] = out_df[date_col_name].dt.month if "day_temp_for_merge" in date_on: out_df.loc[:, "day_temp_for_merge"] = out_df[date_col_name].dt.day return out_df right = convert_col_to_datetime(right, right_date_col) left = convert_col_to_datetime(left, left_date_col) date_on = _add_suffix_to_date_on(date_on) right = separate_date_cols(right, right_date_col, date_on) left = separate_date_cols(left, left_date_col, date_on) merge_cols = date_on + on out = pd.merge(left, right, on=merge_cols, how=how, **kwargs) suffixes = ["", ""] if left_date_col == right_date_col: if "suffixes" in kwargs: suffixes = kwargs["suffixes"] else: suffixes = ["_x", "_y"] # reconstruct the new report date column and clean up columns left_right_date_col = [left_date_col + suffixes[0], right_date_col + suffixes[1]] if report_at_start: # keep the later of the two report dates when determining # the new report date for each row reconstructed_date = out[left_right_date_col].max(axis=1) else: # keep the earlier of the two report dates reconstructed_date = out[left_right_date_col].min(axis=1) out = out.drop(left_right_date_col + date_on, axis=1) out.insert(loc=0, column=new_date_col, value=reconstructed_date) return out
[docs]def expand_timeseries( df: pd.DataFrame, key_cols: list[str], date_col: str = "report_date", freq: str = "MS", fill_through_freq: Literal["year", "month", "day"] = "year", ) -> pd.DataFrame: """Expand a dataframe to a include a full time series at a given frequency. This function adds a full timeseries to the given dataframe for each group of columns specified by ``key_cols``. The data in the timeseries will be filled with the next previous chronological observation for a group of primary key columns specified by ``key_cols``. Arguments: df: The dataframe to expand. Must have ``date_col`` in columns. key_cols: Column names of the non-date primary key columns in the dataframe. The resulting dataframe will have a full timeseries expanded for each unique group of these ID columns that are present in the dataframe. date_col: Name of the datetime column being expanded into a full timeseries. freq: The frequency of the time series to expand the data to. See :ref:`here <timeseries.offset_aliases>` for a list of frequency aliases. fill_through_freq: The frequency in which to fill in the data through. For example, if equal to "year" the data will be filled in through the end of the last reported year for each grouping of `key_cols`. Valid frequencies are only year, month, or day. """ try: pd.tseries.frequencies.to_offset(freq) except ValueError: logger.exception( f"Frequency string {freq} is not valid. \ See Pandas Timeseries Offset Aliases docs for valid strings." ) # For each group of ID columns add a dummy record with the date column # equal to one increment higher than the last record in the group for the # desired fill_through_freq. # This allows records to be filled through the end of the last reported period # and then this dummy record is dropped df = convert_col_to_datetime(df, date_col) end_dates = df.groupby(key_cols).agg({date_col: "max"}) if fill_through_freq == "year": end_dates.loc[:, date_col] = pd.to_datetime( { "year": end_dates[date_col].dt.year + 1, "month": 1, "day": 1, } ) elif fill_through_freq == "month": end_dates.loc[:, date_col] = pd.to_datetime( { "year": end_dates[date_col].dt.year, "month": end_dates[date_col].dt.month + 1, "day": 1, } ) elif fill_through_freq == "day": end_dates.loc[:, date_col] = pd.to_datetime( { "year": end_dates[date_col].dt.year, "month": end_dates[date_col].dt.month, "day": end_dates[date_col].dt.day + 1, } ) else: raise AssertionError( f"{fill_through_freq} is not a valid frequency to fill through." ) end_dates["drop_row"] = True df = pd.concat([df, end_dates.reset_index()]) df = ( df.set_index(date_col) .groupby(key_cols) .resample(freq) .ffill() .drop(key_cols, axis=1) .reset_index() ) df = df[df.drop_row.isnull()].drop("drop_row", axis=1).reset_index(drop=True) return df
[docs]def organize_cols(df, cols): """Organize columns into key ID & name fields & alphabetical data columns. For readability, it's nice to group a few key columns at the beginning of the dataframe (e.g. report_year or report_date, plant_id...) and then put all the rest of the data columns in alphabetical order. Args: df: The DataFrame to be re-organized. cols: The columns to put first, in their desired output ordering. Returns: pandas.DataFrame: A dataframe with the same columns as the input DataFrame df, but with cols first, in the same order as they were passed in, and the remaining columns sorted alphabetically. """ # Generate a list of all the columns in the dataframe that are not # included in cols data_cols = sorted(c for c in df.columns.tolist() if c not in cols) organized_cols = cols + data_cols return df[organized_cols]
