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Merge branch 'develop' into 10229-fix-featured-dv-selection
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@sekmiller
sekmiller committed Feb 6, 2024
2 parents ae9b74f + 98231c5 commit 17637c7
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1 change: 1 addition & 0 deletions doc/sphinx-guides/source/_static/admin/dataverse-external-tools.tsv
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Expand Up @@ -5,3 +5,4 @@ Binder explore dataset Binder allows you to spin up custom computing environment
File Previewers explore file "A set of tools that display the content of files - including audio, html, `Hypothes.is <https://hypothes.is/>`_ annotations, images, PDF, Markdown, text, video, tabular data, spreadsheets, GeoJSON, zip, and NcML files - allowing them to be viewed without downloading the file. The previewers can be run directly from github.io, so the only required step is using the Dataverse API to register the ones you want to use. Documentation, including how to optionally brand the previewers, and an invitation to contribute through github are in the README.md file. Initial development was led by the Qualitative Data Repository and the spreasdheet previewer was added by the Social Sciences and Humanities Open Cloud (SSHOC) project. https://github.com/gdcc/dataverse-previewers"
Data Curation Tool configure file "A GUI for curating data by adding labels, groups, weights and other details to assist with informed reuse. See the README.md file at https://github.com/scholarsportal/Dataverse-Data-Curation-Tool for the installation instructions."
Ask the Data query file Ask the Data is an experimental tool that allows you ask natural language questions about the data contained in Dataverse tables (tabular data). See the README.md file at https://github.com/IQSS/askdataverse/tree/main/askthedata for the instructions on adding Ask the Data to your Dataverse installation.
TurboCurator by ICPSR configure dataset TurboCurator generates metadata improvements for title, description, and keywords. It relies on open AI's ChatGPT & ICPSR best practices. See the `TurboCurator Dataverse Administrator <https://turbocurator.icpsr.umich.edu/tc/adminabout/>`_ page for more details on how it works and adding TurboCurator to your Dataverse installation.
26 changes: 26 additions & 0 deletions src/main/java/edu/harvard/iq/dataverse/api/TestApi.java
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Expand Up @@ -71,5 +71,31 @@ public Response getExternalToolsForFile(@PathParam("id") String idSupplied, @Que
return wr.getResponse();
}
}

@Path("files/{id}/externalTool/{toolId}")
@GET
public Response getExternalToolForFileById(@PathParam("id") String idSupplied, @QueryParam("type") String typeSupplied, @PathParam("toolId") String toolId) {
ExternalTool.Type type;
try {
type = ExternalTool.Type.fromString(typeSupplied);
} catch (IllegalArgumentException ex) {
return error(BAD_REQUEST, ex.getLocalizedMessage());
}
try {
DataFile dataFile = findDataFileOrDie(idSupplied);
List<ExternalTool> datasetTools = externalToolService.findFileToolsByTypeAndContentType(type, dataFile.getContentType());
for (ExternalTool tool : datasetTools) {
ApiToken apiToken = externalToolService.getApiToken(getRequestApiKey());
ExternalToolHandler externalToolHandler = new ExternalToolHandler(tool, dataFile, apiToken, dataFile.getFileMetadata(), null);
JsonObjectBuilder toolToJson = externalToolService.getToolAsJsonWithQueryParameters(externalToolHandler);
if (externalToolService.meetsRequirements(tool, dataFile) && tool.getId().toString().equals(toolId)) {
return ok(toolToJson);
}
}
return error(BAD_REQUEST, "Could not find external tool with id of " + toolId);
} catch (WrappedResponse wr) {
return wr.getResponse();
}
}

}
121 changes: 52 additions & 69 deletions src/test/java/edu/harvard/iq/dataverse/api/ExternalToolsIT.java
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Expand Up @@ -40,21 +40,6 @@ public void testGetExternalTools() {
@Test
public void testFileLevelTool1() {

// Delete all external tools before testing.
Response getTools = UtilIT.getExternalTools();
getTools.prettyPrint();
getTools.then().assertThat()
.statusCode(OK.getStatusCode());
String body = getTools.getBody().asString();
JsonReader bodyObject = Json.createReader(new StringReader(body));
JsonArray tools = bodyObject.readObject().getJsonArray("data");
for (int i = 0; i < tools.size(); i++) {
JsonObject tool = tools.getJsonObject(i);
int id = tool.getInt("id");
Response deleteExternalTool = UtilIT.deleteExternalTool(id);
deleteExternalTool.prettyPrint();
}

Response createUser = UtilIT.createRandomUser();
createUser.prettyPrint();
createUser.then().assertThat()
Expand Down Expand Up @@ -116,7 +101,7 @@ public void testFileLevelTool1() {
.statusCode(OK.getStatusCode())
.body("data.displayName", CoreMatchers.equalTo("AwesomeTool"));

long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");
Long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");

