cleanup unused jars and seqr index

.gitignore

@@ -1,3 +1,4 @@
+/dependency-reduced-pom.xml
 ### JetBrains template
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion
 

.travis.yml

@@ -1,12 +1,12 @@
 language: java
 jdk: oraclejdk8
 before_install:  
-  - "export JAVA_OPTS=-Xmx4G"
-  - "export MAVEN_OPTS=-Xmx4G"
-  
+  - "export JAVA_OPTS=-Xmx2G"
+  - "export MAVEN_OPTS=-Xmx2G"
+
 #install: 
-#  - mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
-#  - sudo pip install robotframework
+#  - travis_wait mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
+#  - travis_wait sudo pip install robotframework
 #script:
 #   - mvn test -B
 #   - pybot scripts/*.robot   

pom.xml

@@ -2,10 +2,6 @@
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> 
  <build>
   <plugins>
-
-
-
-
       <plugin>
           <groupId>org.robotframework</groupId>
           <artifactId>robotframework-maven-plugin</artifactId>
@@ -113,6 +109,11 @@
             <artifactId>junit</artifactId>
             <version>4.12</version>
         </dependency>
+        <dependency>
+            <groupId>net.jcip</groupId>
+            <artifactId>jcip-annotations</artifactId>
+            <version>1.0</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-test-framework</artifactId>

src/test/java/gov/nih/nlm/ncbi/seqr/SeqrArgsTest.java

@@ -0,0 +1,93 @@
+package gov.nih.nlm.ncbi.seqr;
+
+import gov.nih.nlm.ncbi.seqr.solr.FastaStreamParser;
+import gov.nih.nlm.ncbi.seqr.solr.LoadLargeFile2SolrServer;
+import gov.nih.nlm.ncbi.seqr.solr.SeqrController;
+import junit.framework.TestCase;
+import org.apache.solr.client.solrj.SolrServerException;
+import org.apache.solr.client.solrj.embedded.EmbeddedSolrServer;
+import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.SolrDocumentList;
+import org.apache.solr.core.CoreContainer;
+
+import java.io.File;
+
+//import org.codehaus.jackson.JsonNode;
+
+
+import org.junit.*;
+
+import java.io.IOException;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
+@net.jcip.annotations.NotThreadSafe
+public class SeqrArgsTest extends TestCase {
+    private static SeqrController control;
+    static EmbeddedSolrServer solrServer;
+    static CoreContainer container;
+
+    Lock sequential = new ReentrantLock();
+
+    protected void setUp() throws Exception {
+        super.setUp();
+        sequential.lock();
+    }
+
+    protected void tearDown() throws Exception {
+        super.tearDown();
+        sequential.unlock();
+
+    }
+
+    private static void setUpController() throws SolrServerException, InterruptedException, IOException {
+        String solrString = "testdata/solr";
+        container = new CoreContainer(solrString);
+        container.load();
+        solrServer = new EmbeddedSolrServer(container, "sequence");
+        control = new SeqrController(solrServer);
+    }
+
+    public static void tearDownController() {
+        solrServer.shutdown();
+        container.shutdown();
+    }
+
+    public static void ClearData() throws SolrServerException, InterruptedException, IOException {
+        solrServer.deleteByQuery("*:*");
+    }
+
+    public static void loadSampleData() throws SolrServerException, InterruptedException, IOException {
+        ClearData();
+        control.loadJSONDir("testdata/data");
+    }
+
+    @Test
+    public void testFastaIndexingIntegration() throws SolrServerException, InterruptedException, IOException {
+        // verify this is not yet in solr
+        setUpController();
+        ClearData();
+        String seq = "MIKLFCVLAAFISINSACQSSHQQREEFTVATYHSSSICTTYCYSNCVVASQHKGLNVES" +
+                "YTCDKPDPYGRETVCKCTLIKCHDI";
+        SolrDocumentList results = control.search(seq);
+        Assert.assertEquals(0, results.size());
+        tearDownController();
+
+        //and we now index the fasta
+
+        String[] args = {"index", "testdata/data/short.fasta", "--db", "testdata/solr/", "--input_format", "fasta"};
+        Seqr.main(args);
+
+        //the record should be in solr
+        setUpController();
+        results = control.search(seq);
+        Assert.assertEquals(1, results.size());
+        tearDownController();
+    }
+
+    @Test
+    public void testArgParser() {
+        String[] args = {"search", "testdata/data/test.fasta", "--db", "testdata/solr/"};
+        Seqr.main(args);
+    }
+}

src/test/java/gov/nih/nlm/ncbi/seqr/TestMain.java → src/test/java/gov/nih/nlm/ncbi/seqr/SeqrTest.java

@@ -1,51 +1,61 @@
 package gov.nih.nlm.ncbi.seqr;
 
 import gov.nih.nlm.ncbi.seqr.solr.FastaStreamParser;
-import gov.nih.nlm.ncbi.seqr.solr.LoadLargeFile2SolrServer;
 import gov.nih.nlm.ncbi.seqr.solr.SeqrController;
+import junit.framework.TestCase;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.embedded.EmbeddedSolrServer;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.core.CoreContainer;
-import java.io.File;
-
-//import org.codehaus.jackson.JsonNode;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
-import org.junit.*;
+/**
+ * Created by hanl on 9/23/15.
+ */
+@net.jcip.annotations.NotThreadSafe
+public class SeqrTest extends TestCase {
 
-import java.io.IOException;
 
-public class TestMain {
     private static SeqrController control;
     static EmbeddedSolrServer solrServer;
     static CoreContainer container ;
 
