From 6247a1bd281196b5618d3f696a28c5da5beddaf4 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 3 Mar 2025 12:25:47 +0100
Subject: [PATCH 01/14] delete old classes

---
 src/vip_client/classes/VipClient.py | 326 ----------------------
 src/vip_client/classes/VipLoader.py | 405 ----------------------------
 2 files changed, 731 deletions(-)
 delete mode 100644 src/vip_client/classes/VipClient.py
 delete mode 100644 src/vip_client/classes/VipLoader.py

diff --git a/src/vip_client/classes/VipClient.py b/src/vip_client/classes/VipClient.py
deleted file mode 100644
index c9c22cd..0000000
--- a/src/vip_client/classes/VipClient.py
+++ /dev/null
@@ -1,326 +0,0 @@
-from __future__ import annotations
-import json
-import os
-import re
-import time
-from contextlib import contextmanager
-from pathlib import *
-
-from vip_client.utils import vip
-
-class VipClient():
-    """
-    Base class for the client.
-    WORK IN PROGRESS
-    """
-
-                    ##################
-    ################ Class Attributes ##################
-                    ##################
-    
-    # Class name
-    __name__ = "VipClient"
-    # Default verbose state
-    _VERBOSE = True
-    # Vip portal
-    _VIP_PORTAL = "https://vip.creatis.insa-lyon.fr/"
-    # Mail address for support
-    _VIP_SUPPORT = "vip-support@creatis.insa-lyon.fr"
-    # Regular expression for invalid characters
-    _INVALID_CHARS = re.compile(r"[^0-9\.,A-Za-z\-+@/_(): \[\]?&=]")
-
-                    ################
-    ################ Public Methods ##################
-                    ################
-
-    # Login to VIP
-    @classmethod
-    def init(cls, api_key="VIP_API_KEY", verbose=True) -> VipClient:
-        """
-        Handshakes with VIP using your own API key. 
-        Returns a class instance which properties can be provided as keyword arguments.
-        
-        ## Parameters
-        - `api_key` (str): VIP API key. This can be either:
-            A. [unsafe] A **string litteral** containing your API key,
-            B. [safer] A **path to some local file** containing your API key,
-            C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
-        In cases B or C, the API key will be loaded from the local file or the environment variable. 
-        
-        - `verbose` (bool): default verbose mode for all instances.
-            - If True, all instances will display logs by default;
-            - If False, all instance methods will run silently by default.
-
-        - `kwargs` [Optional] (dict): keyword arguments or dictionnary setting properties of the returned instance.     
-        """
-        # Set the default verbose mode for all sessions
-        cls._VERBOSE = verbose
-        # Check if `api_key` is in a local file or environment variable
-        true_key = cls._get_api_key(api_key)
-        # Set User API key
-        try:
-            # setApiKey() may return False
-            assert vip.setApiKey(true_key), \
-                f"(!) Unable to set the VIP API key: {true_key}.\nPlease check the key or retry later."
-        except RuntimeError as vip_error:
-            # setApiKey() may throw RuntimeError in case of bad key
-            cls._printc(f"(!) Unable to set the VIP API key: {true_key}.\n    Original error message:")
-            raise vip_error
-        except(json.decoder.JSONDecodeError) as json_error:
-            # setApiKey() may throw JSONDecodeError in special cases
-            cls._printc(f"(!) Unable to set the VIP API key: {true_key}.\n    Original error message:")
-            raise json_error
-        # Display success
-        cls._printc()
-        cls._printc("----------------------------------")
-        cls._printc("| You are communicating with VIP |")
-        cls._printc("----------------------------------")
-        cls._printc()
-    # ------------------------------------------------
-
-                    #################
-    ################ Private Methods ################
-                    #################
-
-    # Method to check existence of a distant resource.
-    @classmethod
-    def _exists(cls, path, location="vip") -> bool:
-        """
-        Checks existence of a distant resource (`location`="vip").
-        `path` can be a string or Pathlib object.
-        """
-        # Check `location`
-        if location != "vip":
-            raise NotImplementedError(f"Unknown location: {location}")
-        # Check path existence
-        try: 
-            return vip.exists(str(path))
-        except RuntimeError as vip_error:
-            # Connection error with VIP
-            cls._handle_vip_error(vip_error)
-        except json.decoder.JSONDecodeError:
-            raise ValueError(
-                f"The following path generated an error on VIP:\n\t{path}\n"
-                + "Please check this path or retry later."
-                )
-    # ------------------------------------------------
-    
-    # Method to create a distant directory
-    @classmethod
-    def _create_dir(cls, path: PurePath, location="vip") -> None:
-        """
-        Creates a directory at `path`, on VIP servers if `location` is "vip".
-
-        `path`can be a string or PathLib object.
-        Returns the VIP path of the newly created folder.
-        """
-        # Check `location`
-        if location != "vip": 
-            raise NotImplementedError(f"Unknown location: {location}")
-        # Create directory
-        try: 
-            if not vip.create_dir(str(path)):
-                msg = f"The following directoy could not be created on VIP:\n\t{path}\n"
-                msg += f"Please retry later. Contact VIP support ({cls._VIP_SUPPORT}) if this cannot be fixed."
-                raise AssertionError(msg)
-        except RuntimeError as vip_error:
-            cls._handle_vip_error(vip_error)  
-        except json.decoder.JSONDecodeError as json_error:
-            raise ValueError(
-                f"The following path generated an error on VIP:\n\t{path}\n"
-                + "Please check this path is valid and/or consistent with your other inputs."
-                )
-    # ------------------------------------------------
-
-    # Function to delete a path
-    @classmethod
-    def _delete_path(cls, path: PurePath, location="vip") -> None:
-        """
-        Deletes `path` on `location`. Raises an error if the file exists and could not be removed.
-        """
-        # Check `location`
-        if location != "vip":
-            raise NotImplementedError(f"Unknown location: {location}")
-        # Try path deletion
-        done = vip.delete_path(str(path))
-        # VIP Errors are handled by returning False in `vip.delete_path()`.
-        if not done and vip.exists(str(path)):
-            # Raise a generic error if deletion did not work
-            msg = f"\n'{path}' could not be removed from VIP servers.\n"
-            msg += "Check your connection with VIP and path existence on the VIP portal.\n"
-            raise RuntimeError(msg)
-    # ------------------------------------------------
-    
-    # Function to delete a path on VIP with warning
-    @classmethod
-    def _delete_and_check(cls, path: PurePath, location="vip", timeout=300) -> bool:
-        """
-        Deletes `path` on `location` and waits until `path` is actually removed.
-        After `timeout` (seconds), displays a warning if `path` still exist.
-        """
-        # Delete the path
-        cls._delete_path(path, location)
-        # Standby until path is indeed removed (give up after some time)
-        start = time.time()
-        t = time.time() - start
-        while (t < timeout) and cls._exists(path, location):
-            time.sleep(2)
-            t = time.time() - start
-        # Check if the data have indeed been removed
-        return (t < timeout)
-    # ------------------------------------------------
-    
-    ##########################################################
-    # Generic private methods than should work in any subclass
-    ##########################################################
-    
-    # Method to create a directory leaf on the top of any path, at any location
-    @classmethod
-    def _mkdirs(cls, path: PurePath, location: str, **kwargs) -> str:
-        """
-        Creates each non-existent directory in `path` (like os.mkdirs()), 
-        in the file system pointed by `location`.
-        - Directories are created using: cls._create_dir(`path`, `location`, **`kwargs`)
-        - Existence is checked using: cls._exists(`path`, `location`).
-
-        Returns the newly created part of `path` (empty string if `path` already exists).
-        """
-        # Case : the current path exists
-        if cls._exists(path=path, location=location) :
-            return ""
-        # Find the 1rst non-existent node in the arborescence
-        first_node = path
-        while not cls._exists(first_node.parent, location=location):
-            first_node = first_node.parent
-        # Create the first node 
-        cls._create_dir(path=first_node, location=location, **kwargs)
-        # Make the other nodes one by one
-        dir_to_make = first_node
-        while dir_to_make != path:
-            # Find the next directory to make
-            dir_to_make /= path.relative_to(dir_to_make).parts[0]
-            # Make the directory
-            cls._create_dir(path=dir_to_make, location=location, **kwargs)
-        # Return the created nodes
-        return str(path.relative_to(first_node.parent))
-    # ------------------------------------------------
-
-    ##################################################
-    # Context managers
-    ##################################################
-
-    # Simple context manager to silence logs from class methods while executing code
-    @classmethod
-    @contextmanager
-    def _silent_class(cls) -> None:
-        """
-        Under this context, the session will not print anything.
-        """
-        verbose = cls._VERBOSE # save verbose mode
-        cls._VERBOSE = False # silence instance logs
-        yield
-        cls._VERBOSE = verbose # restore verbose mode
-    # ------------------------------------------------
-
-    # init
-    #################################################
-    @classmethod
-    def _get_api_key(cls, api_key: str) -> str:
-        """
-        - `api_key` (str): VIP API key. This can be either:
-            A. [unsafe] A **string litteral** containing your API key,
-            B. [safer] A **path to some local file** containing your API key,
-            C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
-        In cases B or C, the API key will be loaded from the local file or the environment variable. 
-        """
-        # Check if `api_key` is in a local file or environment variable
-        if os.path.isfile(api_key): # local file
-            with open(api_key, "r") as kfile:
-                true_key = kfile.read().strip()
-        elif api_key in os.environ: # environment variable
-            true_key = os.environ[api_key]
-        else: # string litteral
-            true_key = api_key
-        # Return
-        return true_key
-    # ------------------------------------------------
-
-    # Function to check invalid characters in some input string
-    @classmethod
-    def _invalid_chars(cls, value) -> list: 
-        """
-        Returns a list of invalid characters in `value`.
-        Value can be a list or any object convertible to string.
-        """
-        if isinstance(value, list):
-            return sorted(list({v for val in value for v in cls._INVALID_CHARS.findall(str(val))}))
-        else:
-            return sorted(cls._INVALID_CHARS.findall(str(value)))
-    # ------------------------------------------------
-
-    # Function to clean HTML text when loaded from VIP portal
-    @staticmethod
-    def _clean_html(text: str) -> str:
-        """Returns `text` without html tags and newline characters."""
-        return re.sub(r'<[^>]+>|\n', '', text)
-
-    ########################################
-    # SESSION LOGS & USER VIEW
-    ########################################
-
-    @classmethod
-    # Interface to print logs from class methods
-    def _printc(cls, *args, **kwargs) -> None:
-        """
-        Print logs from class methods only when cls._VERBOSE is True.
-        """
-        if cls._VERBOSE:
-            print(*args, **kwargs)
-    # ------------------------------------------------
-
-    # Function to handle VIP runtime errors and provide interpretation to the user
-    @classmethod
-    def _handle_vip_error(cls, vip_error: RuntimeError) -> None:
-        """
-        Rethrows a RuntimeError `vip_error` which occured in the VIP API,
-        with interpretation depending on the error code.
-        """
-        # Enumerate error cases
-        message = vip_error.args[0]
-        if message.startswith("Error 8002") or message.startswith("Error 8003") \
-            or message.startswith("Error 8004"):
-            # "Bad credentials"  / "Full authentication required" / "Authentication error"
-            interpret = (
-                "Unable to communicate with VIP."
-                + f"\nRun {cls.__name__}.init() with a valid API key to handshake with VIP servers"
-                + f"\n({message})"
-            )
-        elif message.startswith("Error 8000"):
-            #  Probably wrong values were fed in `vip.init_exec()`
-            interpret = (
-                f"\n\t'{message}'"
-                + "\nPlease carefully check that session_name / pipeline_id / input_parameters "
-                + "are valid and do not contain any forbidden character"
-                + "\nIf this cannot be fixed, contact VIP support ()"
-            )
-        elif message.startswith("Error 2000") or message.startswith("Error 2001"):
-            #  Maximum number of executions
-            interpret = (
-                f"\n\t'{message}'"
-                + "\nPlease wait until current executions are over, "
-                + f"or contact VIP support ({cls._VIP_SUPPORT}) to increase this limit"
-            )
-        else:
-            # Unhandled runtime error
-            interpret=(
-                f"\n\t{message}"
-                + f"\nIf this cannot be fixed, contact VIP support ({cls._VIP_SUPPORT})"
-            )
-        # Display the error message
-        raise RuntimeError(interpret) from None
-    # ------------------------------------------------
-
-#######################################################
-
-if __name__=="__main__":
-    pass
\ No newline at end of file
diff --git a/src/vip_client/classes/VipLoader.py b/src/vip_client/classes/VipLoader.py
deleted file mode 100644
index df000a3..0000000
--- a/src/vip_client/classes/VipLoader.py
+++ /dev/null
@@ -1,405 +0,0 @@
-from __future__ import annotations
-import os
-import tarfile
-from pathlib import *
-
-from vip_client.utils import vip
-from vip_client.classes.VipClient import VipClient
-
-class VipLoader(VipClient):
-    """
-    Python class to upload / download files to / from VIP servers.
-    WORK IN PROGRESS
-
-    N.B.: all instance methods require that `VipLoader.init()` has been called with a valid API key. 
-    See GitHub documentation to get your own VIP API key.
-    """
-
-                    ##################
-    ################ Class Attributes ##################
-                    ##################
-    
-    # Class name
-    __name__ = "VipLoader"
-    # Default verbose state
-    _VERBOSE = True
-    # List of known directory contents
-    _VIP_TREE = {}
-
-                    ################
-    ################ Public Methods ##################
-                    ################
-
-    @classmethod
-    def list_dir(cls, vip_path: PurePosixPath) -> list[str]:
-        """
-        Returns a list of directories under `vip_path` [str or os.PathLike].
-        """
-        return [
-            PurePosixPath(element["path"]).name
-            for element in cls._list_dir_vip(PurePosixPath(vip_path), update=True)
-        ]
-
-    @classmethod
-    def download_dir(cls, vip_path, local_path, unzip=True):
-        """
-        Download all files from `vip_path` to `local_path` (if needed).
-        Displays what it does if `cls._VERBOSE` is True.
-        Returns a dictionary of failed downloads.
-        """
-        cls._printc("Recursive download from:", vip_path)
-        # Path-ify
-        vip_path = PurePosixPath(vip_path)
-        local_path = Path(local_path)
-        # Assert folder existence on VIP
-        if not cls._exists(vip_path, location='vip'):
-            raise FileNotFoundError("Folder does not exist on VIP.")
-        # Scan the distant and local directories and get a list of files to download
-        cls._printc("\nCloning the distant folder tree")
-        cls._printc("-------------------------------")
-        files_to_download = cls._init_download_dir(vip_path, local_path)
-        cls._printc("-------------------------------")
-        cls._printc("Done.")
-        # Download the files from VIP servers & keep track of the failures
-        cls._printc("\nParallel download of the distant files")
-        cls._printc("--------------------------------------")
-        failures = cls._download_parallel(files_to_download, unzip) 
-        cls._printc("--------------------------------------")
-        cls._printc("End of parallel downloads\n")
-        if not failures :
-            return
-        # Retry in case of failure
-        cls._printc(len(failures), "files could not be downloaded from VIP.")
-        cls._printc("\nGiving a second try")
-        cls._printc("---------------------")
-        failures = cls._download_parallel(failures, unzip)
-        cls._printc("---------------------")
-        cls._printc("End of the process.")
-        if failures :
-            cls._printc("The following files could not be downloaded from VIP:", end="\n\t")
-            cls._printc("\n\t".join([str(file) for file, _ in failures]))
-    # ------------------------------------------------
-
-    
-                    #################
-    ################ Private Methods ################
-                    #################
-
-    @classmethod
-    def _list_content_vip(cls, vip_path: PurePosixPath, update=True) -> list[dict]:
-        """
-        Updates `cls._VIP_TREE` with the content of `vip_path` on VIP servers. 
-        """
-        if update or (vip_path not in cls._VIP_TREE):
-            cls._VIP_TREE[vip_path] = vip.list_content(str(vip_path))
-        return cls._VIP_TREE[vip_path]
-    # ------------------------------------------------
-
-    @classmethod
-    def _list_files_vip(cls, vip_path: PurePosixPath, update=True) -> list[dict]:
-        return [
-            element
-            for element in cls._list_content_vip(vip_path, update)
-            if element['exists'] and not element['isDirectory']
-        ]
-    # ------------------------------------------------
-    
-    @classmethod
-    def _list_dir_vip(cls, vip_path: PurePosixPath, update=True) -> list[dict]:
-        return [
-            element
-            for element in cls._list_content_vip(vip_path, update)
-            if element['exists'] and element['isDirectory']
-        ]
-    # ------------------------------------------------
-    
-    #########################
-    # Methods to be optimized
-    #########################
-
-    # Method to check existence of a distant or local resource.
-    @classmethod
-    def _exists(cls, path: PurePath, location="local") -> bool:
-        """
-        Checks existence of a distant (`location`="vip") or local (`location`="local") resource.
-        `path` can be a string or path-like object.
-        """
-        # Check path existence in `location`
-        if location=="local":
-            return os.path.exists(path)
-        else: 
-            return super()._exists(path=path, location=location)
-    # ------------------------------------------------
-    
-    # Method to create a distant or local directory
-    @classmethod
-    def _create_dir(cls, path: PurePath, location="local", **kwargs) -> None:
-        """
-        Creates a directory at `path` :
-        - locally if `location` is "local";
-        - on VIP if `location` is "vip".
-
-        `kwargs` are passed as keyword arguments to `Path.mkdir()`.
-        Returns the VIP or local path of the newly created folder.
-        """
-        if location == "local": 
-            # Check input type
-            path=Path(path)
-            # Check the parent is a directory
-            assert path.parent.is_dir(),\
-                f"Cannot create subdirectories in '{path.parent}': not a folder"
-            # Create the new directory with additional keyword arguments
-            path.mkdir(**kwargs)
-        else: 
-            return super()._create_dir(path=path, location=location, **kwargs)
-    # ------------------------------------------------
-
-    @classmethod
-    def _init_download_dir(cls, vip_path: PurePosixPath, local_path: Path) -> dict:
-        """
-        Copy the folder tree under `vip_path` to `local_path`
-
-        Returns a dictionary of files within `vip_path` that are not in `local_paths`.
-        Dictionary keys: (vip_path, local_path).
-        Dictionary values: file metadata.
-        """ 
-        # First display
-        cls._printc(f"{local_path} : ", end="")
-        # Scan the current VIP directory
-        cls._list_content_vip(vip_path)
-        # Look for files
-        all_files = cls._list_files_vip(vip_path, update=False)
-        # Scan the local directory and look for files to download
-        if cls._mkdirs(local_path, location="local"):
-            # The local directory did not exist before call
-            cls._printc("Created.")
-            # -> download all the files (no scan to save time)
-        else: 
-            # The local directory already exists
-            cls._printc("Already there.")
-            # Scan it to check if there are more files to download
-            local_filenames = {
-                elem.name for elem in local_path.iterdir() if elem.exists()
-            }
-            # Get the files to download
-            all_files = [ 
-                element for element in all_files 
-                if PurePosixPath(element["path"]).name not in local_filenames
-            ]
-        # Return files to download as a dictionary
-        files_to_download = {}
-        for file in all_files:
-            # Dict key: VIP & local paths
-            file_vip_path = PurePosixPath(file["path"])
-            file_local_path = local_path / file_vip_path.name
-            files_to_download[(file_vip_path, file_local_path)] = {
-                # Dict value: Metadata
-                key: value for key, value in file.items() if key!="path"
-            }
-        # Recurse this function over sub-directories
-        for subdir in cls._list_dir_vip(vip_path, update=False):
-            subdir_path = PurePosixPath(subdir["path"])
-            # Scan the subdirectory
-            new_files = cls._init_download_dir(
-                vip_path = subdir_path,
-                local_path = local_path / subdir_path.name,
-            )
-            # Update the list of files to download
-            files_to_download.update(new_files)
-        return files_to_download
-    # ------------------------------------------------
-
-    # Method do download files using parallel threads
-    @classmethod
-    def _download_parallel(cls, files_to_download: dict, unzip: bool):
-        """
-        Downloads files from VIP using parallel threads.
-        - `files_to_download`: Dictionnary with key: (vip_path, local_path) and value: metadata.
-        - `unzip`: if True, extracts the tarballs inplace after the download.
-
-        Returns a list of failed downloads.
-        """
-        # Copy the input
-        files_to_download = files_to_download.copy()
-        # Return if there is no file to download
-        if not files_to_download:
-            cls._printc("No file to download.")
-            return files_to_download
-        # Check the amount of data
-        try:    total_size = "%.1fMB" % sum([file['size']/(1<<20) for file in files_to_download.values()])
-        except: total_size = "unknown"
-        # Display
-        cls._printc(f"Downloading {len(files_to_download)} file(s) (total size: {total_size})...")
-        # Sort the files to download by size
-        try:
-            file_list = sorted(files_to_download.keys(), key=lambda file: files_to_download[file]["size"])
-        except: 
-            file_list = list(files_to_download)
-        # Download the files from VIP servers
-        nFile = 0 
-        nb_files = len(files_to_download)
-        for file, done in vip.download_parallel(file_list):
-            nFile += 1
-            # Get informations about the new file 
-            vip_path, local_path = file
-            file_info = files_to_download[file]
-            file_size = "[%.1fMB]" % (file_info["size"]/(1<<20)) if "size" in file_info else ""
-            if done: 
-                # Remove file from the list
-                file_info = files_to_download.pop(file)
-                # Display success
-                cls._printc(f"- [{nFile}/{nb_files}] DONE:", local_path, file_size, flush=True)
-                # If the output is a tarball, extract the files and delete the tarball
-                if unzip and tarfile.is_tarfile(local_path):
-                    cls._printc("\tExtracting archive ...", end=" ")
-                    if cls._extract_tarball(local_path):
-                        cls._printc("Done.") # Display success
-                    else:
-                        cls._printc("Extraction failed.") # Display failure
-            else: 
-                # Display failure
-                cls._printc(f"- [{nFile}/{nb_files}] FAILED:", vip_path, file_size, flush=True)
-        # Return failed downloads
-        return files_to_download
-    # ------------------------------------------------
-
-    # Function to download a single file from VIP
-    @classmethod
-    def _download_file(cls, vip_path: PurePosixPath, local_path: Path) -> bool:
-        """
-        Downloads a single file in `vip_path` to `local_path`.
-        Returns a success flag.
-        """
-        # Download (file existence on VIP is not checked to save time)
-        try:
-            return vip.download(str(vip_path), str(local_path))
-        except RuntimeError as vip_error:
-            cls._handle_vip_error(vip_error)
-    # ------------------------------------------------    
-
-    # Method to extract content from a tarball
-    @classmethod
-    def _extract_tarball(cls, local_file: Path):
-        """
-        Replaces tarball `local_file` by a directory with the same name 
-        and extracted content.
-        Returns success flag.
-        """
-        # Rename current archive
-        archive = local_file.parent / "tmp.tgz"
-        os.rename(local_file, archive) # pathlib version does not work it in Python 3.7
-        # Create a new directory to store archive content
-        cls._mkdirs(local_file, location="local")
-        # Extract archive content
-        try:
-            with tarfile.open(archive) as tgz:
-                tgz.extractall(path=local_file)
-            success = True
-        except:
-            success = False
-        # Deal with the temporary archive
-        if success: # Remove the archive
-            os.remove(archive)
-        else: # Rename the archive
-            os.rename(archive, local_file)
-        # Return the flag
-        return success
-    # ------------------------------------------------
-
-    
-    # Function to upload all files from a local directory
-    @classmethod
-    def _upload_dir(cls, local_path: Path, vip_path: PurePosixPath) -> list:
-        """
-        Uploads all files in `local_path` to `vip_path` (if needed).
-        Displays what it does if `cls._VERBOSE` is True.
-        Returns a list of files which failed to be uploaded on VIP.
-        """
-        # Scan the local directory
-        assert cls._exists(local_path, location='local'), f"{local_path} does not exist."
-        # First display
-        cls._printc(f"Cloning: {local_path} ", end="... ")
-        # Scan the distant directory and look for files to upload
-        if cls._mkdirs(vip_path, location="vip"):
-            # The distant directory did not exist before call
-            # -> upload all the data (no scan to save time)
-            files_to_upload = [
-                elem for elem in local_path.iterdir()
-                if elem.is_file()
-            ]
-            cls._printc("(Created on VIP)")
-            if files_to_upload:
-                cls._printc(f"\t{len(files_to_upload)} file(s) to upload.")
-        else: # The distant directory already exists
-            # Scan it to check if there are more files to upload
-            vip_filenames = {
-                PurePosixPath(element["path"]).name
-                for element in vip.list_elements(str(vip_path))
-            }
-            # Get the files to upload
-            files_to_upload = [
-                elem for elem in local_path.iterdir()
-                if elem.is_file() and (elem.name not in vip_filenames)
-            ]
-            # Update the display
-            if files_to_upload: 
-                cls._printc(f"\n\tVIP clone already exists and will be updated with {len(files_to_upload)} file(s).")
-            else:
-                cls._printc("Already on VIP.")
-        # Upload the files
-        nFile = 0
-        failures = []
-        for local_file in files_to_upload :
-            nFile+=1
-            # Get the file size (if possible)
-            try: size = f"{local_file.stat().st_size/(1<<20):,.1f}MB"
-            except: size = "unknown size"
-            # Display the current file
-            cls._printc(f"\t[{nFile}/{len(files_to_upload)}] Uploading file: {local_file.name} ({size}) ...", end=" ")
-            # Upload the file on VIP
-            vip_file = vip_path/local_file.name # file path on VIP
-            if cls._upload_file(local_path=local_file, vip_path=vip_file):
-                # Upload was successful
-                cls._printc("Done.")
-            else:
-                # Update display
-                cls._printc(f"\n(!) Something went wrong during the upload.")
-                # Update missing files
-                failures.append(str(local_file))
-        # Look for sub-directories
-        subdirs = [
-            elem for elem in local_path.iterdir() 
-            if elem.is_dir()
-        ]
-        # Recurse this function over sub-directories
-        for subdir in subdirs:
-            failures += cls._upload_dir(
-                local_path=subdir,
-                vip_path=vip_path/subdir.name
-            )
-        # Return the list of failures
-        return failures
-    # ------------------------------------------------
-
-    # Function to upload a single file on VIP
-    @classmethod
-    def _upload_file(cls, local_path: Path, vip_path: PurePosixPath) -> bool:
-        """
-        Uploads a single file in `local_path` to `vip_path`.
-        Returns a success flag.
-        """
-        # Check
-        assert local_path.exists(), f"{local_path} does not exist."
-        # Upload
-        try:
-            return vip.upload(str(local_path), str(vip_path))
-        except RuntimeError as vip_error:
-            cls._handle_vip_error(vip_error)
-    # ------------------------------------------------   
-
-
-#######################################################
-
-if __name__=="__main__":
-    pass
-    
\ No newline at end of file