[docs]def simplify_strings(df, columns): """Simplify the strings contained in a set of dataframe columns. Performs several operations to simplify strings for comparison and parsing purposes. These include removing Unicode control characters, stripping leading and trailing whitespace, using lowercase characters, and compacting all internal whitespace to a single space. Leaves null values unaltered. Casts other values with astype(str). Args: df (pandas.DataFrame): DataFrame whose columns are being cleaned up. columns (iterable): The labels of the string columns to be simplified. Returns: pandas.DataFrame: The whole DataFrame that was passed in, with the string columns cleaned up. """ out_df = df.copy() for col in columns: if col in out_df.columns: out_df.loc[out_df[col].notnull(), col] = ( out_df.loc[out_df[col].notnull(), col] .astype(str) .str.replace(r"[\x00-\x1f\x7f-\x9f]", "", regex=True) .str.strip() .str.lower() .str.replace(r"\s+", " ", regex=True) ) return out_df
[docs]def cleanstrings_series(col, str_map, unmapped=None, simplify=True): """Clean up the strings in a single column/Series. Args: col (pandas.Series): A pandas Series, typically a single column of a dataframe, containing the freeform strings that are to be cleaned. str_map (dict): A dictionary of lists of strings, in which the keys are the simplified canonical strings, witch which each string found in the corresponding list will be replaced. unmapped (str): A value with which to replace any string found in col that is not found in one of the lists of strings in map. Typically the null string ''. If None, these strings will not be replaced. simplify (bool): If True, strip and compact whitespace, and lowercase all strings in both the list of values to be replaced, and the values found in col. This can reduce the number of strings that need to be kept track of. Returns: pandas.Series: The cleaned up Series / column, suitable for replacing the original messy column in a :class:`pandas.DataFrame`. """ if simplify: col = ( col.astype(str).str.strip().str.lower().str.replace(r"\s+", " ", regex=True) ) for k in str_map: str_map[k] = [re.sub(r"\s+", " ", s.lower().strip()) for s in str_map[k]] for k in str_map: if str_map[k]: col = col.replace(str_map[k], k) if unmapped is not None: badstrings = np.setdiff1d(col.unique(), list(str_map.keys())) # This call to replace can only work if there are actually some # leftover strings to fix -- otherwise it runs forever because we # are replacing nothing with nothing. if len(badstrings) > 0: col = col.replace(badstrings, unmapped) return col
[docs]def cleanstrings(df, columns, stringmaps, unmapped=None, simplify=True): """Consolidate freeform strings in several dataframe columns. This function will consolidate freeform strings found in `columns` into simplified categories, as defined by `stringmaps`. This is useful when a field contains many different strings that are really meant to represent a finite number of categories, e.g. a type of fuel. It can also be used to create simplified categories that apply to similar attributes that are reported in various data sources from different agencies that use their own taxonomies. The function takes and returns a pandas.DataFrame, making it suitable for use with the :func:`pandas.DataFrame.pipe` method in a chain. Args: df (pandas.DataFrame): the DataFrame containing the string columns to be cleaned up. columns (list): a list of string column labels found in the column index of df. These are the columns that will be cleaned. stringmaps (list): a list of dictionaries. The keys of these dictionaries are strings, and the values are lists of strings. Each dictionary in the list corresponds to a column in columns. The keys of the dictionaries are the values with which every string in the list of values will be replaced. unmapped (str, None): the value with which strings not found in the stringmap dictionary will be replaced. Typically the null string ''. If None, then strings found in the columns but not in the stringmap will be left unchanged. simplify (bool): If true, strip whitespace, remove duplicate whitespace, and force lower-case on both the string map and the values found in the columns to be cleaned. This can reduce the overall number of string values that need to be tracked. Returns: pandas.DataFrame: The function returns a new DataFrame containing the cleaned strings. """ out_df = df.copy() for col, str_map in zip(columns, stringmaps): out_df[col] = cleanstrings_series( out_df[col], str_map, unmapped=unmapped, simplify=simplify ) return out_df
