From dc45f1ec88632749e033c197bf7a06edcc696879 Mon Sep 17 00:00:00 2001
From: Michael Gray <mg13@sanger.ac.uk>
Date: Fri, 11 Oct 2013 14:03:17 +0000
Subject: [PATCH] "INSERT INTO table SET col1=val1, col2=val2" does not work
for SQLite.
Use "INSERT INTO table (col1, col2) VALUES (val1, val2) instead.
---
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 7 +--
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 56 ++++++++++---------
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 43 ++++++++------
.../Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm | 26 +++++----
modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm | 14 +++--
modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm | 40 ++++++++-----
.../EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm | 43 ++++++++------
.../EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm | 16 +++++-
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 21 +++----
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 36 +++++++++++-
.../Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 27 ++++++---
11 files changed, 213 insertions(+), 116 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index 1745e9bb98..aeead5a5e6 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -1209,11 +1209,8 @@ sub store {
my $sth =
$db->dbc->prepare( 'INSERT INTO coord_system '
- . 'SET name = ?, '
- . 'version = ?, '
- . 'attrib = ?,'
- . 'rank = ?,'
- . 'species_id = ?' );
+ . '( name, version, attrib, rank, species_id ) '
+ . 'VALUES ( ?, ?, ?, ?, ? )' );
$sth->bind_param( 1, $name, SQL_VARCHAR );
$sth->bind_param( 2, $version, SQL_VARCHAR );
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 4cbb7f9bf8..6b281ad16c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -725,11 +725,12 @@ sub _store_object_xref_mapping {
my $sth = $self->prepare(qq(
INSERT IGNORE INTO object_xref
- SET xref_id = ?,
- ensembl_object_type = ?,
- ensembl_id = ?,
- linkage_annotation = ?,
- analysis_id = ? )
+ ( xref_id,
+ ensembl_object_type,
+ ensembl_id,
+ linkage_annotation,
+ analysis_id )
+ VALUES ( ?, ?, ?, ?, ? ) )
);
$sth->bind_param( 1, $dbEntry->dbID(), SQL_INTEGER );
$sth->bind_param( 2, $ensembl_type, SQL_VARCHAR );
@@ -747,16 +748,17 @@ sub _store_object_xref_mapping {
if ( $dbEntry->isa('Bio::EnsEMBL::IdentityXref') ) {
$sth = $self->prepare( "
INSERT ignore INTO identity_xref
- SET object_xref_id = ?,
- xref_identity = ?,
- ensembl_identity = ?,
- xref_start = ?,
- xref_end = ?,
- ensembl_start = ?,
- ensembl_end = ?,
- cigar_line = ?,
- score = ?,
- evalue = ?" );
+ ( object_xref_id,
+ xref_identity,
+ ensembl_identity,
+ xref_start,
+ xref_end ,
+ ensembl_start,
+ ensembl_end,
+ cigar_line,
+ score,
+ evalue )
+ VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )" );
$sth->bind_param( 1, $object_xref_id, SQL_INTEGER );
$sth->bind_param( 2, $dbEntry->xref_identity, SQL_INTEGER );
$sth->bind_param( 3, $dbEntry->ensembl_identity, SQL_INTEGER );
@@ -771,9 +773,10 @@ sub _store_object_xref_mapping {
} elsif ( $dbEntry->isa('Bio::EnsEMBL::OntologyXref') ) {
$sth = $self->prepare( "
INSERT ignore INTO ontology_xref
- SET object_xref_id = ?,
- source_xref_id = ?,
- linkage_type = ? " );
+ ( object_xref_id,
+ source_xref_id,
+ linkage_type )
+ VALUES ( ?, ?, ? )" );
foreach my $info ( @{ $dbEntry->get_all_linkage_info() } ) {
my ( $linkage_type, $sourceXref ) = @{$info};
my $sourceXid = undef;
@@ -964,13 +967,14 @@ sub _store_or_fetch_xref {
my $sth = $self->prepare( "
INSERT IGNORE INTO xref
- SET dbprimary_acc = ?,
- display_label = ?,
- version = ?,
- description = ?,
- external_db_id = ?,
- info_type = ?,
- info_text = ?");
+ ( dbprimary_acc,
+ display_label,
+ version,
+ description,
+ external_db_id,
+ info_type,
+ info_text )
+ VALUES ( ?, ?, ?, ?, ?, ?, ? ) ");
$sth->bind_param(1, $dbEntry->primary_id,SQL_VARCHAR);
$sth->bind_param(2, $dbEntry->display_id,SQL_VARCHAR);
$sth->bind_param(3, ($dbEntry->version || q{0}),SQL_VARCHAR);
@@ -993,7 +997,7 @@ sub _store_or_fetch_xref {
my $synonym_store_sth = $self->prepare(
"INSERT ignore INTO external_synonym
- SET xref_id = ?, synonym = ?");
+ ( xref_id, synonym ) VALUES ( ?, ? ) ");
my $synonyms = $dbEntry->get_all_synonyms();
foreach my $syn ( @$synonyms ) {
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index b88b900e63..fc94af81c7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -1201,28 +1201,39 @@ sub store {
($gene, $seq_region_id) = $self->_pre_store($gene);
- my $store_gene_sql = qq(
- INSERT INTO gene
- SET biotype = ?,
- analysis_id = ?,
- seq_region_id = ?,
- seq_region_start = ?,
- seq_region_end = ?,
- seq_region_strand = ?,
- description = ?,
- source = ?,
- status = ?,
- is_current = ?,
- canonical_transcript_id = ?
