update database migration toolkit

Signed-off-by: keinsell <[email protected]>

.gitattributes

@@ -1,4 +1,4 @@
 flake.lock linguist-generated=true
-src/lib/migration/sql/*.sql linguist-detectable linguist-language=sql
-src/lib/migration/sql/2_add_substance_data.sql binary linguist-vendored
+src/lib/migration/migrations/*.sql linguist-detectable linguist-language=sql
+src/lib/migration/sql/20250101000002_import_substance.sql binary linguist-vendored
 docs/*.md linguist-detectable

docs/JOURNAL.md

@@ -0,0 +1,17 @@
+# Project's Journal
+
+## 2025
+
+### January
+
+#### 01
+
+- **Spent 4 hours** working on implementing a migration toolkit with `Atlas`, only to realize that it’s not really
+  compatible with code-first ORMs like `SeaORM` and adds more complexity than just writing migrations manually in Rust.
+  Well, these things happen. For now, it’s fine for the current scope, but I’ll likely remove `Atlas` in the future. It
+  seems better suited for cloud-native applications, whereas for our **local-first application**, tools like `Sqitch`
+  and `Prisma` seem like more fitting options. **Atlas** does have its use cases, but it’s not a good fit here.
+
+- **Cleaned up the database schema**—we had a lot of unnecessary, chemical-specific data that wasn’t adding any real
+  value to the project. Now, we’re only storing the essential information, which keeps the database clean and focused,
+  without unnecessary bloat.

src/command/substance/get_substance.rs

@@ -35,7 +35,7 @@ impl CommandHandler for GetSubstance
     {
         let substances = substance::Entity::find()
             .filter(substance::Column::CommonNames.contains(&self.substance_name.to_lowercase()))
-            .order_by_asc(substance::Column::SystematicName)
+            .order_by_asc(substance::Column::Name)
             .all(context.database_connection)
             .await
             .into_diagnostic()?;

src/lib/migration/README.md

@@ -1,4 +1,10 @@
-# Running Migrator CLI
+# Database Management
+
+This directory introduces you to management of database schema in application.
+
+```bash
+curl -sSf https://atlasgo.sh | sh -s -- --community
+```
 
 - Generate a new migration file
     ```sh

src/lib/migration/justfile

@@ -0,0 +1,59 @@
+DEFAULT_DATABASE_CONNECTION_URI := "sqlite:///tmp/neuronek.sqlite"
+schema_format := "{{ sql . }}"
+dev_db := "sqlite://dev?mode=memory"
+migration_dir := "./migrations"
+schema_file := "schema.sql"
+
+inspect connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    atlas schema inspect -u {{ connection_uri }}
+
+pull connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    atlas schema inspect -u "{{ connection_uri }}" --format '{{ schema_format }}' > {{ schema_file }}
+
+push connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    atlas schema apply \
+      -u "{{ connection_uri }}" \
+      --to file://schema.sql \
+      --dev-url "{{ dev_db }}"
+
+plan migration_name connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    @just hash
+    atlas migrate diff {{ migration_name }} \
+      --dir "file://{{ migration_dir }}" \
+      --to "file://{{ schema_file }}" \
+      --dev-url "{{ dev_db }}"
+
+create migration_name:
+    atlas migrate new {{ migration_name }}
+
+up connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    @just hash
+    atlas migrate apply \
+      --url "{{ connection_uri }}"
+
+hash:
+    atlas migrate hash --dir="file://{{ migration_dir }}"
+
+fresh:
+    @just hash
+    @just clean
+    @just up
+    @just pull
+
+clean connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    atlas schema clean -u "{{ connection_uri }}" --auto-approve
+
+baseline connection_uri=DEFAULT_DATABASE_CONNECTION_URI:
+    atlas migrate diff baseline \
+      --dir "file://{{ migration_dir }}" \
+      --dev-url "{{ dev_db }}" \
+      --to "{{ connection_uri }}" \
+
+generate:
+    sea-orm-cli generate entity \
+        --compact-format \
+        --ignore-tables=seaql_migrations,atlas_schema_revisions \
+        --output-dir="./../orm" \
+        -u="{{ DEFAULT_DATABASE_CONNECTION_URI }}" \
+        --with-serde=both \
+        --with-copy-enums

