Initialize database structure

2023-05-24 13:52:24 +02:00
parent 6a265d9a72
commit df64d51445
12 changed files with 532 additions and 1 deletions
--- a/README.md
+++ b/README.md
@@ -1,3 +1,37 @@
 # GeneIT

 WIP project
+
+## Setup dev env
+1. Install prerequisites:
+   1. docker
+   2. docker-compose
+   3. rust
+
+
+2. Start services:
+```bash
+cd geneit_backend
+docker-compose up
+```
+
+
+3. Install Diesel CLI:
+
+```bash
+sudo apt install libpq5 libpq-dev
+cargo install diesel_cli --no-default-features --features postgres
+```
+
+
+4. Initialize database:
+
+```bash
+diesel migation run
+```
+
+> Note: You can access the database directly using this command:
+> 
+> ```bash
+> PGPASSWORD=pass psql -h localhost -p 5432 -U user -d bioclimsol
+> ```
--- a/geneit_backend/.env
+++ b/geneit_backend/.env
@@ -0,0 +1 @@
+DATABASE_URL=postgres://user:pass@localhost/geneit
--- a/geneit_backend/.gitignore
+++ b/geneit_backend/.gitignore
@@ -1,2 +1,3 @@
 target/
 storage/
+.idea
--- a/geneit_backend/Cargo.lock
+++ b/geneit_backend/Cargo.lock
@@ -0,0 +1,414 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+
+[[package]]
+name = "anstream"
+version = "0.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163"
+dependencies = [
+ "anstyle",
+ "anstyle-parse",
+ "anstyle-query",
+ "anstyle-wincon",
+ "colorchoice",
+ "is-terminal",
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "41ed9a86bf92ae6580e0a31281f65a1b1d867c0cc68d5346e2ae128dddfa6a7d"
+
+[[package]]
+name = "anstyle-parse"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e765fd216e48e067936442276d1d57399e37bce53c264d6fefbe298080cb57ee"
+dependencies = [
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle-query"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "anstyle-wincon"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188"
+dependencies = [
+ "anstyle",
+ "windows-sys",
+]
+
+[[package]]
+name = "bitflags"
+version = "1.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
+
+[[package]]
+name = "byteorder"
+version = "1.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610"
+
+[[package]]
+name = "cc"
+version = "1.0.79"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f"
+
+[[package]]
+name = "clap"
+version = "4.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93aae7a4192245f70fe75dd9157fc7b4a5bf53e88d30bd4396f7d8f9284d5acc"
+dependencies = [
+ "clap_builder",
+ "clap_derive",
+ "once_cell",
+]
+
+[[package]]
+name = "clap_builder"
+version = "4.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4f423e341edefb78c9caba2d9c7f7687d0e72e89df3ce3394554754393ac3990"
+dependencies = [
+ "anstream",
+ "anstyle",
+ "bitflags",
+ "clap_lex",
+ "strsim",
+]
+
+[[package]]
+name = "clap_derive"
+version = "4.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "191d9573962933b4027f932c600cd252ce27a8ad5979418fe78e43c07996f27b"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.16",
+]
+
+[[package]]
+name = "clap_lex"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b"
+
+[[package]]
+name = "colorchoice"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
+
+[[package]]
+name = "diesel"
+version = "2.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72eb77396836a4505da85bae0712fa324b74acfe1876d7c2f7e694ef3d0ee373"
+dependencies = [
+ "bitflags",
+ "byteorder",
+ "diesel_derives",
+ "itoa",
+ "pq-sys",
+]
+
+[[package]]
+name = "diesel_derives"
+version = "2.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ad74fdcf086be3d4fdd142f67937678fe60ed431c3b2f08599e7687269410c4"
+dependencies = [
+ "proc-macro-error",
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+]
+
+[[package]]
+name = "errno"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a"
+dependencies = [
+ "errno-dragonfly",
+ "libc",
+ "windows-sys",
+]
+
+[[package]]
+name = "errno-dragonfly"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf"
+dependencies = [
+ "cc",
+ "libc",
+]
+
+[[package]]
+name = "geneit_backend"
+version = "0.1.0"
+dependencies = [
+ "clap",
+ "diesel",
+]
+
+[[package]]
+name = "heck"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
+
+[[package]]
+name = "hermit-abi"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fed44880c466736ef9a5c5b5facefb5ed0785676d0c02d612db14e54f0d84286"
+
+[[package]]
+name = "io-lifetimes"
