store() now only has 1 argument, checks moved into store_or_update_one()

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm

@@ -53,9 +53,11 @@ sub default_table_name {
 sub store_if_needed {
     my ($self, $data) = @_;
 
-    my ($stored_hash) = $self->store({'data'=> $data}, 1);
+    my $storable_hash = {'data'=> $data};
 
-    return '_extended_data_id ' . $stored_hash->{'analysis_data_id'};
+    $self->store_or_update_one( $storable_hash  );
+
+    return '_extended_data_id ' . $storable_hash->{'analysis_data_id'};
 }
 
 1;

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -96,7 +96,7 @@ sub store_jobs_and_adjust_counters {
             # avoid deadlocks when dataflowing under transactional mode (used in Ortheus Runnable for example):
         $dbc->do( "SELECT 1 FROM job WHERE job_id=$semaphored_job_id FOR UPDATE" ) if($need_to_increase_semaphore_count and ($dbc->driver ne 'sqlite'));
 
-        my ($job, $stored_this_time) = $self->store( $job, 0 );
+        my ($job, $stored_this_time) = $self->store( $job );
 
         if($stored_this_time) {
             if($need_to_increase_semaphore_count) { # if we are not creating a new semaphore (where dependent jobs have already been counted),

modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm

@@ -235,7 +235,7 @@ sub _table_info_loader {
         if( $is_ai  # careful! This is only supported by DBD::mysql and will not work with other drivers
          or ($column_name eq $table_name.'_id')
          or ($table_name eq 'analysis_base' and $column_name eq 'analysis_id') ) {    # a special case (historical)
-            $autoinc_id = $column_name;    # careful! This is only supported by DBD::mysql and will not work with other drivers
+            $autoinc_id = $column_name;
         }
     }
     $sth->finish;
@@ -396,6 +396,23 @@ sub update {    # update (some or all) non_primary columns from the primary
     $sth->finish();
 }
 
+sub store_or_update_one {
+    my ($self, $object) = @_;
+
+    if(UNIVERSAL::can($object, 'adaptor') and $object->adaptor and $object->adaptor==$self) {  # looks like it has been previously stored
+        if(@{ $self->primary_key() }) { # updatable ?
+            $self->update( $object );
+            # warn "store_or_update_one: updated [".$object->toString."]\n";
+        }
+    } elsif( my $present = $self->check_object_present_in_db( $object ) ) {
+        $self->mark_stored($object, $present);
+        # warn "store_or_update_one: found [".$object->toString."] in db by content\n";
+    } else {
+        $self->store( $object );
+        # warn "store_or_update_one: stored [".$object->toString."]\n";
+    }
+}
+
 
 sub check_object_present_in_db {    # return autoinc_id/undef if the table has autoinc_id or just 1/undef if not
     my ( $self, $object ) = @_;
@@ -422,7 +439,7 @@ sub check_object_present_in_db {    # return autoinc_id/undef if the table has a
 
 
 sub store {
-    my ($self, $object_or_list, $check_presence_in_db_first) = @_;
+    my ($self, $object_or_list) = @_;
 
     my $objects = (ref($object_or_list) eq 'ARRAY')     # ensure we get an array of objects to store
         ? $object_or_list
@@ -446,9 +463,6 @@ sub store {
     my $stored_this_time        = 0;
 
     foreach my $object (@$objects) {
-        if($check_presence_in_db_first and my $present = $self->check_object_present_in_db($object)) {
-            $self->mark_stored($object, $present);
-        } else {
             my ($columns_being_stored, $column_key) = (ref($object) eq 'HASH') ? $self->keys_to_columns($object) : ($all_storable_columns, '*all*');
             # warn "COLUMN_KEY='$column_key'\n";
 
@@ -474,7 +488,6 @@ sub store {
                 $self->mark_stored($object, $liid );
                 ++$stored_this_time;
             }
-        }
     }
 
     foreach my $sth (values %hashed_sth) {

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -727,21 +727,15 @@ sub run {
     my $dataflow_rule_adaptor       = $hive_dba->get_DataflowRuleAdaptor;
 
     foreach my $resource_class ( $all_rc_coll->list ) {
-        unless( $resource_class->adaptor ) {
-            $resource_class_adaptor->store( $resource_class );
-        }
-        foreach my $resource_description ( $all_rd_coll->find_all_by('resource_class', $resource_class) ) { # code is simplified due to 'REPLACE' mode of the adaptor (NB: not portable!)
-            $resource_description_adaptor->store( $resource_description );
+        $resource_class_adaptor->store_or_update_one( $resource_class );
+        foreach my $resource_description (@{ $all_rd_coll->find_all_by('resource_class', $resource_class) }) {
+            $resource_description_adaptor->store_or_update_one( $resource_description );
         }
     }
 
     foreach my $analysis ( $all_analyses_coll->list ) {
-        my $stats = $analysis->stats;   # should be taking the value cached previously
-
-        unless( $analysis->adaptor ) {  # TODO: check a more thorough condition if moving analyses around, etc
-            $analysis_adaptor->store( $analysis );
-            $analysis_stats_adaptor->store( $stats );
-        }
+        $analysis_adaptor->store_or_update_one( $analysis );
+        $analysis_stats_adaptor->store_or_update_one( $analysis->stats );   # should be taking the value cached previously
 
         if(my $our_jobs = $analysis->jobs_collection ) {
             $job_adaptor->store_jobs_and_adjust_counters( $our_jobs );
@@ -751,11 +745,11 @@ sub run {
     foreach my $analysis ( $all_analyses_coll->list ) {
 
         foreach my $c_rule (@{ $analysis->control_rules_collection }) {
-            $ctrl_rule_adaptor->store( $c_rule, 1 );
+            $ctrl_rule_adaptor->store_or_update_one( $c_rule );
             warn $c_rule->toString."\n";
         }
         foreach my $df_rule (@{ $analysis->dataflow_rules_collection }) {
-            $dataflow_rule_adaptor->store( $df_rule, 1 );
+            $dataflow_rule_adaptor->store_or_update_one( $df_rule );
             warn $df_rule->toString."\n";
         }
     }