From 8a65e51898479dd25a0cc538d4c464e1441c72e4 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 12 Nov 2020 07:47:14 -0800
Subject: [PATCH] Fixed dependencies that blocked the GET /algorithms.
---
pom.xml | 1 -
.../eu/hbp/mip/controllers/AlgorithmsApi.java | 39 +++++++++++--------
src/main/resources/application.yml | 4 +-
3 files changed, 24 insertions(+), 20 deletions(-)
diff --git a/pom.xml b/pom.xml
index b64596e79..0c3f8a8c2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -244,7 +244,6 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
- <version>4.10.0-RC1</version>
</dependency>
<dependency>
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index 07ab6ef29..8fc9fcbf9 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -61,24 +61,26 @@ public class AlgorithmsApi {
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Executing...");
+ String username = userInfo.getUser().getUsername();
+ String endpoint = "(GET) /algorithms";
+ Logging.LogUserAction(username, endpoint, "Executing...");
LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
+ Logging.LogUserAction(username, endpoint, "Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
+ Logging.LogUserAction(username, endpoint, "Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"Getting exareme algorithms failed and returned null");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
} else {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"Getting galaxy workflows failed and returned null");
}
@@ -86,7 +88,7 @@ public class AlgorithmsApi {
try {
disabledAlgorithms = getDisabledAlgorithms();
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"The disabled algorithms could not be loaded.");
}
@@ -97,7 +99,7 @@ public class AlgorithmsApi {
allowedAlgorithms.add(algorithm);
}
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"Successfully listed " + allowedAlgorithms.size() + " algorithms");
return ResponseEntity.ok(allowedAlgorithms);
}
@@ -108,6 +110,8 @@ public class AlgorithmsApi {
* @return a list of AlgorithmDTOs or null if something fails
*/
public LinkedList<AlgorithmDTO> getExaremeAlgorithms() {
+ String username = userInfo.getUser().getUsername();
+ String endpoint = "(GET) /algorithms";
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
// Get exareme algorithms
try {
@@ -120,11 +124,11 @@ public class AlgorithmsApi {
}.getType()
);
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ Logging.LogUserAction(username, endpoint, "An exception occurred: " + e.getMessage());
return null;
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"Completed, returned " + algorithms.size() + " algorithms.");
return algorithms;
}
@@ -135,7 +139,8 @@ public class AlgorithmsApi {
* @return a list of AlgorithmDTOs or null if something fails
*/
public LinkedList<AlgorithmDTO> getGalaxyWorkflows() {
-
+ String username = userInfo.getUser().getUsername();
+ String endpoint = "(GET) /algorithms";
List<Workflow> workflowList;
try {
// Get all the workflows with the galaxy client
@@ -144,7 +149,7 @@ public class AlgorithmsApi {
workflowList = new ArrayList<>(workflowsClient.getWorkflows());
} catch (Exception e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error when calling list galaxy workflows: " + e.getMessage());
+ Logging.LogUserAction(username, endpoint, "Error when calling list galaxy workflows: " + e.getMessage());
return null;
}
@@ -164,28 +169,28 @@ public class AlgorithmsApi {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error Response: " + msgErr);
+ Logging.LogUserAction(username, endpoint, "Error Response: " + msgErr);
return null;
}
} catch (Exception e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ Logging.LogUserAction(username, endpoint, "An exception occurred: " + e.getMessage());
return null;
}
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Workflows fetched: " + workflows.size());
+ Logging.LogUserAction(username, endpoint, "Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Converting workflow: " + workflow);
+ Logging.LogUserAction(username, endpoint, "Converting workflow: " + workflow);
algorithms.add(workflow.convertToAlgorithmDTO());
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
+ Logging.LogUserAction(username, endpoint,
"Converted algorithm: " + algorithms.get(algorithms.size() - 1));
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Completed!");
+ Logging.LogUserAction(username, endpoint, "Completed!");
return algorithms;
}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index a4c205725..1728999c2 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -36,8 +36,8 @@ frontend:
logging:
level:
- root: "DEBUG"
- org: "DEBUG"
+ root: "ERROR"
+ org: "ERROR"
eu:
hbp: "DEBUG"
--
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