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Crisp CSV

This repository helps to build an ETL (Extract-Transform-Load) utility that works with CSV files. The utility applies a range of checks to the input data, merges the files and creates a sanitized, denormalized upload that could be imported into a non-SQL database as a part of an ETL process. The data validation checks are meant to ensure the integrity of the data and avoid ingestion errors triggered by the database engine.

The utility can also be used to read specific CSV fields from the input data and reorder the fields.

Off-the-shelf the utility works with data from the Google COVID-19 Open Data repository. However it has been designed from the outset to be easily customisable and uses templates to simplify the task of reconfiguring the program to work with selected pieces (e.g. fields) of CSV data in other projects. The details are provided under the Customisation heading.

The utility is written in C++ to achieve the high performance required to process large amount of data. This is especially beneficial if your ETL process needs to be recurring and bound to a certain time schedule. The specific performance metrics can be found below.

The utility can be built under Linux or on Windows with WSL. If you have GCC 8 or later installed, then after cloning the repository execute either test.sh/test.cmd to build and test the program or build.sh/build.cmd to perform the production build - it's that simple.

Deployment and usage are straightforward as well. All the work is done by one Linux program that consists of a single executable with an optional configuration file.

Table of Contents

Functionality

Out of the box the utility works with two Google repository files: epidemiology.csv and index.csv. The former contains daily records (e.g. data rows) of COVID-19 case counts applicable to a certain geographical or administrative region denoted by the record's index field. The latter provides a description for the area behind each index.

The CSV field called index will be referred to as geoindex.

The utility performs a set of checks to validate each row, identifies the rows that need to be rejected as invalid, filters the data (by skipping certain rows) and creates an output file by merging the selected CSV fields taken from both files. The output file contains the following columns:

date, geoindex, country, state/province, locality, confirmed cases, recovered cases, deaths, aggregation level

Before exiting the utility prints out a summary with the counts of rejected and filtered rows. Pressing Ctrl+C terminates execution, the utility displays a warning about incomplete output files and exits with non-zero exit code.

The output file (produced by a containerised instance of the utility deployed in the cloud) is imported into a database that powers virusquery.com.

Data Validation

The following checks are performed on each row of data:

  1. Epidemiology.csv

    • Check the date against a regular expression to ensure the date is in the format that can be ingested during import.
    • Check the geoindex against a regular expression to ensure the literal is formed correctly e.g. contains a country code, certain number of correctly positioned underscore characters reflecting its geographical/administrative hierarchy etc.
    • Ensure the geoindex can be found in the index.csv file.

  2. Index.csv

    • Check the geoindex against a regular expression to ensure it is formed correctly.
    • Check the value contained in the aggregation_level field is valid.
    • Verify the geographical/administrative hierarchy of the geoindex is consistent with the value contained in the aggregation_level field.
    • Perform a range of checks to ensure the record is structurally sound. It includes checking the record has country_name data followed by checking it has state/province (e.g. subregion1_name) data if it must be present for this particular geoindex or doesn’t have it in case this data must be missing for a country-wide geoindex. Similar present-or-missing checks for the locality data, e.g. both subregion2_name and locality_name fields which must be either present or missing depending on the aggregation_level value.
    • Check that each xxx_name field mentioned above has length no less than the minimal length applicable to this particular field.
    • Starting with the version 1.1.3 of the utility, examine quoted fields to ensure the quoting is done properly and the quote characters inside fields (if any) are correctly escaped.

If any check fails the row is rejected. The utility creates two error files (next to the output file) used to store the rejected epidemiology and index rows.

Data Filtration

The utility can be built to work with records related to the two levels of geographical (or administrative) hierarchy only: country-wide level (L0) and state/province level (L1). This build configuration filters out records pertaining to the COVID-19 case counts that apply to the localities at the levels L2 and L3. Another build configuration works with all levels - see the Configuration section.