[docs]def fix_int_na(df, columns, float_na=np.nan, int_na=-1, str_na=""): """Convert NA containing integer columns from float to string. Numpy doesn't have a real NA value for integers. When pandas stores integer data which has NA values, it thus upcasts integers to floating point values, using np.nan values for NA. However, in order to dump some of our dataframes to CSV files for use in data packages, we need to write out integer formatted numbers, with empty strings as the NA value. This function replaces np.nan values with a sentinel value, converts the column to integers, and then to strings, finally replacing the sentinel value with the desired NA string. This is an interim solution -- now that pandas extension arrays have been implemented, we need to go back through and convert all of these integer columns that contain NA values to Nullable Integer types like Int64. Args: df (pandas.DataFrame): The dataframe to be fixed. This argument allows method chaining with the pipe() method. columns (iterable of strings): A list of DataFrame column labels indicating which columns need to be reformatted for output. float_na (float): The floating point value to be interpreted as NA and replaced in col. int_na (int): Sentinel value to substitute for float_na prior to conversion of the column to integers. str_na (str): sa.String value to substitute for int_na after the column has been converted to strings. Returns: df (pandas.DataFrame): a new DataFrame, with the selected columns converted to strings that look like integers, compatible with the postgresql COPY FROM command. """ return ( df.replace({c: float_na for c in columns}, int_na) .astype({c: int for c in columns}) .astype({c: str for c in columns}) .replace({c: str(int_na) for c in columns}, str_na) )
[docs]def month_year_to_date(df): """Convert all pairs of year/month fields in a dataframe into Date fields. This function finds all column names within a dataframe that match the regular expression '_month$' and '_year$', and looks for pairs that have identical prefixes before the underscore. These fields are assumed to describe a date, accurate to the month. The two fields are used to construct a new _date column (having the same prefix) and the month/year columns are then dropped. Todo: This function needs to be combined with convert_to_date, and improved: * find and use a _day$ column as well * allow specification of default month & day values, if none are found. * allow specification of lists of year, month, and day columns to be combined, rather than automataically finding all the matching ones. * Do the Right Thing when invalid or NA values are encountered. Args: df (pandas.DataFrame): The DataFrame in which to convert year/months fields to Date fields. Returns: pandas.DataFrame: A DataFrame in which the year/month fields have been converted into Date fields. """ df = df.copy() month_regex = "_month$" year_regex = "_year$" # Columns that match our month or year patterns. month_cols = list(df.filter(regex=month_regex).columns) year_cols = list(df.filter(regex=year_regex).columns) # Base column names that don't include the month or year pattern months_base = [re.sub(month_regex, "", m) for m in month_cols] years_base = [re.sub(year_regex, "", y) for y in year_cols] # We only want to retain columns that have BOTH month and year # matches -- otherwise there's no point in creating a Date. date_base = [base for base in months_base if base in years_base] # For each base column that DOES have both a month and year, # We need to grab the real column names corresponding to each, # so we can access the values in the data frame, and use them # to create a corresponding Date column named [BASE]_date month_year_date = [] for base in date_base: base_month_regex = f"^{base}{month_regex}" month_col = list(df.filter(regex=base_month_regex).columns) if not len(month_col) == 1: raise AssertionError() month_col = month_col[0] base_year_regex = f"^{base}{year_regex}" year_col = list(df.filter(regex=base_year_regex).columns) if not len(year_col) == 1: raise AssertionError() year_col = year_col[0] date_col = f"{base}_date" month_year_date.append((month_col, year_col, date_col)) for month_col, year_col, date_col in month_year_date: df = fix_int_na(df, columns=[year_col, month_col]) date_mask = (df[year_col] != "") & (df[month_col] != "") years = df.loc[date_mask, year_col] months = df.loc[date_mask, month_col] df.loc[date_mask, date_col] = pd.to_datetime( {"year": years, "month": months, "day": 1}, errors="coerce" ) # Now that we've replaced these fields with a date, we drop them. df = df.drop([month_col, year_col], axis=1) return df
