NAME Statistics::Covid - Fetch, store in DB, retrieve and analyse Covid-19 statistics from data providers VERSION Version 0.23 DESCRIPTION This module fetches, stores in a database, retrieves from a database and analyses Covid-19 statistics from online or offline data providers, such as from the John Hopkins University which I hope I am not obstructing (please send an email to the author if that is the case). After specifying one or more data providers (as a url and a header for data and optionally for metadata), this module will attempt to fetch the latest data and store it in a database (SQLite and MySQL, only SQLite was tested so far). Each batch of data should ideally contain information about one or more locations and at a given point in time. All items in this batch are extracted and stored in DB each with its location name and time (it was published, not fetched) as primary keys. Each such data item (Datum) is described in Statistics::Covid::Datum::Table and the relevant class is Statistics::Covid::Datum. It contains fields such as: population, confirmed, unconfirmed, terminal, recovered. Focus was on creating very high-level which distances as much as possible the user from the nitty-gritty details of fetching data using LWP::UserAgent and dealing with the database using DBI and DBIx::Class. This is an early release until the functionality and the table schemata solidify. SYNOPSIS use Statistics::Covid; use Statistics::Covid::Datum; $covid = Statistics::Covid->new({ 'config-file' => 't/example-config.json', 'providers' => ['UK::BBC', 'UK::GOVUK', 'World::JHU'], 'save-to-file' => 1, 'save-to-db' => 1, 'debug' => 2, }) or die "Statistics::Covid->new() failed"; # fetch all the data available (posibly json), process it, # create Datum objects, store it in DB and return an array # of the Datum objects just fetched (and not what is already in DB). my $newobjs = $covid->fetch_and_store(); print $_->toString() for (@$newobjs); print "Confirmed cases for ".$_->name() ." on ".$_->date() ." are: ".$_->confirmed() ."\n" for (@$newobjs); my $someObjs = $covid->select_datums_from_db({ 'conditions' => { belongsto=>'UK', name=>'Hackney' } }); print "Confirmed cases for ".$_->name() ." on ".$_->date() ." are: ".$_->confirmed() ."\n" for (@$someObjs); # or for a single place (this sub sorts results wrt publication time) my $timelineObjs = $covid->select_datums_from_db_for_specific_location_time_ascending('Hackney'); # or for a wildcard match # $covid->select_datums_from_db_for_specific_location_time_ascending({'like'=>'Hack%'}); # and maybe specifying max rows # $covid->select_datums_from_db_for_specific_location_time_ascending({'like'=>'Hack%'}, {'rows'=>10}); for my $anobj (@$timelineObjs){ print $anobj->toString()."\n"; } print "datum rows in DB: ".$covid->db_count_datums()."\n" use Statistics::Covid::Analysis::Plot; # plot something my $objs = $io->db_select({ conditions => {belongsto=>'UK', name=>{'like' => 'Ha%'}} }); my $outfile = 'chartclicker.png'; my $ret = Statistics::Covid::Analysis::Plot::plot_with_chartclicker({ 'datum-objs' => $objs, # saves to this file: 'outfile' => $outfile, # plot this column (x-axis is time always) 'Y' => 'confirmed', # and make several plots, each group must have 'name' common 'GroupBy' => ['name'] }); EXAMPLE SCRIPT script/statistics-covid-fetch-data-and-store.pl is a script which accompanies this distribution. It can be used to fetch any data from specified providers using a specified configuration file. For a quick start: cp t/example-config.json config.json # optionally modify config.json to change the destination data dirs # now fetch data from some default data providers: script/statistics-covid-fetch-data-and-store.pl --config-file config.json The above will fetch the latest data and insert it into an SQLite database in data/db/covid19.sqlite directory. When this script is called again, it will fetch the data again and will be saved into a file timestamped with publication date. So, if data was already fetched it will be simply overwritten by this same data. As far as updating the database is concerned, only newer, up-to-date data will be inserted. So, calling this script, say once or twice will make sure you have the latest data without accummulating it redundantly. But please call this script AT MAXIMUM one or two times per day so as not to obstruct public resources. Please, Please. When the database is up-to-date, analysis of data is the next step. In the synopis, it is shown how to select records from the database, as an array of