stub out GitHub import prototype #5209

scripts/database/upgrades/upgrade_v4.9.4_to_v4.10.sql

@@ -7,3 +7,4 @@ ALTER TABLE pendingworkflowinvocation ADD COLUMN datasetexternallyreleased BOOLE
 INSERT INTO setting(
            name, content)
    VALUES (':UploadMethods', 'native/http');
+ALTER TABLE dataset ADD COLUMN githuburl text;

src/main/java/edu/harvard/iq/dataverse/Dataset.java

@@ -30,6 +30,7 @@
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import edu.harvard.iq.dataverse.util.BundleUtil;
+import javax.persistence.Column;
 
 /**
  *
@@ -108,6 +109,20 @@ public class Dataset extends DvObjectContainer {
     @OneToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
     @JoinColumn(name = "guestbook_id", unique = false, nullable = true, insertable = true, updatable = true)
     private Guestbook guestbook;
+
+    /**
+     * A single repo on GitHub (i.e. https://github.com/IQSS/dataverse)
+     * associated with the dataset for the "code deposit" or "GitHub import"
+     * feature
+     *
+     * TODO: Consider changing this to gitUrl to support GitLab and other git
+     * providers
+     *
+     * TODO: Consider changing this to vcsUrl to support even non-git version
+     * control systems like Subversion. VCS is "version control system".
+     */
+    @Column(nullable = true)
+    private String githubUrl;
 
     @OneToMany(mappedBy="dataset", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     private List<DatasetLinkingDataverse> datasetLinkingDataverses;
@@ -218,6 +233,14 @@ public void setGuestbook(Guestbook guestbook) {
         this.guestbook = guestbook;
     }
 
+    public String getGithubUrl() {
+        return githubUrl;
+    }
+
+    public void setGithubUrl(String githubUrl) {
+        this.githubUrl = githubUrl;
+    }
+
     public boolean isFileAccessRequest() {
         return fileAccessRequest;
     }

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

@@ -0,0 +1,56 @@
+package edu.harvard.iq.dataverse.api;
+
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
+import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
+import java.io.StringReader;
+import javax.json.Json;
+import javax.json.JsonReader;
+import javax.ws.rs.GET;
+import javax.ws.rs.POST;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.core.Response;
+
+@Path("datasets")
+public class GithubApi extends AbstractApiBean {
+
+    @GET
+    @Path("{id}/github")
+    public Response getGithubUrl(@PathParam("id") String idSupplied) {
+        try {
+            Dataset dataset = findDatasetOrDie(idSupplied);
+            final NullSafeJsonBuilder jsonObject = jsonObjectBuilder()
+                    .add("datasetId", dataset.getId())
+                    .add("githubUrl", dataset.getGithubUrl());
+            return ok(jsonObject);
+        } catch (WrappedResponse wr) {
+            return wr.getResponse();
+        }
+    }
+
+    @POST
+    @Path("{id}/github/setUrl")
+    public Response setGithubUrl(String body, @PathParam("id") String idSupplied) {
+        try {
+            Dataset datasetBeforeSave = findDatasetOrDie(idSupplied);
+            JsonReader jsonReader = Json.createReader(new StringReader(body));
+            String githubUrl = jsonReader.readObject().getString("githubUrl");
+            datasetBeforeSave.setGithubUrl(githubUrl);
+            Dataset savedDataset = datasetSvc.merge(datasetBeforeSave);
+            final NullSafeJsonBuilder jsonObject = jsonObjectBuilder()
+                    .add("datasetId", savedDataset.getId())
+                    .add("githubUrl", savedDataset.getGithubUrl());
+            return ok(jsonObject);
+        } catch (WrappedResponse wr) {
+            return wr.getResponse();
+        }
+    }
+
+    @POST
+    @Path("{id}/github/import")
+    public Response importGithubRepo(@PathParam("id") String idSupplied) {
+        return ok("FIXME: download GitHub repo as zip and create a file in dataverse, putting metadata about the repo into the file description.");
+    }
+
+}