[docs]def remove_leading_zeros_from_numeric_strings( df: pd.DataFrame, col_name: str ) -> pd.DataFrame: """Remove leading zeros frame column values that are numeric strings. Sometimes an ID column (like generator_id or unit_id) will be reported with leading zeros and sometimes it won't. For example, in the Excel spreadsheets published by EIA, the same generator may show up with the ID "0001" and "1" in different years This function strips the leading zeros from those numeric strings so the data can be mapped accross years and datasets more reliably. Alphanumeric generator IDs with leadings zeroes are not affected, as we found no instances in which an alphanumeric ID appeared both with and without leading zeroes. The ID "0A1" will stay "0A1". Args: df: A DataFrame containing the column you'd like to remove numeric leading zeros from. col_name: The name of the column you'd like to remove numeric leading zeros from. Returns: A DataFrame without leading zeros for numeric string values in the desired column. """ leading_zeros = df[col_name].str.contains(r"^0+\d+$").fillna(False) if leading_zeros.any(): logger.debug(f"Fixing leading zeros in {col_name} column") df.loc[leading_zeros, col_name] = df[col_name].str.replace( r"^0+", "", regex=True ) else: logger.debug(f"Found no numeric leading zeros in {col_name}") return df
[docs]def convert_to_date( df, date_col="report_date", year_col="report_year", month_col="report_month", day_col="report_day", month_value=1, day_value=1, ): """Convert specified year, month or day columns into a datetime object. If the input ``date_col`` already exists in the input dataframe, then no conversion is applied, and the original dataframe is returned unchanged. Otherwise the constructed date is placed in that column, and the columns which were used to create the date are dropped. Args: df (pandas.DataFrame): dataframe to convert date_col (str): the name of the column you want in the output. year_col (str): the name of the year column in the original table. month_col (str): the name of the month column in the original table. day_col: the name of the day column in the original table. month_value (int): generated month if no month exists. day_value (int): generated day if no month exists. Returns: pandas.DataFrame: A DataFrame in which the year, month, day columns values have been converted into datetime objects. Todo: Update docstring. """ df = df.copy() if date_col in df.columns: return df year = df[year_col] if month_col not in df.columns: month = month_value else: month = df[month_col] if day_col not in df.columns: day = day_value else: day = df[day_col] df[date_col] = pd.to_datetime({"year": year, "month": month, "day": day}) cols_to_drop = [x for x in [day_col, year_col, month_col] if x in df.columns] df.drop(cols_to_drop, axis="columns", inplace=True) return df
[docs]def fix_eia_na(df): """Replace common ill-posed EIA NA spreadsheet values with np.nan. Currently replaces empty string, single decimal points with no numbers, and any single whitespace character with np.nan. Args: df (pandas.DataFrame): The DataFrame to clean. Returns: pandas.DataFrame: The cleaned DataFrame. """ return df.replace( to_replace=[ r"^\.$", # Nothing but a decimal point r"^\s*$", # The empty string and entirely whitespace strings ], value=np.nan, regex=True, )
[docs]def simplify_columns(df): """Simplify column labels for use as snake_case database fields. All columns will be re-labeled by: * Replacing all non-alphanumeric characters with spaces. * Forcing all letters to be lower case. * Compacting internal whitespace to a single " ". * Stripping leading and trailing whitespace. * Replacing all remaining whitespace with underscores. Args: df (pandas.DataFrame): The DataFrame to clean. Returns: pandas.DataFrame: The cleaned DataFrame. Todo: Update docstring. """ df.columns = ( df.columns.str.replace(r"[^0-9a-zA-Z]+", " ", regex=True) .str.strip() .str.lower() .str.replace(r"\s+", " ", regex=True) .str.replace(" ", "_") ) return df