+ my @columns = qw(
+ biotype
+ analysis_id
+ seq_region_id
+ seq_region_start
+ seq_region_end
+ seq_region_strand
+ description
+ source
+ status
+ is_current
+ canonical_transcript_id
);
+ my @canned_columns;
+ my @canned_values;
+
if (defined($gene->stable_id)) {
- my $created = $self->db->dbc->from_seconds_to_date($gene->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($gene->modified_date());
- $store_gene_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;
+ push @columns, 'stable_id', 'version';
+
+ my $created = $self->db->dbc->from_seconds_to_date($gene->created_date());
+ my $modified = $self->db->dbc->from_seconds_to_date($gene->modified_date());
+ push @canned_columns, 'created_date', 'modified_date';
+ push @canned_values, $created, $modified;
}
+ my $columns = join(', ', @columns, @canned_columns);
+ my $values = join(', ', ('?') x @columns, @canned_values);
+ my $store_gene_sql = qq(
+ INSERT INTO gene ( $columns ) VALUES ( $values )
+ );
+
# column status is used from schema version 34 onwards (before it was
# confidence)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index bd3fa764f8..bddb7861d7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -673,17 +673,21 @@ sub store {
my $db = $self->db();
- my $feature_sth = $self->prepare
- ("INSERT INTO misc_feature SET " .
- " seq_region_id = ?, " .
- " seq_region_start = ?, " .
- " seq_region_end = ?, " .
- " seq_region_strand = ?");
-
- my $feature_set_sth = $self->prepare
- ("INSERT IGNORE misc_feature_misc_set SET " .
- " misc_feature_id = ?, " .
- " misc_set_id = ?");
+ my $feature_sth = $self->prepare(
+ q{INSERT INTO misc_feature (
+ seq_region_id,
+ seq_region_start,
+ seq_region_end,
+ seq_region_strand
+ ) VALUES (?, ?, ?, ?)
+ });
+
+ my $feature_set_sth = $self->prepare(
+ qq{INSERT IGNORE INTO misc_feature_misc_set (
+ misc_feature_id,
+ misc_set_id
+ ) VALUES (?, ?)
+ });
my $msa = $db->get_MiscSetAdaptor();
my $aa = $db->get_AttributeAdaptor();
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
index dfc0b0e041..58fddae42d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
@@ -224,12 +224,14 @@ sub store {
# otherwise 2 processes could try to insert at the same time and one
# would fail
- my $sth = $self->prepare
- ("INSERT IGNORE INTO misc_set " .
- "SET code = ?, " .
- " name = ?, " .
- " description = ?, " .
- " max_length = ?");
+ my $sth = $self->prepare(
+ qq{INSERT IGNORE INTO misc_set (
+ code,
+ name,
+ description,
+ max_length
+ ) VALUES (?, ?, ?, ?)
+ });
my $db = $self->db();
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
index b8edcdb482..ccccf55f64 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
@@ -490,21 +490,31 @@ sub store {
( $operon, $seq_region_id ) = $self->_pre_store($operon);
- my $store_operon_sql = qq(
- INSERT INTO operon
- SET seq_region_id = ?,
- seq_region_start = ?,
- seq_region_end = ?,
- seq_region_strand = ?,
- display_label = ?,
- analysis_id = ?
