722e3f4e77c812ebb31bb1533a4918f0cab8fee4
hiram
  Thu May 2 11:37:03 2019 -0700
adding tests to check for extraneous arguments refs #18869

diff --git src/hg/hubApi/tests/jsonConsumer.pl src/hg/hubApi/tests/jsonConsumer.pl
index 1911fa7..30da64a 100755
--- src/hg/hubApi/tests/jsonConsumer.pl
+++ src/hg/hubApi/tests/jsonConsumer.pl
@@ -1,451 +1,484 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use HTTP::Tiny;
 use Time::HiRes;
 use JSON;
 use Getopt::Long;
 
 my $http = HTTP::Tiny->new();
 # my $server = 'https://apibeta.soe.ucsc.edu';
+# my $server = 'http://localhost:1236/cgi-bin/hubApi';
 my $server = 'https://api-test.gi.ucsc.edu';
 # my $server="https://genome-euro.ucsc.edu/cgi-bin/loader/hubApi";
 # my $server = 'https://hgwdev-api.gi.ucsc.edu';
 # my $server = 'https://hgwbeta.soe.ucsc.edu/cgi-bin/hubApi';
+# my $server = 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi';
 my $globalHeaders = { 'Content-Type' => 'application/json' };
 my $lastRequestTime = Time::HiRes::time();
 my $processStartTime = Time::HiRes::time();
 my $requestCount = 0;
 
 ##############################################################################
 # command line options
 my $endpoint = "";
 my $hubUrl = "";
 my $genome = "";
 my $track = "";
 my $chrom = "";
 my $start = "";
 my $end = "";
 my $test0 = 0;
 my $debug = 0;
 my $trackLeavesOnly = 0;
 my $measureTiming = 0;
 my $jsonOutputArrays = 0;
 my $maxItemsOutput = "";
 ##############################################################################
 
 sub usage() {
 printf STDERR "usage: ./jsonConsumer.pl [arguments]\n";
 printf STDERR "arguments:
 -test0 - perform test of /list/publicHubs and /list/ucscGenomes endpoints
 -hubUrl=<URL> - use the URL to access the track or assembly hub
 -genome=<name> - name for UCSC database genome or assembly/track hub genome
 -track=<trackName> - specify a single track in a hub or database
 -chrom=<chromName> - restrict the operation to a single chromosome
 -start=<coordinate> - restrict the operation to a range, use both start and end
 -end=<coordinate> - restrict the operation to a range, use both start and end
 -maxItemsOutput=<N> - limit output to this number of items.  Default 1,000
                       maximum allowed 1,000,000
 -trackLeavesOnly - for list tracks function, no containers listed
 -measureTimeing - turn on timing measurement
 -debug - turn on debugging business
 -endpoint=<function> - where <function> is one of the following:
    /list/publicHubs - provide a listing of all available public hubs
    /list/ucscGenomes - provide a listing of all available UCSC genomes
    /list/hubGenomes - list genomes from a specified hub (with hubUrl=...)
    /list/tracks - list data tracks available in specified hub or database genome
    /list/chromosomes - list chromosomes from specified data track
    /getData/sequence - return sequence from specified hub or database genome
    /getData/track - return data from specified track in hub or database genome
 ";
 }
 
 #########################################################################
 # generic output of a hash pointer
 sub hashOutput($) {
   my ($hashRef) = @_;
   foreach my $key (sort keys %$hashRef) {
     my $value = $hashRef->{$key};
     $value = "<array>" if (ref($value) eq "ARRAY");
     $value = "<hash>" if (ref($value) eq "HASH");
      printf STDERR "%s - %s\n", $key, $hashRef->{$key};
   }
 }
 
 sub arrayOutput($) {
   my ($ary) = @_;
   my $i = 0;
   foreach my $element (@$ary) {
      printf STDERR "# %d\t%s\n", $i++, ref($element);
      if (ref($element) eq "HASH") {
        hashOutput($element);
      }
   }
 }
 #########################################################################
 
 ##############################################################################
 ###
 ### these functions were copied from Ensembl HTTP::Tiny example code:
 ###  https://github.com/Ensembl/ensembl-rest/wiki/Example-Perl-Client
 ###
 ##############################################################################
 
 ##############################################################################
 sub performJsonAction {
   my ($endpoint, $parameters) = @_;
   my $headers = $globalHeaders;
   my $content = performRestAction($endpoint, $parameters, $headers);
   return {} unless $content;
   my $json = decode_json($content);
   return $json;
 }
 
