Merge pull request #3373 from IQSS/sbgrid-json-migration

Allow category of dataverse to be set via native API (using JSON)

doc/sphinx-guides/source/_static/api/dataverse-complete.json

@@ -0,0 +1,15 @@
+{
+  "name": "Scientific Research",
+  "alias": "science",
+  "dataverseContacts": [
+    {
+      "contactEmail": "pi@example.edu"
+    },
+    {
+      "contactEmail": "student@example.edu"
+    }
+  ],
+  "affiliation": "Scientific Research University",
+  "description": "We do all the science.",
+  "dataverseType": "LABORATORY"
+}

doc/sphinx-guides/source/_static/api/dataverse-minimal.json

@@ -0,0 +1,9 @@
+{
+  "name": "Scientific Research",
+  "alias": "science",
+  "dataverseContacts": [
+    {
+      "contactEmail": "pi@example.edu"
+    }
+  ]
+}

doc/sphinx-guides/source/api/native-api.rst

@@ -12,11 +12,24 @@ Endpoints
 
 Dataverses
 ~~~~~~~~~~~
-Generates a new dataverse under ``$id``. Expects a json content describing the dataverse.
+Generates a new dataverse under ``$id``. Expects a JSON content describing the dataverse, as in the example below.
 If ``$id`` is omitted, a root dataverse is created. ``$id`` can either be a dataverse id (long) or a dataverse alias (more robust). ::
 
     POST http://$SERVER/api/dataverses/$id?key=$apiKey
 
+The following JSON example can be `downloaded <../_static/api/dataverse-complete.json>`_ and modified to create dataverses to suit your needs. The fields ``name``, ``alias``, and ``dataverseContacts`` are required. The controlled vocabulary for ``dataverseType`` is
+
+- ``JOURNALS``
+- ``LABORATORY``
+- ``ORGANIZATIONS_INSTITUTIONS``
+- ``RESEARCHERS``
+- ``RESEARCH_GROUP``
+- ``RESEARCH_PROJECTS``
+- ``TEACHING_COURSES``
+- ``UNCATEGORIZED``
+
+.. literalinclude:: ../_static/api/dataverse-complete.json
+
 View data about the dataverse identified by ``$id``. ``$id`` can be the id number of the dataverse, its alias, or the special value ``:root``. ::
 
     GET http://$SERVER/api/dataverses/$id

src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java

@@ -130,6 +130,25 @@ public Response addDataverse( String body, @PathParam("identifier") String paren
             d = execCommand( new CreateDataverseCommand(d, createDataverseRequest(u), null, null) );
 			return createdResponse( "/dataverses/"+d.getAlias(), json(d) );
         } catch ( WrappedResponse ww ) {
+                    Throwable cause = ww.getCause();
+                    StringBuilder sb = new StringBuilder();
+                    while (cause.getCause() != null) {
+                        cause = cause.getCause();
+                        if (cause instanceof ConstraintViolationException) {
+                            ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
+                            for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
+                                sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ")
+                                        .append(violation.getPropertyPath()).append(" at ")
+                                        .append(violation.getLeafBean()).append(" - ")
+                                        .append(violation.getMessage());
+                            }
+                        }
+                    }
+                    String error = sb.toString();
+                    if (!error.isEmpty()) {
+                        LOGGER.log(Level.INFO, error);
+                        return ww.refineResponse(error);
+                    }
             return ww.getResponse();
 
         } catch (EJBException ex) {

src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java

@@ -78,6 +78,13 @@ public void setLenient(boolean lenient) {
     public Dataverse parseDataverse(JsonObject jobj) throws JsonParseException {
         Dataverse dv = new Dataverse();
 
+        /**
+         * @todo Instead of this getMandatoryString method we should run the
+         * String through ConstraintValidator. See EMailValidatorTest and
+         * EMailValidator for examples. That way we can check not only if it's
+         * required or not but other bean validation rules such as "must match
+         * this regex".
+         */
         dv.setAlias(getMandatoryString(jobj, "alias"));
         dv.setName(getMandatoryString(jobj, "name"));
