Bug fixes.

docker-compose.yml

@@ -42,7 +42,7 @@ services:
     image: mongo:6.0.6
     environment:
       MONGO_APP_DATABASE: phyloviz-web-platform
-      MONGO_REPLICA_HOST: host.docker.internal
+      MONGO_REPLICA_HOST: 172.17.0.1
       MONGO_REPLICA_PORT: 27018
 
     entrypoint: >

scripts/flowviz_setup.sh

@@ -8,11 +8,19 @@ cd ./FLOWViZ
 
 echo "Steps 1 and 2 of the manual setup are going to be executed..."
 
+npm install
+
+cd client
+
+npm install
+
+cd ..
+
 ./setupAirflow.sh
 
 echo "Setting up FLOWViZ docker..."
 docker compose up -d
 echo "FLOWViZ docker setup completed!"
 
 echo "Steps 1 and 2 of the manual setup were executed successfully!"
-echo "Now you still need to execute steps 3 to 6 of the manual setup. (https://github.com/devandrepascoa/FLOWViZ?tab=readme-ov-file#manual-setup)"
+echo "Now you still need to execute steps 3 to 6 of the manual setup. (https://github.com/devandrepascoa/FLOWViZ?tab=readme-ov-file#manual-setup)"

scripts/phylodb_cleanup.sh

@@ -6,4 +6,4 @@ docker compose down
 
 cd ..
 
-rm -rf ./phyloDB/
+rm -rf ./phyloDB/

src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepository.java

@@ -28,4 +28,11 @@ public interface S3FileRepository {
      * @return true if the file was deleted successfully, false otherwise
      */
     boolean delete(String url);
+
+    /**
+     * Get location of the repository.
+     *
+     * @return location of the repository
+     */
+    String getLocation();
 }

src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepositoryImpl.java

@@ -27,6 +27,7 @@
 @Repository
 public class S3FileRepositoryImpl implements S3FileRepository {
 
+    private final String s3Endpoint;
     private final String bucketName;
     private final S3AsyncClient s3Client;
     private final S3TransferManager transferManager;
@@ -53,6 +54,7 @@ public S3FileRepositoryImpl(
 
         newS3Client.createBucket(r -> r.bucket(bucketName));
 
+        this.s3Endpoint = s3endpoint;
         this.s3Client = newS3Client;
         this.bucketName = bucketName;
         this.transferManager = S3TransferManager.builder().s3Client(newS3Client).build();
@@ -136,4 +138,10 @@ public boolean delete(String url) {
 
         return true;
     }
+
+    @Override
+    public String getLocation() {
+        return s3Endpoint + "/" + bucketName;
+    }
+
 }

src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java

@@ -20,7 +20,7 @@ public IsolateDataDataRepositorySpecificData uploadIsolateData(String projectId,
 
         s3FileRepository.upload(url, multipartFile);
 
-        return new IsolateDataS3DataRepositorySpecificData(url, multipartFile.getOriginalFilename());
+        return new IsolateDataS3DataRepositorySpecificData(s3FileRepository.getLocation() + "/" + url, multipartFile.getOriginalFilename());
     }
 
     @Override

src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataS3DataRepository.java

@@ -21,7 +21,7 @@ public TypingDataDataRepositorySpecificData uploadTypingData(String projectId, S
 
         s3FileRepository.upload(url, multipartFile);
 
-        return new TypingDataS3DataRepositorySpecificData(url, multipartFile.getOriginalFilename());
+        return new TypingDataS3DataRepositorySpecificData(s3FileRepository.getLocation() + "/" + url, multipartFile.getOriginalFilename());
     }
 
     @Override
@@ -49,4 +49,4 @@ public void deleteTypingData(TypingDataDataRepositorySpecificData typingDataData
 
         s3FileRepository.delete(repositorySpecificData.getUrl());
     }
-}
+}

src/backend/mongo/mongo-init.js

@@ -725,10 +725,10 @@ db['workflow-templates'].insertMany(
                     "taskId": "createMetadata",
                     "tool": "metadata_uploader",
                     "action": {
-                        "command": "--original_url=${url} --url=http://localhost:9444/phyloviz-web-platform/projects/${projectId}/${workflowId} --type=${file_type} --project-id=${projectId} --workflow-id=${workflowId}"
+                        "command": "--original_url=${url} --url=https://s3.eu-west-3.amazonaws.com/phyloviz-web-platform/projects/${projectId}/${workflowId} --type=${file_type} --project-id=${projectId} --workflow-id=${workflowId}"
                     }
                 }
             ]
         }
     ]
-)
+)

src/backend/tools/aws_config

@@ -1,3 +1,3 @@
 [default]
-region = custom
-endpoint_url = http://host.docker.internal:9444
+region = eu-west-3
+endpoint_url = https://s3.eu-west-3.amazonaws.com

src/backend/tools/compute_tree_view/Dockerfile

@@ -9,11 +9,11 @@ COPY compute_tree_view/requirements.txt /app/requirements.txt
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
-ENV PHYLODB_URL="http://host.docker.internal:8081"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
+ENV PHYLODB_URL="http://172.17.0.1:8081"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "compute_tree_view.py"]
+ENTRYPOINT ["python", "compute_tree_view.py"]

src/backend/tools/downloader/Dockerfile

@@ -17,10 +17,10 @@ COPY aws_credentials /root/.aws/credentials
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "downloader.py"]
+ENTRYPOINT ["python", "downloader.py"]

src/backend/tools/downloader/downloader.py

@@ -124,7 +124,7 @@ def download_s3_object(project_id, dataset_id, resource_id, resource_type, out,
     parsed_url = urlparse(s3_url)
     path = parsed_url.path.lstrip('/')
     bucket_name = path.split('/')[0]
-    object_key = path.lstrip(f'{bucket_name}')
+    object_key = path.lstrip(f'{bucket_name}/')
 
