Merge branch 'develop' into fli-iam#fli-iam#1864

youennmerel · Sep 25, 2023 · abd47b1 · abd47b1
2 parents 05c4af1 + 6a7065e
commit abd47b1
Show file tree

Hide file tree

Showing 236 changed files with 3,046 additions and 2,210 deletions.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -21,10 +21,10 @@ jobs:
       packages: write
       contents: read
     steps:
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Check out the repo
         uses: actions/checkout@v3

diff --git a/docker-compose/database/db-changes/datasets/0030_create_dataset_property.sql b/docker-compose/database/db-changes/datasets/0030_create_dataset_property.sql
@@ -0,0 +1,13 @@
+CREATE TABLE `dataset_property` (
+  `id` bigint(20) NOT NULL AUTO_INCREMENT,
+  `name` varchar(255) DEFAULT NULL,
+  `value` varchar(255) DEFAULT NULL,
+  `dataset_id` bigint(20) DEFAULT NULL,
+  `dataset_processing_id` bigint(20) DEFAULT NULL,
+  PRIMARY KEY (`id`),
+  KEY `FK1mcyt0h60808jmj3shlvge9c8` (`dataset_id`),
+  KEY `FKl09g6qevg8filjycsylycbdxw` (`dataset_processing_id`),
+  CONSTRAINT `FK1mcyt0h60808jmj3shlvge9c8` FOREIGN KEY (`dataset_id`) REFERENCES `dataset` (`id`),
+  CONSTRAINT `FKl09g6qevg8filjycsylycbdxw` FOREIGN KEY (`dataset_processing_id`) REFERENCES `dataset_processing` (`id`)
+)
+
diff --git a/docker-compose/database/db-changes/datasets/0031_create_processing_resource.sql b/docker-compose/database/db-changes/datasets/0031_create_processing_resource.sql
@@ -0,0 +1,11 @@
+CREATE TABLE `processing_resource` (
+  `id` bigint(20) NOT NULL AUTO_INCREMENT,
+  `resource_id` varchar(255) NOT NULL,
+  `dataset_id` bigint(20) DEFAULT NULL,
+  `processing_id` bigint(20) DEFAULT NULL,
+  PRIMARY KEY (`id`),
+  KEY `FK7971ykr4l94b3qgns4do405qe` (`dataset_id`),
+  KEY `FKtkm1ww8m49x3jdwdtocijhrha` (`processing_id`),
+  CONSTRAINT `FK7971ykr4l94b3qgns4do405qe` FOREIGN KEY (`dataset_id`) REFERENCES `dataset` (`id`),
+  CONSTRAINT `FKtkm1ww8m49x3jdwdtocijhrha` FOREIGN KEY (`processing_id`) REFERENCES `dataset_processing` (`id`)
+)
diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/ShanoirDatasetApplication.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/ShanoirDatasetApplication.java
@@ -14,6 +14,10 @@
 
 package org.shanoir.ng;
 
+import com.fasterxml.jackson.core.Version;
+import com.fasterxml.jackson.databind.Module;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+import io.swagger.v3.oas.annotations.OpenAPIDefinition;
 import org.shanoir.ng.shared.paging.PageSerializer;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
@@ -22,12 +26,6 @@
 import org.springframework.data.web.config.EnableSpringDataWebSupport;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
-import com.fasterxml.jackson.core.Version;
-import com.fasterxml.jackson.databind.Module;
-import com.fasterxml.jackson.databind.module.SimpleModule;
-
-import io.swagger.v3.oas.annotations.OpenAPIDefinition;
-
 /**
  * Shanoir-NG microservice datasets application.
  */

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/controller/BidsApi.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/controller/BidsApi.java
@@ -1,8 +1,13 @@
 
 package org.shanoir.ng.bids.controller;
 
-import java.io.IOException;
-
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.responses.ApiResponses;
+import io.swagger.v3.oas.annotations.tags.Tag;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.validation.Valid;
 import org.shanoir.ng.bids.model.BidsElement;
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.springframework.http.ResponseEntity;
@@ -12,13 +17,7 @@
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import io.swagger.v3.oas.annotations.Operation;
-import io.swagger.v3.oas.annotations.Parameter;
-import io.swagger.v3.oas.annotations.responses.ApiResponse;
-import io.swagger.v3.oas.annotations.responses.ApiResponses;
-import io.swagger.v3.oas.annotations.tags.Tag;
-import jakarta.servlet.http.HttpServletResponse;
-import jakarta.validation.Valid;
+import java.io.IOException;
 
