add enclosed by to pgx ontoloy map load command

Author: boycer

linkedSPLs/LinkedSPLs-update/README

@@ -1,6 +1,11 @@
 CODE TO GENERATE THE SQL AND LINKED-DATA VERSION OF LINKEDSPLS
 Authors: Richard Boyce, Greg Gardner, Yifan Ning
-Date: 09/25/2015
+
+Last updated Date: 09/25/2015
+
+problematic labels:
+spls/e8ae0b66-25de-41b1-8013-7f414bbb7568.xml
+
 
 ################################################################################
 OVERVIEW
@@ -37,8 +42,12 @@ Update all linkedSPLs mappings by command below
 $ ant linkedSPLs-update
 
 Update piece by piece (recommended)
-$ ant loadDailymedSPLsToRDB
-$ ant load-loincSection
+create schema linkedSPLs
+modify db connection information in db-connection.properties (if creating linkedSPLs)
+$ ant unzip-spls (if creating linkedSPLs)
+$ ant createTableSchema (if creating linkedSPLs)
+$ ant load-loincSection (if creating linkedSPLs)
+$ ant loadDailymedSPLsToRDB (ensure tables are truncated)
 
 $ ant load-FDAPreferredSubstanceToUNII          
 $ ant load-FDA_UNII_to_ChEBI         
@@ -61,12 +70,17 @@ $ ant load-OMOPId-RXCUIs-from-OHDSI
 
 
 
-
-
 ################################################################################
 PRE-REQUISITES (Download all source data before run any ant command)
 ################################################################################
 
+Install python libs if deploy linkedSPLs on new environment
+
+apt-get install libxml2-dev libxslt1-dev python-dev
+apt-get install python-lxml
+apt-get install python-feedparser
+
+
 Download and organize all source data files in data folder
 
 --------------------------------------------------------

linkedSPLs/LinkedSPLs-update/build.xml

@@ -171,7 +171,7 @@
 
   <target name ="check-mapping-sources">
 
-    <property name="datasource" value="${FDA_UNII_NAMES},${FDA_UNII_RECORDS},${DRUGBANK_XML},${PG_CLASS_INDEXING_SPLS},${RXNORM_SETID},${RXNCONSO_RRF},${RXNORM_FULL_SCHEMA},${DRON_RXCUI_INGREDIENT},${DRON_RXNORM_DRUG},${ERROR_LOG}"/>
+    <property name="datasource" value="${FDA_UNII_NAMES},${FDA_UNII_RECORDS},${DRUGBANK_XML},${PG_CLASS_INDEXING_SPLS},${RXNORM_SETID},${RXNCONSO_RRF},${RXNORM_FULL_SCHEMA},${DRON_RXCUI_INGREDIENT},${DRON_RXCUI_INGREDIENT},${DRON_RXCUI_DRUG},${ERROR_LOG}"/>
     <filelist id="data.sources" dir="." files="${datasource}" />
 
     <restrict id="missing.files">
@@ -232,10 +232,10 @@
     <!-- <antcall target="load-FDAPharmgxTable" /> -->
     <!-- <antcall target="load-FDAPharmgxTableToOntologyMap"  /> -->
 
-    <!-- <antcall target="load-DrOn_RXCUI_DRUG" />  -->
-    <!-- <antcall target="load-DrOn_RXCUI_INGREDIENT" />  -->
+    <!-- <antcall target="load-DrOn_RXCUI_DRUG" /> -->
+    <!-- <antcall target="load-DrOn_RXCUI_INGREDIENT" /> -->
 
-    <!-- <antcall target="load-OMOPId-RXCUIs-from-OHDSI" />  -->
+    <!-- <antcall target="load-OMOPId-RXCUIs-from-OHDSI" /> -->
 
     <antcall target="set.timestamp">
       <param name="message" value="updated all mappings in ${mysql-schema}" />
@@ -327,13 +327,13 @@
     </java>
 
     <!-- old apporach that query bioportal -->
-    <exec executable="python" failonerror="true">
-      <arg line="${PT-UNII-ChEBI-mapping}/getChebiMappingsFromJSON.py data/FDA/FDAPreferredSubstanceToUNII.txt" />
-      <redirector append="true">
-        <outputmapper type="merge" to="${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt"/>
-        <errormapper type="merge" to="${ERROR_LOG}"/>
-      </redirector>
-    </exec>
+    <!-- <exec executable="python" failonerror="true"> -->
+    <!--   <arg line="${PT-UNII-ChEBI-mapping}/getChebiMappingsFromJSON.py data/FDA/FDAPreferredSubstanceToUNII.txt" /> -->
+    <!--   <redirector append="true"> -->
+    <!--     <outputmapper type="merge" to="${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt"/> -->
+    <!--     <errormapper type="merge" to="${ERROR_LOG}"/> -->
+    <!--   </redirector> -->
+    <!-- </exec> -->
 
     <antcall target="set.timestamp">
       <param name="message" value="mappings of FDA preferred term and ChEBI is created at ${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt" />
@@ -868,7 +868,7 @@
    </classpath>
       <transaction>
 	truncate FDAPharmgxTableToOntologyMap;
-	LOAD DATA LOCAL INFILE "${BIOMARKER}" INTO TABLE FDAPharmgxTableToOntologyMap FIELDS TERMINATED BY ',' LINES TERMINATED BY '\n' IGNORE 1 LINES(FDAReferencedSubgroup,HGNCGeneSymbol,Synonymns,AlleleVariant,Pharmgkb,URI,Ontology,CuratorComments);
+	LOAD DATA LOCAL INFILE "${BIOMARKER}" INTO TABLE FDAPharmgxTableToOntologyMap FIELDS TERMINATED BY ',' ENCLOSED BY '"' LINES TERMINATED BY '\n' IGNORE 1 LINES(FDAReferencedSubgroup,HGNCGeneSymbol,Synonymns,AlleleVariant,Pharmgkb,URI,Ontology,CuratorComments);
       </transaction>
     </sql>