Response getTool = UtilIT.getExternalTool(toolId);
getTool.prettyPrint();
Expand All @@ -130,41 +115,34 @@ public void testFileLevelTool1() {
.statusCode(BAD_REQUEST.getStatusCode())
.body("message", CoreMatchers.equalTo("Type must be one of these values: [explore, configure, preview, query]."));

Response getExternalToolsForTabularFiles = UtilIT.getExternalToolsForFile(tabularFileId.toString(), "explore", apiToken);
// Getting tool by tool Id to avoid issue where there are existing tools
String toolIdString = toolId.toString();
Response getExternalToolsForTabularFiles = UtilIT.getExternalToolForFileById(tabularFileId.toString(), "explore", apiToken, toolIdString);
getExternalToolsForTabularFiles.prettyPrint();

getExternalToolsForTabularFiles.then().assertThat()
.statusCode(OK.getStatusCode())
.body("data[0].displayName", CoreMatchers.equalTo("AwesomeTool"))
.body("data[0].scope", CoreMatchers.equalTo("file"))
.body("data[0].contentType", CoreMatchers.equalTo("text/tab-separated-values"))
.body("data[0].toolUrlWithQueryParams", CoreMatchers.equalTo("http://awesometool.com?fileid=" + tabularFileId + "&key=" + apiToken));
.body("data.displayName", CoreMatchers.equalTo("AwesomeTool"))
.body("data.scope", CoreMatchers.equalTo("file"))
.body("data.contentType", CoreMatchers.equalTo("text/tab-separated-values"))
.body("data.toolUrlWithQueryParams", CoreMatchers.equalTo("http://awesometool.com?fileid=" + tabularFileId + "&key=" + apiToken));

Response getExternalToolsForJuptyerNotebooks = UtilIT.getExternalToolsForFile(jupyterNotebookFileId.toString(), "explore", apiToken);
getExternalToolsForJuptyerNotebooks.prettyPrint();
getExternalToolsForJuptyerNotebooks.then().assertThat()
.statusCode(OK.getStatusCode())
// No tools for this file type.
.body("data", Matchers.hasSize(0));

//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());
}

@Test
public void testDatasetLevelTool1() {

// Delete all external tools before testing.
Response getTools = UtilIT.getExternalTools();
getTools.prettyPrint();
getTools.then().assertThat()
.statusCode(OK.getStatusCode());
String body = getTools.getBody().asString();
JsonReader bodyObject = Json.createReader(new StringReader(body));
JsonArray tools = bodyObject.readObject().getJsonArray("data");
for (int i = 0; i < tools.size(); i++) {
JsonObject tool = tools.getJsonObject(i);
int id = tool.getInt("id");
Response deleteExternalTool = UtilIT.deleteExternalTool(id);
deleteExternalTool.prettyPrint();
}

Response createUser = UtilIT.createRandomUser();
createUser.prettyPrint();
createUser.then().assertThat()
Expand All @@ -184,7 +162,6 @@ public void testDatasetLevelTool1() {
createDataset.then().assertThat()
.statusCode(CREATED.getStatusCode());

// Integer datasetId = UtilIT.getDatasetIdFromResponse(createDataset);
Integer datasetId = JsonPath.from(createDataset.getBody().asString()).getInt("data.id");
String datasetPid = JsonPath.from(createDataset.getBody().asString()).getString("data.persistentId");

Expand Down Expand Up @@ -219,6 +196,8 @@ public void testDatasetLevelTool1() {
addExternalTool.then().assertThat()
.statusCode(OK.getStatusCode())
.body("data.displayName", CoreMatchers.equalTo("DatasetTool1"));

long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");

Response getExternalToolsByDatasetIdInvalidType = UtilIT.getExternalToolsForDataset(datasetId.toString(), "invalidType", apiToken);
getExternalToolsByDatasetIdInvalidType.prettyPrint();
Expand All @@ -233,27 +212,16 @@ public void testDatasetLevelTool1() {
.body("data[0].scope", CoreMatchers.equalTo("dataset"))
.body("data[0].toolUrlWithQueryParams", CoreMatchers.equalTo("http://datasettool1.com?datasetPid=" + datasetPid + "&key=" + apiToken))
.statusCode(OK.getStatusCode());


//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());
}

@Test
public void testDatasetLevelToolConfigure() {

// Delete all external tools before testing.
Response getTools = UtilIT.getExternalTools();
getTools.prettyPrint();
getTools.then().assertThat()
.statusCode(OK.getStatusCode());
String body = getTools.getBody().asString();
JsonReader bodyObject = Json.createReader(new StringReader(body));
JsonArray tools = bodyObject.readObject().getJsonArray("data");
for (int i = 0; i < tools.size(); i++) {
JsonObject tool = tools.getJsonObject(i);
int id = tool.getInt("id");
Response deleteExternalTool = UtilIT.deleteExternalTool(id);
deleteExternalTool.prettyPrint();
}

