From c830fc1dc4afc20efc4b2b9319808ece631afb4b Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 2 Aug 2022 17:38:40 +0300
Subject: [PATCH 1/4] Remove Exareme algorithms that exist in the Exareme2 from
the /algorithms endpoint
---
src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index af7b96607..f103306f6 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -30,6 +30,7 @@ import java.io.IOException;
import java.net.ConnectException;
import java.util.ArrayList;
import java.util.List;
+import java.util.Objects;
import static eu.hbp.mip.utils.InputStreamConverter.convertInputStreamToString;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -100,6 +101,13 @@ public class AlgorithmsAPI {
logger.LogUserAction("The disabled algorithms could not be loaded.");
}
+ // Remove Exareme algorithms that exist in the Exareme2
+ if (mipengineAlgorithms != null && exaremeAlgorithms != null){
+ for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) {
+ exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
+ }
+ }
+
// Remove any disabled algorithm
ArrayList<ExaremeAlgorithmDTO> allowedAlgorithms = new ArrayList<>();
for (ExaremeAlgorithmDTO algorithm : algorithms) {
--
GitLab
From 70875558c46ba38db1c1c42df20de8a312f1f1b5 Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Tue, 2 Aug 2022 17:49:18 +0300
Subject: [PATCH 2/4] Removal of exareme deprecated algorithms are on the
proper place
---
.../eu/hbp/mip/controllers/AlgorithmsAPI.java | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index f103306f6..1fb02b09d 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -75,6 +75,14 @@ public class AlgorithmsAPI {
ArrayList<ExaremeAlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
ArrayList<ExaremeAlgorithmDTO> algorithms = new ArrayList<>();
+
+ // Remove Exareme algorithms that exist in the Exareme2
+ if (mipengineAlgorithms != null && exaremeAlgorithms != null){
+ for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) {
+ exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
+ }
+ }
+
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
@@ -101,12 +109,7 @@ public class AlgorithmsAPI {
logger.LogUserAction("The disabled algorithms could not be loaded.");
}
- // Remove Exareme algorithms that exist in the Exareme2
- if (mipengineAlgorithms != null && exaremeAlgorithms != null){
- for (ExaremeAlgorithmDTO algorithm : mipengineAlgorithms) {
- exaremeAlgorithms.removeIf(obj -> Objects.equals(obj.getName(), algorithm.getName()));
- }
- }
+
// Remove any disabled algorithm
ArrayList<ExaremeAlgorithmDTO> allowedAlgorithms = new ArrayList<>();
--
GitLab
From 1ef56cf52539b9bacb2de531712c93155f5aa74c Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 12 Aug 2022 15:01:18 +0300
Subject: [PATCH 3/4] Fixed small typo
---
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
index 8f908902c..a7974d378 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -49,7 +49,7 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("multiple")
private String multiple;
- @SerializedName("types")
+ @SerializedName("type")
private String type;
@SerializedName("desc")
--
GitLab
From 2820f0fa1af6d67887ebcb1ab955afac8edf7ec9 Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 18 Aug 2022 14:53:54 +0300
Subject: [PATCH 4/4] Default value to default
---
src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
index a7974d378..8a9e0cc56 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmDTO.java
@@ -61,7 +61,7 @@ public class MIPEngineAlgorithmDTO {
@SerializedName("max")
private String max;
- @SerializedName("default_value")
+ @SerializedName("default")
private String default_value;
@SerializedName("enums")
--
GitLab