Merge branch 'main' into homepage

backend/.gitignore

@@ -1,3 +1,4 @@
 __pycache__/
 .venv
-foldseek/
+foldseek/
+tmalign/

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
  */
@@ -25,13 +27,14 @@ 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, 
+ 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
+ date_published timestamp with time zone DEFAULT CURRENT_TIMESTAMP,
  FOREIGN KEY (species_id) REFERENCES species(id) ON UPDATE CASCADE ON DELETE CASCADE
 );
 
@@ -46,17 +49,66 @@ CREATE TABLE users (
  admin boolean NOT NULL
 );
 
+
+/*
+* Articles Table
+*/
+CREATE TABLE articles (
+ id serial PRIMARY KEY,
+ title text NOT NULL UNIQUE,
+ description text,
+ date_published timestamp with time zone DEFAULT CURRENT_TIMESTAMP,
+ refs text -- bibtex references mentioned in the content/article
+);
+CREATE TABLE components (
+ id serial PRIMARY KEY,
+ article_id integer NOT NULL,
+ component_order integer NOT NULL, -- where this component is within a particular article 
+ FOREIGN KEY (article_id) REFERENCES articles(id) ON UPDATE CASCADE ON DELETE CASCADE
+);
+CREATE TABLE text_components (
+ id serial PRIMARY KEY,
+ component_id integer NOT NULL,
+
+ -- component specific info
+ markdown text DEFAULT '',
+
+ FOREIGN KEY (component_id) REFERENCES components(id) ON UPDATE CASCADE ON DELETE CASCADE
+);
+CREATE TABLE protein_components (
+ id serial PRIMARY KEY,
+ component_id integer NOT NULL,
+
+ -- component specific info
+ name text NOT NULL,
+ aligned_with_name text, 
+
+ FOREIGN KEY (component_id) REFERENCES components(id) ON UPDATE CASCADE ON DELETE CASCADE
+);
+CREATE TABLE image_components (
+ id serial PRIMARY KEY,
+ component_id integer NOT NULL,
+
+ -- component specific info
+ src bytea NOT NULL, --bytes of the image
+ width integer,
+ height integer,
+
+ FOREIGN KEY (component_id) REFERENCES components(id) ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+
 /*
  * Inserts example species into species table
  */
-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 ('ganaspis hookeri');
+INSERT INTO species(name) VALUES ('leptopilina boulardi');
+INSERT INTO species(name) VALUES ('leptopilina heterotoma');
 INSERT INTO species(name) VALUES ('unknown');
 
 /*
  * Inserts test user into user table
  * Email: test
  * Password: test
  */
-INSERT INTO users(username, email, pword, admin) VALUES ('test', 'test', '$2b$12$PFoNf7YM0KNIPP8WGsJjveIOhiJjitsMtfwRcCjdcyTuqjdk/q//u', '1');
+INSERT INTO users(username, email, pword, admin) VALUES ('test', 'test', '$2b$12$PFoNf7YM0KNIPP8WGsJjveIOhiJjitsMtfwRcCjdcyTuqjdk/q//u', '1');