From 583ffb893c1b681a2a2e8edf4b53d60f21e90035 Mon Sep 17 00:00:00 2001
From: xnought <bertuccd@oregonstate.edu>
Date: Thu, 16 Nov 2023 21:19:25 -0800
Subject: [PATCH] feat: remove id as integer in place of name pk

---
 backend/init.sql         |  4 +---
 backend/src/api_types.py |  1 -
 backend/src/server.py    | 32 ++++++++++++--------------------
 3 files changed, 13 insertions(+), 24 deletions(-)

diff --git a/backend/init.sql b/backend/init.sql
index a922101c..a52d2497 100644
--- a/backend/init.sql
+++ b/backend/init.sql
@@ -10,9 +10,7 @@
 -- Note: "Numeric" data types have arbitrary precision which are good for calculations. This seems like what we want.
 -- https://www.postgresql.org/docs/current/datatype-numeric.html#DATATYPE-NUMERIC-DECIMAL
 CREATE TABLE proteins (
-    -- todo: make the id meaningful, like Lb17_comp535_c2_seq1, discuss this
-    id integer GENERATED ALWAYS AS IDENTITY PRIMARY KEY,  -- increment id for now
-    name text NOT NULL UNIQUE,
+    name text NOT NULL UNIQUE PRIMARY KEY,
     length integer,
     mass numeric
 );
diff --git a/backend/src/api_types.py b/backend/src/api_types.py
index d66bfd25..ca954ad4 100644
--- a/backend/src/api_types.py
+++ b/backend/src/api_types.py
@@ -25,7 +25,6 @@ class CamelModel(BaseModel):
 
 class ProteinEntry(CamelModel):
     name: str
-    id: str
     length: int
     mass: float
 
diff --git a/backend/src/server.py b/backend/src/server.py
index d9e28389..2c16f7ec 100644
--- a/backend/src/server.py
+++ b/backend/src/server.py
@@ -1,5 +1,5 @@
 from .setup import init_fastapi_app, disable_cors
-from .api_types import ProteinEntry, UploadBody, UploadStatus, UploadError
+from .api_types import ProteinEntry, UploadBody, UploadError
 from .db import Database
 from .protein import Protein
 import logging as log
@@ -21,48 +21,40 @@ def get_all_entries():
     with Database() as db:
         try:
             entries_sql = db.execute_return(
-                """SELECT id, name, length, mass FROM proteins"""
+                """SELECT name, length, mass FROM proteins"""
             )
             log.warn(entries_sql)
 
             # if we got a result back
             if entries_sql is not None:
                 return [
-                    ProteinEntry(
-                        id=str(entry[0]),
-                        name=entry[1],
-                        length=entry[2],
-                        mass=entry[3],
-                    )
-                    for entry in entries_sql
+                    ProteinEntry(name=name, length=length, mass=mass)
+                    for name, length, mass in entries_sql
                 ]
         except Exception as e:
             log.error(e)
 
 
-@app.get("/protein-entry/{protein_id:str}", response_model=ProteinEntry | None)
-def get_protein_entry(protein_id: str):
+@app.get("/protein-entry/{protein_name:str}", response_model=ProteinEntry | None)
+def get_protein_entry(protein_name: str):
     """Get a single protein entry by its id
     Returns: ProteinEntry if found | None if not found
     """
     with Database() as db:
         try:
             entry_sql = db.execute_return(
-                """SELECT id, name, length, mass FROM proteins
-                    WHERE id = %s""",
-                [protein_id],
+                """SELECT name, length, mass FROM proteins
+                    WHERE name = %s""",
+                [protein_name],
             )
             log.warn(entry_sql)
 
             # if we got a result back
             if entry_sql is not None and len(entry_sql) != 0:
                 # return the only entry
-                return ProteinEntry(
-                    id=str(entry_sql[0][0]),
-                    name=entry_sql[0][1],
-                    length=entry_sql[0][2],
-                    mass=entry_sql[0][3],
-                )
+                only_returned_entry = entry_sql[0]
+                name, length, mass = only_returned_entry
+                return ProteinEntry(name=name, length=length, mass=mass)
 
         except Exception as e:
             log.error(e)