Merge remote-tracking branch 'origin/feature/web-extjs' into develop

Conflicts:
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/FilesWSServer.java
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/GeneWSServer.java
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/RegionWSServer.java
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/StudyWSServer.java
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/VariantWSServer.java
	eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/ga4gh/GA4GHVariantCallSetWSServer.java
	eva-web/src/js/eva-variant-widget-panel.js
	eva-web/src/js/variant-widget/eva-variant-widget.js

eva-server/pom.xml

@@ -68,7 +68,11 @@
             <artifactId>jersey-media-multipart</artifactId>
             <version>2.7</version>
         </dependency>
-
+        <dependency>
+            <groupId>com.wordnik</groupId>
+            <artifactId>swagger-jersey2-jaxrs_2.11</artifactId>
+            <version>1.3.10</version>
+        </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
             <artifactId>javax.servlet-api</artifactId>

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/CORSResponseFilter.java → eva-server/src/main/java/uk/ac/ebi/variation/eva/server/CORSResponseFilter.java

@@ -1,4 +1,4 @@
-package uk.ac.ebi.variation.eva.server.ws;
+package uk.ac.ebi.variation.eva.server;
 
 import java.io.IOException;
 

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/EvaWSRegistry.java

@@ -1,15 +1,15 @@
 package uk.ac.ebi.variation.eva.server;
 
 import org.glassfish.jersey.server.ResourceConfig;
-import uk.ac.ebi.variation.eva.server.ws.CORSResponseFilter;
 
 /**
  * Created by imedina on 01/04/14.
+ * @author imedina
  */
 public class EvaWSRegistry extends ResourceConfig {
 
     public EvaWSRegistry() {
-        packages("uk.ac.ebi.variation.eva.server.ws");
+//        packages("uk.ac.ebi.variation.eva.server.ws");
         register(CORSResponseFilter.class);
     }
 

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/exception/SpeciesException.java

@@ -0,0 +1,9 @@
+package uk.ac.ebi.variation.eva.server.exception;
+
+@SuppressWarnings("serial")
+public class SpeciesException extends Exception {
+
+	public SpeciesException(String msg) {
+		super(msg);
+	}
+}

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/exception/VersionException.java

@@ -0,0 +1,11 @@
+package uk.ac.ebi.variation.eva.server.exception;
+
+
+@SuppressWarnings("serial")
+public class VersionException extends Exception {
+
+	public VersionException(String msg) {
+		super(msg);
+	}
+
+}

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/EvaWSServer.java

@@ -5,40 +5,47 @@
 import com.fasterxml.jackson.databind.ObjectWriter;
 import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import com.google.common.base.Splitter;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
+import javax.ws.rs.*;
 import javax.ws.rs.core.*;
+
+import com.wordnik.swagger.annotations.ApiParam;
 import org.opencb.biodata.models.feature.Genotype;
 import org.opencb.biodata.models.variant.VariantSourceEntry;
 import org.opencb.biodata.models.variant.VariantSource;
 import org.opencb.biodata.models.variant.stats.VariantStats;
 import org.opencb.datastore.core.QueryOptions;
 import org.opencb.datastore.core.QueryResponse;
-import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException;
 import org.opencb.opencga.storage.core.variant.io.json.VariantSourceEntryJsonMixin;
 import org.opencb.opencga.storage.core.variant.io.json.GenotypeJsonMixin;
 import org.opencb.opencga.storage.core.variant.io.json.VariantSourceJsonMixin;
 import org.opencb.opencga.storage.core.variant.io.json.VariantStatsJsonMixin;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import uk.ac.ebi.variation.eva.server.exception.SpeciesException;
+import uk.ac.ebi.variation.eva.server.exception.VersionException;
 
 /**
  * Created by imedina on 01/04/14.
  */
 @Path("/{version}")
-//@Produces(MediaType.APPLICATION_JSON)
+@Produces("application/json")
 public class EvaWSServer {
 
-    // output content format: txt or text, json, xml, das
-    protected String outputFormat;
-
+    @DefaultValue("")
+    @PathParam("version")
+    @ApiParam(name = "version", value = "EVA REST WS version", defaultValue = "v1")
     protected String version;
+
+    @DefaultValue("Homo sapiens")
+    @QueryParam("species")
+    @ApiParam(name = "species", value = "Excluded fields will not be returned. Comma separated JSON paths must be provided",
+            defaultValue = "hsapiens", allowableValues = "hsapiens,mmusculus")
+    protected String species;
+
     protected UriInfo uriInfo;
     protected HttpServletRequest httpServletRequest;
 
