Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Revert changes made in the last PR regarding Pubmetric endpoint #76

Merged
merged 1 commit into from
Dec 16, 2024
Merged

Revert changes made in the last PR regarding Pubmetric endpoint #76

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
107 changes: 53 additions & 54 deletions src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ static boolean computeBenchmarks(SolutionsList candidateSolutions, String runID)
if (!additionalBenchmarks.isEmpty() && additionalBenchmarks.has("benchmarks")) {
additionalBenchmarks.getJSONArray("benchmarks").forEach(benchmark -> benchmarks.put(benchmark));
}

workflowBenchmarks.put("benchmarks", benchmarks);

String titleBenchmark = workflow.getFileName() + ".json";
Expand All @@ -96,64 +96,62 @@ static boolean computeBenchmarks(SolutionsList candidateSolutions, String runID)
}

/**
* Get the Pubmetric benchmarks for the workflow.
* @param workflow the SolutionWorkflow instance
* @return JSON response from Pubmetric API
*/
public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
* Get the Pubmetric benchmarks for the workflow.
*
* @param workflow the SolutionWorkflow instance
* @return JSON response from Pubmetric API
*/
public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
DefaultCWLCreator cwlCreator = new DefaultCWLCreator(workflow);
String cwlFileContent = cwlCreator.generate();
byte[] cwlFileBytes = cwlFileContent.getBytes();

return sendPostToPubmetric(cwlFileBytes);
}

/**
* Send a POST request to the Pubmetric API to get benchmarks.
* @param cwlFileBytes byte array of CWL file content
* @return JSON response from Pubmetric API
*/
public static JSONObject sendPostToPubmetric(byte[] cwlFileBytes) {
try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
HttpPost uploadFile = createHttpPost(cwlFileBytes);
return executeRequest(httpClient, uploadFile);
} catch (IOException | JSONException e) {
log.error("Error while processing Pubmetric benchmarks", e);
return new JSONObject(); // return empty JSON if an error occurs
}
}

/**
* Creates an HttpPost request with the provided CWL content.
* @param cwlFileBytes byte array of CWL file content
* @return configured HttpPost request
*/
private static HttpPost createHttpPost(byte[] cwlFileBytes) {
HttpPost uploadFile = new HttpPost("http://localhost:8000/score_workflow/");
}

/**
* Send a POST request to the Pubmetric API to get benchmarks.
*
* @param cwlFileBytes byte array of CWL file content
* @return JSON response from Pubmetric API
*/
public static JSONObject sendPostToPubmetric(byte[] cwlFileBytes) {
// Create the HTTP client
CloseableHttpClient httpClient = HttpClients.createDefault();
HttpPost uploadFile = new HttpPost("http://pubmetric:8000/score_workflow/");

// Create a multipart entity with the CWL file
MultipartEntityBuilder builder = MultipartEntityBuilder.create();
builder.addBinaryBody("cwl_file", cwlFileBytes, org.apache.http.entity.ContentType.DEFAULT_BINARY, "workflow.cwl");
uploadFile.setEntity(builder.build());
return uploadFile;
}

/**
* Executes the HTTP request and returns the response as a JSONObject.
* @param httpClient the HTTP client
* @param uploadFile the configured HttpPost request
* @return JSON response from Pubmetric API
* @throws IOException if an error occurs during the HTTP call
*/
private static JSONObject executeRequest(CloseableHttpClient httpClient, HttpPost uploadFile) throws IOException {
try (CloseableHttpResponse response = httpClient.execute(uploadFile)) {
HttpEntity responseEntity = response.getEntity();
if (responseEntity != null) {
String responseString = EntityUtils.toString(responseEntity);
return new JSONObject(responseString);
}
return new JSONObject(); // return empty JSON if no response entity
builder.addBinaryBody("cwl_file", cwlFileBytes, org.apache.http.entity.ContentType.DEFAULT_BINARY,
"workflow.cwl");

HttpEntity multipart = builder.build();
uploadFile.setEntity(multipart);

// Execute the request
CloseableHttpResponse response;
try {
response = httpClient.execute(uploadFile);
HttpEntity responseEntity = response.getEntity();

// Print the response
if (responseEntity != null) {
String responseString = EntityUtils.toString(responseEntity);
return new JSONObject(responseString);
}

// Close resources
response.close();
httpClient.close();
} catch (IOException e) {
log.error("Error while fetching the Pubmetric benchmarks");
} catch (JSONException e) {
log.error("Error while parsing the Pubmetric benchmarks");
}
}


return new JSONObject();
}

/**
* Compute the benchmarks (based on bio.tools and OpenEBench APIs) for the
* workflows and return it in JSON format.
Expand Down Expand Up @@ -200,7 +198,7 @@ private static List<Benchmark> computeBiotoolsBenchmark(SolutionWorkflow workflo
try {
biotoolsEntry = BioToolsRestClient.fetchToolFromBioTools(toolID);
} catch (JSONException | IOException e) {
log.warn(e.getMessage());
log.warn(e.getMessage());
} finally {
biotoolsEntry.put(ToolBenchmarkingAPIs.restAPEtoolID, toolNode.getUsedModule().getPredicateLabel());
biotoolsAnnotations.add(biotoolsEntry);
Expand Down Expand Up @@ -265,7 +263,8 @@ private static List<Benchmark> computeOpenEBenchmarks(SolutionWorkflow workflow)

BenchmarkBase citationsBenchmark = new BenchmarkBase("Citations", "Bibliometrics", "Citations annotated per tool",
"citation count", "citation", null);
benchmarks.add(OpenEBenchBenchmarkProcessor.countCitationsBenchmark(openEBenchBiotoolsMetrics, citationsBenchmark));
benchmarks
.add(OpenEBenchBenchmarkProcessor.countCitationsBenchmark(openEBenchBiotoolsMetrics, citationsBenchmark));

return benchmarks;

Expand Down
Loading