Skip to content
Snippets Groups Projects
Commit 84102302 authored by ThanKarab's avatar ThanKarab
Browse files

Adding config file to disable algorithms.

parent 769b6119
No related branches found
No related tags found
1 merge request!14Adding config file to disable algorithms.
Hide whitespace changes
Inline Side-by-side
Showing
with 93 additions and 30 deletions
config/disabledAlgorithms.json 0 → 100644
+ 3
− 0
View file @ 84102302
[
"3C"
]
\ No newline at end of file
src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+ 56
− 10
View file @ 84102302
......@@ -5,17 +5,20 @@ import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.model.AlgorithmDTO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.galaxy.WorkflowDTO;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.UserActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
......@@ -28,6 +31,8 @@ import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import static eu.hbp.mip.utils.ErrorMessages.disabledAlgorithmsCouldNotBeLoaded;
import static eu.hbp.mip.utils.InputStreamConverter.convertInputStreamToString;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
......@@ -54,10 +59,10 @@ public class AlgorithmsApi {
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms", "");
List<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
List<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
List<AlgorithmDTO> algorithms = new LinkedList<>();
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
......@@ -71,7 +76,23 @@ public class AlgorithmsApi {
"Getting galaxy workflows failed and returned null");
}
return ResponseEntity.ok(algorithms);
List<String> disabledAlgorithms = new ArrayList<>();
try {
disabledAlgorithms = getDisabledAlgorithms();
} catch (IOException e) {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List all algorithms",
disabledAlgorithmsCouldNotBeLoaded);
}
// Remove any disabled algorithm
LinkedList<AlgorithmDTO> allowedAlgorithms = new LinkedList<>();
for (AlgorithmDTO algorithm : algorithms) {
if (!disabledAlgorithms.contains(algorithm.getName())) {
allowedAlgorithms.add(algorithm);
}
}
return ResponseEntity.ok(allowedAlgorithms);
}
/**
......@@ -79,16 +100,20 @@ public class AlgorithmsApi {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
public List<AlgorithmDTO> getExaremeAlgorithms() {
public LinkedList<AlgorithmDTO> getExaremeAlgorithms() {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List exareme algorithms", "");
List<AlgorithmDTO> algorithms = new LinkedList<>();
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
// Get exareme algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
algorithms = gson.fromJson(response.toString(), algorithms.getClass());
algorithms = gson.fromJson(
response.toString(),
new TypeToken<LinkedList<AlgorithmDTO>>() {
}.getType()
);
} catch (IOException e) {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List exareme algorithms", "An exception occurred: " + e.getMessage());
return null;
......@@ -104,10 +129,10 @@ public class AlgorithmsApi {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
public List<AlgorithmDTO> getGalaxyWorkflows() {
public LinkedList<AlgorithmDTO> getGalaxyWorkflows() {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "");
List<Workflow> workflowList = null;
List<Workflow> workflowList;
try {
// Get all the workflows with the galaxy client
final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
......@@ -146,7 +171,7 @@ public class AlgorithmsApi {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
List<AlgorithmDTO> algorithms = new LinkedList<>();
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Converting workflow: " + workflow);
......@@ -159,4 +184,25 @@ public class AlgorithmsApi {
UserActionLogging.LogUserAction(userInfo.getUser().getUsername(), "List Galaxy workflows", "Completed!");
return algorithms;
}
@Autowired
private CustomResourceLoader resourceLoader;
/**
* Fetches the disabled algorithms from a .json file
*
* @return a list with their names
* @throws IOException when the file could not be loaded
*/
List<String> getDisabledAlgorithms() throws IOException {
Resource resource = resourceLoader.getResource("file:/opt/portal/api/disabledAlgorithms.json");
List<String> response = gson.fromJson(convertInputStreamToString(
resource.getInputStream()),
new TypeToken<List<String>>() {
}.getType()
);
return response;
}
}
src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+ 5
− 19
View file @ 84102302
......@@ -10,9 +10,11 @@ import eu.hbp.mip.model.PathologyDTO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.InputStreamConverter;
import eu.hbp.mip.utils.UserActionLogging;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
......@@ -21,12 +23,10 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.List;
import static eu.hbp.mip.utils.ErrorMessages.pathologiesCouldNotBeLoaded;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
......@@ -54,10 +54,10 @@ public class PathologiesApi {
Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
List<PathologyDTO> allPathologies;
try {
allPathologies = gson.fromJson(convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
}.getType());
} catch (IOException e) {
return ResponseEntity.badRequest().body("The pathologies.json file could not be read.");
return ResponseEntity.badRequest().body(pathologiesCouldNotBeLoaded);
}
// If authentication is disabled return everything
......@@ -68,18 +68,4 @@ public class PathologiesApi {
return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
userInfo.getUser().getUsername(), authentication.getAuthorities(), allPathologies));
}
// Pure Java
private static String convertInputStreamToString(InputStream inputStream) throws IOException {
ByteArrayOutputStream result = new ByteArrayOutputStream();
byte[] buffer = new byte[1024];
int length;
while ((length = inputStream.read(buffer)) != -1) {
result.write(buffer, 0, length);
}
return result.toString(StandardCharsets.UTF_8.name());
}
}
src/main/java/eu/hbp/mip/model/UserInfo.java
+ 1
− 1
View file @ 84102302
......@@ -13,7 +13,7 @@ import org.springframework.stereotype.Component;
import javax.inject.Named;
@Component
@Scope(value = "session", proxyMode=ScopedProxyMode.TARGET_CLASS)
@Scope(value = "session", proxyMode = ScopedProxyMode.TARGET_CLASS)
@Named("userInfo")
public class UserInfo {
......
src/main/java/eu/hbp/mip/utils/ErrorMessages.java 0 → 100644
+ 7
− 0
View file @ 84102302
package eu.hbp.mip.utils;
public class ErrorMessages {
public static String pathologiesCouldNotBeLoaded = "The pathologies could not be loaded.";
public static String disabledAlgorithmsCouldNotBeLoaded = "The disabled algorithms could not be loaded.";
}
src/main/java/eu/hbp/mip/utils/InputStreamConverter.java 0 → 100644
+ 21
− 0
View file @ 84102302
package eu.hbp.mip.utils;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
public class InputStreamConverter {
// Pure Java
public static String convertInputStreamToString(InputStream inputStream) throws IOException {
ByteArrayOutputStream result = new ByteArrayOutputStream();
byte[] buffer = new byte[1024];
int length;
while ((length = inputStream.read(buffer)) != -1) {
result.write(buffer, 0, length);
}
return result.toString(StandardCharsets.UTF_8.name());
}
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment