Merge pull request #486 from jjgao/master

release v0.1.1
cBioPortal · Nov 17, 2015 · e9a6aa5 · e9a6aa5
2 parents 8b1001e + 87f2afe
commit e9a6aa5
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Showing 47 changed files with 1,029 additions and 442 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 nb-configuration.xml
+nbactions-private.xml
 oncotator/src/main/resources/db.properties
 portal/Portal-Google-Code.ipr
 portal/Portal-Google-Code.iws

diff --git a/business/pom.xml b/business/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>0.1.0-SNAPSHOT</version>
+    <version>0.1.1</version>
   </parent>
 
   <!-- module metadata -->

diff --git a/core/pom.xml b/core/pom.xml
@@ -1,13 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
   <!-- module meta data -->
   <parent>
 	<artifactId>master</artifactId>
 	<groupId>org.mskcc.cbio</groupId>
-	<version>0.1.0-SNAPSHOT</version>
+	<version>0.1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>

diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java
@@ -40,7 +40,6 @@
 import java.sql.*;
 import java.util.*;
 import java.text.*;
-import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * Analogous to and replaces the old DaoCancerType. A CancerStudy has a NAME and
@@ -59,24 +58,31 @@ public static enum Status
 
     private DaoCancerStudy() {}
 
-    private static final Map<String, java.util.Date> cacheDateByStableId = new ConcurrentHashMap<String, java.util.Date>();
-    private static final Map<Integer, java.util.Date> cacheDateByInternalId = new ConcurrentHashMap<Integer, java.util.Date>();
-    private static final Map<String,CancerStudy> byStableId = new ConcurrentHashMap<String,CancerStudy>();
-    private static final Map<Integer,CancerStudy> byInternalId = new ConcurrentHashMap<Integer,CancerStudy>();
+    private static final Map<String, java.util.Date> cacheDateByStableId = new HashMap<String, java.util.Date>();
+    private static final Map<Integer, java.util.Date> cacheDateByInternalId = new HashMap<Integer, java.util.Date>();
+    private static final Map<String,CancerStudy> byStableId = new HashMap<String,CancerStudy>();
+    private static final Map<Integer,CancerStudy> byInternalId = new HashMap<Integer,CancerStudy>();
+    private static long lastCached = Long.MIN_VALUE;
 
     static {
         SpringUtil.initDataSource();
-        reCache();
+        reCacheAll(System.currentTimeMillis());
     }
 
-	public static void reCacheAll()
-	{
-		reCache();
-		DaoGeneticProfile.reCache();
-		DaoPatient.reCache();
-		DaoSample.reCache();
-		DaoClinicalData.reCache();
-	}
+    private static synchronized void reCacheAll(long time) {
+        if (lastCached >= time) {
+            return;
+        }
+
+        System.out.println("Recaching... ");
+        DaoCancerStudy.reCache();
+        DaoGeneticProfile.reCache();
+        DaoPatient.reCache();
+        DaoSample.reCache();
+        DaoClinicalData.reCache();
+        System.out.println("Finished recaching... ");
+        lastCached = System.currentTimeMillis();
+    }
 
