Alex/add caregivers (#25)

* Alex/form submission history (#20)

* added history of every form submission

* added history to the router

* created history search

* deleted file i accidentally created

* added tokens and caregiver adding function (#21)

* Add jager to default deployment

* Fix tracing and logging

Least disorganized git repository

* remove unneeded imports

* added form finding for caregivers

* added find caregivers listing, and remove caregiver functionality

* add medication tracking (#22)

* add medication tracking

also some other files got hit by `cargo fmt` 🤷

* forgot `$set`

* improved history and other features

* fixed cookie issue

* re-added medication

---------

Co-authored-by: Chris Graham <Chrisgraham908@gmail.com>
Co-authored-by: LeavesOfFall <131100486+LeavesOfFall@users.noreply.github.com>

.dockerignore

@@ -0,0 +1,97 @@
+# flyctl launch added from .gitignore
+# no compiled
+**\debug
+**\target
+target
+
+# If you commit keys I will personally remove you from this earth
+**\.env
+
+**\**\*.rs.bk
+**\*.pdb
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+**\.idea\**\workspace.xml
+**\.idea\**\tasks.xml
+**\.idea\**\usage.statistics.xml
+**\.idea\**\dictionaries
+**\.idea\**\shelf
+
+# AWS User-specific
+**\.idea\**\aws.xml
+
+# Generated files
+**\.idea\**\contentModel.xml
+
+# Sensitive or high-churn files
+**\.idea\**\dataSources
+**\.idea\**\dataSources.ids
+**\.idea\**\dataSources.local.xml
+**\.idea\**\sqlDataSources.xml
+**\.idea\**\dynamic.xml
+**\.idea\**\uiDesigner.xml
+**\.idea\**\dbnavigator.xml
+
+# Gradle
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+**\.idea\**\gradle.xml
+**\.idea\**\libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+**\cmake-build-*
+
+# Mongo Explorer plugin
+**\.idea\**\mongoSettings.xml
+
+# File-based project format
+**\*.iws
+
+# IntelliJ
+**\out
+
+# mpeltonen/sbt-idea plugin
+**\.idea_modules
+
+# JIRA plugin
+**\atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+**\.idea\replstate.xml
+
+# SonarLint plugin
+**\.idea\sonarlint
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+**\com_crashlytics_export_strings.xml
+**\crashlytics.properties
+**\crashlytics-build.properties
+**\fabric.properties
+
+# Editor-based Rest Client
+**\.idea\httpRequests
+
+# Android studio 3.1+ serialized cache file
+**\.idea\caches\build_file_checksums.ser
+fly.toml

.github/workflows/fly-deploy.yml

@@ -0,0 +1,18 @@
+# See https://fly.io/docs/app-guides/continuous-deployment-with-github-actions/
+
+name: Fly Deploy
+on:
+  push:
+    branches:
+      - main
+jobs:
+  deploy:
+    name: Deploy app
+    runs-on: ubuntu-latest
+    concurrency: deploy-group    # optional: ensure only one action runs at a time
+    steps:
+      - uses: actions/checkout@v4
+      - uses: superfly/flyctl-actions/setup-flyctl@master
+      - run: flyctl deploy --remote-only
+        env:
+          FLY_API_TOKEN: ${{ secrets.FLY_API_TOKEN }}

Cargo.toml

@@ -4,7 +4,7 @@ version = "0.1.0"
 edition = "2021"
 
 [features]
-default = ["local_log", "journal_log"]
+default = ["local_log", "journal_log", "jaeger_tracing"]
 local_log = []
 journal_log = []
 jaeger_tracing = []
@@ -20,10 +20,13 @@ serde_json = "1.0.120"
 tracing = { version = "0.1" }
 tracing-subscriber = { version = "0.3" }
 tracing-journald = { version = "0.3" }
+tracing-opentelemetry = "0.27.0"
+opentelemetry = { version = "0.26", features = ["trace", "metrics"] }
+opentelemetry-stdout = { version = "0.26", features = ["trace", "metrics"] }
+opentelemetry_sdk = { version = "0.26.0", features = ["rt-tokio", "trace"] }
+opentelemetry-otlp = { version = "0.26.0", features = ["grpc-tonic", "metrics"] }
+opentelemetry-semantic-conventions = "0.26.0"
 