@@ -47,6 +54,36 @@ public class EvaWSServer {
     protected long startTime;
     protected long endTime;
 
+    @DefaultValue("")
+    @QueryParam("exclude")
+    @ApiParam(name = "excluded fields", value = "Excluded fields will not be returned. Comma separated JSON paths must be provided")
+    protected String exclude;
+
+    @DefaultValue("")
+    @QueryParam("include")
+    @ApiParam(name = "included fields", value = "Included fields are the only to be returned. Comma separated JSON path must be provided")
+    protected String include;
+
+    @DefaultValue("-1")
+    @QueryParam("limit")
+    @ApiParam(name = "limit", value = "Max number of results to be returned. No limit applied when -1 [-1]")
+    protected int limit;
+
+    @DefaultValue("-1")
+    @QueryParam("skip")
+    @ApiParam(name = "skip", value = "Number of results to be skipped. No skip applied when -1 [-1]")
+    protected int skip;
+
+    @DefaultValue("false")
+    @QueryParam("count")
+    @ApiParam(name = "count", value = "The total number of results is returned [false]")
+    protected String count;
+
+    @DefaultValue("json")
+    @QueryParam("of")
+    @ApiParam(name = "Output format", value = "Output format, Protobuf is not yet implemented", defaultValue = "json", allowableValues = "json,pb (Not implemented yet)")
+    protected String outputFormat;
+
     protected static ObjectMapper jsonObjectMapper;
     protected static ObjectWriter jsonObjectWriter;
     protected static XmlMapper xmlObjectMapper;
@@ -69,6 +106,7 @@ public class EvaWSServer {
         logger.info("EvaWSServer: Initialising attributes inside static block");
     }
 
+    @Deprecated
     public EvaWSServer() {
         logger.info("EvaWSServer: in 'constructor'");
     }
@@ -88,49 +126,46 @@ protected void init(String version, UriInfo uriInfo) {
         startTime = System.currentTimeMillis();
         queryResponse = new QueryResponse();
 
-
+        // TODO A properties files may be needed to load valid versions and species
         // load properties file
         // ResourceBundle databaseConfig =
         // ResourceBundle.getBundle("org.bioinfo.infrared.ws.application");
         // config = new Config(databaseConfig);
 
-
         // mediaType = MediaType.valueOf("text/plain");
         queryOptions = new QueryOptions();
         // logger = new Logger();
         // logger.setLevel(Logger.DEBUG_LEVEL);
         logger.info("GenericrestWSServer: in 'init' method");
-
-        /**
-         * Check version parameter, must be: v1, v2, ... If 'latest' then is
-         * converted to appropriate version
-         */
-        // if(version != null && version.equals("latest") &&
-        // config.getProperty("CELLBASE.LATEST.VERSION") != null) {
-        // version = config.getProperty("CELLBASE.LATEST.VERSION");
-        // System.out.println("version init: "+version);
-        // }
-
-        // this code MUST be run before the checking
-        parseCommonQueryParameters(uriInfo.getQueryParameters());
     }
 
