feat: species dropdown connected to backend (#100)

* feat: change the dropdown to a select

* feat: reduce species down to organism name

* feat: join on integer id

* feat: serial id primary key

* feat: get entry and search entry use joins

* feat: fetch all species for the dropdown

* feat: upload the species name

* fix: name might change

* refac: simplify if someone can edit or not

* feat: delete species

* sh run.sh gen_api

* fix: remove link from method

* fix: cascade

backend/init.sql

@@ -15,7 +15,8 @@
  * Proteins Table
  */
 CREATE TABLE proteins (
- name text NOT NULL UNIQUE PRIMARY KEY, -- user specified name of the protein (TODO: consider having a string limit)
+ id serial PRIMARY KEY,
+ name text NOT NULL UNIQUE, -- user specified name of the protein (TODO: consider having a string limit)
  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)
@@ -26,20 +27,22 @@ CREATE TABLE proteins (
  * Species Table
  */
 CREATE TABLE species (
- id text NOT NULL UNIQUE PRIMARY KEY, -- This should be the first letters in the scientific name - e.g. "gh", the prefix to the files, for simplicity.
- tax_genus text NOT NULL,
- tax_species text NOT NULL,
- scientific_name text UNIQUE GENERATED ALWAYS AS (tax_genus || ' ' || tax_species) STORED,
- content bytea
+ id serial PRIMARY KEY,
+ name text NOT NULL UNIQUE -- combined genus and species name, provided for now by the user
+ -- -- removed now to reduce complexity for v0
+ -- tax_genus text NOT NULL,
+ -- tax_species text NOT NULL,
+ -- scientific_name text UNIQUE GENERATED ALWAYS AS (tax_genus || ' ' || tax_species) STORED,
+ -- content bytea
 );
 
 /*
  * Table: species_proteins
  * Description: Join table for N:M connection between Species and Proteins
  */
  CREATE TABLE species_proteins (
- species_id text references species(id) ON UPDATE CASCADE ON DELETE CASCADE,
- protein_id text references proteins(name) ON UPDATE CASCADE ON DELETE CASCADE,
+ species_id serial references species(id) ON UPDATE CASCADE ON DELETE CASCADE,
+ protein_id serial references proteins(id) ON UPDATE CASCADE ON DELETE CASCADE,
  PRIMARY KEY (species_id, protein_id)
  );
 
@@ -73,48 +76,32 @@ INSERT INTO proteins (name, length, mass, content, refs) VALUES (
 /*
  * Inserts example species into species table
  */
-INSERT INTO species(id, tax_genus, tax_species, content) VALUES (
- 'Gh',
- 'Ganaspis',
- 'hookeri',
- null
-);
-
-INSERT INTO species(id, tax_genus, tax_species, content) VALUES (
- 'Lb',
- 'Leptopilina',
- 'boulardi',
- null
-);
+INSERT INTO species(name) VALUES ('ganaspis hookeri'); 
+INSERT INTO species(name) VALUES ('leptopilina boulardi'); 
+INSERT INTO species(name) VALUES ('leptopilina heterotoma'); 
+INSERT INTO species(name) VALUES ('unknown');
 
-INSERT INTO species(id, tax_genus, tax_species, content) VALUES (
- 'Lh',
- 'Leptopilina',
- 'heterotoma',
- null
-);
-
- /*
+/*
  * Inserts connections between species and proteins
- */ 
+*/ 
 INSERT INTO species_proteins(species_id, protein_id) VALUES (
- 'Gh',
- 'Gh_comp271_c0_seq1'
+ 1, -- 'ganaspis hookeri',
+ 1 -- 'Gh_comp271_c0_seq1'
  );
 
  /*
  * Inserts connections between species and proteins
  */ 
 INSERT INTO species_proteins(species_id, protein_id) VALUES (
- 'Lb',
- 'Lb17_comp535_c2_seq1'
+ 2, -- 'leptopilina boulardi',
+ 2 -- 'Lb17_comp535_c2_seq1'
  );
 
  /*
  * Inserts connections between species and proteins
  */ 
 INSERT INTO species_proteins(species_id, protein_id) VALUES (
- 'Lh',
- 'Lh14_comp2336_c0_seq1'
+ 3, -- 'leptopilina heterotoma',
+ 3 --'Lh14_comp2336_c0_seq1'
  );
 

backend/src/api_types.py

@@ -27,6 +27,7 @@ class ProteinEntry(CamelModel):
  name: str
  length: int
  mass: float
+ species_name: str
  content: str | None = None
  refs: str | None = None
 