Statistics::Covid::Datum objects. Feel free to share any modules you create on analysing this data, either under this namespace (for example Statistics::Covid::Analysis::XYZ) or any other you see appropriate. CONFIGURATION FILE Below is an example configuration file which is essentially JSON with comments. It can be found in t/example-config.json relative to the root directory of this distribution. # comments are allowed, otherwise it is json # this file does not get eval'ed, it is parsed # only double quotes! and no excess commas { # fileparams options "fileparams" : { # dir to store datafiles, each DataProvider class # then has its own path to append "datafiles-dir" : "datazz/files" }, # database IO options "dbparams" : { # which DB to use: SQLite, MySQL (case sensitive) "dbtype" : "SQLite", # the name of DB # in the case of SQLite, this is a filepath # all non-existing dirs will be created (by module, not by DBI) "dbdir" : "datazz/db", "dbname" : "covid19.sqlite", # how to handle duplicates in DB? (duplicate=have same PrimaryKey) # only-better : replace records in DB if outdated (meaning number of markers is less, e.g. terminal or confirmed) # replace : force replace irrespective of markers # ignore : if there is a duplicate in DB DONT REPLACE/DONT INSERT # (see also Statistics::Covid::Datum for up-to-date info) "replace-existing-db-record" : "only-better", # username and password if needed # unfortunately this is in plain text # BE WARNED: do not store your main DB password here!!!! # perhaps create a new user or use SQLite # there is no need for these when using SQLite "hostname" : "", # must be a string (MySQL-related) "port" : "", # must be a string (MySQL-related) "username" : "", # must be a string "password" : "", # must be a string # options to pass to DBI::connect # see https://metacpan.org/pod/DBI for all options "dbi-connect-params" : { "RaiseError" : 1, # die on error "PrintError" : 0 # do not print errors or warnings } } } DATABASE SUPPORT SQLite and MySQL database types are supported through the abstraction offered by DBI and DBIx::Class. However, only the SQLite support has been tested. Support for MySQL is totally untested. AUTHOR Andreas Hadjiprocopis, , BENCHMARKS There are some benchmark tests to time database insertion and retrieval performance. These are optional and will not be run unless explicitly stated via make bench These tests do not hit the online data providers at all. And they should not, see ADDITIONAL TESTING for more information on this. They only time the creation of objects and insertion to the database. ADDITIONAL TESTING Testing the DataProviders is not done because it requires network access and hits on the providers which is not fair. However, there are targets in the Makefile for initiating the "network" tests by doing make network . CAVEATS This module has been put together very quickly and under pressure. There are must exist quite a few bugs. In addition, the database schema, the class functionality and attributes are bound to change. A migration database script may accompany new versions in order to use the data previously collected and stored. Support for MySQL is totally untested. Please use SQLite for now or test the MySQL interface. Support for Postgres has been somehow missed but is underway!. BUGS This module has been put together very quickly and under pressure. There are must exist quite a few bugs. Please report any bugs or feature requests to bug-statistics-Covid at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Statistics-Covid. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. SUPPORT You can find documentation for this module with the perldoc command. perldoc Statistics::Covid You can also look for information at: * github repository which will host data and alpha releases * RT: CPAN's request tracker (report bugs here) http://rt.cpan.org/NoAuth/Bugs.html?Dist=Statistics-Covid * AnnoCPAN: Annotated CPAN documentation http://annocpan.org/dist/Statistics-Covid * CPAN Ratings http://cpanratings.perl.org/d/Statistics-Covid * Search CPAN http://search.cpan.org/dist/Statistics-Covid/ * Information about the basis module DBIx::Class http://search.cpan.org/dist/DBIx-Class/ DEDICATIONS Almaz ACKNOWLEDGEMENTS Perlmonks for supporting the world with answers and programming enlightment DBIx::Class the data providers: John Hopkins University , UK government , https://www.bbc.co.uk (for disseminating official results) LICENSE AND COPYRIGHT Copyright 2020 Andreas Hadjiprocopis. 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