     private static synchronized void reCache() {
         cacheDateByStableId.clear();
@@ -356,8 +362,10 @@ public static void addCancerStudy(CancerStudy cancerStudy, boolean overwrite) th
      */
     public static CancerStudy getCancerStudyByInternalId(int internalId) throws DaoException
 	{
-		if (studyNeedsRecaching(null, internalId)) {
-			reCacheAll();
+		if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && studyNeedsRecaching(null, internalId)) {
+                    System.out.print("Study with internal ID of "+internalId+" updated.");
+                    reCacheAll(System.currentTimeMillis());
 		}
         return byInternalId.get(internalId);
     }
@@ -370,8 +378,10 @@ public static CancerStudy getCancerStudyByInternalId(int internalId) throws DaoE
      */
     public static CancerStudy getCancerStudyByStableId(String stableId) throws DaoException
 	{
-		if (studyNeedsRecaching(stableId)) {
-			reCacheAll();
+		if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && studyNeedsRecaching(stableId)) {
+                    System.out.print("Study "+stableId+" updated.");
+                    reCacheAll(System.currentTimeMillis());
 		}
         return byStableId.get(stableId);
     }
@@ -383,8 +393,10 @@ public static CancerStudy getCancerStudyByStableId(String stableId) throws DaoEx
      * @return true if the CancerStudy exists, otherwise false
      */
     public static boolean doesCancerStudyExistByStableId(String cancerStudyStableId) {
-        if (studyNeedsRecaching(cancerStudyStableId)) {
-            reCacheAll();
+        if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && studyNeedsRecaching(cancerStudyStableId)) {
+            System.out.print("Study "+cancerStudyStableId+" updated.");
+            reCacheAll(System.currentTimeMillis());
         }
         return byStableId.containsKey(cancerStudyStableId);
     }
@@ -397,8 +409,10 @@ public static boolean doesCancerStudyExistByStableId(String cancerStudyStableId)
      * @return true if the CancerStudy exists, otherwise false
      */
     public static boolean doesCancerStudyExistByInternalId(int internalCancerStudyId) {
-        if (studyNeedsRecaching(null, internalCancerStudyId)) {
-            reCacheAll();
+        if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && studyNeedsRecaching(null, internalCancerStudyId)) {
+            System.out.print("Study with internal ID of "+internalCancerStudyId+" updated.");
+            reCacheAll(System.currentTimeMillis());
         }
         return byInternalId.containsKey(internalCancerStudyId);
     }
@@ -409,8 +423,10 @@ public static boolean doesCancerStudyExistByInternalId(int internalCancerStudyId
      * @return ArrayList of all CancerStudy Objects.
      */
     public static ArrayList<CancerStudy> getAllCancerStudies() {
-        if (cacheOutOfSyncWithDb()) {
-            reCacheAll();
+        if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && cacheOutOfSyncWithDb()) {
+            System.out.print("cache out of sync updated.");
+            reCacheAll(System.currentTimeMillis());
         }
         return new ArrayList<CancerStudy>(byStableId.values());
     }
@@ -420,8 +436,10 @@ public static ArrayList<CancerStudy> getAllCancerStudies() {
      * @return number of cancer studies.
      */
     public static int getCount() {
-        if (cacheOutOfSyncWithDb()) {
-            reCacheAll();
+        if (GlobalProperties.getRecacheStudyAfterUpdate()
+                        && cacheOutOfSyncWithDb()) {
+            System.out.print("cache out of sync updated.");
+            reCacheAll(System.currentTimeMillis());
         }
         return byStableId.size();
     }
@@ -535,7 +553,10 @@ static void deleteCancerStudy(int internalCancerStudyId) throws DaoException {
         } finally {
             JdbcUtil.closeAll(DaoCancerStudy.class, con, pstmt, rs);
         }
-        reCacheAll();
+        System.out.print("delete a study "+internalCancerStudyId);
+        if (GlobalProperties.getRecacheStudyAfterUpdate()) {           
+            reCacheAll(System.currentTimeMillis());
+        }
     }
 
     /**
@@ -556,30 +577,29 @@ private static CancerStudy extractCancerStudy(ResultSet rs) throws SQLException
         return cancerStudy;
     }
 
-	private static boolean studyNeedsRecaching(String stableId, Integer ... internalId)
-	{
-        if (cacheOutOfSyncWithDb()) {
-            return true;
-        }
-		try {
-			java.util.Date importDate = null;
-			java.util.Date cacheDate = null;
-    		if (internalId.length > 0) {
-				importDate = getImportDate(null, internalId[0]);
-				cacheDate = cacheDateByInternalId.get(internalId[0]);
-			}
-			else {
-				if (stableId.equals(org.mskcc.cbio.portal.util.AccessControl.ALL_CANCER_STUDIES_ID)) {
-					return false;
-				}
-				importDate = getImportDate(stableId);
-				cacheDate = cacheDateByStableId.get(stableId);
-			}
-			return (importDate == null || cacheDate == null) ? true : cacheDate.before(importDate);
-		}
-		catch (ParseException e) {
-			return false;
-		}
+	private static boolean studyNeedsRecaching(String stableId, Integer ... internalId) {
+            if (cacheOutOfSyncWithDb()) {
+                return true;
+            }
+
+            try {
+                java.util.Date importDate = null;
+                java.util.Date cacheDate = null;
+                if (internalId.length > 0) {
+                    importDate = getImportDate(null, internalId[0]);
+                    cacheDate = cacheDateByInternalId.get(internalId[0]);
+                } else {
+                    if (stableId.equals(org.mskcc.cbio.portal.util.AccessControl.ALL_CANCER_STUDIES_ID)) {
+                        return false;
+                    }
+                    importDate = getImportDate(stableId);
+                    cacheDate = cacheDateByStableId.get(stableId);
+                }
+
+                return (importDate == null || cacheDate == null) ? false : cacheDate.before(importDate);
+            } catch (ParseException e) {
+                    return false;
+            }
         catch (DaoException e) {
             return false;
         }

diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoClinicalData.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoClinicalData.java
@@ -35,12 +35,10 @@
 import org.mskcc.cbio.portal.model.*;
 import org.mskcc.cbio.portal.util.InternalIdUtil;
 