src/lib/migration/migrations/20250101000001_add_ingestion_table.sql

@@ -0,0 +1,18 @@
+-- Create "ingestion" table
+CREATE TABLE `ingestion`
+(
+    `id`                      integer       NOT NULL PRIMARY KEY AUTOINCREMENT,
+    `substance_name`          varchar       NOT NULL,
+    `route_of_administration` varchar       NOT NULL,
+    `dosage`                  float         NOT NULL,
+    `ingested_at`             datetime_text NOT NULL,
+    `updated_at`              datetime_text NOT NULL,
+    `created_at`              datetime_text NOT NULL
+);
+-- Create "seaql_migrations" table
+CREATE TABLE IF NOT EXISTS `seaql_migrations`
+(
+    `version`    varchar NOT NULL,
+    `applied_at` bigint  NOT NULL,
+    PRIMARY KEY (`version`)
+);

src/lib/migration/sql/2_add_substance_data.sql → src/lib/migration/migrations/20250101000002_import_substance.sql

@@ -1,3 +1,159 @@
+-- Create "substance" table
+CREATE TABLE `substance`
+(
+    `id`                 text    NOT NULL,
+    `name`               text    NOT NULL,
+    `common_names`       text    NOT NULL,
+    `brand_names`        text    NOT NULL,
+    `substitutive_name`  text    NULL,
+    `systematic_name`    text    NOT NULL,
+    `pubchem_cid`        integer NOT NULL,
+    `unii`               text    NULL,
+    `cas_number`         text    NULL,
+    `inchi_key`          text    NOT NULL,
+    `smiles`             text    NOT NULL,
+    `psychonautwiki_url` text    NULL,
+    `psychoactive_class` text    NOT NULL,
+    `chemical_class`     text    NULL,
+    `description`        text    NULL,
+    PRIMARY KEY (`id`)
+);
+-- Create index "substance_id_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_id_key` ON `substance` (`id`);
+-- Create index "substance_name_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_name_key` ON `substance` (`name`);
+-- Create index "substance_substitutive_name_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_substitutive_name_key` ON `substance` (`substitutive_name`);
+-- Create index "substance_systematic_name_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_systematic_name_key` ON `substance` (`systematic_name`);
+-- Create index "substance_pubchem_cid_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_pubchem_cid_key` ON `substance` (`pubchem_cid`);
+-- Create index "substance_cas_number_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_cas_number_key` ON `substance` (`cas_number`);
+-- Create index "substance_inchi_key_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_inchi_key_key` ON `substance` (`inchi_key`);
+-- Create index "substance_smiles_key" to table: "substance"
+CREATE UNIQUE INDEX `substance_smiles_key` ON `substance` (`smiles`);
+-- Create "substance_synonym" table
+CREATE TABLE `substance_synonym`
+(
+    `id`          text NOT NULL,
+    `substanceId` text NOT NULL,
+    `name`        text NOT NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `substance_synonym_substanceId_fkey` FOREIGN KEY (`substanceId`) REFERENCES `substance` (`id`) ON UPDATE CASCADE ON DELETE RESTRICT
+);
+-- Create index "substance_synonym_name_key" to table: "substance_synonym"
+CREATE UNIQUE INDEX `substance_synonym_name_key` ON `substance_synonym` (`name`);
+-- Create "substance_tolerance" table
+CREATE TABLE `substance_tolerance`
+(
+    `id`                           text NOT NULL,
+    `substanceId`                  text NOT NULL,
+    `mechanism`                    text NOT NULL,
