updated swagger API and update several annotation. Now this version i…

…s ready to use

README

@@ -27,9 +27,11 @@ Step 1. Init the Database
 
 Step 2. Check the API
 1. in pdb-annotation/pdb-alignment-api/: mvn spring-boot:run
-2. open your web browser:
-http://localhost:8080/StructureMappingQuery?ensemblid=ENSP00000483207.2
-http://localhost:8080/ProteinIdentifierRecognitionQuery?ensemblid=ENSP00000483207.2
+2. Swagger-UI:
+http://localhost:8080/swagger-ui.html
+3. Directly using API:
+http://localhost:8080/pdb_annotation/StructureMappingQuery?ensemblId=ENSP00000483207.2
+http://localhost:8080/pdb_annotation/ProteinIdentifierRecognitionQuery?ensemblId=ENSP00000483207.2
 
 Step 3. Weekly update
 1. in pdb-annotation/pdb-alignment-pipeline/target/: java -jar -Xmx7000m pdb-0.1.0.jar update

pdb-alignment-api/pom.xml

@@ -24,6 +24,18 @@
       <groupId>mysql</groupId>
       <artifactId>mysql-connector-java</artifactId>
     </dependency>
+    <dependency>
+            <groupId>io.springfox</groupId>
+            <artifactId>springfox-swagger-ui</artifactId>
+            <version>2.4.0</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>io.springfox</groupId>
+            <artifactId>springfox-swagger2</artifactId>
+            <version>2.4.0</version>
+            <scope>compile</scope>
+        </dependency>
   </dependencies>
 
   <properties>

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/Application.java

@@ -1,13 +1,52 @@
 package org.cbioportal.pdb_annotation.web;
 
 import org.springframework.boot.SpringApplication;
-import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.Bean;
 
+import springfox.documentation.builders.ApiInfoBuilder;
+import springfox.documentation.builders.PathSelectors;
+import springfox.documentation.service.ApiInfo;
+import springfox.documentation.spi.DocumentationType;
+import springfox.documentation.spring.web.plugins.Docket;
+import springfox.documentation.swagger2.annotations.EnableSwagger2;
+
+/**
+ * Main SpringBoot Application
+ * 
+ * @author Juexin Wang
+ *
+ */
 @SpringBootApplication
-@EnableAutoConfiguration
+@EnableSwagger2 
 public class Application {
 	public static void main(String[] args) {
 		SpringApplication.run(Application.class, args);
-	}
+	}	
+
+	@Bean
+    public Docket annotationApi()
+    {
+        // default swagger definition file location: <root>/v2/api-docs?group=pdb_annotation
+        // default swagger UI location: <root>/swagger-ui.html
+        return new Docket(DocumentationType.SWAGGER_2)
+            .groupName("pdb_annotation")
+            .apiInfo(annotationApiInfo())
+            .select()
+            .paths(PathSelectors.regex("/pdb_annotation.*"))
+            .build();
+    }
+
+    private ApiInfo annotationApiInfo()
+    {
+        return new ApiInfoBuilder()
+            .title("PDB Annotation API")
+            .description("PDB Annotation API")
+            //.termsOfServiceUrl("http://terms-of-service-url")
+            .contact("CMO, MSKCC")
+            .license("GNU AFFERO GENERAL PUBLIC LICENSE Version 3")
+            .licenseUrl("https://github.com/cBioPortal/pdb-annotation/blob/master/LICENSE")
+            .version("2.0")
+            .build();
+    }
 }

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/controllers/AlignmentController.java

@@ -1,73 +1,90 @@
 package org.cbioportal.pdb_annotation.web.controllers;
 
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 
+import org.cbioportal.pdb_annotation.web.domain.AlignmentRepository;
+import org.cbioportal.pdb_annotation.web.domain.EnsemblRepository;
+import org.cbioportal.pdb_annotation.web.domain.PdbRepository;
 import org.cbioportal.pdb_annotation.web.models.Alignment;
-import org.cbioportal.pdb_annotation.web.persistancy.AlignmentRepository;
-import org.cbioportal.pdb_annotation.web.persistancy.EnsemblRepository;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Controller;
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.ResponseStatus;
+import org.springframework.web.bind.annotation.RestController;
 
