Merge pull request #168 from xnought/desc

feat: add description to proteins

backend/init.sql

@@ -25,6 +25,7 @@ CREATE TABLE species (
 CREATE TABLE proteins (
  id serial PRIMARY KEY,
  name text NOT NULL UNIQUE, -- user specified name of the protein (TODO: consider having a string limit)
+ description text, 
  length integer, -- length of amino acid sequence
  mass numeric, -- mass in amu/daltons
  content bytea, -- stored markdown for the protein article (TODO: consider having a limit to how big this can be)

backend/src/api/protein.py

@@ -115,7 +115,14 @@ def get_protein_entry(protein_name: str):
  """
  with Database() as db:
  try:
- query = """SELECT proteins.name, proteins.length, proteins.mass, proteins.content, proteins.refs, species.name as species_name FROM proteins
+ query = """SELECT proteins.name, 
+ proteins.description,
+ proteins.length, 
+ proteins.mass, 
+ proteins.content, 
+ proteins.refs, 
+ species.name
+ FROM proteins
  JOIN species ON species.id = proteins.species_id
  WHERE proteins.name = %s;"""
  entry_sql = db.execute_return(query, [protein_name])
@@ -125,7 +132,15 @@ def get_protein_entry(protein_name: str):
  if entry_sql is not None and len(entry_sql) != 0:
  # return the only entry
  only_returned_entry = entry_sql[0]
- name, length, mass, content, refs, species_name = only_returned_entry
+ (
+ name,
+ description,
+ length,
+ mass,
+ content,
+ refs,
+ species_name,
+ ) = only_returned_entry
 
  # if byte arrays are present, decode them into a string
  if content is not None:
@@ -135,6 +150,7 @@ def get_protein_entry(protein_name: str):
 
  return ProteinEntry(
  name=name,
+ description=description,
  length=length,
  mass=mass,
  content=content,
@@ -200,12 +216,13 @@ def upload_protein_entry(body: UploadBody):
 
  try:
  # add the protein itself
- query = """INSERT INTO proteins (name, length, mass, content, refs, species_id) 
- VALUES (%s, %s, %s, %s, %s, (SELECT id FROM species WHERE name = %s));"""
+ query = """INSERT INTO proteins (name, description, length, mass, content, refs, species_id) 
+ VALUES (%s, %s, %s, %s, %s, %s, (SELECT id FROM species WHERE name = %s));"""
  db.execute(
  query,
  [
  pdb.name,
+ body.description,
  pdb.num_amino_acids,
  pdb.mass_daltons,
  str_to_bytea(body.content),
@@ -267,5 +284,14 @@ def edit_protein_entry(body: EditBody):
  ],
  )
 
+ if body.new_description is not None:
+ db.execute(
+ """UPDATE proteins SET description = %s WHERE name = %s""",
+ [
+ body.new_description,
+ body.old_name if not name_changed else body.new_name,
+ ],
+ )
+
  except Exception:
  return UploadError.WRITE_ERROR

backend/src/api/search.py

@@ -72,10 +72,14 @@ def search_proteins(body: SearchProteinsBody):
  filter_clauses = gen_sql_filters(
  body.species_filter, body.length_filter, body.mass_filter
  )
- entries_query = """SELECT proteins.name, proteins.length, proteins.mass, species.name as species_name FROM proteins 
- JOIN species ON species.id = proteins.species_id 
- WHERE proteins.name ILIKE %s"""
-
+ entries_query = """SELECT proteins.name, 
+ proteins.description, 
+ proteins.length, 
+ proteins.mass, 
+ species.name 
+ FROM proteins 
+ JOIN species ON species.id = proteins.species_id 
+ WHERE proteins.name ILIKE %s"""
  log.warn(filter_clauses)
  entries_result = db.execute_return(
  sanitize_query(entries_query + filter_clauses),
@@ -91,8 +95,9 @@ def search_proteins(body: SearchProteinsBody):
  length=length,
  mass=mass,
  species_name=species_name,
+ description=description,
  )
- for name, length, mass, species_name in entries_result
+ for name, description, length, mass, species_name in entries_result
  ],
  total_found=len(entries_result),
  )

