Merge pull request #312 from OHDSI/release-1.13.0

1.13.0 release
OHDSI · Aug 31, 2022 · 911c55b · 911c55b
2 parents 7e2f273 + 8ecc640
commit 911c55b
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Showing 28 changed files with 78 additions and 149 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>com.odysseusinc.athena</groupId>
     <artifactId>athena</artifactId>
-    <version>1.12.2</version>
+    <version>1.13.0</version>
     <packaging>jar</packaging>
 
 
@@ -21,19 +21,20 @@
         <java.version>1.8</java.version>
         <jjwt.version>0.9.1</jjwt.version>
         <opensaml.version>2.6.6-patched</opensaml.version>
-        <solr.version>7.7.1</solr.version>
-        <spring-security-pac4j.version>3.1.0</spring-security-pac4j.version>
-        <pac4j.version>2.3.1</pac4j.version>
+        <solr.version>8.11.2</solr.version>
+        <spring-security-pac4j.version>4.1.0</spring-security-pac4j.version>
+        <pac4j.version>3.3.0</pac4j.version>
         <opencsv.version>3.9</opencsv.version>
-        <javax.mail.version>1.4</javax.mail.version>
+        <jakarta.mail.version>1.6.7</jakarta.mail.version>
         <dockerImagePrefix>hub.odysseusinc.com</dockerImagePrefix>
-        <arachne.version>1.16.2</arachne.version>
+        <arachne.version>1.19.0</arachne.version>
         <disruptor.version>3.4.2</disruptor.version>
         <commons-lang3.version>3.11</commons-lang3.version>
         <build.number>${BUILD_NUMBER}</build.number>
         <build.id>${BUILD_TIMESTAMP}</build.id>
         <guava.verson>30.1-jre</guava.verson>
         <lombok.version>1.18.18</lombok.version>
+        <postgresql.version>42.2.26</postgresql.version>
     </properties>
 
     <profiles>
@@ -132,6 +133,7 @@
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
+            <version>${postgresql.version}</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.jtds</groupId>
@@ -187,9 +189,9 @@
         </dependency>
 
         <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>mail</artifactId>
-            <version>${javax.mail.version}</version>
+            <groupId>com.sun.mail</groupId>
+            <artifactId>jakarta.mail</artifactId>
+            <version>${jakarta.mail.version}</version>
         </dependency>
 
         <dependency>
@@ -216,6 +218,11 @@
             <artifactId>pac4j-jwt</artifactId>
             <version>${pac4j.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.pac4j</groupId>
+            <artifactId>pac4j-core</artifactId>
+            <version>${pac4j.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
             <artifactId>hamcrest-core</artifactId>
@@ -259,6 +266,11 @@
             <groupId>org.springframework.retry</groupId>
             <artifactId>spring-retry</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+            <version>4.4</version>
+        </dependency>
     </dependencies>
 
     <build>
@@ -327,43 +339,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>com.spotify</groupId>
-                <artifactId>docker-maven-plugin</artifactId>
-                <version>0.4.13</version>
-                <configuration>
-                    <imageName>${dockerImagePrefix}/${project.artifactId}</imageName>
-                    <imageTags>
-                        <imageTag>${project.version}</imageTag>
-                        <imageTag>latest</imageTag>
-                    </imageTags>
-                    <dockerDirectory>src/main/docker</dockerDirectory>
-                    <resources>
-                        <resource>
-                            <!--<targetPath>/</targetPath>-->
-                            <directory>${project.build.directory}</directory>
-                            <include>${project.build.finalName}.${project.packaging}</include>
-                        </resource>
-                    </resources>
-                    <serverId>arachne-hub</serverId>
-                    <registryUrl>https://hub.odysseusinc.com/v2/</registryUrl>
-                </configuration>
-                <executions>
-                    <execution>
-                        <phase>install</phase>
-                        <goals>
-                            <goal>build</goal>
-                        </goals>
-                    </execution>
-                    <execution>
-                        <id>deploy</id>
-                        <phase>deploy</phase>
-                        <goals>
-                            <goal>push</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>

diff --git a/properties/dev/application.properties b/properties/dev/application.properties
@@ -81,7 +81,7 @@ saved.files.storage.days=7
 cpt4.dir.v4=/opt/athena/addons/cpt4_4_5
 cpt4.dir.v5=/opt/athena/addons/cpt4_5
 
-vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel
+vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel/tree/v5.3.1
 vocabularies.download.forum.url=http://forums.ohdsi.org/c/implementers
 vocabularies.download.umls.url=https://uts.nlm.nih.gov/uts/login
 

diff --git a/properties/prod/application.properties b/properties/prod/application.properties
@@ -77,7 +77,7 @@ saved.files.storage.days=7
 cpt4.dir.v4=/opt/athena/addons/cpt4_4_5
 cpt4.dir.v5=/opt/athena/addons/cpt4_5
 
-vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel
+vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel/tree/v5.3.1
 vocabularies.download.forum.url=http://forums.ohdsi.org/c/implementers
 vocabularies.download.umls.url=https://uts.nlm.nih.gov/uts/login
 

diff --git a/properties/qa/application.properties b/properties/qa/application.properties
@@ -77,7 +77,7 @@ saved.files.storage.days=7
 cpt4.dir.v4=/opt/athena/addons/cpt4_4_5
 cpt4.dir.v5=/opt/athena/addons/cpt4_5
 
-vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel
+vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel/tree/v5.3.1
 vocabularies.download.forum.url=http://forums.ohdsi.org/c/implementers
 vocabularies.download.umls.url=https://uts.nlm.nih.gov/uts/login
 

diff --git a/properties/test/application.properties b/properties/test/application.properties
@@ -68,7 +68,7 @@ spring.mail.properties.mail.smtp.starttls.required=true
 
 athena.url=https://athenatest.odysseusinc.com
 athena.mail.notifier=Athena
-athena.mail.admin=[email protected],[email protected],gregory.klebanov@odysseusinc.com
+athena.mail.admin=admin@admin.com
 
 csv.separator=\t
 csv.file.name.searched.concepts=Athena search.csv
@@ -78,7 +78,7 @@ saved.files.storage.days=7
 cpt4.dir.v4=/opt/athena/addons/cpt4_4_5
 cpt4.dir.v5=/opt/athena/addons/cpt4_5
 
-vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel
+vocabularies.download.control.files.url=https://github.com/OHDSI/CommonDataModel/tree/v5.3.1
 vocabularies.download.forum.url=http://forums.ohdsi.org/c/implementers
 vocabularies.download.umls.url=https://uts.nlm.nih.gov/uts/login
 

diff --git a/src/main/docker/Dockerfile b/src/main/docker/Dockerfile
diff --git a/src/main/docker/cpt4.jar b/src/main/docker/cpt4.jar
diff --git a/src/main/docker/cpt4_4_5/cpt.bat b/src/main/docker/cpt4_4_5/cpt.bat
diff --git a/src/main/docker/cpt4_4_5/cpt.sh b/src/main/docker/cpt4_4_5/cpt.sh
diff --git a/src/main/docker/cpt4_4_5/readme.txt b/src/main/docker/cpt4_4_5/readme.txt
diff --git a/src/main/docker/cpt4_5/cpt.bat b/src/main/docker/cpt4_5/cpt.bat
diff --git a/src/main/docker/cpt4_5/cpt.sh b/src/main/docker/cpt4_5/cpt.sh
diff --git a/src/main/docker/cpt4_5/readme.txt b/src/main/docker/cpt4_5/readme.txt
diff --git a/src/main/docker/run.sh b/src/main/docker/run.sh
diff --git a/.../java/com/odysseusinc/athena/api/v1/controller/converter/ConceptSearchDTOToSolrQuery.java b/.../java/com/odysseusinc/athena/api/v1/controller/converter/ConceptSearchDTOToSolrQuery.java
@@ -168,7 +168,7 @@ private void putIntoJsonFacet(JSONObject jsonFacet, String facetField) {
         jsonFacet.put(getFacetLabel(facetField), new JSONObject()
                 .put("type", "terms")
                 .put("field", facetField)
-                .put("limit", 100)
+                .put("limit", -1)
                 .put("missing", true)
                 .put("mincount", 0)
                 .put("domain",

diff --git a/src/main/java/com/odysseusinc/athena/config/CustomLogoutLogic.java b/src/main/java/com/odysseusinc/athena/config/CustomLogoutLogic.java
@@ -26,7 +26,6 @@
 
 import com.odysseusinc.athena.model.security.AthenaProfile;
 import com.odysseusinc.athena.service.security.RevokedTokenStore;
-import com.odysseusinc.athena.util.UserProfileUtil;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -39,7 +38,7 @@
 import org.pac4j.core.context.session.SessionStore;
 import org.pac4j.core.engine.DefaultLogoutLogic;
 import org.pac4j.core.exception.HttpAction;
-import org.pac4j.core.http.HttpActionAdapter;
+import org.pac4j.core.http.adapter.HttpActionAdapter;
 import org.pac4j.core.profile.CommonProfile;
 import org.pac4j.core.profile.ProfileManager;
 import org.pac4j.core.redirect.RedirectAction;
@@ -88,7 +87,7 @@ public R perform(C context, Config config,
             centralLogout = inputCentralLogout;
         }
 
-        Object sessionAttribute = context.getSessionAttribute(Pac4jConstants.USER_PROFILES);
+        Object sessionAttribute = context.getSessionStore().get(context, Pac4jConstants.USER_PROFILES);
         if (sessionAttribute instanceof Map) {
             Map<String, CommonProfile> profileMap = (Map<String, CommonProfile>) sessionAttribute;
             profileMap.forEach((k, v) -> {
@@ -115,9 +114,9 @@ public R perform(C context, Config config,
         }
         HttpAction action;
         if (redirectUrl != null) {
-            action = HttpAction.redirect("redirect", context, redirectUrl);
+            action = HttpAction.redirect(context, redirectUrl);
         } else {
-            action = HttpAction.ok("ok", context);
+            action = HttpAction.ok(context, "ok");
         }
 
