Merge pull request ga4gh#168 from david4096/va_created_check

Check created time of analysis field

ctk-schemas/src/main/resources/avro/alleleAnnotations.avdl

@@ -182,8 +182,8 @@ record VariantAnnotation {
   /** The ID of the variant annotation set this record belongs to. */
   string variantAnnotationSetId;
 
-  /** The date this annotation was created in milliseconds from the epoch. */
-  union { null, long } created = null;
+  /** The :ref:`ISO 8601 <metadata_date_time>` time at which this record was created. */
+  union { null, string } created = null;
 
   /**
   The transcript effect annotation for the alleles of this variant. Each one

ctk-schemas/src/main/resources/avro/metadata.avdl

@@ -58,20 +58,20 @@ record Experiment {
 
   /**
   The time at which this record was created. 
-  Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
+  Format: :ref:`ISO 8601 <metadata_date_time>`
   */
-  string recordCreateTime;
+  string created;
 
   /**
   The time at which this record was last updated.
-  Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
+  Format: :ref:`ISO 8601 <metadata_date_time>`
   */
-  string recordUpdateTime;
+  string updated;
 
   /**
   The time at which this experiment was performed.
   Granularity here is variable (e.g. date only).
-  Format: ISO 8601, YYYY-MM-DDTHH:MM:SS (e.g. 2015-02-10T00:03:42)
+  Format: :ref:`ISO 8601 <metadata_date_time>`
   */
   union { null, string } runTime = null;
 
@@ -168,15 +168,15 @@ record Analysis {
 
   /**
   The time at which this record was created. 
-  Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
+  Format: :ref:`ISO 8601 <metadata_date_time>`
   */
-  union { null, string } recordCreateTime = null;
+  union { null, string } created = null;
 
   /**
   The time at which this record was last updated.
-  Format: ISO 8601, YYYY-MM-DDTHH:MM:SS.SSS (e.g. 2015-02-10T00:03:42.123Z)
+  Format: :ref:`ISO 8601 <metadata_date_time>`
   */
-  string recordUpdateTime;
+  string updated;
 
   /** The type of analysis. */
   union { null, string } type = null;

ctk-schemas/src/main/resources/avro/metadatamethods.avdl

@@ -0,0 +1,70 @@
+@namespace("org.ga4gh.methods")
+
+protocol MetadataMethods {
+
+import idl "metadata.avdl";
+import idl "common.avdl";
+import idl "methods.avdl";
+
+/******************  /datasets/search  *********************/
+/**
+This request maps to the body of `POST /datasets/search` as JSON.
+*/
+record SearchDatasetsRequest {
+
+  /**
+  Specifies the maximum number of results to return in a single page.
+  If unspecified, a system default will be used.
+  */
+  union { null, int } pageSize = null;
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  To get the next page of results, set this parameter to the value of
+  `nextPageToken` from the previous response.
+  */
+  union { null, string } pageToken = null;
+}
+
+/**
+This is the response from `POST /datasets/search` expressed as JSON.
+*/
+record SearchDatasetsResponse {
+  /** The list of datasets. */
+  array<org.ga4gh.models.Dataset> datasets = [];
+
+  /**
+  The continuation token, which is used to page through large result sets.
+  Provide this value in a subsequent request to return the next page of
+  results. This field will be empty if there aren't any additional results.
+  */
+  union { null, string } nextPageToken = null;
+}
+
+/**
+Gets a list of datasets accessible through the API.
+
+TODO: Reads and variants both want to have datasets. Are they the same object?
+
+`POST /datasets/search` must accept a JSON version of
+`SearchDatasetsRequest` as the post body and will return a JSON version
+of `SearchDatasetsResponse`.
+*/
+SearchDatasetsResponse searchDatasets(
+  /**
+  This request maps to the body of `POST /datasets/search` as JSON.
+  */
+  SearchDatasetsRequest request) throws GAException;
+
+/****************  /datasets/{id}  *******************/
+/**
+Gets a `Dataset` by ID.
+`GET /datasets/{id}` will return a JSON version of `Dataset`.
+*/
+org.ga4gh.models.Dataset getDataset(
+  /**
+  The ID of the `Dataset`.
+  */
+  string id) throws GAException;
+
+}

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

@@ -62,7 +62,7 @@ private TestData() {
      * The names of the variant annotation sets used for variant annotation in the standard test data.
      */
     public static final List<String> VARIANT_ANNOTATION_SET_NAMES =
-            Arrays.asList("WASH7P_annotation", "OR4F_annotation");
+            Arrays.asList("WASH7P", "OR4F");
 
     /**
      * The names of known-good read groups.

cts-java/src/test/java/org/ga4gh/cts/api/variantAnnotation/VariantAnnotationSetsSearchIT.java

@@ -2,25 +2,20 @@
 
 import org.apache.avro.AvroRemoteException;
 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.ga4gh.methods.*;
-import org.ga4gh.models.VariantSet;
 import org.ga4gh.models.VariantAnnotationSet;
-import org.ga4gh.models.AnalysisResult;
-import org.ga4gh.models.Analysis;
-import org.ga4gh.models.OntologyTerm;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 
-import java.net.HttpURLConnection;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.List;
 
 import static org.assertj.core.api.Assertions.*;
-import static org.ga4gh.cts.api.Utils.catchGAWrapperException;
 
 /**
  * Tests dealing with searching for VariantAnnotationSets.
@@ -80,7 +75,7 @@ public void checkGetVariantAnnotationSetById() throws AvroRemoteException {
      *@throws AvroRemoteException if there's a communication problem or server exception ({@link GAException})
      */
     @Test
-    public void checkVariantAnnotationAnalysis() throws AvroRemoteException {
+    public void checkVariantAnnotationAnalysis() throws AvroRemoteException, ParseException {
 
         // Seek a list of VariantAnnotationSets for the compliance dataset.
         final List<VariantAnnotationSet> variantAnnotationSets =  Utils.getAllVariantAnnotationSets(client);
@@ -91,12 +86,17 @@ public void checkVariantAnnotationAnalysis() throws AvroRemoteException {
         // Check the Analysis record within the VariantAnnotationSet matches the test data
         final String name        = "compliance1";
         final String description = "variant annotation test data";
-        final String created     = "2015-11-18T00:00:00.000000Z";
+        final String created     = "2015-11-18";
+        // TODO make a more robust ISO8601 parser
+        // Date formatting can be ISO compliant but still break these
+        // However, the second, df2 matches python's datetime.isoformat function
+        DateFormat df1 = new SimpleDateFormat("yyyy-MM-dd");
+        DateFormat df2 = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
         final String software    = "SnpEff";
 
         assertThat(vSet.getAnalysis().getName()).isEqualTo(name);
         assertThat(vSet.getAnalysis().getDescription()).isEqualTo(description);
-        assertThat(vSet.getAnalysis().getRecordCreateTime()).isEqualTo(created);
+        assertThat(df2.parse(vSet.getAnalysis().getCreated())).isEqualTo(df1.parse(created));
         assertThat(vSet.getAnalysis().getSoftware().get(0)).isEqualTo(software);
 
     }

cts-java/src/test/java/org/ga4gh/cts/api/variants/VariantSetsSearchIT.java

@@ -52,7 +52,7 @@ public void checkSearchingVariantSetsReturnsSome() throws AvroRemoteException {
      */
     @Test
     public void checkExpectedVariantSets() throws AvroRemoteException {
-        final int expectedNumberOfVariantSets = 2;
+        final int expectedNumberOfVariantSets = 3;
 
         final SearchVariantSetsRequest req =
                 SearchVariantSetsRequest.newBuilder()