-import org.apache.commons.logging.*;
 import org.apache.commons.lang.StringUtils;
 
 import java.sql.*;
 import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * Data Access Object for `clinical` table
@@ -55,15 +53,11 @@ public final class DaoClinicalData {
     private static final String SAMPLE_INSERT = "INSERT INTO " + SAMPLE_TABLE + "(`INTERAL_ID`,`ATTR_ID`,`ATTR_VALUE` VALUES(?,?,?)";
     private static final String PATIENT_INSERT = "INSERT INTO " + PATIENT_TABLE + "(`INTERNAL_ID`,`ATTR_ID`,`ATTR_VALUE` VALUES(?,?,?)";
 
-    private static final Map<String, String> sampleAttributes = new ConcurrentHashMap<String, String>();
-    private static final Map<String, String> patientAttributes = new ConcurrentHashMap<String, String>();
+    private static final Map<String, String> sampleAttributes = new HashMap<String, String>();
+    private static final Map<String, String> patientAttributes = new HashMap<String, String>();
 
     private DaoClinicalData() {}
 
-    static {
-        reCache();
-    }
-
     public static synchronized void reCache()
     {
         clearCache();

diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfile.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfile.java
@@ -36,7 +36,6 @@
 
 import java.sql.*;
 import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * Analogous to and replaces the old DaoCancerType. A CancerStudy has a NAME and
@@ -48,14 +47,10 @@
 public final class DaoGeneticProfile {
     private DaoGeneticProfile() {}
 
-    private static final Map<String,GeneticProfile> byStableId = new ConcurrentHashMap<String,GeneticProfile>();
-    private static final Map<Integer,GeneticProfile> byInternalId = new ConcurrentHashMap<Integer,GeneticProfile>();
-    private static final Map<Integer,List<GeneticProfile>> byStudy = new ConcurrentHashMap<Integer,List<GeneticProfile>>();
-
-    static {
-        reCache();
-    }
-
+    private static final Map<String,GeneticProfile> byStableId = new HashMap<String,GeneticProfile>();
+    private static final Map<Integer,GeneticProfile> byInternalId = new HashMap<Integer,GeneticProfile>();
+    private static final Map<Integer,List<GeneticProfile>> byStudy = new HashMap<Integer,List<GeneticProfile>>();
+
     public static synchronized void reCache() {
         byStableId.clear();
         byInternalId.clear();

diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoPatient.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoPatient.java
@@ -38,7 +38,6 @@
 
 import java.sql.*;
 import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * DAO to `patient`.
@@ -47,14 +46,10 @@
  */
 public class DaoPatient {
 
-    private static final Map<Integer, Patient> byInternalId = new ConcurrentHashMap<Integer, Patient>();
-    private static final Map<Integer, Set<Patient>> byInternalCancerStudyId = new ConcurrentHashMap<Integer, Set<Patient>>();
+    private static final Map<Integer, Patient> byInternalId = new HashMap<Integer, Patient>();
+    private static final Map<Integer, Set<Patient>> byInternalCancerStudyId = new HashMap<Integer, Set<Patient>>();
     private static final MultiKeyMap byCancerIdAndStablePatientId = new MultiKeyMap();
 
-    static {
-        reCache();
-    }
-
     private static void clearCache()
     {
         byInternalId.clear();

diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoSample.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoSample.java
@@ -38,7 +38,6 @@
 
 import java.sql.*;
 import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
 
 /**
  * DAO to `sample`.
@@ -49,15 +48,11 @@ public class DaoSample {
 
     private static final int MISSING_CANCER_STUDY_ID = -1;
 
-    private static final Map<String, Sample> byStableId = new ConcurrentHashMap<String, Sample>();
-    private static final Map<Integer, Sample> byInternalId = new ConcurrentHashMap<Integer, Sample>();
+    private static final Map<String, Sample> byStableId = new HashMap<String, Sample>();
+    private static final Map<Integer, Sample> byInternalId = new HashMap<Integer, Sample>();
     private static final Map<Integer, Map<String, Sample>> byInternalPatientAndStableSampleId = new HashMap<Integer, Map<String, Sample>>();
     private static final Map<Integer, Map<String, Sample>> byCancerStudyIdAndStableSampleId = new HashMap<Integer, Map<String, Sample>>();
 
-    static {
-        reCache();
-    }
-
     private static void clearCache()
     {
         byStableId.clear();
@@ -204,6 +199,7 @@ public static Sample getSampleByCancerStudyAndSampleId(int cancerStudyId, String
     {
         Map<String, Sample> samples = byCancerStudyIdAndStableSampleId.get(cancerStudyId);
         if (samples==null) {
+            System.err.println("Couldn't find sample "+stableSampleId+" in study "+cancerStudyId);
             return null;
         }