         // local logout if requested or multiple profiles

diff --git a/src/main/java/com/odysseusinc/athena/config/CustomPac4jCallbackLogic.java b/src/main/java/com/odysseusinc/athena/config/CustomPac4jCallbackLogic.java
@@ -22,48 +22,51 @@
 
 package com.odysseusinc.athena.config;
 
+import lombok.extern.slf4j.Slf4j;
 import org.pac4j.core.client.Client;
 import org.pac4j.core.client.Clients;
 import org.pac4j.core.config.Config;
 import org.pac4j.core.context.WebContext;
 import org.pac4j.core.credentials.Credentials;
 import org.pac4j.core.engine.CallbackLogic;
 import org.pac4j.core.exception.HttpAction;
-import org.pac4j.core.http.HttpActionAdapter;
+import org.pac4j.core.http.adapter.HttpActionAdapter;
 import org.pac4j.core.profile.CommonProfile;
-import org.pac4j.core.profile.UserProfile;
 import org.pac4j.jwt.profile.JwtGenerator;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import org.pac4j.saml.client.SAML2Client;
 import org.springframework.beans.factory.annotation.Value;
 
+@Slf4j
 public class CustomPac4jCallbackLogic<R, C extends WebContext> implements CallbackLogic<R, C> {
-    protected Logger logger = LoggerFactory.getLogger(this.getClass());
 
     @Value("${salt}")
     private String salt;
 
     @Value("${athena.async-auth-redirect}")
     private String redirectPath;
 
-    private JwtGenerator<CommonProfile> jwtGenerator;
+    private final JwtGenerator<CommonProfile> jwtGenerator;
 
     public CustomPac4jCallbackLogic(JwtGenerator<CommonProfile> jwtGenerator) {
         this.jwtGenerator = jwtGenerator;
     }
 
+    @Override
     public R perform(
             C context,
             Config config,
             HttpActionAdapter<R, C> httpActionAdapter,
             String inputDefaultUrl,
             Boolean inputMultiProfile,
-            Boolean inputRenewSession) {
+            Boolean inputRenewSession,
+            Boolean renewSession,
+            String clientName
+    ) {
 
-        this.logger.debug("=== CALLBACK ===");
+        log.debug("=== CALLBACK ===");
 
         Clients clients = config.getClients();
-        Client client = clients.findClient(context);
+        Client client = clients.findClient(SAML2Client.class);
 
         HttpAction action;
         try {
@@ -72,16 +75,15 @@ public R perform(
 
             String token = jwtGenerator.generate(profile);
 
-            logger.debug("jwt: " + token);
+            log.debug("jwt: " + token);
 
             action = HttpAction.redirect(
-                    "redirect",
                     context,
                     redirectPath + "?token=" + token
             );
-        } catch (HttpAction var15) {
-            this.logger.debug("extra HTTP action required in callback: {}", Integer.valueOf(var15.getCode()));
-            action = var15;
+        } catch (HttpAction ex) {
+            log.debug("extra HTTP action required in callback: {}", Integer.valueOf(ex.getCode()));
+            action = ex;
         }
 
         return httpActionAdapter.adapt(action.getCode(), context);

diff --git a/src/main/java/com/odysseusinc/athena/service/impl/ConceptSearchPhraseToSolrQueryService.java b/src/main/java/com/odysseusinc/athena/service/impl/ConceptSearchPhraseToSolrQueryService.java
@@ -1,7 +1,7 @@
 package com.odysseusinc.athena.service.impl;
 
-import static org.apache.commons.collections.CollectionUtils.isEmpty;
-import static org.apache.commons.collections.CollectionUtils.isNotEmpty;
+import static org.apache.commons.collections4.CollectionUtils.isEmpty;
+import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
 import static org.apache.commons.lang3.StringUtils.EMPTY;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.remove;

diff --git a/src/main/java/com/odysseusinc/athena/service/impl/QueryDebugUtils.java b/src/main/java/com/odysseusinc/athena/service/impl/QueryDebugUtils.java
@@ -101,9 +101,9 @@ public static QueryResponse debug(String baseDir, String conceptQueryDir, SolrQu
         File fileWithQuery = new File(String.format("%s%s", dir,  "query"));
         FileUtils.writeStringToFile(fileWithQuery, QueryDebugUtils.getQuery(query.getQuery()), Charset.defaultCharset());
 
-        for (Map.Entry<String, String> stringStringEntry : response.getExplainMap().entrySet()) {
+        for (Map.Entry<String, Object> stringStringEntry : response.getExplainMap().entrySet()) {
             String k = stringStringEntry.getKey();
-            String v = stringStringEntry.getValue();
+            String v = stringStringEntry.getValue().toString();
             File file = new File(dir + org.apache.commons.lang3.StringUtils.substringBetween(v, "\n", "=") + "_" + k);
             FileUtils.writeStringToFile(file, v, Charset.defaultCharset());
         }