PT-497: Add the possibility to reindex OMIM from the administration

Store the current version
phenotips · Oct 6, 2015 · a60856e · a60856e
1 parent 88cb93d
commit a60856e
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Showing 3 changed files with 36 additions and 0 deletions.
diff --git a/...m/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java b/...m/api/src/main/java/org/phenotips/vocabulary/internal/solr/MendelianInheritanceInMan.java
@@ -37,9 +37,13 @@
 import javax.inject.Singleton;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
+import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.client.solrj.util.ClientUtils;
 import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.SolrDocumentList;
+import org.apache.solr.common.SolrException;
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.common.params.CommonParams;
 import org.apache.solr.common.params.DisMaxParams;
@@ -158,6 +162,26 @@ private SolrParams produceDynamicSolrParams(String originalQuery, Integer rows,
         return params;
     }
 
+    @Override
+    public String getVersion()
+    {
+        SolrQuery query = new SolrQuery();
+        query.setQuery("version:*");
+        query.set(CommonParams.ROWS, "1");
+        try {
+            QueryResponse response = this.externalServicesAccess.getSolrConnection().query(query);
+            SolrDocumentList termList = response.getResults();
+            if (!termList.isEmpty()) {
+                return termList.get(0).getFieldValue("version").toString();
+            }
+        } catch (SolrServerException | SolrException ex) {
+            this.logger.warn("Failed to query vocabulary version: {}", ex.getMessage());
+        } catch (IOException ex) {
+            this.logger.error("IOException while getting vocabulary version", ex);
+        }
+        return null;
+    }
+
     @Override
     public synchronized int reindex(String sourceURL)
     {

diff --git a/...aries/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java b/...aries/omim/api/src/main/java/org/phenotips/vocabulary/internal/solr/OmimSourceParser.java
@@ -36,6 +36,8 @@
 import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.solr.common.SolrInputDocument;
+import org.joda.time.DateTime;
+import org.joda.time.format.ISODateTimeFormat;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -123,6 +125,7 @@ public OmimSourceParser(Vocabulary hpo, String sourceURL)
             loadSymptoms(true);
             loadSymptoms(false);
             loadGeneReviews();
+            loadVersion();
         } catch (NullPointerException | CompressorException | IOException ex) {
             this.logger.error("Failed to prepare the OMIM index: {}", ex.getMessage(), ex);
         }
@@ -282,4 +285,12 @@ private void loadGeneReviews()
             this.logger.error("Failed to load OMIM-GeneReviews links: {}", ex.getMessage(), ex);
         }
     }
+
+    private void loadVersion()
+    {
+        SolrInputDocument metaTerm = new SolrInputDocument();
+        metaTerm.addField(ID_FIELD, "HEADER_INFO");
+        metaTerm.addField("version", ISODateTimeFormat.dateTime().withZoneUTC().print(new DateTime()));
+        this.data.put("VERSION", metaTerm);
+    }
 }
diff --git a/resources/solr-configuration/src/main/resources/omim/conf/schema.xml b/resources/solr-configuration/src/main/resources/omim/conf/schema.xml
@@ -115,6 +115,7 @@
   </types>
 
   <fields>
+    <field name="version" type="string" indexed="true" stored="true" omitNorms="true"/>
     <field name="id" type="string" indexed="true" stored="true" required="true" />
     <field name="name" type="text_general" indexed="true" stored="true"/>
     <field name="nameSpell" type="text_spell" indexed="true" stored="false"/>