refac: simplify if someone can edit or not

backend/src/api_types.py

@@ -27,7 +27,7 @@ class ProteinEntry(CamelModel):
  name: str
  length: int
  mass: float
- species_name: str | None = None
+ species_name: str
  content: str | None = None
  refs: str | None = None
 
@@ -58,5 +58,7 @@ class UploadStatus(CamelModel):
 class EditBody(CamelModel):
  old_name: str # so we can identify the exact row we need to change
  new_name: str
+ old_species_name: str # so we can identify the exact row we need to change
+ new_species_name: str
  new_content: str | None = None
  new_refs: str | None = None

backend/src/server.py

@@ -213,8 +213,8 @@ def edit_protein_entry(body: EditBody):
  if body.new_name != body.old_name:
  os.rename(pdb_file_name(body.old_name), pdb_file_name(body.new_name))
 
- name_changed = False
  with Database() as db:
+ name_changed = False
  if body.new_name != body.old_name:
  db.execute(
  """UPDATE proteins SET name = %s WHERE name = %s""",
@@ -225,6 +225,15 @@ def edit_protein_entry(body: EditBody):
  )
  name_changed = True
 
+ if body.new_species_name != body.old_species_name:
+ db.execute(
+ """UPDATE species_proteins SET species_id = (SELECT id FROM species WHERE name = %s) WHERE protein_id = (SELECT id FROM proteins WHERE name = %s)""",
+ [
+ body.new_species_name,
+ body.old_name if not name_changed else body.new_name,
+ ],
+ )
+
  if body.new_content is not None:
  db.execute(
  """UPDATE proteins SET content = %s WHERE name = %s""",

frontend/src/routes/edit/[proteinName]/+page.svelte

@@ -1,6 +1,6 @@
 <script lang="ts">
  import { Backend, UploadError, type ProteinEntry } from "$lib/backend";
- import { Button, Input, Label, Helper } from "flowbite-svelte";
+ import { Button, Input, Label, Helper, Select } from "flowbite-svelte";
  import { goto } from "$app/navigation";
  import { onMount } from "svelte";
  import ArticleEditor from "$lib/ArticleEditor.svelte";
@@ -9,17 +9,20 @@
  // and reuploaded/edited
  export let data;
 
- let name: string;
-
  // store original too so we can see if the user changed/edited the content
+ let name: string;
+ let ogName: string;
  let ogContent: string;
  let content: string;
  let ogRefs: string;
  let refs: string;
+ let ogSpecies: string;
+ let species: string;
 
  let uploadError: UploadError | undefined;
  let entry: ProteinEntry | null = null;
  let error = false;
+ let allSpecies: string[] | null;
 
  // when this component mounts, request protein wikipedia entry from backend
  onMount(async () => {
@@ -32,14 +35,25 @@
  error = true;
  } else {
  name = entry.name;
+ ogName = name;
 
  content = entry.content ?? "";
  ogContent = content; // log original content
 
  refs = entry.refs ?? "";
  ogRefs = refs; // log original refs
+
+ species = entry.speciesName;
+ ogSpecies = species;
  }
+
+ allSpecies = await Backend.getAllSpecies();
  });
+ $: changed =
+ name !== ogName ||
+ content !== ogContent ||
+ refs !== ogRefs ||
+ species !== ogSpecies;
 </script>
 
 <section>
@@ -64,24 +78,35 @@
  >
  {/if}
  </div>
+
+ <div class="flex gap-5 mb-2">
+ <div>
+ <Label for="species-select" class="mb-2">Select a Species</Label>
+ {#if allSpecies}
+ <Select
+ id="species-select"
+ items={allSpecies.map((s) => ({ name: s, value: s }))}
+ bind:value={species}
+ />
+ {:else}
+ <Helper color="red">Error loading species</Helper>
+ {/if}
+ </div>
+ </div>
+
  <div>
  <ArticleEditor bind:content bind:refs />
  </div>
  <div>
  <Button
  on:click={async () => {
  if (entry) {
- if (
- name === entry.name &&
- content === ogContent &&
- refs === ogRefs
- )
- return; // no changes no edits!
-
  try {
  const err = await Backend.editProteinEntry({
  newName: name,
  oldName: entry.name,
+ newSpeciesName: species,
+ oldSpeciesName: ogSpecies,
  newContent: content !== ogContent ? content : undefined,
  newRefs: refs !== ogRefs ? refs : undefined,
  });
@@ -97,10 +122,7 @@
  }
  }
  }}
- disabled={(name === entry.name &&
- content === ogContent &&
- refs === ogRefs) ||
- name.length === 0}>Edit Protein</Button
+ disabled={!changed || name.length === 0}>Edit Protein</Button
  >
 
  <Button outline on:click={() => goto(`/protein/${name}`)}>Cancel</Button

frontend/src/routes/upload/+page.svelte

@@ -49,7 +49,6 @@
  {/if}
  </div>
 
- <!-- Species dropdown (hardcoded, not hooked up to backend for now) -->
  <div class="flex gap-5 mb-2">
  <div>
  <Label for="species-select" class="mb-2">Select a Species</Label>