From c03d396b10a76911eb8eb286dfb4ba1a8b8c50e8 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 20 Apr 2009 07:41:14 +0000
Subject: [PATCH] add product_cvname and synonym_cvname to the options file
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10550 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/options | 12 +++++++++--
.../chado/ChadoTransactionManager.java | 20 ++++++++++---------
2 files changed, 21 insertions(+), 11 deletions(-)
diff --git a/etc/options b/etc/options
index e2acc2f8b..d44429daa 100644
--- a/etc/options
+++ b/etc/options
@@ -2,7 +2,7 @@
# (Note that comment lines start with a hash (#) symbol)
-# $Header: //tmp/pathsoft/artemis/etc/options,v 1.62 2009-04-08 15:15:40 tjc Exp $
+# $Header: //tmp/pathsoft/artemis/etc/options,v 1.63 2009-04-20 07:41:14 tjc Exp $
# This file should contain option settings that look like this:
#
@@ -822,9 +822,14 @@ hyperlinks = \
# Lookseq url
#lookseq = http://www.sanger.ac.uk/cgi-bin/teams/team112/lookseq/get_data.pl?
-#lookseq_chr = MAL3
+#lookseq_chr = MAL1
#lookseq_lane = sample_7a
+#lookseq = http://intwebdev.sanger.ac.uk/cgi-bin/teams/team81/lookseq/get_data.pl?
+#lookseq_chr = seq2
+#lookseq_lane = aln_srt.bam
+
+
#
# CHADO DATABASE OPTIONS
#
@@ -839,6 +844,9 @@ chado_exon_model=CDS
# define how product qualifiers are stored (as a cv or as a featureprop)
product_cv=yes
+product_cvname = genedb_products
+# cv containing synonym names
+synonym_cvname = genedb_synonym_type
# set default delete behaviour to make things obsolete, if
# this is not provided the default is to permanently delete
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index bb5e2bd94..e4fd69d82 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -123,24 +123,25 @@ public class ChadoTransactionManager
//controlled vocab tags
public static String CV_NAME[];
- static
- {
- initCV();
- }
-
-
//synonym tags from cv
private static String synonym_tags[] = null;
- public static String SYNONYM_TAG_CVNAME = "genedb_synonym_type";
+ public static String SYNONYM_TAG_CVNAME =
+ Options.getOptions().getProperty("synonym_cvname");
private EntryGroup entryGroup;
// Db where db entries are stored corresponding to controlled curation CV terms
public static String CONTROLLED_CURATION_DB = "CCGEN";
public static String PRODUCT_DB = "PRODUCT";
- public static String PRODUCT_CV = "genedb_products";
+ public static String PRODUCT_CV =
+ Options.getOptions().getProperty("product_cvname");
// number of SQL commands successfully processed during a commit
public static int commitReturnValue = 0;
+ static
+ {
+ initCV();
+ }
+
public ChadoTransactionManager()
{
@@ -150,7 +151,7 @@ public class ChadoTransactionManager
{
if(Options.getOptions().getPropertyTruthValue("product_cv"))
{
- logger4j.debug("PRODUCT STORED AS A CV (product_cv=yes)");
+ logger4j.debug("PRODUCT STORED AS A CV (product_cv=yes) IN "+PRODUCT_CV);
CV_NAME = new String[]
{ "GO",
"controlled_curation",
@@ -165,6 +166,7 @@ public class ChadoTransactionManager
"controlled_curation",
"class" };
}
+ logger4j.debug("SYNONYM NAMES ARE STORED IN "+SYNONYM_TAG_CVNAME);
}
public void setEntryGroup(final EntryGroup entryGroup)
--
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