From 7d9a5055e910a7d509b2758c53a0bf899b822c81 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 3 Mar 2025 13:09:18 +0100
Subject: [PATCH 02/14] allow keeping outputs on vip

---
 src/vip_client/classes/VipLauncher.py |  8 ++++----
 src/vip_client/classes/VipSession.py  | 17 +++++++++++------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/vip_client/classes/VipLauncher.py b/src/vip_client/classes/VipLauncher.py
index b24804c..bf1405c 100644
--- a/src/vip_client/classes/VipLauncher.py
+++ b/src/vip_client/classes/VipLauncher.py
@@ -614,7 +614,7 @@ def run_session( self, nb_runs=1, refresh_time=30) -> VipLauncher:
     # ------------------------------------------------
 
     # Clean session data on VIP
-    def finish(self, timeout=300) -> VipLauncher:
+    def finish(self, timeout=300, **kwargs) -> VipLauncher:
         """
         Removes session's output data from VIP servers. 
 
@@ -641,7 +641,7 @@ def finish(self, timeout=300) -> VipLauncher:
         self._print("---------------------")
         # Browse paths to delete
         success = True
-        for path, location in self._path_to_delete().items():
+        for path, location in self._path_to_delete(**kwargs).items():
             # Display progression
             self._print(f"[{location}] {path} ... ", end="", flush=True)
             # Check data existence
@@ -694,7 +694,7 @@ def finish(self, timeout=300) -> VipLauncher:
         else:
             self._print("(!) There may still be temporary data on VIP.")
             self._print(f"Please run finish() again or check the following path(s) on the VIP portal ({self._VIP_PORTAL}):")
-            self._print('\n\t'.join([str(path) for path in self._path_to_delete()]))
+            self._print('\n\t'.join([str(path) for path in self._path_to_delete(**kwargs)]))
             # Finish display
             self._print()
         # Return 
@@ -838,7 +838,7 @@ def display(self) -> VipLauncher:
     ###################################################################
 
     # Path to delete during session finish
-    def _path_to_delete(self) -> dict:
+    def _path_to_delete(self, **kwargs) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
         return {
             self._vip_output_dir: "vip"
diff --git a/src/vip_client/classes/VipSession.py b/src/vip_client/classes/VipSession.py
index 00ad805..7485c28 100644
--- a/src/vip_client/classes/VipSession.py
+++ b/src/vip_client/classes/VipSession.py
@@ -563,7 +563,7 @@ def run_session(
         )
 
     # Clean session data on VIP
-    def finish(self, timeout=300) -> VipSession:
+    def finish(self, timeout=300, keep_output=False) -> VipSession:
         """
         Removes session's data from VIP servers (INPUTS and OUTPUTS). 
         The downloaded outputs and the input dataset are kept on the local machine.
@@ -574,7 +574,7 @@ def finish(self, timeout=300) -> VipSession:
         - Workflows status are set to "Removed" when the corresponding outputs have been removed from VIP servers.
         """
         # Finish the session based on self._path_to_delete()
-        super().finish(timeout=timeout)
+        super().finish(timeout=timeout, keep_output=keep_output)
         # Check if the input data have been erased (this is not the case when get_inputs have been used)
         if (self._vip_input_dir != self._vip_dir / "INPUTS"
                 and self._exists(self._vip_input_dir, location="vip")):
@@ -673,11 +673,16 @@ def get_inputs(self, session: VipSession, get_pipeline=False, get_settings=False
     ###################################################################
 
     # Path to delete during session finish()
-    def _path_to_delete(self) -> dict:
+    def _path_to_delete(self, **kwargs) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
-        return {
-            self._vip_dir: "vip"
-        }
+        if (kwargs.get("keep_output", False)):
+            return {
+                self._vip_dir / "INPUTS": "vip"
+            }
+        else:
+            return {
+                self._vip_dir: "vip"
+            }
 
     # Method to check existence of a distant or local resource.
     @classmethod

From e36966d8d5616b111c9e9da8f55ec975883cc79e Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 3 Mar 2025 13:42:55 +0100
Subject: [PATCH 03/14] renaming VipCI to VipGirder

---
 doc/history.md                             |   4 +-
 doc/source.md                              |   2 +-
 examples/tutorials/exemple_VipCI.ipynb     |  16 +-
 src/vip_client/classes/VipCI.py            | 671 ---------------------
 src/vip_client/classes/__init__.py         |   6 +-
 tests/README.md                            |   4 +-
 tests/{test_VipCI.py => test_VipGirder.py} |  24 +-
 tests/test_VipLauncher.py                  |   2 -
 tests/test_VipSession.py                   |   3 -
 tests/test_global.py                       |  12 +-
 tests/try_viploader.py                     |  18 -
 11 files changed, 31 insertions(+), 731 deletions(-)
 delete mode 100644 src/vip_client/classes/VipCI.py
 rename tests/{test_VipCI.py => test_VipGirder.py} (90%)
 delete mode 100644 tests/try_viploader.py

diff --git a/doc/history.md b/doc/history.md
index c2d0ee1..504ccdc 100644
--- a/doc/history.md
+++ b/doc/history.md
@@ -22,12 +22,12 @@
 
 ### June 2023
 
-- Class [`VipLauncher`](#viplauncher) is introduced for specific user needs, as a parent of `VipSession` & `VipCI`;
+- Class [`VipLauncher`](#viplauncher) is introduced for specific user needs, as a parent of `VipSession` & `VipGirder`;
 - Session properties (`session_name`, `pipeline_id`, *etc.*) can be safely accessed and modified in all "`Vip*`" classes;
 - A list of available pipelines and detailed informations about each pipeline can be displayed through new class method `show_pipeline()`;
 
 ### April 2023
-- Class [`VipCI`](#vipci) to interacts with Girder datasets (tailored for CI tests in the ReproVIP project).
+- Class [`VipGirder`](#VipGirder) to interacts with Girder datasets (tailored for CI tests in the ReproVIP project).
 
 ### March 2023
 - Class [`VipSession`](#vipsession): user-friendly interface to run VIP jobs on local datasets.
diff --git a/doc/source.md b/doc/source.md
index b3a5539..34f71e4 100644
--- a/doc/source.md
+++ b/doc/source.md
@@ -12,7 +12,7 @@ The most user-friendly class to interact with VIP. See the documentation [here](
 
 A parent class of `VipSession` that implements everything needed to launch VIP applications on remote data sets. *More information to come*.
 
-### [vip_client.classes.**VipCI**](../src/vip_client/classes/VipCI.py)
+### [vip_client.classes.**VipGirder**](../src/vip_client/classes/VipGirder.py)
 
 [Prototype] A `VipLauncher` implementation to launch VIP application on [Girder](https://girder.readthedocs.io/en/latest/) datasets. Currently used for continuous integration (CI) tests on the VIP platform.
 