+    `mechanism_desciption`         text NULL,
+    `onset_mechanism`              text NOT NULL,
+    `onset_description`            text NULL,
+    `decline_mechanism`            text NOT NULL,
+    `decline_description`          text NULL,
+    `onset_duration`               text NULL,
+    `decline_to_baseline_duration` text NULL,
+    `decline_to_half_duration`     text NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `substance_tolerance_substanceId_fkey` FOREIGN KEY (`substanceId`) REFERENCES `substance` (`id`) ON UPDATE CASCADE ON DELETE RESTRICT
+);
+-- Create index "substance_tolerance_substanceId_key" to table: "substance_tolerance"
+CREATE UNIQUE INDEX `substance_tolerance_substanceId_key` ON `substance_tolerance` (`substanceId`);
+-- Create "chemical_class" table
+CREATE TABLE `chemical_class`
+(
+    `id`          text NOT NULL,
+    `name`        text NOT NULL,
+    `description` text NULL,
+    PRIMARY KEY (`id`)
+);
+-- Create index "chemical_class_name_key" to table: "chemical_class"
+CREATE UNIQUE INDEX `chemical_class_name_key` ON `chemical_class` (`name`);
+-- Create "psychoactive_class" table
+CREATE TABLE `psychoactive_class`
+(
+    `id`          text NOT NULL,
+    `name`        text NOT NULL,
+    `summary`     text NULL,
+    `description` text NULL,
+    `substanceId` text NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `psychoactive_class_substanceId_fkey` FOREIGN KEY (`substanceId`) REFERENCES `substance` (`id`) ON UPDATE CASCADE ON DELETE SET NULL
+);
+-- Create index "psychoactive_class_name_key" to table: "psychoactive_class"
+CREATE UNIQUE INDEX `psychoactive_class_name_key` ON `psychoactive_class` (`name`);
+-- Create "substance_route_of_administration" table
+CREATE TABLE `substance_route_of_administration`
+(
+    `id`            text NOT NULL,
+    `substanceName` text NOT NULL,
+    `name`          text NOT NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `substance_route_of_administration_substanceName_fkey` FOREIGN KEY (`substanceName`) REFERENCES `substance` (`name`) ON UPDATE CASCADE ON DELETE RESTRICT
+);
+-- Create index "substance_route_of_administration_name_substanceName_key" to table: "substance_route_of_administration"
+CREATE UNIQUE INDEX `substance_route_of_administration_name_substanceName_key` ON `substance_route_of_administration` (`name`, `substanceName`);
+-- Create "substance_interactions" table
+CREATE TABLE `substance_interactions`
+(
+    `id`          text NOT NULL,
+    `substanceId` text NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `SubstanceInteraction_substanceId_fkey` FOREIGN KEY (`substanceId`) REFERENCES `substance` (`id`) ON UPDATE CASCADE ON DELETE SET NULL
+);
+-- Create "effect" table
+CREATE TABLE `effect`
+(
+    `id`             text NOT NULL,
+    `name`           text NOT NULL,
+    `slug`           text NOT NULL,
+    `category`       text NULL,
+    `type`           text NULL,
+    `tags`           text NOT NULL,
+    `summary`        text NULL,
+    `description`    text NOT NULL,
+    `parameters`     text NOT NULL,
+    `see_also`       text NOT NULL,
+    `effectindex`    text NULL,
+    `psychonautwiki` text NULL,
+    PRIMARY KEY (`id`)
+);
+-- Create index "Effect_name_key" to table: "effect"
+CREATE UNIQUE INDEX `Effect_name_key` ON `effect` (`name`);
+-- Create index "Effect_slug_key" to table: "effect"
+CREATE UNIQUE INDEX `Effect_slug_key` ON `effect` (`slug`);
