update database migration toolkit

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

Author: keinsell

.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

.idea/dataSources.xml

@@ -4,7 +4,7 @@ cargo-features = ["edition2024"]
 name = "neuronek"
 description = "🧬 Intelligent dosage tracker application for monitoring supplements, nootropics and psychoactive substances along with their long-term influence on one's mind and body."
 authors = ["Jakub Olan <[email protected]>"]
-version = "0.0.0-dev.5"
+version = "0.0.0-dev.6"
 edition = "2024"
 repository = "https://github.com/keinsell/neuronek"
 
@@ -28,25 +28,19 @@ serde = { version = "1.0.216", features = ["derive", "std", "unstable"] }
 lazy_static = "1.5.0"
 figlet-rs = "0.1.5"
 serde_json = "1.0.133"
-chrono ={version = "0.4.39", features = ["std", "serde", "iana-time-zone"]}
+chrono = { version = "0.4.39", features = ["std", "serde", "iana-time-zone"] }
 log = { version = "0.4.22", features = ["serde", "kv"] }
 measurements = { version = "0.11.0", features = ["std", "serde", "from_str", "regex"] }
 pubchem = "0.1.1"
 tabled = "0.17.0"
 rust-embed = "8.5.0"
-predicates = "3.1.2"
 assert_cmd = "2.0.16"
 logforth = "0.19.0"
-bupropion = "0.0.20"
 typed-builder = "0.20.0"
 date_time_parser = "0.2.0"
-chrono-humanize = "0.2.3"
 chrono-english = "0.1.7"
 clap-verbosity-flag = "3.0.1"
-clap_autocomplete = "0.4.2"
-tantivy = "0.22.0"
 clap_complete = "4.5.40"
-clap_complete_command = "0.6.1"
 atty = "0.2.14"
 [dependencies.sea-orm-migration]
 version = "1.1.0"
@@ -64,4 +58,4 @@ atty = "0.2"
 
 [profile.dist]
 inherits = "release"
-lto = "fat"
+lto = "fat"

Cargo.toml

@@ -7,14 +7,11 @@ their long-term influence on one's mind and body.
 
 ## About
 
-Neuronek is an intelligent dosage tracking application designed to monitor and log the use of supplements, nootropics, and
+Neuronek is an intelligent dosage tracking application designed to monitor and log the use of supplements, nootropics,
+and
 psychoactive substances. By recording and analyzing ingestion, it helps users better understand the long-term effects
 of these compounds on their physical and mental health.
 
-### Motivation
-
-As pretty irresponsible autist I do not count times when I was literally forgetting to take a meds, skipped days, took twice, took too late and so on.
-
 ## Getting Started
 
 ### Installation
@@ -65,7 +62,7 @@ After installation, you can start using the application by running the `psylog`
 application provides a command-line interface (CLI) for interacting with its features and functionalities.
 
 ```bash
-❯ psylog --help
+❯ neuronek --help
 ```
 
 ## Features
@@ -233,7 +230,8 @@ friendly human interface.
 
 *Roadmap is a subject to change and one that is presented here is a high-level overview of direction of the project.*
 
-neuronek is an ongoing project with many planned features and improvements. Some of the key areas of development include:
+neuronek is an ongoing project with many planned features and improvements. Some of the key areas of development
+include:
 
 - **Journaling**: A user-friendly interface for creating and managing journal entries related to ingestions, thoughts,
   and experiences.
@@ -242,10 +240,10 @@ neuronek is an ongoing project with many planned features and improvements. Some
 - **Desktop/Mobile Application**
 - **Cloud Sync**
 
-
 ## Contributing
 
-Project do not expect any external contribution. If you want to contribute, please contact me directly via [[email protected]]() and we can discuss the project together and move code to
+Project do not expect any external contribution. If you want to contribute, please contact me directly
+via [[email protected]]() and we can discuss the project together and move code to
 organization out of my profile.
 
 See [CONTRIBUTING.md](CONTRIBUTING.md) for more information.

README.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.

docs/JOURNAL.md

@@ -1,6 +1,9 @@
 default:
     @just --list
 
+install-requirements:
+    cargo install cargo-machete sccache
+
 lint:
     cargo lint
 
@@ -14,6 +17,7 @@ format:
 fix:
     @just format
     cargo fix
+    cargo-machete --fix
 
 build:
     cargo build

justfile

@@ -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/command/substance/get_substance.rs

@@ -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/README.md

@@ -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/justfile

@@ -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`)
+);