From ddc2775ee3c0dd59c2a12f15ff22ca173c34cdc4 Mon Sep 17 00:00:00 2001
From: Robert Tisma <942951+rtisma@users.noreply.github.com>
Date: Tue, 14 Jan 2020 15:50:36 -0500
Subject: [PATCH 1/3] Merge back from master @ 3.0.0-SNAPSHOT
---
pom.xml | 2 +-
score-client/pom.xml | 2 +-
score-core/pom.xml | 2 +-
score-fs/pom.xml | 2 +-
score-server/pom.xml | 2 +-
score-test/pom.xml | 2 +-
6 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/pom.xml b/pom.xml
index 15c17f3c..e0bccbce 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
pom
${project.artifactId}
diff --git a/score-client/pom.xml b/score-client/pom.xml
index 549c6981..10f64667 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
../pom.xml
diff --git a/score-core/pom.xml b/score-core/pom.xml
index 9e778509..ea5cd62b 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
../pom.xml
diff --git a/score-fs/pom.xml b/score-fs/pom.xml
index b0ce7722..db79de92 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
../pom.xml
diff --git a/score-server/pom.xml b/score-server/pom.xml
index 25054d30..9945bb5f 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
../pom.xml
diff --git a/score-test/pom.xml b/score-test/pom.xml
index d81a3fa1..0a9d43c2 100644
--- 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
bio.overture
score
- 3.0.0
+ 3.0.0-SNAPSHOT
../pom.xml
From 6ca0077066e043969f747b4739860919c1a004fe Mon Sep 17 00:00:00 2001
From: khartmann
Date: Tue, 14 Jan 2020 18:48:42 -0500
Subject: [PATCH 2/3] Bugfix: Can't stream a ArrayNode object
---
.../metadata/legacy/LegacyMetadataClient.java | 43 +++++++++----------
1 file changed, 21 insertions(+), 22 deletions(-)
diff --git a/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataClient.java b/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataClient.java
index 2ef031b6..eb6d370a 100644
--- a/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataClient.java
+++ b/score-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 .
- *
- * 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 .
+ *
+ * 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 readAll(@NonNull String path) {
- val results = Lists. newArrayList();
+ val results = Lists.newArrayList();
boolean last = false;
int pageNumber = 0;
@@ -114,7 +112,8 @@ private List readAll(@NonNull String path) {
val result = MAPPER.readValue(url, ObjectNode.class);
last = result.path("last").asBoolean();
- List page = MAPPER.convertValue(result.path("content"), new TypeReference>() {});
+ List page = MAPPER.convertValue(result.path("content"), new TypeReference>() {
+ });
results.addAll(page);
pageNumber++;
@@ -134,7 +133,7 @@ public List 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).
From 540a3d54a1b23b1f482cfa2dc5db5b50395eff7b Mon Sep 17 00:00:00 2001
From: Robert Tisma <942951+rtisma@users.noreply.github.com>
Date: Wed, 15 Jan 2020 10:40:05 -0500
Subject: [PATCH 3/3] Release Candidate 3.0.1
---
pom.xml | 2 +-
score-client/pom.xml | 2 +-
score-core/pom.xml | 2 +-
score-fs/pom.xml | 2 +-
score-server/pom.xml | 2 +-
score-test/pom.xml | 2 +-
6 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/pom.xml b/pom.xml
index e0bccbce..86c2e16f 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
pom
${project.artifactId}
diff --git a/score-client/pom.xml b/score-client/pom.xml
index 10f64667..a14d2774 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
../pom.xml
diff --git a/score-core/pom.xml b/score-core/pom.xml
index ea5cd62b..c3e71f55 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
../pom.xml
diff --git a/score-fs/pom.xml b/score-fs/pom.xml
index db79de92..3748c2c9 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
../pom.xml
diff --git a/score-server/pom.xml b/score-server/pom.xml
index 9945bb5f..953c84b8 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
../pom.xml
diff --git a/score-test/pom.xml b/score-test/pom.xml
index 0a9d43c2..dd50d143 100644
--- 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
bio.overture
score
- 3.0.0-SNAPSHOT
+ 3.0.1
../pom.xml