The following data rows are filtered:

  1. Epidemiology.csv

    • Records below the state/province level - depending on the build configuration.
    • Records with all the three cumulative epidemiology metrics missing.
    • Records for today's Australian data if the cumulative confirmed case count is present with the other two cumulative metrics missing.
    • Records pertaining to UK NUTS regions.

  2. Index.csv

    • Records below the state/province level - depending on the build configuration.

The counts of the filtered rows are included into the summary printed out when the utility finishes, however the rows are not saved.

Performance

On Google Cloud Platform's f1-micro VM the utility running inside a Docker container processes ~2 mil epidemiology rows with 18000 index rows in 15 seconds producing 140 MB output file and generating the following summary upon exit:

crisp-csv - version 1.1.2
crisp-csv - processed 2164142 data rows
crisp-csv - rejected 266 data rows due to index processing failure
crisp-csv - rejected 1 data row
crisp-csv - filtered 2073 data rows
crisp-csv - rejected 5 index rows
crisp-csv - execution time: 15 seconds

The first row in both input files contains column names and is rejected as invalid data. It explains the rejection of 1 data row and 1 index row. The remaining 4 rejected index rows are not included into the validated geoindex which causes 266 data rows (with the rejected geoindices) to be rejected as well.

Building the configuration that filters out records below the state/province level cuts the execution time approximately in half.

Build

The utility is built and runs under Linux. It can be built on Windows with WSL in which case install Debian or Ubuntu 20.04 LTS from Microsoft Store, alternatively perform a manual installation.

Prerequisites

On Debian 10 or Ubunty 20.04 the only build prerequisite is the build-essential package.

  • To install the package on Debian/Ubunty run the following command:
    sudo apt update && apt install build-essential

    If you have an earlier version of Linux distribution with older GCC installed then it might not support C++17 features. In this case you will need to install GCC 8 by following the install steps in the .travis.yml file. The steps ensure that Travis CI VM, which comes with Ubuntu 18.04 and GCC 7, gets upgraded to GCC 8.

  • To install the package on WSL follow the steps described in this link.

If you intend to use VS Code, install the Remote - WSL extension.

Build Steps

  • On Linux execute: ./build.sh
  • On Windows execute: build.cmd
  • If you prefer to build using VS Code execute: ide.cmd.
    Once VS Code starts, press Ctrl+Shift+B to execute the Default Build Task or simply type make in the Terminal window.

After the build process finishes, the crisp-csv executable can be found in the ./build/ subdirectory. It is named after the top-level project directory so in order to rename the program you can change the directory name. Then run make clean && make to rebuild. Alternatively edit the .cmd files replacing crisp-csv with the new name and execute clean.cmd followed by build.cmd.

Testing

  • On Linux execute: ./test.sh
  • On Windows execute: test.cmd

This will build the test configuration and overwrite the executable located in the build/ subdirectory. Executing build.cmd builds the production configuration overwriting the same executable.

Switching from one configuration to another triggers a full rebuild that takes more time than an incremental build typically facilitated by make during development.

The repository is integrated with travis-ci.com for Continuous Integration so that every push causes Travis CI to start a VM, clone the repository, perform a build and run the tests. The build/test outcome is shown by the CI icon at the top (next to the last commit hash). To access the build/test log, click on the icon.

Usage

Data Location

At run-time the production build of the utility requires a readable and writeable subdirectory csv/ to exist in the directory that contains the executable. It will look for the epidemiology.csv and index.csv files in the subdirectory. To satisfy this requirement for the cloned repository download the epidemiology.csv and index.csv files into the crisp-csv/build/csv/ directory.

Running the Utility

  • On Linux execute: ./run.sh
  • On Windows execute: run.cmd
    The utility will run in WSL.
  • If using VS Code (started by ide.cmd), type build/crisp-csv in the Terminal window.

The output file and the two error files with rejected epidemiology and index records will be created in the csv/ subdirectory. Already existing files will be overwritten.