+version = "1.0.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9c66c74d2ae7e79a5a8f7ac924adbe38ee42a859c6539ad869eb51f0b52dc220"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "windows-sys",
+]
+
+[[package]]
+name = "is-terminal"
+version = "0.4.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f"
+dependencies = [
+ "hermit-abi",
+ "io-lifetimes",
+ "rustix",
+ "windows-sys",
+]
+
+[[package]]
+name = "itoa"
+version = "1.0.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6"
+
+[[package]]
+name = "libc"
+version = "0.2.144"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1"
+
+[[package]]
+name = "linux-raw-sys"
+version = "0.3.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519"
+
+[[package]]
+name = "once_cell"
+version = "1.17.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b7e5500299e16ebb147ae15a00a942af264cf3688f47923b8fc2cd5858f23ad3"
+
+[[package]]
+name = "pq-sys"
+version = "0.4.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "31c0052426df997c0cbd30789eb44ca097e3541717a7b8fa36b1c464ee7edebd"
+dependencies = [
+ "vcpkg",
+]
+
+[[package]]
+name = "proc-macro-error"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c"
+dependencies = [
+ "proc-macro-error-attr",
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+ "version_check",
+]
+
+[[package]]
+name = "proc-macro-error-attr"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "version_check",
+]
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.58"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fa1fb82fc0c281dd9671101b66b771ebbe1eaf967b96ac8740dcba4b70005ca8"
+dependencies = [
+ "unicode-ident",
+]
+
+[[package]]
+name = "quote"
+version = "1.0.27"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f4f29d145265ec1c483c7c654450edde0bfe043d3938d6972630663356d9500"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "rustix"
+version = "0.37.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "acf8729d8542766f1b2cf77eb034d52f40d375bb8b615d0b147089946e16613d"
+dependencies = [
+ "bitflags",
+ "errno",
+ "io-lifetimes",
+ "libc",
+ "linux-raw-sys",
+ "windows-sys",
+]
+
+[[package]]
+name = "strsim"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
+
+[[package]]
+name = "syn"
+version = "1.0.109"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "syn"
+version = "2.0.16"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a6f671d4b5ffdb8eadec19c0ae67fe2639df8684bd7bc4b83d986b8db549cf01"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "unicode-ident"
+version = "1.0.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e5464a87b239f13a63a501f2701565754bae92d243d4bb7eb12f6d57d2269bf4"
+
+[[package]]
+name = "utf8parse"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+
+[[package]]
+name = "vcpkg"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+
+[[package]]
+name = "version_check"
+version = "0.9.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+
+[[package]]
+name = "windows-sys"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
+dependencies = [
+ "windows-targets",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7b1eb6f0cd7c80c79759c929114ef071b87354ce476d9d94271031c0497adfd5"
+dependencies = [
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
+
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc"
+
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3"
+
+[[package]]
+name = "windows_i686_gnu"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a"
--- a/geneit_backend/Cargo.toml
+++ b/geneit_backend/Cargo.toml
@@ -6,3 +6,5 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

 [dependencies]
+clap = { version = "4.3.0", features = ["derive", "env"] }
+diesel = { version = "2.0.4", features = ["postgres"] }
--- a/geneit_backend/diesel.toml
+++ b/geneit_backend/diesel.toml
@@ -0,0 +1,8 @@
+# For documentation on how to configure this file,
+# see https://diesel.rs/guides/configuring-diesel-cli
+
+[print_schema]
+file = "src/schema.rs"
+
+[migrations_directory]
+dir = "migrations"
--- a/geneit_backend/migrations/.keep
+++ b/geneit_backend/migrations/.keep
--- a/geneit_backend/migrations/00000000000000_diesel_initial_setup/down.sql
+++ b/geneit_backend/migrations/00000000000000_diesel_initial_setup/down.sql
@@ -0,0 +1,6 @@
+-- This file was automatically created by Diesel to setup helper functions
+-- and other internal bookkeeping. This file is safe to edit, any future
+-- changes will be added to existing projects as new migrations.
