refactor and bugfix

refactored ast.py into multiple modules and added another validation test
belbio · Feb 4, 2021 · 7f3d182 · 7f3d182
1 parent fa64a11
commit 7f3d182
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Showing 10 changed files with 815 additions and 763 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -16,7 +16,7 @@
     "statusBarItem.hoverBackground": "#f7df1e",
     "statusBar.foreground": "#15202b"
   },
-  "python.pythonPath": ".venv/bin/python3",
+  "python.pythonPath": ".venv/bin/python",
   "python.analysis.openFilesOnly": false,
   "python.analysis.memory.keepLibraryLocalVariables": true,
   "python.autoComplete.addBrackets": true,
@@ -30,8 +30,13 @@
   "cSpell.ignoreWords": [
     "arango",
     "equivalenced",
+    "mult",
+    "orthologizing",
+    "paren",
+    "pmod",
     "schem",
     "scomp",
+    "tloc",
     "zfin"
   ],
   "python.formatting.provider": "black",

diff --git a/bel/core/settings.py b/bel/core/settings.py
@@ -67,20 +67,24 @@ def getenv_boolean(var_name, default=False):
 """
 
 # BEL API
-BEL_API = os.getenv("BEL_API", default="http://localhost:8888")
+BEL_API = os.getenv("BEL_API", default="http://localhost:8888")  # DevSkim: ignore DS137138
 
 # Redis Info
 REDIS_HOST = os.getenv("REDIS_HOST", default="localhost")
 REDIS_PORT = os.getenv("REDIS_PORT", default=6379)
 REDIS_QUEUE = os.getenv("NANOPUBSTORE_TYPE", default="belservice")
 
 # Elasticsearch Info
-ELASTICSEARCH_URL = os.getenv("BEL_ELASTICSEARCH_URL", default="http://localhost:9200")
+ELASTICSEARCH_URL = os.getenv(
+    "BEL_ELASTICSEARCH_URL", default="http://localhost:9200"  # DevSkim: ignore DS137138
+)  # DevSkim: ignore DS137138
 TERMS_INDEX = os.getenv("TERMS_INDEX", default="terms")  # Elasticsearch terms index
 TERMS_DOCUMENT_TYPE = os.getenv("TERMS_DOCUMENT_TYPE", default="_doc")
 
 # Arango Databases
-ARANGO_URL = os.getenv("BEL_ARANGO_URL", default="http://localhost:8529")
+ARANGO_URL = os.getenv(
+    "BEL_ARANGO_URL", default="http://localhost:8529"  # DevSkim: ignore DS137138
+)  # DevSkim: ignore DS137138
 ARANGO_USER = os.getenv("BEL_ARANGO_USER", default="root")
 ARANGO_PASSWORD = os.getenv("BEL_ARANGO_PASSWORD", default="Set a password, please")
 
@@ -96,7 +100,7 @@ def getenv_boolean(var_name, default=False):
 BEL_SPECIFICATION_URLS = json.loads(os.getenv("BEL_SPECIFICATION_URLS", default="[]"))
 if not BEL_SPECIFICATION_URLS:
     BEL_SPECIFICATION_URLS = [
-        "http://resources.bel.bio.s3-us-east-2.amazonaws.com/specifications/bel_latest.yaml"
+        "http://resources.bel.bio.s3-us-east-2.amazonaws.com/specifications/bel_latest.yaml"  # DevSkim: ignore DS137138
     ]
 
 bel_canonicalize_default = {