Merge pull request #67 from rohankatyal29/master

[ FIX #51, #52 & #53 ] Update Python, NodeJS & Java BDK to API 0.2
mcupak · Mar 17, 2015 · 8ab733f · 8ab733f
2 parents 0ef6724 + 148dd14
commit 8ab733f
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diff --git a/beacon-adapters/beacon-java/README.md b/beacon-adapters/beacon-java/README.md
@@ -17,8 +17,8 @@ All you need to build this project is Java 7.0 (Java SDK 1.7) or later, Maven 3.
 ##How to run it
 Start the JBoss server:
 
-    For Linux:   JBOSS_HOME/bin/standalone.sh
-    For Windows: JBOSS_HOME\bin\standalone.bat
+    For Linux/Unix: JBOSS_HOME/bin/standalone.sh
+    For Windows: 	JBOSS_HOME\bin\standalone.bat
 
 Build and deploy the archive:
 
@@ -45,8 +45,8 @@ In order to create your own beacon, we suggest you do the following:
 
 The API takes care of the rest and provides the following endpoints upon deployment of your beacon:
 
-    http://localhost:8080/beacon-java/rest/info - information about your beacon
-    http://localhost:8080/beacon-java/rest/query - access to query service
+    http://localhost:8080/beacon-java/info - information about your beacon
+    http://localhost:8080/beacon-java/query - access to query service
 
 ##Technologies
 Java EE. CDI, JAX-RS, JAXB. Tested with Arquillian/ShrinkWrap.
diff --git a/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/Beacon.java b/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/Beacon.java
@@ -24,9 +24,16 @@
 package com.dnastack.beacon.entity;
 
 import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 import java.util.Objects;
+
 import javax.xml.bind.annotation.XmlRootElement;
 
+import com.dnastack.beacon.entity.resources.DataSetResource;
+import com.dnastack.beacon.entity.resources.QueryResource;
+
 /**
  * Beacon.
  *
@@ -42,18 +49,79 @@ public class Beacon implements Serializable {
     private String name;
     private String organization;
     private String description;
+	private String api;
+    private String homepage;
+    private String email;
+    private String auth = null;
+
+    private List<DataSetResource> queries;
+    private List<QueryResource> datasets;
 
     public Beacon() {
         // needed for JAXB
     }
 
-    public Beacon(String id, String name, String organization, String description) {
-        this.id = id;
+    public Beacon(String id, String name, String organization, String description, String api, String homepage, String email, String auth, List<DataSetResource> queries,  List<QueryResource> datasets) {
+    	this.id = id;
         this.name = name;
         this.organization = organization;
         this.description = description;
+        this.api = api;
+        this.homepage = homepage;
+        this.email = email;
+        this.auth = auth;
+        this.queries = queries;
+        this.datasets = datasets;
     }
 
+    public String getApi() {
+		return api;
+	}
+
+	public void setApi(String api) {
+		this.api = api;
+	}
+
+	public String getHomepage() {
+		return homepage;
+	}
+
+	public void setHomepage(String homepage) {
+		this.homepage = homepage;
+	}
+
+	public String getEmail() {
+		return email;
+	}
+
+	public void setEmail(String email) {
+		this.email = email;
+	}
+
+	public String getAuth() {
+		return auth;
+	}
+
+	public void setAuth(String auth) {
+		this.auth = auth;
+	}
+
+    public List<DataSetResource> getQueries() {
+		return queries;
+	}
+
+	public void setQueries(List<DataSetResource> queries) {
+		this.queries = queries;
+	}
+
+	public List<QueryResource> getDatasets() {
+		return datasets;
+	}
+
+	public void setDatasets(List<QueryResource> datasets) {
+		this.datasets = datasets;
+	}
+
     public String getId() {
         return id;
     }
@@ -93,6 +161,12 @@ public int hashCode() {
         hash = 61 * hash + Objects.hashCode(this.name);
         hash = 61 * hash + Objects.hashCode(this.organization);
         hash = 61 * hash + Objects.hashCode(this.description);
+        hash = 61 * hash + Objects.hashCode(this.api);
+        hash = 61 * hash + Objects.hashCode(this.homepage);
+        hash = 61 * hash + Objects.hashCode(this.email);
+        hash = 61 * hash + Objects.hashCode(this.auth);
+        hash = 61 * hash + Objects.hashCode(this.queries);
+        hash = 61 * hash + Objects.hashCode(this.datasets);
         return hash;
     }
 