diff --git a/examples/tutorials/exemple_VipCI.ipynb b/examples/tutorials/exemple_VipCI.ipynb
index fa78792..06798bc 100644
--- a/examples/tutorials/exemple_VipCI.ipynb
+++ b/examples/tutorials/exemple_VipCI.ipynb
@@ -11,12 +11,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import the class\n",
-    "from vip_client.classes import VipCI\n",
+    "from vip_client.classes import VipGirder\n",
     "import time\n",
     "\n",
     "# Pipeline identifier\n",
@@ -66,7 +66,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -131,13 +131,13 @@
    ],
    "source": [
     "# Connect with Vip & Girder\n",
-    "VipCI.init(\n",
+    "VipGirder.init(\n",
     "  vip_key=\"VIP_API_KEY\", # My environment variable for the VIP API key (also works with litteral string or file name)\n",
     "  girder_key=\"GIRDER_API_KEY\" # My environment variable for the Girder API key (also works with litteral string or file name)\n",
     ")\n",
     "\n",
     "# Create a Session\n",
-    "session = VipCI(\n",
+    "session = VipGirder(\n",
     "  session_name=\"Test_Girder\", # Session Name\n",
     ")\n",
     "\n",
@@ -170,7 +170,7 @@
    "source": [
     "__N.B.__: The last cell could also be written with a single line of code:\n",
     "```python\n",
-    "VipCI.init(\n",
+    "VipGirder.init(\n",
     "    vip_key=\"VIP_API_KEY\", # My environment variable for the VIP API key \n",
     "    girder_key=\"GIRDER_API_KEY\", # My environment variable for the Girder API key\n",
     "    session_name = \"Test_Girder\", # Session Name\n",
@@ -194,7 +194,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -260,7 +260,7 @@
     }
    ],
    "source": [
-    "VipCI(my_output_dir).run_session(nb_runs=2)"
+    "VipGirder(my_output_dir).run_session(nb_runs=2)"
    ]
   },
   {
diff --git a/src/vip_client/classes/VipCI.py b/src/vip_client/classes/VipCI.py
deleted file mode 100644
index 456bd7b..0000000
--- a/src/vip_client/classes/VipCI.py
+++ /dev/null
@@ -1,671 +0,0 @@
-# Builtins
-from __future__ import annotations
-import os
-import time
-from pathlib import *
-# Try importing the Girder client
-try:
-    import girder_client
-except:
-    from warnings import warn
-    warn("vip_client.classes.VipCI is unavailable (missing package: girder-client)")
-# Other classes from VIP client
-from vip_client.utils import vip
-from vip_client.classes.VipLauncher import VipLauncher
-
-class VipCI(VipLauncher):
-    """
-    Python class to run VIP pipelines on datasets located on Girder.
-
-    A single instance allows to run 1 pipeline with 1 parameter set (any number of runs).
-    Pipeline runs need at least three inputs:
-    - `pipeline_id` (str) Name of the pipeline. 
-    - `input_settings` (dict) All parameters needed to run the pipeline.
-    - `output_dir` (str) Path to a Girder folder where execution results will be stored.
-
-    N.B.: all instance methods require that `VipCI.init()` has been called with:
-    - a valid VIP API key;
-    - a valid Girder API key.
-    """
-
-                    ##################
-    ################ Class Attributes ##################
-                    ##################
-
-    # --- Overriden from the parent class ---
-
-    # Class name
-    __name__ = "VipCI"
-    # Properties to save / display for this class
-    _PROPERTIES = [
-        "session_name", 
-        "pipeline_id",
-        "vip_output_dir", 
-        "input_settings", 
-        "workflows"
-    ]
-    # Default location for VIP inputs/outputs (different from the parent class)
-    _SERVER_NAME = "girder"
-    # Prefix that defines a Girder path 
-    _SERVER_PATH_PREFIX = "/collection"
-    # Default backup location 
-    # (set to None to avoid saving and loading backup files)
-    _BACKUP_LOCATION = "girder"
-    
-    # Prefix that defines a Girder ID
-    _GIRDER_ID_PREFIX = "pilotGirder"
-    # Grider portal
-    _GIRDER_PORTAL = 'https://pilot-warehouse.creatis.insa-lyon.fr/api/v1'
-    
-
-                    #################
-    ################ Main Properties ##################
-                    #################
-    
-    @property
-    def custom_wf_metadata(self) -> dict:
-        return self._custom_wf_metadata
-    
-    @custom_wf_metadata.setter
-    def custom_wf_metadata(self, value: dict) -> None:
-        if value != None:
-            assert isinstance(value, dict), f"Custom metadata must be a dictionary, not {type(value)}"
-        self._custom_wf_metadata = value
-
-
-
-                    #############
-    ################ Constructor ##################
-                    ############# 
-    def __init__(
-        self, output_dir=None, pipeline_id: str=None, input_settings: dict=None, 
-        session_name: str=None, verbose: bool=None, custom_wf_metadata: dict=None
-    ) -> None:
-        """
-        Creates a VipCI instance and sets its properties from keyword arguments.
-
-        ## Parameters
-        - `output_dir` (str | os.PathLike) Path to a Girder folder where execution results will be stored.
-            - Does not need to exist
-            - Usually in format : "/collection/[collection_name]/[path_to_folder]"
-            - User must have read/write permissions on the Girder collection/folder.
-
-        - `pipeline_id` (str) Name of your pipeline in VIP. 
-            - Usually in format : *application_name*/*version*.
-            - Run VipLauncher.show_pipeline() to display available pipelines.
-
-        - `input_settings` (dict) All parameters needed to run the pipeline.
-            - Run VipSession.show_pipeline(`pipeline_id`) to display these parameters.
-            - The dictionary can contain any object that can be converted to strings, or lists of such objects.
-            - Lists of parameters launch parallel workflows on VIP.
-
-        - `session_name` [Optional/Recommended] (str) A name to identify this session.
-            - Default value: 'VipCI-[date]-[time]-[id]'
-        
-        - `verbose` [Optional] (bool) Verbose mode for this instance.
-            - If True, instance methods will display logs;
-            - If False, instance methods will run silently.
-        
-        - `custom_wf_metadata` [Optional] (dict) Custom metadata to add to each workflow.
-
-        `session_name` is only set at instantiation; other properties can be set later in function calls.
-        If `output_dir` leads to data from a previous session, properties will be loaded from the metadata on Girder.
-        """
-        # Initialize with the name, pipeline and input settings
-        super().__init__(
-            output_dir = output_dir,
-            session_name = session_name, 
-            pipeline_id = pipeline_id, 
-            input_settings = input_settings,
-            verbose = verbose
-        )
-        # Set custom properties
-        self.custom_wf_metadata = custom_wf_metadata
-        # End display
-        if any([session_name, output_dir]) and (self.__name__ == "VipCI"): 
-            self._print()
-    # ------------------------------------------------
-
-                    ################
-    ################ Public Methods ##################
-                    ################
-
-    #################################################
-    # Manage a session from start to finish
-    #################################################
-
-    # Login to VIP and Girder
-    @classmethod
-    def init(
-            cls, 
-            vip_key="VIP_API_KEY", 
-            girder_key="GIRDER_API_KEY", 
-            verbose=True, 
-            girder_api_url=None,
-            girder_id_prefix=None,
-            **kwargs
-        ) -> VipCI:
-        """
-        Handshakes with VIP using your own API key. 
-        Returns a class instance which properties can be provided as keyword arguments.
-        
-        ## Parameters
-        - `vip_key` (str): VIP API key. This can be either:
-            A. [unsafe] A **string litteral** containing your API key,
-            B. [safer] A **path to some local file** containing your API key,
-            C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
-        In cases B or C, the API key will be loaded from the local file or the environment variable. 
-
-        - `girder_key` (str): Girder API key. Can take the same values as `vip_key`.
-        
-        - `verbose` (bool): default verbose mode for all instances.
-            - If True, all instances will display logs by default;
-            - If False, all instance methods will run silently by default.
-
-        - `kwargs` [Optional] (dict): keyword arguments or dictionnary setting properties of the returned instance.     
-        """
-        # Initiate a Vip Session silently
-        super().init(api_key=vip_key, verbose=False)
-        # Restore the verbose state
-        cls._VERBOSE = verbose
-        # Set the Girder ID prefix
-        cls._GIRDER_ID_PREFIX = girder_id_prefix if girder_id_prefix is not None else cls._GIRDER_ID_PREFIX
-        cls._GIRDER_PORTAL = girder_api_url if girder_api_url is not None else cls._GIRDER_PORTAL
-        # Instantiate a Girder client
-        cls._girder_client = girder_client.GirderClient(apiUrl=girder_api_url)
-        # Check if `girder_key` is in a local file or environment variable
-        true_key = cls._get_api_key(girder_key)
-        # Authenticate with Girder API key
-        cls._girder_client.authenticate(apiKey=true_key)
-        # Diplay success
-        cls._printc()
-        cls._printc("---------------------------------------------")
-        cls._printc("| You are communicating with VIP and Girder |")
-        cls._printc("---------------------------------------------")
-        cls._printc()
-        # Return a VipCI instance for method cascading
-        return cls(verbose=(verbose and kwargs), **kwargs)
-    # ------------------------------------------------
-
-    # Launch the pipeline on VIP
-    def launch_pipeline(
-            self, pipeline_id: str=None, input_settings: dict=None, output_dir=None, nb_runs=1, 
-            verbose: bool=None
-        ) -> VipCI:
-        """
-        Launches pipeline executions on VIP.
-
-        Input parameters :
-        - `pipeline_id` (str) The name of your pipeline in VIP, 
-            usually in format : *application_name*/*version*.
-        - `input_settings` (dict) All parameters needed to run the pipeline.
-            - Run VipSession.show_pipeline(`pipeline_id`) to display these parameters.
-            - The dictionary can contain any object that can be converted to strings, or lists of such objects.
-            - Lists of parameters launch parallel workflows on VIP.
-        - `output_dir` (str) Path to the VIP folder where execution results will be stored.
-        - `nb_runs` (int) Number of parallel workflows to launch with the same settings.
-        
-        Default behaviour:
-        - Raises AssertionError in case of wrong inputs 
-        - Raises RuntimeError in case of failure on VIP servers.
-        - In any case, session is backed up after pipeline launch
-        """
-        return super().launch_pipeline(
-            pipeline_id = pipeline_id, # default
-            input_settings = input_settings, # default
-            output_dir = output_dir, # default
-            nb_runs = nb_runs, # default
-        )
-    # ------------------------------------------------
-
-    # Monitor worflow executions on VIP 
-    def monitor_workflows(self, refresh_time=30) -> VipCI:
-        """
-        Updates and displays the status of each execution launched in the current session.
-        - If an execution is still runnig, updates status every `refresh_time` (seconds) until all runs are done.
-        - Displays a full report when all executions are done.
-        """
-        return super().monitor_workflows(refresh_time=refresh_time)
-    # ------------------------------------------------
-
-    # Run a full VipCI session 
-    def run_session(self, nb_runs=1, refresh_time=30) -> VipCI:
-        """
-        Runs a full session from Girder data:
-        1. Launches pipeline executions on VIP;
-        2. Monitors pipeline executions until they are all over;
-            and Adds metadata on Girder output folder.
-
-        |!| This function assumes that all session properties are already set.
-        Optional arguments can be provided:
-        - Increase `nb_runs` to run more than 1 execution at once;
-        - Set `refresh_time` to modify the default refresh time.
-        """
-        return super().run_session(nb_runs=nb_runs, refresh_time=refresh_time)
-    # ------------------------------------------------
-
-    # Display session properties in their current state
-    def display(self) -> VipCI:
-        """
-        Displays useful properties in JSON format.
-        - `session_name` : current session name
-        - `pipeline_id`: pipeline identifier
-        - `output_dir` : path to the pipeline outputs
-        - `input_settings` : input parameters sent to VIP
-        - `workflows`: workflow inventory, identifying all pipeline runs in this session.
-        """
-        # Return for method cascading
-        return super().display()
-    # ------------------------------------------------
-
-    # Return error in case of call to finish()
-    def finish(self, verbose: bool=None) -> None:
-        """
-        This function does not work in VipCI.
-        """
-        # Update the verbose state and display
-        self._verbose = verbose
-        self._print("\n=== FINISH ===\n", max_space=2)
-        # Raise error message
-        raise NotImplementedError(f"Class {self.__name__} cannot delete the distant data.")
-    # ------------------------------------------------
-
-                    #################
-    ################ Private Methods ################
-                    #################
-
-    ###################################################################
-    # Methods that must be overwritten to adapt VipLauncher methods to
-    # new location: "girder"
-    ###################################################################
-
-    # Path to delete during session finish
-    def _path_to_delete(self) -> dict:
-        """Returns the folders to delete during session finish, with appropriate location."""
-        return {}
-    # ------------------------------------------------
-
-    # Method to check existence of a resource on Girder.
-    @classmethod
-    def _exists(cls, path: PurePath, location="girder") -> bool:
-        """
-        Checks existence of a resource on Girder.
-        """
-        # Check path existence in `location`
-        if location=="girder":
-            try: 
-                cls._girder_client.resourceLookup(path=str(path))
-                return True
-            except girder_client.HttpError: 
-                return False
-        else: 
-            raise NotImplementedError(f"Unknown location: {location}")
-    # ------------------------------------------------
-    
-    # Method to create a distant or local directory
-    @classmethod
-    def _create_dir(cls, path: PurePath, location="girder", **kwargs) -> str:
-        """
-        Creates a directory at `path` on Girder if `location` is "girder".
-
-        `path` should be a PathLib object.
-        `kwargs` can be passed as keyword arguments to `girder-client.createFolder()`.
-        Returns the Girder ID of the newly created folder.
-        """
-        if location == "girder": 
-            # Find the parent ID and type
-            parentId, parentType = cls._girder_path_to_id(str(path.parent))
-            # Check the parent is a directory
-            if not (parentType == "folder"):
-                raise ValueError(f"Cannot create folder {path} in '{path.parent}': parent is not a Girder folder")
-            # Create the new directory with additional keyword arguments
-            return cls._girder_client.createFolder(
-                parentId=parentId, name=str(path.name), reuseExisting=True, **kwargs
-                )["_id"]
-        else: 
-            raise NotImplementedError(f"Unknown location: {location}")
-    # ------------------------------------------------
-
-    # Function to delete a path
-    @classmethod
-    def _delete_path(cls, path: PurePath, location="vip") -> None:
-        raise NotImplementedError("VipCI cannot delete data.")
-
-    # Function to delete a path on VIP with warning
-    @classmethod
-    def _delete_and_check(cls, path: PurePath, location="vip", timeout=300) -> bool:
-        raise NotImplementedError("VipCI cannot delete data.")
-    
-    ####################################################
-    # Launch & Monitor pipeline executions from Girder #
-    ####################################################
-
-    def _init_exec(self) -> str:
-        """
-        Initiates one VIP workflow with `pipeline_id`, `session_name`, `input_settings`, `output_dir`.
-        Returns the workflow identifier.
-        """
-        # Get function arguments
-        # input_settings = self._vip_input_settings(self._input_settings)
-        input_settings = self._get_input_settings(location="vip-girder")
-        # Create a workflow-specific result directory
-        res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime()) 
-            # no simple way to rename later with workflow_id
-        res_id = self._create_dir(
-            path=res_path, location="girder", 
-            description=f"VIP outputs from one workflow in Session '{self._session_name}'"
-        )
-        res_vip = self._vip_girder_id(res_id)
-        # Launch execution
-        workflow_id = vip.init_exec(
-            pipeline = self.pipeline_id, 
-            name = self.session_name, 
-            inputValues = input_settings,
-            resultsLocation = res_vip
-        )
-        # Record the path to output files (create the workflow entry)
-        self._workflows[workflow_id] = {"output_path": str(res_path)}
-        return workflow_id
-    # ------------------------------------------------
-
-    # Function extract metadata from a single workflow
-    def _meta_workflow(self, workflow_id: str) -> dict:
-        metadata = {
-            "session_name": self._session_name,
-            "workflow_id": workflow_id,
-            "workflow_start": self._workflows[workflow_id]["start"],
-            "workflow_status": self._workflows[workflow_id]["status"]
-        }
-        # If custom metadata is provided, add it to the metadata
-        if self.custom_wf_metadata is not None:
-            metadata = {**metadata, **self.custom_wf_metadata}
-        return metadata
-
-    # Overwrite _get_exec_infos() to bypass call to vip.get_exec_results() (does not work at this time)
-    @classmethod
-    def _get_exec_infos(cls, workflow_id: str) -> dict:
-        """
-        Returns succint information on `workflow_id`:
-        - Execution status (VIP notations)
-        - Starting time (local time, format '%Y/%m/%d %H:%M:%S')
-        - List of paths to the output files.
-        """
-        try :
-            # Get execution infos
-            infos = vip.execution_info(workflow_id)
-            # Secure way to get execution results
-            # files = vip.get_exec_results(workflow_id)
-        except RuntimeError as vip_error:
-            cls._handle_vip_error(vip_error)
-        # Return filtered information
-        return {
-            # Execution status (VIP notations)
-            "status": infos["status"],
-            # Starting time (human readable)
-            "start": time.strftime(
-                '%Y/%m/%d %H:%M:%S', time.localtime(infos["startDate"]/1000)
-                ),
-            # # Returned files
-            # "outputs": infos["returnedFiles"]["output_file"]
-        }
-    # ------------------------------------------------
-
-    ###################################################
-    # Save (/load) Session to (/from) Girder metadata #
-    ###################################################
-
-    # Save session properties in a JSON file
-    def _save_session(self, session_data: dict, location="girder") -> bool:
-        """
-        Saves dictionary `session_data` as metadata in the output directory on Girder.
-        Returns a success flag.
-        Displays success / failure unless `_verbose` is False.
-        """
-        # Thow error if location is not "girder" because this session does no interact with VIP
-        if location != "girder":
-            return NotImplementedError(f"Location '{location}' is unknown for {self.__name__}")
-        # Ensure the output directory exists on Girder
-        is_new = self._mkdirs(path=self._vip_output_dir, location=location)
-        # Save metadata in the global output directory
-        folderId, _ = self._girder_path_to_id(self._vip_output_dir)
-        self._girder_client.addMetadataToFolder(folderId=folderId, metadata=session_data)
-        # Update metadata for each workflow
-        for workflow_id in self._workflows:
-            metadata = self._meta_workflow(workflow_id=workflow_id)
-            folderId, _ = self._girder_path_to_id(path=self._workflows[workflow_id]["output_path"])
-            self._girder_client.addMetadataToFolder(folderId=folderId, metadata=metadata)
-        # Display
-        self._print()
-        if is_new:
-            self._print(">> Session was backed up as Girder metadata in:")
-            self._print(f"\t{self._vip_output_dir} (Girder ID: {folderId})\n")
-        else:
-            self._print(">> Session backed up\n")
-        # Return
-        return True
-    # ------------------------------------------------
-
-    def _load_session(self, location="girder") -> dict:
-        """
-        Loads backup data from the metadata stored in the output directory on Girder.
-        If the metadata could not be found, returns None.
-        Otherwise, returns session properties as a dictionary.
-        """
-        # Thow error if location is not "girder"
-        if location != "girder":
-            return NotImplementedError(f"Location '{location}' is unknown for {self.__name__}")
-        # Check the output directory is defined
-        if self.vip_output_dir is None: 
-            return None
-        # Load the metadata on Girder
-        with self._silent_class():
-            try:
-                girder_id, _ = self._girder_path_to_id(self.vip_output_dir)
-                folder = self._girder_client.getFolder(folderId=girder_id)
-            except girder_client.HttpError as e:
-                if e.status == 400: # Folder was not found
-                    return None
-        # Display success if the folder was found
-        self._print("<< Session restored from its output directory\n")
-        # Return session metadata
-        return folder["meta"]
-    # ------------------------------------------------
-    
-    ##################################
-    # Manipulate Resources on Girder #
-    ##################################
-
-    # Function to get a resource ID
-    @classmethod
-    def _girder_path_to_id(cls, path) -> tuple[str, str]:
-        """
-        Returns a resource ID from its `path` within a Girder collection.
-        `path` should begin with: "/collection/[collection_name]/...".
-        `path` can be a string or PathLib object.
-
-        Raises `girder_client.HttpError` if the resource was not found. 
-        Adds intepretation message unless `cls._VERBOSE` is False.
-        """
-        try :
-            resource = cls._girder_client.resourceLookup(str(path))
-        except girder_client.HttpError as e:
-            if e.status == 400:
-                cls._printc("(!) The following path is invalid or refers to a resource that does not exist:")
-                cls._printc("    %s" % path)
-                cls._printc("    Original error from Girder API:")
-            raise e
-        # Return the resource ID and type
-        try:
-            return resource['_id'], resource['_modelType']
-        except KeyError as ke:
-            cls._printc(f"Unhandled type of resource: \n\t{resource}\n")
-            raise ke
-    # ------------------------------------------------
-    
-    # Function to get a resource path
-    @classmethod
-    def _girder_id_to_path(cls, id: str, type: str) -> PurePosixPath:
-        """
-        Returns a resource path from its Girder `id`.
-        The resource `type` (item, folder, collection) must be provided.
-
-        Raises `girder_client.HttpError` if the resource was not found.
-        """
-        try :
-            return PurePosixPath(cls._girder_client.get(f"/resource/{id}/path", {"type": type}))
-        except girder_client.HttpError as e:
-            if e.status == 400:
-                cls._printc(f"(!) Invalid Girder ID: {id} with resource type:{type}")
-                cls._printc("    Original error from Girder API:")
-            raise e
-    # ------------------------------------------------
-    
-    # Function to convert a Girder ID to Girder-VIP standard
-    @classmethod
-    def _vip_girder_id(cls, resource) -> str:
-        """
-        Prefixes a Girder ID with the VIP standard. 
-        Input `resource` should be a Girder Id (str) or a Girder path (PurePosixPath)
-        """
-        if isinstance(resource, str):
-            # Prefix the ID
-            return ":".join([cls._GIRDER_ID_PREFIX, resource])
-        elif isinstance(resource, PurePath):
-            # Get the Girder ID
-            girder_id, _ = cls._girder_path_to_id(resource)
-            # Prefix the ID
-            return ":".join([cls._GIRDER_ID_PREFIX, girder_id])
-    # ------------------------------------------------
-
-    ###################################################################
-    # Adapt `input_settings` to the Vip-Girder communication protocol #
-    ###################################################################
-
-    # Store the VIP paths as PathLib objects.
-    def _parse_input_settings(self, input_settings) -> dict:
-        """
-        Parses the input settings, i.e.:
-        - Resolves any reference to a Girder collection and turns a folder name 
-            into a list of files
-        - Converts all Girder paths to PathLib objects 
-        - Leaves the other parameters untouched.
-        """
-        # Function to extract file from Girder item
-        def get_file_from_item(itemId: str) -> str:
-            """Returns the Girder ID of a single file contained in `itemId`"""
-            files = [
-                f["_id"] for f in self._girder_client.listFile(itemId=itemId)
-            ]
-            # Check the number of files (1 per item)
-            if len(files) != 1:
-                msg = f"Unable to parse the Girder item : {self._girder_id_to_path(id=itemId, type='item')}"
-                msg += "Contains more than 1 file."
-                raise NotImplementedError(msg)
-            return files[0]
-        # -- End of get_file_from_item() --
-        # Function to extract all files from a Girder resource
-        def get_files(input_path: str):
-            """
-            Returns the path of all files contained in the Girder resource pointed by `input_path`.
-            The Girder resource can be a file, an item with 1 file or a folder with multiple items.
-            """
-            # Look up for the resource in Girder & get the Girder ID
-            girder_id, girder_type = self._girder_path_to_id(input_path)
-            # Retrieve all files based on the resource type
-            if girder_type == "file":
-                # Return the Girder path
-                return PurePosixPath(input_path)
-            elif girder_type == "item":
-                # Retrieve the corresponding file
-                fileId = get_file_from_item(girder_id)
-                # Return the Girder path
-                return self._girder_id_to_path(id=fileId, type='file')
-            elif girder_type == "folder":
-                # Retrieve all items
-                items = [ it["_id"] for it in self._girder_client.listItem(folderId=girder_id) ]
-                new_inputs = []
-                # Browse items
-                for itemId in items:
-                    # Retrieve the corresponding file
-                    fileId = get_file_from_item(itemId)
-                    # Update the file list with new Girder path
-                    new_inputs.append(self._girder_id_to_path(id=fileId, type='file'))
-                # Return the list of files
-                return new_inputs
-            else: 
-                # Girder type = collection or other
-                raise ValueError(f"Bad resource: {input_path}\n\tGirder type '{girder_type}' is not permitted in this context.")
-        # -- End of get_files() --
-        # Function to parse Girder paths
-        def parse_value(input):
-            # Case: single input, string or path-like
-            if isinstance(input, (str, os.PathLike)):
-                # Case: Girder path
-                if str(input).startswith(self._SERVER_PATH_PREFIX): 
-                    return get_files(input)
-                # Case: any other input
-                else: return input
-            # Case: multiple inputs
-            elif isinstance(input, list):
-                new_input = []
-                # Browse elements
-                for element in input:
-                    # Parse element
-                    parsed = parse_value(element)
-                    # Merge the lists if `element` is a folder
-                    if isinstance(parsed, list): new_input += parsed
-                    # Append if `element` is a file
-                    else: new_input.append(parsed)
-                # Return the list of files
-                return new_input
-           # Case not string nor path-like: return as is
-            else: return input
-        # -- End of parse_value() --
-        # Return the parsed value of each parameter
-        return {
-            key: parse_value(value)
-            for key, value in input_settings.items()
-        }
-    # ------------------------------------------------
-
-    # Get the input settings after files are parsed as PathLib objects
-    def _get_input_settings(self, location="girder") -> dict:
-        """
-        Returns the input settings with filenames adapted to `location`.
-        - if `location` = "girder", returns Girder paths string format.
-        - if `location` = "vip-girder", returns the prefixed Girder ID for VIP.
-
-        Returns a string version of any other parameter.
-        """
-        # Function to get the VIP-Girder standard from 1 input path
-        def get_input(value, location) -> str:
-            """
-            If `value` is a path, returns the corresponding string.
-            Value can be a single input or a list of inputs.
-            """
-            # Case: multiple inputs
-            if isinstance(value, list):
-                return [ get_input(element, location) for element in value ]
-            # Case : path to Girder resource
-            elif isinstance(value, PurePath): 
-                if location == "girder":
-                    return str(value)
-                elif location == "vip-girder":
-                    return self._vip_girder_id(value)
-            # Case: other parameter
-            else: return str(value)
-        # --------------------
-        # Raise an error if `location` cannot be parsed
-        if location not in ("girder", "vip-girder"):
-            raise NotImplementedError(f"Unknown location: {location}")
-        # Browse input settings
-        return {
-            key: get_input(value, location)
-            for key, value in self._input_settings.items()
-        }
-    # ------------------------------------------------
-
-######################################################
-        
-if __name__=="__main__":
-    pass
\ No newline at end of file
diff --git a/src/vip_client/classes/__init__.py b/src/vip_client/classes/__init__.py
index cc36a19..09eb4d4 100644
--- a/src/vip_client/classes/__init__.py
+++ b/src/vip_client/classes/__init__.py
@@ -2,7 +2,7 @@
 All classes for the client.
 - VipSession: main user class. To run a VIP application on local datasets.
 - VipLauncher: to run a Vip application on datasets located on VIP servers.
-- VipCI (alpha): to run a Vip application on datasets located on CREATIS data warehouse.
+- VipGirder (alpha): to run a Vip application on datasets located on CREATIS data warehouse.
 - VipLoader (planned): to upload / download data to / from VIP servers.
 - VipLoader (planned): base class.
 """
@@ -10,6 +10,4 @@
 # Replace each class module by its class in the namespace
 from vip_client.classes.VipSession import VipSession 
 from vip_client.classes.VipLauncher import VipLauncher
-from vip_client.classes.VipCI import VipCI
-from vip_client.classes.VipLoader import VipLoader
-from vip_client.classes.VipClient import VipClient
+from vip_client.classes.VipGirder import VipGirder
diff --git a/tests/README.md b/tests/README.md
index 2be2e22..50e159e 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -1,3 +1,3 @@
-# Test Suite for VIP Pyhton Client
+# Test Suite for VIP Python Client
 