@@ -37,6 +38,7 @@ class AllEntries(CamelModel):
 
 class UploadBody(CamelModel):
  name: str
+ species_name: str
  content: str # markdown content from user
  refs: str # references used in content (bibtex form)
  pdb_file_str: str
@@ -56,5 +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

@@ -40,40 +40,45 @@ def get_all_entries():
  """
  with Database() as db:
  try:
- entries_sql = db.execute_return(
- """SELECT name, length, mass FROM proteins"""
- )
+ query = """SELECT proteins.name, proteins.length, proteins.mass, species.name as species_name FROM species_proteins 
+ JOIN proteins ON species_proteins.protein_id = proteins.id
+ JOIN species ON species_proteins.species_id = species.id;"""
+ entries_sql = db.execute_return(query)
  log.warn(entries_sql)
 
  # if we got a result back
  if entries_sql is not None:
  return [
- ProteinEntry(name=name, length=length, mass=mass)
- for name, length, mass in entries_sql
+ ProteinEntry(
+ name=name, length=length, mass=mass, species_name=species_name
+ )
+ for name, length, mass, species_name in entries_sql
  ]
  except Exception as e:
  log.error(e)
 
 
-@app.get("/search-entries/{query:str}", response_model=list[ProteinEntry] | None)
-def search_entries(query: str):
+@app.get("/search-entries/{protein_name:str}", response_model=list[ProteinEntry] | None)
+def search_entries(protein_name: str):
  """Gets a list of protein entries by a search string
  Returns: list[ProteinEntry] if found | None if not found
  """
  with Database() as db:
  try:
- entries_sql = db.execute_return(
- """SELECT name, length, mass FROM proteins
- WHERE name ILIKE %s""",
- [f"%{query}%"],
- )
+ query = """SELECT proteins.name, proteins.length, proteins.mass, species.name as species_name FROM species_proteins 
+  JOIN proteins ON species_proteins.protein_id = proteins.id
+  JOIN species ON species_proteins.species_id = species.id
+  WHERE proteins.name ILIKE %s;"""
+ entries_sql = db.execute_return(query, [f"%{protein_name}%"])
  log.warn(entries_sql)
 
  # if we got a result back
  if entries_sql is not None:
  return [
- ProteinEntry(name=name, length=length, mass=mass)
- for name, length, mass in entries_sql
+ ProteinEntry(
+ name=name, length=length, mass=mass, species_name=species_name
+ )
+ for name, length, mass, species_name in entries_sql
  ]
  except Exception as e:
  log.error(e)
@@ -86,18 +91,18 @@ def get_protein_entry(protein_name: str):
  """
  with Database() as db:
  try:
- entry_sql = db.execute_return(
- """SELECT name, length, mass, content, refs FROM proteins
- WHERE name = %s""",
- [protein_name],
- )
+ query = """SELECT proteins.name, proteins.length, proteins.mass, proteins.content, proteins.refs, species.name as species_name FROM species_proteins 
+  JOIN proteins ON species_proteins.protein_id = proteins.id
+  JOIN species ON species_proteins.species_id = species.id
+  WHERE proteins.name = %s;"""
+ entry_sql = db.execute_return(query, [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
  only_returned_entry = entry_sql[0]
- name, length, mass, content, refs = only_returned_entry
+ name, length, mass, content, refs, species_name = only_returned_entry
 
  # if byte arrays are present, decode them into a string
  if content is not None:
@@ -106,7 +111,12 @@ def get_protein_entry(protein_name: str):
  refs = bytea_to_str(refs)
 
  return ProteinEntry(
- name=name, length=length, mass=mass, content=content, refs=refs
+ name=name,
+ length=length,
+ mass=mass,
+ content=content,
+ refs=refs,
+ species_name=species_name,
  )
 
  except Exception as e:
@@ -117,17 +127,18 @@ def get_protein_entry(protein_name: str):
 @app.delete("/protein-entry/{protein_name:str}", response_model=None)
 def delete_protein_entry(protein_name: str):
  # Todo, have a meaningful error if the delete fails
- try:
- with Database() as db:
+ with Database() as db:
+ # remove protein
+ try:
  db.execute(
  """DELETE FROM proteins
  WHERE name = %s""",
  [protein_name],
  )
- # delete the file from the data/ folder
- os.remove(pdb_file_name(protein_name))
- except Exception as e:
- log.error(e)
+  # delete the file from the data/ folder
+  os.remove(pdb_file_name(protein_name))
+  except Exception as e:
+  log.error(e)
 
