Several fixes : Changing VIP portal / Girder URL, working route to check api key, check for empty file (#40)

* Adding set_vip_url function

* fix bad route used to check api key

* allow user to choose the url of the girder instance

* better name for girder url

* Allow user to change vip portal url when using classes

* setting new vip url with utils/vip.py

* check for empty file and code refactor

* Better way to check file size

* refactor

* Renaming

Author: hippolyteblot

src/vip_client/classes/VipCI.py

@@ -51,13 +51,12 @@ class VipCI(VipLauncher):
     # Default backup location 
     # (set to None to avoid saving and loading backup files)
     _BACKUP_LOCATION = "girder"
-
-    # --- New Attributes ---
-
+    
     # 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 ##################
@@ -137,7 +136,15 @@ def __init__(
 
     # Login to VIP and Girder
     @classmethod
-    def init(cls, vip_key="VIP_API_KEY", girder_key="GIRDER_API_KEY", verbose=True, **kwargs) -> VipCI:
+    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.
@@ -161,8 +168,11 @@ def init(cls, vip_key="VIP_API_KEY", girder_key="GIRDER_API_KEY", verbose=True,
         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=cls._GIRDER_PORTAL)
+        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

src/vip_client/classes/VipLauncher.py

@@ -371,7 +371,8 @@ def __init__(
 
     # ($A.1) Login to VIP
     @classmethod
-    def init(cls, api_key="VIP_API_KEY", verbose=True, **kwargs) -> VipLauncher:
+    def init(cls, api_key="VIP_API_KEY", verbose=True, vip_portal_url=None,
+             **kwargs) -> VipLauncher:
         """
         Handshakes with VIP using your own API key. 
         Returns a class instance which properties can be provided as keyword arguments.
@@ -391,11 +392,14 @@ def init(cls, api_key="VIP_API_KEY", verbose=True, **kwargs) -> VipLauncher:
         """
         # Set the default verbose mode for all sessions
         cls._VERBOSE = verbose
+        # Set the VIP portal URL
+        cls._VIP_PORTAL = vip_portal_url if vip_portal_url else cls._VIP_PORTAL
         # 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
+            vip.set_vip_url(cls._VIP_PORTAL)
             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:
@@ -1641,6 +1645,7 @@ def _check_input_values(self, input_settings: dict, location: str) -> None:
         self._check_invalid_input(input_settings, self._pipeline_def['parameters'])
 
         wrong_type_inputs = []
+        missing_files = []
         for param in self._pipeline_def['parameters']:
             name = param['name']
             # Check only defined inputs
@@ -1650,11 +1655,10 @@ def _check_input_values(self, input_settings: dict, location: str) -> None:
             # If input is a File, check file(s) existence
             if param["type"] == "File":
                 # Ensure every file exists at `location`
-                missing_file = self._first_missing_file(value, location)
-                if missing_file:
-                    raise FileNotFoundError(
-                        f"Parameter '{name}': The following file is missing in the {location.upper()} file system: {missing_file}"
-                    )
+                missing_files_found = self._missing_files(value, location)
+                if missing_files_found:
+                    missing_files.extend(missing_files_found)
+                    continue
             if param["type"] == "Boolean":
                 if value not in ["true", "false"]:
                     wrong_type_inputs.append(name)
@@ -1666,6 +1670,10 @@ def _check_input_values(self, input_settings: dict, location: str) -> None:
             raise ValueError(
                 f"Wrong type(s) for parameter(s): {', '.join(sorted(wrong_type_inputs))}"
             )
+        if missing_files:
+            raise FileNotFoundError(
+                f"Missing file(s) for parameter(s): {', '.join(sorted(missing_files))}"
+            )
 
     # ------------------------------------------------
 
@@ -1713,21 +1721,27 @@ def _invalid_chars_for_vip(cls, value) -> list:
 
     # Function to assert file existence in the input settings
     @classmethod
-    def _first_missing_file(cls, value, location: str) -> str: 
+    def _missing_files(cls, value, location: str) -> list[str]:
         """
-        Returns the path the first non-existent file in `value` (None by default).
-        - `value` can contain a single file path or a list of paths.
-        - `location` refers to the storage infrastructure (e.g., "vip") to feed in cls._exists().
+        Returns a list of missing files for `value` at `location`.
+        
+        - `value` can be either a single file path or a list of paths.
+        - `location` refers to the storage infrastructure (e.g., "vip") used by cls._exists().
         """
-        # Case : list of files
+        missing_files = []
+        
+        # Case: list of files
         if isinstance(value, list):
-            for file in value : 
-                if cls._first_missing_file(value=file, location=location) is not None:
-                    return file
-            return None
+            for file in value:
+                if not cls._exists(file, location=location):
+                    missing_files.append(file)
         # Case: single file
         else:
-            return value if not cls._exists(path=value, location=location) else None 
+            if not cls._exists(value, location=location):
+                missing_files.append(value)
+        
+        return missing_files
+
     # ------------------------------------------------
 
     ########################################

src/vip_client/classes/VipSession.py

@@ -350,8 +350,8 @@ def upload_inputs(self, input_dir=None, update_files=True) -> VipSession:
         elif not self._is_defined("_local_input_dir"): 
             raise TypeError(f"Session '{self._session_name}': Please provide an input directory.")
         # Check local input directory
-        if not self._exists(self._local_input_dir, location="local"): 
-            raise FileNotFoundError(f"Session '{self._session_name}': Input directory does not exist.")
+        if not self._exists(self._local_input_dir, location="local"):
+            raise FileNotFoundError(f"Session '{self._session_name}': Input directory '{self._local_input_dir}' does not exist.")
         # Check the local values of `input_settings` before uploading
         if self._is_defined("_input_settings"):
             self._print("Checking references to the dataset within Input Settings ... ", end="", flush=True)
@@ -684,11 +684,12 @@ def _path_to_delete(self) -> dict:
     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.
+        `path` can be a string or path-like object. If `location` is "local", empty folders are 
+        considered as non-existent.
         """
         # Check path existence in `location`
         if location=="local":
-            return os.path.exists(path)
+            return os.path.exists(path) and os.path.isdir(path) and os.listdir(path)
         else: 
             return super()._exists(path=path, location=location)
     # ------------------------------------------------
@@ -831,9 +832,10 @@ def _upload_dir(self, local_path: Path, vip_path: PurePosixPath) -> list:
         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"
+            # Check the file size
+            size = local_file.stat().st_size
+            if size == 0: raise ValueError(f"{local_file} is an empty file. Empty file are not supported on VIP")
+            size = f"{size/(1<<20):,.1f}MB"
             # Display the current file
             self._print(f"\t[{nFile}/{len(files_to_upload)}] Uploading file: {local_file.name} ({size}) ...", end=" ")
             # Upload the file on VIP

src/vip_client/utils/vip.py

@@ -20,6 +20,11 @@
 # API URL
 __PREFIX = "https://vip.creatis.insa-lyon.fr/rest/"
 
+def set_vip_url(vip_portal_url: str) -> None:
+    """Change the API prefix"""
+    global __PREFIX
+    __PREFIX = vip_portal_url + "/rest/"
+
 # API key
 __apikey = None
 __headers = {'apikey': __apikey}
@@ -80,7 +85,7 @@ def setApiKey(value) -> bool:
     Return True is correct apikey, False otherwise.
     Raise an error if an other problems occured 
     """
-    url = __PREFIX + 'plateform'
+    url = __PREFIX + 'platform'
     head_test = {
                  'apikey': value,
                 }