Merge remote-tracking branch 'IQSS/develop' into IQSS/11126-Payara6.2…

…024.12

doc/release-notes/10541-root-alias-name2.md

@@ -0,0 +1 @@
+The [tutorial](https://dataverse-guide--11201.org.readthedocs.build/en/11201/container/running/demo.html#root-collection-customization-alias-name-etc) on running Dataverse in Docker has been updated to explain how to configure the root collection using a JSON file. See also #10541 and #11201.

doc/sphinx-guides/source/container/running/demo.rst

@@ -29,6 +29,8 @@ To stop the containers hit ``Ctrl-c`` (hold down the ``Ctrl`` key and then hit t
 
 To start the containers, run ``docker compose up``.
 
+.. _starting-over:
+
 Deleting Data and Starting Over
 -------------------------------
 
@@ -46,6 +48,8 @@ Starting Fresh
 
 For this exercise, please start fresh by stopping all containers and removing the ``data`` directory.
 
+.. _demo-persona:
+
 Creating and Running a Demo Persona
 +++++++++++++++++++++++++++++++++++
 
@@ -137,6 +141,29 @@ In the example below of configuring :ref:`:FooterCopyright` we use the default u
 
 One you make this change it should be visible in the copyright in the bottom left of every page.
 
+Root Collection Customization (Alias, Name, etc.)
++++++++++++++++++++++++++++++++++++++++++++++++++
+
+Before running ``docker compose up`` for the first time, you can customize the root collection by placing a JSON file in the right place.
+
+First, in the "demo" directory you created (see :ref:`demo-persona`), create a subdirectory called "config":
+
+``mkdir demo/config``
+
+Next, download :download:`dataverse-complete.json <../../_static/api/dataverse-complete.json>` and put it in the "config" directory you just created. The contents of your "demo" directory should look something like this:
+
+.. code-block:: bash
+
+        % find demo
+        demo
+        demo/config
+        demo/config/dataverse-complete.json
+        demo/init.sh
+
+Edit ``dataverse-complete.json`` to have the values you want. You'll want to refer to :ref:`update-dataverse-api` in the API Guide to understand the format. In that documentation you can find optional parameters as well.
+
+To test your JSON file, run ``docker compose up``. Again, this only works when you are running ``docker compose up`` for the first time. (You can always start over. See :ref:`starting-over`.)
+
 Multiple Languages
 ++++++++++++++++++
 

modules/container-configbaker/scripts/bootstrap/demo/init.sh

@@ -19,6 +19,16 @@ echo ""
 echo "Setting DOI provider to \"FAKE\"..."
 curl -sS -X PUT -d FAKE "${DATAVERSE_URL}/api/admin/settings/:DoiProvider"
 
+API_TOKEN=$(grep apiToken "/tmp/setup-all.sh.out" | jq ".data.apiToken" | tr -d \")
+export API_TOKEN
+
+ROOT_COLLECTION_JSON=/scripts/bootstrap/demo/config/dataverse-complete.json
+if [ -f $ROOT_COLLECTION_JSON ]; then
+  echo ""
+  echo "Updating root collection based on $ROOT_COLLECTION_JSON..."
+  curl -sS -X PUT -H "X-Dataverse-key:$API_TOKEN" "$DATAVERSE_URL/api/dataverses/:root" --upload-file $ROOT_COLLECTION_JSON
+fi
+
 echo ""
 echo "Revoke the key that allows for creation of builtin users..."
 curl -sS -X DELETE "${DATAVERSE_URL}/api/admin/settings/BuiltinUsers.KEY"

src/main/java/edu/harvard/iq/dataverse/ingest/IngestMessageBean.java

@@ -23,6 +23,7 @@
 import edu.harvard.iq.dataverse.*;
 import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
+import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 
 import java.sql.Timestamp;
@@ -60,6 +61,7 @@ public class IngestMessageBean implements MessageListener {
     @EJB IngestServiceBean ingestService;
     @EJB UserNotificationServiceBean userNotificationService;
     @EJB AuthenticationServiceBean authenticationServiceBean;
+    @EJB IndexServiceBean indexService;
 
 
     public IngestMessageBean() {
@@ -111,6 +113,7 @@ public void onMessage(Message message) {
                         // and "mixed success and failure" emails. Now we never list successfully
                         // ingested files so this line is commented out.
                         // sbIngestedFiles.append(String.format("<li>%s</li>", datafile.getCurrentName()));
+                        indexService.asyncIndexDataset(datafile.getOwner(), true);
                     } else {
                         logger.warning("Error occurred during ingest job for file id " + datafile_id + "!");
                         sbIngestedFiles.append(String.format("<li>%s</li>", datafile.getCurrentName()));

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

@@ -33,6 +33,10 @@
 
 import static jakarta.ws.rs.core.Response.Status.*;
 import static java.lang.Thread.sleep;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import static org.hamcrest.CoreMatchers.equalTo;
+import static org.hamcrest.CoreMatchers.is;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
@@ -1838,4 +1842,53 @@ public void testShowTypeCounts() throws InterruptedException  {
                 .body("data.total_count_per_object_type.Datasets", CoreMatchers.is(0))
                 .body("data.total_count_per_object_type.Files", CoreMatchers.is(0));        
     }
+
+    @Test
+    public void testTabularFiles() throws IOException {
+        Response createUser = UtilIT.createRandomUser();
+        createUser.then().assertThat().statusCode(OK.getStatusCode());
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+
+        Response createDataverseResponse = UtilIT.createRandomDataverse(apiToken);
+        createDataverseResponse.prettyPrint();
+        createDataverseResponse.then().assertThat()
+                .statusCode(CREATED.getStatusCode());
+
+        String dataverseAlias = UtilIT.getAliasFromResponse(createDataverseResponse);
+
+        Response createDataset = UtilIT.createRandomDatasetViaNativeApi(dataverseAlias, apiToken);
+        createDataset.prettyPrint();
+        createDataset.then().assertThat()
+                .statusCode(CREATED.getStatusCode());
+
+        Integer datasetId = UtilIT.getDatasetIdFromResponse(createDataset);
+        String datasetPid = UtilIT.getDatasetPersistentIdFromResponse(createDataset);
+
+        Path pathToDataFile = Paths.get(java.nio.file.Files.createTempDirectory(null) + File.separator + "data.csv");
+        String contentOfCsv = ""
+                + "name,pounds,species,treats\n"
+                + "Midnight,15,dog,milkbones\n"
+                + "Tiger,17,cat,cat grass\n"
+                + "Panther,21,cat,cat nip\n";
+        java.nio.file.Files.write(pathToDataFile, contentOfCsv.getBytes());
+
+        Response uploadFile = UtilIT.uploadFileViaNative(datasetId.toString(), pathToDataFile.toString(), apiToken);
+        uploadFile.prettyPrint();
+        uploadFile.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.files[0].label", equalTo("data.csv"));
+
+        assertTrue(UtilIT.sleepForLock(datasetId.longValue(), "Ingest", apiToken, UtilIT.MAXIMUM_INGEST_LOCK_DURATION), "Failed test if Ingest Lock exceeds max duration " + pathToDataFile);
+
+        Long fileId = JsonPath.from(uploadFile.body().asString()).getLong("data.files[0].dataFile.id");
+
+        Response search = UtilIT.search("entityId:" + fileId, apiToken);
+        search.prettyPrint();
+        search.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.items[0].name", is("data.tab"))
+                .body("data.items[0].variables", is(4))
+                .body("data.items[0].observations", is(3));
+    }
+
 }