continuous data compliance finished (#248)

* continuous data compliance finsihed

* Move parent pom to master

ctk-transport/src/main/java/org/ga4gh/ctk/transport/URLMAPPING.java

@@ -146,6 +146,18 @@ public interface URLMAPPING {
 
     void setGetFeature(String getFeature);
 
+    String getSearchContinuousSets();
+
+    void setSearchContinuousSets(String searchContinuousSets);
+
+    String getGetContinuousSet();
+
+    void setGetContinuousSet(String getContinuousSet);
+
+    String getSearchContinuous();
+
+    void setSearchContinuous(String searchContinuous);
+
 
     String getGetRnaQuantification();
 

ctk-transport/src/main/java/org/ga4gh/ctk/transport/URLMAPPINGImpl.java

@@ -91,6 +91,9 @@ public class URLMAPPINGImpl implements URLMAPPING {
         defaultEndpoints.put("ctk.tgt.getFeatureSets", "featuresets/{id}");
         defaultEndpoints.put("ctk.tgt.searchFeatures", "features/search");
         defaultEndpoints.put("ctk.tgt.getFeatures", "features/{id}");
+        defaultEndpoints.put("ctk.tgt.searchContinuousSets", "continuoussets/search");
+        defaultEndpoints.put("ctk.tgt.getContinuousSets", "continuoussets/{id}");
+        defaultEndpoints.put("ctk.tgt.searchContinuous", "continuous/search");
         defaultEndpoints.put("ctk.tgt.searchPhenotypeAssociationSets","phenotypeassociationsets/search");
 
         defaultEndpoints.put("ctk.tgt.searchGenotypePhenotype", "featurephenotypeassociations/search");
@@ -547,6 +550,36 @@ public String getGetFeature() {
         return endpoints.get("ctk.tgt.getFeatures");
     }
 
+    @Override
+    public String getSearchContinuousSets() {
+        return endpoints.get("ctk.tgt.searchContinuousSets");
+    }
+
+    @Override
+    public void setSearchContinuousSets(String searchContinuousSets) {
+        endpoints.put("ctk.tgt.searchContinuousSets", searchContinuousSets);
+    }
+
+    @Override
+    public void setGetContinuousSet(String getContinuousSets) {
+        endpoints.put("ctk.tgt.getContinuousSets", getContinuousSets);
+    }
+
+    @Override
+    public String getGetContinuousSet() {
+        return endpoints.get("ctk.tgt.getContinuousSets");
+    }
+
+    @Override
+    public String getSearchContinuous() {
+        return endpoints.get("ctk.tgt.searchContinuous");
+    }
+
+    @Override
+    public void setSearchContinuous(String searchContinuous) {
+        endpoints.put("ctk.tgt.searchContinuouss", searchContinuous);
+    }
+
     @Override
     public String getGetRnaQuantification() { return endpoints.get("ctk.tgt.getRnaQuantification"); }
 

ctk-transport/src/main/java/org/ga4gh/ctk/transport/protocols/Client.java

@@ -36,6 +36,11 @@
 import ga4gh.SequenceAnnotationServiceOuterClass.SearchFeaturesResponse;
 import ga4gh.SequenceAnnotations.Feature;
 import ga4gh.SequenceAnnotations.FeatureSet;
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousSetsRequest;
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousSetsResponse;
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousResponse;
+import ga4gh.SequenceAnnotations.Continuous;
+import ga4gh.SequenceAnnotations.ContinuousSet;
 import ga4gh.VariantServiceOuterClass.*;
 import ga4gh.Variants.CallSet;
 import ga4gh.Variants.Variant;
@@ -515,7 +520,31 @@ public Feature getFeature(String id) throws InvalidProtocolBufferException, GAWr
             return builder.build();
         }
 
+        public SearchContinuousSetsResponse searchContinuousSets(SearchContinuousSetsRequest request) throws InvalidProtocolBufferException, GAWrapperException, UnirestException {
+            String path = urls.getSearchContinuousSets();
+            SearchContinuousSetsResponse.Builder responseBuilder = SearchContinuousSetsResponse.newBuilder();
+            new Post<>(urls.getUrlRoot(), path, request, responseBuilder, wireTracker).performQuery();
+            return responseBuilder.build();
+        }
+
+
+        public ContinuousSet getContinuousSet(String id) throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+            String path = urls.getGetContinuousSet();
+            ContinuousSet.Builder builder = ContinuousSet.newBuilder();
+            new Get<>(urls.getUrlRoot(), path, id, null, builder, wireTracker).performQuery();
+            return builder.build();
+        }
+
+        public SearchContinuousResponse searchContinuous(SequenceAnnotationServiceOuterClass.SearchContinuousRequest request)
+                throws InvalidProtocolBufferException, GAWrapperException, UnirestException {
+            String path = urls.getSearchContinuous();
+            SearchContinuousResponse.Builder responseBuilder = SearchContinuousResponse.newBuilder();
+            new Post<>(urls.getUrlRoot(), path, request, responseBuilder, wireTracker).performQuery();
+            return responseBuilder.build();
+        }
+
     }
+
     /**
      * Inner class holding all biodata-related methods.  Gathering them in an inner class like
      * this makes it a little easier for someone writing tests to use their IDE's auto-complete

