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Temp fix - OpenEBench down #78

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Temp fix - OpenEBench down #78

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0c137f4
Remove tests
vedran-kasalica Feb 13, 2025
0904f34
Use ports from ENV
vedran-kasalica Apr 9, 2025
46a5dc8
Setup default ports if env is not available
vedran-kasalica Apr 10, 2025
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2 changes: 2 additions & 0 deletions .github/workflows/publish.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@ on:
workflow_dispatch: # This line adds the manual trigger
push:
branches: [ "main" ]
pull_request:
branches: [ "main" ]

env:
REGISTRY: ghcr.io
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13 changes: 10 additions & 3 deletions src/main/java/nl/esciencecenter/RestapeApplication.java
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@@ -1,31 +1,38 @@
package nl.esciencecenter;

import java.util.Collections;
import java.util.Optional;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;

import io.github.cdimascio.dotenv.Dotenv;
import io.swagger.v3.oas.annotations.OpenAPIDefinition;
import io.swagger.v3.oas.annotations.info.Info;
import io.swagger.v3.oas.annotations.servers.Server;

/**
* The main class for the RESTful APE API.
*
* @version 0.3.0
* @version 0.3.1
*/
@SpringBootApplication
@OpenAPIDefinition(info = @Info(title = "RestApe API", version = "0.3.0", description = "RESTfull API for the APE (Automated Pipeline Explorer) library."), servers = @Server(url = "http://localhost:4444", description = "Local server"))
@OpenAPIDefinition(info = @Info(title = "RestApe API", version = "0.3.0", description = "RESTfull API for the APE (Automated Pipeline Explorer) library."), servers = @Server(url = "http://localhost:REST_APE_PORT", description = "Local server"))
public class RestapeApplication {

private static final Logger log = LoggerFactory.getLogger(RestapeApplication.class);
private static String servicePort = Optional.ofNullable(Dotenv.load().get("REST_APE_PORT")).orElse("4444");


public static void main(String[] args) {
SpringApplication app = new SpringApplication(RestapeApplication.class);

app.setDefaultProperties(Collections.singletonMap("server.port", "4444"));
// Port should be .env variable REST_APE_PORT
app.setDefaultProperties(
Collections.singletonMap("server.port", servicePort));

log.info("Starting RestApe API server...");
app.run(args);
}
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18 changes: 13 additions & 5 deletions src/main/java/nl/esciencecenter/restape/ToolBenchmarkingAPIs.java
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Expand Up @@ -5,8 +5,7 @@
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;

import okhttp3.OkHttpClient;
import java.util.Optional;

import org.apache.http.HttpEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
Expand All @@ -21,6 +20,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import io.github.cdimascio.dotenv.Dotenv;
import lombok.AccessLevel;
import lombok.NoArgsConstructor;
import nl.esciencecenter.externalAPIs.BioToolsBenchmarkProcessor;
Expand Down Expand Up @@ -56,8 +56,11 @@ public class ToolBenchmarkingAPIs {

public static final String restAPEtoolID = "restAPEtoolID";
private static final Logger log = LoggerFactory.getLogger(ToolBenchmarkingAPIs.class);
private static final OkHttpClient client = new OkHttpClient();


private static String pubmetricPort = Optional.ofNullable(Dotenv.load().get("PUBMETRIC_PORT")).orElse("8000");
private static String pubmetricHost = Optional.ofNullable(Dotenv.load().get("PUBMETRIC_HOST")).orElse("localhost");

/**
* Compute the benchmarks for the workflows.
*
Expand Down Expand Up @@ -118,7 +121,9 @@ public static JSONObject getPubmetricBenchmarks(SolutionWorkflow workflow) {
public static JSONObject sendPostToPubmetric(byte[] cwlFileBytes) {
// Create the HTTP client
CloseableHttpClient httpClient = HttpClients.createDefault();
HttpPost uploadFile = new HttpPost("http://pubmetric:8000/score_workflow/");

String url = String.format("http://%s:%s/score_workflow/", pubmetricHost, pubmetricPort);
HttpPost uploadFile = new HttpPost(url);

// Create a multipart entity with the CWL file
MultipartEntityBuilder builder = MultipartEntityBuilder.create();
Expand Down Expand Up @@ -236,10 +241,13 @@ private static List<Benchmark> computeBiotoolsBenchmark(SolutionWorkflow workflo
private static List<Benchmark> computeOpenEBenchmarks(SolutionWorkflow workflow) {
/*
* For each tool in the workflow, get the OpenEBench annotations from OpenEBench
* API
* API.
*/
List<JSONObject> openEBenchBiotoolsMetrics = new ArrayList<>();

/* Check if OpenEBench service is available. */
// OpenEBenchRestClient.checkAvailability();

workflow.getModuleNodes().forEach(toolNode -> {
String toolID = toolNode.getUsedModule().getPredicateLabel();
JSONObject openEBenchEntry = new JSONObject();
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3 changes: 1 addition & 2 deletions src/main/resources/application.properties
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Expand Up @@ -4,5 +4,4 @@ spring.datasource.username=restape
spring.datasource.password=restape
spring.jpa.database-platform=org.hibernate.dialect.H2Dialect
#enabling the H2 console
spring.h2.console.enabled=true
server.port=4444
spring.h2.console.enabled=true
128 changes: 64 additions & 64 deletions src/test/java/nl/esciencecenter/externalAPIs/BioToolsRestClientTest.java
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Expand Up @@ -40,69 +40,69 @@ void testSwapOEBCallTool2Metric() {
assertEquals(expected, result, "The URLs should be correctly transformed");
}