     print("Retrieving S3 object from bucket: " + bucket_name + " and key: " + object_key)
 

src/backend/tools/isolate_data_indexer/Dockerfile

@@ -9,11 +9,11 @@ COPY isolate_data_indexer/requirements.txt /app/requirements.txt
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
-ENV PHYLODB_URL="http://host.docker.internal:8081"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
+ENV PHYLODB_URL="http://172.17.0.1:8081"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "isolate_data_indexer.py"]
+ENTRYPOINT ["python", "isolate_data_indexer.py"]

src/backend/tools/metadata_uploader/Dockerfile

@@ -16,10 +16,10 @@ COPY aws_credentials /root/.aws/credentials
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "metadata_uploader.py"]
+ENTRYPOINT ["python", "metadata_uploader.py"]

src/backend/tools/rclone/rclone.conf

@@ -3,4 +3,4 @@ type = s3
 provider = other
 access_key_id = AKIAIOSFODNN7EXAMPLE
 secret_access_key = wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY
-endpoint = http://host.docker.internal:9444
+endpoint = https://s3.eu-west-3.amazonaws.com

src/backend/tools/tree_indexer/Dockerfile

@@ -9,11 +9,11 @@ COPY tree_indexer/requirements.txt /app/requirements.txt
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
-ENV PHYLODB_URL="http://host.docker.internal:8081"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
+ENV PHYLODB_URL="http://172.17.0.1:8081"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "tree_indexer.py"]
+ENTRYPOINT ["python", "tree_indexer.py"]

src/backend/tools/typing_data_indexer/Dockerfile

@@ -9,11 +9,11 @@ COPY typing_data_indexer/requirements.txt /app/requirements.txt
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
-ENV PHYLODB_URL="http://host.docker.internal:8081"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
+ENV PHYLODB_URL="http://172.17.0.1:8081"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "typing_data_indexer.py"]
+ENTRYPOINT ["python", "typing_data_indexer.py"]

src/backend/tools/uploader/Dockerfile

@@ -16,10 +16,10 @@ COPY aws_credentials /root/.aws/credentials
 # Set the working directory to /app
 WORKDIR /app
 
-ENV MONGO_URI="mongodb://host.docker.internal:28017/?directConnection=true"
+ENV MONGO_URI="mongodb://172.17.0.1:28017/?directConnection=true"
 
 # Install any required packages
 RUN pip install --trusted-host pypi.python.org -r requirements.txt
 
 # Run the script when the container launches
-ENTRYPOINT ["python", "uploader.py"]
+ENTRYPOINT ["python", "uploader.py"]

src/backend/tools/uploader/uploader.py

@@ -25,7 +25,7 @@
 datasets_collection = db['datasets']
 
 
-def tree_handler(s3_output_path, project_id, dataset_id, tree_id):
+def tree_handler(object_key, project_id, dataset_id, tree_id):
     trees_collection = db['trees']
 
     # Tree should already be indexed, so its metadata exists
@@ -38,15 +38,15 @@ def tree_handler(s3_output_path, project_id, dataset_id, tree_id):
         },
         {'$set': {
             'repositorySpecificData.s3': {
-                'url': f'http://localhost:9444/{bucket_name}{s3_output_path}'
+                'url': f'https://s3.eu-west-3.amazonaws.com/{bucket_name}/{object_key}'
             }
         }}
     )
 
     print(f'File uploaded to S3 and tree metadata updated of tree with treeId: {tree_id}')
 
 
-def distance_matrix_handler(s3_output_path, project_id, dataset_id, workflow_id, distance_matrix_id, source_type,
+def distance_matrix_handler(object_key, project_id, dataset_id, workflow_id, distance_matrix_id, source_type,
                             function):
     distance_matrix_collection = db['distance-matrices']
 
@@ -69,7 +69,7 @@ def distance_matrix_handler(s3_output_path, project_id, dataset_id, workflow_id,
         'source': source,
         'repositorySpecificData': {
             's3': {
-                'url': f'http://localhost:9444/{bucket_name}{s3_output_path}'
+                'url': f'https://s3.eu-west-3.amazonaws.com/{bucket_name}/{object_key}'
             }
         }
     }
@@ -119,17 +119,18 @@ def upload_file_to_s3(file_path, project_id, dataset_id, workflow_id, resource_i
 
     collection_name = get_collection_from_resource_type(resource_type)
 
-    s3_output_path = f'/{project_id}/{collection_name}/{resource_id}'
+    object_key = f'{project_id}/{collection_name}/{resource_id}'
+
     # Upload the file to S3
     with open(file_path, 'rb') as file:
-        s3.upload_fileobj(file, bucket_name, s3_output_path)
+        s3.upload_fileobj(file, bucket_name, object_key)
 
     if resource_type == "tree":
         tree_id = resource_id
-        tree_handler(s3_output_path, project_id, dataset_id, tree_id)
+        tree_handler(object_key, project_id, dataset_id, tree_id)
     elif resource_type == "distance-matrix":
         distance_matrix_id = resource_id
-        distance_matrix_handler(s3_output_path, project_id, dataset_id, workflow_id, distance_matrix_id, source_type,
+        distance_matrix_handler(object_key, project_id, dataset_id, workflow_id, distance_matrix_id, source_type,
                                 function)
     else:
         raise Exception(f'Unknown resource type: {resource_type}')

start.sh

@@ -9,6 +9,6 @@ npm install
 npm start &
 
 docker compose up -d --build
-sleep 60
 echo "Doing very heavy work..."
+sleep 90
 docker compose up -d