Merge branch 'release/0.4.2'

Author: emersonf

README.md

@@ -1,4 +1,4 @@
-# Shimmer [![Build Status](https://travis-ci.org/openmhealth/shimmer.svg?branch=master)](https://travis-ci.org/openmhealth/shimmer)
+# Shimmer [![Build Status](https://travis-ci.org/openmhealth/shimmer.svg?branch=develop)](https://travis-ci.org/openmhealth/shimmer)
 
 Shimmer is an application that makes it easy to pull health data from popular third-party APIs like Runkeeper and Fitbit.
 It converts that data into an [Open mHealth](http://www.openmhealth.org) compliant format, letting your application work with clean and clinically meaningful data.   
@@ -98,6 +98,7 @@ If you want to build and run the code natively, in a terminal
 1. Run the `./run-natively.sh` script and follow the instructions.
 1. When the script blocks with the message `Started Application`, the components are running.
   * Press Ctrl-C to stop them.
+  * The script creates a WAR file which you can alternatively drop into an application server. [This issue](https://github.com/openmhealth/shimmer/issues/31) has details.
 1. Visit `http://localhost:8083` in a browser.
 
 If you want to build and run the code in Docker, in a terminal 

build.gradle

@@ -10,7 +10,7 @@ subprojects {
 
     ext {
         javaVersion = 1.8
-        shimmerVersion = '0.4.1'
+        shimmerVersion = '0.4.2'
         omhSchemaSdkVersion = '1.0.3'
     }
 

java-shim-sdk/build.gradle

@@ -31,14 +31,13 @@ archivesBaseName = 'omh-shim-sdk'
 version = '1.0.0'
 
 ext {
-    jacksonVersion = '2.5.3'
+    jacksonVersion = '2.6.1'
 }
 
 dependencies {
     compile "com.google.guava:guava:18.0"
     compile "com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}"
     compile "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
-    compile "joda-time:joda-time:2.5" // TODO remove this when refactored to java.time
     compile "org.openmhealth.schema:omh-schema-sdk:${omhSchemaSdkVersion}"
     compile 'org.slf4j:slf4j-api:1.7.12'
 

java-shim-sdk/src/main/java/org/openmhealth/shim/ShimDataRequest.java

@@ -16,14 +16,11 @@
 
 package org.openmhealth.shim;
 
-import org.joda.time.DateTime;
-
 import java.time.OffsetDateTime;
-import java.util.List;
+
 
 /**
- * A wrapper for encapsulating data requests sent
- * to shims. Prevents from having long method signatures.
+ * A wrapper for encapsulating data requests sent to shims. Prevents from having long method signatures.
  *
  * @author Danilo Bonilla
  */
@@ -34,15 +31,14 @@ public class ShimDataRequest {
      */
     private String dataTypeKey;
     /**
-     * parameters required for acessing data, this
-     * will likely be oauth token + any extras or some
-     * kind of trusted access.
+     * parameters required for acessing data, this will likely be oauth token + any extras or some kind of trusted
+     * access.
      */
     private AccessParameters accessParameters;
 
     /**
-     * // TODO replace this with filters on effective time, using the Data Point API
-     * The start date for the data being retrieved
+     * // TODO replace this with filters on effective time, using the Data Point API The start date for the data being
+     * retrieved
      */
     private OffsetDateTime startDateTime;
 
@@ -52,47 +48,10 @@ public class ShimDataRequest {
     private OffsetDateTime endDateTime;
 
     /**
-     * List of columns required
-     */
-    private List<String> columnList;
-
-    /**
-     * The starting row for the data (for pagination purposes)
-     */
-    private Long numToSkip;
-
-    /**
-     * Number of rows to return
-     */
-    private Long numToReturn;
-
-    /**
-     * If true, returns normalized results
-     * from the external data provider, otherwise
-     * returns raw data.
+     * If true, returns normalized results from the external data provider, otherwise returns raw data.
      */
     private boolean normalize = true;
 
-    public ShimDataRequest() {
-    }
-
-    public ShimDataRequest(String dataTypeKey,
-                           AccessParameters accessParameters,
-                           OffsetDateTime startDateTime,
-                           OffsetDateTime endDateTime,
-                           List<String> columnList,
-                           Long numToSkip,
-                           Long numToReturn,
-                           boolean normalize) {
-        this.dataTypeKey = dataTypeKey;
-        this.accessParameters = accessParameters;
-        this.startDateTime = startDateTime;
-        this.endDateTime = endDateTime;
-        this.columnList = columnList;
-        this.numToSkip = numToSkip;
-        this.numToReturn = numToReturn;
-        this.normalize = false;
-    }
 
     public void setDataTypeKey(String dataTypeKey) {
         this.dataTypeKey = dataTypeKey;
@@ -106,10 +65,6 @@ public OffsetDateTime getStartDateTime() {
         return startDateTime;
     }
 
-    public DateTime getStartDate() {
-        return getStartDateTime() == null ? null : new DateTime(getStartDateTime().toInstant());
-    }
-
     public void setStartDateTime(OffsetDateTime startDateTime) {
         this.startDateTime = startDateTime;
     }
@@ -118,25 +73,10 @@ public OffsetDateTime getEndDateTime() {
         return endDateTime;
     }
 
