From bcee550a5cdd5eaedffae00c05a2c2700eaf29fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 12 Nov 2007 12:52:00 +0000
Subject: [PATCH] Added creation of new 'analysis' if one does not already
exist AND if $do_upload is true.
TODO: testing
---
.../XrefMapper/CoordinateMapper.pm | 58 +++++++++++++------
1 file changed, 41 insertions(+), 17 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
index 9cc4c6b9c8..22887585b7 100644
--- a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
@@ -115,8 +115,33 @@ sub run_coordinatemapping {
log_progress("Can not find analysis ID for this analysis:\n");
log_progress(" logic_name = 'XrefCoordinateMapping'\n");
log_progress( " parameters = '%s'\n", $analysis_params );
- log_progress("A new analysis will be added\n");
- } else {
+
+ if ($do_upload) {
+ ##################################################################
+ # Store a new analysis. #
+ ##################################################################
+
+ log_progress("A new analysis will be added\n");
+
+ $analysis_id = $core_dbh->selectall_arrayref(
+ 'SELECT MAX(analysis_id) FROM analysis')->[0][0];
+ log_progress( "Last used analysis_id is %d\n", $analysis_id );
+
+ my $sql = 'INSERT INTO analysis '
+ . 'VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)';
+ my $sth = $core_dbh->prepare($sql);
+
+ $sth->execute( ++$analysis_id, 'now()',
+ 'XrefCoordinateMapping', '\N',
+ '\N', '\N',
+ 'xref_mapper.pl', '\N',
+ '\N', $analysis_params,
+ 'CoordinateMapper.pm', '\N',
+ '\N', '\N' );
+ }
+ } ## end if ( !defined($analysis_id...
+
+ if ( defined($analysis_id) ) {
log_progress( "Analysis ID is %d\n",
$analysis_id );
}
@@ -476,15 +501,17 @@ sub dump_xref {
# Assign 'xref_id' to this Xref.
$xref->{'xref_id'} = ++$xref_id;
- $fh->printf("%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n",
- $xref->{'xref_id'},
- $xref->{'external_db_id'},
- $xref->{'accession'},
- $xref->{'accession'},
- '0',
- '\N',
- 'MISC', # FIXME
- '\N' # FIXME (possibly)
+ $fh->printf(
+ "%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n",
+ $xref->{'xref_id'},
+ $xref->{'external_db_id'},
+ $xref->{'accession'},
+ $xref->{'accession'},
+ '0',
+ '\N',
+ 'MISC', # FIXME (add new 'info_type' enum 'COORDINATEOVERLAP'
+ # in release v49)
+ '\N' # FIXME (possibly)
);
}
$fh->close();
@@ -677,11 +704,11 @@ sub dump_unmapped_object {
$xref->{'unmapped_object_id'} = ++$unmapped_object_id;
$fh->printf(
- "%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n",
+ "%d\t%s\t%s\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n",
$xref->{'unmapped_object_id'},
'xref',
- $analysis_id || -1, # -1 means create analysis for
- # this when uploading
+ $analysis_id || '\N', # '\N' (NULL) means no analysis exists
+ # and uploading this table will fail.
$xref->{'external_db_id'},
$xref->{'accession'},
$xref->{'reason'}->{'unmapped_reason_id'}, (
@@ -722,9 +749,6 @@ sub upload_unmapped_reason {
while ( my $line = $fh->getline() ) {
chomp($line);
my @fields = split( /\t/, $line );
-
- # FIXME (when 'analysis_id' is -1)
-
$sth->execute(@fields);
}
$fh->close();
--
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