@@ -117,12 +191,30 @@ public boolean equals(Object obj) {
         if (!Objects.equals(this.description, other.description)) {
             return false;
         }
+        if (!Objects.equals(this.api, other.api)) {
+            return false;
+        }
+        if (!Objects.equals(this.homepage, other.homepage)) {
+            return false;
+        }
+        if (!Objects.equals(this.email, other.email)) {
+            return false;
+        }
+        if (!Objects.equals(this.auth, other.auth)) {
+            return false;
+        }
+        if (!Objects.equals(this.queries, other.queries)) {
+            return false;
+        }
+        if (!Objects.equals(this.datasets, other.datasets)) {
+            return false;
+        }
         return true;
     }
 
     @Override
     public String toString() {
-        return "Beacon{" + "id=" + id + ", name=" + name + ", organization=" + organization + ", description=" + description + '}';
+        return "Beacon{" + "id=" + id + ", name=" + name + ", organization=" + organization + ", description=" + description + ", api=" + api + ", homepage=" + ", email=" + email +  ", auth=" + auth + " + " + ", queries=" + queries + ", datasets=" + datasets + "}";
     }
 
 }
diff --git a/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/BeaconResponse.java b/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/BeaconResponse.java
@@ -24,8 +24,12 @@
 package com.dnastack.beacon.entity;
 
 import java.io.Serializable;
+import java.util.Objects;
+
 import javax.xml.bind.annotation.XmlRootElement;
 
+import com.dnastack.beacon.entity.resources.ResponseResource;
+
 /**
  * Beacon response.
  *
@@ -37,48 +41,48 @@ public class BeaconResponse implements Serializable {
 
     private static final long serialVersionUID = 54L;
 
-    private Beacon beacon;
+    private String beacon_id;
     private Query query;
-    private Boolean response = null;
+    private ResponseResource response = null;
 
     public BeaconResponse() {
         // needed for JAXB
     }
 
-    public BeaconResponse(Beacon beacon, Query query, Boolean response) {
-        this.beacon = beacon;
+    public BeaconResponse(String beacon_id, Query query, ResponseResource response) {
+        this.beacon_id = beacon_id;
         this.query = query;
         this.response = response;
     }
 
-    public Beacon getBeacon() {
-        return beacon;
-    }
+    public String getBeacon_id() {
+		return beacon_id;
+	}
 
-    public void setBeacon(Beacon beacon) {
-        this.beacon = beacon;
-    }
+	public void setBeacon_id(String beacon_id) {
+		this.beacon_id = beacon_id;
+	}
 
-    public Query getQuery() {
+	public Query getQuery() {
         return query;
     }
 
     public void setQuery(Query query) {
         this.query = query;
     }
 
-    public Boolean getResponse() {
+    public ResponseResource getResponse() {
         return response;
     }
 
-    public void setResponse(Boolean response) {
+    public void setResponse(ResponseResource response) {
         this.response = response;
     }
 
