Add a date option. Comment code

extractCases.pl

@@ -6,17 +6,38 @@
 use Getopt::Long;
 use List::Util qw{sum0 none};
 
+# Not sure if the site address or the name prefix will work allways. Check.
+#Downloads address
 my $site= "https://www.ecdc.europa.eu/sites/default/files/documents/";
-my $sheetname;
-my $ids;
-my $ws;
-GetOptions("sheet=s"=>\$sheetname, "ids=s"=>\$ids, "ws=i"=>\$ws) or usage('Bad options');
-usage("missing --sheet") unless defined $sheetname;
+#File name. Notice orthograpic mistake. Might have to change.
+my $nameprefix0="COVID-19-geographic-disbtribution-worldwide-";
+my $nameprefix1="COVID-19-geographic-distribution-worldwide-";
+my $sheetname; #user supplied and actual sheetname
+my $date; #user supplied date
+my $ids; #user supplied comma separated country codes
+my $ws; #user supplied averaging window size
+my $help; #help flag
+GetOptions("sheet=s"=>\$sheetname, "date=s"=>\$date, "ids=s"=>\$ids,
+	   "ws=i"=>\$ws, "help|?"=>\$help) or usage('Bad options');
+# check options
+usage() if $help;
+usage("missing --sheet or --date") unless defined $sheetname or
+    defined $date;
+usage("Only one of --sheet or --date allowed") if defined $sheetname
+    and defined $date;
 usage("missing --ws") unless defined $ws;
 usage("ws should be positive") unless $ws>0;
-$ids=lc $ids;
-my @ids=split /\s*,\s*/, $ids;
-system "wget $site$sheetname" unless -r $sheetname;
+usage("missing country ids") unless defined $ids;
+$ids=lc $ids; #normalize to lower case
+my @ids=split /\s*,\s*/, $ids; #get list of comma separated codes.
+# possible sheet names (accounting for orthographic mistake above)
+my ($sheetname0, $sheetname1)=map {"$_$date.xlsx"} ($nameprefix0,$nameprefix1) if defined $date;
+# test each possible sheetname
+foreach($sheetname, $sheetname0, $sheetname1){
+    next unless defined;
+    $sheetname=$_,last if -r $_; #already downloaded
+    $sheetname=$_,last if system("wget", "$site$_")==0; #download it
+}
 my $book=Spreadsheet::Read->new($sheetname) or die "Couldn't open spreadsheet";
 my $sheet=$book->sheet(1);
 my $maxcol=$sheet->maxcol;
@@ -25,31 +46,34 @@
 #dateRep, day, month, year, cases, deaths, countriesAndTerritories,
 #geoId, countryterritoryCode, popData2018
 my %cols;
-map {$cols{lc $colnames[$_]}=$_} (0..$maxcol-1);
+map {$cols{lc $colnames[$_]}=$_} (0..$maxcol-1); #array of column names
 #say "maxcol $maxcol maxrow $maxrow";
 my %data;
 for my $r(2..$maxrow){
     my @row=$sheet->row($r);
     my $geoid=lc $row[$cols{geoid}];
-    next if none {$_ eq $geoid} @ids;
-    #next unless $row[$cols{cases}];
+    next if none {$_ eq $geoid} @ids; #skip other countries
+    # one data array for each country
+    # each entry is an array of values: day month year cases deaths
     push @{$data{$geoid}}, [map {$row[$cols{$_}]} qw(day month year cases deaths)];
 }
 
-for my $id(@ids){
+for my $id(@ids){ #for each country
+    #writed one file per country
     open (OUT, "> $id.txt") or die "Couldn't open $id.txt";
-    my @data=@{$data{$id}};
-    @data=reverse @data;
+    my @data=@{$data{$id}}; #country data
+    @data=reverse @data; #put in temporal order
     my $totalcases=0;
-    my @recent; #keep a few for a moving window average
+    my @recent; #keep a fifo for the moving window average
     foreach(@data){
-	my ($day, $month, $year, $cases, $deaths)=@$_;
-	$totalcases+=$cases;
-	push @recent, [($cases, $deaths)];
-	next if scalar @recent <=$ws;
-	shift @recent;
-	my @avg=map {my $i=$_; sum0(map {$_->[$i]} @recent)/@recent} (0,1);
-	say OUT join " ", $totalcases, @avg;
+	my ($day, $month, $year, $cases, $deaths)=@$_; #fetch data
+	$totalcases+=$cases; #accumulate
+	push @recent, [($cases, $deaths)]; #push into fifo
+	next if scalar @recent <=$ws; #wait for fifo to grow
+	shift @recent; #throw oldest
+	#average new cases and deaths
+	my @avg=map {my $i=$_; sum0(map {$_->[$i]} @recent)/@recent}(0,1);
+	say OUT join " ", $totalcases, @avg; #write to output file.
     }
 }
 
@@ -58,7 +82,26 @@
 sub usage{
     say @_;
     say <<FIN;
-    GetOptions("sheet=s"=>\$sheetname, "ids=s"=>\$ids, "ws=>i"=>\$ws)
+Usage:
+
+    ./extractCases.pl --date 2020-02-25 --ids=cn,de,es,it,jp,kr,mx,ru,us --ws=5
+    ./extractCases.pl \
+       --sheet COVID-19-geographic-disbtribution-worldwide-2020-02-25.xlsx \
+       --ids=cn,de,es,it,jp,kr,mx,ru,us --ws=5
+
+    Extracts information about the COVID-19 pandemic
+
+    Downloads (if necessary) a data sheet from the European CDC and
+    extracts info for the desired countries and writes them into
+    country-named files such as cn.txt, es.txt, etc. in three columns:
+    total number of cases, averaged number of daily cases and averaged
+    number of deceases.
+
+    Options:
+        --sheet  Filename of sheet to download
+        --date   iso formatted date of the sheet to download
+        --ids    Comma separated iso 2-letter country-codes of desired countries
+        --ws     Size of the moving average window. 1 means don't average.
 FIN
     exit 1;
 }