From d1c2859496b44517c61768658496d10fdfade326 Mon Sep 17 00:00:00 2001
From: ThanKarab <tkarabatsis@hotmail.com>
Date: Fri, 13 Nov 2020 03:57:25 -0800
Subject: [PATCH] Beautification of non_docker additions.
---
docker/config/application.tmpl | 9 ++++-----
pom.xml | 3 ++-
.../java/eu/hbp/mip/controllers/AlgorithmsApi.java | 6 +++---
.../java/eu/hbp/mip/controllers/PathologiesApi.java | 10 +++-------
src/main/java/eu/hbp/mip/controllers/SecurityApi.java | 2 +-
src/main/resources/application.yml | 9 ++++-----
6 files changed, 17 insertions(+), 22 deletions(-)
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index f25878893..5bdfa36a1 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -77,8 +77,7 @@ services:
keycloak:
keycloakUrl: {{ .Env.KEYCLOAK_URL }}
-pathologies:
- pathologiesUrl: "file:/opt/portal/api/pathologies.json"
-
-algorithms:
- disabledAlgorithmsUrl: "file:/opt/portal/api/disabledAlgorithms.json"
\ No newline at end of file
+# Files are imported when building the docker image
+files:
+ pathologies_json: "file:/opt/portal/api/pathologies.json"
+ disabledAlgorithms_json: "file:/opt/portal/api/disabledAlgorithms.json"
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index b64596e79..ba87e5423 100644
--- a/pom.xml
+++ b/pom.xml
@@ -268,8 +268,9 @@
<include>**/*.yml</include> <!-- Only for development -->
</includes>
<filtering>true</filtering>
-
</resource>
+
+ <!-- Used for development. Docker/config folder files added as resources -->
<resource>
<directory>config</directory>
<includes>
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index 07ab6ef29..e2c3b6e0e 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -55,8 +55,8 @@ public class AlgorithmsApi {
@Value("#{'${services.galaxy.galaxyApiKey}'}")
private String galaxyApiKey;
- @Value("#{'${services.algorithms.disabledAlgorithmsUrl}'}")
- private String disabledAlgorithmsUrl;
+ @Value("#{'${files.disabledAlgorithms_json}'}")
+ private String disabledAlgorithmsFilePath;
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
@@ -200,7 +200,7 @@ public class AlgorithmsApi {
*/
List<String> getDisabledAlgorithms() throws IOException {
- Resource resource = resourceLoader.getResource(disabledAlgorithmsUrl);
+ Resource resource = resourceLoader.getResource(disabledAlgorithmsFilePath);
List<String> response = gson.fromJson(convertInputStreamToString(
resource.getInputStream()),
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index a6979e70c..383515660 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -1,7 +1,3 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
package eu.hbp.mip.controllers;
import com.google.gson.Gson;
@@ -44,8 +40,8 @@ public class PathologiesApi {
@Value("#{'${hbp.authentication.enabled:1}'}")
private boolean authenticationIsEnabled;
- @Value("#{'${services.pathologies.pathologiesUrl}'}")
- private String pathologiesUrl;
+ @Value("#{'${files.pathologies_json}'}")
+ private String pathologiesFilePath;
@Autowired
private CustomResourceLoader resourceLoader;
@@ -57,7 +53,7 @@ public class PathologiesApi {
Logging.LogUserAction(username, endpoint, "Loading pathologies ...");
// Load pathologies from file
- Resource resource = resourceLoader.getResource(pathologiesUrl);
+ Resource resource = resourceLoader.getResource(pathologiesFilePath);
List<PathologyDTO> allPathologies;
try {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
diff --git a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
index e179b3172..77b22fae8 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -96,7 +96,7 @@ public class SecurityApi {
@Value("#{'${services.galaxy.galaxyPassword:password}'}")
private String galaxyPassword;
- @Value("#{'${services.galaxy.galaxyContext:nativeGalaxy}'}")
+ @Value("#{'${services.galaxy.galaxpathoyContext:nativeGalaxy}'}")
private String galaxyContext;
/**
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index a4c205725..5fda7331d 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -74,8 +74,7 @@ services:
keycloak:
keycloakUrl: "127.0.0.1"
- pathologies:
- pathologiesUrl: "classPath:/pathologies.json"
-
- algorithms:
- disabledAlgorithmsUrl: "classPath:/disableAlgorithms.json"
\ No newline at end of file
+# Files are loaded from the resources
+files:
+ pathologies_json: "classPath:/pathologies.json"
+ disabledAlgorithms_json: "classPath:/disabledAlgorithms.json"
\ No newline at end of file
--
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