Configuration

The functionality provided by the utility can be customised during builds and at run-time.

  1. Build time configuration
    Out of the box the utility processes all levels of the geographical (or administrative) hierarchy. It can be restricted to the first two (country and state/province) levels by editing the makefile and changing the CFLAGS variable from -DSKIP_LOCALITIES=0 to -DSKIP_LOCALITIES=1. This requires a full rebuild so execute clean.cmd or its Linux equivalent after changing the makefile.

  2. Run-time configuration
    At run-time the utility looks for a configuration file <executable-file-name>.cfg e.g. crisp-csv.cfg located in the same directory. The file contains a JSON object with the following keys:

    {
 "processedDataRows": 1500000,
 "rejectedDataRows": 200,
 "rejectedIndexRows": 20,
 "relaxIndexChecks": false,
 "filterUkNuts": true,
 "filterAuData": true
}

    The first three keys represent the thresholds that affect the utility exit code. If the respective row counts are less than the first threshold or greater than the other two thresholds, the utility returns a non-zero exit code indicating a failure. This can be used to terminate an ETL pipeline, disable data copying from staging environment to production, etc.

    The last two keys affect filtering described in the Data Filtration section. The relaxIndexChecks setting, if set to true, drops several geoindex checks and makes the utility accept UA_KBP as a valid geoindex, see this issue for more details.

    If the configuration file cannot be found, the utility falls back to the defaults specified inRuntimeConfig.h In case the configuration file is found but cannot be parsed the utility terminates.

Customisation

Customising the utility to work with CSV data structured differently requires familiarity with the existing design.

Existing Design

The class CsvFile acts as CSV processing engine and reads the input file with epidemiology data line by line. The class is configured to read only certain CSV fields from the input file and combined together, those selected fields form a CSV record that needs to be processed further. The class constructor gets an array of CSV field indices from a Factory that creates an instance of the class. Each index denotes a CSV field from the input file.

CsvFile is data-agnostic e.g. it has no knowledge of what data is contained in which CSV field. Therefore it is unable to perform data processing on its own and needs to delegate the work to handlers which are the classes derived from CsvScanner or CsvProcessor. Both handlers are created by a Factory.

The handler derived from CsvScanner is called by CsvFile to scan each CSV record and decide if the record should be rejected as invalid or filtered as not needed or accepted. If the record is accepted then CsvFile passes the selected fields of the CSV record to CsvProcessor for additional processing. The array of indices passed to CsvFile constructor actually contains tuples so it's an array of tuples. Each tuple consists of a CSV field index and a boolean flag. If set to true, the flag tells CsvFile to call CsvProcessor and pass the field's content to it for processing.

The handler derived from CsvProcessor reads the secondary data file (which is the index.csv file in the implementation related to Google COVID-19 Open Data repository), sanitizes the geoindex by rejecting or filtering or accepting index rows and then responds to calls from CsvFile by merging geoindex related information into the CSV record.

Making Changes

Create your custom CSV record scanner and field processor. Extend the Factory to produce both and inject smart pointers holding their instances into the CsvFile along with a modified array of CSV field indices. Decide which CSV field(s) require further processing and alter the tuples accordingly. Add or replace members of the CsvFieldCounts structure to adjust the lengths of the CSV records and modify the RuntimeConfig class as necessary.

Adding new .h or .cpp files and renaming the existing source files doesn't require changing the makefile. It requires changes if you add a subdirectory to the src/ directory in which case the changes should reflect the actions applied in the makefile to the existing subdirectories, namely config/, handlers/ and test/.

Credits

The source code includes the json.hpp file taken from the JSON for Modern C++ repository to implement parsing of the JSON configuration file.

Tests include the file catch.hpp taken from the Catch2 test framework repository.

The makefile utilises several recipes mentioned in the comments.

License

The software is licensed under the MIT License.