Prepare for v2.12.0 Release (#2130)

OHDSI · Oct 11, 2022 · fad7c7c · fad7c7c
1 parent e4230e5
commit fad7c7c
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Showing 6 changed files with 61 additions and 33 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
   <groupId>org.ohdsi</groupId>
   <artifactId>WebAPI</artifactId>
   <packaging>war</packaging>
-  <version>2.12.0-SNAPSHOT</version>
+  <version>2.12.0</version>
   <name>WebAPI</name>
   <properties>
     <build.number>${BUILD_NUMBER}</build.number>
@@ -776,16 +776,11 @@
                 <groupId>com.vaadin.external.google</groupId>
                 <artifactId>android-json</artifactId>
             </exclusion>
-            <!-- To have an explicit json-smart dependency in the dependencies block effective -->
-            <!-- For some reason it is not overriden as the other dependencies like jackson-databind -->
-            <exclusion>
-              <groupId>net.minidev</groupId>
-              <artifactId>json-smart</artifactId>
-            </exclusion>
         </exclusions>
     </dependency>
     <!-- It is overriding a transitive dependency from the dependency above -->
     <!-- After migrating to Spring Boot 2.x we should get rid of it -->
+    <!-- It is currently inefficient as com.nimbusds:nimbus-jose-jwt has hard bounds [1.3.1,2.3] -->
     <dependency>
       <groupId>net.minidev</groupId>
       <artifactId>json-smart</artifactId>
@@ -861,14 +856,6 @@
       <groupId>com.microsoft.azure</groupId>
       <artifactId>msal4j</artifactId>
       <version>1.9.0</version>
-      <!-- To have an explicit json-smart dependency in the dependencies block effective -->
-      <!-- For some reason it is not overriden as the other dependencies like jackson-databind -->
-      <exclusions>
-        <exclusion>
-          <groupId>net.minidev</groupId>
-          <artifactId>json-smart</artifactId>
-        </exclusion>
-      </exclusions>
     </dependency>
     <dependency>
       <groupId>com.opencsv</groupId>
@@ -973,12 +960,6 @@
           <groupId>com.fasterxml.jackson.core</groupId>
           <artifactId>jackson-databind</artifactId>
         </exclusion>
-        <!-- To have an explicit json-smart dependency in the dependencies block effective -->
-        <!-- For some reason it is not overriden as the other dependencies like jackson-databind -->
-        <exclusion>
-          <groupId>net.minidev</groupId>
-          <artifactId>json-smart</artifactId>
-        </exclusion>
       </exclusions>
     </dependency>
     <dependency>
@@ -1561,6 +1542,26 @@
           <artifactId>google-auth-library-credentials</artifactId>
           <version>0.16.2</version>
         </dependency>
+        <dependency>
+          <groupId>com.google.api</groupId>
+          <artifactId>gax</artifactId>
+          <version>1.47.0</version>
+        </dependency>
+        <dependency>
+          <groupId>com.google.api</groupId>
+          <artifactId>gax-grpc</artifactId>
+          <version>1.47.0</version>
+        </dependency>
+        <dependency>
+          <groupId>com.google.api.grpc</groupId>
+          <artifactId>proto-google-cloud-bigquerystorage-v1beta1</artifactId>
+          <version>0.66.0</version>
+        </dependency>
+        <dependency>
+          <groupId>io.opencensus</groupId>
+          <artifactId>opencensus-contrib-http-util</artifactId>
+          <version>0.18.0</version>
+        </dependency>
       </dependencies>
       <build>
         <plugins>

diff --git a/src/main/java/org/ohdsi/webapi/Constants.java b/src/main/java/org/ohdsi/webapi/Constants.java
@@ -56,7 +56,7 @@ interface Params {
     String COHORT_CHARACTERIZATION_ID = "cohort_characterization_id";
     String PATHWAY_ANALYSIS_ID = "pathway_analysis_id";
     String PREDICTION_ANALYSIS_ID = "prediction_analysis_id";
-    String PREDICTION_SKELETON_VERSION = "v0.0.6";
+    String PREDICTION_SKELETON_VERSION = "v0.0.1";
     String ESTIMATION_ANALYSIS_ID = "estimation_analysis_id";
     String UPDATE_PASSWORD = "update_password";
     String SOURCE_ID = "source_id";

diff --git a/src/main/java/org/ohdsi/webapi/service/VocabularyService.java b/src/main/java/org/ohdsi/webapi/service/VocabularyService.java
@@ -576,9 +576,9 @@ protected PreparedStatementRenderer prepareExecuteSearch(ConceptSearch search, S
       if (!search.query.isEmpty()) {
         String queryFilter = "LOWER(CONCEPT_NAME) LIKE '%@query%' or LOWER(CONCEPT_CODE) LIKE '%@query%'";
         if (StringUtils.isNumeric(search.query)) {
-          queryFilter += "or CONCEPT_ID = @query";
+          queryFilter += " or CONCEPT_ID = CAST(@query as int)";
         }
-        filters += "AND (" + queryFilter + ")";
+        filters += " AND (" + queryFilter + ")";
         variableNameList.add("query");
         variableValueList.add(search.query.toLowerCase());
       }

diff --git a/src/main/java/org/ohdsi/webapi/tag/TagSecurityUtils.java b/src/main/java/org/ohdsi/webapi/tag/TagSecurityUtils.java
@@ -9,6 +9,8 @@
 import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
 import org.ohdsi.webapi.reusable.domain.Reusable;
 