Response createUser = UtilIT.createRandomUser();
createUser.prettyPrint();
createUser.then().assertThat()
Expand Down Expand Up @@ -302,6 +270,8 @@ public void testDatasetLevelToolConfigure() {
addExternalTool.then().assertThat()
.statusCode(OK.getStatusCode())
.body("data.displayName", CoreMatchers.equalTo("Dataset Configurator"));

long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");

Response getExternalToolsByDatasetId = UtilIT.getExternalToolsForDataset(datasetId.toString(), "configure", apiToken);
getExternalToolsByDatasetId.prettyPrint();
Expand All @@ -311,6 +281,11 @@ public void testDatasetLevelToolConfigure() {
.body("data[0].types[0]", CoreMatchers.equalTo("configure"))
.body("data[0].toolUrlWithQueryParams", CoreMatchers.equalTo("https://datasetconfigurator.com?datasetPid=" + datasetPid))
.statusCode(OK.getStatusCode());

//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());

}

Expand Down Expand Up @@ -400,12 +375,13 @@ public void deleteTools() {
String body = getTools.getBody().asString();
JsonReader bodyObject = Json.createReader(new StringReader(body));
JsonArray tools = bodyObject.readObject().getJsonArray("data");
/*
for (int i = 0; i < tools.size(); i++) {
JsonObject tool = tools.getJsonObject(i);
int id = tool.getInt("id");
Response deleteExternalTool = UtilIT.deleteExternalTool(id);
deleteExternalTool.prettyPrint();
}
}*/
}

// preview only
Expand Down Expand Up @@ -446,12 +422,20 @@ public void createToolShellScript() {
addExternalTool.prettyPrint();
addExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());

long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");

//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());
}

// explore only
@Disabled
@Test
public void createToolDataExplorer() {
/*
JsonObjectBuilder job = Json.createObjectBuilder();
job.add("displayName", "Data Explorer");
job.add("description", "");
Expand Down Expand Up @@ -479,6 +463,14 @@ public void createToolDataExplorer() {
addExternalTool.prettyPrint();
addExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());
long toolId = JsonPath.from(addExternalTool.getBody().asString()).getLong("data.id");
//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());
*/
}

// both preview and explore
Expand Down Expand Up @@ -527,21 +519,6 @@ public void createToolSpreadsheetViewer() {
@Test
public void testFileLevelToolWithAuxFileReq() throws IOException {

// Delete all external tools before testing.
Response getTools = UtilIT.getExternalTools();
getTools.prettyPrint();
getTools.then().assertThat()
.statusCode(OK.getStatusCode());
String body = getTools.getBody().asString();
JsonReader bodyObject = Json.createReader(new StringReader(body));
JsonArray tools = bodyObject.readObject().getJsonArray("data");
for (int i = 0; i < tools.size(); i++) {
JsonObject tool = tools.getJsonObject(i);
int id = tool.getInt("id");
Response deleteExternalTool = UtilIT.deleteExternalTool(id);
deleteExternalTool.prettyPrint();
}

Response createUser = UtilIT.createRandomUser();
createUser.prettyPrint();
createUser.then().assertThat()
Expand Down Expand Up @@ -640,6 +617,12 @@ public void testFileLevelToolWithAuxFileReq() throws IOException {
.body("data[0].displayName", CoreMatchers.equalTo("HDF5 Tool"))
.body("data[0].scope", CoreMatchers.equalTo("file"))
.body("data[0].contentType", CoreMatchers.equalTo("application/x-hdf5"));

//Delete the tool added by this test...
Response deleteExternalTool = UtilIT.deleteExternalTool(toolId);
deleteExternalTool.then().assertThat()
.statusCode(OK.getStatusCode());

}

}
15 changes: 15 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java
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Expand Up @@ -2354,6 +2354,21 @@ static Response getExternalToolsForFile(String idOrPersistentIdOfFile, String ty
}
return requestSpecification.get("/api/admin/test/files/" + idInPath + "/externalTools?type=" + type + optionalQueryParam);
}

static Response getExternalToolForFileById(String idOrPersistentIdOfFile, String type, String apiToken, String toolId) {
String idInPath = idOrPersistentIdOfFile; // Assume it's a number.
String optionalQueryParam = ""; // If idOrPersistentId is a number we'll just put it in the path.
if (!NumberUtils.isCreatable(idOrPersistentIdOfFile)) {
idInPath = ":persistentId";
optionalQueryParam = "&persistentId=" + idOrPersistentIdOfFile;
}
RequestSpecification requestSpecification = given();
if (apiToken != null) {
requestSpecification = given()
.header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken);
}
return requestSpecification.get("/api/admin/test/files/" + idInPath + "/externalTool/" + toolId + "?type=" + type + optionalQueryParam);
}

static Response submitFeedback(JsonObjectBuilder job) {
return given()
Expand Down

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