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
+import io.swagger.annotations.ApiResponse;
+import io.swagger.annotations.ApiResponses;
 
-@Controller
+/**
+ * 
+ * Controller of the main API: AlignmentController
+ * 
+ * @author Juexin Wang
+ *
+ */
+@RestController // shorthand for @Controller, @ResponseBody
+@CrossOrigin(origins = "*") // allow all cross-domain requests
+@RequestMapping(value = "/pdb_annotation/")
 public class AlignmentController {
-
-	@RequestMapping("/StructureMappingQuery")
-	  @ResponseBody
-	  public List<Alignment> findByEnsemblidinAlignment(String ensemblid) {
-
-		List<Alignment> list = new ArrayList<Alignment>();
-	    try {
-	      Iterator<Alignment> it = alignmentDao.findByEnsemblId(ensemblid).iterator();
-	       while(it.hasNext()){
-	    	   Alignment alignment = (Alignment)it.next();
-	    	   list.add(alignment);
-	       }	
-	    }
-	    catch (Exception ex) {
-	    	ex.printStackTrace();
-	    }
-	    return list;
-
-	  }
-
-
-	@RequestMapping("/ProteinIdentifierRecognitionQuery")
-	  @ResponseBody
-	  public boolean isExistedEnsemblidinAlignment(String ensemblid) {
-	    try {
-	      Iterator<Alignment> it = alignmentDao.findByEnsemblId(ensemblid).iterator(); 
-	      if(it.hasNext()){
-	    	   return true;
-	       }else{
-	    	   return false;
-	       }
-	    }
-	    catch (Exception ex) {
-	    	ex.printStackTrace();
-	    }
-	    return false;
-	  }
-
-
-
-
-
-	  // ------------------------
-	  // PRIVATE FIELDS
-	  // ------------------------
 
-	  @Autowired
-	  private AlignmentRepository alignmentDao;
-
-	  //@Autowired
-	  //private EnsemblDAO ensemblDao;
-
-
+	private AlignmentRepository alignmentRepository;
+	private EnsemblRepository ensemblRepository;
+	private PdbRepository pdbRepository;
 
+	@Autowired
+	public AlignmentController(AlignmentRepository alignmentRepository, EnsemblRepository ensemblRepository,
+			PdbRepository pdbRepository) {
+		this.alignmentRepository = alignmentRepository;
+		this.ensemblRepository = ensemblRepository;
+		this.pdbRepository = pdbRepository;
+	}
+
+	@ApiOperation(value = "get pdb alignments by ensemblId", nickname = "getPdbAlignmentByEnsemblId")
+	@ApiResponses(value = {
+			@ApiResponse(code = 200, message = "Success", response = Alignment.class, responseContainer = "List"),
+			@ApiResponse(code = 400, message = "Bad Request") })
+	@RequestMapping(value = "/StructureMappingQuery", method = RequestMethod.GET, produces = "application/json")
+	@ResponseBody
+	@ResponseStatus(HttpStatus.OK)
+	public List<Alignment> getPdbAlignmentByEnsemblId(
+			@RequestParam @ApiParam(value = "Input ensembl id. For example ENSP00000483207.2", required = true, allowMultiple = true) String ensemblId) {
+		List<Alignment> list = new ArrayList();
+		try {
+			List<Alignment> it = alignmentRepository.findByEnsemblId(ensemblId);
+			list.addAll(it);
+		} catch (Exception ex) {
+			ex.printStackTrace();
+		}
+		return list;
+	}
+
+	@ApiOperation(value = "get whether ensemblId exists by ensemblId", nickname = "getExistedEnsemblidinAlignment")
+	@ApiResponses(value = {
+			@ApiResponse(code = 200, message = "Success", response = Alignment.class, responseContainer = "boolean"),
+			@ApiResponse(code = 400, message = "Bad Request") })
+	@RequestMapping(value = "/ProteinIdentifierRecognitionQuery", method = RequestMethod.GET, produces = "application/json")
+	@ResponseBody
+	@ResponseStatus(HttpStatus.OK)
+	public boolean getExistedEnsemblidinAlignment(
+			@RequestParam @ApiParam(value = "Input ensembl id. For example ENSP00000483207.2", required = true, allowMultiple = true) String ensemblId) {
+		try {
+			List<Alignment> it = alignmentRepository.findByEnsemblId(ensemblId);
+			if (it.size() != 0) {
+				return true;
+			} else {
+				return false;
+			}
+		} catch (Exception ex) {
+			ex.printStackTrace();
+		}
+		return false;
+	}
 