[docs]def drop_tables(engine: sa.engine.Engine, clobber: bool = False): """Drops all tables from a SQLite database. Creates an sa.schema.MetaData object reflecting the structure of the database that the passed in ``engine`` refers to, and uses that schema to drop all existing tables. Todo: Treat DB connection as a context manager (with/as). Args: engine: An SQL Alchemy SQLite database Engine pointing at an exising SQLite database to be deleted. clobber: Whether or not to allow a non-empty DB to be removed. Raises: AssertionError: if clobber is False and there are any tables in the database. Returns: None """ md = sa.MetaData() md.reflect(engine) insp = sa.inspect(engine) if len(insp.get_table_names()) > 0 and not clobber: raise AssertionError( f"You are attempting to drop your database without setting clobber to {clobber}" ) md.drop_all(engine) conn = engine.connect() conn.exec_driver_sql("VACUUM") conn.close()
[docs]def merge_dicts(list_of_dicts): """Merge multipe dictionaries together. Given any number of dicts, shallow copy and merge into a new dict, precedence goes to key value pairs in latter dicts. Args: dict_args (list): a list of dictionaries. Returns: dict """ merge_dict = {} for dictionary in list_of_dicts: merge_dict.update(dictionary) return merge_dict
[docs]def convert_cols_dtypes( df: pd.DataFrame, data_source: str | None = None, name: str | None = None, ) -> pd.DataFrame: """Convert a PUDL dataframe's columns to the correct data type. Boolean type conversions created a special problem, because null values in boolean columns get converted to True (which is bonkers!)... we generally want to preserve the null values and definitely don't want them to be True, so we are keeping those columns as objects and preforming a simple mask for the boolean columns. The other exception in here is with the `utility_id_eia` column. It is often an object column of strings. All of the strings are numbers, so it should be possible to convert to :func:`pandas.Int32Dtype` directly, but it is requiring us to convert to int first. There will probably be other columns that have this problem... and hopefully pandas just enables this direct conversion. Args: df: dataframe with columns that appear in the PUDL tables. data_source: the name of the datasource (eia, ferc1, etc.) name: name of the table (for logging only!) Returns: Input dataframe, but with column types as specified by :py:const:`pudl.metadata.fields.FIELD_METADATA` """ # get me all of the columns for the table in the constants dtype dict dtypes = { col: dtype for col, dtype in get_pudl_dtypes(group=data_source).items() if col in df.columns } # grab only the boolean columns (we only need their names) bool_cols = [col for col in dtypes if dtypes[col] == "boolean"] # grab all of the non boolean columns non_bool_cols = {col: dtypes[col] for col in dtypes if col not in bool_cols} # Grab only the string columns... string_cols = [col for col in dtypes if dtypes[col] == "string"] for col in bool_cols: # Bc the og bool values were sometimes coming across as actual bools or # strings, for some reason we need to map both types (I'm not sure # why!). We use na_action to preserve the og NaN's. I've also added in # the string version of a null value bc I am sure it will exist. df[col] = df[col].map( { "False": False, "True": True, False: False, True: True, "nan": pd.NA, } ) if name: logger.debug(f"Converting the dtypes of: {name}") # unfortunately, the pd.Int32Dtype() doesn't allow a conversion from object # columns to this nullable int type column. `utility_id_eia` shows up as a # column of strings (!) of numbers so it is an object column, and therefor # needs to be converted beforehand. if "utility_id_eia" in df.columns: # we want to be able to use this dtype cleaning at many stages, and # sometimes this column has been converted to a float and therefor # we need to skip this conversion if df.utility_id_eia.dtypes is np.dtype("object"): df = df.astype({"utility_id_eia": "float"}) df = ( df.astype(non_bool_cols) .astype({col: "boolean" for col in bool_cols}) .replace(to_replace="nan", value={col: pd.NA for col in string_cols}) .replace(to_replace="<NA>", value={col: pd.NA for col in string_cols}) ) # Zip codes are highly correlated with datatype. If they datatype gets # converted at any point it may mess up the accuracy of the data. For # example: 08401.0 or 8401 are both incorrect versions of 08401 that a # simple datatype conversion cannot fix. For this reason, we use the # zero_pad_numeric_string function. if any("zip_code" for col in df.columns): zip_cols = [col for col in df.columns if "zip_code" in col] for col in zip_cols: if "4" in col: df.loc[:, col] = zero_pad_numeric_string(df[col], n_digits=4) else: df.loc[:, col] = zero_pad_numeric_string(df[col], n_digits=5) return df