 @Tag(name = "bids")
 @RequestMapping("/bids")

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/controller/BidsApiController.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/controller/BidsApiController.java
@@ -1,21 +1,9 @@
 package org.shanoir.ng.bids.controller;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.text.SimpleDateFormat;
-import java.util.stream.Stream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
-
+import io.swagger.v3.oas.annotations.Parameter;
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.servlet.http.HttpServletResponse;
 import jakarta.validation.Valid;
-
 import org.apache.commons.io.FileUtils;
 import org.joda.time.DateTime;
 import org.shanoir.ng.bids.BidsDeserializer;
@@ -35,7 +23,17 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import io.swagger.v3.oas.annotations.Parameter;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.stream.Stream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 @Controller
 public class BidsApiController implements BidsApi {

diff --git a/...-ng-datasets/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQDatasetsService.java b/...-ng-datasets/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQDatasetsService.java
@@ -14,10 +14,8 @@
 
 package org.shanoir.ng.configuration.amqp;
 
-import java.io.IOException;
-import java.util.*;
-
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.shanoir.ng.bids.service.BIDSService;
 import org.shanoir.ng.dataset.dto.StudyStorageVolumeDTO;
@@ -46,11 +44,8 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.amqp.AmqpRejectAndDontRequeueException;
 import org.springframework.amqp.core.ExchangeTypes;
-import org.springframework.amqp.rabbit.annotation.Exchange;
 import org.springframework.amqp.rabbit.annotation.Queue;
-import org.springframework.amqp.rabbit.annotation.QueueBinding;
-import org.springframework.amqp.rabbit.annotation.RabbitHandler;
-import org.springframework.amqp.rabbit.annotation.RabbitListener;
+import org.springframework.amqp.rabbit.annotation.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.stereotype.Component;
@@ -59,7 +54,8 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.util.CollectionUtils;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.IOException;
+import java.util.*;
 
 /**
  * RabbitMQ configuration.

diff --git a/...g-datasets/src/main/java/org/shanoir/ng/configuration/security/SecurityConfiguration.java b/...g-datasets/src/main/java/org/shanoir/ng/configuration/security/SecurityConfiguration.java
@@ -14,10 +14,6 @@
 
 package org.shanoir.ng.configuration.security;
 
-import java.util.Collection;
-import java.util.Map;
-import java.util.stream.Collectors;
-
 import org.shanoir.ng.dicom.web.StowRSMultipartRelatedRequestFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
@@ -40,6 +36,10 @@
 import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
 import org.springframework.web.filter.CorsFilter;
 
+import java.util.Collection;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 /**
  * Spring security configuration.
  *

diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApi.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApi.java
@@ -15,15 +15,6 @@
 
 package org.shanoir.ng.dataset.controler;
 
-import java.io.IOException;
-
-import org.shanoir.ng.shared.exception.RestServiceException;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-
 import io.swagger.v3.oas.annotations.Operation;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
@@ -32,6 +23,15 @@
 import jakarta.servlet.http.HttpServletResponse;
 import jakarta.validation.Valid;
 import jakarta.validation.constraints.NotNull;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
+import org.shanoir.ng.shared.exception.RestServiceException;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import java.io.IOException;
 
 /**
  * @author Alae Es-saki
@@ -51,6 +51,6 @@ public interface CarminDataApi {
             produces = { "application/json", "application/octet-stream" },
             method = RequestMethod.GET)
     ResponseEntity<?> getPath(@Parameter(name = "the complete path on which to request information. It can contain non-encoded slashes. Except for the \"exists\" action, any request on a non-existing path should return an error", required=true) @PathVariable("completePath") String completePath, @NotNull @Parameter(name = "The \"content\" action downloads the raw file. If the path points to a directory, a tarball of this directory is returned. The \"exists\" action returns a BooleanResponse object (see definition) indicating if the path exists or not. The \"properties\" action returns a Path object (see definition) with the path properties. The \"list\" action returns a DirectoryList object (see definition) with the properties of all the files of the directory (if the path is not a directory an error must be returned). The \"md5\" action is optional and returns a PathMd5 object (see definition)." ,required=true
-    ) @Valid @RequestParam(value = "action", required = true) String action, @Valid @RequestParam(value = "format", required = false, defaultValue = "dcm") final String format, HttpServletResponse response) throws IOException, RestServiceException;
+    ) @Valid @RequestParam(value = "action", required = true) String action, @Valid @RequestParam(value = "format", required = false, defaultValue = "dcm") final String format, HttpServletResponse response) throws IOException, RestServiceException, EntityNotFoundException;
 