-This is an unfinished work proposing test scripts for VipLauncher, VipCI and VipSession using pytest. It also tests low-level client functions.
\ No newline at end of file
+This is an unfinished work proposing test scripts for VipLauncher, VipGirder and VipSession using pytest. It also tests low-level client functions.
\ No newline at end of file
diff --git a/tests/test_VipCI.py b/tests/test_VipGirder.py
similarity index 90%
rename from tests/test_VipCI.py
rename to tests/test_VipGirder.py
index 92fa6b5..f3100ce 100644
--- a/tests/test_VipCI.py
+++ b/tests/test_VipGirder.py
@@ -1,11 +1,7 @@
-import io
-from urllib.error import HTTPError
 import pytest
 from pathlib import *
 
-import pytest_mock
-from vip_client.utils import vip
-from vip_client.classes import VipCI
+from vip_client.classes import VipGirder
 from mocked_services import mock_vip_api, mock_girder_client, mock_pathlib, mock_os
 from FakeGirderClient import FakeGirderClient
 
@@ -41,7 +37,7 @@ def setup_teardown_vip_launcher(request, mocker):
     
     # Setup code before running the tests in the class
     print("Handshake with VIP")
-    VipCI.init(vip_key="FAKE_KEY", girder_key="FAKE_KEY")
+    VipGirder.init(vip_key="FAKE_KEY", girder_key="FAKE_KEY")
     print("Setup done")
 
 @pytest.fixture(scope="function", autouse=True)
@@ -86,7 +82,7 @@ def fake_execution_info(workflow_id):
     mocker.patch("vip_client.utils.vip.execution_info").side_effect = fake_execution_info
     
     # Launch a Full Session Run
-    s = VipCI()
+    s = VipGirder()
     s.pipeline_id = pipeline_id
     s.output_dir = PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS")
     s.input_settings = {
@@ -131,19 +127,19 @@ def fake_execution_info(workflow_id):
 )
 def test_backup(mocker, backup_location, input_settings, pipeline_id, output_dir):
 
-    VipCI._BACKUP_LOCATION = backup_location
+    VipGirder._BACKUP_LOCATION = backup_location
         
     # Create session
-    s1 = VipCI(pipeline_id=pipeline_id, input_settings=input_settings)
+    s1 = VipGirder(pipeline_id=pipeline_id, input_settings=input_settings)
     s1.output_dir = output_dir
     
-    assert s1._save() is not (VipCI._BACKUP_LOCATION is None) # Return False if no backup location
+    assert s1._save() is not (VipGirder._BACKUP_LOCATION is None) # Return False if no backup location
     
     # Load backup
-    s2 = VipCI(output_dir=s1.output_dir)
+    s2 = VipGirder(output_dir=s1.output_dir)
     # Check parameters
     assert s2.output_dir == s1.output_dir
-    if VipCI._BACKUP_LOCATION is None:
+    if VipGirder._BACKUP_LOCATION is None:
         assert not s2._load()
         assert s2.input_settings != s1.input_settings
         assert s2.pipeline_id != s1.pipeline_id
@@ -154,10 +150,10 @@ def test_backup(mocker, backup_location, input_settings, pipeline_id, output_dir
 
 def test_properties_interface(mocker):
 
-    VipCI._BACKUP_LOCATION = "girder"
+    VipGirder._BACKUP_LOCATION = "girder"
 
     # Copy the first session
-    s = VipCI()
+    s = VipGirder()
     s.input_settings = {
         "zipped_folder": 'fake_value1',
         "basis_file": 'fake_value2',
diff --git a/tests/test_VipLauncher.py b/tests/test_VipLauncher.py
index 366fe86..cae305d 100644
--- a/tests/test_VipLauncher.py
+++ b/tests/test_VipLauncher.py
@@ -1,8 +1,6 @@
-import io
 import pytest
 from pathlib import *
 
-from vip_client.utils import vip
 from vip_client.classes import VipLauncher
 from mocked_services import mock_vip_api, mock_pathlib, mock_os
 
diff --git a/tests/test_VipSession.py b/tests/test_VipSession.py
index f1b2d9e..f1d62b0 100644
--- a/tests/test_VipSession.py
+++ b/tests/test_VipSession.py
@@ -1,10 +1,7 @@
-import io
 from unittest.mock import patch
 import pytest
 from pathlib import *
 
-import pytest_mock
-from vip_client.utils import vip
 from vip_client.classes import VipSession
 from mocked_services import mock_vip_api, mock_pathlib, mock_os
 
diff --git a/tests/test_global.py b/tests/test_global.py
index d6beb14..16d5479 100644
--- a/tests/test_global.py
+++ b/tests/test_global.py
@@ -1,4 +1,4 @@
-from vip_client.classes import VipSession, VipCI, VipLauncher
+from vip_client.classes import VipSession, VipGirder, VipLauncher
 from mocked_services import mock_vip_api, mock_pathlib, mock_os, mock_girder_client
 import pytest
 
@@ -48,8 +48,8 @@
     }
 ]
 
-test_cases_missing_input_fields = [(input_settings, tested_class) for input_settings in test_cases_missing_input_fields for tested_class in [VipSession, VipLauncher, VipCI]]
-test_cases_missing_input_values = [(input_settings, tested_class) for input_settings in test_cases_missing_input_values for tested_class in [VipSession, VipLauncher, VipCI]]
+test_cases_missing_input_fields = [(input_settings, tested_class) for input_settings in test_cases_missing_input_fields for tested_class in [VipSession, VipLauncher, VipGirder]]
+test_cases_missing_input_values = [(input_settings, tested_class) for input_settings in test_cases_missing_input_values for tested_class in [VipSession, VipLauncher, VipGirder]]
 
 @pytest.fixture(scope="function", autouse=True)
 def setup_teardown_vip_launcher(request, mocker):
@@ -63,7 +63,7 @@ def setup_teardown_vip_launcher(request, mocker):
     print("Handshake with VIP")
     VipSession.init(api_key="FAKE_KEY")
     VipLauncher.init(api_key="FAKE_KEY")
-    VipCI.init(vip_key="FAKE_KEY", girder_key="FAKE_KEY")
+    VipGirder.init(vip_key="FAKE_KEY", girder_key="FAKE_KEY")
     print("Setup done")
 
 
@@ -72,10 +72,10 @@ def setup_teardown_vip_launcher(request, mocker):
 )
 def test_missing_input_settings(input_settings, tested_class):
 
-    VipCI._BACKUP_LOCATION = None
+    VipGirder._BACKUP_LOCATION = None
     
     # Copy the first session
-    s = VipCI()
+    s = VipGirder()
     s.pipeline_id = "LCModel/0.1"
     s.output_dir = "/path/to/output"
     s.input_settings = input_settings
diff --git a/tests/try_viploader.py b/tests/try_viploader.py
deleted file mode 100644
index 8032c3f..0000000
--- a/tests/try_viploader.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import sys
-from pathlib import Path
-SOURCE_ROOT = str(Path(__file__).parents[1] / "src") # <=> /src/
-sys.path.append(SOURCE_ROOT)
-import vip_client
-
-from vip_client.classes import VipLoader
-from pathlib import *
-
-VipLoader.init()
-path = "/vip/EGI tutorial (group)/outputs"
-print(f"Under '{path}':")
-print("\n".join(VipLoader.list_dir(path)))
-print()
-VipLoader.download_dir(
-    vip_path=path, 
-    local_path=Path("Here")
-)
\ No newline at end of file

From 3810a144b568837feefff38e568fc740659375f5 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 3 Mar 2025 16:46:05 +0100
Subject: [PATCH 04/14] file renaming

---
 src/vip_client/classes/VipGirder.py | 679 ++++++++++++++++++++++++++++
 1 file changed, 679 insertions(+)
 create mode 100644 src/vip_client/classes/VipGirder.py

diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
new file mode 100644
index 0000000..a72bb11
--- /dev/null
+++ b/src/vip_client/classes/VipGirder.py
@@ -0,0 +1,679 @@
+# Builtins
+from __future__ import annotations
+import os
+import time
+from pathlib import *
+# Try importing the Girder client
+try:
+    import girder_client
+except:
+    from warnings import warn
+    warn("vip_client.classes.VipGirder is unavailable (missing package: girder-client)")
+# Other classes from VIP client
+from vip_client.utils import vip
+from vip_client.classes.VipLauncher import VipLauncher
+
+class VipGirder(VipLauncher):
+    """
+    Python class to run VIP pipelines on datasets located on Girder.
+
+    A single instance allows to run 1 pipeline with 1 parameter set (any number of runs).
+    Pipeline runs need at least three inputs:
+    - `pipeline_id` (str) Name of the pipeline. 
+    - `input_settings` (dict) All parameters needed to run the pipeline.
+    - `output_dir` (str) Path to a Girder folder where execution results will be stored.
+
+    N.B.: all instance methods require that `VipGirder.init()` has been called with:
+    - a valid VIP API key;
+    - a valid Girder API key.
+    """
+
+                    ##################
+    ################ Class Attributes ##################
+                    ##################
+
+    # --- Overriden from the parent class ---
+
+    # Class name
+    __name__ = "VipGirder"
+    # Properties to save / display for this class
+    _PROPERTIES = [
+        "session_name", 
+        "pipeline_id",
+        "vip_output_dir", 
+        "input_settings", 
+        "workflows"
+    ]
+    # Default location for VIP inputs/outputs (different from the parent class)
+    _INPUT_SERVER_NAME = "girder"
+    _OUTPUT_SERVER_NAME = "girder"
+    # Prefix that defines a Girder path 
+    _SERVER_PATH_PREFIX = "/collection"
+    # Default backup location 
+    # (set to None to avoid saving and loading backup files)
+    _BACKUP_LOCATION = "girder"
+    
+    # Prefix that defines a Girder ID
+    _GIRDER_ID_PREFIX = "pilotGirder"
+    # Grider portal
+    _GIRDER_PORTAL = 'https://pilot-warehouse.creatis.insa-lyon.fr/api/v1'
+    
+
+                    #################
+    ################ Main Properties ##################
+                    #################
+    
+    @property
+    def custom_wf_metadata(self) -> dict:
+        return self._custom_wf_metadata
+    
+    @custom_wf_metadata.setter
+    def custom_wf_metadata(self, value: dict) -> None:
+        if value != None:
+            assert isinstance(value, dict), f"Custom metadata must be a dictionary, not {type(value)}"
+        self._custom_wf_metadata = value
+
+
+
+                    #############
+    ################ Constructor ##################
+                    ############# 
+    def __init__(
+        self, output_dir=None, pipeline_id: str=None, input_settings: dict=None, 
+        session_name: str=None, verbose: bool=None, custom_wf_metadata: dict=None, **kwargs
+    ) -> None:
+        """
+        Creates a VipGirder instance and sets its properties from keyword arguments.
+
+        ## Parameters
+        - `output_dir` (str | os.PathLike) Path to a Girder folder where execution results will be stored.
+            - Does not need to exist
+            - Usually in format : "/collection/[collection_name]/[path_to_folder]"
+            - User must have read/write permissions on the Girder collection/folder.
+
+        - `pipeline_id` (str) Name of your pipeline in VIP. 
+            - Usually in format : *application_name*/*version*.
+            - Run VipLauncher.show_pipeline() to display available pipelines.
+
+        - `input_settings` (dict) All parameters needed to run the pipeline.
+            - Run VipSession.show_pipeline(`pipeline_id`) to display these parameters.
+            - The dictionary can contain any object that can be converted to strings, or lists of such objects.
+            - Lists of parameters launch parallel workflows on VIP.
+
+        - `session_name` [Optional/Recommended] (str) A name to identify this session.
+            - Default value: 'VipGirder-[date]-[time]-[id]'
+        
+        - `verbose` [Optional] (bool) Verbose mode for this instance.
+            - If True, instance methods will display logs;
+            - If False, instance methods will run silently.
+        
+        - `custom_wf_metadata` [Optional] (dict) Custom metadata to add to each workflow.
+
+        `session_name` is only set at instantiation; other properties can be set later in function calls.
+        If `output_dir` leads to data from a previous session, properties will be loaded from the metadata on Girder.
+        """
+        # Initialize with the name, pipeline and input settings
+        super().__init__(
+            output_dir = output_dir,
+            session_name = session_name, 
+            pipeline_id = pipeline_id, 
+            input_settings = input_settings,
+            verbose = verbose
+        )
+        # Set custom properties
+        self.custom_wf_metadata = custom_wf_metadata
+        # End display
+        if any([session_name, output_dir]) and (self.__name__ == "VipGirder"): 
+            self._print()
+    # ------------------------------------------------
+
+                    ################
+    ################ Public Methods ##################
+                    ################
+
+    #################################################
+    # Manage a session from start to finish
+    #################################################
+
+    # Login to VIP and Girder
+    @classmethod
+    def init(
+            cls, 
+            vip_key="VIP_API_KEY", 
+            girder_key="GIRDER_API_KEY", 
+            verbose=True, 
+            girder_api_url=None,
+            girder_id_prefix=None,
+            **kwargs
+        ) -> VipGirder:
+        """
+        Handshakes with VIP using your own API key. 
+        Returns a class instance which properties can be provided as keyword arguments.
+        
+        ## Parameters
+        - `vip_key` (str): VIP API key. This can be either:
+            A. [unsafe] A **string litteral** containing your API key,
+            B. [safer] A **path to some local file** containing your API key,
+            C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
+        In cases B or C, the API key will be loaded from the local file or the environment variable. 
+
+        - `girder_key` (str): Girder API key. Can take the same values as `vip_key`.
+        
+        - `verbose` (bool): default verbose mode for all instances.
+            - If True, all instances will display logs by default;
+            - If False, all instance methods will run silently by default.
+
+        - `kwargs` [Optional] (dict): keyword arguments or dictionnary setting properties of the returned instance.     
+        """
+        # Initiate a Vip Session silently
+        super().init(api_key=vip_key, verbose=False, **kwargs)
+        # Restore the verbose state
+        cls._VERBOSE = verbose
+        # Set the Girder ID prefix
+        cls._GIRDER_ID_PREFIX = girder_id_prefix if girder_id_prefix is not None else cls._GIRDER_ID_PREFIX
+        cls._GIRDER_PORTAL = girder_api_url if girder_api_url is not None else cls._GIRDER_PORTAL
+        # Instantiate a Girder client
+        cls._girder_client = girder_client.GirderClient(apiUrl=girder_api_url)
+        # Check if `girder_key` is in a local file or environment variable
+        true_key = cls._get_api_key(girder_key)
+        # Authenticate with Girder API key
+        cls._girder_client.authenticate(apiKey=true_key)
+        # Diplay success
+        cls._printc()
+        cls._printc("---------------------------------------------")
+        cls._printc("| You are communicating with VIP and Girder |")
+        cls._printc("---------------------------------------------")
+        cls._printc()
+        # Return a VipGirder instance for method cascading
+        return cls(verbose=(verbose and kwargs), **kwargs)
+    # ------------------------------------------------
+
+    # Launch the pipeline on VIP
+    def launch_pipeline(
+            self, pipeline_id: str=None, input_settings: dict=None, output_dir=None, nb_runs=1, 
+            verbose: bool=None
+        ) -> VipGirder:
+        """
+        Launches pipeline executions on VIP.
+
+        Input parameters :
+        - `pipeline_id` (str) The name of your pipeline in VIP, 
+            usually in format : *application_name*/*version*.
+        - `input_settings` (dict) All parameters needed to run the pipeline.
+            - Run VipSession.show_pipeline(`pipeline_id`) to display these parameters.
+            - The dictionary can contain any object that can be converted to strings, or lists of such objects.
+            - Lists of parameters launch parallel workflows on VIP.
+        - `output_dir` (str) Path to the VIP folder where execution results will be stored.
+        - `nb_runs` (int) Number of parallel workflows to launch with the same settings.
+        
+        Default behaviour:
+        - Raises AssertionError in case of wrong inputs 
+        - Raises RuntimeError in case of failure on VIP servers.
+        - In any case, session is backed up after pipeline launch
+        """
+        return super().launch_pipeline(
+            pipeline_id = pipeline_id, # default
+            input_settings = input_settings, # default
+            output_dir = output_dir, # default
+            nb_runs = nb_runs, # default
+        )
+    # ------------------------------------------------
+
+    # Monitor worflow executions on VIP 
+    def monitor_workflows(self, refresh_time=30) -> VipGirder:
+        """
+        Updates and displays the status of each execution launched in the current session.
+        - If an execution is still runnig, updates status every `refresh_time` (seconds) until all runs are done.
+        - Displays a full report when all executions are done.
+        """
+        return super().monitor_workflows(refresh_time=refresh_time)
+    # ------------------------------------------------
+
+    # Run a full VipGirder session 
+    def run_session(self, nb_runs=1, refresh_time=30) -> VipGirder:
+        """
+        Runs a full session from Girder data:
+        1. Launches pipeline executions on VIP;
+        2. Monitors pipeline executions until they are all over;
+            and Adds metadata on Girder output folder.
+
+        |!| This function assumes that all session properties are already set.
+        Optional arguments can be provided:
+        - Increase `nb_runs` to run more than 1 execution at once;
+        - Set `refresh_time` to modify the default refresh time.
+        """
+        return super().run_session(nb_runs=nb_runs, refresh_time=refresh_time)
+    # ------------------------------------------------
+
+    # Display session properties in their current state
+    def display(self) -> VipGirder:
+        """
+        Displays useful properties in JSON format.
+        - `session_name` : current session name
+        - `pipeline_id`: pipeline identifier
+        - `output_dir` : path to the pipeline outputs
+        - `input_settings` : input parameters sent to VIP
+        - `workflows`: workflow inventory, identifying all pipeline runs in this session.
+        """
+        # Return for method cascading
+        return super().display()
+    # ------------------------------------------------
+
+    # Return error in case of call to finish()
+    def finish(self, verbose: bool=None) -> None:
+        """
+        This function does not work in VipGirder.
+        """
+        # Update the verbose state and display
+        self._verbose = verbose
+        self._print("\n=== FINISH ===\n", max_space=2)
+        # Raise error message
+        raise NotImplementedError(f"Class {self.__name__} cannot delete the distant data.")
+    # ------------------------------------------------
+
+                    #################
+    ################ Private Methods ################
+                    #################
+
+    ###################################################################
+    # Methods that must be overwritten to adapt VipLauncher methods to
+    # new location: "girder"
+    ###################################################################
+
+    # Path to delete during session finish
+    def _path_to_delete(self) -> dict:
+        """Returns the folders to delete during session finish, with appropriate location."""
+        return {}
+    # ------------------------------------------------
+
+    # Method to check existence of a resource on Girder.
+    @classmethod
+    def _exists(cls, path: PurePath, location="girder") -> bool:
+        """
+        Checks existence of a resource on Girder.
+        """
+        # Check path existence in `location`
+        if location=="girder":
+            try: 
+                cls._girder_client.resourceLookup(path=str(path))
+                return True
+            except girder_client.HttpError: 
+                return False
+        else:
+            return super()._exists(path, location)
+    # ------------------------------------------------
+    
+    # Method to create a distant or local directory
+    @classmethod
+    def _create_dir(cls, path: PurePath, location="girder", **kwargs) -> str:
+        """
+        Creates a directory at `path` on Girder if `location` is "girder".
+
+        `path` should be a PathLib object.
+        `kwargs` can be passed as keyword arguments to `girder-client.createFolder()`.
+        Returns the Girder ID of the newly created folder.
+        """
+        if location == "girder": 
+            # Find the parent ID and type
+            parentId, parentType = cls._girder_path_to_id(str(path.parent))
+            # Check the parent is a directory
+            if not (parentType == "folder"):
+                raise ValueError(f"Cannot create folder {path} in '{path.parent}': parent is not a Girder folder")
+            # Create the new directory with additional keyword arguments
+            return cls._girder_client.createFolder(
+                parentId=parentId, name=str(path.name), reuseExisting=True, **kwargs
+                )["_id"]
+        else:
+            super()._create_dir(path, location)
+            return ""
+    # ------------------------------------------------
+
+    # Function to delete a path
+    @classmethod
+    def _delete_path(cls, path: PurePath, location="vip") -> None:
+        if location == "girder":
+            raise NotImplementedError("VipGirder cannot delete data.")
+        else:
+            return super()._delete_path(path, location)
+
+    # Function to delete a path on VIP with warning
+    @classmethod
+    def _delete_and_check(cls, path: PurePath, location="vip", timeout=300) -> bool:
+        if location == "girder":
+            raise NotImplementedError("VipGirder cannot delete data.")
+        else:
+            return super()._delete_and_check(path, location, timeout)
+    
+    ####################################################
+    # Launch & Monitor pipeline executions from Girder #
+    ####################################################
+
+    def _init_exec(self) -> str:
+        """
+        Initiates one VIP workflow with `pipeline_id`, `session_name`, `input_settings`, `output_dir`.
+        Returns the workflow identifier.
+        """
+        # Get function arguments
+        # input_settings = self._vip_input_settings(self._input_settings)
+        input_settings = self._get_input_settings(location="vip-girder")
+        # Create a workflow-specific result directory
+        res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime()) 
+            # no simple way to rename later with workflow_id
+        res_id = self._create_dir(
+            path=res_path, location=self._OUTPUT_SERVER_NAME, 
+            description=f"VIP outputs from one workflow in Session '{self._session_name}'"
+        )
+        res_vip = self._vip_girder_id(res_id)
+        # Launch execution
+        workflow_id = vip.init_exec(
+            pipeline = self.pipeline_id, 
+            name = self.session_name, 
+            inputValues = input_settings,
+            resultsLocation = res_vip
+        )
+        # Record the path to output files (create the workflow entry)
+        self._workflows[workflow_id] = {"output_path": str(res_path)}
+        return workflow_id
+    # ------------------------------------------------
+
+    # Function extract metadata from a single workflow
+    def _meta_workflow(self, workflow_id: str) -> dict:
+        metadata = {
+            "session_name": self._session_name,
+            "workflow_id": workflow_id,
+            "workflow_start": self._workflows[workflow_id]["start"],
+            "workflow_status": self._workflows[workflow_id]["status"]
+        }
+        # If custom metadata is provided, add it to the metadata
+        if self.custom_wf_metadata is not None:
+            metadata = {**metadata, **self.custom_wf_metadata}
+        return metadata
+
+    # Overwrite _get_exec_infos() to bypass call to vip.get_exec_results() (does not work at this time)
+    @classmethod
+    def _get_exec_infos(cls, workflow_id: str) -> dict:
+        """
+        Returns succint information on `workflow_id`:
+        - Execution status (VIP notations)
+        - Starting time (local time, format '%Y/%m/%d %H:%M:%S')
+        - List of paths to the output files.
+        """
+        try :
+            # Get execution infos
+            infos = vip.execution_info(workflow_id)
+            # Secure way to get execution results
+            # files = vip.get_exec_results(workflow_id)
+        except RuntimeError as vip_error:
+            cls._handle_vip_error(vip_error)
+        # Return filtered information
+        return {
+            # Execution status (VIP notations)
+            "status": infos["status"],
+            # Starting time (human readable)
+            "start": time.strftime(
+                '%Y/%m/%d %H:%M:%S', time.localtime(infos["startDate"]/1000)
+                ),
+            # # Returned files
+            # "outputs": infos["returnedFiles"]["output_file"]
+        }
+    # ------------------------------------------------
+
+    ###################################################
+    # Save (/load) Session to (/from) Girder metadata #
+    ###################################################
+
+    # Save session properties in a JSON file
+    def _save_session(self, session_data: dict, location="girder") -> bool:
+        """
+        Saves dictionary `session_data` as metadata in the output directory on Girder.
+        Returns a success flag.
+        Displays success / failure unless `_verbose` is False.
+        """
+        # Thow error if location is not "girder" because this session does no interact with VIP
+        if location != "girder":
+            return super()._save_session(session_data, location)
+        # Ensure the output directory exists on Girder
+        is_new = self._mkdirs(path=self._vip_output_dir, location=location)
+        # Save metadata in the global output directory
+        folderId, _ = self._girder_path_to_id(self._vip_output_dir)
+        self._girder_client.addMetadataToFolder(folderId=folderId, metadata=session_data)
+        # Update metadata for each workflow
+        for workflow_id in self._workflows:
+            metadata = self._meta_workflow(workflow_id=workflow_id)
+            folderId, _ = self._girder_path_to_id(path=self._workflows[workflow_id]["output_path"])
+            self._girder_client.addMetadataToFolder(folderId=folderId, metadata=metadata)
+        # Display
+        self._print()
+        if is_new:
+            self._print(">> Session was backed up as Girder metadata in:")
+            self._print(f"\t{self._vip_output_dir} (Girder ID: {folderId})\n")
+        else:
+            self._print(">> Session backed up\n")
+        # Return
+        return True
+    # ------------------------------------------------
+
+    def _load_session(self, location="girder") -> dict:
+        """
+        Loads backup data from the metadata stored in the output directory on Girder.
+        If the metadata could not be found, returns None.
+        Otherwise, returns session properties as a dictionary.
+        """
+        # Thow error if location is not "girder"
+        if location != "girder":
+            return super()._load_session(location)
+        # Check the output directory is defined
+        if self.vip_output_dir is None: 
+            return None
+        # Load the metadata on Girder
+        with self._silent_class():
+            try:
+                girder_id, _ = self._girder_path_to_id(self.vip_output_dir)
+                folder = self._girder_client.getFolder(folderId=girder_id)
+            except girder_client.HttpError as e:
+                if e.status == 400: # Folder was not found
+                    return None
+        # Display success if the folder was found
+        self._print("<< Session restored from its output directory\n")
+        # Return session metadata
+        return folder["meta"]
+    # ------------------------------------------------
+    
+    ##################################
+    # Manipulate Resources on Girder #
+    ##################################
+
+    # Function to get a resource ID
+    @classmethod
+    def _girder_path_to_id(cls, path) -> tuple[str, str]:
+        """
+        Returns a resource ID from its `path` within a Girder collection.
+        `path` should begin with: "/collection/[collection_name]/...".
+        `path` can be a string or PathLib object.
+
+        Raises `girder_client.HttpError` if the resource was not found. 
+        Adds intepretation message unless `cls._VERBOSE` is False.
+        """
+        try :
+            resource = cls._girder_client.resourceLookup(str(path))
+        except girder_client.HttpError as e:
+            if e.status == 400:
+                cls._printc("(!) The following path is invalid or refers to a resource that does not exist:")
+                cls._printc("    %s" % path)
+                cls._printc("    Original error from Girder API:")
+            raise e
+        # Return the resource ID and type
+        try:
+            return resource['_id'], resource['_modelType']
+        except KeyError as ke:
+            cls._printc(f"Unhandled type of resource: \n\t{resource}\n")
+            raise ke
+    # ------------------------------------------------
+    
+    # Function to get a resource path
+    @classmethod
+    def _girder_id_to_path(cls, id: str, type: str) -> PurePosixPath:
+        """
+        Returns a resource path from its Girder `id`.
+        The resource `type` (item, folder, collection) must be provided.
+
+        Raises `girder_client.HttpError` if the resource was not found.
+        """
+        try :
+            return PurePosixPath(cls._girder_client.get(f"/resource/{id}/path", {"type": type}))
+        except girder_client.HttpError as e:
+            if e.status == 400:
+                cls._printc(f"(!) Invalid Girder ID: {id} with resource type:{type}")
+                cls._printc("    Original error from Girder API:")
+            raise e
+    # ------------------------------------------------
+    
+    # Function to convert a Girder ID to Girder-VIP standard
+    @classmethod
+    def _vip_girder_id(cls, resource) -> str:
+        """
+        Prefixes a Girder ID with the VIP standard. 
+        Input `resource` should be a Girder Id (str) or a Girder path (PurePosixPath)
+        """
+        if isinstance(resource, str):
+            # Prefix the ID
+            return ":".join([cls._GIRDER_ID_PREFIX, resource])
+        elif isinstance(resource, PurePath):
+            # Get the Girder ID
+            girder_id, _ = cls._girder_path_to_id(resource)
+            # Prefix the ID
+            return ":".join([cls._GIRDER_ID_PREFIX, girder_id])
+    # ------------------------------------------------
+
+    ###################################################################
+    # Adapt `input_settings` to the Vip-Girder communication protocol #
+    ###################################################################
+
+    # Store the VIP paths as PathLib objects.
+    def _parse_input_settings(self, input_settings) -> dict:
+        """
+        Parses the input settings, i.e.:
+        - Resolves any reference to a Girder collection and turns a folder name 
+            into a list of files
+        - Converts all Girder paths to PathLib objects 
+        - Leaves the other parameters untouched.
+        """
+        # Function to extract file from Girder item
+        def get_file_from_item(itemId: str) -> str:
+            """Returns the Girder ID of a single file contained in `itemId`"""
+            files = [
+                f["_id"] for f in self._girder_client.listFile(itemId=itemId)
+            ]
+            # Check the number of files (1 per item)
+            if len(files) != 1:
+                msg = f"Unable to parse the Girder item : {self._girder_id_to_path(id=itemId, type='item')}"
+                msg += "Contains more than 1 file."
+                raise NotImplementedError(msg)
+            return files[0]
+        # -- End of get_file_from_item() --
+        # Function to extract all files from a Girder resource
+        def get_files(input_path: str):
+            """
+            Returns the path of all files contained in the Girder resource pointed by `input_path`.
+            The Girder resource can be a file, an item with 1 file or a folder with multiple items.
+            """
+            # Look up for the resource in Girder & get the Girder ID
+            girder_id, girder_type = self._girder_path_to_id(input_path)
+            # Retrieve all files based on the resource type
+            if girder_type == "file":
+                # Return the Girder path
+                return PurePosixPath(input_path)
+            elif girder_type == "item":
+                # Retrieve the corresponding file
+                fileId = get_file_from_item(girder_id)
+                # Return the Girder path
+                return self._girder_id_to_path(id=fileId, type='file')
+            elif girder_type == "folder":
+                # Retrieve all items
+                items = [ it["_id"] for it in self._girder_client.listItem(folderId=girder_id) ]
+                new_inputs = []
+                # Browse items
+                for itemId in items:
+                    # Retrieve the corresponding file
+                    fileId = get_file_from_item(itemId)
+                    # Update the file list with new Girder path
+                    new_inputs.append(self._girder_id_to_path(id=fileId, type='file'))
+                # Return the list of files
+                return new_inputs
+            else: 
+                # Girder type = collection or other
+                raise ValueError(f"Bad resource: {input_path}\n\tGirder type '{girder_type}' is not permitted in this context.")
+        # -- End of get_files() --
+        # Function to parse Girder paths
+        def parse_value(input):
+            # Case: single input, string or path-like
+            if isinstance(input, (str, os.PathLike)):
+                # Case: Girder path
+                if str(input).startswith(self._SERVER_PATH_PREFIX): 
+                    return get_files(input)
+                # Case: any other input
+                else: return input
+            # Case: multiple inputs
+            elif isinstance(input, list):
+                new_input = []
+                # Browse elements
+                for element in input:
+                    # Parse element
+                    parsed = parse_value(element)
+                    # Merge the lists if `element` is a folder
+                    if isinstance(parsed, list): new_input += parsed
+                    # Append if `element` is a file
+                    else: new_input.append(parsed)
+                # Return the list of files
+                return new_input
+           # Case not string nor path-like: return as is
+            else: return input
+        # -- End of parse_value() --
+        # Return the parsed value of each parameter
+        return {
+            key: parse_value(value)
+            for key, value in input_settings.items()
+        }
+    # ------------------------------------------------
+
+    # Get the input settings after files are parsed as PathLib objects
+    def _get_input_settings(self, location="girder") -> dict:
+        """
+        Returns the input settings with filenames adapted to `location`.
+        - if `location` = "girder", returns Girder paths string format.
+        - if `location` = "vip-girder", returns the prefixed Girder ID for VIP.
+
+        Returns a string version of any other parameter.
+        """
+        # Function to get the VIP-Girder standard from 1 input path
+        def get_input(value, location) -> str:
+            """
+            If `value` is a path, returns the corresponding string.
+            Value can be a single input or a list of inputs.
+            """
+            # Case: multiple inputs
+            if isinstance(value, list):
+                return [ get_input(element, location) for element in value ]
+            # Case : path to Girder resource
+            elif isinstance(value, PurePath): 
+                if location == "girder":
+                    return str(value)
+                elif location == "vip-girder":
+                    return self._vip_girder_id(value)
+            # Case: other parameter
+            else: return str(value)
+        # --------------------
+        # Raise an error if `location` cannot be parsed
+        if location not in ("girder", "vip-girder"):
+            return super()._get_input_settings(location)
+        # Browse input settings
+        return {
+            key: get_input(value, location)
+            for key, value in self._input_settings.items()
+        }
+    # ------------------------------------------------
+
+######################################################
+        
+if __name__=="__main__":
+    pass
\ No newline at end of file

From 85de883a534ea140c7f1dc5abb07cac076fea65a Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 3 Mar 2025 16:54:51 +0100
Subject: [PATCH 05/14] support of local vip as an output instead of girder

---
 src/vip_client/classes/VipGirder.py   | 21 ++++++++++++---------
 src/vip_client/classes/VipLauncher.py | 23 ++++++++++++++---------
 2 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
index a72bb11..9d0502e 100644
--- a/src/vip_client/classes/VipGirder.py
+++ b/src/vip_client/classes/VipGirder.py
@@ -354,16 +354,19 @@ def _init_exec(self) -> str:
         Returns the workflow identifier.
         """
         # Get function arguments
-        # input_settings = self._vip_input_settings(self._input_settings)
         input_settings = self._get_input_settings(location="vip-girder")
-        # Create a workflow-specific result directory
-        res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime()) 
-            # no simple way to rename later with workflow_id
-        res_id = self._create_dir(
-            path=res_path, location=self._OUTPUT_SERVER_NAME, 
-            description=f"VIP outputs from one workflow in Session '{self._session_name}'"
-        )
-        res_vip = self._vip_girder_id(res_id)
+        res_path = str(self._vip_output_dir) + "/OUTPUTS"
+        res_vip = res_path
+        if (self._OUTPUT_SERVER_NAME == "girder"):
+            # Create a workflow-specific result directory
+            res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime()) 
+                # no simple way to rename later with workflow_id
+            res_id = self._create_dir(
+                path=res_path, location=self._OUTPUT_SERVER_NAME, 
+                description=f"VIP outputs from one workflow in Session '{self._session_name}'"
+            )
+            res_vip = self._vip_girder_id(res_id)
+
         # Launch execution
         workflow_id = vip.init_exec(
             pipeline = self.pipeline_id, 
diff --git a/src/vip_client/classes/VipLauncher.py b/src/vip_client/classes/VipLauncher.py
index bf1405c..1d96e20 100644
--- a/src/vip_client/classes/VipLauncher.py
+++ b/src/vip_client/classes/VipLauncher.py
@@ -43,7 +43,8 @@ class VipLauncher():
     # (set to None to avoid saving and loading backup files)
     _BACKUP_LOCATION = None
     # Default location for VIP inputs/outputs (can be different for subclasses)
-    _SERVER_NAME = "vip"
+    _INPUT_SERVER_NAME = "vip"
+    _OUTPUT_SERVER_NAME = "vip"
     # Prefix that defines a path from VIP
     _SERVER_PATH_PREFIX = "/vip"
     # Default file name to save session properties 
@@ -482,15 +483,15 @@ def launch_pipeline(
         if not self._is_defined("_vip_output_dir"):
             raise TypeError("Please provide an output directory for Session: %s" %self._session_name)
         else: self._print("Output directory: ", end="", flush=True)
-            # Ensure the directory exists
-        if self._mkdirs(path=self._vip_output_dir, location=self._SERVER_NAME):
-            self._print(f"Created on {self._SERVER_NAME.upper()}")
+        # Ensure the directory exists
+        if self._mkdirs(path=self._vip_output_dir, location=self._OUTPUT_SERVER_NAME):
+            self._print(f"Created on {self._OUTPUT_SERVER_NAME.upper()}")
         else:
             self._print("OK")
         # Check the input parameters
         self._print("Input settings: ", end="", flush=True)
         # Check content
-        self._check_input_settings(location=self._SERVER_NAME)
+        self._check_input_settings(location=self._INPUT_SERVER_NAME)
         self._print("OK")
         # End parameters checks
         self._print("----------------\n")
@@ -921,6 +922,8 @@ def _delete_and_check(cls, path: PurePath, location="vip", timeout=300) -> bool:
         Deletes `path` on `location` and waits until `path` is actually removed.
         After `timeout` (seconds), displays a warning if `path` still exist.
         """
+        if location != "vip":
+            raise NotImplementedError(f"Unknown location: {location}")
         # Delete the path
         cls._delete_path(path, location)
         # Standby until path is indeed removed (give up after some time)
@@ -1004,7 +1007,7 @@ def _set(self, **kwargs) -> None:
 