 ##############################################################################
 sub performRestAction {
   my ($endpoint, $parameters, $headers) = @_;
   $parameters ||= {};
   $headers ||= {};
   $headers->{'Content-Type'} = 'application/json' unless exists $headers->{'Content-Type'};
   if($requestCount == 15) { # check every 15
     my $currentTime = Time::HiRes::time();
     my $diff = $currentTime - $lastRequestTime;
     # if less than a second then sleep for the remainder of the second
     if($diff < 1) {
       Time::HiRes::sleep(1-$diff);
     }
     # reset
     $lastRequestTime = Time::HiRes::time();
     $requestCount = 0;
   }
 
   $endpoint =~ s#^/##;
   my $url = "$server/$endpoint";
 
   if(%{$parameters}) {
     my @params;
     foreach my $key (keys %{$parameters}) {
       my $value = $parameters->{$key};
       push(@params, "$key=$value");
     }
     my $param_string = join(';', @params);
     $url.= '?'.$param_string;
   }
   if ($debug) { $url .= ";debug=1"; }
   if ($measureTiming) { $url .= ";measureTiming=1"; }
   if ($jsonOutputArrays) { $url .= ";jsonOutputArrays=1"; }
   if (length($maxItemsOutput)) { $url .= ";maxItemsOutput=$maxItemsOutput"; }
   printf STDERR "### '%s'\n", $url;
   my $response = $http->get($url, {headers => $headers});
   my $status = $response->{status};
   if(!$response->{success}) {
     # Quickly check for rate limit exceeded & Retry-After (lowercase due to our client)
     if($status == 429 && exists $response->{headers}->{'retry-after'}) {
       my ($status, $reason) = ($response->{status}, $response->{reason});
       my $retry = $response->{headers}->{'retry-after'};
       printf STDERR "Failed for $endpoint! Status code: ${status}. Reason: ${reason}, retry-after: $retry seconds\n";
 #      hashOutput($response->{headers});
       Time::HiRes::sleep($retry);
       # After sleeping see that we re-request
       return performRestAction($endpoint, $parameters, $headers);
     }
     else {
       my ($status, $reason) = ($response->{status}, $response->{reason});
 #      die "Failed for $endpoint! Status code: ${status}. Reason: ${reason}\n";
       printf STDERR "Failed for $endpoint! Status code: ${status}. Reason: ${reason}\n";
 # hashOutput($response->{headers});
 # hashOutput($response->{content});
 # printf STDERR "'%s'\n", $response->{content};
 # printf STDERR "'%s'\n", $response->{headers};
       return return $response->{content};
     }
   }
   $requestCount++;
   if(length $response->{content}) {
     return $response->{content};
   }
   return;
 }
 
 #############################################################################
 sub columnNames($) {
   my ($nameArray) = @_;
   if (ref($nameArray) ne "ARRAY") {
     printf "ERROR: do not have an array reference in columnNames\n";
   } else {
     printf "### Column names in table return:\n";
     my $i = 0;
     foreach my $name (@$nameArray) {
       printf "%d\t\"%s\"\n", ++$i, $name;
     }
   }
 }
 
 sub topLevelKeys($) {
   my ($topHash) = @_;
   printf "### keys in top level hash:\n";
   foreach my $topKey ( sort keys %$topHash) {
     # do not print out the downloadTime and downloadTimeStamps since that
     # would make it difficult to have a consistent test output.
     next if ($topKey eq "downloadTime");
     next if ($topKey eq "downloadTimeStamp");
     next if ($topKey eq "botDelay");
     next if ($topKey eq "dataTime");
     next if ($topKey eq "dataTimeStamp");
     my $value = $topHash->{$topKey};
     $value = "<array>" if (ref($value) eq "ARRAY");
     $value = "<hash>" if (ref($value) eq "HASH");
     printf "\"%s\":\"%s\"\n", $topKey,$value;
   }
 }
 
 #############################################################################
 sub checkError($$$) {
   my ($json, $endpoint, $expect) = @_;
   my $jsonReturn = performJsonAction($endpoint, "");
 #   printf "%s", $json->pretty->encode( $jsonReturn );
   if (! defined($jsonReturn->{'error'}) ) {
      printf "ERROR: no error received from endpoint: '%s', received:\n", $endpoint;
      printf "%s", $json->pretty->encode( $jsonReturn );
   } else {
      if ($jsonReturn->{'error'} ne "$expect '$endpoint'") {
 	printf "incorrect error received from endpoint '%s':\n\t'%s'\n", $endpoint, $jsonReturn->{'error'};
      }
      printf "%s", $json->pretty->encode( $jsonReturn );
   }
 }
 
