From cc95264d0f713e30b5c81a3bdb97b16fe3529b49 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 16 Nov 2007 09:24:43 +0000
Subject: [PATCH] Added lots of sanity checking to track down formatting
errors.
---
.../external_db/update_external_dbs.pl | 65 ++++++++++++++-----
1 file changed, 48 insertions(+), 17 deletions(-)
diff --git a/misc-scripts/external_db/update_external_dbs.pl b/misc-scripts/external_db/update_external_dbs.pl
index d05685208a..e06b0b9096 100644
--- a/misc-scripts/external_db/update_external_dbs.pl
+++ b/misc-scripts/external_db/update_external_dbs.pl
@@ -53,6 +53,9 @@ if($release_num) {
@dbnames = grep {/^[a-zA-Z]+\_[a-zA-Z]+\_(core|est|estgene|vega|otherfeatures|cdna)\_${release_num}\_\d+[A-Za-z]?$/} @dbnames;
}
+my @field_names = qw(external_db_id db_name release status dbprimary_acc_linkable display_label_linkable priority db_display_name type);
+
+my @types = qw(ARRAY ALT_TRANS MISC LIT PRIMARY_DB_SYNONYM);
#
# make sure the user wishes to continue
@@ -77,8 +80,9 @@ if ($input ne 'yes') {
my $fh = IO::File->new();
$fh->open($file) or die("Could not open input file $file");
my @rows;
-my $row;
-while ($row = <$fh>) {
+my %bad_lines;
+
+while (my $row = <$fh>) {
chomp($row);
next if ($row =~ /^#/); # skip comments
next if ($row =~ /^$/); # and blank lines
@@ -104,16 +108,45 @@ while ($row = <$fh>) {
exit(1);
}
- if ( $a[1] =~ /^$/ || $a[1] =~ /^\s+$/ || $a[1] =~ /^\d+$/ ) {
- print STDERR "Cannot parse the following line:\n"
- . $row
- . "\nIt probably has spaces separating the fields "
- . "rather than tabs.\n";
- exit(1);
+ # do some formatting checks
+ my $blank;
+ for (my $i=0; $i < scalar(@a); $i++) {
+ if ($a[$i] eq '') {
+ $bad_lines{$row} = $field_names[$i] . " - field blank - check all tabs/spaces in line";
+ }
+ }
+
+ if ($a[1] =~ /\s/) {
+ $bad_lines{$row} = "db_name field appears to contain spaces";
}
+ if ($a[1] =~ /^$/) {
+ $bad_lines{$row} = "db_name field appears to be missing";
+ }
+ if ($a[1] =~ /^\s+$/) {
+ $bad_lines{$row} = "db_name field appears to be blank";
+ }
+ if ($a[1] =~ /^\d+$/) {
+ $bad_lines{$row} = "db_name field appears to be numeric - check formatting";
+ }
+
+ my $type_ok;
+ foreach my $type (@types) {
+ $type_ok = 1 if ($a[8] eq $type);
+ }
+ $bad_lines{$row} = "type field is " . $a[8] . ", not one of the recognised types" if (!$type_ok);
+
}
$fh->close();
+if (%bad_lines) {
+ print STDERR "Cannot parse the following line(s) from $file; check that all fields are present and are separated by one tab (not spaces). \n";
+ print STDERR "Name of problem field, and the error is printed in brackets first\n\n";
+ foreach my $row (keys %bad_lines) {
+ print STDERR "[". $bad_lines{$row} . "]" . " $row\n";
+ }
+ exit(1);
+}
+
# Load into master database
if(!$nonreleasemode){
load_database($db, $master, @rows);
@@ -121,30 +154,28 @@ $fh->close();
# Check each other database in turn
# Load if no extra rows in db that aren't in master
# Warn and skip if there are
-
+
foreach my $dbname (@dbnames) {
-
+
print STDERR "Looking at $dbname ... \n";
if ($force || $nonreleasemode) {
-
+
print STDERR "Forcing overwrite of external_db table in "
. "$dbname from $file\n";
load_database( $db, $dbname, @rows );
-
+
} elsif (compare_external_db($db, $master, $dbname)) {
-
+
print STDERR "$dbname has no additional rows. "
. "Overwriting external_db table from $file\n";
load_database( $db, $dbname, @rows );
-
+
} else {
-
+
print STDERR "$dbname has extra rows "
. "that are not in $file, skipping\n";
}
-
-
}
--
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