diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index ed802879..57445f9a 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -51,13 +51,18 @@ jobs:
path: opencga-enterprise
fetch-depth: "10"
- id: get_opencga_branch
- name: Get OpenCGA branch from 'pom.xml' property
+ name: Get OpenCGA branch
run: |
- pwd
- ls -lrtha
- ls -lrtha ./opencga-enterprise
- chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
- opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
+ # If the task exists in the opencga repository, this is the branch to be tested
+ if [[ "${{ inputs.task }}" == TASK* ]]; then
+ if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}" ] ; then
+ opencga_branch="${{ inputs.task }}";
+ return 0;
+ fi
+ else
+ chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
+ opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
+ fi
echo "opencga_branch=${opencga_branch}"
echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
- name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'
diff --git a/commons-datastore/commons-datastore-solr/src/main/java/org/opencb/commons/datastore/solr/SolrManager.java b/commons-datastore/commons-datastore-solr/src/main/java/org/opencb/commons/datastore/solr/SolrManager.java
index d6258f88..15f65bf0 100644
--- a/commons-datastore/commons-datastore-solr/src/main/java/org/opencb/commons/datastore/solr/SolrManager.java
+++ b/commons-datastore/commons-datastore-solr/src/main/java/org/opencb/commons/datastore/solr/SolrManager.java
@@ -23,7 +23,10 @@
import org.apache.solr.client.solrj.impl.CloudSolrClient;
import org.apache.solr.client.solrj.impl.HttpSolrClient;
import org.apache.solr.client.solrj.impl.LBHttpSolrClient;
-import org.apache.solr.client.solrj.request.*;
+import org.apache.solr.client.solrj.request.CollectionAdminRequest;
+import org.apache.solr.client.solrj.request.CoreAdminRequest;
+import org.apache.solr.client.solrj.request.CoreStatus;
+import org.apache.solr.client.solrj.request.SolrPing;
import org.apache.solr.client.solrj.response.SolrPingResponse;
import org.apache.solr.common.SolrException;
import org.slf4j.Logger;
@@ -31,14 +34,15 @@
import java.io.IOException;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
public class SolrManager {
- private String host;
- private String mode;
- private SolrClient solrClient;
+ private final List<String> hosts;
+ private final String mode;
+ private final SolrClient solrClient;
private final Logger logger = LoggerFactory.getLogger(SolrManager.class);
@@ -65,49 +69,14 @@ public SolrManager(String host, String mode, int timeout) {
* @param timeout Read timeout
*/
public SolrManager(List<String> hosts, String mode, int timeout) {
- hosts = hosts.stream().flatMap(s -> Arrays.stream(s.split(","))).collect(Collectors.toList());
-
- this.host = String.join(",", hosts);
+ this.hosts = hosts.stream().flatMap(s -> Arrays.stream(s.split(","))).collect(Collectors.toList());
this.mode = mode;
-
- if (hosts.get(0).startsWith("http")) {
- if (hosts.size() == 1) {
- // Single HTTP endpoint.
- this.solrClient = new HttpSolrClient.Builder(host).build();
- ((HttpSolrClient) this.solrClient).setRequestWriter(new BinaryRequestWriter());
- ((HttpSolrClient) this.solrClient).setSoTimeout(timeout);
- } else {
- // Use a LoadBalancer if there are multiple http hosts
- this.solrClient = new LBHttpSolrClient.Builder().withBaseSolrUrls(hosts.toArray(new String[0])).build();
-
- ((LBHttpSolrClient) this.solrClient).setRequestWriter(new BinaryRequestWriter());
- ((LBHttpSolrClient) this.solrClient).setSoTimeout(timeout);
- }
- } else {
- // If the provided hosts are not http, assume zookeeper hosts like HOST:PORT
- // This client will use Zookeeper to discover Solr endpoints for SolrCloud collections, and then use the
- // LBHttpSolrClient to issue requests.
