dependencys added so that for a source to be loaded then all of its...

dependencys added so that for a source to be loaded then all of its dependecies must be loaded before it. Stored in a table dependent_source.

misc-scripts/xref_mapping/sql/table.sql

@@ -75,6 +75,15 @@ CREATE TABLE synonym (
 
 ################################################################################
 
+CREATE TABLE dependent_source (
+  master_source_id           int unsigned not null,
+  dependent_source_id        int unsigned not null,
+
+  PRIMARY KEY (master_source_id, dependent_source_id)
+) COLLATE=latin1_swedish_ci TYPE=InnoDB;
+
+################################################################################
+
 CREATE TABLE source (
 
   source_id                   int unsigned not null auto_increment,

misc-scripts/xref_mapping/xref_config.ini

@@ -1089,7 +1089,6 @@ data_uri        =
 name            = HGNC
 download        = Y
 order           = 30
-#order 51
 priority        = 2
 prio_descr      = ccds
 parser          = HGNC_CCDSParser
@@ -1128,6 +1127,7 @@ order           = 29
 priority        = 4
 prio_descr      = entrezgene_manual
 parser          = HGNCParser
+dependent       = EntrezGene::MULTI,Uniprot/SWISSPROT::MULTI,RefSeq_dna::homo_sapiens,RefSeq_dna::homo_sapiens#01,RefSeq_peptide::homo_sapiens
 release_uri     =
 data_uri        = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
 

misc-scripts/xref_mapping/xref_config2sql.pl

@@ -172,5 +172,21 @@ foreach my $species_section ( sort( $config->GroupMembers('species') ) )
             $config->val( $source_section, 'parser' ) );
 
     print("\n");
+    
+    my @dependents =
+       split( /\,/, $config->val( $source_section, 'dependent', '' ) );
+
+    foreach my $dep (@dependents){
+      my $dep_name = "source $dep";
+      print "# adding source dependency that $source_section needs $dep_name loaded first\n";
+      if ( !exists( $source_ids{$dep_name} ) ) {
+	die( sprintf( "Can not find dependent source section '[%s]'\n"
+                      . "while reading species section '[%s]'\n",
+		      $dep, $species_section ) );
+      }
+      print "INSERT INTO dependent_source (master_source_id, dependent_source_id)\n";
+      printf( "VALUES (%d, %d);\n\n", $source_ids{$source_section}, $source_ids{$dep_name});
+    }
+
   } ## end foreach my $source_name ( sort...)
 } ## end foreach my $species_section...