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

@@ -0,0 +1,70 @@
+package edu.harvard.iq.dataverse.api;
+
+import com.jayway.restassured.RestAssured;
+import com.jayway.restassured.path.json.JsonPath;
+import com.jayway.restassured.response.Response;
+import java.util.logging.Logger;
+import static javax.ws.rs.core.Response.Status.CREATED;
+import static javax.ws.rs.core.Response.Status.OK;
+import static org.hamcrest.CoreMatchers.equalTo;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class GithubApiIT {
+
+    private static final Logger logger = Logger.getLogger(GithubApiIT.class.getCanonicalName());
+
+    @BeforeClass
+    public static void setUpClass() {
+        RestAssured.baseURI = UtilIT.getRestAssuredBaseUri();
+    }
+
+    @Test
+    public void testGithubDeposit() {
+
+        Response createUser = UtilIT.createRandomUser();
+        createUser.prettyPrint();
+        createUser.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        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 datasetPersistentId = JsonPath.from(createDataset.getBody().asString()).getString("data.persistentId");
+
+        Response githubUrlShouldBeAbsent = UtilIT.getGithubUrl(datasetPersistentId, apitoken);
+        githubUrlShouldBeAbsent.prettyPrint();
+        githubUrlShouldBeAbsent.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.githubUrl", equalTo(null));
+
+        String githubUrl = "https://github.com/IQSS/metrics.dataverse.org";
+        Response setGithubUrl = UtilIT.setGithubUrl(datasetPersistentId, githubUrl, apitoken);
+        setGithubUrl.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        setGithubUrl.prettyPrint();
+
+        Response getGithubUrl = UtilIT.getGithubUrl(datasetPersistentId, apitoken);
+        getGithubUrl.prettyPrint();
+        getGithubUrl.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.githubUrl", equalTo(githubUrl));
+
+        Response importGithubRepo = UtilIT.importGithubRepo(datasetPersistentId, apitoken);
+        importGithubRepo.prettyPrint();
+
+    }
+
+}

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

@@ -1162,7 +1162,62 @@ static Response removeDatasetThumbnail(String datasetPersistentId, String apiTok
                 .header(API_TOKEN_HTTP_HEADER, apiToken)
                 .delete("/api/datasets/:persistentId/thumbnail" + "?persistentId=" + datasetPersistentId);
     }
-
+
+    static Response getGithubUrl(String idOrPersistentId, String apiToken) {
+        logger.info("Getting GitHub URL");
+        String idInPath = idOrPersistentId; // Assume it's a number.
+        String optionalQueryParam = ""; // If idOrPersistentId is a number we'll just put it in the path.
+        if (!NumberUtils.isNumber(idOrPersistentId)) {
+            idInPath = ":persistentId";
+            optionalQueryParam = "?persistentId=" + idOrPersistentId;
+        }
+        RequestSpecification requestSpecification = given();
+        if (apiToken != null) {
+            requestSpecification = given()
+                    .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken);
+        }
+        return requestSpecification.get("/api/datasets/" + idInPath + "/github" + optionalQueryParam);
+    }
+
+    static Response setGithubUrl(String idOrPersistentId, String githubUrl, String apiToken) {
+        logger.info("Setting GitHub URL");
+        JsonObjectBuilder roleBuilder = Json.createObjectBuilder();
+        roleBuilder.add("githubUrl", githubUrl);
+        JsonObject roleObject = roleBuilder.build();
+        String idInPath = idOrPersistentId; // Assume it's a number.
+        String optionalQueryParam = ""; // If idOrPersistentId is a number we'll just put it in the path.
+        if (!NumberUtils.isNumber(idOrPersistentId)) {
+            idInPath = ":persistentId";
+            optionalQueryParam = "?persistentId=" + idOrPersistentId;
+        }
+        RequestSpecification requestSpecification = given();
+        if (apiToken != null) {
+            requestSpecification = given()
+                    .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken);
+        }
+        return requestSpecification
+                .body(roleObject.toString())
+                .contentType(ContentType.JSON)
+                .post("/api/datasets/" + idInPath + "/github/setUrl" + optionalQueryParam);
+    }
+
+    static Response importGithubRepo(String idOrPersistentId, String apiToken) {
+        logger.info("Importing GitHub repo into dataset " + idOrPersistentId);
+        String idInPath = idOrPersistentId; // Assume it's a number.
+        String optionalQueryParam = ""; // If idOrPersistentId is a number we'll just put it in the path.
+        if (!NumberUtils.isNumber(idOrPersistentId)) {
+            idInPath = ":persistentId";
+            optionalQueryParam = "?persistentId=" + idOrPersistentId;
+        }
+        RequestSpecification requestSpecification = given();
+        if (apiToken != null) {
+            requestSpecification = given()
+                    .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken);
+        }
+        return requestSpecification
+                .post("/api/datasets/" + idInPath + "/github/import" + optionalQueryParam);
+    }
+
     static Response getDatasetVersions(String idOrPersistentId, String apiToken) {
         logger.info("Getting Dataset Versions");
         String idInPath = idOrPersistentId; // Assume it's a number.