Merge pull request #193 from xnought/search

feat: title, description, and content fuzzy search

backend/init.sql

@@ -11,6 +11,8 @@
 -- Generated columns:
 -- https://www.postgresql.org/docs/current/ddl-generated-columns.html
 
+CREATE EXTENSION pg_trgm; -- for trigram matching fuzzy search similarity() func
+
 /*
  * Species Table
  */
@@ -28,8 +30,8 @@ CREATE TABLE proteins (
  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)
- refs bytea, -- bibtex references mentioned in the content/article
+ content text, -- stored markdown for the protein article (TODO: consider having a limit to how big this can be)
+ refs text, -- bibtex references mentioned in the content/article
  species_id integer NOT NULL,
  thumbnail bytea, -- thumbnail image of the protein in base64 format
  FOREIGN KEY (species_id) REFERENCES species(id) ON UPDATE CASCADE ON DELETE CASCADE

backend/src/api/protein.py

@@ -164,10 +164,6 @@ def get_protein_entry(protein_name: str):
  ) = only_returned_entry
 
  # if byte arrays are present, decode them into a string
- if content is not None:
- content = bytea_to_str(content)
- if refs is not None:
- refs = bytea_to_str(refs)
  if thumbnail is not None:
  thumbnail = bytea_to_str(thumbnail)
 
@@ -263,8 +259,8 @@ def upload_protein_entry(body: UploadBody, req: Request):
  body.description,
  pdb.num_amino_acids,
  pdb.mass_daltons,
- str_to_bytea(body.content),
- str_to_bytea(body.refs),
+ body.content,
+ body.refs,
  body.species_name,
  ],
  )
@@ -310,7 +306,7 @@ def edit_protein_entry(body: EditBody, req: Request):
  db.execute(
  """UPDATE proteins SET content = %s WHERE name = %s""",
  [
- str_to_bytea(body.new_content),
+ body.new_content,
  body.old_name if not name_changed else body.new_name,
  ],
  )
@@ -319,7 +315,7 @@ def edit_protein_entry(body: EditBody, req: Request):
  db.execute(
  """UPDATE proteins SET refs = %s WHERE name = %s""",
  [
- str_to_bytea(body.new_refs),
+ body.new_refs,
  body.old_name if not name_changed else body.new_name,
  ],
  )

backend/src/api/search.py

@@ -74,41 +74,61 @@ def get_descriptions(protein_names: list[str]):
 
 
 def gen_sql_filters(
+ species_table: str,
+ proteins_table: str,
  species_filter: str | None,
  length_filter: RangeFilter | None = None,
  mass_filter: RangeFilter | None = None,
 ) -> str:
  filters = [
- category_where_clause("species.name", species_filter),
- range_where_clause("proteins.length", length_filter),
- range_where_clause("proteins.mass", mass_filter),
+ category_where_clause(f"{species_table}.name", species_filter),
+ range_where_clause(f"{proteins_table}.length", length_filter),
+ range_where_clause(f"{proteins_table}.mass", mass_filter),
  ]
  return " AND " + combine_where_clauses(filters) if any(filters) else ""
 
 
 @router.post("/search/proteins", response_model=SearchProteinsResults)
 def search_proteins(body: SearchProteinsBody):
- title_query = sanitize_query(body.query)
+ text_query = sanitize_query(body.query)
  with Database() as db:
  try:
  filter_clauses = gen_sql_filters(
- body.species_filter, body.length_filter, body.mass_filter
+ "species",
+ "proteins_scores",
+ body.species_filter,
+ body.length_filter,
+ body.mass_filter,
  )
- entries_query = """SELECT proteins.name, 
- proteins.description, 
- proteins.length, 
- proteins.mass, 
+ threshold = 0
+ score_filter = (
+ f"(proteins_scores.name_score >= {threshold} OR proteins_scores.desc_score >= {threshold} OR proteins_scores.content_score >= {threshold})" # show only the scores > 0
+ if len(text_query) > 0
+ else "TRUE" # show all scores
+ )
+ # cursed shit, edit this at some point
+ # note that we have a sub query since postgres can't do where clauses on aliased tables
+ entries_query = """SELECT proteins_scores.name, 
+ proteins_scores.description, 
+ proteins_scores.length, 
+ proteins_scores.mass, 
  species.name,
- proteins.thumbnail
- FROM proteins 
- JOIN species ON species.id = proteins.species_id 
- WHERE proteins.name ILIKE %s"""
+ proteins_scores.thumbnail
+ FROM (SELECT *, 
+ similarity(name, %s) as name_score, 
+ similarity(description, %s) as desc_score,
+ similarity(content, %s) as content_score
+ FROM proteins) as proteins_scores
+ JOIN species ON species.id = proteins_scores.species_id
+ WHERE {} {}
+ ORDER BY (proteins_scores.name_score*4 + proteins_scores.desc_score*2 + proteins_scores.content_score) DESC;
+ """.format(
+ score_filter, filter_clauses
+ ) # numbers in order by correspond to weighting
  log.warn(filter_clauses)
  entries_result = db.execute_return(
- sanitize_query(entries_query + filter_clauses),
- [
- f"%{title_query}%",
- ],
+ sanitize_query(entries_query),
+ [text_query, text_query, text_query],
  )
  if entries_result is not None:
  return SearchProteinsResults(

galaxy/.gitignore

@@ -0,0 +1 @@
+master_venom_galaxy/