[docs]def generate_rolling_avg(df, group_cols, data_col, window, **kwargs): """Generate a rolling average. For a given dataframe with a ``report_date`` column, generate a monthly rolling average and use this rolling average to impute missing values. Args: df (pandas.DataFrame): Original dataframe. Must have group_cols column, a data_col column and a ``report_date`` column. group_cols (iterable): a list of columns to groupby. data_col (str): the name of the data column. window (int): window from :func:`pandas.Series.rolling`. kwargs : Additional arguments to pass to :func:`pandas.Series.rolling`. Returns: pandas.DataFrame """ df = df.astype({"report_date": "datetime64[ns]"}) # create a full date range for this df date_range = pd.DataFrame( pd.date_range( start=min(df["report_date"]), end=max(df["report_date"]), freq="MS", name="report_date", ) ).assign( tmp=1 ) # assiging a temp column to merge on groups = ( df[group_cols + ["report_date"]] .drop_duplicates() .assign(tmp=1) # assiging a temp column to merge on ) # merge the date range and the groups together # to get the backbone/complete date range/groups bones = ( date_range.merge(groups) .drop("tmp", axis=1) # drop the temp column .merge(df, on=group_cols + ["report_date"]) .set_index(group_cols + ["report_date"]) .groupby(by=group_cols + ["report_date"]) .mean() ) # with the aggregated data, get a rolling average roll = bones.rolling(window=window, center=True, **kwargs).agg({data_col: "mean"}) # return the merged return bones.merge( roll, on=group_cols + ["report_date"], suffixes=("", "_rolling") ).reset_index()
[docs]def fillna_w_rolling_avg(df_og, group_cols, data_col, window=12, **kwargs): """Filling NaNs with a rolling average. Imputes null values from a dataframe on a rolling monthly average. To note, this was designed to work with the PudlTabl object's tables. Args: df_og (pandas.DataFrame): Original dataframe. Must have group_cols column, a data_col column and a 'report_date' column. group_cols (iterable): a list of columns to groupby. data_col (str): the name of the data column. window (int): window from pandas.Series.rolling kwargs : Additional arguments to pass to :class:`pandas.Series.rolling`. Returns: pandas.DataFrame: dataframe with nulls filled in. """ df_og = df_og.astype({"report_date": "datetime64[ns]"}) df_roll = generate_rolling_avg(df_og, group_cols, data_col, window, **kwargs) df_roll[data_col] = df_roll[data_col].fillna(df_roll[f"{data_col}_rolling"]) df_new = df_og.merge( df_roll, how="left", on=group_cols + ["report_date"], suffixes=("", "_rollfilled"), ) df_new[data_col] = df_new[data_col].fillna(df_new[f"{data_col}_rollfilled"]) return df_new.drop(columns=[f"{data_col}_rollfilled", f"{data_col}_rolling"])
[docs]def count_records(df, cols, new_count_col_name): """Count the number of unique records in group in a dataframe. Args: df (panda.DataFrame) : dataframe you would like to groupby and count. cols (iterable) : list of columns to group and count by. new_count_col_name (string) : the name that will be assigned to the column that will contain the count. Returns: pandas.DataFrame: dataframe containing only ``cols`` and ``new_count_col_name``. """ return ( df.assign(count_me=1) .groupby(cols, observed=True) .count_me.count() .reset_index() .rename(columns={"count_me": new_count_col_name}) )
[docs]def cleanstrings_snake(df, cols): """Clean the strings in a columns in a dataframe with snake case. Args: df (panda.DataFrame) : original dataframe. cols (list): list of columns in `df` to apply snake case to. """ for col in cols: df.loc[:, col] = ( df[col] .astype(str) .str.strip() .str.lower() .str.replace(r"\s+", "_", regex=True) ) return df
