Merge pull request #5 from wcmc-its/dev

Upgrade to Java 11 and swagger 3.0
wcmc-its · Dec 29, 2020 · e486887 · e486887
2 parents 508a63a + 59b12e3
commit e486887
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Showing 13 changed files with 83 additions and 75 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM openjdk:8-jre-slim
+FROM openjdk:11-jre-slim
 
 RUN mkdir -p /app
 WORKDIR /app

diff --git a/Procfile b/Procfile
@@ -1 +1 @@
-web: java -jar reciter-scopus-retrieval-tool-0.0.1-SNAPSHOT.jar
+web: java -jar reciter-scopus-retrieval-tool-1.1.0.jar
diff --git a/buildspec.yml b/buildspec.yml
@@ -2,6 +2,8 @@ version: 0.2
 # https://docs.aws.amazon.com/codebuild/latest/userguide/getting-started.html
 phases:
   install:
+    runtime-versions:
+      java: openjdk11
     commands:
       - echo Nothing to do in the install phase...
   pre_build:
@@ -14,9 +16,9 @@ phases:
   post_build:
     commands:
       - echo Build completed on `date`
-      - cp target/reciter-scopus-retrieval-tool-0.0.1-SNAPSHOT.jar .
+      - cp target/reciter-scopus-retrieval-tool-1.1.0.jar .
 artifacts:
   files:
-    - reciter-scopus-retrieval-tool-0.0.1-SNAPSHOT.jar
+    - reciter-scopus-retrieval-tool-1.1.0.jar
     - .ebextensions/**/* 
     - Procfile
diff --git a/k8-buildspec.yml b/k8-buildspec.yml
@@ -2,6 +2,8 @@
 version: 0.2
 phases:
   install:
+    runtime-versions:
+      java: openjdk11
     commands:
       - kubectl version --short --client   
   pre_build:

diff --git a/kubernetes/k8-configmap.yaml b/kubernetes/k8-configmap.yaml
@@ -14,7 +14,7 @@ data:
         listen [::]:80 default_server;
 
         location /scopus {
-            rewrite ^/scopus/swagger-ui.html$ /swagger-ui.html break;
+            rewrite ^/scopus/swagger-ui/index.html$ /swagger-ui/index.html break;
             rewrite ^/scopus/(.*)$ /scopus/$1 break;
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
             proxy_set_header X-Forwarded-Proto $scheme;

diff --git a/kubernetes/k8-deployment.yaml b/kubernetes/k8-deployment.yaml
@@ -60,15 +60,15 @@ spec:
             cpu: 0.6
         livenessProbe:
           httpGet:
-            path: "/swagger-ui.html"
+            path: "/scopus/ping"
             port: 5000
           initialDelaySeconds: 10
           periodSeconds: 10
           failureThreshold: 3
           timeoutSeconds: 3
         readinessProbe:
           httpGet:
-            path: "/swagger-ui.html"
+            path: "/scopus/ping"
             port: 5000
           initialDelaySeconds: 10
           periodSeconds: 10

diff --git a/kubernetes/k8-service.yaml b/kubernetes/k8-service.yaml
@@ -4,7 +4,7 @@ metadata:
   name: reciter-scopus
   namespace: reciter
   annotations:
-    alb.ingress.kubernetes.io/healthcheck-path: /scopus/swagger-ui.html
+    alb.ingress.kubernetes.io/healthcheck-path: /scopus/ping
     alb.ingress.kubernetes.io/success-codes: 200-302
     alb.ingress.kubernetes.io/healthcheck-protocol: HTTP
     alb.ingress.kubernetes.io/healthcheck-interval-seconds: '15'

diff --git a/pom.xml b/pom.xml
@@ -2,20 +2,20 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.wcmc.reciter</groupId>
   <artifactId>reciter-scopus-retrieval-tool</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
+  <version>1.1.0</version>
   <name>ReCiter-Scopus-Retrieval-Tool</name>
   <description>A tool to retrieve Scopus articles.</description>
   <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>1.4.2.RELEASE</version>
-        <relativePath /> <!-- lookup parent from repository -->
+        <version>2.3.7.RELEASE</version>
+        <relativePath />
     </parent>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <java.version>1.8</java.version>
+        <java.version>11</java.version>
     </properties>
 