+
+DROP FUNCTION IF EXISTS diesel_manage_updated_at(_tbl regclass);
+DROP FUNCTION IF EXISTS diesel_set_updated_at();
--- a/geneit_backend/migrations/00000000000000_diesel_initial_setup/up.sql
+++ b/geneit_backend/migrations/00000000000000_diesel_initial_setup/up.sql
@@ -0,0 +1,36 @@
+-- This file was automatically created by Diesel to setup helper functions
+-- and other internal bookkeeping. This file is safe to edit, any future
+-- changes will be added to existing projects as new migrations.
+
+
+
+
+-- Sets up a trigger for the given table to automatically set a column called
+-- `updated_at` whenever the row is modified (unless `updated_at` was included
+-- in the modified columns)
+--
+-- # Example
+--
+-- ```sql
+-- CREATE TABLE users (id SERIAL PRIMARY KEY, updated_at TIMESTAMP NOT NULL DEFAULT NOW());
+--
+-- SELECT diesel_manage_updated_at('users');
+-- ```
+CREATE OR REPLACE FUNCTION diesel_manage_updated_at(_tbl regclass) RETURNS VOID AS $$
+BEGIN
+    EXECUTE format('CREATE TRIGGER set_updated_at BEFORE UPDATE ON %s
+                    FOR EACH ROW EXECUTE PROCEDURE diesel_set_updated_at()', _tbl);
+END;
+$$ LANGUAGE plpgsql;
+
+CREATE OR REPLACE FUNCTION diesel_set_updated_at() RETURNS trigger AS $$
+BEGIN
+    IF (
+        NEW IS DISTINCT FROM OLD AND
+        NEW.updated_at IS NOT DISTINCT FROM OLD.updated_at
+    ) THEN
+        NEW.updated_at := current_timestamp;
+    END IF;
+    RETURN NEW;
+END;
+$$ LANGUAGE plpgsql;
--- a/geneit_backend/migrations/2023-05-24-102711_create_users/down.sql
+++ b/geneit_backend/migrations/2023-05-24-102711_create_users/down.sql
@@ -0,0 +1,2 @@
+-- This file should undo anything in `up.sql`
+DROP table users;
--- a/geneit_backend/migrations/2023-05-24-102711_create_users/up.sql
+++ b/geneit_backend/migrations/2023-05-24-102711_create_users/up.sql
@@ -0,0 +1,12 @@
+-- Create table
+CREATE TABLE users (
+    id SERIAL PRIMARY KEY,
+    email VARCHAR(255) NOT NULL,
+    password VARCHAR NULL,
+    reset_password_token VARCHAR(150) NULL,
+    time_create BIGINT NOT NULL,
+    time_gen_reset_token BIGINT NOT NULL DEFAULT 0,
+    time_activate BIGINT NOT NULL DEFAULT 0,
+    active BOOLEAN NOT NULL DEFAULT TRUE,
+    admin BOOLEAN NOT NULL DEFAULT FALSE
+)
--- a/geneit_backend/src/schema.rs
+++ b/geneit_backend/src/schema.rs
@@ -0,0 +1,15 @@
+// @generated automatically by Diesel CLI.
+
+diesel::table! {
+    users (id) {
+        id -> Int4,
+        email -> Varchar,
+        password -> Nullable<Varchar>,
+        reset_password_token -> Nullable<Varchar>,
+        time_create -> Int8,
+        time_gen_reset_token -> Int8,
+        time_activate -> Int8,
+        active -> Bool,
+        admin -> Bool,
+    }
+}
				`@@ -0,0 +1 @@`
				`DATABASE_URL=postgres://user:pass@localhost/geneit`