 #############################################################################
 sub verifyCommandProcessing()
 {
     my $json = JSON->new;
     # verify command processing can detected bad input
     my $endpoint = "/list/noSubCommand";
     my $expect = "do not recognize endpoint function:";
     checkError($json, $endpoint,$expect);
 }	#	sub verifyCommandProcessing()
 
 
 #############################################################################
 sub processEndPoint() {
   my $errReturn = 0;
   if (length($endpoint)) {
      my $json = JSON->new;
      my $jsonReturn = {};
      if ($endpoint eq "/list/hubGenomes") {
 	my %parameters;
 	# allow no hubUrl argument to test error reports
         if (length($hubUrl)) {
 	   $parameters{"hubUrl"} = "$hubUrl";
         }
         if (length($genome)) {
 	   $parameters{"genome"} = "$genome";
         }
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      } elsif ($endpoint eq "/list/tracks") {
 	# no need to verify arguments here, pass them along, or not,
 	# so that error returns can be verified
 	my %parameters;
+	if (length($chrom)) {
+	    $parameters{"chrom"} = "$chrom";
+	}
 	if ($trackLeavesOnly) {
 	    $parameters{"trackLeavesOnly"} = "1";
 	}
 	# allow no hubUrl argument to test error reports
         if (length($hubUrl)) {
 	  $parameters{"hubUrl"} = "$hubUrl";
 	}
 	# allow call to go through without a genome specified to test error
 	if (length($genome)) {
 	  $parameters{"genome"} = "$genome";
 	}
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      } elsif ($endpoint eq "/list/chromosomes") {
 	my %parameters;
+	if (length($chrom)) {
+	    $parameters{"chrom"} = "$chrom";
+	}
+	if ($trackLeavesOnly) {
+	    $parameters{"trackLeavesOnly"} = "1";
+	}
 	if (length($hubUrl)) {
 	    $parameters{"hubUrl"} = "$hubUrl";
 	}
 	# allow call to go through without a genome specified to test error
 	if (length($genome)) {
 	    $parameters{"genome"} = "$genome";
 	}
 	if (length($track)) {
 	    $parameters{"track"} = "$track";
 	}
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      } elsif ($endpoint eq "/getData/sequence") {
 	my %parameters;
+	if ($trackLeavesOnly) {
+	    $parameters{"trackLeavesOnly"} = "1";
+	}
 	if (length($hubUrl)) {
 	  $parameters{"hubUrl"} = "$hubUrl";
 	}
 	# allow call to go through without a genome specified to test error
 	if (length($genome)) {
 	  $parameters{"genome"} = "$genome";
 	}
 	if (length($chrom)) {
 	    $parameters{"chrom"} = "$chrom";
 	}
 	if (length($start)) {
 	    $parameters{"start"} = "$start";
 	    $parameters{"end"} = "$end";
 	}
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      } elsif ($endpoint eq "/getData/track") {
 	my %parameters;
 	if (length($hubUrl)) {
 	  $parameters{"hubUrl"} = "$hubUrl";
 	}
+	if ($trackLeavesOnly) {
+	    $parameters{"trackLeavesOnly"} = "1";
+	}
 	# allow call to go through without a genome specified to test error
 	if (length($genome)) {
 	    $parameters{"genome"} = "$genome";
 	}
 	if (length($track)) {
 	    $parameters{"track"} = "$track";
 	}
 	if (length($chrom)) {
 	    $parameters{"chrom"} = "$chrom";
 	}
 	if (length($start)) {
 	    $parameters{"start"} = "$start";
 	    $parameters{"end"} = "$end";
 	}
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      } else {
 #	printf STDERR "# endpoint not supported at this time: '%s'\n", $endpoint;
 #	Pass along the bogus request just to test the error handling.
 	my %parameters;
+	if (length($hubUrl)) {
+	  $parameters{"hubUrl"} = "$hubUrl";
+	}
+	if (length($genome)) {
+	    $parameters{"genome"} = "$genome";
+	}
+	if (length($track)) {
+	    $parameters{"track"} = "$track";
+	}
+	if (length($chrom)) {
+	    $parameters{"chrom"} = "$chrom";
+	}
+	if (length($start)) {
+	    $parameters{"start"} = "$start";
+	    $parameters{"end"} = "$end";
+	}
 	$jsonReturn = performJsonAction($endpoint, \%parameters);
 	$errReturn = 1 if (defined ($jsonReturn->{'error'}));
 	printf "%s", $json->pretty->encode( $jsonReturn );
      }
   } else {
     printf STDERR "ERROR: no endpoint given ?\n";
     exit 255;
   }
   return $errReturn;
 }	# sub processEndPoint()
 