-opentelemetry = "0.17.0"
-tracing-opentelemetry = "0.17.2"
-opentelemetry-jaeger = "0.16.0"
 mongodb = "3.0.1"
 dotenvy = "0.15.7"
 anyhow = { version = "1.0.86", features = [] }
@@ -37,4 +40,5 @@ rand = "0.8.5"
 rust-argon2 = "2.1.0"
 tower-cookies = "0.10.0"
 jsonwebtoken = "9.3.0"
-bson = "2.13.0"
+bson = { version = "2.13.0", features = ["chrono-0_4"] }
+chrono-humanize = "0.2.3"

Dockerfile

@@ -19,4 +19,5 @@ COPY --from=build /app/app /usr/local/bin/
 
 HEALTHCHECK --start-period=10s --interval=10s --timeout=3s CMD ["bash", "./healthcheck.sh"]
 
+EXPOSE 8080
 ENTRYPOINT ["/usr/local/bin/app"]

fly.toml

@@ -0,0 +1,22 @@
+# fly.toml app configuration file generated for parkinsons-pulse-service on 2024-10-23T11:24:44+13:00
+#
+# See https://fly.io/docs/reference/configuration/ for information about how to use this file.
+#
+
+app = 'parkinsons-pulse-service'
+primary_region = 'syd'
+
+[build]
+
+[http_service]
+  internal_port = 8080
+  force_https = true
+  auto_stop_machines = 'stop'
+  auto_start_machines = true
+  min_machines_running = 0
+  processes = ['app']
+
+[[vm]]
+  memory = '1gb'
+  cpu_kind = 'shared'
+  cpus = 1

src/app/auth/middleware.rs

@@ -7,7 +7,7 @@ use mongodb::bson::oid::ObjectId;
 use tower_cookies::Cookies;
 use tracing::info;
 
-use crate::app::{auth::utils::decode_jwt, auth::LoginUserBody, models::User};
+use crate::app::{auth::utils::decode_jwt, models::User};
 
 #[derive(serde::Deserialize, serde::Serialize, Clone, Debug)]
 pub struct UserClaims {
@@ -17,6 +17,7 @@ pub struct UserClaims {
     pub last_name: String,
     // national_health_identifer: String,
     pub email_address: String,
+    pub is_patient: bool,
 }
 
 impl TryInto<UserClaims> for User {
@@ -27,6 +28,7 @@ impl TryInto<UserClaims> for User {
             first_name: self.first_name,
             last_name: self.last_name,
             email_address: self.email_address,
+            is_patient: self.is_patient,
         })
     }
 }

src/app/auth/mod.rs

@@ -167,7 +167,8 @@ pub async fn login(
     info!("{:#?}", auth_cookie);
     cookies.add(auth_cookie);
 
-    StatusCode::OK.into_response()
+    (StatusCode::OK, Json(user_without_password)).into_response()
+
 }
 
 async fn logout(cookies: Cookies) -> Response {

src/app/auth/utils.rs

@@ -23,11 +23,11 @@ impl<'a> AuthCookieBuilder<'a> {
     pub fn new(value: String) -> Self {
         Self {
             cookie: CookieBuilder::new("auth_token", value)
-                // .domain(config::get_domain())
+                .domain(config::get_domain())
                 .path("/")
                 .http_only(true)
-                .same_site(tower_cookies::cookie::SameSite::Lax)
-                .secure(false),
+                .same_site(tower_cookies::cookie::SameSite::None)
+                .secure(config::get_is_production() == "PRODUCTION"),
         }
     }
     #[must_use]

src/app/caregiver/add.rs

@@ -21,25 +21,7 @@ use crate::app::{
     },
 };
 
