From 4c987a1a731dd896b495ebd73ed6347a8a4baafa Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 22 Jul 2022 16:17:14 +0300
Subject: [PATCH 1/2] Now a pathology has a version until Exareme is completely
replaced by Exareme2 the portalbackend will ignore the version for the
algorithms that run on Exareme.
---
.../models/DTOs/MIPEngineAlgorithmRequestDTO.java | 2 +-
.../java/eu/hbp/mip/models/DTOs/PathologyDTO.java | 4 ++++
.../eu/hbp/mip/services/ExperimentService.java | 15 ++++++++++++++-
3 files changed, 19 insertions(+), 2 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
index 7b330e419..1e582b923 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAlgorithmRequestDTO.java
@@ -41,7 +41,7 @@ public class MIPEngineAlgorithmRequestDTO {
inputData.setData_model(parameter.getValue());
break;
case "filter":
- if (!parameter.getValue().equals(""))
+ if (parameter.getValue() != null && !parameter.getValue().equals(""))
inputData.setFilters(JsonConverters.convertJsonStringToObject(parameter.getValue(), MIPEngineAlgorithmRequestDTO.Filter.class));
break;
default:
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
index ecc5b723b..c1b0f434f 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -13,6 +13,10 @@ public class PathologyDTO {
@SerializedName("code")
private String code;
+ @SerializedName("version")
+ private String version;
+
+
@SerializedName("label")
private String label;
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 747b5acdd..327f9ecf8 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -465,7 +465,20 @@ public class ExperimentService {
String algorithmEndpoint = queryExaremeUrl + "/" + algorithmName;
List<ExaremeAlgorithmRequestParamDTO> algorithmParameters
= experimentDTO.getAlgorithm().getParameters();
- String algorithmBody = gson.toJson(algorithmParameters);
+ List<ExaremeAlgorithmRequestParamDTO> algorithmParametersWithoutPathologyVersion = new ArrayList<>();
+
+ for (ExaremeAlgorithmRequestParamDTO algorithmParameter : algorithmParameters)
+ {
+ if (algorithmParameter.getName().equals("pathology")) {
+ List<String> pathology_info = Arrays.asList(algorithmParameter.getValue().split(":", 2));
+ String pathology_code = pathology_info.get(0);
+ algorithmParameter.setValue(pathology_code);
+ }
+ algorithmParametersWithoutPathologyVersion.add(algorithmParameter);
+
+ }
+
+ String algorithmBody = gson.toJson(algorithmParametersWithoutPathologyVersion);
logger.LogUserAction("Exareme algorithm execution. Endpoint: " + algorithmEndpoint);
logger.LogUserAction("Exareme algorithm execution. Body: " + algorithmBody);
--
GitLab
From 94687d7281e14a732c853fa5dff71b8cdb19b182 Mon Sep 17 00:00:00 2001
From: Kfilippopolitis <kostasfilippop@gmail.com>
Date: Fri, 22 Jul 2022 16:31:20 +0300
Subject: [PATCH 2/2] Now on a new pr a portalbackend testing image will be
created.
---
.github/workflows/publish_testing_images.yml | 49 ++++++++++++++++++++
1 file changed, 49 insertions(+)
create mode 100644 .github/workflows/publish_testing_images.yml
diff --git a/.github/workflows/publish_testing_images.yml b/.github/workflows/publish_testing_images.yml
new file mode 100644
index 000000000..ffce4b047
--- /dev/null
+++ b/.github/workflows/publish_testing_images.yml
@@ -0,0 +1,49 @@
+name: Publish testing images
+
+on:
+ pull_request:
+ branches:
+ - master
+
+jobs:
+ build_and_push:
+ name: Build image and push to dockerhub
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v2
+
+ - name: Set up Docker Buildx
+ uses: docker/setup-buildx-action@v1
+
+ - name: Log in to Docker Hub
+ uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+ with:
+ username: ${{ secrets.DOCKER_USERNAME }}
+ password: ${{ secrets.DOCKER_PASSWORD }}
+
+ - name: Load cached image
+ uses: actions/cache@v2
+ with:
+ path: /tmp/.buildx-cache/portal-backend
+ key: buildx-backend
+ restore-keys: buildx-backend
+
+ - name: Build and Push image to dockerhub
+ uses: docker/build-push-action@v2
+ with:
+ context: .
+ file: ./Dockerfile
+ push: true
+ tags: hbpmip/portal-backend:testing
+ cache-from: type=local,src=/tmp/.buildx-cache/portal-backend
+ cache-to: type=local,dest=/tmp/.buildx-cache-new/portal-backend
+
+ # Temp fix
+ # https://github.com/docker/build-push-action/issues/252
+ # https://github.com/moby/buildkit/issues/1896
+ - name: Move Docker images cache
+ run: |
+ rm -rf /tmp/.buildx-cache
+ mv /tmp/.buildx-cache-new /tmp/.buildx-cache
+
--
GitLab