 }
diff --git a/...r-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApiController.java b/...r-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApiController.java
@@ -15,46 +15,73 @@
 
 package org.shanoir.ng.dataset.controler;
 
-import java.io.IOException;
-
+import io.swagger.v3.oas.annotations.Parameter;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotNull;
+import org.shanoir.ng.dataset.model.Dataset;
 import org.shanoir.ng.dataset.service.DatasetDownloaderServiceImpl;
+import org.shanoir.ng.processing.carmin.service.ProcessingResourceService;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
 import org.shanoir.ng.shared.exception.RestServiceException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import io.swagger.v3.oas.annotations.Parameter;
-import jakarta.servlet.http.HttpServletResponse;
-import jakarta.validation.Valid;
-import jakarta.validation.constraints.NotNull;
+import java.io.IOException;
+import java.util.List;
 
 @Controller
 public class CarminDataApiController implements CarminDataApi{
 
+    private static final Logger LOG = LoggerFactory.getLogger(CarminDataApiController.class);
+
     private static final String DCM = "dcm";
 
     @Autowired
     private DatasetDownloaderServiceImpl datasetDownloaderService;
 
+    @Autowired
+    private ProcessingResourceService processingResourceService;
+
     @Override
-    public ResponseEntity<?> getPath(@Parameter(name = "the complete path on which to request information. It can contain non-encoded slashes. Except for the \"exists\" action, any request on a non-existing path should return an error", required=true) @PathVariable("completePath") String completePath, @NotNull @Parameter(name = "The \"content\" action downloads the raw file. If the path points to a directory, a tarball of this directory is returned. The \"exists\" action returns a BooleanResponse object (see definition) indicating if the path exists or not. The \"properties\" action returns a Path object (see definition) with the path properties. The \"list\" action returns a DirectoryList object (see definition) with the properties of all the files of the directory (if the path is not a directory an error must be returned). The \"md5\" action is optional and returns a PathMd5 object (see definition)." ,required=true
-        ) @Valid @RequestParam(value = "action", required = true, defaultValue = "content") String action, @Valid @RequestParam(value = "format", required = false, defaultValue = DCM) final String format, HttpServletResponse response) throws IOException, RestServiceException {
+    public ResponseEntity<?> getPath(
+            @Parameter(name = "the complete path on which to request information. It can contain non-encoded slashes. Except for the \"exists\" action, any request on a non-existing path should return an error",
+                    required=true)
+            @PathVariable("completePath") String completePath,
+            @NotNull @Parameter(name = "The \"content\" action downloads the raw file. If the path points to a directory, a tarball of this directory is returned. The \"exists\" action returns a BooleanResponse object (see definition) indicating if the path exists or not. The \"properties\" action returns a Path object (see definition) with the path properties. The \"list\" action returns a DirectoryList object (see definition) with the properties of all the files of the directory (if the path is not a directory an error must be returned). The \"md5\" action is optional and returns a PathMd5 object (see definition).",
+                    required=true)
+            @Valid @RequestParam(value = "action", required = true, defaultValue = "content") String action,
+            @Valid @RequestParam(value = "format", required = false, defaultValue = DCM) final String format,
+            HttpServletResponse response) throws IOException, RestServiceException, EntityNotFoundException {
         // TODO implement those actions
         switch (action){
             case "exists":
             case "list":
             case "md5":
             case "properties":
                 return new ResponseEntity<Void>(HttpStatus.NOT_IMPLEMENTED);
-            case "content":{
-            	datasetDownloaderService.downloadDatasetById(Long.parseLong(completePath),null, format, response, true);
+            case "content":
+
+                List<Dataset> datasets = this.processingResourceService.findDatasetsByResourceId(completePath);
+
+                if(datasets.isEmpty()){
+                    LOG.error("No dataset found for resource id [{}]", completePath);
+                    return new ResponseEntity<Void>(HttpStatus.BAD_REQUEST);
+                }
+
+                datasetDownloaderService.massiveDownload(format, datasets, response, true);
+
                 return new ResponseEntity<Void>(HttpStatus.OK);
-            }
         }
+
         return new ResponseEntity<Void>(HttpStatus.BAD_REQUEST);
+
     }
 
 }