     # Simple context manager to unlock session properties while executing code
     @contextmanager
-    def _unlocked_properties(self) -> None:
+    def _unlocked_properties(self):
         """
         Under this context, session properties can be modified without raising an error.
         """
@@ -1016,7 +1019,7 @@ def _unlocked_properties(self) -> None:
 
     # Simple context manager to silence session logs while executing code
     @contextmanager
-    def _silent_session(self) -> None:
+    def _silent_session(self):
         """
         Under this context, the session will not print anything.
         """
@@ -1029,7 +1032,7 @@ def _silent_session(self) -> None:
     # Simple context manager to silence logs from class methods while executing code
     @classmethod
     @contextmanager
-    def _silent_class(cls) -> None:
+    def _silent_class(cls):
         """
         Under this context, the session will not print anything.
         """
@@ -1528,6 +1531,8 @@ def _get_input_settings(self, location="vip") -> dict:
         Returns the input settings with their orignal values in string format.
         `location` is destined to subclasses.
         """
+        if location != "vip":
+            raise NotImplementedError(f"Unknown location: {location}")
         return {
             key: [str(v) for v in value] if isinstance(value, list) else str(value)
             for key, value in self._input_settings.items()
@@ -1553,7 +1558,7 @@ def _check_input_settings(self, input_settings: dict=None, location: str=None) -
         """
         # If location is not provided, default to server
         if location is None:
-            location = self._SERVER_NAME
+            location = self._INPUT_SERVER_NAME
         # If input_settings are not provided, get instance attribute instead
         if not input_settings:
             if self._is_defined("_input_settings"):

From b5f0cf1a7f000a789499fcb3e4e22d6474dae4fe Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Tue, 4 Mar 2025 13:07:05 +0100
Subject: [PATCH 06/14] download_outputs and finish on vipgirder mode

---
 src/vip_client/classes/VipGirder.py | 40 ++++++++++++++++++++++++-----
 1 file changed, 33 insertions(+), 7 deletions(-)

diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
index 9d0502e..86caf66 100644
--- a/src/vip_client/classes/VipGirder.py
+++ b/src/vip_client/classes/VipGirder.py
@@ -259,16 +259,42 @@ def display(self) -> VipGirder:
         return super().display()
     # ------------------------------------------------
 
+    def download_outputs(self, output_dir: str):
+        """This will works only when girder isn't the output location."""
+        output_path = PurePath(output_dir)
+
+        os.mkdir(output_path)
+        for workflow in self._workflows.keys():
+            files = vip.get_exec_results(workflow)
+            files = vip.get_exec_results(workflow)
+            to_download = [file["path"] for file in files]
+            linked_download = []
+
+            for path in to_download:
+                posixPath = PosixPath(path)
+                linked_download.append((path, output_path / posixPath.name))
+
+            for v in linked_download:
+                if not (vip.download(v[0], v[1])):
+                    print(f"Failed to download {v[0]} to {v[1]}")
+            print("Workflow outputs successfully downloaded locally!")
+
+    # ------------------------------------------------
+
     # Return error in case of call to finish()
-    def finish(self, verbose: bool=None) -> None:
+    def finish(self, verbose: bool=None, keep_output=False) -> None:
         """
-        This function does not work in VipGirder.
+        This function does nothing when using girder as output location else it erase the data on vip.
         """
-        # Update the verbose state and display
-        self._verbose = verbose
-        self._print("\n=== FINISH ===\n", max_space=2)
-        # Raise error message
-        raise NotImplementedError(f"Class {self.__name__} cannot delete the distant data.")
+        if (self._OUTPUT_SERVER_NAME == "girder"):
+            # Update the verbose state and display
+            self._verbose = verbose
+            self._print("\n=== FINISH ===\n", max_space=2)
+        elif not keep_output:
+            for values in self._workflows.values():
+                self._delete_and_check(PurePath(values["output_path"]).parent)
+                print(f"Workflow successfully cleaned on VIP ({str(PurePath(values["output_path"]).parent)})")
+
     # ------------------------------------------------
 
                     #################

From 5a682d41c3665ae833c40c2f3fe064fc6923388d Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Tue, 4 Mar 2025 15:47:05 +0100
Subject: [PATCH 07/14] fix

---
 src/vip_client/classes/VipGirder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
index 86caf66..f3ede45 100644
--- a/src/vip_client/classes/VipGirder.py
+++ b/src/vip_client/classes/VipGirder.py
@@ -293,7 +293,7 @@ def finish(self, verbose: bool=None, keep_output=False) -> None:
         elif not keep_output:
             for values in self._workflows.values():
                 self._delete_and_check(PurePath(values["output_path"]).parent)
-                print(f"Workflow successfully cleaned on VIP ({str(PurePath(values["output_path"]).parent)})")
+                print(f"Workflow successfully cleaned on VIP ({str(PurePath(values['output_path']).parent)})")
 
     # ------------------------------------------------
 

From 46d5201211b08f97e3a6021adc6bd546cf7851c3 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Fri, 14 Mar 2025 10:40:31 +0100
Subject: [PATCH 08/14] fix already existing output folder

---
 src/vip_client/classes/VipGirder.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
index f3ede45..bb628f5 100644
--- a/src/vip_client/classes/VipGirder.py
+++ b/src/vip_client/classes/VipGirder.py
@@ -263,7 +263,7 @@ def download_outputs(self, output_dir: str):
         """This will works only when girder isn't the output location."""
         output_path = PurePath(output_dir)
 
-        os.mkdir(output_path)
+        os.makedirs(output_path, exist_ok=True)
         for workflow in self._workflows.keys():
             files = vip.get_exec_results(workflow)
             files = vip.get_exec_results(workflow)

From d5b9c0426f3d274930e718c9834c430f3194a220 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 17 Mar 2025 13:34:59 +0100
Subject: [PATCH 09/14] documentation

---
 doc/vipsession.md                    | 5 ++++-
 src/vip_client/classes/VipSession.py | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/vipsession.md b/doc/vipsession.md
index ec8c143..5002890 100644
--- a/doc/vipsession.md
+++ b/doc/vipsession.md
@@ -169,7 +169,10 @@ When all properties are set, the full *upload-run-download* process ([steps 2-5]
 ```python
 session.run_session()
 ```
-*Do not forget to remove your temporary data from VIP after downloading the outputs (`session.finish()`).*
+*Do not forget to remove your temporary data from VIP after downloading the outputs (`session.finish(keep_output=False)`).*
+
+> [!NOTE]
+> By default `session.finish()` will remove the outputs from the VIP platform, but if you want to keep them you use the option `keep_output=True`
 