- );
-
+ my @columns = qw(
+ seq_region_id
+ seq_region_start
+ seq_region_end
+ seq_region_strand
+ display_label
+ analysis_id
+ );
+
+ my ($created, $modified);
if ( defined($operon->stable_id()) ) {
- my $created = $self->db->dbc->from_seconds_to_date($operon->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($operon->modified_date());
- $store_operon_sql .= ", stable_id = ?, version = ?, created_date = " . $created . ",modified_date = " . $modified;
+ $created = $self->db->dbc->from_seconds_to_date($operon->created_date());
+ $modified = $self->db->dbc->from_seconds_to_date($operon->modified_date());
+ push @columns, qw(
+ stable_id
+ version
+ created_date
+ modified_date
+ );
}
+ my $i_columns = join(', ', @columns);
+ my $i_values = join(', ', ('?') x @columns);
+ my $store_operon_sql = qq(
+ INSERT INTO operon ( ${i_columns} ) VALUES ( $i_values )
+ );
# column status is used from schema version 34 onwards (before it was
# confidence)
@@ -520,7 +530,9 @@ sub store {
if ( defined($operon->stable_id()) ) {
$sth->bind_param( 7, $operon->stable_id(), SQL_VARCHAR );
my $version = ($operon->version()) ? $operon->version() : 1;
- $sth->bind_param( 8, $version, SQL_INTEGER );
+ $sth->bind_param( 8, $version, SQL_INTEGER );
+ $sth->bind_param( 9, $created, SQL_DATETIME );
+ $sth->bind_param(10, $modified, SQL_DATETIME );
}
$sth->execute();
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
index af7f06677f..b6cecf03f7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
@@ -544,23 +544,32 @@ sub store {
} else {
$analysis_id = $db->get_AnalysisAdaptor->store($analysis);
}
- my $store_operon_transcript_sql = qq(
- INSERT INTO operon_transcript
- SET seq_region_id = ?,
- seq_region_start = ?,
- seq_region_end = ?,
- seq_region_strand = ?,
- display_label = ?,
- operon_id = ?,
- analysis_id =?
- );
-
+ my @columns = qw(
+ seq_region_id
+ seq_region_start
+ seq_region_end
+ seq_region_strand
+ display_label
+ operon_id
+ analysis_id
+ );
+
+ my ($created, $modified);
if ( defined($operon_transcript->stable_id()) ) {
- my $created = $self->db->dbc->from_seconds_to_date($operon_transcript->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($operon_transcript->modified_date());
- $store_operon_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . ",modified_date = " . $modified;
+ $created = $self->db->dbc->from_seconds_to_date($operon_transcript->created_date());
+ $modified = $self->db->dbc->from_seconds_to_date($operon_transcript->modified_date());
+ push @columns, qw(
+ stable_id
+ version
+ created_date
+ modified_date
+ );
}
-
+ my $i_columns = join(', ', @columns);
+ my $i_values = join(', ', ('?') x @columns);
+ my $store_operon_transcript_sql = qq(
+ INSERT INTO operon_transcript ( ${i_columns} ) VALUES ( $i_values )
+ );
# column status is used from schema version 34 onwards (before it was
# confidence)
@@ -577,7 +586,9 @@ sub store {
if ( defined($operon_transcript->stable_id()) ) {
$sth->bind_param( 8, $operon_transcript->stable_id(), SQL_VARCHAR );
my $version = ($operon_transcript->version()) ? $operon_transcript->version() : 1;
- $sth->bind_param( 9, $version, SQL_INTEGER );
+ $sth->bind_param( 9, $version, SQL_INTEGER );
+ $sth->bind_param(10, $created, SQL_DATETIME );
+ $sth->bind_param(11, $modified, SQL_DATETIME );
}
$sth->execute();
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
index 5e9269b1a3..df64c6e104 100755
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
@@ -220,7 +220,21 @@ sub store {
$db->get_AnalysisAdaptor->store($analysis);
}
- my $sth = $self->prepare("INSERT INTO protein_feature " . " SET translation_id = ?, " . " seq_start = ?, " . " seq_end = ?, " . " analysis_id = ?, " . " hit_start = ?, " . " hit_end = ?, " . " hit_name = ?, " . " hit_description = ?, " . " score = ?, " . " perc_ident = ?, " . " evalue = ?");
+ my $sth = $self->prepare(q{
+ INSERT INTO protein_feature
+ ( translation_id,
+ seq_start,
+ seq_end,
+ analysis_id,
+ hit_start,
+ hit_end,
+ hit_name,
+ hit_description,
+ score,
+ perc_ident,
+ evalue )
+ VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
+ });
$sth->bind_param(1, $translation_id, SQL_INTEGER);
$sth->bind_param(2, $feature->start, SQL_INTEGER);
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index ca4c883c1a..45a3e9a3d2 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -2018,9 +2018,9 @@ sub store {
#store the seq_region
my $sth = $db->dbc->prepare("INSERT INTO seq_region " .
- "SET name = ?, " .
- " length = ?, " .
- " coord_system_id = ?" );
+ " ( name, length, coord_system_id ) " .