ctk-transport/src/main/resources/defaulttransport.properties

@@ -31,4 +31,6 @@ ctk.tgt.searchGenotypePhenotype=featurephenotypeassociations/search
 ctk.tgt.searchPhenotypes=phenotypes/search
 ctk.tgt.searchFeatures=features/search
 ctk.tgt.searchFeatureSets=featuresets/search
+ctk.tgt.searchContinuous=continuous/search
+ctk.tgt.searchContinuousSets=continuoussets/search
 ctk.tgt.searchPhenotypeAssociationSets=phenotypeassociationsets/search

cts-java/src/main/resources/defaulttransport.properties

@@ -31,4 +31,6 @@ ctk.tgt.searchGenotypePhenotype=featurephenotypeassociations/search
 ctk.tgt.searchPhenotypes=phenotypes/search
 ctk.tgt.searchFeatures=features/search
 ctk.tgt.searchFeatureSets=featuresets/search
+ctk.tgt.searchContinuous=continuous/search
+ctk.tgt.searchContinuousSets=continuoussets/search
 ctk.tgt.searchPhenotypeAssociationSets=phenotypeassociationsets/search

cts-java/src/test/java/org/ga4gh/cts/api/Utils.java

@@ -20,6 +20,7 @@
 import ga4gh.References.*;
 import ga4gh.ReferenceServiceOuterClass.*;
 import ga4gh.SequenceAnnotationServiceOuterClass.SearchFeatureSetsRequest;
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousSetsRequest;
 import ga4gh.SequenceAnnotations.*;
 import ga4gh.Variants.*;
 import ga4gh.VariantServiceOuterClass.*;
@@ -794,6 +795,72 @@ public static FeatureSet getFeatureSetByName(Client client, String name) throws
         }
         return featureSets.get(0);
     }
+
+    /**
+     * Search for and return all {@link ContinuousSet}s.
+     *
+     * @param client the connection to the server
+     * @return the {@link List} of results
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    public static List<ContinuousSet> getAllContinuousSets(Client client) throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+
+        final List<ContinuousSet> result = new LinkedList<>();
+        String pageToken = "";
+        do {
+            final SearchContinuousSetsRequest req =
+                    SearchContinuousSetsRequest.newBuilder()
+                            .setDatasetId(TestData.getDatasetId())
+                            .setPageSize(100)
+                            .setPageToken(pageToken)
+                            .build();
+            final SearchContinuousSetsResponse resp = client.sequenceAnnotations.searchContinuousSets(req);
+            pageToken = resp.getNextPageToken();
+            result.addAll(resp.getContinuousSetsList());
+        } while (!pageToken.equals(""));
+
+        return result;
+    }
+
+    /**
+     * Utility method to fetch the Id of a {@link ContinuousSet} for the compliance dataset.
+     * @param client the connection to the server
+     * @return the ID of a {@link ContinuousSet}
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    public static String getContinuousSetId(Client client) throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+
+        // get all compliance continuous sets
+        final List<ContinuousSet> continuousSets = getAllContinuousSets(client);
+        return continuousSets.get(0).getId();
+    }
+
+    /**
+     * Given a name, return the continuous  set corresponding to that name. When that name
+     * is not found returns the first continuous  set found.
+     * @param client the connection to the server
+     * @param name the string name of the annotation set
+     * @return a {@link ContinuousSet} with the requested name
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    public static ContinuousSet getContinuousSetByName(Client client, String name) throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+
+        // get all compliance continuous sets
+        final List<ContinuousSet> continuousSets = getAllContinuousSets(client);
+        for (ContinuousSet fs : continuousSets) {
+            if (fs.getName().equals(name)) {
+                return fs;
+            }
+        }
+        return continuousSets.get(0);
+    }
+
     /**
      * Sugar for getting the first Biosample result that matches the name search request.
      * @param client

cts-java/src/test/java/org/ga4gh/cts/api/sequenceAnnotations/ContinuousSearchIT.java