backend/src/api_types.py

@@ -30,6 +30,7 @@ class ProteinEntry(CamelModel):
  species_name: str
  content: str | None = None
  refs: str | None = None
+ description: str | None = None
 
 
 class AllEntries(CamelModel):
@@ -38,6 +39,7 @@ class AllEntries(CamelModel):
 
 class UploadBody(CamelModel):
  name: str
+ description: str
  species_name: str
  content: str # markdown content from user
  refs: str # references used in content (bibtex form)
@@ -62,6 +64,7 @@ class EditBody(CamelModel):
  new_species_name: str
  new_content: str | None = None
  new_refs: str | None = None
+ new_description: str | None = None
 
 
 class LoginBody(CamelModel):

frontend/src/lib/ListProteins.svelte

@@ -5,8 +5,6 @@
  import dummy from "../images/dummy.png";
 
  export let allEntries: ProteinEntry[] | null = null;
- const dummyDesc =
- "scriptionDescriptionDescription DescriptionDescription Description Description";
 </script>
 
 <div class="prot-grid">
@@ -17,7 +15,7 @@
  <div
  class="prot-container"
  on:click={() => navigate(`/protein/${entry.name}`)}
- title={`Name:${entry.name}\nDescription:${dummyDesc}`}
+ title={`Name:${entry.name}\nDescription:${entry.description}`}
  >
  <div class="prot-thumb mr-2">
  <img class="prot-thumb" src={dummy} alt="dummy" />
@@ -27,7 +25,9 @@
  {entry.name}
  </div>
  <div class="prot-desc">
- {dummyDesc}
+ {#if entry.description}
+ {entry.description}
+ {/if}
  </div>
  <div>
  <div><b>Organism</b>: {entry.speciesName}</div>
@@ -87,6 +87,7 @@
  .prot-grid {
  display: flex;
  gap: 20px;
+ align-content: flex-start;
  flex-wrap: wrap;
  padding: 10px;
  margin-left: 10px;

frontend/src/lib/openapi/models/EditBody.ts

@@ -9,5 +9,6 @@ export type EditBody = {
  newSpeciesName: string;
  newContent?: (string | null);
  newRefs?: (string | null);
+ newDescription?: (string | null);
 };
 

frontend/src/lib/openapi/models/ProteinEntry.ts

@@ -9,5 +9,6 @@ export type ProteinEntry = {
  speciesName: string;
  content?: (string | null);
  refs?: (string | null);
+ description?: (string | null);
 };
 

frontend/src/lib/openapi/models/UploadBody.ts

@@ -4,6 +4,7 @@
 /* eslint-disable */
 export type UploadBody = {
  name: string;
+ description: string;
  speciesName: string;
  content: string;
  refs: string;

frontend/src/routes/Edit.svelte

@@ -4,15 +4,18 @@
  import { navigate } from "svelte-routing";
  import { onMount } from "svelte";
  import ArticleEditor from "../lib/ArticleEditor.svelte";
- import {user} from "../lib/stores/user"
+ import { user } from "../lib/stores/user";
 
  // key difference, here we get the information, then populate it in the upload form that can be edited
  // and reuploaded/edited
  export let urlId: string;
 
  // store original too so we can see if the user changed/edited the content
+
  let name: string;
  let ogName: string;
+ let description: string;
+ let ogDescription: string;
  let ogContent: string;
  let content: string;
  let ogRefs: string;
@@ -28,8 +31,10 @@
  // when this component mounts, request protein wikipedia entry from backend
  onMount(async () => {
  if (!$user.loggedIn) {
- alert("You are not logged in. You are being redirected to home. TODO: Make this better.")
- navigate("/")
+ alert(
+ "You are not logged in. You are being redirected to home. TODO: Make this better."
+ );
+ navigate("/");
  }
 
  // Request the protein from backend given ID
@@ -40,17 +45,21 @@
  if (entry == null) {
  error = true;
  } else {
+ // keep track of db value and the value we change (og denotes original / db)
  name = entry.name;
  ogName = name;
 
  content = entry.content ?? "";
- ogContent = content; // log original content
+ ogContent = content;
 
  refs = entry.refs ?? "";
- ogRefs = refs; // log original refs
+ ogRefs = refs;
 
  species = entry.speciesName;
  ogSpecies = species;
+
+ description = entry.description ?? "";
+ ogDescription = description;
  }
 
  allSpecies = await Backend.searchSpecies();
@@ -59,7 +68,8 @@
  name !== ogName ||
  content !== ogContent ||
  refs !== ogRefs ||
- species !== ogSpecies;
+ species !== ogSpecies ||
+ ogDescription !== description;
 </script>
 