     <dependencies>
@@ -29,19 +29,11 @@
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
-
-        <!-- https://mvnrepository.com/artifact/io.springfox/springfox-swagger2 -->
-        <dependency>
-            <groupId>io.springfox</groupId>
-            <artifactId>springfox-swagger2</artifactId>
-            <version>2.8.0</version>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/io.springfox/springfox-swagger-ui -->
         <dependency>
-            <groupId>io.springfox</groupId>
-            <artifactId>springfox-swagger-ui</artifactId>
-            <version>2.8.0</version>
-        </dependency>
+			<groupId>io.springfox</groupId>
+			<artifactId>springfox-boot-starter</artifactId>
+			<version>3.0.0</version>
+		</dependency>
         <dependency>
         	<groupId>edu.cornell.weill.reciter</groupId>
         	<artifactId>reciter-scopus-model</artifactId>
@@ -68,15 +60,4 @@
             </plugin>
         </plugins>
     </build>
-    <!-- <repositories>
-        <repository>
-            <id>wcmc-its</id>
-            <name>ReCiter-Maven-Repository</name>
-            <url>https://github.com/wcmc-its/ReCiter-Maven-Repository/raw/master/snapshots</url>
-            <snapshots>
-                <enabled>true</enabled>
-                <updatePolicy>always</updatePolicy>
-            </snapshots>
-        </repository>
-    </repositories> -->
 </project>
diff --git a/src/main/java/reciter/controller/PingController.java b/src/main/java/reciter/controller/PingController.java
@@ -0,0 +1,23 @@
+package reciter.controller;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.ResponseBody;
+
+@Controller
+@RequestMapping("/scopus")
+@Api(value = "PingController", tags = {"Health Check"})
+public class PingController {
+
+    @ApiOperation(value = "Health check", response = ResponseEntity.class)
+    @GetMapping(value = "/ping", produces = "text/plain")
+    @ResponseBody
+    public ResponseEntity<String> ping() {
+        return ResponseEntity.ok("Healthy");
+    }
+}
diff --git a/src/main/java/reciter/controller/ScopusController.java b/src/main/java/reciter/controller/ScopusController.java
@@ -1,35 +1,39 @@
 package reciter.controller;
 
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiResponse;
-import io.swagger.annotations.ApiResponses;
+import java.util.ArrayList;
+import java.util.List;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiResponse;
+import io.swagger.annotations.ApiResponses;
 import reciter.model.scopus.ScopusArticle;
 import reciter.model.scopus.ScopusQuery;
 import reciter.scopus.retriever.ScopusArticleRetriever;
 
-import java.util.ArrayList;
-import java.util.List;
-
 @Controller
 @RequestMapping("/scopus")
-@Api(value="ScopusController", description="Operations on querying the Scopus API.")
+@Api(value="ScopusController", tags = {"Querying Scopus with PMID, SCOPUS-ID or DOI"})
 public class ScopusController {
     private static final Logger slf4jLogger = LoggerFactory.getLogger(ScopusController.class);
 
-    @ApiOperation(value = "Querying Scopus with PMIDs.", response = List.class)
+    @ApiOperation(value = "Querying Scopus with PMID, SCOPUS-ID or DOI. Add type it only accepts PMID,SCOPUS-ID or DOI(case-insensitive)", response = List.class)
     @ApiResponses(value = {
             @ApiResponse(code = 200, message = "Successfully retrieved list"),
             @ApiResponse(code = 401, message = "You are not authorized to view the resource"),
             @ApiResponse(code = 403, message = "Accessing the resource you were trying to reach is forbidden"),
             @ApiResponse(code = 404, message = "The resource you were trying to reach is not found")
     })
-    @RequestMapping(value = "/query/", method = RequestMethod.POST, produces = "application/json")
+    @PostMapping(value = "/query/", produces = "application/json")
     @ResponseBody
     public ResponseEntity<List<ScopusArticle>> retrieve(@RequestBody ScopusQuery scopusQuery) {
         slf4jLogger.info("calling retrieve with pmids size=[" + scopusQuery.getQuery().size() + "]");