+ " VALUES ( ?, ?, ? )"
+ );
$sth->bind_param(1,$sr_name,SQL_VARCHAR);
$sth->bind_param(2,$sr_len,SQL_INTEGER);
@@ -2332,13 +2332,14 @@ sub store_assembly{
#
my $sth = $self->db->dbc->prepare
("INSERT INTO assembly " .
- "SET asm_seq_region_id = ?, " .
- " cmp_seq_region_id = ?, " .
- " asm_start = ?, " .
- " asm_end = ?, " .
- " cmp_start = ?, " .
- " cmp_end = ?, " .
- " ori = ?" );
+ " ( asm_seq_region_id, " .
+ " cmp_seq_region_id, " .
+ " asm_start, " .
+ " asm_end , " .
+ " cmp_start, " .
+ " cmp_end , " .
+ " ori )" .
+ "VALUES ( ?, ?, ?, ?, ?, ?, ? )");
my $asm_seq_region_id = $self->get_seq_region_id( $asm_slice );
my $cmp_seq_region_id = $self->get_seq_region_id( $cmp_slice );
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 2882756054..2d7e889399 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -973,18 +973,48 @@ sub store {
#
# Store transcript
#
- my $store_transcript_sql =
- sprintf "INSERT INTO transcript SET gene_id = ?, analysis_id = ?, seq_region_id = ?, seq_region_start = ?, seq_region_end = ?, seq_region_strand = ?,%s biotype = ?, status = ?, description = ?, is_current = ?, canonical_translation_id = ?", ($self->schema_version > 74)?" source = ?,":'';
+# my $store_transcript_sql =
+# sprintf "INSERT INTO transcript SET gene_id = ?, analysis_id = ?, seq_region_id = ?, seq_region_start = ?, seq_region_end = ?, seq_region_strand = ?,%s biotype = ?, status = ?, description = ?, is_current = ?, canonical_translation_id = ?", ($self->schema_version > 74)?" source = ?,":'';
+
+ my @columns = qw(
+ gene_id
+ analysis_id
+ seq_region_id
+ seq_region_start
+ seq_region_end
+ seq_region_strand
+ );
+
+ push @columns, 'source' if ($self->schema_version > 74);
+
+ push @columns, qw(
+ biotype
+ status
+ description
+ is_current
+ canonical_translation_id
+ );
+
+ my @canned_columns;
+ my @canned_values;
if ( defined( $transcript->stable_id() ) ) {
+ push @columns, 'stable_id', 'version';
my $created = $self->db->dbc->from_seconds_to_date($transcript->created_date());
my $modified = $self->db->dbc->from_seconds_to_date($transcript->modified_date());
- $store_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;
+ push @canned_columns, 'created_date', 'modified_date';
+ push @canned_values, $created, $modified;
}
+ my $columns = join(', ', @columns, @canned_columns);
+ my $values = join(', ', ('?') x @columns, @canned_values);
+ my $store_transcript_sql = qq(
+ INSERT INTO transcript ( $columns ) VALUES ( $values )
+ );
+
my $tst = $self->prepare($store_transcript_sql);
my $i = 0;
$tst->bind_param( ++$i, $gene_dbID, SQL_INTEGER );
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 661e69e767..cf063d4786 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -477,22 +477,33 @@ sub store {
throw("end_Exon must have a dbID for Translation to be stored.");
}
- my $store_translation_sql = qq(
- INSERT INTO translation
- SET seq_start = ?,
- start_exon_id = ?,
- seq_end = ?,
- end_exon_id = ?,
- transcript_id = ?
+ my @columns = qw(
+ seq_start
+ start_exon_id
+ seq_end
+ end_exon_id
+ transcript_id
);
+ my @canned_columns;
+ my @canned_values;
+
if (defined($translation->stable_id)) {
+ push @columns, 'stable_id', 'version';
+
my $created = $self->db->dbc->from_seconds_to_date($translation->created_date());
my $modified = $self->db->dbc->from_seconds_to_date($translation->modified_date());
- $store_translation_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;
+ push @canned_columns, 'created_date', 'modified_date';
+ push @canned_values, $created, $modified;
}
+ my $columns = join(', ', @columns, @canned_columns);
+ my $values = join(', ', ('?') x @columns, @canned_values);
+ my $store_translation_sql = qq(
+ INSERT INTO translation ( $columns ) VALUES ( $values )
+ );
+
my $sth = $self->prepare($store_translation_sql);
$sth->bind_param(1,$translation->start,SQL_INTEGER);
$sth->bind_param(2,$translation->start_Exon->dbID,SQL_INTEGER);
--
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