[docs]def zero_pad_numeric_string( col: pd.Series, n_digits: int, ) -> pd.Series: """Clean up fixed-width leading zero padded numeric (e.g. ZIP, FIPS) codes. Often values like ZIP and FIPS codes are stored as integers, or get converted to floating point numbers because there are NA values in the column. Sometimes other non-digit strings are included like Canadian postal codes mixed in with ZIP codes, or IMP (imported) instead of a FIPS county code. This function attempts to manage these irregularities and produce either fixed-width leading zero padded strings of digits having a specified length (n_digits) or NA. * Convert the Series to a nullable string. * Remove any decimal point and all digits following it. * Remove any non-digit characters. * Replace any empty strings with NA. * Replace any strings longer than n_digits with NA. * Pad remaining digit-only strings to n_digits length. * Replace (invalid) all-zero codes with NA. Args: col: The Series to clean. May be numeric, string, object, etc. n_digits: the desired length of the output strings. Returns: A Series of nullable strings, containing only all-numeric strings having length n_digits, padded with leading zeroes if necessary. """ out_col = ( col.astype("string") # Remove decimal points and any digits following them. # This turns floating point strings into integer strings .replace(r"[\.]+\d*", "", regex=True) # Remove any whitespace .replace(r"\s+", "", regex=True) # Replace anything that's not entirely digits with NA .replace(r"[^\d]+", pd.NA, regex=True) # Set any string longer than n_digits to NA .replace(f"[\\d]{{{n_digits+1},}}", pd.NA, regex=True) # Pad the numeric string with leading zeroes to n_digits length .str.zfill(n_digits) # All-zero ZIP & FIPS codes are invalid. # Also catches empty strings that were zero padded. .replace({n_digits * "0": pd.NA}) ) if not out_col.str.match(f"^[\\d]{{{n_digits}}}$").all(): raise ValueError( f"Failed to generate zero-padded numeric strings of length {n_digits}." ) return out_col
[docs]def iterate_multivalue_dict(**kwargs): """Make dicts from dict with main dict key and one value of main dict.""" single_valued = { k: v for k, v in kwargs.items() if not (isinstance(v, list) or isinstance(v, tuple)) } # Transform multi-valued {k: vlist} into {k1: [{k1: v1}, {k1: v2}, ...], k2: [...], ...} multi_valued = { k: [{k: v} for v in vlist] for k, vlist in kwargs.items() if (isinstance(vlist, list) or isinstance(vlist, tuple)) } for value_assignments in itertools.product(*multi_valued.values()): result = dict(single_valued) for k_v in value_assignments: result.update(k_v) yield result
[docs]def get_working_dates_by_datasource(datasource): """Get all working dates of a datasource as a DatetimeIndex.""" import pudl.metadata.classes dates = pd.DatetimeIndex([]) for data_source in pudl.metadata.classes.DataSource.from_field_namespace( datasource ): working_partitions = data_source.working_partitions if "years" in working_partitions: dates = dates.append( pd.to_datetime(working_partitions["years"], format="%Y") ) if "year_month" in working_partitions: dates = dates.append( pd.DatetimeIndex([pd.to_datetime(working_partitions["year_month"])]) ) return dates
[docs]def dedupe_on_category( dedup_df: pd.DataFrame, base_cols: list[str], category_name: str, sorter: list[str] ) -> pd.DataFrame: """Deduplicate a df using a sorted category to retain prefered values. Use a sorted category column to retain your prefered values when a dataframe is deduplicated. Args: dedup_df: the dataframe with the records to deduplicate. base_cols: list of columns which must not be duplicated. category_name: name of the categorical column to order values for deduplication. sorter: sorted list of categorical values found in the ``category_name`` column. Returns: The deduplicated dataframe. """ dedup_df[category_name] = dedup_df[category_name].astype( pd.CategoricalDtype(categories=sorter, ordered=True) ) return dedup_df.drop_duplicates(subset=base_cols, keep="first")
[docs]def calc_capacity_factor(df, freq, min_cap_fact=None, max_cap_fact=None): """Calculate capacity factor. Capacity factor is calcuated from the capcity, the net generation over a time period and the hours in that same time period. The dates from that dataframe are pulled out to determine the hours in each period based on the frequency. The number of hours is used in calculating the capacity factor. Then records with capacity factors outside the range specified by `min_cap_fact` and `max_cap_fact` are dropped. Args: df (pandas.DataFrame): table with components of capacity factor ( `report_date`, `net_generation_mwh` and `capacity_mw`) min_cap_fact (float): Lower bound, below which values are set to NaN. If None, don't use a lower bound. Default is None. max_cap_fact (float): Upper bound, below which values are set to NaN. If None, don't use an upper bound. Default is None. freq (str): String describing time frequency at which to aggregate the reported data, such as 'MS' (month start) or 'AS' (annual start). Returns: pandas.DataFrame: modified version of input `df` with one additional column (`capacity_factor`). """ # get a unique set of dates to generate the number of hours dates = df["report_date"].drop_duplicates() dates_to_hours = pd.DataFrame( data={ "report_date": dates, "hours": dates.apply( lambda d: ( pd.date_range(d, periods=2, freq=freq)[1] - pd.date_range(d, periods=2, freq=freq)[0] ) / pd.Timedelta(hours=1) ), } ) df = ( # merge in the hours for the calculation df.merge(dates_to_hours, on=["report_date"]) # actually calculate capacity factor wooo! .assign( capacity_factor=lambda x: x.net_generation_mwh / (x.capacity_mw * x.hours) ) # Replace unrealistic capacity factors with NaN .pipe(oob_to_nan, ["capacity_factor"], lb=min_cap_fact, ub=max_cap_fact).drop( ["hours"], axis=1 ) ) return df