 <svelte:head>
@@ -90,6 +100,18 @@
  {/if}
  </div>
 
+ <div>
+ <Label for="protein-desc" class="block mb-2"
+ >Protein Description</Label
+ >
+ <Input
+ bind:value={description}
+ style="width: 600px"
+ id="protein-desc"
+ placeholder="Description"
+ />
+ </div>
+
  <div class="flex gap-5 mb-2">
  <div>
  <Label for="species-select" class="mb-2"
@@ -128,6 +150,10 @@
  ? content
  : undefined,
  newRefs: refs !== ogRefs ? refs : undefined,
+ newDescription:
+ description !== ogDescription
+ ? description
+ : undefined,
  });
  if (err) {
  uploadError = err;

frontend/src/routes/Protein.svelte

@@ -45,8 +45,9 @@
  </h1>
 
  <div id="description">
- DescriptionDescriptionDescriptionDescriptionDescriptionDescriptionDescriptionDescriptionDescription
- Description Description Description Description
+ {#if entry.description}
+ {entry.description}
+ {/if}
  </div>
 
  <EntryCard title="Computed Insights">

frontend/src/routes/Upload.svelte

@@ -13,21 +13,24 @@
  import ArticleEditor from "../lib/ArticleEditor.svelte";
  import { onMount } from "svelte";
  import Cookies from "js-cookie";
- import {user} from "../lib/stores/user"
+ import { user } from "../lib/stores/user";
 
  let species: string[] | null;
  let selectedSpecies: string = "unknown";
 
- const authToken = Cookies.get("auth")
+ const authToken = Cookies.get("auth");
  onMount(async () => {
  if (!$user.loggedIn) {
- alert("You are not logged in. You are being redirected to home. TODO: Make this better.")
- navigate("/")
+ alert(
+ "You are not logged in. You are being redirected to home. TODO: Make this better."
+ );
+ navigate("/");
  }
  species = await Backend.searchSpecies();
  });
 
  let name: string = "";
+ let description: string = "";
  let content: string = "";
  let files: FileList | undefined; // bind:files on the Fileupload
  let uploadError: UploadError | undefined;
@@ -62,6 +65,18 @@
  {/if}
  </div>
 
+ <div>
+ <Label for="protein-desc" class="block mb-2"
+ >Protein Description</Label
+ >
+ <Input
+ bind:value={description}
+ style="width: 600px"
+ id="protein-desc"
+ placeholder="Description"
+ />
+ </div>
+
  <div class="flex gap-5 mb-2">
  <div>
  <Label for="species-select" class="mb-2">Select a Species</Label
@@ -95,6 +110,7 @@
  try {
  const err = await Backend.uploadProteinEntry({
  name,
+ description,
  pdbFileStr,
  content,
  refs,

galaxy/upload_all.py

@@ -14,7 +14,7 @@ def remove_box():
  os.system(f"rm -rf {DIR}")
 
 
-def upload_protein_file(path, name, species_name, content="", refs=""):
+def upload_protein_file(path, name, species_name, content="", refs="", desc=""):
  with open(path, "r") as f:
  pdb_file_str = f.read()
 
@@ -24,6 +24,7 @@ def upload_protein_file(path, name, species_name, content="", refs=""):
  "content": content,
  "refs": refs,
  "pdb_file_str": pdb_file_str,
+ "description": desc,
  }
  out = requests.post("http://localhost:8000/protein/upload", json=payload)
  return out
@@ -43,7 +44,12 @@ def upload_all():
  name = fn.split(".")[0].replace("_", " ")
  species_name = available_species[fn[:2]]
  upload_protein_file(
- full_path, name, species_name, content=CONTENT, refs=REFS
+ full_path,
+ name,
+ species_name,
+ content=CONTENT,
+ refs=REFS,
+ desc="from the venom lab at osu",
  )
  print("uploaded", full_path, name, species_name)
  remove_box()