fli-iam#2388-automatic executions - front

docker-compose/Dockerfile

@@ -13,7 +13,7 @@
 
 ################ base debian image #########################################
 
-FROM debian:bookworm as base-debian
+FROM debian:bookworm AS  base-debian
 
 # - disable the automatic "apt-get clean" command (because we mount
 #   /var/cache/apt from an external volume to speed-up the build)
@@ -30,13 +30,13 @@ RUN rm /etc/apt/apt.conf.d/docker-clean \
 #   (rather that temurin's default /etc/ssl/certs/adoptium/cacerts)
 #   to keep the location independent of the implementation (in case users need
 #   to mount it from an external volume)
-FROM base-debian as adoptium-key
+FROM base-debian AS  adoptium-key
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq && apt-get install -qqy wget gnupg
 RUN wget -qO - https://packages.adoptium.net/artifactory/api/gpg/key/public \
     | gpg --dearmor > /adoptium.gpg
 
-FROM base-debian as base-debian-with-adoptium
+FROM base-debian AS  base-debian-with-adoptium
 COPY --link --from=adoptium-key /adoptium.gpg /etc/apt/keyrings/
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq && apt install -qqy apt-transport-https ca-certificates \
@@ -45,11 +45,11 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
             "$(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" \
     | tee /etc/apt/sources.list.d/adoptium.list
 
-FROM base-debian-with-adoptium as jdk
+FROM base-debian-with-adoptium AS  jdk
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq && apt-get install -qqy temurin-21-jdk maven bzip2 git
 
-FROM base-debian-with-adoptium as base-microservice
+FROM base-debian-with-adoptium AS  base-microservice
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq \
     && apt-get install -qqy temurin-21-jre ca-certificates-java \
@@ -69,7 +69,7 @@ ENTRYPOINT ["/bin/entrypoint", "java", "-Djava.security.egd=file:/dev/urandom",
 
 ################ datasets ##################################################
 
-FROM alpine as datasets-download
+FROM alpine AS  datasets-download
 
 # Installation of dcm4che into /opt/dcm4che to manage the store-scu into the
 # PACS dcm4che3, used last version 5.21.0 as available on the 2020-02-14
@@ -81,7 +81,7 @@ RUN wget -qO dcm4che-bin.zip \
     && rm    /dcm4che-bin.zip
 
 
-FROM base-microservice as datasets
+FROM base-microservice AS  datasets
 
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq \
@@ -111,7 +111,7 @@ CMD ["-jar", "/shanoir-ng-datasets.jar"]
 
 ################ import ####################################################
 
-FROM base-microservice as import
+FROM base-microservice AS  import
 
 COPY --link import/entrypoint /usr/bin/
 COPY --link import/shanoir-ng-import.jar shanoir-ng-import.jar
@@ -124,7 +124,7 @@ CMD ["-jar", "/shanoir-ng-import.jar"]
 
 ################ nifti-conversion ##########################################
 
-FROM base-debian as nifti-conversion-conda
+FROM base-debian AS  nifti-conversion-conda
 
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked,id=apt-conda \
     apt-get -qqy update \
@@ -141,7 +141,7 @@ RUN --mount=type=cache,target=/opt/miniconda3/pkgs \
     /opt/miniconda3/bin/conda install -c conda-forge dicomifier -y
 
 
-FROM base-debian as nifti-conversion-builder
+FROM base-debian AS  nifti-conversion-builder
 
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked,id=apt-builder \
     apt-get -qqy update \
@@ -168,7 +168,7 @@ RUN mkdir -p /target/opt/nifti-converters/mriconverter \
     && chmod 0777 . MRIFileManager/MRIManager.jar
 
 
-FROM base-microservice as nifti-conversion
+FROM base-microservice AS  nifti-conversion
 
 # xvfb+gtk2 needed by mri_conv (headless mode not supported by DicomToNifti)
 # see: https://populse.github.io/mri_conv/Installation/installation.html#scriptwithoutGUI
@@ -218,7 +218,7 @@ CMD ["-jar", "/nifti-conversion.jar"]
 
 ################ preclinical ###############################################
 
-FROM base-microservice as preclinical
+FROM base-microservice AS  preclinical
 
 COPY --link preclinical/shanoir-ng-preclinical.jar shanoir-ng-preclinical.jar
 COPY --link preclinical/entrypoint /usr/bin/
@@ -231,7 +231,7 @@ CMD ["-jar", "/shanoir-ng-preclinical.jar", "-Xmx6g", "-Xms1g"]
 