- if (isCloud()) {
- this.solrClient = new CloudSolrClient.Builder().withZkHost(hosts).build();
-
- ((CloudSolrClient) this.solrClient).setRequestWriter(new BinaryRequestWriter());
- ((CloudSolrClient) this.solrClient).setSoTimeout(timeout);
- } else {
- throw new IllegalArgumentException("Can not initialize SolrManager from Zookeeper host not in Cloud mode");
- }
- }
+ this.solrClient = newSolrClient(timeout);
}
public SolrManager(SolrClient solrClient, String host, String mode) {
this.solrClient = solrClient;
- this.host = host;
- this.mode = mode;
- }
-
- @Deprecated
- public SolrManager(SolrClient solrClient, String host, String mode, int timeout) {
- this.solrClient = solrClient;
- this.host = host;
+ this.hosts = Collections.singletonList(host);
this.mode = mode;
}
@@ -188,7 +157,7 @@ public void create(String dbName, String configSet) throws SolrException {
*/
public void createCore(String coreName, String configSet) throws SolrException {
try {
- logger.debug("Creating core: host={}, core={}, configSet={}", host, coreName, configSet);
+ logger.debug("Creating core: host={}, core={}, configSet={}", StringUtils.join(",", hosts), coreName, configSet);
CoreAdminRequest.Create request = new CoreAdminRequest.Create();
request.setCoreName(coreName);
request.setConfigSet(configSet);
@@ -210,7 +179,7 @@ public void createCore(String coreName, String configSet) throws SolrException {
*/
public void createCollection(String collectionName, String configSet) throws SolrException {
logger.debug("Creating collection: host={}, collection={}, config={}, numShards={}, numReplicas={}",
- host, collectionName, configSet, 1, 1);
+ StringUtils.join(",", hosts), collectionName, configSet, 1, 1);
try {
CollectionAdminRequest request = CollectionAdminRequest.createCollection(collectionName, configSet, 1, 1);
request.process(solrClient);
@@ -353,11 +322,39 @@ public void close() throws IOException {
}
}
- private boolean isCloud() {
- if (StringUtils.isEmpty(mode)) {
- logger.warn("Solr 'mode' is empty, setting default 'cloud'");
- mode = "cloud";
+ public SolrClient newSolrClient(int timeout) {
+ final SolrClient solrClient;
+ if (hosts.get(0).startsWith("http")) {
+ if (hosts.size() == 1) {
+ // Single HTTP endpoint.
+ solrClient = new HttpSolrClient.Builder(hosts.get(0)).build();
+ ((HttpSolrClient) solrClient).setRequestWriter(new BinaryRequestWriter());
+ ((HttpSolrClient) solrClient).setSoTimeout(timeout);
+ } else {
+ // Use a LoadBalancer if there are multiple http hosts
+ solrClient = new LBHttpSolrClient.Builder().withBaseSolrUrls(hosts.toArray(new String[0])).build();
+
+ ((LBHttpSolrClient) solrClient).setRequestWriter(new BinaryRequestWriter());
+ ((LBHttpSolrClient) solrClient).setSoTimeout(timeout);
+ }
+ } else {
+ // If the provided hosts are not http, assume zookeeper hosts like HOST:PORT
+ // This client will use Zookeeper to discover Solr endpoints for SolrCloud collections, and then use the
+ // LBHttpSolrClient to issue requests.
+ if (isCloud()) {
+ solrClient = new CloudSolrClient.Builder().withZkHost(hosts).build();
+
+ ((CloudSolrClient) solrClient).setRequestWriter(new BinaryRequestWriter());
+ ((CloudSolrClient) solrClient).setSoTimeout(timeout);
+ } else {
+ throw new IllegalArgumentException("Can not initialize SolrManager from Zookeeper host not in Cloud mode");
+ }
}
+
+ return solrClient;
+ }
+
+ private boolean isCloud() {
switch (mode.toLowerCase()) {
case "collection":
case "cloud": {
@@ -376,37 +373,22 @@ private boolean isCloud() {
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("SolrManager{");
- sb.append("host='").append(host).append('\'');
+ sb.append("hosts='").append(hosts).append('\'');
sb.append(", mode='").append(mode).append('\'');
sb.append(", solrClient=").append(solrClient);
sb.append('}');
return sb.toString();
}
- public String getHost() {
- return host;
- }
-
- public SolrManager setHost(String host) {
- this.host = host;
- return this;
+ public List<String> getHosts() {
+ return hosts;
}
public String getMode() {
return mode;
}
- public SolrManager setMode(String mode) {
- this.mode = mode;
- return this;
- }
-
public SolrClient getSolrClient() {
return solrClient;
}
-
- public SolrManager setSolrClient(SolrClient solrClient) {
- this.solrClient = solrClient;
- return this;
- }
}