Merge pull request #97 from inab/76-wfexs-backend-init-issues

76 wfexs backend init issues

tests/pushers/test_cache.py

@@ -119,7 +119,7 @@ def test_cache_push(tmpdir) -> "None":  # type: ignore[no-untyped-def]
     # First, instantiate WfExS backend
     temppath = tmpdir.mkdir("TEMP")
 
-    bootstrap_ok, test_local_config = WfExSBackend.bootstrap(
+    bootstrap_ok, test_local_config, config_directory = WfExSBackend.bootstrap(
         local_config_ro={
             "cacheDir": "CACHE",
             "workDir": "WORKDIRS",
@@ -129,7 +129,7 @@ def test_cache_push(tmpdir) -> "None":  # type: ignore[no-untyped-def]
     )
     wfexs = WfExSBackend(
         local_config=test_local_config,
-        config_directory=tmpdir.strpath,
+        config_directory=config_directory,
     )
 
     # Second, instantiate the cache plugin

wfexs_backend/__main__.py

@@ -1255,7 +1255,7 @@ def main() -> None:
             )
 
     if args.cacheDir:
-        local_config["cache-directory"] = args.cacheDir
+        local_config["cacheDir"] = args.cacheDir
 
     # In any case, assuring the cache directory does exist
     cacheDir = local_config.get("cacheDir")
@@ -1273,11 +1273,12 @@ def main() -> None:
 
     # A filename is needed later, in order to initialize installation keys
     if not localConfigFilename:
-        localConfigFilename = defaultLocalConfigFilename
-
-    # Hints for the the default path for the Crypt4GH keys
-    config_directory = os.path.dirname(localConfigFilename)
-    config_relname = os.path.basename(localConfigFilename)
+        config_directory = None
+        config_relname = os.path.basename(defaultLocalConfigFilename)
+    else:
+        # Hints for the the default path for the Crypt4GH keys
+        config_directory = os.path.dirname(localConfigFilename)
+        config_relname = os.path.basename(localConfigFilename)
 
     # Initialize (and create config file)
     if command in (
@@ -1290,9 +1291,11 @@ def main() -> None:
         WfExS_Commands.Import,
         WfExS_Commands.Execute,
     ):
-        updated_config, local_config = WfExSBackend.bootstrap(
+        updated_config, local_config, config_directory = WfExSBackend.bootstrap(
             local_config, config_directory, key_prefix=config_relname
         )
+        # This is needed because config directory could have been empty
+        localConfigFilename = os.path.join(config_directory, config_relname)
 
         # Last, should config be saved back?
         if updated_config or not os.path.exists(localConfigFilename):

wfexs_backend/wfexs_backend.py

@@ -278,7 +278,7 @@ def bootstrap(
         local_config_ro: "WfExSConfigBlock",
         config_directory: "Optional[AnyPath]" = None,
         key_prefix: "Optional[str]" = None,
-    ) -> "Tuple[bool, WfExSConfigBlock]":
+    ) -> "Tuple[bool, WfExSConfigBlock, AnyPath]":
         """
         :param local_config: Relevant local configuration, like the cache directory.
         :param config_directory: The filename to be used to resolve relative paths
@@ -292,11 +292,20 @@ def bootstrap(
 
         updated = False
 
+        valErrors = config_validate(local_config_ro, cls.CONFIG_SCHEMA)
+        if len(valErrors) > 0:
+            logging.error(
+                f"ERROR on incoming local configuration block for bootstrap: {valErrors}"
+            )
+            sys.exit(1)
+
         local_config = cast("WritableWfExSConfigBlock", copy.deepcopy(local_config_ro))
 
         # Getting the config directory
         if config_directory is None:
-            config_directory = cast("AbsPath", os.getcwd())
+            config_directory = cast(
+                "AbsPath", tempfile.mkdtemp(prefix="WfExS", suffix="config")
+            )
         if not os.path.isabs(config_directory):
             config_directory = cast("AbsPath", os.path.abspath(config_directory))
 
@@ -395,7 +404,16 @@ def bootstrap(
                 "Python interpreter does not support scrypt, so encoded crypt4gh keys with that algorithm cannot be used"
             )
 
-        return updated, local_config
+        # Validate, again, as it changed
+        if updated:
+            valErrors = config_validate(local_config, cls.CONFIG_SCHEMA)
+            if len(valErrors) > 0:
+                logging.error(
+                    f"ERROR in bootstrapped updated local configuration block: {valErrors}"
+                )
+                sys.exit(1)
+
+        return updated, local_config, config_directory
 
     @classmethod
     def FromDescription(
@@ -425,7 +443,7 @@ def FromDescription(
             stacklevel=2,
         )
 
-        _, updated_local_config = cls.bootstrap(
+        _, updated_local_config, config_directory = cls.bootstrap(
             local_config, config_directory=config_directory
         )
 
@@ -464,7 +482,8 @@ def __init__(
         )
 
         if not isinstance(local_config, dict):
-            local_config = {}
+            # Minimal bootstrapping for embedded cases
+            _, local_config, config_directory = self.bootstrap({}, config_directory)
 
         # validate the local configuration object
         valErrors = config_validate(local_config, self.CONFIG_SCHEMA)
@@ -1654,7 +1673,9 @@ def listStagedWorkflows(
                             creation,
                             orcids,  # TODO: give some use to this
                             instanceRawWorkdir,
-                        ) = self.parseOrCreateRawWorkDir(entry.path, create_ok=False)
+                        ) = self.parseOrCreateRawWorkDir(
+                            cast("AbsPath", entry.path), create_ok=False
+                        )
                     except:
                         self.logger.warning(f"Skipped {entry.name} on listing")
                         continue