Implemented species and species_proteins tables

backend/init.sql

@@ -5,18 +5,45 @@
 -- To rerun this file, you'll need to do `sh run.sh reload_init_sql`
 -- Keep in mind this will backup the data to `backend/backups` folder and wipe everything in the docker container DB
 
-
--- TODO: modify for https://lucid.app/lucidchart/4958d57d-101d-4c33-aef3-717c381af45c/edit?invitationId=inv_94f4d938-33ba-4f8d-a758-4ac7f452a594&page=0_0#
--- Note: "Numeric" data types have arbitrary precision which are good for calculations. This seems like what we want.
+-- Note: "Numeric" data types have arbitrary precision which are good for calculations, which seems ideal for this project.
 -- https://www.postgresql.org/docs/current/datatype-numeric.html#DATATYPE-NUMERIC-DECIMAL
+
+-- Generated columns:
+-- https://www.postgresql.org/docs/current/ddl-generated-columns.html
+
+/*
+ * Proteins Table
+ */
 CREATE TABLE proteins (
  name text NOT NULL UNIQUE PRIMARY KEY,
- length integer,
+ length integer, -- 
  mass numeric
 );
 
--- NOTE: These file path links are off-the-cuff, and might not be useful to the frontend, so
--- TODO: Change file path links to something useful
+/*
+ * 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
+);
+
+/*
+ * 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,
+ PRIMARY KEY (species_id, protein_id)
+ );
+
+/*
+ * Inserts example proteins into proteins table
+ */
 INSERT INTO proteins (name, length, mass) VALUES (
  'Gh_comp271_c0_seq1', 
  0,
@@ -30,4 +57,53 @@ INSERT INTO proteins (name, length, mass) VALUES (
 INSERT INTO proteins (name, length, mass) VALUES (
  'Lh14_comp2336_c0_seq1', 
  0,
- 0.0);
+ 0.0);
+
+/*
+ * 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(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'
+ );
+
+ /*
+ * Inserts connections between species and proteins
+ */ 
+INSERT INTO species_proteins(species_id, protein_id) VALUES (
+ 'Lb',
+ 'Lb17_comp535_c2_seq1'
+ );
+
+ /*
+ * Inserts connections between species and proteins
+ */ 
+INSERT INTO species_proteins(species_id, protein_id) VALUES (
+ 'Lh',
+ 'Lh14_comp2336_c0_seq1'
+ );
+