diff --git a/config/disabledAlgorithms.json b/config/disabledAlgorithms.json
new file mode 100644
index 0000000000000000000000000000000000000000..d92a3b2f1421d2dad3a140503d1c0effa964bdfb
--- /dev/null
+++ b/config/disabledAlgorithms.json
@@ -0,0 +1,3 @@
+[
+ "3C"
+]
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index 6b92c691a633ecbd4c16ccea813fc8b3c3533742..27e9b8e5db7cf2339bfea34fee0d17893ee97336 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -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;
+ }
}
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index f4eb2a7d623583cbdf3a00753a26dc499ffc1f39..7b6b3e65017204ea3e52897e15a2345a82deeda4 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -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());
-
- }
}
diff --git a/src/main/java/eu/hbp/mip/model/UserInfo.java b/src/main/java/eu/hbp/mip/model/UserInfo.java
index 293ce9534cf78c0f27b5f742ca924540072e2fea..71eee3573b485d690c810b42c1344cc2170fb9f5 100644
--- a/src/main/java/eu/hbp/mip/model/UserInfo.java
+++ b/src/main/java/eu/hbp/mip/model/UserInfo.java
@@ -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 {
diff --git a/src/main/java/eu/hbp/mip/utils/ErrorMessages.java b/src/main/java/eu/hbp/mip/utils/ErrorMessages.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f672f81b8bb57c559015a52bc65e44a0da7bd72
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/ErrorMessages.java
@@ -0,0 +1,7 @@
+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.";
+}
diff --git a/src/main/java/eu/hbp/mip/utils/InputStreamConverter.java b/src/main/java/eu/hbp/mip/utils/InputStreamConverter.java
new file mode 100644
index 0000000000000000000000000000000000000000..ebb8f9d999dd73381ae9f203c12361fb381cba9b
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/InputStreamConverter.java
@@ -0,0 +1,21 @@
+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());
+ }
+}