 All `VipSession` methods can be run in cascade, so everything holds in a single command:
 ```python
diff --git a/src/vip_client/classes/VipSession.py b/src/vip_client/classes/VipSession.py
index 7485c28..47544e5 100644
--- a/src/vip_client/classes/VipSession.py
+++ b/src/vip_client/classes/VipSession.py
@@ -565,13 +565,14 @@ def run_session(
     # Clean session data on VIP
     def finish(self, timeout=300, keep_output=False) -> VipSession:
         """
-        Removes session's data from VIP servers (INPUTS and OUTPUTS). 
+        Removes session's data from VIP servers (INPUTS and by default OUTPUTS). 
         The downloaded outputs and the input dataset are kept on the local machine.
 
         Detailed behaviour:
         - This process checks for actual deletion on VIP servers until `timeout` (seconds) is reached.
             If deletion could not be verified, the procedure ends with a warning message.
         - Workflows status are set to "Removed" when the corresponding outputs have been removed from VIP servers.
+        - OUTPUTS are by default deleted from VIP servers, the option `keep_output` override this behavior
         """
         # Finish the session based on self._path_to_delete()
         super().finish(timeout=timeout, keep_output=keep_output)

From a76a4004e205dd0d907668f209d2059715fbd302 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Fri, 21 Mar 2025 14:35:22 +0100
Subject: [PATCH 10/14] documentation update

---
 examples/tutorials/demo-vipsession.ipynb | 78 ++++++++++++++++++++++++
 1 file changed, 78 insertions(+)

diff --git a/examples/tutorials/demo-vipsession.ipynb b/examples/tutorials/demo-vipsession.ipynb
index ed5c402..fc40a84 100644
--- a/examples/tutorials/demo-vipsession.ipynb
+++ b/examples/tutorials/demo-vipsession.ipynb
@@ -499,6 +499,84 @@
     "! tree {new_session.output_dir}"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Re-use a same dataset multiples times\n",
+    "You can re-use the same dataset multiples times. For that you will only need to keep the trace of where the inputs where uploaded on VIP.  \n",
+    "You will also need to not run `finish()` at the end of the session which has uploaded the dataset, it will prevent your dataset from being deleted.  \n",
+    "When you will reuse the data don't forget to adapt the paths in `inputs_settings` by using the path where they were initially uploaded."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session = VipSession(\"session-A\")\n",
+    "session.upload_inputs(input_dir)\n",
+    "\n",
+    "inputs_settings = {\n",
+    "    \"file\": \"initial.file\",\n",
+    "    \"value\": 5\n",
+    "}\n",
+    "\n",
+    "input_folder_on_vip = session._vip_input_dir\n",
+    "print(f\"The dataset is located on VIP here: {input_folder_on_vip}\") # keep this information somewhere\n",
+    "\n",
+    "session.launch_pipeline(pipeline_id, input_settings)\n",
+    "session.monitor_workflows()\n",
+    "# no finish for the first session"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session = VipSession(\"session-B\")\n",
+    "# do not forget to prepend your inputs !\n",
+    "adapted_inputs_settings = {\n",
+    "    \"file\" : f\"{input_folder_on_vip}/initial.file\", # reuse the stored inforation !\n",
+    "    \"value\": 5\n",
+    "}\n",
+    "session.launch_pipeline(pipeline_id, adapted_inputs_settings)\n",
+    "session.monitor_workflows()\n",
+    "session.finish()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> [!NOTE]\n",
+    "> At the very end when you won't need the dataset anymore don't forget to run `VipSession(session-A).finish()` for cleaning the data from VIP servers.\n",
+    "> You must name your session like you named it for uploading your dataset."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "upload_session = VipSession(\"upload-session\")\n",
+    "upload_session.upload_inputs(input_dir)\n",
+    "# * running the session * #\n",
+    "\n",
+    "reuse_session_a = VipSession(\"reuse-session_a\")\n",
+    "# * reunning the session on the previous dataset * #\n",
+    "\n",
+    "reuse_session_b = VipSession(\"reuse-session_b\")\n",
+    "# * reunning the session on the previous dataset * #\n",
+    "\n",
+    "# finally deleting the dataset\n",
+    "VipSession(\"upload-session\").finish()"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",

From 72180c1f344481ef7513969f9b6d4d4ac9ead6a7 Mon Sep 17 00:00:00 2001
From: Ethaniel <30417812+ethaaalpha@users.noreply.github.com>
Date: Mon, 24 Mar 2025 15:29:53 +0100
Subject: [PATCH 11/14] typo

---
 examples/tutorials/demo-vipsession.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/tutorials/demo-vipsession.ipynb b/examples/tutorials/demo-vipsession.ipynb
index fc40a84..b2f2c08 100644
--- a/examples/tutorials/demo-vipsession.ipynb
+++ b/examples/tutorials/demo-vipsession.ipynb
@@ -540,7 +540,7 @@
     "session = VipSession(\"session-B\")\n",
     "# do not forget to prepend your inputs !\n",
     "adapted_inputs_settings = {\n",
-    "    \"file\" : f\"{input_folder_on_vip}/initial.file\", # reuse the stored inforation !\n",
+    "    \"file\" : f\"{input_folder_on_vip}/initial.file\", # reuse the stored information !\n",
     "    \"value\": 5\n",
     "}\n",
     "session.launch_pipeline(pipeline_id, adapted_inputs_settings)\n",

From ab25ec769fcd18f2c6c569e432606d5cbcde1ed5 Mon Sep 17 00:00:00 2001
From: Ethaniel Billon <ebillon@student.42lyon.fr>
Date: Mon, 28 Apr 2025 12:20:27 +0200
Subject: [PATCH 12/14] add option keep_input finish

---
 src/vip_client/classes/VipSession.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/vip_client/classes/VipSession.py b/src/vip_client/classes/VipSession.py
index 47544e5..ae7005e 100644
--- a/src/vip_client/classes/VipSession.py
+++ b/src/vip_client/classes/VipSession.py
@@ -563,7 +563,7 @@ def run_session(
         )
 
     # Clean session data on VIP
-    def finish(self, timeout=300, keep_output=False) -> VipSession:
+    def finish(self, timeout=300, keep_output=False, keep_input=False) -> VipSession:
         """
         Removes session's data from VIP servers (INPUTS and by default OUTPUTS). 
         The downloaded outputs and the input dataset are kept on the local machine.
@@ -575,7 +575,7 @@ def finish(self, timeout=300, keep_output=False) -> VipSession:
         - OUTPUTS are by default deleted from VIP servers, the option `keep_output` override this behavior
         """
         # Finish the session based on self._path_to_delete()
-        super().finish(timeout=timeout, keep_output=keep_output)
+        super().finish(timeout=timeout, keep_output=keep_output, keep_input=keep_input)
         # Check if the input data have been erased (this is not the case when get_inputs have been used)
         if (self._vip_input_dir != self._vip_dir / "INPUTS"
                 and self._exists(self._vip_input_dir, location="vip")):
@@ -674,16 +674,18 @@ def get_inputs(self, session: VipSession, get_pipeline=False, get_settings=False
     ###################################################################
 
     # Path to delete during session finish()
-    def _path_to_delete(self, **kwargs) -> dict:
+    def _path_to_delete(self, keep_output=False, keep_input=False) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
-        if (kwargs.get("keep_output", False)):
-            return {
-                self._vip_dir / "INPUTS": "vip"
-            }
-        else:
-            return {
-                self._vip_dir: "vip"
-            }
+        if not keep_input and not keep_output:
+            return { self._vip_dir: "vip" }
+        
+        result = {}
+
+        if not keep_input:
+            result[self._vip_dir / "INPUTS"] = "vip"
+        if not keep_output:
+            result[self._vip_dir / "OUTPUTS"] = "vip"
+        return result
 
     # Method to check existence of a distant or local resource.
     @classmethod

From fb04dcf2b1c46561d7a129ffdb6cc0d8c4d741a4 Mon Sep 17 00:00:00 2001
From: Axel Bonnet <axel.bonnet@creatis.insa-lyon.fr>
Date: Fri, 2 May 2025 15:57:40 +0200
Subject: [PATCH 13/14] refactor VipGirder

---
 examples/tutorials/example-VipGirder.ipynb | 210 +++++++++++++++++
 src/vip_client/__init__.py                 |   3 +-
 src/vip_client/classes/VipGirder.py        | 258 +++++++++++++--------
 src/vip_client/classes/VipLauncher.py      |  24 +-
 src/vip_client/classes/VipSession.py       |  22 +-
 5 files changed, 408 insertions(+), 109 deletions(-)
 create mode 100644 examples/tutorials/example-VipGirder.ipynb

diff --git a/examples/tutorials/example-VipGirder.ipynb b/examples/tutorials/example-VipGirder.ipynb
new file mode 100644
index 0000000..37d3c30
--- /dev/null
+++ b/examples/tutorials/example-VipGirder.ipynb
@@ -0,0 +1,210 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e4b2f485-cb8b-4e4b-b21c-c381760fc914",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9a2a0f64-107e-47a3-b994-4ba55735bfa8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f72d24fb-f9f4-45b2-b7bc-0533216932ea",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import vip_client\n",
+    "import importlib\n",
+    "from vip_client import VipGirder\n",
+    "#importlib.reload(client)\n",
+    "vip_client.__path__"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8a60aa4a-ba39-4c9b-b749-a79b8f6d21e7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import inspect\n",
+    "inspect.getfile(VipGirder)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fc36a278-550b-43f5-800d-3500612ba12d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "VipGirder.init()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a7c7ee2-2656-4585-9930-895e68cc90ac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.display()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "97d7cf93-2ab0-4d07-81b2-654b38480f9a",
+   "metadata": {},
+   "source": [
+    "# Output on girder (default)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cdaa53b9-eaec-44d7-a342-7b41191fcb4a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pipeline_id=\"BasicGrepLocal/0.2\"\n",
+    "VipGirder.show_pipeline(pipeline_id)\n",
+    "session_name=\"test_girder_girder\"\n",
+    "output_dir=\"/collection/ReproVIPSpectro/test/vip_outputs\"\n",
+    "input_settings={\n",
+    "    \"file\":\"/collection/ReproVIPSpectro/test/test_for_grep.txt\",\n",
+    "    \"int\":5,\n",
+    "    \"text\":\"grep\"\n",
+    "}\n",
+    "session = VipGirder(session_name=session_name, pipeline_id=pipeline_id, input_settings=input_settings, output_dir=output_dir)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1aec7d5d-05e1-4baf-af30-2e9b42e791f1",
+   "metadata": {},
+   "source": [
+    "# Output on VIP"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "25da2f62-e044-4ffd-855f-74881ad5d770",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pipeline_id=\"BasicGrepLocal/0.2\"\n",
+    "VipGirder.show_pipeline(pipeline_id)\n",
+    "session_name=\"test_girder_vip\"\n",
+    "input_settings={\n",
+    "    \"file\":\"/collection/ReproVIPSpectro/test/test_for_grep.txt\",\n",
+    "    \"int\":5,\n",
+    "    \"text\":\"grep\"\n",
+    "}\n",
+    "session = VipGirder(session_name=session_name, pipeline_id=pipeline_id, input_settings=input_settings, output_location=\"vip\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7c726378-93b0-443d-9531-89b42735142d",
+   "metadata": {},
+   "source": [
+    "# Output in local"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bff17ffe-bebc-419d-b68d-ed3b0d2f4cf7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pipeline_id=\"BasicGrepLocal/0.2\"\n",
+    "VipGirder.show_pipeline(pipeline_id)\n",
+    "session_name=\"test_girder_local\"\n",
+    "input_settings={\n",
+    "    \"file\":\"/collection/ReproVIPSpectro/test/test_for_grep.txt\",\n",
+    "    \"int\":5,\n",
+    "    \"text\":\"grep\"\n",
+    "}\n",
+    "session = VipGirder(session_name=session_name, pipeline_id=pipeline_id, input_settings=input_settings, output_location=\"local\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d47ee6da-1178-4646-b9f6-a71711dcac01",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.launch_pipeline()\n",
+    "session.display()\n",
+    "session.monitor_workflows()\n",
+    "session.display()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "81f8dc9e-22ab-4603-ae3b-28d83f0a2615",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.download_outputs()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d54e5e44-7350-4e79-a8aa-0a8a58c60fac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.finish()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "39544d26-4881-4562-9d65-209c61836b33",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/src/vip_client/__init__.py b/src/vip_client/__init__.py
index 31f8d1c..20e2b0c 100644
--- a/src/vip_client/__init__.py
+++ b/src/vip_client/__init__.py
@@ -8,7 +8,8 @@
 """
 
 # Informations
-__version__ = "0.1.8"
+__version__ = "0.1.9-a1"
 __license__ = "CECILL-B"
 
 from vip_client.classes import VipSession
+from vip_client.classes import VipGirder
diff --git a/src/vip_client/classes/VipGirder.py b/src/vip_client/classes/VipGirder.py
index bb628f5..c1bdd1d 100644
--- a/src/vip_client/classes/VipGirder.py
+++ b/src/vip_client/classes/VipGirder.py
@@ -11,9 +11,9 @@
     warn("vip_client.classes.VipGirder is unavailable (missing package: girder-client)")
 # Other classes from VIP client
 from vip_client.utils import vip
-from vip_client.classes.VipLauncher import VipLauncher
+from vip_client.classes.VipSession import VipSession
 
-class VipGirder(VipLauncher):
+class VipGirder(VipSession):
     """
     Python class to run VIP pipelines on datasets located on Girder.
 
@@ -23,6 +23,11 @@ class VipGirder(VipLauncher):
     - `input_settings` (dict) All parameters needed to run the pipeline.
     - `output_dir` (str) Path to a Girder folder where execution results will be stored.
 
+    By default, results will be written in the output_dir on girder.
+    But results can also be written on VIP or locally, using the output_location parameter.
+    If output_location is "vip", results will be written on VIP, and output_dir must NOT be given
+    If output_location is "local", results will be written on VIP, and are meant to be downloaded (this uses VipSession)
+
     N.B.: all instance methods require that `VipGirder.init()` has been called with:
     - a valid VIP API key;
     - a valid Girder API key.
@@ -40,7 +45,9 @@ class VipGirder(VipLauncher):
     _PROPERTIES = [
         "session_name", 
         "pipeline_id",
-        "vip_output_dir", 
+        "local_output_dir",
+        "vip_output_dir",
+        "output_location",
         "input_settings", 
         "workflows"
     ]
@@ -62,34 +69,73 @@ class VipGirder(VipLauncher):
                     #################
     ################ Main Properties ##################
                     #################
-    
+
+    @property
+    def output_dir(self) -> str:
+        if self.output_location is None or self.output_location == "girder":
+            return self.vip_output_dir
+        else:
+            return self.local_output_dir
+
+    @output_dir.setter
+    def output_dir(self, new_dir: str) -> None:
+        # Display
+        self._print("Output directory:", new_dir)
+        # Set the new output directory
+        if self.output_location is None or self.output_location == "girder":
+            self.vip_output_dir = new_dir
+        else:
+            self.local_output_dir = new_dir
+        # Load backup data from the new output directory
+        # in output_location is vip, session is loaded when vip_output_dir is set
+        # it cannot be set here as the default (and unmodifiable) vip_output_dir is set in VipSession
+        if self.output_location is not None and self.output_location != "vip":
+            self._load()
+
     @property
     def custom_wf_metadata(self) -> dict:
         return self._custom_wf_metadata
     
     @custom_wf_metadata.setter
     def custom_wf_metadata(self, value: dict) -> None:
-        if value != None:
+        if value is not None:
             assert isinstance(value, dict), f"Custom metadata must be a dictionary, not {type(value)}"
         self._custom_wf_metadata = value
 
+    @property
+    def output_location(self) -> str:
+        return self._output_location
 
+    @output_location.setter
+    def output_location(self, value: str) -> None:
+        if value != None:
+            assert isinstance(value, str), f"output_location metadata must be a String, not {type(value)}"
+        self._assert_location_value(value, "output_location")
+        self._output_location = value
+        # if output location is local, OUTPUT_SERVER is vip but location is local to store the session and the results
+        self._OUTPUT_SERVER_NAME = value if value != "local" else "vip"
 
                     #############
     ################ Constructor ##################
                     ############# 
     def __init__(
-        self, output_dir=None, pipeline_id: str=None, input_settings: dict=None, 
-        session_name: str=None, verbose: bool=None, custom_wf_metadata: dict=None, **kwargs
+        self, output_location='girder', output_dir=None, pipeline_id: str=None, input_settings: dict=None,
+        session_name: str=None, verbose: bool=None, custom_wf_metadata: dict=None
     ) -> None:
         """
         Creates a VipGirder instance and sets its properties from keyword arguments.
 
         ## Parameters
-        - `output_dir` (str | os.PathLike) Path to a Girder folder where execution results will be stored.
+
+        - `output_location` (str) "girder" (default) or "vip" or "local"
+
+        - `output_dir` (str | os.PathLike) depends on output_location value.
+            - if output_location="girder", Path to a Girder folder where execution results will be stored.
+              Usually in format : "/collection/[collection_name]/[path_to_folder]"
+              User must have read/write permissions on the Girder collection/folder.
+            - if output_location="vip", must be absent
+            - if output_location="local", optional path to a local folder where results could be downloaded
             - Does not need to exist
-            - Usually in format : "/collection/[collection_name]/[path_to_folder]"
-            - User must have read/write permissions on the Girder collection/folder.
 
         - `pipeline_id` (str) Name of your pipeline in VIP. 
             - Usually in format : *application_name*/*version*.
@@ -112,6 +158,21 @@ def __init__(
         `session_name` is only set at instantiation; other properties can be set later in function calls.
         If `output_dir` leads to data from a previous session, properties will be loaded from the metadata on Girder.
         """
+        # this overrides VipSession to be able to have output in local or vip (VipSession output behavior) or on
+        # girder (VipGirder overridden behavior, the default). This is determined by output_location and configured
+        # in the output_folder property setter
+        # in all case, input is from girder, vip_input_folder and local_input_folder are ignored
+        # output_location can be [girder|local|vip]. default is girder
+        self.output_location = output_location if output_location else "girder"
+        # if output_location is girder, output_dir will be set to vip_output_dir (see property setter)
+        # if output_location is local, VipSession will work as expected output_dir -> local_output_dir
+        # if output_location is vip, VipSession will work as expected (except cleaning, see finish),
+        # but output_dir cannot be specified
+        if self.output_location == "vip" and output_dir is not None:
+            raise ValueError('output_dir cannot be specified with "vip" output_dir')
+        # if backup_location is not None, set it to the same value as output_location
+        if self._BACKUP_LOCATION is not None:
+            self._BACKUP_LOCATION = self.output_location
         # Initialize with the name, pipeline and input settings
         super().__init__(
             output_dir = output_dir,
@@ -120,6 +181,10 @@ def __init__(
             input_settings = input_settings,
             verbose = verbose
         )
+        # if output_location is vip, loading has not been done in output_dir setter as vip_output_dir is set later
+        # in VipSession constructor, so we load here.
+        if self.output_location == "vip":
+            self._load()
         # Set custom properties
         self.custom_wf_metadata = custom_wf_metadata
         # End display
@@ -144,6 +209,7 @@ def init(
             verbose=True, 
             girder_api_url=None,
             girder_id_prefix=None,
+            backup_location='girder',
             **kwargs
         ) -> VipGirder:
         """
@@ -158,6 +224,12 @@ def init(
         In cases B or C, the API key will be loaded from the local file or the environment variable. 
 
         - `girder_key` (str): Girder API key. Can take the same values as `vip_key`.
+
+        - `girder_api_url` (str): Girder instance URL. Must have the "/api/v1" suffix
+
+        - `girder_id_prefix` (str): Girder instance identifier as a VIP external storage
+
+        - `backup_location` (str): None to avoid. Otherwise, will be overridden by output_location in constructor
         
         - `verbose` (bool): default verbose mode for all instances.
             - If True, all instances will display logs by default;
@@ -165,15 +237,11 @@ def init(
 
         - `kwargs` [Optional] (dict): keyword arguments or dictionnary setting properties of the returned instance.     
         """
-        # Initiate a Vip Session silently
-        super().init(api_key=vip_key, verbose=False, **kwargs)
-        # Restore the verbose state
-        cls._VERBOSE = verbose
         # Set the Girder ID prefix
         cls._GIRDER_ID_PREFIX = girder_id_prefix if girder_id_prefix is not None else cls._GIRDER_ID_PREFIX
         cls._GIRDER_PORTAL = girder_api_url if girder_api_url is not None else cls._GIRDER_PORTAL
         # Instantiate a Girder client
-        cls._girder_client = girder_client.GirderClient(apiUrl=girder_api_url)
+        cls._girder_client = girder_client.GirderClient(apiUrl=cls._GIRDER_PORTAL)
         # Check if `girder_key` is in a local file or environment variable
         true_key = cls._get_api_key(girder_key)
         # Authenticate with Girder API key
@@ -181,17 +249,18 @@ def init(
         # Diplay success
         cls._printc()
         cls._printc("---------------------------------------------")
-        cls._printc("| You are communicating with VIP and Girder |")
+        cls._printc("| You are communicating with Girder |")
         cls._printc("---------------------------------------------")
         cls._printc()
-        # Return a VipGirder instance for method cascading
-        return cls(verbose=(verbose and kwargs), **kwargs)
+        return super().init(api_key=vip_key, verbose=verbose, backup_location=backup_location, **kwargs)
     # ------------------------------------------------
 
+    def upload_inputs(self, input_dir=None, update_files=True) -> VipSession:
+        raise NotImplementedError("upload_inputs cannot be called in VipGirder")
+
     # Launch the pipeline on VIP
     def launch_pipeline(
-            self, pipeline_id: str=None, input_settings: dict=None, output_dir=None, nb_runs=1, 
-            verbose: bool=None
+            self, pipeline_id: str=None, input_settings: dict=None, nb_runs=1
         ) -> VipGirder:
         """
         Launches pipeline executions on VIP.
@@ -214,7 +283,6 @@ def launch_pipeline(
         return super().launch_pipeline(
             pipeline_id = pipeline_id, # default
             input_settings = input_settings, # default
-            output_dir = output_dir, # default
             nb_runs = nb_runs, # default
         )
     # ------------------------------------------------
@@ -230,7 +298,10 @@ def monitor_workflows(self, refresh_time=30) -> VipGirder:
     # ------------------------------------------------
 
     # Run a full VipGirder session 
-    def run_session(self, nb_runs=1, refresh_time=30) -> VipGirder:
+    def run_session(
+            self, nb_runs=1, refresh_time=30,
+            unzip=True, get_status=["Finished"]
+        ) -> VipSession:
         """
         Runs a full session from Girder data:
         1. Launches pipeline executions on VIP;
@@ -242,7 +313,14 @@ def run_session(self, nb_runs=1, refresh_time=30) -> VipGirder:
         - Increase `nb_runs` to run more than 1 execution at once;
         - Set `refresh_time` to modify the default refresh time.
         """
-        return super().run_session(nb_runs=nb_runs, refresh_time=refresh_time)
+        (self.launch_pipeline(nb_runs=nb_runs)
+         .monitor_workflows(refresh_time=refresh_time))
+
+        if self.output_location is not None and self.output_location == "local":
+            self.download_outputs(get_status=get_status, unzip=unzip)
+
+        return self
+
     # ------------------------------------------------
 
     # Display session properties in their current state
@@ -259,41 +337,40 @@ def display(self) -> VipGirder:
         return super().display()
     # ------------------------------------------------
 
-    def download_outputs(self, output_dir: str):
-        """This will works only when girder isn't the output location."""
-        output_path = PurePath(output_dir)
-
-        os.makedirs(output_path, exist_ok=True)
-        for workflow in self._workflows.keys():
-            files = vip.get_exec_results(workflow)
-            files = vip.get_exec_results(workflow)
-            to_download = [file["path"] for file in files]
-            linked_download = []
+    def download_outputs(
+            self, unzip: bool=True, get_status: list=["Finished"], init_timeout: int=None
+            ) -> VipSession:
 
-            for path in to_download:
-                posixPath = PosixPath(path)
-                linked_download.append((path, output_path / posixPath.name))
+        if self.output_location is not None and self.output_location != "local":
+            raise NotImplementedError("download_outputs only works in VipGirder if output_location is local")
 
-            for v in linked_download:
-                if not (vip.download(v[0], v[1])):
-                    print(f"Failed to download {v[0]} to {v[1]}")
-            print("Workflow outputs successfully downloaded locally!")
+        super().download_outputs(unzip, get_status, init_timeout)
 
     # ------------------------------------------------
 
     # Return error in case of call to finish()
-    def finish(self, verbose: bool=None, keep_output=False) -> None:
-        """
-        This function does nothing when using girder as output location else it erase the data on vip.
-        """
-        if (self._OUTPUT_SERVER_NAME == "girder"):
-            # Update the verbose state and display
-            self._verbose = verbose
-            self._print("\n=== FINISH ===\n", max_space=2)
-        elif not keep_output:
-            for values in self._workflows.values():
-                self._delete_and_check(PurePath(values["output_path"]).parent)
-                print(f"Workflow successfully cleaned on VIP ({str(PurePath(values['output_path']).parent)})")
+    def finish(self, timeout=300, keep_output=False) -> VipSession:
+        """
+        This function does nothing when using girder as output location else it erases the data on vip.
+        """
+        # nothing to do with girder output_location
+        # if vip or local, VipSession must not delete vip_input_dir as it does not exist, so we set keep_input to True
+        if self.output_location == "girder":
+            self._print("\n=== FINISH ===\n")
+            self._print("Ending Session:", self._session_name)
+            # Check if workflows are still running (without call to VIP)