     @Override
     public int hashCode() {
         int hash = 7;
-        hash = 41 * hash + (this.beacon != null ? this.beacon.hashCode() : 0);
+        hash = 41 * hash + Objects.hashCode(this.beacon_id);
         hash = 41 * hash + (this.query != null ? this.query.hashCode() : 0);
         hash = 41 * hash + (this.response != null ? this.response.hashCode() : 0);
         return hash;
@@ -93,7 +97,7 @@ public boolean equals(Object obj) {
             return false;
         }
         final BeaconResponse other = (BeaconResponse) obj;
-        if (this.beacon != other.beacon && (this.beacon == null || !this.beacon.equals(other.beacon))) {
+        if (this.beacon_id != other.beacon_id && (this.beacon_id == null || !this.beacon_id.equals(other.beacon_id))) {
             return false;
         }
         if (this.query != other.query && (this.query == null || !this.query.equals(other.query))) {
@@ -107,7 +111,7 @@ public boolean equals(Object obj) {
 
     @Override
     public String toString() {
-        return "Response of '" + beacon + "' to '" + query + "': '" + response + "'";
+        return "Response of '" + beacon_id + "' to '" + query + "': '" + response + "'";
     }
 
 }
diff --git a/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/Query.java b/beacon-adapters/beacon-java/src/main/java/com/dnastack/beacon/entity/Query.java
@@ -42,16 +42,18 @@ public class Query implements Serializable {
     private Long position;
     private String allele;
     private Reference reference;
+    private String dataset;
 
     public Query() {
         // needed for JAXB
     }
 
-    public Query(Chromosome chromosome, Long position, String allele, Reference reference) {
+    public Query(Chromosome chromosome, Long position, String allele, Reference reference, String dataset) {
         this.chromosome = chromosome;
         this.position = position;
         this.allele = allele;
         this.reference = reference;
+        this.dataset = dataset;
     }
 
     public Chromosome getChromosome() {
@@ -86,13 +88,22 @@ public void setReference(Reference reference) {
         this.reference = reference;
     }
 
-    @Override
+    public String getDataset() {
+		return dataset;
+	}
+
+	public void setDataset(String dataset) {
+		this.dataset = dataset;
+	}
+
+	@Override
     public int hashCode() {
         int hash = 3;
         hash = 89 * hash + Objects.hashCode(this.chromosome);
         hash = 89 * hash + Objects.hashCode(this.position);
         hash = 89 * hash + Objects.hashCode(this.allele);
         hash = 89 * hash + Objects.hashCode(this.reference);
+        hash = 89 * hash + Objects.hashCode(this.dataset);
         return hash;
     }
 
@@ -117,12 +128,15 @@ public boolean equals(Object obj) {
         if (this.reference != other.reference) {
             return false;
         }
+        if (this.dataset != other.dataset) {
+            return false;
+        }
         return true;
     }
 
     @Override
     public String toString() {
-        return "Query{" + "chromosome=" + chromosome + ", position=" + position + ", allele=" + allele + ", reference=" + reference + '}';
+        return "Query{" + "chromosome=" + chromosome + ", position=" + position + ", allele=" + allele + ", reference=" + reference + ", dataset=" + dataset + '}';
     }
 
 }
diff --git a/...apters/beacon-java/src/main/java/com/dnastack/beacon/entity/resources/AlleleResource.java b/...apters/beacon-java/src/main/java/com/dnastack/beacon/entity/resources/AlleleResource.java
@@ -0,0 +1,36 @@
+package com.dnastack.beacon.entity.resources;
+
+public class AlleleResource {
+
+	private String allele;
+	private Double frequency;
+
+	public AlleleResource() {
+		// needed for JAXB
+	}
+
+	/* 
+	 * Required field(s): allele  
+	 * frequency is a double between 0 & 1
+	*/
+	public AlleleResource(String allele, Double frequency) {
+		this.allele = allele;
+		this.frequency = frequency;
+	}
+
+	public String getAllele() {
+		return allele;
+	}
+
+	public void setAllele(String allele) {
+		this.allele = allele;
+	}
+
+	public Double getFrequency() {
+		return frequency;
+	}
+
+	public void setFrequency(Double frequency) {
+		this.frequency = frequency;
+	}
+}