Merge pull request #105 from newgene/enhancement-autohub-validator

Enhancement autohub: allow easily customize validation logic

biothings/hub/__init__.py

@@ -359,6 +359,7 @@ class HubServer(object):
         "version_urls": getattr(config, "VERSION_URLS", []),
         "indexer_factory": getattr(config, "AUTOHUB_INDEXER_FACTORY", None),
         "es_host": getattr(config, "AUTOHUB_ES_HOST", None),
+        "validator_class": getattr(config, "AUTOHUB_VALIDATOR_CLASS", None),
     }
 
     def __init__(
@@ -830,6 +831,7 @@ def configure_autohub_feature(self):
         version_urls = self.autohub_config["version_urls"]
         indexer_factory = self.autohub_config["indexer_factory"]
         es_host = self.autohub_config["es_host"]
+        validator_class = self.autohub_config["validator_class"]
         factory = None
         if indexer_factory:
             assert (
@@ -842,7 +844,9 @@ def configure_autohub_feature(self):
                 self.logger.error(
                     "Couldn't find indexer factory class from '%s': %s" % (indexer_factory, e)
                 )
-        self.autohub_feature = AutoHubFeature(autohub_managers, version_urls, factory)
+        self.autohub_feature = AutoHubFeature(
+            autohub_managers, version_urls, factory, validator_class=validator_class,
+        )
         try:
             self.autohub_feature.configure()
             self.autohub_feature.configure_auto_release(config)

biothings/hub/default_config.py

@@ -342,6 +342,10 @@
 # A list of URLs to the versions.json files, which contain data release metadata
 VERSION_URLS = []
 
+# Use this configuration to customize validation logic of the auto hub feature.
+# the AutoHubValidator will be use as default. Any customize class must be extended from it.
+AUTOHUB_VALIDATOR_CLASS = None
+
 # Set to True to skip checking application/biothings version matching, before installing
 # a data release, in version settings like "app_version", "standalone_version", "biothings_version"
 SKIP_CHECK_COMPAT = True

biothings/hub/standalone/__init__.py

@@ -2,16 +2,18 @@
     This standalone module is originally located at "biothings/standalone" repo.
     It's used for Standalone/Autohub instance.
 """
-import os
+import asyncio
+import importlib
 import logging
+import os
 import sys
-import asyncio
 from copy import deepcopy
 from functools import partial
 
 from biothings import config as btconfig
 from biothings.hub import HubServer
 from biothings.hub.autoupdate import BiothingsDumper, BiothingsUploader
+from biothings.hub.standalone.validators import AutoHubValidator
 from biothings.utils.es import ESIndexer
 from biothings.utils.backend import DocESBackend
 from biothings.utils.loggers import get_logger
@@ -26,8 +28,9 @@ class AutoHubFeature(object):
 
     DEFAULT_DUMPER_CLASS = BiothingsDumper
     DEFAULT_UPLOADER_CLASS = BiothingsUploader
+    DEFAULT_VALIDATOR_CLASS = AutoHubValidator
 
-    def __init__(self, managers, version_urls, indexer_factory=None, *args, **kwargs):
+    def __init__(self, managers, version_urls, indexer_factory=None, validator_class=None, *args, **kwargs):
         """
         version_urls is a list of URLs pointing to versions.json file. The name
         of the data release is taken from the URL (http://...s3.amazon.com/<the_name>/versions.json)
@@ -48,13 +51,30 @@ def __init__(self, managers, version_urls, indexer_factory=None, *args, **kwargs
 
         When a data release named (from URL) matches an entry, it's used to configured
         which ES backend to target, otherwise the default one is used.
+
+        If validator_class is passed, it'll be used to provide validation methods for installing step.
+        If validator_class is None, the AutoHubValidator will be used as fallback.
+
         """
         super().__init__(*args, **kwargs)
         self.version_urls = self.extract(version_urls)
         self.indexer_factory = indexer_factory
         self.managers = managers
         self.logger, _ = get_logger("autohub")
 
+        if validator_class:
+            if isinstance(validator_class, str):
+                parts = validator_class.split(".")
+                validator_module = ".".join(parts[:-1])
+                validator_class = parts[-1]
+                validator_class = getattr(importlib.import_module(validator_module), validator_class)
+            assert issubclass(validator_class, AutoHubValidator), (
+                "validator_class must be a subclass of biothings.hub.standalone.AutoHubValidator"
+            )
+            self.validator = validator_class(self)
+        else:
+            self.validator = self.DEFAULT_VALIDATOR_CLASS(self)
+
     def extract(self, urls):
         vurls = []
         for url in urls:
@@ -66,10 +86,6 @@ def extract(self, urls):
 
         return vurls
 
-    def validate_release(self, version_path, force=False):
-        """Check if the release is valid to install. If not, it should raise an Exception to stop the progress"""
-        pass
-
     def install(self, src_name, version="latest", dry=False, force=False, use_no_downtime_method=True):
         """
         Update hub's data up to the given version (default is latest available),
@@ -91,7 +107,7 @@ async def do(version):
                 if dry:
                     return version_path
 
-                self.validate_release(version_path=version_path, force=force)
+                self.validator.validate(version_path=version_path, force=force)
 
                 for step_version in version_path:
                     logging.info("Downloading data for version '%s'", step_version)

biothings/hub/standalone/validators.py

@@ -0,0 +1,22 @@
+class AutoHubValidateError(Exception):
+    reason = None
+
+    def __init__(self, reason, *args, **kwargs):
+        self.reason = reason
+        super().__init__(*args, **kwargs)
+
+
+class AutoHubValidator:
+    """
+    This class aims to provide an easy way to customize validation logic for installing a hub from a release.
+    """
+
+    def __init__(self, auto_hub_feature):
+        self.auto_hub_feature = auto_hub_feature
+
+    def validate(self, force=False, **kwargs):
+        """
+        Check if the release is valid to install.
+        If invalid, it should raise an AutoHubValidateError include any reason to stop the progress.
+        """
+        pass