         dv.setDescription(jobj.getString("description", null));
@@ -102,7 +109,16 @@ public Dataverse parseDataverse(JsonObject jobj) throws JsonParseException {
             dv.setDataverseTheme(theme);
             theme.setDataverse(dv);
         }
-
+
+        dv.setDataverseType(Dataverse.DataverseType.UNCATEGORIZED); // default
+        if (jobj.containsKey("dataverseType")) {
+            for (Dataverse.DataverseType dvtype : Dataverse.DataverseType.values()) {
+                if (dvtype.name().equals(jobj.getString("dataverseType"))) {
+                    dv.setDataverseType(dvtype);
+                }
+            }
+        }
+
         /*  We decided that subject is not user set, but gotten from the subject of the dataverse's
             datasets - leavig this code in for now, in case we need to go back to it at some point
         

src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java

@@ -200,7 +200,8 @@ public static JsonObjectBuilder json(Dataverse dv) {
                 .add("affiliation", dv.getAffiliation())
                 .add("dataverseContacts", json(dv.getDataverseContacts()))
                 .add("permissionRoot", dv.isPermissionRoot())
-                .add("description", dv.getDescription());
+                .add("description", dv.getDescription())
+                .add("dataverseType", dv.getDataverseType().name());
         if (dv.getOwner() != null) {
             bld.add("ownerId", dv.getOwner().getId());
         }

src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java

@@ -2,39 +2,39 @@
 
 import com.jayway.restassured.RestAssured;
 import com.jayway.restassured.response.Response;
+import edu.harvard.iq.dataverse.Dataverse;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
 import java.util.logging.Logger;
-import org.junit.AfterClass;
+import javax.json.Json;
+import javax.json.JsonObject;
+import javax.ws.rs.core.Response.Status;
+import static javax.ws.rs.core.Response.Status.CREATED;
+import static javax.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR;
+import static javax.ws.rs.core.Response.Status.OK;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import static junit.framework.Assert.assertEquals;
+import static org.hamcrest.CoreMatchers.equalTo;
 
 public class DataversesIT {
 
     private static final Logger logger = Logger.getLogger(DataversesIT.class.getCanonicalName());
 
-    private static String username1;
-    private static String apiToken1;
-    private static String dataverseAlias1;
-    private static String dataverseAlias2;
-
     @BeforeClass
     public static void setUpClass() {
-
         RestAssured.baseURI = UtilIT.getRestAssuredBaseUri();
-
-        Response createUserResponse = UtilIT.createRandomUser();
-//        createUserResponse.prettyPrint();
-        assertEquals(200, createUserResponse.getStatusCode());
-
-        apiToken1 = UtilIT.getApiTokenFromResponse(createUserResponse);
-        username1 = UtilIT.getUsernameFromResponse(createUserResponse);
-
     }
 
     @Test
     public void testAttemptToCreateDuplicateAlias() throws Exception {
 
-        Response createDataverse1Response = UtilIT.createRandomDataverse(apiToken1);
+        Response createUser = UtilIT.createRandomUser();
+//        createUser.prettyPrint();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+
+        Response createDataverse1Response = UtilIT.createRandomDataverse(apiToken);
         if (createDataverse1Response.getStatusCode() != 201) {
             // purposefully using println here to the error shows under "Test Results" in Netbeans
             System.out.println("A workspace for testing (a dataverse) couldn't be created in the root dataverse. The output was:\n\n" + createDataverse1Response.body().asString());
@@ -44,37 +44,96 @@ public void testAttemptToCreateDuplicateAlias() throws Exception {
         }
         assertEquals(201, createDataverse1Response.getStatusCode());
 
-        dataverseAlias1 = UtilIT.getAliasFromResponse(createDataverse1Response);
-        dataverseAlias2 = dataverseAlias1.toUpperCase();
+        String dataverseAlias1 = UtilIT.getAliasFromResponse(createDataverse1Response);
+        String dataverseAlias2 = dataverseAlias1.toUpperCase();
