From 5eca8a04e75e74553afb792eb8bc2199fd7ff4ca Mon Sep 17 00:00:00 2001
From: "Francisco J. Ossandon" <fco.j.ossandon@gmail.com>
Date: Wed, 30 Apr 2014 18:58:35 -0400
Subject: [PATCH] RemoteBlast_rpsblast.t: Fixed a few number of skipped tests,
 and cleaned format and indentation

---
 t/Tools/Run/RemoteBlast_rpsblast.t | 120 +++++++++++++++++++------------------
 1 file changed, 61 insertions(+), 59 deletions(-)

diff --git a/t/Tools/Run/RemoteBlast_rpsblast.t b/t/Tools/Run/RemoteBlast_rpsblast.t
index 3676abec9..f4f66832a 100644
--- a/t/Tools/Run/RemoteBlast_rpsblast.t
+++ b/t/Tools/Run/RemoteBlast_rpsblast.t
@@ -1,5 +1,5 @@
 # -*-Perl-*- Test Harness script for Bioperl
-# 	$Id$	
+# $Id$
 
 # malcolm_cook@stowers.org: this test is in a separate file from
 # RemoteBlast.t (on which it is modelled) since there is some sort of
@@ -14,8 +14,10 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 7,
-               -requires_modules => [qw(IO::String LWP LWP::UserAgent)],
+    test_begin(-tests               => 7,
+               -requires_modules    => [qw(IO::String
+                                           LWP
+                                           LWP::UserAgent)],
                -requires_networking => 1);
 
     use_ok('Bio::Tools::Run::RemoteBlast');
@@ -23,81 +25,81 @@ BEGIN {
 
 my $v = test_debug();
 my $inputfilename = test_input_file('ecolitst.fa');
-ok( -e $inputfilename);	
-
-my $remote_rpsblast = Bio::Tools::Run::RemoteBlast->new
-  ('-verbose'    => test_debug(),
-   '-prog'       => 'blastp',
-   '-data'       => 'cdsearch/cdd',
-   '-readmethod' => 'blasttable',
-   '-expect'     => '1e-10',
-  );
+ok( -e $inputfilename);
 
+my $remote_rpsblast
+    = Bio::Tools::Run::RemoteBlast->new(-verbose    => test_debug(),
+                                        -prog       => 'blastp',
+                                        -data       => 'cdsearch/cdd',
+                                        -readmethod => 'blasttable',
+                                        -expect     => '1e-10',
+                                        );
 $remote_rpsblast->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');
 
 # This is the key to getting job run using rpsblast:
-$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; 
+$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
 
 my $attempt = 1;
 
 SKIP: {
     my $status;
     eval{
-	$status = $remote_rpsblast->submit_blast($inputfilename);
+        $status = $remote_rpsblast->submit_blast($inputfilename);
     };
-    
+
     ok($status,'rpsblast blasttable submitted');
-    
-    skip("Error accessing remote BLAST interface: $@", 3) if $@;
-    
+    skip("Error accessing remote BLAST interface: $@", 4) if $@;
+
     my @rids = $remote_rpsblast->each_rid;
     is(@rids, 1, 'should only be one RID');
-    skip("Wrong number of RIDs: ".scalar(@rids), 2) if @rids != 1;
-    
-    print STDERR "waiting [$rids[0]]..." if( $v > 0 );
+    skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
+
+    diag("Retrieving $rids[0]...\n") if $v;
     my $rc;
     while (defined($rc = $remote_rpsblast->retrieve_blast($rids[0]))) {
-	if ( !ref($rc) ) {
-	    if ( $rc < 0 ) {
-		skip("need a better solution for when 'Server failed to return any data'",2);
-	    }
-	    sleep 5;
-	    print STDERR "Retrieval attempt: $attempt\n" if ( $v > 0 );
-	    $attempt++ < 10 ? next : last;
-	} else {
-	    last
-	}
+        if ( !ref($rc) ) {
+            if ( $rc < 0 ) {
+                skip("need a better solution for when 'Server failed to return any data'",2);
+            }
+            sleep 5;
+            diag("Retrieval attempt: $attempt\n") if $v;
+            $attempt++ < 10 ? next : last;
+        }
+        else {
+            last;
+        }
     }
     $remote_rpsblast->remove_rid($rids[0]);
-    
+
     if ($rc) {
-	ok(1,'retrieve_blast succeeded');
-	$remote_rpsblast->remove_rid($rids[0]);
-	my $count = 0;
-	isa_ok($rc, 'Bio::SearchIO');
-	while (my $result = $rc->next_result) {
-	    while ( my $hit = $result->next_hit ) {
-		$count++;
-		next unless ( $v > 0);
-		print "sbjct name is ", $hit->name, "\n";
-		while ( my $hsp = $hit->next_hsp ) {
-		    print "score is ", $hsp->bits, "\n";
-		} 
-	    }
-	}
-	cmp_ok($count, '>=', 45, 'HSPs returned');
-    } elsif ($attempt > 10) {
-	# have a test fail here (there should not be repeated failed attempts to
-	# get reports)
-	
-	ok(0,'Exceeded maximum attempts on server to retrieve report');
-	skip("Timeout, did not return report after ".($attempt - 1)." attempts", 2);
-    } else {
-	# have a test fail here (whatever is returned should be eval as true and
-	# be a SearchIO)
-	
-	ok(0,"Other problem on remote server, no report returned: $rc");
-	skip('Possible remote server problems', 1);
+        ok(1,'retrieve_blast succeeded');
+        $remote_rpsblast->remove_rid($rids[0]);
+        my $count = 0;
+        isa_ok($rc, 'Bio::SearchIO');
+        while (my $result = $rc->next_result) {
+            while ( my $hit = $result->next_hit ) {
+                $count++;
+                next unless ( $v > 0);
+                print "sbjct name is ", $hit->name, "\n";
+                while ( my $hsp = $hit->next_hsp ) {
+                    print "score is ", $hsp->bits, "\n";
+                }
+            }
+        }
+        cmp_ok($count, '>=', 45, 'HSPs returned');
+    }
+    elsif ($attempt > 10) {
+        # have a test fail here (there should not be repeated failed attempts to
+        # get reports)
+        ok(0,'Exceeded maximum attempts on server to retrieve report');
+        diag("Timeout, did not return report after ".($attempt - 1)." attempts");
+        skip('Remote server timeout problems', 2);
+    }
+    else {
+        # have a test fail here (whatever is returned should be eval as true and
+        # be a SearchIO)
+        ok(0,"Other problem on remote server, no report returned: $rc");
+        skip('Possible remote server problems', 2);
     }
 }
 
-- 
2.11.4.GIT