 }

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/domain/AlignmentRepository.java

@@ -0,0 +1,20 @@
+package org.cbioportal.pdb_annotation.web.domain;
+
+import java.util.List;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+/**
+ * 
+ * @author Juexin Wang
+ *
+ */
+@Transactional
+public interface AlignmentRepository extends JpaRepository<Alignment, Long>{
+
+	public List<Alignment> findByEnsemblId(String ensemblId);	
+
+}

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/domain/EnsemblRepository.java

@@ -0,0 +1,20 @@
+package org.cbioportal.pdb_annotation.web.domain;
+
+import java.util.List;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.cbioportal.pdb_annotation.web.models.Ensembl;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+/**
+ * 
+ * @author Juexin Wang
+ *
+ */
+@Transactional
+public interface EnsemblRepository extends JpaRepository<Alignment, Long>{
+
+	public List<Ensembl> findByEnsemblId(String ensemblId);
+}

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/domain/PdbRepository.java

@@ -0,0 +1,16 @@
+package org.cbioportal.pdb_annotation.web.domain;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+/**
+ * 
+ * @author Juexin Wang
+ *
+ */
+@Transactional
+public interface PdbRepository extends JpaRepository<Alignment, Long>{
+
+}

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/models/Alignment.java

@@ -6,7 +6,12 @@
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.Table;
-import javax.validation.constraints.NotNull;
+
+/**
+ * 
+ * @author Juexin Wang
+ *
+ */
 
 @Entity
 @Table(name = "pdb_ensembl_alignment")
@@ -55,16 +60,14 @@ public class Alignment {
 	  @Column(name = "IDENTP")
 	  private float identp;
 
-	  /*
 	  @Column(name = "ENSEMBL_ALIGN")
-	  private String ensemblalign;
+	  private String ensemblAlign;
 
 	  @Column(name = "PDB_ALIGN")
-	  private String pdbalign;
+	  private String pdbAlign;
 
 	  @Column(name = "MIDLINE_ALIGN")
-	  private String midlinealign;
-	  */
+	  private String midlineAlign;
 
 
 	  // ------------------------
@@ -175,33 +178,32 @@ public float getIdentp() {
 	public void setIdentp(float identp) {
 		this.identp = identp;
 	}
-
-	/*
-	public String getEnsemblalign() {
-		return ensemblalign;
+	
+
+	public String getEnsemblAlign() {
+		return ensemblAlign;
 	}
 
-	public void setEnsemblalign(String ensemblalign) {
-		this.ensemblalign = ensemblalign;
+	public void setEnsemblAlign(String ensemblAlign) {
+		this.ensemblAlign = ensemblAlign;
 	}
 
-	public String getPdbalign() {
-		return pdbalign;
+	public String getPdbAlign() {
+		return pdbAlign;
 	}
 
-	public void setPdbalgin(String pdbalign) {
-		this.pdbalign = pdbalign;
+	public void setPdbAlign(String pdbAlign) {
+		this.pdbAlign = pdbAlign;
 	}
 
-	public String getMidlinealign() {
-		return midlinealign;
+	public String getMidlineAlign() {
+		return midlineAlign;
 	}
 
-	public void setMidlinealign(String midlinealign) {
-		this.midlinealign = midlinealign;
+	public void setMidlineAlign(String midlineAlign) {
+		this.midlineAlign = midlineAlign;
 	}
-	*/
-
+
 	/**
 	 * Construction Function
 	 */