-async fn delete_expired_tokens(
-    collection: &Collection<CaregiverToken>,
-) -> mongodb::error::Result<()> {
-    let now = DateTime::now();
-
-    let filter = doc! {
-      "expired_by": {
-        "$lt": now
-      }
-    };
-
-    let delete_result = collection.delete_many(filter).await?;
-    info!(
-        "Deleted {} expired caregiver tokens",
-        delete_result.deleted_count
-    );
-
-    Ok(())
-}
+use super::delete_expired_tokens;
 
 #[tracing::instrument]
 #[axum::debug_handler]

src/app/caregiver/find.rs

@@ -0,0 +1,96 @@
+use axum::{
+    extract::{Path, State},
+    http::StatusCode,
+    response::{IntoResponse, Response},
+    Json,
+};
+use bson::DateTime;
+use chrono::Utc;
+use futures::StreamExt;
+use mongodb::{
+    bson::{doc, oid::ObjectId, to_document},
+    Collection, Cursor, Database,
+};
+use serde::{Deserialize, Serialize};
+use serde_json::json;
+use tracing::info;
+
+use crate::app::{
+    auth::{self, middleware::Auth},
+    models::{
+        dto::{caregiver::CaregiverTokenPath, form::CreateFormPayload},
+        CaregiverToken, Form, User,
+    },
+};
+
+#[derive(Serialize, Deserialize)]
+struct CaregiverInfo {
+    id: ObjectId,
+    first_name: String,
+    last_name: String,
+    email_address: String,
+}
+
+#[tracing::instrument]
+#[axum::debug_handler]
+pub async fn find_caregiver(State(db): State<Database>, Auth(auth): Auth) -> Response {
+    let Some(auth) = auth else {
+        return (
+            StatusCode::UNAUTHORIZED,
+            String::from("You must be signed in to find caregivers"),
+        )
+            .into_response();
+    };
+
+    // Perform the aggregation using $lookup
+    let pipeline = vec![
+        doc! {
+          "$match": {
+            "_id": auth.id
+          }
+        },
+        doc! {
+            "$lookup": {
+                "from": "users",  // The caregivers collection
+                "localField": "caregivers",  // The field in users that holds caregiver IDs
+                "foreignField": "_id",  // The field in caregivers that matches the user_id
+                "as": "caregivers_info"  // The result will be stored in this field
+            }
+        },
+        doc! {
+            "$project": {
+                "caregivers_info._id": 1,
+                "caregivers_info.first_name": 1,  // Only retrieve caregiver ID and name
+                "caregivers_info.last_name": 1,  // Only retrieve caregiver ID and name
+                "caregivers_info.email_address": 1,  // Only retrieve caregiver ID and name
+            }
+        },
+    ];
+
+    let Ok(mut cursor): Result<Cursor<bson::document::Document>, mongodb::error::Error> =
+        db.collection::<User>("users").aggregate(pipeline).await
+    else {
+        return (
+            StatusCode::INTERNAL_SERVER_ERROR,
+            String::from("could not find caregivers"),
+        )
+            .into_response();
+    };
+
+    let Some(Ok(caregiver)) = cursor.next().await else {
+        return (
+            StatusCode::INTERNAL_SERVER_ERROR,
+            String::from("could not find caregiver list"),
+        )
+            .into_response();
+    };
+
+    let Some(caregiver_info) = caregiver.get("caregivers_info") else {
+        return (
+            StatusCode::INTERNAL_SERVER_ERROR,
+            String::from("cannot extract caregiver information"),
+        )
+            .into_response();
+    };
+    (StatusCode::OK, Json(caregiver_info)).into_response()
+}

src/app/caregiver/generate.rs

@@ -17,13 +17,15 @@ use crate::app::{
     models::{dto::form::CreateFormPayload, CaregiverToken, Form, User},
 };
 
+use super::delete_expired_tokens;
+
 #[tracing::instrument]
 #[axum::debug_handler]
 pub async fn generate(State(db): State<Database>, Auth(auth): Auth) -> Response {
     let Some(auth) = auth else {
         return (
             StatusCode::UNAUTHORIZED,
-            String::from("You must be signed in to create a form"),
+            String::from("You must be signed in to generate a caregiver token"),
         )
             .into_response();
     };