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
<
https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6>
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, <bliako at cpan.org>, <andreashad2 at gmail.com>
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
<
https://github.com/hadjiprocopis/statistics-covid> 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 <
https://www.perlmonks.org> for supporting the world with
answers and programming enlightment
DBIx::Class
the data providers:
John Hopkins University
<
https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6>,
UK government
<
https://www.gov.uk/government/publications/covid-19-track-coronavirus-cases>,
https://www.bbc.co.uk (for disseminating official results)
LICENSE AND COPYRIGHT
Copyright 2020 Andreas Hadjiprocopis.
This program is free software; you can redistribute it and/or modify it
under the terms of the the Artistic License (2.0). You may obtain a
copy of the full license at:
http://www.perlfoundation.org/artistic_license_2_0
Any use, modification, and distribution of the Standard or Modified
Versions is governed by this Artistic License. By using, modifying or
distributing the Package, you accept this license. Do not use, modify,
or distribute the Package, if you do not accept this license.
If your Modified Version has been derived from a Modified Version made
by someone other than you, you are nevertheless required to ensure that
your Modified Version complies with the requirements of this license.
This license does not grant you the right to use any trademark, service
mark, tradename, or logo of the Copyright Holder.
This license includes the non-exclusive, worldwide, free-of-charge
patent license to make, have made, use, offer to sell, sell, import and
otherwise transfer the Package with respect to any patent claims
licensable by the Copyright Holder that are necessarily infringed by
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