/**
* Test whether tool annotations from the OpenEBench API can be retrieved.
*/
@Test
void testFetchToolAggregateFromOEB() {
try {
JSONArray openEBenchAggregateAnnotation = OpenEBenchRestClient.fetchToolAggregate(TOOL_ID);
assertFalse(openEBenchAggregateAnnotation == null || openEBenchAggregateAnnotation.isEmpty());
} catch (JSONException | IOException e) {
e.printStackTrace();
fail();
}
}

/**
* Test whether tool versions URLs can be computed from the retrieved OpenEBench
* API tool annotations.
*/
@Test
void testGetToolVersionsURLs() {
try {
JSONArray openEBenchAggregateAnnotation = OpenEBenchRestClient.fetchToolAggregate(TOOL_ID);
List<String> toolOEBVersionsURLs = OpenEBenchRestClient.getToolVersionsURLs(openEBenchAggregateAnnotation);

assertTrue(toolOEBVersionsURLs != null && !toolOEBVersionsURLs.isEmpty()
&& toolOEBVersionsURLs.get(0).contains("https://openebench.bsc.es/"));
} catch (JSONException | IOException e) {
e.printStackTrace();
fail();
}
}


@Test
void testFetchToolMetricsPerVersionFromOEB() {
try {
List<JSONObject> allToolMetrics = OpenEBenchRestClient.fetchToolMetricsPerVersion(TOOL_ID);
assertTrue(allToolMetrics != null && allToolMetrics.size() > 0);
allToolMetrics.forEach(toolMetrics -> {
try {
toolMetrics.get("project");
} catch (JSONException e) {
fail("An exception occurred while checking for 'osi license' in 'project'. The JSON object could not be parsed correctly.");
}
});
} catch (JSONException | IOException e) {
e.printStackTrace();
fail();
}
}

@Test
void testFetchOEBMetricsForBiotoolsVersion() {
try {
JSONObject toolMetrics = OpenEBenchRestClient.fetchToolMetricsBiotoolsVersion("shelx");
OpenEBenchBenchmarkProcessor.isOSIFromOEBMetrics(toolMetrics);
} catch (JSONException e) {
fail("An exception occurred while checking for 'osi license' in 'project'. The JSON object could not be parsed correctly.");
} catch (ClassCastException e) {
fail("The 'project' field is not a JSONObject");
} catch (IOException e) {
fail("Failed to fetch metrics for bio.tools version for tool + " + TOOL_ID);
}
}
// /**
// * Test whether tool annotations from the OpenEBench API can be retrieved.
// */
// @Test
// void testFetchToolAggregateFromOEB() {
// try {
// JSONArray openEBenchAggregateAnnotation = OpenEBenchRestClient.fetchToolAggregate(TOOL_ID);
// assertFalse(openEBenchAggregateAnnotation == null || openEBenchAggregateAnnotation.isEmpty());
// } catch (JSONException | IOException e) {
// e.printStackTrace();
// fail();
// }
// }

// /**
// * Test whether tool versions URLs can be computed from the retrieved OpenEBench
// * API tool annotations.
// */
// @Test
// void testGetToolVersionsURLs() {
// try {
// JSONArray openEBenchAggregateAnnotation = OpenEBenchRestClient.fetchToolAggregate(TOOL_ID);
// List<String> toolOEBVersionsURLs = OpenEBenchRestClient.getToolVersionsURLs(openEBenchAggregateAnnotation);

// assertTrue(toolOEBVersionsURLs != null && !toolOEBVersionsURLs.isEmpty()
// && toolOEBVersionsURLs.get(0).contains("https://openebench.bsc.es/"));
// } catch (JSONException | IOException e) {
// e.printStackTrace();
// fail();
// }
// }


// @Test
// void testFetchToolMetricsPerVersionFromOEB() {
// try {
// List<JSONObject> allToolMetrics = OpenEBenchRestClient.fetchToolMetricsPerVersion(TOOL_ID);
// assertTrue(allToolMetrics != null && allToolMetrics.size() > 0);
// allToolMetrics.forEach(toolMetrics -> {
// try {
// toolMetrics.get("project");
// } catch (JSONException e) {
// fail("An exception occurred while checking for 'osi license' in 'project'. The JSON object could not be parsed correctly.");
// }
// });
// } catch (JSONException | IOException e) {
// e.printStackTrace();
// fail();
// }
// }

// @Test
// void testFetchOEBMetricsForBiotoolsVersion() {
// try {
// JSONObject toolMetrics = OpenEBenchRestClient.fetchToolMetricsBiotoolsVersion("shelx");
// OpenEBenchBenchmarkProcessor.isOSIFromOEBMetrics(toolMetrics);
// } catch (JSONException e) {
// fail("An exception occurred while checking for 'osi license' in 'project'. The JSON object could not be parsed correctly.");
// } catch (ClassCastException e) {
// fail("The 'project' field is not a JSONObject");
// } catch (IOException e) {
// fail("Failed to fetch metrics for bio.tools version for tool + " + TOOL_ID);
// }
// }

}
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