EVA-3414 add Writable config script

ebi_eva_common_pyutils/WritableConfig.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+import os
+
+import yaml
+from ebi_eva_common_pyutils.config import Configuration, cfg
+
+
+class WritableConfig(Configuration):
+    """Configuration object that allows writes to the config file"""
+
+    def __init__(self, *search_path, version=None):
+        super().__init__(search_path)
+        self.version = version
+
+    def load_config_file(self, *search_path):
+        try:
+            super().load_config_file(*search_path)
+        except FileNotFoundError:
+            # expected if it's the first time we are creating the config file
+            # In that case the first search path is set to be the config files
+            self.config_file = search_path[0]
+            pass
+
+    def backup(self):
+        """
+        Rename the config file by adding a '.1' at the end. If the '.1' file exists it move it to a '.2' and so on.
+        """
+        if os.path.isfile(self.config_file):
+            file_name = self.config_file
+            suffix = 1
+            backup_name = f'{file_name}.{suffix}'
+            while os.path.exists(backup_name):
+                suffix += 1
+                backup_name = f'{file_name}.{suffix}'
+
+            for i in range(suffix, 1, -1):
+                os.rename(f'{file_name}.{i - 1}', f'{file_name}.{i}')
+            os.rename(file_name, file_name + '.1')
+
+    def write(self):
+        if self.config_file and self.content and os.path.isdir(os.path.dirname(self.config_file)):
+            with open(self.config_file, 'w') as open_config:
+                yaml.safe_dump(self.content, open_config)
+
+    def set(self, *path, value):
+        self._set_version()
+        top_level = self.content
+        for p in path[:-1]:
+            if p not in top_level:
+                top_level[p] = {}
+            top_level = top_level[p]
+        top_level[path[-1]] = value
+
+    def pop(self, *path, default=None):
+        """Recursive dictionary pop with default"""
+        top_level = self.content
+        for p in path[:-1]:
+            if p not in top_level:
+                return default
+            top_level = top_level[p]
+        return top_level.pop(path[-1], default)
+
+    def is_empty(self):
+        return not self.content
+
+    def clear(self):
+        self.content = {}
+
+    def _set_version(self):
+        # If we're starting to fill in an empty config, set the version if available
+        if self.is_empty() and self.version:
+            self.content['version'] = self.version
+
+    def __contains__(self, item):
+        return item in self.content
+
+    def __setitem__(self, item, value):
+        """Allow dict-style write access, e.g. config['this']='that'."""
+        self._set_version()
+        self.content[item] = value
+
+
+def load_config(*args):
+    """Load a config file from any path provided.
+    If none are provided then read from a file path provided in the environment variable CONFIG."""
+    cfg.load_config_file(
+        *args,
+        os.getenv('CONFIG')
+    )

tests/common/test_config.py

@@ -1,5 +1,4 @@
 import os
-from os import environ
 from os.path import join
 
 import pytest