-    private static void setUpController() {
+    Lock sequential = new ReentrantLock();
+
+
+    public void setUp() throws Exception {
+        super.setUp();
+        sequential.lock();
         String solrString = "testdata/solr";
         container = new CoreContainer(solrString);
         container.load();
         solrServer = new EmbeddedSolrServer(container, "sequence");
         control = new SeqrController(solrServer);
+        solrServer.deleteByQuery("*:*");
+        control.loadJSONDir("testdata/data");
+
+    }
+
+    public void tearDown() throws Exception {
+        this.tearDownController();
+        sequential.unlock();
+        //LoadLargeFile2SolrServer server = new LoadLargeFile2SolrServer(solrServer);
+        //server.loadFastaFile(new File("testdata/data/short.fasta"));
     }
 
-//    @AfterClass
-//    public static void afterEverything() throws SolrServerException, InterruptedException, IOException {
-//        setUpController();
-//        solrServer.deleteByQuery("*:*");
-//        tearDownController();
-//    }
 
     @BeforeClass
     public static void beforeEverything() throws SolrServerException, InterruptedException, IOException {
-        setUpController();
-        solrServer.deleteByQuery("*:*");
-        control.loadJSONDir("testdata/data");
+        //setUpController();
         tearDownController();
-//        LoadLargeFile2SolrServer server = new LoadLargeFile2SolrServer(solrServer);
-//        server.loadFastaFile(new File("testdata/data/short.fasta"));
-
     }
     public static void tearDownController() {
         solrServer.shutdown();
@@ -60,27 +70,11 @@ public static void tearDownController() {
 //        tearDownController();
 //    }
 
-    @Test
-    public void testFastaIndexingIntegration() throws SolrServerException {
-        // check that it's not already in solr
-        setUpController();
-        String seq = "MIKLFCVLAAFISINSACQSSHQQREEFTVATYHSSSICTTYCYSNCVVASQHKGLNVES" +
-                "YTCDKPDPYGRETVCKCTLIKCHDI";
-        SolrDocumentList results = control.search(seq);
-        Assert.assertEquals(0, results.size());
-        tearDownController();
 
-        String[] args = {"index",  "testdata/data/short.fasta", "--db", "testdata/solr/", "--input_format", "fasta"};
-        Seqr.main(args);
-        setUpController();
-        results = control.search(seq);
-        Assert.assertEquals(1, results.size());
-        tearDownController();
-    }
 
     @Test
     public void testAbSolrSimple() throws Exception {
-        setUpController();
+
         //String seq = "MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWKFTPL";
         //String seq = "MSFKVYDPIAELIATQFPTSNPDLQIINNDVLVVSPHKITLPMGPQNAGDVTNKAYVDQAVMSAAVPVASSTTVGTIQMAGDLEGSSGTNPIIAANKITLNKLQKIGPKMVIGNPNSDWNNTQEIELDSSFRIVDNRLNAGIVPISSTDPNKSNTVIPAPQQNGLFYLDSSGRVWVWAEHYYKCITPSRYISKWMGVGDFQELTVGQSVMWDSGRPSIETVSTQGLEVEWISSTNFTLSSLYLIPIVVKVTICIPLLGQPDQMAKFVLYSVSSAQQPRTGIVLTTDSSRSSAPIVSEYITVNWFEPKSYSVQLKEVNSDSGTTVTICSDKWLANPFLDCWITIEEVG";
         String seq = "MNTLYLGSNSPRRMEILTQLGYRVIQLPAGIDESVKAGETPFAYVQRMAEEKNRTALTLFCETNGTMPDFPLITADTCVVSDGIILGKPRSQAEAIEFLNRLSGKQHTVLTAVCIHYRGKTSSRVQTNRVVFKPLSSEEISAYVQSGEPMDKAGAYAVQGIGGIFIQSIEGSFSGIMGLPVYETVSMLQDLGYRSPLSALKP";
@@ -90,22 +84,13 @@ public void testAbSolrSimple() throws Exception {
             System.out.println(document);
         }
         Assert.assertEquals(1, results.size());
-        tearDownController();
     }
 
-
-    @Test
-    public void testArgParse() {
-        String[] args = {"search",  "testdata/data/test.fasta", "--db", "testdata/solr/"};
-        Seqr.main(args);
-        }
-
     @Test
     //TODO: check this works with an assertion
     public void testFastaToJsonFileConversion() throws Exception {
         FastaStreamParser converter = new FastaStreamParser("testdata/data/short.fasta");
         converter.convertToJsonFile("testdata/data/short.json");
         new File("testdata/data/short.json").delete();
     }
-
-}
+}

testdata/solr/sequence/conf/solrconfig.xml

@@ -135,16 +135,15 @@
      <lst name="defaults">
       <bool name="terms">true</bool>
       <bool name="distrib">false</bool>
-    </lst>     R
+    </lst>
     <arr name="components">
       <str>terms</str>
     </arr>
   </requestHandler>
   <queryResponseWriter name="json" class="solr.JSONResponseWriter">
     <str name="content-type">text/plain; charset=UTF-8</str>
   </queryResponseWriter>
-	<queryResponseWriter name="xbin" class="org.apache.solr.export.BinaryExportWriter"/>
-  <queryResponseWriter name="xslt" class="solr.XSLTResponseWriter">
+    <queryResponseWriter name="xslt" class="solr.XSLTResponseWriter">
     <int name="xsltCacheLifetimeSeconds">5</int>
   </queryResponseWriter>
   <queryParser name="cutoff"  class="org.apache.lucene.analysis.tanimoto.tanimotoCutoffPostFilterPlugin" />

testdata/solr/sequence/conf/solrcore.properties

@@ -1,4 +1,4 @@
 POLL_TIME=00:00:60
 #master.core.url=127.0.0.1:8980/solr
 master.user=updater
-master.password=updater
+master.password=password of your choice