-    public DateTime getEndDate() {
-        return getStartDateTime() == null ? null : new DateTime(getStartDateTime().toInstant());
-    }
-
     public void setEndDateTime(OffsetDateTime endDateTime) {
         this.endDateTime = endDateTime;
     }
 
-    public void setColumnList(List<String> columnList) {
-        this.columnList = columnList;
-    }
-
-    public void setNumToSkip(Long numToSkip) {
-        this.numToSkip = numToSkip;
-    }
-
-    public void setNumToReturn(Long numToReturn) {
-        this.numToReturn = numToReturn;
-    }
 
     public String getDataTypeKey() {
         return dataTypeKey;
@@ -146,18 +86,6 @@ public AccessParameters getAccessParameters() {
         return accessParameters;
     }
 
-    public List<String> getColumnList() {
-        return columnList;
-    }
-
-    public Long getNumToSkip() {
-        return numToSkip;
-    }
-
-    public Long getNumToReturn() {
-        return numToReturn;
-    }
-
     public boolean getNormalize() {
         return normalize;
     }

java-shim-sdk/src/main/java/org/openmhealth/shim/common/mapper/DataPointMapper.java

@@ -2,9 +2,16 @@
 
 
 import org.openmhealth.schema.domain.omh.DataPoint;
+import org.openmhealth.schema.domain.omh.SchemaId;
+import org.openmhealth.schema.domain.omh.SchemaSupport;
 
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.ParameterizedType;
 import java.util.List;
 
+import static java.util.Collections.singletonList;
+
 
 /**
  * A mapper that creates data points from one or more inputs.
@@ -13,15 +20,46 @@
  * @param <I> the input type
  * @author Emerson Farrugia
  */
-public interface DataPointMapper<B, I> {
+public interface DataPointMapper<B extends SchemaSupport, I> {
 
     /**
-     * Maps one or more inputs into one or more data points. This cardinality allows a mapper to use different inputs
-     * to assemble a data point, e.g. combining a user profile API response and a blood pressure API response to build
-     * an identified blood pressure data point.
+     * Maps one or more inputs into one or more data points. The parameter cardinality allows a mapper to use different
+     * inputs to assemble a data point, e.g. combining a user profile API response and a blood pressure API response to
+     * build an identified blood pressure data point.
      *
      * @param inputs the list of inputs
-     * @return the list of data points
+     * @return the list of data points mapped from those inputs
      */
     List<DataPoint<B>> asDataPoints(List<I> inputs);
+
+    /**
+     * @see #asDataPoints(List)
+     */
+    default List<DataPoint<B>> asDataPoints(I input) {
+
+        return asDataPoints(singletonList(input));
+    }
+
+    /**
+     * Gets the schema identifier of the data point body that this mapper creates. This default implementation assumes
+     * that body classes have a default constructor used for serialization, and must be overridden if they don't.
+     *
+     * @return the schema identifier of the body type
+     */
+    @SuppressWarnings("unchecked")
+    default SchemaId getBodySchemaId() {
+
+        try {
+            Class<B> bodyClass = (Class<B>)
+                    ((ParameterizedType) getClass().getGenericSuperclass()).getActualTypeArguments()[0];
+
+            Constructor<B> bodyClassConstructor = bodyClass.getDeclaredConstructor();
+            bodyClassConstructor.setAccessible(true);
+
+            return bodyClassConstructor.newInstance().getSchemaId();
+        }
+        catch (NoSuchMethodException | InstantiationException | InvocationTargetException | IllegalAccessException e) {
+            throw new RuntimeException(e);
+        }
+    }
 }

java-shim-sdk/src/main/java/org/openmhealth/shim/common/mapper/JsonNodeDataPointMapper.java

@@ -1,6 +1,7 @@
 package org.openmhealth.shim.common.mapper;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import org.openmhealth.schema.domain.omh.SchemaSupport;
 
 
 /**
@@ -9,6 +10,6 @@
  * @param <B> the body type of the data points to create
  * @author Emerson Farrugia
  */
-public interface JsonNodeDataPointMapper<B> extends DataPointMapper<B, JsonNode> {
+public interface JsonNodeDataPointMapper<B extends SchemaSupport> extends DataPointMapper<B, JsonNode> {
 
 }

shim-server-ui/app/views/authorizationComplete.html

@@ -1,9 +1,9 @@
 <div ng-controller="MainCtrl">
-  <div class="authorization-complete-message">
-    <span ng-show="error">We're sorry, </span>
-    <span ng-show="!error">Great, </span>
-    authorization was <span ng-show="error">not </span>successful.<br/>
-    <br/>
-    This window should now close automatically.<br/>
-  </div>
-</div>
+    <div class="authorization-complete-message">
+        <span ng-show="error">We're sorry, </span>
+        <span ng-show="!error">Great, </span>
+        authorization was <span ng-show="error">not </span>successful.<br/>
+        <br/>
+        This window should now close automatically.<br/>
+    </div>
+</div>

shim-server-ui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "shim-server-ui",
-  "version": "0.4.1",
+  "version": "0.4.2",
   "dependencies": {},
   "devDependencies": {
     "grunt": "~0.4.5",