feat: added file bundle task when downloading file archive

obiba_opal/core.py

@@ -25,6 +25,8 @@ def __init__(self, server=None):
         self.base_url = self.__ensure_entry("Opal address", server)
         self.id = None
         self.rid = None
+        self.profile = None
+        self.version = None
 
     def __del__(self):
         self.close()
@@ -67,13 +69,14 @@ def buildWithCertificate(cls, server, cert, key, no_ssl_verify: bool = False):
         :param key - private key (must be named as 'privatekey.pem')
         :param no_ssl_verify - if True, the SSL certificate is not verified
         (not recommended)
+        :return: the client instance
         """
 
         client = cls(server)
         if client.base_url.startswith("https:"):
             client.session.verify = not no_ssl_verify
         client.session.cert = (cert, key)
-
+        client.init()
         return client
 
     @classmethod
@@ -86,6 +89,7 @@ def buildWithAuthentication(cls, server, user, password, no_ssl_verify: bool = F
         :param password - user password
         :param no_ssl_verify - if True, the SSL certificate is not verified
         (not recommended)
+        :return: the client instance
         """
         client = cls(server)
         if client.base_url.startswith("https:"):
@@ -114,6 +118,7 @@ def buildWithToken(cls, server, token, no_ssl_verify: bool = False):
         :param token - token key
         :param no_ssl_verify - if True, the SSL certificate is not verified
         (not recommended)
+        :return: the client instance
         """
         client = cls(server)
         if client.base_url.startswith("https:"):
@@ -134,6 +139,7 @@ def credentials(self, user, password):
 
         :param user - username
         :param password - user password
+        :return: the client instance
         """
         u = self.__ensure_entry("User name", user)
         p = self.__ensure_entry("Password", password, True)
@@ -147,17 +153,18 @@ def token(self, token):
         Creates the authorization header and attempts to input the required token
 
         :param token - token key
+        :return: the client instance
         """
         tk = self.__ensure_entry("Token", token, True)
-        return self.header("X-Opal-Auth", tk)
+        self.header("X-Opal-Auth", tk)
+        self.init()
+        return self
 
     def init_otp(self):
         """
         Checks if an OTP is needed and if yes, prompts the user for the security code
         """
-        request = self.new_request()
-        profile_url = "/system/subject-profile/_current"
-        response = request.accept_json().get().resource(profile_url).send()
+        response = self.init()
         if response.code == 401:
             auth_header = response.get_header("WWW-Authenticate")
             if auth_header:
@@ -166,7 +173,41 @@ def init_otp(self):
                     val = input("Enter 6-digits code: ")
                     # validate code and get the opalsid cookie for further requests
                     request = self.new_request()
-                    request.header(otp_header, val).accept_json().get().resource(profile_url).send()
+                    self.init(request.header(otp_header, val))
+
+    def init(self, request=None):
+        """
+        Initializes the client profile and version information by calling the system profile endpoint
+
+        :return: the response of the profile endpoint
+        """
+        _request = self.new_request() if request is None else request
+        profile_url = "/system/subject-profile/_current"
+        response = _request.accept_json().get().resource(profile_url).send()
+        if response.code == 200:
+            self.profile = response.from_json()
+            self.version = response.get_version()
+        return response
+
+    def compare_version(self, version):
+        """
+        Compares the Opal version with the provided version and raises an exception if the Opal version is lower than the provided version
+
+        :param version - the version to compare with
+        :return: -1 if the Opal version is lower than the provided version, 0 if they are equal, 1 if the Opal version is higher than the provided version
+        :raises Exception: if the Opal version is not initialized
+        """
+        if self.version is None:
+            raise Exception("Opal version is not initialized")
+        clean_version = self.version.split("-")[0]  # Remove any suffix like "-SNAPSHOT"
+        opal_version = tuple(map(int, clean_version.split(".")))
+        required_version = tuple(map(int, version.split(".")))
+        if opal_version < required_version:
+            return -1
+        elif opal_version > required_version:
+            return 1
+        else:
+            return 0
 
     def verify(self, value):
         """
@@ -500,6 +541,9 @@ def get_header(self, header: str) -> str | None:
     def get_location(self):
         return self.get_header("Location")
 
+    def get_version(self):
+        return self.get_header("X-Opal-Version")
+
     def extract_cookie_value(self, name: str) -> str | None:
         if "set-cookie" in self.response.headers:
             if isinstance(self.response.headers["set-cookie"], str):

obiba_opal/file.py

@@ -2,10 +2,13 @@
 Opal file management.
 """
 
