misc commit

belbio · Apr 9, 2021 · 61f874b · 61f874b
1 parent 7f3d182
commit 61f874b
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Showing 33 changed files with 1,203 additions and 1,020 deletions.
diff --git a/api/app/__init__.py b/api/app/__init__.py
diff --git a/api/app/core/jwt.py b/api/app/core/jwt.py
diff --git a/api/app/core/middleware.py b/api/app/core/middleware.py
diff --git a/api/app/gunicorn_conf.py b/api/app/gunicorn_conf.py
diff --git a/api/app/main.py b/api/app/main.py
diff --git a/bel/api/endpoints/bel.py b/bel/api/endpoints/bel.py
@@ -5,14 +5,14 @@
 
 # Third Party
 import fastapi
-from fastapi import APIRouter, Depends, Query
+from fastapi import APIRouter, Body, Depends, Query
 from loguru import logger
 
 # Local
 import bel.belspec.crud
 import bel.lang.ast
 import bel.nanopub.validate
-from bel.schemas.bel import AssertionStr
+from bel.schemas.bel import AssertionRequest, AssertionStr
 
 router = APIRouter()
 
@@ -68,3 +68,34 @@ def validate_assertion(bel_assertion: str):
     logger.info(f"Validated: {validated}")
 
     return validated
+
+
+@router.post("/optimize")
+def optimize_assertion(
+    assertion: AssertionStr,
+    triple: bool = Query(
+        False,
+        description="Return Assertion as a Triple in a dictionary, default is to return Assertion as a single string",
+    ),
+):
+    """Optimize BEL Assertion
+
+    Transform BEL Assertion into more canonical BEL format
+
+    Current transformations implemented:
+
+    1. reactants(A, B) -> products(complex(A, B))  CONVERTED TO complex(A, B)
+    1. reactants(A, loc(X)) -> products(A, loc(Y)) CONVERTED TO tloc(A, fromLoc(X), toLoc(Y))
+    1. tloc(A, fromLoc(X), toLoc(extracellular region)) CONVERTED TO sec(A)
+    1. tloc(A, fromLoc(X), toLoc(plasma membrane)) CONVERTED TO surf(A)
+
+    """
+
+    # BEL AST optimizations
+    ast = bel.lang.ast.BELAst(assertion=assertion)
+    ast.optimize()
+
+    if triple:
+        return ast.to_triple()
+
+    return ast.to_string()
diff --git a/bel/belspec/enhance.py b/bel/belspec/enhance.py
@@ -182,7 +182,7 @@ def add_functions(specification: Mapping[str, Any]) -> Mapping[str, Any]:
         specification["functions"]["list_long"].append(func_name)
         specification["functions"]["list_short"].append(abbreviated_name)
 
-        if specification["functions"]["info"][func_name]["type"] == "primary":
+        if specification["functions"]["info"][func_name]["type"] == "Primary":
             specification["functions"]["primary"].append(func_name)
             specification["functions"]["primary"].append(abbreviated_name)
             specification["functions"]["primary_list_long"].append(func_name)
@@ -248,7 +248,7 @@ def enhance_function_signatures(specification: Mapping[str, Any]) -> Mapping[str
     for func in specification["functions"]["signatures"]:
 
         # Add primary parent functions to modifier functions
-        if specification["functions"]["signatures"][func]["func_type"] == "modifier":
+        if specification["functions"]["signatures"][func]["func_type"] == "Modifier":
             specification["functions"]["signatures"][func]["primary_function"] = specification[
                 "functions"
             ]["info"][func]["primary_function"]
@@ -342,14 +342,14 @@ def create_ebnf_parser(specification):
     functions_list = [
         (function, specification["functions"]["info"][function]["abbreviation"])
         for function in specification["functions"]["info"]
-        if specification["functions"]["info"][function]["type"] == "primary"
+        if specification["functions"]["info"][function]["type"] == "Primary"
     ]
     functions_list = sorted(list(itertools.chain(*functions_list)), key=len, reverse=True)
 
     modifiers_list = [
         (function, specification["functions"]["info"][function]["abbreviation"])
         for function in specification["functions"]["info"]
-        if specification["functions"]["info"][function]["type"] == "modifier"
+        if specification["functions"]["info"][function]["type"] == "Modifier"
     ]
     modifiers_list = sorted(list(itertools.chain(*modifiers_list)), key=len, reverse=True)
 

diff --git a/bel/core/mail.py b/bel/core/mail.py
@@ -2,7 +2,7 @@
 from typing import List
 
 # Third Party
-import requests
+import httpx
 from loguru import logger
 
 # Local
@@ -22,7 +22,7 @@ def send_simple_email(to: List[str], subject: str, body: str, body_html: str = "
     if body_html:
         data["html"] = body_html
 
-    r = requests.post(
+    r = httpx.post(
         f"{settings.MAIL_API}/messages",
         auth=("api", settings.MAIL_API_TOKEN),
         data=data,