Changeset 547

Timestamp:

11/22/11 02:14:14 (6 months ago)

Author:

AlexanderPico

Message:

switched from EnXXXXXX to En

Location:

trunk/dbbuilder/src/org/bridgedb/build/scripts

Files:

• PathVisioMySQL_BUILD.sql.template (modified) (5 diffs)
• buildPathVisio.sh (modified) (1 diff)

trunk/dbbuilder/src/org/bridgedb/build/scripts/PathVisioMySQL_BUILD.sql.template

@@ -12 +12 @@
 from gene left join link
 on gene.ID = link.ID_Right
-where gene.Code = 'L' and link.Code_Left = 'EnXXXXXX' and link.ID_Left is not null group by ID;
+where gene.Code = 'L' and link.Code_Left = 'En' and link.ID_Left is not null group by ID;
 create index index_id_left_temp on gene_temp (ID_Left);
 
@@ -19 +19 @@
 from gene_temp left join gene
 on gene_temp.ID_Left = gene.ID
-where gene.Code = 'EnXXXXXX';
+where gene.Code = 'En';
 
 update gene, gene_temp2
@@ -84 +84 @@
 genmapp_XXXXXX_CS_YYYYYY.attr.Name, genmapp_XXXXXX_CS_YYYYYY.attr.Value
 FROM genmapp_XXXXXX_CS_YYYYYY.attr
-WHERE genmapp_XXXXXX_CS_YYYYYY.attr.Value != '';
+WHERE genmapp_XXXXXX_CS_YYYYYY.attr.Value != ''
+AND genmapp_XXXXXX_CS_YYYYYY.attr.Code IN ("En","Mb","L","X","Il","Ag","Q","Om","U","Rf","S","Ip","T","Pd","H","M","R","D","Z","F","W","Gg","A","Ti","Ir","N","Uc","Pl","Gm","Bg","Ec","Wg","Gw","Kg","Bc","Tb");
 
 ## Fill 'datanode'
@@ -92 +93 @@
 FROM genmapp_XXXXXX_CS_YYYYYY.gene
 WHERE genmapp_XXXXXX_CS_YYYYYY.gene.ID != '' 
-AND genmapp_XXXXXX_CS_YYYYYY.gene.Code IN ("EnXXXXXX","Mb","L","X","Il","Ag","Q","Om","U","Rf","S","Ip","T","Pd","H","M","R","D","Z","F","W","Gg","A","Ti","Ir","N","Uc","Pl","Gm","Bg","Ec","Wg","Gw","Kg","Bc","Tb");
+AND genmapp_XXXXXX_CS_YYYYYY.gene.Code IN ("En","Mb","L","X","Il","Ag","Q","Om","U","Rf","S","Ip","T","Pd","H","M","R","D","Z","F","W","Gg","A","Ti","Ir","N","Uc","Pl","Gm","Bg","Ec","Wg","Gw","Kg","Bc","Tb");
 
 ## Fill 'link'
@@ -99 +100 @@
 SELECT DISTINCT *
 FROM genmapp_XXXXXX_CS_YYYYYY.link
-WHERE genmapp_XXXXXX_CS_YYYYYY.link.Code_Right IN ("EnXXXXXX","Mb","L","X","Il","Ag","Q","Om","U","Rf","S","Ip","T","Pd","H","M","R","D","Z","F","W","Gg","A","Ti","Ir","N","Uc","Pl","Gm","Bg","Ec","Wg","Gw","Kg","Bc","Tb");
+WHERE genmapp_XXXXXX_CS_YYYYYY.link.Code_Right IN ("En,"Mb","L","X","Il","Ag","Q","Om","U","Rf","S","Ip","T","Pd","H","M","R","D","Z","F","W","Gg","A","Ti","Ir","N","Uc","Pl","Gm","Bg","Ec","Wg","Gw","Kg","Bc","Tb");
 
 ##Add Ensembl IDs to right side of 'link' table
 INSERT INTO link
-SELECT datanode.id, "EnXXXXXX", datanode.id, "EnXXXXXX"
+SELECT datanode.id, "En", datanode.id, "En"
 FROM datanode
-WHERE datanode.code = "EnXXXXXX";
+WHERE datanode.code = "En";
 
 ## Add one more index to link

trunk/dbbuilder/src/org/bridgedb/build/scripts/buildPathVisio.sh

@@ -78 +78 @@
 
 #Run qc.sh
-./qc.sh ${DatabaseSpecies} ${PriorDatabaseDate} ${DatabaseDate} > temp.${DatabaseDb}.qc 
+(
+cd ${ScriptsDir}
+./qc.sh ${DatabaseSpecies} ${PriorDatabaseDate} ${DatabaseDate} > ../temp.${DatabaseSpecies}.${DatabaseDate}.qc
+)
 
 # report on products (check size > 1.9M)