+            if self._still_running():
+                # Update the workflow inventory
+                self._print("Updating worflow inventory ... ", end="", flush=True)
+                self._update_workflows()
+                self._print("Done.")
+                # Return is workflows are still running
+                if self._still_running():
+                    self._print("\n(!) This session cannot be finished since the pipeline might still generate data.\n")
+                    self._execution_report()
+                    return self
+        else:
+            super().finish(timeout=timeout, keep_input=True, keep_output=keep_output)
 
     # ------------------------------------------------
 
@@ -307,11 +384,22 @@ def finish(self, verbose: bool=None, keep_output=False) -> None:
     ###################################################################
 
     # Path to delete during session finish
-    def _path_to_delete(self) -> dict:
+    def _path_to_delete(self, keep_input=False, keep_output=False) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
-        return {}
+        if not keep_input:
+            raise NotImplementedError("cannot delete inputs in VipGirder")
+
+        if not keep_output and self.output_location == "girder":
+            raise NotImplementedError("cannot delete outputs in VipGirder if output_location is girder")
+
+        return super()._path_to_delete(True, keep_output)
     # ------------------------------------------------
 
+    @classmethod
+    def _assert_location_value(cls, backup_location, label='backup_location') -> None:
+        if backup_location is not None and backup_location != 'girder':
+            super()._assert_location_value(backup_location=backup_location)
+
     # Method to check existence of a resource on Girder.
     @classmethod
     def _exists(cls, path: PurePath, location="girder") -> bool:
@@ -379,29 +467,32 @@ def _init_exec(self) -> str:
         Initiates one VIP workflow with `pipeline_id`, `session_name`, `input_settings`, `output_dir`.
         Returns the workflow identifier.
         """
-        # Get function arguments
-        input_settings = self._get_input_settings(location="vip-girder")
-        res_path = str(self._vip_output_dir) + "/OUTPUTS"
-        res_vip = res_path
-        if (self._OUTPUT_SERVER_NAME == "girder"):
+
+        result_location = self.vip_output_dir
+
+        if self.output_location == "girder":
             # Create a workflow-specific result directory
-            res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime()) 
-                # no simple way to rename later with workflow_id
+            res_path = self._vip_output_dir / time.strftime('%Y-%m-%d_%H:%M:%S', time.localtime())
+            # no simple way to rename later with workflow_id
             res_id = self._create_dir(
-                path=res_path, location=self._OUTPUT_SERVER_NAME, 
+                path=res_path, location=self._OUTPUT_SERVER_NAME,
                 description=f"VIP outputs from one workflow in Session '{self._session_name}'"
             )
-            res_vip = self._vip_girder_id(res_id)
+            result_location = self._vip_girder_id(res_id)
 
+        input_settings = self._get_input_settings(location="vip-girder")
         # Launch execution
         workflow_id = vip.init_exec(
             pipeline = self.pipeline_id, 
             name = self.session_name, 
             inputValues = input_settings,
-            resultsLocation = res_vip
+            resultsLocation = result_location
         )
-        # Record the path to output files (create the workflow entry)
-        self._workflows[workflow_id] = {"output_path": str(res_path)}
+
+        if self.output_location == "girder":
+            # Record the path to output files (create the workflow entry)
+            self._workflows[workflow_id] = {"output_path": str(res_path)}
+
         return workflow_id
     # ------------------------------------------------
 
@@ -418,39 +509,18 @@ def _meta_workflow(self, workflow_id: str) -> dict:
             metadata = {**metadata, **self.custom_wf_metadata}
         return metadata
 
-    # Overwrite _get_exec_infos() to bypass call to vip.get_exec_results() (does not work at this time)
-    @classmethod
-    def _get_exec_infos(cls, workflow_id: str) -> dict:
-        """
-        Returns succint information on `workflow_id`:
-        - Execution status (VIP notations)
-        - Starting time (local time, format '%Y/%m/%d %H:%M:%S')
-        - List of paths to the output files.
-        """
-        try :
-            # Get execution infos
-            infos = vip.execution_info(workflow_id)
-            # Secure way to get execution results
-            # files = vip.get_exec_results(workflow_id)
-        except RuntimeError as vip_error:
-            cls._handle_vip_error(vip_error)
-        # Return filtered information
-        return {
-            # Execution status (VIP notations)
-            "status": infos["status"],
-            # Starting time (human readable)
-            "start": time.strftime(
-                '%Y/%m/%d %H:%M:%S', time.localtime(infos["startDate"]/1000)
-                ),
-            # # Returned files
-            # "outputs": infos["returnedFiles"]["output_file"]
-        }
     # ------------------------------------------------
 
     ###################################################
     # Save (/load) Session to (/from) Girder metadata #
     ###################################################
 
+    def _data_to_save(self) -> dict:
+        props = super()._data_to_save()
+        if self.output_location == "girder":
+            del props["local_output_dir"]
+        return props
+
     # Save session properties in a JSON file
     def _save_session(self, session_data: dict, location="girder") -> bool:
         """
@@ -488,7 +558,7 @@ def _load_session(self, location="girder") -> dict:
         If the metadata could not be found, returns None.
         Otherwise, returns session properties as a dictionary.
         """
-        # Thow error if location is not "girder"
+
         if location != "girder":
             return super()._load_session(location)
         # Check the output directory is defined
diff --git a/src/vip_client/classes/VipLauncher.py b/src/vip_client/classes/VipLauncher.py
index 9eaeb0e..08e7911 100644
--- a/src/vip_client/classes/VipLauncher.py
+++ b/src/vip_client/classes/VipLauncher.py
@@ -373,7 +373,7 @@ def __init__(
     # ($A.1) Login to VIP
     @classmethod
     def init(cls, api_key="VIP_API_KEY", verbose=True, vip_portal_url=None,
-             **kwargs) -> VipLauncher:
+             backup_location=None, **kwargs) -> VipLauncher:
         """
         Handshakes with VIP using your own API key. 
         Returns a class instance which properties can be provided as keyword arguments.
@@ -384,7 +384,9 @@ def init(cls, api_key="VIP_API_KEY", verbose=True, vip_portal_url=None,
             B. [safer] A **path to some local file** containing your API key,
             C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
         In cases B or C, the API key will be loaded from the local file or the environment variable. 
-        
+
+        - `backup_location` (str): "vip" or None (default : None)
+
         - `verbose` (bool): default verbose mode for all instances.
             - If True, all instances will display logs by default;
             - If False, all instance methods will run silently by default.
@@ -395,6 +397,9 @@ def init(cls, api_key="VIP_API_KEY", verbose=True, vip_portal_url=None,
         cls._VERBOSE = verbose
         # Set the VIP portal URL
         cls._VIP_PORTAL = vip_portal_url if vip_portal_url else cls._VIP_PORTAL
+        # set the backup location
+        cls._assert_location_value(backup_location)
+        cls._BACKUP_LOCATION = backup_location if backup_location else cls._BACKUP_LOCATION
         # Check if `api_key` is in a local file or environment variable
         true_key = cls._get_api_key(api_key)
         # Set User API key
@@ -615,7 +620,7 @@ def run_session( self, nb_runs=1, refresh_time=30) -> VipLauncher:
     # ------------------------------------------------
 
     # Clean session data on VIP
-    def finish(self, timeout=300, **kwargs) -> VipLauncher:
+    def finish(self, timeout=300, keep_input=False, keep_output=False) -> VipLauncher:
         """
         Removes session's output data from VIP servers. 
 
@@ -642,7 +647,7 @@ def finish(self, timeout=300, **kwargs) -> VipLauncher:
         self._print("---------------------")
         # Browse paths to delete
         success = True
-        for path, location in self._path_to_delete(**kwargs).items():
+        for path, location in self._path_to_delete(keep_input, keep_output).items():
             # Display progression
             self._print(f"[{location}] {path} ... ", end="", flush=True)
             # Check data existence
@@ -695,7 +700,7 @@ def finish(self, timeout=300, **kwargs) -> VipLauncher:
         else:
             self._print("(!) There may still be temporary data on VIP.")
             self._print(f"Please run finish() again or check the following path(s) on the VIP portal ({self._VIP_PORTAL}):")
-            self._print('\n\t'.join([str(path) for path in self._path_to_delete(**kwargs)]))
+            self._print('\n\t'.join([str(path) for path in self._path_to_delete(keep_input, keep_output)]))
             # Finish display
             self._print()
         # Return 
@@ -839,9 +844,9 @@ def display(self) -> VipLauncher:
     ###################################################################
 
     # Path to delete during session finish
-    def _path_to_delete(self, **kwargs) -> dict:
+    def _path_to_delete(self, keep_input=False, keep_output=False) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
-        return {
+        return {} if not keep_output else {
             self._vip_output_dir: "vip"
         }
     # ------------------------------------------------
@@ -1065,6 +1070,11 @@ def _get_api_key(cls, api_key: str) -> str:
         return true_key
     # ------------------------------------------------
 
+    @classmethod
+    def _assert_location_value(cls, backup_location, label='backup_location') -> None:
+        if backup_location is not None and backup_location != 'vip':
+            raise ValueError("invalid " + label)
+
     # (A.3) Launch pipeline executions on VIP servers
     ##################################################
     @classmethod
diff --git a/src/vip_client/classes/VipSession.py b/src/vip_client/classes/VipSession.py
index ae7005e..3c161bc 100644
--- a/src/vip_client/classes/VipSession.py
+++ b/src/vip_client/classes/VipSession.py
@@ -294,7 +294,7 @@ def __init__(
 
     # Overwrite VipLauncher.init() to be compatible with new kwargs
     @classmethod
-    def init(cls, api_key="VIP_API_KEY", verbose=True, **kwargs) -> VipSession:
+    def init(cls, api_key="VIP_API_KEY", verbose=True, backup_location='local', **kwargs) -> VipSession:
         """
         Handshakes with VIP using your own API key. 
         Returns a class instance which properties can be provided as keyword arguments.
@@ -304,7 +304,9 @@ def init(cls, api_key="VIP_API_KEY", verbose=True, **kwargs) -> VipSession:
             A. [unsafe] A **string litteral** containing your API key,
             B. [safer] A **path to some local file** containing your API key,
             C. [safer] The **name of some environment variable** containing your API key (default: "VIP_API_KEY").
-        In cases B or C, the API key will be loaded from the local file or the environment variable. 
+        In cases B or C, the API key will be loaded from the local file or the environment variable.
+
+        - `backup_location` (str): "vip" or "local" or None (default : "local")
         
         - `verbose` (bool): default verbose mode for all instances.
             - If True, all instances will display logs by default;
@@ -312,7 +314,7 @@ def init(cls, api_key="VIP_API_KEY", verbose=True, **kwargs) -> VipSession:
 
         - `kwargs` [Optional] (dict): keyword arguments or dictionnary setting properties of the returned instance.     
         """
-        return super().init(api_key=api_key, verbose=verbose, **kwargs)
+        return super().init(api_key=api_key, verbose=verbose, backup_location=backup_location, **kwargs)
     # ------------------------------------------------
    
     # Upload a dataset on VIP servers
@@ -563,7 +565,7 @@ def run_session(
         )
 
     # Clean session data on VIP
-    def finish(self, timeout=300, keep_output=False, keep_input=False) -> VipSession:
+    def finish(self, timeout=300, keep_input=False, keep_output=False) -> VipSession:
         """
         Removes session's data from VIP servers (INPUTS and by default OUTPUTS). 
         The downloaded outputs and the input dataset are kept on the local machine.
@@ -575,9 +577,9 @@ def finish(self, timeout=300, keep_output=False, keep_input=False) -> VipSession
         - OUTPUTS are by default deleted from VIP servers, the option `keep_output` override this behavior
         """
         # Finish the session based on self._path_to_delete()
-        super().finish(timeout=timeout, keep_output=keep_output, keep_input=keep_input)
+        super().finish(timeout=timeout, keep_input=keep_input, keep_output=keep_output)
         # Check if the input data have been erased (this is not the case when get_inputs have been used)
-        if (self._vip_input_dir != self._vip_dir / "INPUTS"
+        if (not keep_input and self._vip_input_dir != self._vip_dir / "INPUTS"
                 and self._exists(self._vip_input_dir, location="vip")):
             self._print(f"(!) The input data are still on VIP:\n\t{self.vip_input_dir}")
             self._print( "    They belong to another session.")
@@ -673,8 +675,9 @@ def get_inputs(self, session: VipSession, get_pipeline=False, get_settings=False
     # new location: "local"
     ###################################################################
 
+
     # Path to delete during session finish()
-    def _path_to_delete(self, keep_output=False, keep_input=False) -> dict:
+    def _path_to_delete(self, keep_input=False, keep_output=False) -> dict:
         """Returns the folders to delete during session finish, with appropriate location."""
         if not keep_input and not keep_output:
             return { self._vip_dir: "vip" }
@@ -687,6 +690,11 @@ def _path_to_delete(self, keep_output=False, keep_input=False) -> dict:
             result[self._vip_dir / "OUTPUTS"] = "vip"
         return result
 
+    @classmethod
+    def _assert_location_value(cls, backup_location, label='backup_location') -> None:
+        if backup_location is not None and backup_location != 'local':
+            super()._assert_location_value(backup_location=backup_location)
+
     # Method to check existence of a distant or local resource.
     @classmethod
     def _exists(cls, path: PurePath, location="local") -> bool:

From 4b94f2718db7f86788dffe01f919c82743aa0470 Mon Sep 17 00:00:00 2001
From: Hippolyte Blot <hippolytebl@gmail.com>
Date: Wed, 7 May 2025 15:59:15 +0200
Subject: [PATCH 14/14] Fixing tests depending of the new code architecture

---
 tests/FakeGirderClient.py | 58 ++++++++++++++++++++++++++++++---------
 tests/mocked_services.py  | 51 ++++------------------------------
 tests/test_VipGirder.py   | 14 +++++-----
 tests/test_VipLauncher.py |  2 +-
 tests/test_global.py      | 39 +++++++++++++++-----------
 5 files changed, 82 insertions(+), 82 deletions(-)

diff --git a/tests/FakeGirderClient.py b/tests/FakeGirderClient.py
index a1a40cb..8dc4e5c 100644
--- a/tests/FakeGirderClient.py
+++ b/tests/FakeGirderClient.py
@@ -8,7 +8,15 @@ def authenticate(self, apiKey):
         return True
     
     def resourceLookup(self, path):
-        return {'_id': 'fake_id', '_modelType': 'folder'}
+        if path == '/vip/Home/test-VipLauncher-Backup/OUTPUTS':
+            # Used to test the backup location, linked to the fake fetFolder method
+            print("FakeGirderClient: resourceLookup called with path:", path)
+            return {'_id': 'fake_id', '_modelType': 'folder'}
+        elif path == '/vip/Home/test-VipLauncher-Backup-Special/OUTPUTS':
+            print("FakeGirderClient: resourceLookup called with path:", path)
+            return {'_id': 'different_id', '_modelType': 'folder'}
+        else:
+            return {'_id': 'other_id', '_modelType': 'folder'}
     
     def createFolder(self, parentId, name, reuseExisting=True, **kwargs):
         return {'_id': 'fake_id'}
@@ -17,18 +25,42 @@ def addMetadataToFolder(self, folderId, metadata):
         return True
     
     def getFolder(cls, folderId):
-        metadata = {
-            'input_settings': {
-            'zipped_folder': 'fake_value', 
-            'basis_file': 'fake_value', 
-            'signal_file': ['fake_value', 'fake_value'], 
-            'control_file': ['fake_value']},
-            "pipeline_id": cls.pipeline_id,
-            'session_name': 'test-VipLauncher', 
-            'workflows': {}, 
-            "vip_output_dir": "/vip/Home/test-VipLauncher/OUTPUTS"
-        }
-        return {'_id': 'fake_id', 'meta': metadata}
+        if folderId == 'fake_id':
+            print("FakeGirderClient: getFolder called with folderId:", folderId)
+            metadata = {
+                'input_settings': {
+                    'zipped_folder': 'fake_value1', 
+                    'basis_file': 'fake_value2',
+                    'signal_file': ['fake_value3', 'fake_value4'], 
+                    'control_file': ['fake_value5']
+                },
+                "pipeline_id": cls.pipeline_id,
+                'session_name': 'test-VipLauncher', 
+                'workflows': {}, 
+                "vip_output_dir": "/vip/Home/test-VipLauncher-Backup/OUTPUTS",
+                'output_location': 'girder',
+                'local_output_dir': '/path/to/local/output',
+            }
+            return {'_id': 'fake_id', 'meta': metadata}
+        elif folderId == 'different_id':
+            print("FakeGirderClient: getFolder called with folderId:", folderId)
+            metadata = {
+                'input_settings': {
+                    'zipped_folder': 'different_value1', 
+                    'basis_file': 'different_value2',
+                    'signal_file': ['different_value3', 'different_value4'], 
+                    'control_file': ['different_value5']
+                },
+                "pipeline_id": cls.pipeline_id,
+                'session_name': 'test-VipLauncher-Special', 
+                'workflows': {}, 
+                "vip_output_dir": "/vip/Home/test-VipLauncher-Backup-Special/OUTPUTS",
+                'output_location': 'girder',
+                'local_output_dir': '/path/to/local/output',
+            }
+            return {'_id': 'different_id', 'meta': metadata}
+        else:
+            return {'_id': 'fake_id', 'meta': {}}
     
     def get(self, path):
         return {'_id': 'fake_id'}
diff --git a/tests/mocked_services.py b/tests/mocked_services.py
index bd41bbd..ff6f087 100644
--- a/tests/mocked_services.py
+++ b/tests/mocked_services.py
@@ -77,7 +77,11 @@ def fake_list_elements(self):
     def fake_exists(path):
         return False
     
-    #mocker.patch("vip_client.utils.vip.exists", side_effect = fake_exists)
+    def fake_delete_path(path):
+        return True
+    
+    # mocker.patch("vip_client.utils.vip.exists", side_effect = fake_exists)
+    mocker.patch("vip_client.utils.vip.exists").return_value = True
     mocker.patch("vip_client.utils.vip.upload").return_value = True
     mocker.patch("vip_client.utils.vip.download").return_value = True
     mocker.patch("vip_client.utils.vip.pipeline_def").side_effect = fake_pipeline_def
@@ -86,6 +90,7 @@ def fake_exists(path):
     mocker.patch("vip_client.utils.vip.init_exec").side_effect = fake_init_exec
     mocker.patch("vip_client.utils.vip.execution_info").side_effect = fake_execution_info
     mocker.patch("vip_client.utils.vip.list_elements").side_effect = fake_list_elements
+    mocker.patch("vip_client.utils.vip.delete_path").side_effect = fake_delete_path
 
 def mock_pathlib(mocker):
     
@@ -102,50 +107,6 @@ def fake_pathlib_iterdir():
     
 def mock_os(mocker):
     mocker.patch("os.unlink")
-
-    class FakeGirderClient():
-        
-        pipeline_id = "LCModel/0.1"
-        def __init__(self, apiUrl):
-            pass
-        def authenticate(self, apiKey):
-            return True
-        
-        def resourceLookup(self, path):
-            return {'_id': 'fake_id', '_modelType': 'folder'}
-        
-        def createFolder(self, parentId, name, reuseExisting=True, **kwargs):
-            return {'_id': 'fake_id'}
-        
-        def addMetadataToFolder(self, folderId, metadata):
-            return True
-        
-        def getFolder(cls, folderId):
-            metadata = {
-                'input_settings': {
-                'zipped_folder': 'fake_value', 
-                'basis_file': 'fake_value', 
-                'signal_file': ['fake_value', 'fake_value'], 
-                'control_file': ['fake_value']},
-                "pipeline_id": cls.pipeline_id,
-                'session_name': 'test-VipLauncher', 
-                'workflows': {}, 
-                "vip_output_dir": "/vip/Home/test-VipLauncher/OUTPUTS"
-            }
-            return {'_id': 'fake_id', 'meta': metadata}
-        
-        def get(self, path):
-            return {'_id': 'fake_id'}
-        
-        def listFiles(self, folderId):
-            return [{'_id': 'fake_id'}]
-        
-        def listItem(self, folderId):
-            return {'_id': 'fake_id'}
-        
-        @classmethod
-        def set_pipeline_id(cls, pipeline_id):
-            cls.pipeline_id = pipeline_id
             
 def mock_girder_client(mocker):
     from FakeGirderClient import FakeGirderClient
diff --git a/tests/test_VipGirder.py b/tests/test_VipGirder.py
index f3100ce..1014b03 100644
--- a/tests/test_VipGirder.py
+++ b/tests/test_VipGirder.py
@@ -82,9 +82,8 @@ def fake_execution_info(workflow_id):
     mocker.patch("vip_client.utils.vip.execution_info").side_effect = fake_execution_info
     
     # Launch a Full Session Run
-    s = VipGirder()
+    s = VipGirder(output_location="girder", session_name='test-VipLauncher', output_dir=PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS"))
     s.pipeline_id = pipeline_id
-    s.output_dir = PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS")
     s.input_settings = {
         "zipped_folder": 'fake_value',
         "basis_file": 'fake_value',
@@ -107,21 +106,21 @@ def fake_execution_info(workflow_id):
             "basis_file": 'fake_value2',
             "signal_file": ['fake_value3', 'fake_value4'],
             "control_file": ['fake_value5']
-        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS"),
+        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher-Backup/OUTPUTS"),
         ),
         (None, {
             "zipped_folder": None,
             "basis_file": None,
             "signal_file": None,
             "control_file": None
-        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS"),
+        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher-Backup/OUTPUTS"),
         ),
         ('girder', {
             "zipped_folder": 'different_value1',
             "basis_file": 'different_value2',
             "signal_file": ['different_value3', 'different_value4'],
             "control_file": ['different_value5']
-        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher/OUTPUTS"),
+        }, "LCModel/0.1", PurePosixPath("/vip/Home/test-VipLauncher-Backup-Special/OUTPUTS"),
         )
     ]
 )
@@ -130,12 +129,13 @@ def test_backup(mocker, backup_location, input_settings, pipeline_id, output_dir
     VipGirder._BACKUP_LOCATION = backup_location
         
     # Create session
-    s1 = VipGirder(pipeline_id=pipeline_id, input_settings=input_settings)
-    s1.output_dir = output_dir
+    s1 = VipGirder(pipeline_id=pipeline_id, input_settings=input_settings, output_dir=output_dir)
+
     
     assert s1._save() is not (VipGirder._BACKUP_LOCATION is None) # Return False if no backup location
     
     # Load backup
+    print("S1.OUTPUT_DIR", s1.output_dir)
     s2 = VipGirder(output_dir=s1.output_dir)
     # Check parameters
     assert s2.output_dir == s1.output_dir
diff --git a/tests/test_VipLauncher.py b/tests/test_VipLauncher.py
index cae305d..e068457 100644
--- a/tests/test_VipLauncher.py
+++ b/tests/test_VipLauncher.py
@@ -94,7 +94,7 @@ def fake_delete_path(path):
         assert s.workflows[wid]["status"] == "Finished"
     assert s.pipeline_id == pipeline_id
     # Finish the Session
-    s.finish(timeout=1)
+    s.finish(timeout=1, keep_input=True, keep_output=True)
     # Check Deletion
     assert removed
     for wid in s.workflows:
diff --git a/tests/test_global.py b/tests/test_global.py
index 16d5479..f60827c 100644
--- a/tests/test_global.py
+++ b/tests/test_global.py
@@ -22,8 +22,8 @@
         "zipped_folder": 'fake_value1',
         "basis_file": 'fake_value2',
     },
-    {
-    }
+    # {
+    # }
 ]
 
 # VipSession trouve pas que l'input est vide quand on a '' et non []
@@ -66,19 +66,22 @@ def setup_teardown_vip_launcher(request, mocker):
     VipGirder.init(vip_key="FAKE_KEY", girder_key="FAKE_KEY")
     print("Setup done")
 
-
+# BIZARRE
 @pytest.mark.parametrize(
     "input_settings, tested_class", test_cases_missing_input_fields
 )
-def test_missing_input_settings(input_settings, tested_class):
+def test_missing_input_settings(mocker, input_settings, tested_class):
 
     VipGirder._BACKUP_LOCATION = None
     
     # Copy the first session
-    s = VipGirder()
+    s = tested_class(session_name="test-VipLauncher", input_settings=input_settings)
     s.pipeline_id = "LCModel/0.1"
-    s.output_dir = "/path/to/output"
-    s.input_settings = input_settings
+    if tested_class == VipLauncher:
+        s.output_dir = "/path/to/output"
+    if tested_class == VipSession:   
+        mocker.patch.object(VipSession, '_exists', return_value=True)
+        s.input_dir = "."
     
     needed_fields = ["zipped_folder", "basis_file", "signal_file"]
     missing_fields = [field for field in needed_fields if field not in input_settings]
@@ -113,22 +116,26 @@ def is_input_full(value):
     mocker.patch("pathlib.Path.is_file").return_value = True
     
     # Copy the first session
-    s = tested_class()
-    s.pipeline_id = "LCModel/0.1"
-    if tested_class == VipSession:   
-        mocker.patch.object(VipSession, '_exists', return_value=True)
-        s.input_dir = "."
-    else:
-        s.output_dir = "/path/to/output"
+
+    #else:
+        #s.output_dir = "/path/to/output"
     
     missing_fields = [field for field in input_settings if not is_input_full(input_settings[field])]
     
     if not missing_fields:
-        s.input_settings = input_settings
+        s = tested_class(input_settings=input_settings, session_name="test-VipLauncher")
+        s.pipeline_id = "LCModel/0.1"
+        if tested_class == VipSession:   
+            mocker.patch.object(VipSession, '_exists', return_value=True)
+            s.input_dir = "."
         s.run_session()
         return
     # Catch the exception message
     with pytest.raises(ValueError) as e:
-        s.input_settings = input_settings
+        s = tested_class(input_settings=input_settings, session_name="test-VipLauncher")
+        s.pipeline_id = "LCModel/0.1"
+        if tested_class == VipSession:   
+            mocker.patch.object(VipSession, '_exists', return_value=True)
+            s.input_dir = "."
         s.run_session()
     assert str(e.value) == "Missing input value(s) for parameter(s): " + ", ".join(sorted(missing_fields))