 ################ studies ###################################################
 
-FROM base-microservice as studies
+FROM base-microservice AS  studies
 
 COPY --link studies/shanoir-ng-studies.jar shanoir-ng-studies.jar
 COPY --link studies/entrypoint /usr/bin/
@@ -244,7 +244,7 @@ CMD ["-jar", "/shanoir-ng-studies.jar"]
 
 ################ users #####################################################
 
-FROM base-microservice as users
+FROM base-microservice AS  users
 
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update -qq && apt-get install -qqy openssl
@@ -265,7 +265,7 @@ CMD ["-jar", "/shanoir-ng-users.jar"]
 
 ################ keycloak ##################################################
 
-FROM quay.io/keycloak/keycloak:25.0.4 as keycloak-base
+FROM quay.io/keycloak/keycloak:25.0.4 AS  keycloak-base
 
 # keycloak options (https://www.keycloak.org/server/all-config)
 #
@@ -284,7 +284,7 @@ ENV KC_DB="mysql" \
 #
 # Use builder to integrate custom provider
 #
-FROM keycloak-base as keycloak-builder
+FROM keycloak-base AS  keycloak-builder
 
 COPY keycloak/shanoir-ng-keycloak-auth.jar /opt/keycloak/providers
 
@@ -294,7 +294,7 @@ RUN /opt/keycloak/bin/kc.sh build
 #
 # Create actual image, based on builder before
 #
-FROM keycloak-base as keycloak
+FROM keycloak-base AS  keycloak
 
 COPY --from=keycloak-builder /opt/keycloak/ /opt/keycloak/
 COPY --chown=keycloak keycloak/themes/. /opt/keycloak/themes
@@ -313,7 +313,7 @@ CMD []
 
 FROM ohif/app:v3.9.0-beta.76 AS nginx-viewer
 
-FROM nginx as nginx
+FROM nginx AS  nginx
 
 COPY --link \
     nginx/http.conf \
@@ -342,7 +342,7 @@ CMD ["nginx", "-g", "daemon off;"]
 
 ################ front-dev #################################################
 
-FROM node:lts-alpine3.17 as front-dev
+FROM node:lts-alpine3.17 AS  front-dev
 
 WORKDIR /app
 
@@ -352,7 +352,7 @@ RUN npm install -g @angular/[email protected]
 
 ################ database ##################################################
 
-FROM mysql/mysql-server:5.7 as database
+FROM mysql/mysql-server:5.7 AS database
 
 COPY --link --chmod=0755 database/shanoir-entrypoint.sh /
 ENTRYPOINT ["/shanoir-entrypoint.sh"]
@@ -371,15 +371,15 @@ COPY --link database/db-changes /opt/db-changes
 
 ################ keycloak-database ##################################################
 
-FROM mysql/mysql-server:5.7 as keycloak-database
+FROM mysql/mysql-server:5.7 AS keycloak-database
 
 COPY --link --chmod=0755 keycloak-database/1_add_users.sql /docker-entrypoint-initdb.d/
 
 
 
 ################ solr ###############################################################
 
-FROM solr:8.1 as solr
+FROM solr:8.1 AS solr
 
 USER root
 RUN mkdir -p /etc/shanoir-core-template \

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/controller/ExecutionApi.java

@@ -24,9 +24,9 @@
 import org.shanoir.ng.shared.exception.EntityNotFoundException;
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.shanoir.ng.shared.exception.SecurityException;
-import org.shanoir.ng.vip.AutomaticExecution;
 import org.shanoir.ng.vip.dto.ExecutionCandidateDTO;
 import org.shanoir.ng.vip.dto.VipExecutionDTO;
+import org.shanoir.ng.vip.model.AutomaticExecution;
 import org.shanoir.ng.vip.monitoring.model.ExecutionStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/controller/ExecutionApiController.java

@@ -27,10 +27,10 @@
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.shanoir.ng.shared.exception.SecurityException;
 import org.shanoir.ng.utils.KeycloakUtil;
-import org.shanoir.ng.vip.AutomaticExecution;
 import org.shanoir.ng.vip.dto.DatasetParameterDTO;
 import org.shanoir.ng.vip.dto.ExecutionCandidateDTO;
 import org.shanoir.ng.vip.dto.VipExecutionDTO;
+import org.shanoir.ng.vip.model.AutomaticExecution;
 import org.shanoir.ng.vip.monitoring.model.ExecutionMonitoring;
 import org.shanoir.ng.vip.monitoring.model.ExecutionStatus;
 import org.shanoir.ng.vip.monitoring.schedule.ExecutionStatusMonitorService;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/model/AutomaticExecution.java