         logger.info("Attempting to creating dataverse with alias '" + dataverseAlias2 + "' (uppercase version of existing '" + dataverseAlias1 + "' dataverse, should fail)...");
-        Response attemptToCreateDataverseWithDuplicateAlias = UtilIT.createDataverse(dataverseAlias2, apiToken1);
+        String category = null;
+        Response attemptToCreateDataverseWithDuplicateAlias = UtilIT.createDataverse(dataverseAlias2, category, apiToken);
         attemptToCreateDataverseWithDuplicateAlias.prettyPrint();
         assertEquals(400, attemptToCreateDataverseWithDuplicateAlias.getStatusCode());
 
         logger.info("Deleting dataverse " + dataverseAlias1);
-        Response deleteDataverse1Response = UtilIT.deleteDataverse(dataverseAlias1, apiToken1);
+        Response deleteDataverse1Response = UtilIT.deleteDataverse(dataverseAlias1, apiToken);
         deleteDataverse1Response.prettyPrint();
         assertEquals(200, deleteDataverse1Response.getStatusCode());
 
         logger.info("Checking response code for attempting to delete a non-existent dataverse.");
-        Response attemptToDeleteDataverseThatShouldNotHaveBeenCreated = UtilIT.deleteDataverse(dataverseAlias2, apiToken1);
+        Response attemptToDeleteDataverseThatShouldNotHaveBeenCreated = UtilIT.deleteDataverse(dataverseAlias2, apiToken);
         attemptToDeleteDataverseThatShouldNotHaveBeenCreated.prettyPrint();
         assertEquals(404, attemptToDeleteDataverseThatShouldNotHaveBeenCreated.getStatusCode());
 
     }
 
-    @AfterClass
-    public static void tearDownClass() {
-        boolean disabled = false;
+    @Test
+    public void testDataverseCategory() {
+        Response createUser = UtilIT.createRandomUser();
+        createUser.prettyPrint();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+
+        Response createDataverseWithoutCategory = UtilIT.createRandomDataverse(apiToken);
+        createDataverseWithoutCategory.prettyPrint();
+        createDataverseWithoutCategory.then().assertThat()
+                .body("data.dataverseType", equalTo("UNCATEGORIZED"))
+                .statusCode(Status.CREATED.getStatusCode());
+
+        String alias1 = UtilIT.getRandomIdentifier();
+        String category1 = Dataverse.DataverseType.LABORATORY.toString();
+        Response createDataverseWithCategory = UtilIT.createDataverse(alias1, category1, apiToken);
+        createDataverseWithCategory.prettyPrint();
+        createDataverseWithCategory.then().assertThat()
+                .body("data.dataverseType", equalTo("LABORATORY"))
+                .statusCode(Status.CREATED.getStatusCode());
+
+        String alias2 = UtilIT.getRandomIdentifier();
+        String madeUpCategory = "madeUpCategory";
+        Response createDataverseWithInvalidCategory = UtilIT.createDataverse(alias2, madeUpCategory, apiToken);
+        createDataverseWithInvalidCategory.prettyPrint();
+        createDataverseWithInvalidCategory.then().assertThat()
+                .body("data.dataverseType", equalTo("UNCATEGORIZED"))
+                .statusCode(Status.CREATED.getStatusCode());
+
+        String alias3 = UtilIT.getRandomIdentifier();
+        String category3 = Dataverse.DataverseType.LABORATORY.toString().toLowerCase();
+        Response createDataverseWithLowerCaseCategory = UtilIT.createDataverse(alias3, category3, apiToken);
+        createDataverseWithLowerCaseCategory.prettyPrint();
+        createDataverseWithLowerCaseCategory.then().assertThat()
+                .body("data.dataverseType", equalTo("UNCATEGORIZED"))
+                .statusCode(Status.CREATED.getStatusCode());
 
-        if (disabled) {
-            return;
-        }
+    }
 
-        Response deleteUser1Response = UtilIT.deleteUser(username1);
-        deleteUser1Response.prettyPrint();
-        assertEquals(200, deleteUser1Response.getStatusCode());
+    @Test
+    public void testMinimalDataverse() throws FileNotFoundException {
+        Response createUser = UtilIT.createRandomUser();
+        createUser.prettyPrint();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+        JsonObject dvJson;
+        FileReader reader = new FileReader("doc/sphinx-guides/source/_static/api/dataverse-minimal.json");
+        dvJson = Json.createReader(reader).readObject();