-    private void parseCommonQueryParameters(MultivaluedMap<String, String> multivaluedMap) {
+
+    protected void checkParams() throws VersionException, SpeciesException {
+        // TODO A Version and Species checker must be implemented
+        if (version == null || !version.equals("v1")) {
+            throw new VersionException("Version not valid: '" + version + "'");
+        }
+        if (species == null || species.isEmpty()/*|| !isValidSpecies(species)*/) {
+            throw new SpeciesException("Species not valid: '" + species + "'");
+        }
+
+        MultivaluedMap<String, String> multivaluedMap = uriInfo.getQueryParameters();
+        queryOptions.put("species", species);
+
         queryOptions.put("metadata", (multivaluedMap.get("metadata") != null) ? multivaluedMap.get("metadata").get(0).equals("true") : true);
-        queryOptions.put("exclude", (multivaluedMap.get("exclude") != null) ? Splitter.on(",").splitToList(multivaluedMap.get("exclude").get(0)) : null);
-        queryOptions.put("include", (multivaluedMap.get("include") != null) ? Splitter.on(",").splitToList(multivaluedMap.get("include").get(0)) : null);
-        queryOptions.put("limit", (multivaluedMap.get("limit") != null) ? multivaluedMap.get("limit").get(0) : -1);
-        queryOptions.put("skip", (multivaluedMap.get("skip") != null) ? multivaluedMap.get("skip").get(0) : -1);
-        queryOptions.put("count", (multivaluedMap.get("count") != null) ? Boolean.parseBoolean(multivaluedMap.get("count").get(0)) : false);
-
-        outputFormat = (multivaluedMap.get("of") != null) ? multivaluedMap.get("of").get(0) : "json";
-//        outputCompress = (multivaluedMap.get("outputcompress") != null) ? multivaluedMap.get("outputcompress").get(0) : "false";
+        queryOptions.put("exclude", (exclude != null && !exclude.equals("")) ? Splitter.on(",").splitToList(exclude) : null);
+        queryOptions.put("include", (include != null && !include.equals("")) ? Splitter.on(",").splitToList(include) : null);
+        queryOptions.put("limit", (limit > 0) ? limit : -1);
+        queryOptions.put("skip", (skip > 0) ? skip : -1);
+        queryOptions.put("count", (count != null && !count.equals("")) ? Boolean.parseBoolean(count) : false);
+
+        outputFormat = (outputFormat != null && !outputFormat.equals("")) ? outputFormat : "json";
     }
-    
+
     @GET
     @Path("/test")
     public Response help() {
-        return createOkResponse("No help available");
+        return createOkResponse("No help available yet");
     }
 
 

eva-server/src/main/java/uk/ac/ebi/variation/eva/server/ws/FilesWSServer.java

@@ -5,56 +5,66 @@
 import java.util.Arrays;
 import javax.naming.NamingException;
 import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
+import javax.ws.rs.*;
 import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 import javax.ws.rs.core.UriInfo;
+
+import com.wordnik.swagger.annotations.Api;
+import com.wordnik.swagger.annotations.ApiOperation;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantSourceDBAdaptor;
 import uk.ac.ebi.variation.eva.lib.datastore.DBAdaptorConnector;
 import uk.ac.ebi.variation.eva.lib.storage.metadata.VariantSourceEvaproDBAdaptor;
+import uk.ac.ebi.variation.eva.server.exception.SpeciesException;
+import uk.ac.ebi.variation.eva.server.exception.VersionException;
 
 /**
  *
  * @author Cristina Yenyxe Gonzalez Garcia <cyenyxe@ebi.ac.uk>
  */
 @Path("/{version}/files")
-@Produces(MediaType.APPLICATION_JSON)
+@Produces("application/json")
+@Api(value = "Files", description = "Files RESTful Web Services API")
 public class FilesWSServer extends EvaWSServer {
-    
+
     private VariantSourceDBAdaptor variantSourceEvaproDbAdaptor;
 
-    public FilesWSServer() throws IllegalOpenCGACredentialsException {
-        super();
-    }
 
-    public FilesWSServer(@DefaultValue("") @PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) 
-            throws NamingException {
+    public FilesWSServer(@DefaultValue("") @PathParam("version") String version,
+                         @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws NamingException {
         super(version, uriInfo, hsr);
         variantSourceEvaproDbAdaptor = new VariantSourceEvaproDBAdaptor();
     }
 
     @GET
     @Path("/all")
+    @ApiOperation(httpMethod = "GET", value = "Gets the files of a species")
     public Response getFiles(@QueryParam("species") String species) 
             throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
-        if (species != null && !species.isEmpty()) {
-            queryOptions.put("species", species);
+        try {
+            checkParams();
+        } catch (VersionException | SpeciesException ex) {
+            return createErrorResponse(ex.toString());
         }
+
         VariantSourceDBAdaptor variantSourceMongoDbAdaptor = DBAdaptorConnector.getVariantSourceDBAdaptor(species);
         return createOkResponse(variantSourceMongoDbAdaptor.getAllSources(queryOptions));
     }
-    
+
     @GET
     @Path("/{files}/url")
+    @ApiOperation(httpMethod = "GET", value = "Gets the URL of a file")
     public Response getFileUrl(@PathParam("files") String filenames) {
+        try {
+            checkParams();
+        } catch (VersionException | SpeciesException ex) {
+            return createErrorResponse(ex.toString());
+        }
+
         return createOkResponse(variantSourceEvaproDbAdaptor.getSourceDownloadUrlByName(Arrays.asList(filenames.split(","))));
     }
-    
+
 }