Merge pull request #225 from overture-stack/rc/3.0.1

Release Candidate 3.0.1
overture-stack · Jan 15, 2020 · a7cef70 · a7cef70
2 parents 942e0ba + 540a3d5
commit a7cef70
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Showing 7 changed files with 27 additions and 28 deletions.
diff --git a/pom.xml b/pom.xml
@@ -20,7 +20,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
 
   <groupId>bio.overture</groupId>
   <artifactId>score</artifactId>
-  <version>3.0.0</version>
+  <version>3.0.1</version>
   <packaging>pom</packaging>
 
   <name>${project.artifactId}</name>

diff --git a/score-client/pom.xml b/score-client/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/...-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataClient.java b/...-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataClient.java
@@ -1,18 +1,18 @@
 /*
- * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved.                             
- *                                                                                                               
+ * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved.
+ *
  * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
- * You should have received a copy of the GNU General Public License along with                                  
- * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
- *                                                                                                               
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
- * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
- * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
- * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
- * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 package bio.overture.score.client.metadata.legacy;
@@ -25,7 +25,6 @@
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.google.common.collect.Lists;
-import com.sun.xml.bind.v2.model.core.TypeRef;
 import lombok.Getter;
 import lombok.NonNull;
 import lombok.SneakyThrows;
@@ -39,13 +38,11 @@
 import java.io.FileNotFoundException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
 import java.util.List;
 import java.util.stream.Stream;
 
 import static java.util.stream.Collectors.joining;
-import static java.util.stream.Collectors.maxBy;
+import static java.util.stream.StreamSupport.stream;
 import static org.icgc.dcc.common.core.util.stream.Collectors.toImmutableList;
 
 /**
@@ -66,9 +63,10 @@ public class LegacyMetadataClient {
   @NonNull
   @Getter
   private final String serverUrl;
-
+  
   @Autowired
-  public LegacyMetadataClient(@Value("${metadata.url}") String serverUrl, @Value("${metadata.ssl.enabled}") boolean ssl) {
+  public LegacyMetadataClient(@Value("${metadata.url}") String serverUrl,
+    @Value("${metadata.ssl.enabled}") boolean ssl) {
     if (!ssl) {
       SSLCertificateValidation.disable();
     }
@@ -103,7 +101,7 @@ private Entity read(@NonNull String path) {
 
   @SneakyThrows
   private List<Entity> readAll(@NonNull String path) {
-    val results = Lists.<Entity> newArrayList();
+    val results = Lists.<Entity>newArrayList();
     boolean last = false;
     int pageNumber = 0;
 
@@ -114,7 +112,8 @@ private List<Entity> readAll(@NonNull String path) {
 
         val result = MAPPER.readValue(url, ObjectNode.class);
         last = result.path("last").asBoolean();
-        List<Entity> page = MAPPER.convertValue(result.path("content"), new TypeReference<ArrayList<Entity>>() {});
+        List<Entity> page = MAPPER.convertValue(result.path("content"), new TypeReference<ArrayList<Entity>>() {
+        });
 
         results.addAll(page);
         pageNumber++;
@@ -134,7 +133,7 @@ public List<String> getObjectIdsByAnalysisId(@NonNull String programId, @NonNull
 
     log.debug("Fetching analysis files from url '{}'", url);
 
-    return Stream.of(MAPPER.readValue(url, ArrayNode.class)).
+    return stream(MAPPER.readValue(url, ArrayNode.class).spliterator(), false).
       peek(r -> log.debug("Got result {}", r)).
       map(x -> x.path("objectId")).
       map(JsonNode::textValue).

diff --git a/score-core/pom.xml b/score-core/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-fs/pom.xml b/score-fs/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-server/pom.xml b/score-server/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-test/pom.xml b/score-test/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.1</version>
     <relativePath>../pom.xml</relativePath>
   </parent>