-import obiba_opal.core as core
+import json
 import sys
 import os
 
+import obiba_opal.core as core
+from obiba_opal.system import TaskService
+
 
 class FileService:
     """
@@ -90,7 +93,11 @@ def download_file(self, path: str, fd: int | os.PathLike, download_password: str
         :param fd: The file descriptor or path to the destination file
         :param download_password: The password to use to encrypt the
                                 downloaded zip archive
+        :raises Exception: If the file is not readable
         """
+        info = self.file_info(path)
+        if not info["readable"]:
+            raise Exception(f"File {path} is not readable")
         request = self.client.new_request()
         request.fail_on_error()
 
@@ -100,8 +107,42 @@ def download_file(self, path: str, fd: int | os.PathLike, download_password: str
         file = FileService.OpalFile(path)
         fp = os.fdopen(fd, "wb") if isinstance(fd, int) else fd
 
-        request.get().resource(file.get_ws()).accept("*/*").header("X-File-Key", download_password).send(fp)
-        fp.flush()
+        if self.client.compare_version("5.7.0") < 0:
+            # File download before Opal 5.7.0
+            request.get().resource(file.get_ws()).accept("*/*").header("X-File-Key", download_password).send(fp)
+            fp.flush()
+        else:
+            # File download with Opal 5.7.0 or later
+            if download_password or info["type"] == "FOLDER":
+                # File to be bundled as zip archive
+                options = file.make_bundle_options(download_password)
+                bundle_request = self.client.new_request().fail_on_error()
+                if self.verbose:
+                    bundle_request.verbose()
+                response = bundle_request.post().resource("/shell/commands/_file-bundle").accept_json().content_type_json().content(json.dumps(options)).send()
+                task = response.from_json()
+                task_service = TaskService(self.client)
+                try:
+                    status = task_service.wait_task(task["id"], True)
+                    if status == "SUCCEEDED":
+                        # Task succeeded, downloading file
+                        download_request = self.client.new_request().fail_on_error()
+                        if self.verbose:
+                            download_request.verbose()
+                        download_request.get().resource(f"/shell/command/{task['id']}/_result").accept("*/*").send(fp)
+                        fp.flush()
+                    else:
+                        raise Exception(f"File bundle task failed with status: {status}")
+                finally:
+                    # Ensure task is deleted in any case to avoid leaving pending tasks on the server
+                    delete_request = self.client.new_request().fail_on_error()
+                    if self.verbose:
+                        delete_request.verbose()
+                    delete_request.delete().resource(f"/shell/command/{task['id']}").send()
+            else:
+                # File to be downloaded as is
+                request.get().resource(file.get_ws()).accept("*/*").header("X-File-Key", download_password).send(fp)
+                fp.flush()
 
     def upload_file(self, upload: str, path: str):
         """
@@ -167,3 +208,11 @@ def get_meta_ws(self):
 
         def get_ws(self):
             return f"/files{self.path}"
+
+        def make_bundle_options(self, download_password):
+            options = {
+                "paths": [self.path]
+            }
+            if download_password:
+                options["password"] = download_password
+            return options

obiba_opal/system.py

@@ -452,18 +452,20 @@ def cancel_task(self, id: str | int):
         request.content("CANCELED")
         request.put().resource(f"/shell/command/{id}/status").send()
 
-    def wait_task(self, id: str | int):
+    def wait_task(self, id: str | int, silently: bool = False):
+        """ Wait for the task to complete or being canceled, and return its status. """
         task = self.get_task(id)
-        while task["status"] not in ["SUCCEEDED", "CANCELED", "FAILED"]:
-            if "progress" in task:
-                progress = task["progress"]
-                if "message" in progress:
-                    sys.stdout.write("\r\033[K" + str(progress["percent"]) + "% " + progress["message"])
+        while task["status"] not in ["SUCCEEDED", "CANCELED", "FAILED", "CANCEL_PENDING"]:
+            if not silently:
+                if "progress" in task:
+                    progress = task["progress"]
+                    if "message" in progress:
+                        sys.stdout.write("\r\033[K" + str(progress["percent"]) + "% " + progress["message"])
+                    else:
+                        sys.stdout.write("\r\033[K" + str(progress["percent"]) + "%")
                 else:
-                    sys.stdout.write("\r\033[K" + str(progress["percent"]) + "%")
-            else:
-                sys.stdout.write(".")
-            sys.stdout.flush()
+                    sys.stdout.write(".")
+                sys.stdout.flush()
             time.sleep(1)
             task = self.get_task(id)
         return task["status"]

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "obiba-opal"
-version = "6.0.2"
+version = "6.1.0"
 description = "OBiBa/Opal python client."
 authors = [
     {name = "Yannick Marcon", email = "yannick.marcon@obiba.org"}
@@ -52,3 +52,8 @@ build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
 packages = ["obiba_opal"]
+
+[tool.pytest.ini_options]
+markers = [
+    "integration: marks tests that require a running Opal instance",
+]