@@ -0,0 +1,65 @@
+package org.ga4gh.cts.api.sequenceAnnotations;
+
+import com.google.protobuf.InvalidProtocolBufferException;
+
+import com.mashape.unirest.http.exceptions.UnirestException;
+
+import org.ga4gh.ctk.CtkLogs;
+import org.ga4gh.ctk.transport.GAWrapperException;
+import org.ga4gh.ctk.transport.URLMAPPING;
+import org.ga4gh.ctk.transport.protocols.Client;
+import org.ga4gh.cts.api.TestData;
+import org.ga4gh.cts.api.Utils;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+import java.util.List;
+import java.util.function.Consumer;
+
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousRequest;
+import ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousResponse;
+import ga4gh.SequenceAnnotations.Continuous;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Test searching continuous data.
+ */
+@Category(SequenceAnnotationTests.class)
+public class ContinuousSearchIT implements CtkLogs {
+
+    private static Client client = new Client(URLMAPPING.getInstance());
+
+
+    /**
+     * Fetch continuous data between two positions in the reference.  The number of values  must
+     * equal what we're expecting by examination of the continuous data.
+     *
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+
+    @Test
+    public void checkExpectedNumberOfValues() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+        final long start = 50083750;
+        final long end = 50083800;
+        final String referenceName = "chr19";
+        final int expectedNumberOfValues = 25;
+
+        final String id = Utils.getContinuousSetId(client);
+
+        final SearchContinuousRequest fReq =
+                SearchContinuousRequest.newBuilder()
+                                     .setContinuousSetId(id)
+                                     .setReferenceName(referenceName)
+                                     .setStart(start).setEnd(end)
+                                     .build();
+        final SearchContinuousResponse fResp = client.sequenceAnnotations.searchContinuous(fReq);
+        final List<Continuous> searchContinuous = fResp.getContinuousList();
+
+        assertThat(searchContinuous).isNotEmpty();
+        Continuous msg = searchContinuous.get(0);
+        assertThat(msg.getValuesList()).hasSize(expectedNumberOfValues);
+    }
+}

cts-java/src/test/java/org/ga4gh/cts/api/sequenceAnnotations/ContinuousSetsGetByIdIT.java

@@ -0,0 +1,58 @@
+package org.ga4gh.cts.api.sequenceAnnotations;
+
+import com.google.protobuf.InvalidProtocolBufferException;
+
+import com.mashape.unirest.http.exceptions.UnirestException;
+
+import org.ga4gh.ctk.transport.GAWrapperException;
+import org.ga4gh.ctk.transport.URLMAPPING;
+import org.ga4gh.ctk.transport.protocols.Client;
+import org.ga4gh.cts.api.Utils;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+import org.junit.runner.RunWith;
+
+import java.util.List;
+
+import ga4gh.SequenceAnnotations.ContinuousSet;
+import junitparams.JUnitParamsRunner;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Tests for <tt>GET /continuousSets/{id}</tt>.
+ *
+ * @author Maciek Smuga-Otto
+ */
+@Category(SequenceAnnotationTests.class)
+@RunWith(JUnitParamsRunner.class)
+public class ContinuousSetsGetByIdIT {
+
+    private static Client client = new Client(URLMAPPING.getInstance());
+
+    /**
+     * Verify that ContinuousSets that we obtain by way of {@link ga4gh.SequenceAnnotationServiceOuterClass.SearchContinuousSetsRequest }
+     * match the ones we get via <tt>GET /continuousSets/{id}</tt>.
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    @Test
+    public void checkContinuousSetsGetResults() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+        final int expectedNumberOfContinuousSets = 1;
+
+        final List<ContinuousSet> continuousSets = Utils.getAllContinuousSets(client);
+
+        assertThat(continuousSets).hasSize(expectedNumberOfContinuousSets);
+
+        for (final ContinuousSet continuousSetFromSearch : continuousSets) {
+            final ContinuousSet continuousSetFromGet = client.sequenceAnnotations.getContinuousSet(continuousSetFromSearch.getId());
+            assertThat(continuousSetFromGet).isNotNull();
+
+            assertThat(continuousSetFromGet).isEqualTo(continuousSetFromSearch);
+        }
+
+    }
+
+
+}

cts-java/src/test/java/org/ga4gh/cts/api/sequenceAnnotations/ContinuousSetsSearchIT.java

@@ -0,0 +1,55 @@
+package org.ga4gh.cts.api.sequenceAnnotations;
+
+import com.google.protobuf.InvalidProtocolBufferException;
+
+import com.mashape.unirest.http.exceptions.UnirestException;
+
+import org.assertj.core.api.StrictAssertions;
+import org.ga4gh.ctk.transport.GAWrapperException;
+import org.ga4gh.ctk.transport.URLMAPPING;
+import org.ga4gh.ctk.transport.protocols.Client;
+import org.ga4gh.cts.api.Utils;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+import java.util.List;
+
+import ga4gh.SequenceAnnotations.ContinuousSet;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ *  Tests for <tt>POST /continuousSets/search</tt>.
+ *
+ * @author Maciek Smuga-Otto
+ */
+@Category(SequenceAnnotationTests.class)
+public class ContinuousSetsSearchIT {
+
+
+    private static Client client = new Client(URLMAPPING.getInstance());
+
+    /**
+     * Check SequenceAnnotationSets contain some analysis data.
+     * @throws GAWrapperException if the server finds the request invalid in some way
+     * @throws UnirestException if there's a problem speaking HTTP to the server
+     * @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
+     */
+    @Test
+    public void checkSearchingContinuousSets() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
+
+        // Seek a list of SequenceAnnotationSets for the compliance dataset.
+        final List<ContinuousSet> continuousSets = Utils.getAllContinuousSets(client);
+
+        // check some are available
+        assertThat(continuousSets).isNotEmpty();
+
+        // Check the continuousSetId is as expected.
+        continuousSets.stream()
+                .forEach(sas -> StrictAssertions.assertThat(sas.getName()).isNotNull());
+    }
+
+
+}
+
+