@@ -0,0 +1,55 @@
+package org.shanoir.ng.vip.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import org.shanoir.ng.shared.model.Study;
+
+/**
+ * This class represents the associated criterias for an automatic execution realized after an import in shanoir.
+ */
+@Entity
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class AutomaticExecution {
+
+    @Id
+    private Long id;
+
+    private String name;
+
+    @ManyToOne
+    @JoinColumn(name = "study_id")
+    private Study study;
+
+    /*
+    @OneToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+    @JoinTable(name = "pipeline_parameter")
+    private List<PipelineParameter> parameters;
+     */
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public Long getId() {
+        return id;
+    }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
+    public Study getStudy() {
+        return study;
+    }
+
+    public void setStudy(Study study) {
+        this.study = study;
+    }
+}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/monitoring/model/PipelineParameter.java

@@ -15,14 +15,18 @@
 
 package org.shanoir.ng.vip.monitoring.model;
 
-import java.util.List;
-import java.util.Map;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
 
 /**
  * This class represents the parameter of a VIP pipeline.
  */
+@Entity
 public class PipelineParameter {
 
+    @Id
+    private Long id;
+
     private String name;
     private String type;
     private String value;
@@ -77,4 +81,12 @@ public String getValue() {
     public void setValue(String value) {
         this.value = value;
     }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
+    public Long getId() {
+        return id;
+    }
 }

shanoir-ng-front/src/app/studies/study/study.component.html

@@ -426,7 +426,7 @@ <h2 class="header command-zone" i18n="Create study|Title@@studyDetailCreateTitle
             </fieldset>
             <fieldset [class.hidden-tab]="activeTab != 'executions'" tab="executions">
                 <legend>Execution planning</legend>
-                <execution-planning-list/>
+                <execution-planning-list [studyId]="study.id" [mode]="mode"/>
             </fieldset>
 		</form>
 	</div>

shanoir-ng-front/src/app/vip/execution-planning/execution-planning-list.component.html

@@ -1,8 +1,12 @@
+<label i18n="Execution planning">Execution's planification</label>
+
 <ol>
     <li>
-        <label i18n="Execution planning">Execution's planification</label>
             <ol *ngFor="let planifiedExec of executions let i = index; let even = even; let odd = odd;" [class.even]="even" [class.odd]="odd">
-                <execution-planning executionPlanning="{{planifiedExec}}"/>
+                <execution-planning executionPlanning="{{planifiedExec}}" [mode]="mode"/>
+                <button *ngIf="mode =='edit' " (click)="deleteExec(planifiedExec)"> Delete </button>
             </ol>
     </li>
+    <button *ngIf="mode == 'edit'" (click)="addNewExec()"> New </button>
 </ol>
+

shanoir-ng-front/src/app/vip/execution-planning/execution-planning-list.component.ts

@@ -1,15 +1,20 @@
-import {Component, Input, OnInit} from '@angular/core';
+import {Component, Input, model, OnInit} from '@angular/core';
 import {ExecutionService} from "../execution/execution.service";
 import {AutomaticExecution} from "../models/automatic-execution";
+import {ModesAware} from "../../preclinical/shared/mode/mode.decorator";
+import { Mode } from '../../shared/components/entity/entity.component.abstract';
+import {ExecutionPlanning} from "./execution-planning.component";
 
 @Component({
     selector: 'execution-planning-list',
     templateUrl: './execution-planning-list.component.html',
     styleUrls: ['./execution-planning-list.component.css']
 })
+@ModesAware
 export class ExecutionPlanningList {
 
     @Input() studyId: number
+    @Input() mode: Mode
     executions: AutomaticExecution[]
 
     constructor(protected executionService: ExecutionService) {}
@@ -20,4 +25,14 @@ export class ExecutionPlanningList {
         )
     }
 
+    addNewExec() {
+        let exec = new AutomaticExecution();
+        exec.name = "new one yay";
+        this.executions.push(exec)
+    }
+
+    deleteExec(execution) {
+        this.executions = this.executions.slice(this.executions.indexOf(execution));
+    }
+
 }