diff --git a/src/main/java/reciter/scopus/retriever/ScopusArticleRetriever.java b/src/main/java/reciter/scopus/retriever/ScopusArticleRetriever.java
@@ -4,29 +4,28 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
-import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import com.github.rholder.retry.Retryer;
 import com.github.rholder.retry.Retryer.RetryerCallable;
 import com.github.rholder.retry.RetryerBuilder;
 import com.github.rholder.retry.StopStrategies;
 import com.github.rholder.retry.WaitStrategies;
 import com.google.common.base.Predicates;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import reciter.model.scopus.ScopusArticle;
 import reciter.scopus.callable.ScopusUriParserCallable;
 import reciter.scopus.querybuilder.ScopusXmlQuery;
 import reciter.scopus.xmlparser.ScopusXmlHandler;
 
 public class ScopusArticleRetriever {
 
-	private final static Logger slf4jLogger = LoggerFactory.getLogger(ScopusArticleRetriever.class);
+	private static final Logger slf4jLogger = LoggerFactory.getLogger(ScopusArticleRetriever.class);
 
 	/**
 	 * Scopus retrieval threshold.
@@ -49,7 +48,7 @@ public List<ScopusArticle> retrieveScopus(List<Object> pmids, String type) {
 		if (pmids.size() == 1) {
 			pmidQueries.add(type + "(" + pmids.get(0) + ")");
 		} else {
-			StringBuffer sb = new StringBuffer();
+			StringBuilder sb = new StringBuilder();
 			int i = 0;
 			Iterator<Object> itr = pmids.iterator();
 			while (itr.hasNext()) {
@@ -65,7 +64,7 @@ public List<ScopusArticle> retrieveScopus(List<Object> pmids, String type) {
 				}
 				if (i != 0 && i % SCOPUS_DEFAULT_THRESHOLD == 0) {
 					pmidQueries.add(sb.toString());
-					sb = new StringBuffer();
+					sb = new StringBuilder();
 				}
 				i++;
 			}
@@ -76,7 +75,7 @@ public List<ScopusArticle> retrieveScopus(List<Object> pmids, String type) {
 			}
 		}
 
-		List<RetryerCallable<List<ScopusArticle>>> callables = new ArrayList<RetryerCallable<List<ScopusArticle>>>();
+		List<RetryerCallable<List<ScopusArticle>>> callables = new ArrayList<>();
 
 		Retryer<List<ScopusArticle>> retryer = RetryerBuilder.<List<ScopusArticle>>newBuilder()
                 .retryIfResult(Predicates.<List<ScopusArticle>>isNull())

diff --git a/src/main/java/reciter/scopus/xmlparser/ScopusXmlHandler.java b/src/main/java/reciter/scopus/xmlparser/ScopusXmlHandler.java
@@ -2,13 +2,9 @@
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.xml.sax.Attributes;
 import org.xml.sax.SAXException;
 import org.xml.sax.helpers.DefaultHandler;
@@ -25,16 +21,13 @@
  */
 public class ScopusXmlHandler extends DefaultHandler {
 
-	private final static Logger slf4jLogger = LoggerFactory.getLogger(ScopusXmlHandler.class);
-
 	private ScopusArticle scopusArticle;
 
 	private boolean bScopusDocId;
 
 	private boolean bAffiliation;
 	private boolean bAfid;
 	private boolean bAffilname;
-//	private boolean bNameVariant;
 	private boolean bAffiliationCity;
 	private boolean bAffiliationCountry;
 