+        Response create = UtilIT.createDataverse(dvJson, apiToken);
+        create.prettyPrint();
+        create.then().assertThat().statusCode(CREATED.getStatusCode());
+        Response deleteDataverse = UtilIT.deleteDataverse("science", apiToken);
+        deleteDataverse.prettyPrint();
+        deleteDataverse.then().assertThat().statusCode(OK.getStatusCode());
+    }
 
+    @Test
+    public void testNotEnoughJson() {
+        Response createUser = UtilIT.createRandomUser();
+        createUser.prettyPrint();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+        Response createFail = UtilIT.createDataverse(Json.createObjectBuilder().add("name", "notEnough").add("alias", "notEnough").build(), apiToken);
+        createFail.prettyPrint();
+        createFail.then().assertThat()
+                /**
+                 * @todo We really don't want Dataverse to throw a 500 error
+                 * when not enough JSON is supplied to create a dataverse.
+                 */
+                .statusCode(INTERNAL_SERVER_ERROR.getStatusCode());
     }
 
 }

src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java

@@ -73,7 +73,6 @@ public class SearchIT {
     private static TestUser homer;
     private static TestUser ned;
     private static TestUser clancy;
-    private static final String categoryTestDataverse = "categoryTestDataverse";
     private static final String dvForPermsTesting = "dvForPermsTesting";
     private static String dataset1;
     private static String dataset2;
@@ -89,7 +88,6 @@ public class SearchIT {
     private static final boolean disableTestPermsonRootDv = false;
     private static final boolean disableTestPermsOnNewDv = false;
     private static final boolean homerPublishesVersion2AfterDeletingFile = false;
-    private static final boolean disableTestCategory = false;
     private Stopwatch timer;
     private boolean haveToUseCurlForUpload = false;
 
@@ -731,40 +729,6 @@ public void homerPublishesVersion2AfterDeletingFile() throws InterruptedExceptio
 
     }
 
-    @Ignore
-    @Test
-    public void dataverseCategory() {
-
-        if (disableTestCategory) {
-            return;
-        }
-
-        Response enableNonPublicSearch = enableSetting(SettingsServiceBean.Key.SearchApiNonPublicAllowed);
-        assertEquals(200, enableNonPublicSearch.getStatusCode());
-
-        /**
-         * Unfortunately, it appears that the ability to specify the category of
-         * a dataverse when creating it is a GUI-only feature. It can't
-         * currently be done via the API, to our knowledge. You also can't tell
-         * from the API which category was persisted but it always seems to be
-         * "UNCATEGORIZED"
-         */
-        TestDataverse dataverseToCreate = new TestDataverse(categoryTestDataverse, categoryTestDataverse, Dataverse.DataverseType.ORGANIZATIONS_INSTITUTIONS);
-        Response createDvResponse = createDataverse(dataverseToCreate, homer);
-        assertEquals(201, createDvResponse.getStatusCode());
-
-        TestSearchQuery query = new TestSearchQuery(categoryTestDataverse);
-        Response searchResponse = search(query, homer);
-//        searchResponse.prettyPrint();
-        JsonPath jsonPath = JsonPath.from(searchResponse.body().asString());
-        String category = jsonPath.get("data.facets." + SearchFields.DATAVERSE_CATEGORY).toString();
-        String msg = "category: " + category;
-        assertEquals("category: [null]", msg);
-
-        Response disableNonPublicSearch = deleteSetting(SettingsServiceBean.Key.SearchApiNonPublicAllowed);
-        assertEquals(200, disableNonPublicSearch.getStatusCode());
-    }
-
     @AfterClass
     public static void cleanup() {
 
@@ -805,11 +769,6 @@ public static void cleanup() {
             assertEquals(200, destroyDataset.getStatusCode());
         }
 
-        if (!disableTestCategory) {
-            Response deleteCategoryDataverseResponse = deleteDataverse(categoryTestDataverse, homer);
-            assertEquals(200, deleteCategoryDataverseResponse.getStatusCode());
-        }
-
         if (!disableTestPermsOnNewDv) {
             Response deleteDvResponse = deleteDataverse(dvForPermsTesting, homer);
             assertEquals(200, deleteDvResponse.getStatusCode());