+import javax.ws.rs.BadRequestException;
+
 public class TagSecurityUtils {
     public static String COHORT_DEFINITION = "cohortdefinition";
     public static String CONCEPT_SET = "conceptset";
@@ -40,7 +42,19 @@ public static boolean checkPermission(final String asset, final String method) {
             return false;
         }
 
-        final String permission = String.format("%s:*:protectedtag:*:%s", asset, method);
+        final String template;
+        switch (method) {
+            case "post":
+                template = "%s:*:protectedtag:post";
+                break;
+            case "delete":
+                template = "%s:*:protectedtag:*:delete";
+                break;
+            default:
+                throw new BadRequestException(String.format("Unsupported method: %s", method));
+
+        }
+        final String permission = String.format(template, asset);
         return SecurityUtils.getSubject().isPermitted(permission);
     }
 

diff --git a/src/main/resources/resources/estimation/r/runAnalysis.R b/src/main/resources/resources/estimation/r/runAnalysis.R
@@ -56,7 +56,9 @@ tryCatch({
                 runAnalyses = TRUE,
                 packageResults = TRUE,
                 maxCores = maxCores,
-                minCellCount = 5)
+                minCellCount = 5,
+                # a workaround as renv.lock file is unreachable after the analysis package has been installed
+                verifyDependencies = FALSE)
 }, finally = {
         remove.packages('@packageName')
 })
diff --git a/src/main/resources/resources/prediction/r/runAnalysis.R b/src/main/resources/resources/prediction/r/runAnalysis.R
@@ -21,8 +21,9 @@ tryCatch({
         user <- Sys.getenv("DBMS_USERNAME")
         pwd <- Sys.getenv("DBMS_PASSWORD")
         cdmDatabaseSchema <- Sys.getenv("DBMS_SCHEMA")
+        cdmDatabaseName <- Sys.getenv("DATA_SOURCE_NAME")
         resultsDatabaseSchema <- Sys.getenv("RESULT_SCHEMA")
-        cohortsDatabaseSchema <- Sys.getenv("TARGET_SCHEMA")
+        cohortDatabaseSchema <- Sys.getenv("TARGET_SCHEMA")
         cohortTable <- Sys.getenv("COHORT_TARGET_TABLE")
         driversPath <- (function(path) if (path == "") NULL else path)( Sys.getenv("JDBC_DRIVER_PATH") )
 
@@ -32,6 +33,19 @@ tryCatch({
                                                                         password = pwd,
                                                                         pathToDriver = driversPath)
 
+        databaseDetails <- PatientLevelPrediction::createDatabaseDetails(connectionDetails = connectionDetails,
+                                                                         cdmDatabaseSchema = cdmDatabaseSchema,
+                                                                         cdmDatabaseName = cdmDatabaseName,
+                                                                         cohortDatabaseSchema = cohortDatabaseSchema,
+                                                                         cohortTable = cohortTable,
+                                                                         outcomeDatabaseSchema = cohortDatabaseSchema,
+                                                                         outcomeTable = cohortTable,
+                                                                         cdmVersion = 5)
+
+        logSettings <- PatientLevelPrediction::createLogSettings(verbosity = "INFO",
+                                                                 timeStamp = T,
+                                                                 logName = 'skeletonPlp')
+
         # Evaluating can't use global environment in child threads
         connectionDetails$user <- function() Sys.getenv("DBMS_USERNAME")
         connectionDetails$password <- function() Sys.getenv("DBMS_PASSWORD")
@@ -41,18 +55,15 @@ tryCatch({
         dir.create(outputFolder)
 
         PatientLevelPrediction::setPythonEnvironment(envname = 'PLP', envtype = 'conda')
-        execute(connectionDetails = connectionDetails,
-                cdmDatabaseSchema = cdmDatabaseSchema,
-                cohortDatabaseSchema = cohortsDatabaseSchema,
-                cohortTable = cohortTable,
+        execute(databaseDetails = databaseDetails,
                 outputFolder = outputFolder,
                 createCohorts = T,
                 runAnalyses = T,
                 createValidationPackage = F,
                 packageResults = T,
                 minCellCount = 5,
-                cdmVersion = 5,
-                createShiny = T)
+                viewShiny = T,
+                logSettings = logSettings)
         # To run PLP Viewer shiny app call:
         # PatientLevelPrediction::viewMultiplePlp(outputFolder)
 }, finally = {