[docs]def weighted_average(df, data_col, weight_col, by): """Generate a weighted average. Args: df (pandas.DataFrame): A DataFrame containing, at minimum, the columns specified in the other parameters data_col and weight_col. data_col (string): column name of data column to average weight_col (string): column name to weight on by (list): A list of the columns to group by when calcuating the weighted average value. Returns: pandas.DataFrame: a table with ``by`` columns as the index and the weighted ``data_col``. """ df["_data_times_weight"] = df[data_col] * df[weight_col] df["_weight_where_notnull"] = df.loc[df[data_col].notnull(), weight_col] g = df.groupby(by, observed=True) result = g["_data_times_weight"].sum(min_count=1) / g["_weight_where_notnull"].sum( min_count=1 ) del df["_data_times_weight"], df["_weight_where_notnull"] return result.to_frame(name=data_col) # .reset_index()
[docs]def sum_and_weighted_average_agg( df_in: pd.DataFrame, by: list, sum_cols: list, wtavg_dict: dict[str, str], ) -> pd.DataFrame: """Aggregate dataframe by summing and using weighted averages. Many times we want to aggreate a data table using the same groupby columns but with different aggregation methods. This function combines two of our most common aggregation methods (summing and applying a weighted average) into one function. Because pandas does not have a built-in weighted average method for groupby we use :func:``weighted_average``. Args: df_in (pandas.DataFrame): input table to aggregate. Must have columns in ``id_cols``, ``sum_cols`` and keys from ``wtavg_dict``. by (list): columns to group/aggregate based on. These columns will be passed as an argument into grouby as ``by`` arg. sum_cols (list): columns to sum. wtavg_dict (dictionary): dictionary of columns to average (keys) and columns to weight by (values). Returns: table with join of columns from ``by``, ``sum_cols`` and keys of ``wtavg_dict``. Primary key of table will be ``by``. """ logger.debug(f"grouping by {by}") # we are keeping the index here for easy merging of the weighted cols below df_out = df_in.groupby(by=by, as_index=True, observed=True)[sum_cols].sum( min_count=1 ) for data_col, weight_col in wtavg_dict.items(): df_out.loc[:, data_col] = weighted_average( df_in, data_col=data_col, weight_col=weight_col, by=by )[data_col] return df_out.reset_index()
[docs]def get_eia_ferc_acct_map(): """Get map of EIA technology_description/pm codes <> ferc accounts. Returns: pandas.DataFrame: table which maps the combination of EIA's technology description and prime mover code to FERC Uniform System of Accounts (USOA) accouting names. Read more about USOA `here <https://www.ferc.gov/enforcement-legal/enforcement/accounting-matters>`__ The output table has the following columns: `['technology_description', 'prime_mover_code', 'ferc_acct_name']` """ eia_ferc_acct_map = pd.read_csv( resources.open_text("pudl.package_data.glue", "ferc_acct_to_pm_tech_map.csv") ) return eia_ferc_acct_map
[docs]def dedupe_n_flatten_list_of_lists(mega_list): """Flatten a list of lists and remove duplicates.""" return list({item for sublist in mega_list for item in sublist})
[docs]def flatten_list(xs: Iterable) -> Generator: """Flatten an irregular (arbitrarily nested) list of lists (or sets). Inspiration from `here <https://stackoverflow.com/questions/2158395/flatten-an-irregular-arbitrarily-nested-list-of-lists>`__ """ for x in xs: if isinstance(x, Iterable) and not isinstance(x, (str, bytes)): yield from flatten_list(x) else: yield x
[docs]def convert_df_to_excel_file(df: pd.DataFrame, **kwargs) -> pd.ExcelFile: """Converts a pandas dataframe to a pandas ExcelFile object. You can pass parameters for pandas.to_excel() function. """ bio = BytesIO() writer = pd.ExcelWriter(bio, engine="xlsxwriter") df.to_excel(writer, **kwargs) writer.save() bio.seek(0) workbook = bio.read() return pd.ExcelFile(workbook)