feat: ✨ add get file structure endpoint (#11)

* feat: add get file tree

* fix: format

* fix: format

* style: format

function_app.py

@@ -1,7 +1,7 @@
 """Azure Function App for ETL pipeline."""
+import json
 
 import logging
-
 import azure.functions as func
 
 from publish_pipeline.generate_high_level_metadata.generate_changelog import (
@@ -191,3 +191,18 @@ def moving_folders(req: func.HttpRequest) -> func.HttpResponse:
 def copying_folders(req: func.HttpRequest) -> func.HttpResponse:
     """Copies the directories along with the files in the Azure Database."""
     return file_operations.file_operation(file_operations.copy_directory, req)
+
+
+@app.route(route="listing-structure", auth_level=func.AuthLevel.FUNCTION)
+def listing_folder_structure(req: func.HttpRequest) -> func.HttpResponse:
+    """List the directories along with the files in the Azure Database."""
+    try:
+        file_operations.pipeline()
+        file_operations.get_file_tree()
+        # return func.HttpResponse("Success", status_code=200)
+        return func.HttpResponse(
+            json.dumps(file_operations.get_file_tree().to_dict()), status_code=200
+        )
+    except Exception as e:
+        print(f"Exception: {e}")
+        return func.HttpResponse("Internal Server Error", status_code=500)

utils/file_operations.py

@@ -1,20 +1,46 @@
 import os
-from typing import Callable
-import config
+from typing import Callable, List
 from azure.storage.filedatalake import FileSystemClient
 import azure.functions as func
+import datetime
+
+import azure.storage.blob as azureblob
+import psycopg2
+
+import config
 
 
 class FileException(Exception):
     pass
 
 
-def move_directory(container: str, source: str, destination: str, overwrite_permitted: bool):
-    file_system = FileSystemClient.from_connection_string(
-        config.AZURE_STORAGE_CONNECTION_STRING,
-        file_system_name=container,
-    )
+class FileStructure:
+    label: str
+
+    def __init__(self, label: str):
+        self.label = label
+
+    def to_dict(self):
+        return {
+            "label": self.label
+        }
+
 
+class FolderStructure(FileStructure):
+    children: List['FileStructure']
+
+    def __init__(self, label: str, children: List['FileStructure']):
+        super().__init__(label)
+        self.children = children
+
+    def to_dict(self):
+        return {
+            "children": [child.to_dict() for child in self.children],
+            "label": self.label
+        }
+
+
+def move_directory(file_system: FileSystemClient, source: str, destination: str, overwrite_permitted: bool):
     source_client = file_system.get_directory_client(source)
     destination_client = file_system.get_directory_client(destination)
 
@@ -31,12 +57,9 @@ def move_directory(container: str, source: str, destination: str, overwrite_perm
         )
 
 
-def copy_directory(container: str, source: str, destination: str, overwrite_permitted: bool) -> None:
+def copy_directory(file_system: FileSystemClient, source: str, destination: str, overwrite_permitted: bool) -> None:
     """Moving directories while implementing subsequent copies (recursion)"""
-    file_system = FileSystemClient.from_connection_string(
-        config.AZURE_STORAGE_CONNECTION_STRING,
-        file_system_name=container,
-    )
+
     source_client = file_system.get_directory_client(source)
 
     if not source_client.exists():
@@ -68,7 +91,7 @@ def copy_directory(container: str, source: str, destination: str, overwrite_perm
                 destination_file.create_file()
             destination_file.upload_data(source_file_bytes, overwrite=True)
         else:
-            copy_directory(container, child_path, target_path, overwrite_permitted)
+            copy_directory(file_system, child_path, target_path, overwrite_permitted)
 
 
 def file_operation(operation: Callable, req: func.HttpRequest) -> func.HttpResponse:
@@ -83,15 +106,95 @@ def file_operation(operation: Callable, req: func.HttpRequest) -> func.HttpRespo
 
     overwrite: bool = overwrite_permitted.lower().strip() == "true"
 
-    source: str = "AI-READI/metadata/test2/t1"
-    destination: str = "AI-READI/metadata/test2/t2"
+    source: str = "AI-READI/metadata/test2/t1/test"
+    destination: str = "AI-READI/metadata/test2/t3/t4"
     container = "stage-1-container"
 
     try:
-        operation(container, source, destination, overwrite)
+        file_system = FileSystemClient.from_connection_string(
+            config.AZURE_STORAGE_CONNECTION_STRING,
+            file_system_name=container,
+        )
+        operation(file_system, source, destination, overwrite)
         return func.HttpResponse("Success", status_code=200)
     except FileException as e:
         return func.HttpResponse(e.args[0], status_code=500)
     except Exception as e:
         print(f"Exception: {e}")
     return func.HttpResponse("Internal Server Error", status_code=500)
+
+
+def get_file_tree():
+    container = "stage-1-container"
+    file_system = FileSystemClient.from_connection_string(
+        config.AZURE_STORAGE_CONNECTION_STRING,
+        file_system_name=container,
+    )
+    source: str = "AI-READI/metadata/test2/t1"
+
+    return recurse_file_tree(file_system, source)
+
+
+def recurse_file_tree(file_system: FileSystemClient, source: str) -> FileStructure:
+    source_client = file_system.get_directory_client(source)
+
+    if not source_client.exists():
+        raise FileException("source directory does not exist!")
+
+    source_path: str = source_client.get_directory_properties().name
+    return FolderStructure(os.path.basename(source_path),
+                           [recurse_file_tree(file_system, child_path)
+                            if child_path.is_directory
+                            else FileStructure(os.path.basename(child_path.name))
+                            for child_path
+                            in file_system.get_paths(source_path, recursive=False)
+                            ])
+
+
+def pipeline():
+    """
+        Reads the file structure from azure
+    """
+
+    conn = psycopg2.connect(
+        host=config.FAIRHUB_DATABASE_HOST,
+        database=config.FAIRHUB_DATABASE_NAME,
+        user=config.FAIRHUB_DATABASE_USER,
+        password=config.FAIRHUB_DATABASE_PASSWORD,
+        port=config.FAIRHUB_DATABASE_PORT,
+    )
+
+    cur = conn.cursor()
+
+    study_id = "c588f59c-cacb-4e52-99dd-95b37dcbfd5c"
+    dataset_id = "af4be921-e507-41a9-9328-4cbb4b7dca1c"
+
+    cur.execute(
+        "SELECT * FROM dataset WHERE id = %s AND study_id = %s",
+        (dataset_id, study_id),
+    )
+    dataset = cur.fetchone()
+
+    if dataset is None:
+        return "Dataset not found"
+
+    conn.close()
+    # upload the file to the metadata folder
+
+    # metadata_folder = "AI-READI/metadata"
+    #
+    # sas_token = azureblob.generate_account_sas(
+    #     account_name="b2aistaging",
+    #     account_key=config.AZURE_STORAGE_ACCESS_KEY,
+    #     resource_types=azureblob.ResourceTypes(container=True, object=True),
+    #     permission=azureblob.AccountSasPermissions(read=True, write=True, list=True),
+    #     expiry=datetime.datetime.now(datetime.timezone.utc)
+    #            + datetime.timedelta(hours=1),
+    # )
+    #
+    # # Get the blob service client
+    # blob_service_client = azureblob.BlobServiceClient(
+    #     account_url="https://b2aistaging.blob.core.windows.net/",
+    #     credential=sas_token,
+    # )
+    return