+-- Create "substance_route_of_administration_phase" table
+CREATE TABLE `substance_route_of_administration_phase`
+(
+    `id`                      text NOT NULL,
+    `classification`          text NOT NULL,
+    `lower_duration`          text NULL,
+    `upper_duration`          text NULL,
+    `routeOfAdministrationId` text NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `route_of_administration_phase_routeOfAdministrationId_fkey` FOREIGN KEY (`routeOfAdministrationId`) REFERENCES `substance_route_of_administration` (`id`) ON UPDATE CASCADE ON DELETE SET NULL
+);
+-- Create index "route_of_administration_phase_routeOfAdministrationId_classification_key" to table: "substance_route_of_administration_phase"
+CREATE UNIQUE INDEX `route_of_administration_phase_routeOfAdministrationId_classification_key` ON `substance_route_of_administration_phase` (`routeOfAdministrationId`, `classification`);
+-- Create "substance_route_of_administration_dosage" table
+CREATE TABLE `substance_route_of_administration_dosage`
+(
+    `id`                      text NOT NULL,
+    `intensity`               text NOT NULL,
+    `lower_bound_amount`      real NULL,
+    `upper_bound_amount`      real NULL,
+    `unit`                    text NOT NULL,
+    `routeOfAdministrationId` text NULL,
+    PRIMARY KEY (`id`),
+    CONSTRAINT `route_of_administration_dosage_routeOfAdministrationId_fkey` FOREIGN KEY (`routeOfAdministrationId`) REFERENCES `substance_route_of_administration` (`id`) ON UPDATE CASCADE ON DELETE SET NULL
+);
+-- Create index "route_of_administration_dosage_intensivity_routeOfAdministrationId_key" to table: "substance_route_of_administration_dosage"
+CREATE UNIQUE INDEX `route_of_administration_dosage_intensivity_routeOfAdministrationId_key` ON `substance_route_of_administration_dosage` (`intensity`, `routeOfAdministrationId`);
 -- Disable the enforcement of foreign-keys constraints
 PRAGMA foreign_keys = off;
 -- Create "new_substance_route_of_administration_phase" table
@@ -54,7 +210,6 @@ DELETE
 FROM "substance_route_of_administration";
 DELETE
 FROM "substance";
-BEGIN;
 INSERT INTO substance
 VALUES ('3ab37fdea136ae2c01e5d7670e7ee0d7ea1c700367f9d4dfb65d4249fc7c0282f6fe70443f2506c6a5de71bda8e220b1c94de53ff0d4e34e697341e2728c4259',
         '1,3-dimethylbutylamine', '', '', NULL, '4-methylpentan-2-amine', 7908, NULL, NULL,
@@ -13499,5 +13654,21 @@ INSERT INTO substance_route_of_administration_dosage
 VALUES ('3b54f9aead9bf6a954607ca9314b57461b19ec95a0681499d5acad2547d11122d5cc9e6374c3df018a6c11964f3742d6bdeab47a4051ea354872f3beacee5a10',
         'heavy', 15.0, 0.0, 'mg',
         '319bdcc6327775a15fbce77e9fc1a3bb22a2a62acca3fe71f00b57c5d1094607047975ae4e88c548a8d6711be13d82c27bb45dba92e061df92feb834aeb3a8b7');
-END;
-PRAGMA foreign_keys = on;
+PRAGMA foreign_keys = on;
+-- Create "atlas_schema_revisions" table
+CREATE TABLE IF NOT EXISTS `atlas_schema_revisions`
+(
+    `version`          text     NOT NULL,
+    `description`      text     NOT NULL,
+    `type`             integer  NOT NULL DEFAULT 2,
+    `applied`          integer  NOT NULL DEFAULT 0,
+    `total`            integer  NOT NULL DEFAULT 0,
+    `executed_at`      datetime NOT NULL,
+    `execution_time`   integer  NOT NULL,
+    `error`            text     NULL,
+    `error_stmt`       text     NULL,
+    `hash`             text     NOT NULL,
+    `partial_hashes`   json     NULL,
+    `operator_version` text     NOT NULL,
+    PRIMARY KEY (`version`)
+);