 
 # None return means success
@@ -148,9 +159,24 @@ def upload_protein_entry(body: UploadBody):
  # write to file to data/ folder
  with open(pdb_file_name(pdb.name), "w") as f:
  f.write(pdb.file_contents)
+ except Exception:
+ log.warn("Failed to write to file")
+ return UploadError.WRITE_ERROR
 
- # save to db
- with Database() as db:
+ # save to db
+ with Database() as db:
+ try:
+ # first add the species if it doesn't exist
+ db.execute(
+ """INSERT INTO species (name) VALUES (%s) ON CONFLICT DO NOTHING;""",
+ [body.species_name],
+ )
+ except Exception:
+ log.warn("Failed to insert into species table")
+ return UploadError.QUERY_ERROR
+
+ try:
+ # add the protein itself
  db.execute(
  """INSERT INTO proteins (name, length, mass, content, refs) VALUES (%s, %s, %s, %s, %s);""",
  [
@@ -161,8 +187,21 @@ def upload_protein_entry(body: UploadBody):
  str_to_bytea(body.refs),
  ],
  )
- except Exception:
- return UploadError.WRITE_ERROR
+ except Exception:
+ log.warn("Failed to insert into proteins table")
+ return UploadError.QUERY_ERROR
+
+ try:
+ # connect them with the intermediate table
+ db.execute(
+ """INSERT INTO species_proteins (species_id, protein_id)
+ VALUES ((SELECT id FROM species WHERE name = %s),
+ (SELECT id FROM proteins WHERE name = %s));""",
+ [body.species_name, body.name],
+ )
+ except Exception:
+ log.warn("Failed to insert into join table")
+ return UploadError.QUERY_ERROR
 
 
 # TODO: add more edits, now only does name and content edits
@@ -176,6 +215,7 @@ def edit_protein_entry(body: EditBody):
  os.rename(pdb_file_name(body.old_name), pdb_file_name(body.new_name))
 
  with Database() as db:
+ name_changed = False
  if body.new_name != body.old_name:
  db.execute(
  """UPDATE proteins SET name = %s WHERE name = %s""",
@@ -184,13 +224,23 @@ def edit_protein_entry(body: EditBody):
  body.old_name,
  ],
  )
+ 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""",
  [
  str_to_bytea(body.new_content),
- body.old_name,
+ body.old_name if not name_changed else body.new_name,
  ],
  )
 
@@ -199,14 +249,26 @@ def edit_protein_entry(body: EditBody):
  """UPDATE proteins SET refs = %s WHERE name = %s""",
  [
  str_to_bytea(body.new_refs),
- body.old_name,
+ body.old_name if not name_changed else body.new_name,
  ],
  )
 
  except Exception:
  return UploadError.WRITE_ERROR
 
 
+@app.get("/all-species", response_model=list[str] | None)
+def get_all_species():
+ try:
+ with Database() as db:
+ query = """SELECT name as species_name FROM species"""
+ entry_sql = db.execute_return(query)
+ if entry_sql is not None:
+ return [d[0] for d in entry_sql]
+ except Exception:
+ return
+
+
 def export_app_for_docker():
  """Needed for the [docker-compose.yml](../../docker-compose.yml)
  Example: `uvicorn src.server:export_app_for_docker --reload --host 0.0.0.0`

frontend/src/lib/ListProteins.svelte

@@ -21,6 +21,7 @@
  <Table>
  <TableHead>
  <TableHeadCell>Protein name</TableHeadCell>
+ <TableHeadCell>Organism</TableHeadCell>
  <TableHeadCell>Length</TableHeadCell>
  <TableHeadCell>Mass (Da)</TableHeadCell>
  </TableHead>
@@ -37,6 +38,7 @@
  ><span class="text-primary-700">{entry.name}</span
  ></TableBodyCell
  >
+ <TableBodyCell>{entry.speciesName}</TableBodyCell>
  <TableBodyCell>{entry.length}</TableBodyCell>
  <TableBodyCell>{numberWithCommas(entry.mass)}</TableBodyCell>
  </TableBodyRow>

frontend/src/openapi/models/EditBody.ts

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

frontend/src/openapi/models/HTTPValidationError.ts

@@ -8,3 +8,4 @@ import type { ValidationError } from './ValidationError';
 export type HTTPValidationError = {
  detail?: Array<ValidationError>;
 };
+