@@ -65,7 +58,6 @@ public class ScopusXmlHandler extends DefaultHandler {
 
 	private int afid;
 	private StringBuilder affilname = new StringBuilder();
-//	private String nameVariant;
 	private String affiliationCity;
 	private String affiliationCountry;
 	private Map<Integer, Affiliation> affiliations = new HashMap<>();
@@ -112,9 +104,6 @@ public void startElement(String uri, String localName, String qName, Attributes
 				affilname.setLength(0);
 				bAffilname = true;
 			}
-//			if (qName.equalsIgnoreCase("name-variant")) {
-//				bNameVariant = true;
-//			}
 			if (qName.equalsIgnoreCase("affiliation-city")) {
 				bAffiliationCity = true;
 			}
@@ -234,12 +223,8 @@ public void characters(char[] ch, int start, int length) throws SAXException {
 				afid = Integer.parseInt(new String(ch, start, length));
 			} 
 			if (bAffilname) {
-				//affilname = new String(ch, start, length);
 				affilname.append(ch, start, length);
 			}
-//			if (bNameVariant) {
-//				nameVariant = new String(ch, start, length);
-//			}
 			if (bAffiliationCity) {
 				affiliationCity = new String(ch, start, length);
 			}
@@ -360,9 +345,6 @@ public void endElement(String uri, String localName, String qName) throws SAXExc
 			if (qName.equalsIgnoreCase("affilname")) {
 				bAffilname = false;
 			}
-//			if (qName.equalsIgnoreCase("name-variant")) {
-//				bNameVariant = false;
-//			}
 			if (qName.equalsIgnoreCase("affiliation-city")) {
 				bAffiliationCity = false;
 			}
@@ -472,8 +454,8 @@ public void endElement(String uri, String localName, String qName) throws SAXExc
 			if (bError) {
 				scopusArticle = null;
 			} else {
-				List<Affiliation> affiliationList = new ArrayList<Affiliation>();
-				List<Author> authorList = new ArrayList<Author>();
+				List<Affiliation> affiliationList = new ArrayList<>();
+				List<Author> authorList = new ArrayList<>();
 				for (Affiliation affiliation : affiliations.values()) {
 					affiliationList.add(affiliation);
 				}
@@ -499,7 +481,6 @@ public void endElement(String uri, String localName, String qName) throws SAXExc
 						.citedByCount(citedByCount)
 						.authors(authorList).build();
 				scopusArticles.add(scopusArticle);
-				// TODO refactor
 				scopusArticle = null;
 				doi=null;
 				affiliations.clear();

diff --git a/src/main/java/reciter/swagger/SwaggerConfig.java b/src/main/java/reciter/swagger/SwaggerConfig.java
@@ -2,7 +2,11 @@
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+
+import springfox.documentation.builders.ApiInfoBuilder;
 import springfox.documentation.builders.RequestHandlerSelectors;
+import springfox.documentation.service.ApiInfo;
+import springfox.documentation.service.Contact;
 import springfox.documentation.spi.DocumentationType;
 import springfox.documentation.spring.web.plugins.Docket;
 import springfox.documentation.swagger2.annotations.EnableSwagger2;
@@ -18,6 +22,18 @@ public Docket productApi() {
                 .select()
                 .apis(RequestHandlerSelectors.basePackage("reciter.controller"))
                 .paths(regex("/scopus.*"))
+                .build()
+                .apiInfo(apiInfo());
+    }
+
+    private ApiInfo apiInfo() {
+        return new ApiInfoBuilder().title("ReCiter publication management system - Scopus Retrieval Tool")
+                .description("Retrieve publications from Scopus. More info here: http://github.com/wcmc-its/ReCiter-Scopus-Retrieval-Tool/").termsOfServiceUrl("")
+                .contact(new Contact("Paul J. Albert", "https://github.com/wcmc-its/ReCiter", "[email protected]"))
+                .contact(new Contact("Sarbajit Dutta", "https://github.com/wcmc-its/ReCiter", "[email protected]"))
+                .license("Apache License Version 2.0")
+                .licenseUrl("https://www.apache.org/licenses/LICENSE-2.0")
+                .version("1.1.0")
                 .build();
     }
 }
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		web: java -jar reciter-scopus-retrieval-tool-0.0.1-SNAPSHOT.jar
		web: java -jar reciter-scopus-retrieval-tool-1.1.0.jar