 ###########################################################################
 ### test /list/publicHubs and /list/ucscGenomes
 sub test0() {
 
 my $json = JSON->new;
 my $jsonReturn = {};
 
 verifyCommandProcessing();	# check 'command' and 'subCommand'
 
 $jsonReturn = performJsonAction("/list/publicHubs", "");
 
 # this prints everything out indented nicely:
 # printf "%s", $json->pretty->encode( $jsonReturn );
 
 # exit 255;
 # __END__
 
 #	"dataTimeStamp" : 1552320994,
 #	"downloadTime" : "2019:03:26T21:40:10Z",
 #	"botDelay" : 2,
 #	"downloadTimeStamp" : 1553636410,
 #	"dataTime" : "2019-03-11T09:16:34"
 
 # look for the specific public hub named "Plants" to print out
 # for a verify test case
 #
 if (ref($jsonReturn) eq "HASH") {
   topLevelKeys($jsonReturn);
 
   if (defined($jsonReturn->{"publicHubs"})) {
      my $arrayData = $jsonReturn->{"publicHubs"};
      foreach my $data (@$arrayData) {
 	if ($data->{'shortLabel'} eq "Plants") {
         printf "### Plants public hub data\n";
 	  foreach my $key (sort keys %$data) {
 	  next if ($key eq "registrationTime");
 	  printf "'%s'\t'%s'\n", $key, $data->{$key};
 	  }
 	}
      }
   }
 } elsif (ref($jsonReturn) eq "ARRAY") {
   printf "ERROR: top level returns ARRAY of size: %d\n", scalar(@$jsonReturn);
   printf "should have been a HASH to the publicHub data\n";
 }
 
 $jsonReturn = performJsonAction("/list/ucscGenomes", "");
 # printf "%s", $json->pretty->encode( $jsonReturn );
 
 
 if (ref($jsonReturn) eq "HASH") {
   topLevelKeys($jsonReturn);
   if (defined($jsonReturn->{"ucscGenomes"})) {
      my $ucscGenomes = $jsonReturn->{"ucscGenomes"};
      if (exists($ucscGenomes->{'hg38'})) {
 	my $hg38 = $ucscGenomes->{'hg38'};
         printf "### hg38/Human information\n";
      foreach my $key (sort keys %$hg38) {
 	   printf "\"%s\"\t\"%s\"\n", $key, $hg38->{$key};
          }
        }
      }
 } elsif (ref($jsonReturn) eq "ARRAY") {
   printf "ERROR: top level returns ARRAY of size: %d\n", scalar(@$jsonReturn);
   printf "should have been a HASH to the ucscGenomes\n";
 }
 
 }	#	sub test0()
 
 sub elapsedTime() {
 if ($measureTiming) {
   my $endTime = Time::HiRes::time();
   my $et = $endTime - $processStartTime;
   printf STDERR "# procesing time: %.3fs\n", $et;
 }
 }
 
 #############################################################################
 ### main()
 #############################################################################
 
 my $argc = scalar(@ARGV);
 
 GetOptions ("hubUrl=s" => \$hubUrl,
     "endpoint=s"  => \$endpoint,
     "genome=s"  => \$genome,
     "track=s"  => \$track,
     "chrom=s"  => \$chrom,
     "start=s"  => \$start,
     "end=s"    => \$end,
     "test0"    => \$test0,
     "debug"    => \$debug,
     "trackLeavesOnly"    => \$trackLeavesOnly,
     "measureTiming"    => \$measureTiming,
     "jsonOutputArrays"    => \$jsonOutputArrays,
     "maxItemsOutput=s"   => \$maxItemsOutput)
     or die "Error in command line arguments\n";
 
 if ($test0) {
    test0;
    elapsedTime();
    exit 0;
 }
 
 if ($argc > 0) {
    if (processEndPoint()) {
 	elapsedTime();
 	exit 255;
    } else {
 	elapsedTime();
 	exit 0;
    }
 }
 
 usage();