From 637956835974eb57d74ad061462845c81d007a38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= <bneron@pasteur.fr>
Date: Wed, 20 Jan 2016 16:00:24 +0100
Subject: [PATCH] remove t3ss_family info add predicted_system and ncbi_id

replace all t3ss_family info and search by predicted_system

and add info ncbi_id and search system using ncbi_id
---
 src/couchapp/txssdb/views/by_replicon_name/map.js   |  5 +++--
 .../txssdb/views/by_replicon_ncbi_id/map.js         | 13 +++++++++++++
 src/couchapp/txssdb/views/by_replicon_strain/map.js |  5 +++--
 src/couchapp/txssdb/views/by_replicon_taxid/map.js  |  5 +++--
 .../txssdb/views/by_replicon_taxonomy/map.js        |  5 +++--
 src/couchapp/txssdb/views/predicted_system/map.js   |  2 +-
 6 files changed, 26 insertions(+), 9 deletions(-)
 create mode 100644 src/couchapp/txssdb/views/by_replicon_ncbi_id/map.js

diff --git a/src/couchapp/txssdb/views/by_replicon_name/map.js b/src/couchapp/txssdb/views/by_replicon_name/map.js
index ab85317..6257a83 100644
--- a/src/couchapp/txssdb/views/by_replicon_name/map.js
+++ b/src/couchapp/txssdb/views/by_replicon_name/map.js
@@ -3,10 +3,11 @@ function(doc) {
     	"id" : doc._id,
     	"code" : doc.code ,
     	"name" : doc.replicon.name ,
-    	"T3SS_family" : doc.T3SS_family,
+    	"predicted_system" : doc.predicted_system,
     	"taxid" : doc.replicon.taxid,
+    	"ncbi_id": doc.replicon.ncbi_id,
     	"strain" : doc.replicon.strain ,
-    	"taxonomy" : doc.replicon.taxonomy.join( ", ") ,
+    	"taxonomy" : doc.replicon.taxonomy.join(", ") ,
     	"type" : doc.replicon.type
     });
   }
\ No newline at end of file
diff --git a/src/couchapp/txssdb/views/by_replicon_ncbi_id/map.js b/src/couchapp/txssdb/views/by_replicon_ncbi_id/map.js
new file mode 100644
index 0000000..701c3dd
--- /dev/null
+++ b/src/couchapp/txssdb/views/by_replicon_ncbi_id/map.js
@@ -0,0 +1,13 @@
+function(doc) {
+    emit(doc.replicon.ncbi_id, {
+    	"id" : doc._id,
+    	"code" : doc.code ,
+    	"name" : doc.replicon.name ,
+    	"predicted_system" : doc.predicted_system,
+    	"taxid" : doc.replicon.taxid,
+    	"ncbi_id": doc.replicon.ncbi_id,
+    	"strain" : doc.replicon.strain ,
+    	"taxonomy" : doc.replicon.taxonomy.join(", ") ,
+    	"type" : doc.replicon.type
+    });
+  }
\ No newline at end of file
diff --git a/src/couchapp/txssdb/views/by_replicon_strain/map.js b/src/couchapp/txssdb/views/by_replicon_strain/map.js
index c03ec69..b6cb110 100644
--- a/src/couchapp/txssdb/views/by_replicon_strain/map.js
+++ b/src/couchapp/txssdb/views/by_replicon_strain/map.js
@@ -3,10 +3,11 @@ function(doc) {
     	"id" : doc._id,
     	"code" : doc.code ,
     	"name" : doc.replicon.name ,
-    	"T3SS_family" : doc.T3SS_family,
+    	"predicted_system" : doc.predicted_system,
     	"taxid" : doc.replicon.taxid,
+    	"ncbi_id": doc.replicon.ncbi_id,
     	"strain" : doc.replicon.strain ,
-    	"taxonomy" : doc.replicon.taxonomy.join( ", ") ,
+    	"taxonomy" : doc.replicon.taxonomy.join(", ") ,
     	"type" : doc.replicon.type
     });
   }
\ No newline at end of file
diff --git a/src/couchapp/txssdb/views/by_replicon_taxid/map.js b/src/couchapp/txssdb/views/by_replicon_taxid/map.js
index 254578b..439787a 100644
--- a/src/couchapp/txssdb/views/by_replicon_taxid/map.js
+++ b/src/couchapp/txssdb/views/by_replicon_taxid/map.js
@@ -3,10 +3,11 @@ function(doc) {
     	"id" : doc._id,
     	"code" : doc.code ,
     	"name" : doc.replicon.name ,
-    	"T3SS_family" : doc.T3SS_family,
+    	"predicted_system" : doc.predicted_system,
     	"taxid" : doc.replicon.taxid,
+    	"ncbi_id": doc.replicon.ncbi_id,
     	"strain" : doc.replicon.strain ,
-    	"taxonomy" : doc.replicon.taxonomy.join( ", ") ,
+    	"taxonomy" : doc.replicon.taxonomy.join(", ") ,
     	"type" : doc.replicon.type
     });
   }
\ No newline at end of file
diff --git a/src/couchapp/txssdb/views/by_replicon_taxonomy/map.js b/src/couchapp/txssdb/views/by_replicon_taxonomy/map.js
index f22363c..f7d026d 100644
--- a/src/couchapp/txssdb/views/by_replicon_taxonomy/map.js
+++ b/src/couchapp/txssdb/views/by_replicon_taxonomy/map.js
@@ -1,12 +1,13 @@
 function(doc) {
 	taxonomy =  doc.replicon.taxonomy;
-	for( var j=0; j< taxonomy.length ; j++ ){
+	for(var j = 0; j < taxonomy.length; j++){
 		emit(taxonomy[j], {
 	    	"id" : doc._id,
 	    	"code" : doc.code ,
 	    	"name" : doc.replicon.name ,
-	    	"T3SS_family" : doc.T3SS_family,
+	    	"predicted_system" : doc.predicted_system,
 	    	"taxid" : doc.replicon.taxid,
+	    	"ncbi_id": doc.replicon.ncbi_id,
 	    	"strain" : doc.replicon.strain ,
 	    	"taxonomy" : doc.replicon.taxonomy.join( ", ") ,
 	    	"type" : doc.replicon.type
diff --git a/src/couchapp/txssdb/views/predicted_system/map.js b/src/couchapp/txssdb/views/predicted_system/map.js
index f8532a0..4363c9a 100644
--- a/src/couchapp/txssdb/views/predicted_system/map.js
+++ b/src/couchapp/txssdb/views/predicted_system/map.js
@@ -1,3 +1,3 @@
 function(doc) {
-	emit(doc.T3SS_family , 1);
+	emit(doc.predicted_system, 1);
 }
\ No newline at end of file
-- 
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