feat: remove id as integer in place of name pk

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
 );

backend/src/api_types.py

@@ -25,7 +25,6 @@ class CamelModel(BaseModel):
 
 class ProteinEntry(CamelModel):
  name: str
- id: str
  length: int
  mass: float
 

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)