Mostly working state

.gitea/workflows/release-linux.yml

@@ -0,0 +1,67 @@
+name: Build and Package JRuby Rails App
+
+#on:
+#  push:
+#    branches:
+#      - main
+#      - second_try
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install Java and JRuby
+        run: |
+          apt-get update && apt-get install -y wget curl libgmp-dev
+          # Install Java (needed for JRuby and jpackage)
+          apt-get install -y openjdk-17-jdk
+          
+          # Download and install JRuby directly
+          JRUBY_VERSION="9.4.6.0"
+          curl -O https://repo1.maven.org/maven2/org/jruby/jruby-dist/${JRUBY_VERSION}/jruby-dist-${JRUBY_VERSION}-bin.tar.gz
+          tar -xzf jruby-dist-${JRUBY_VERSION}-bin.tar.gz -C /opt/
+          ln -s /opt/jruby-${JRUBY_VERSION}/bin/jruby /usr/local/bin/jruby
+          ln -s /opt/jruby-${JRUBY_VERSION}/bin/bundle /usr/local/bin/bundle
+
+      - name: Install Dependencies
+        run: |
+          bundle install
+
+      - name: Build JAR with Jarbler
+        run: |
+          gem install jarbler
+          jarble
+
+      - name: Generate Unique App Name with Git Hash
+        id: vars
+        run: |
+          SHORT_HASH=$(git rev-parse --short HEAD)
+          echo "app_name=custom-app-${SHORT_HASH}" >> $GITHUB_OUTPUT
+
+      - name: Package with jpackage
+        run: |
+          # Find the generated jar file name dynamically
+          JAR_FILE=$(ls build/*.jar | head -n 1)
+          
+          # Run jpackage to bundle the application and runtime into an app-image directory
+          jpackage \
+            --type app-image \
+            --name "${{ steps.vars.outputs.app_name }}" \
+            --input "$(dirname "$JAR_FILE")" \
+            --main-jar "$(basename "$JAR_FILE")" \
+            --dest dist
+
+      - name: Compress Executable Package
+        run: |
+          cd dist
+          tar -czvf "${{ steps.vars.outputs.app_name }}.tar.gz" "${{ steps.vars.outputs.app_name }}"
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ steps.vars.outputs.app_name }}
+          path: dist/*.tar.gz

.github/workflows/ci.yml

@@ -3,7 +3,7 @@ name: CI
 on:
   pull_request:
   push:
-    branches: [ main ]
+    branches: [ main, second_try ]
 
 jobs:
   scan_ruby:
@@ -76,7 +76,7 @@ jobs:
     #    options: --health-cmd "redis-cli ping" --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - name: Install packages
-        run: sudo apt-get update && sudo apt-get install --no-install-recommends -y libvips
+        run: apt-get update && apt-get install --no-install-recommends -y libvips
 
       - name: Checkout code
         uses: actions/checkout@v6
@@ -104,7 +104,7 @@ jobs:
     #    options: --health-cmd "redis-cli ping" --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - name: Install packages
-        run: sudo apt-get update && sudo apt-get install --no-install-recommends -y libvips
+        run: apt-get update && apt-get install --no-install-recommends -y libvips
 
       - name: Checkout code
         uses: actions/checkout@v6

NOTES.md

@@ -0,0 +1,13 @@
+# Setting up the application
+
+## Create the database connections:
+
+bin/rails generate model Joints --no-migration
+bin/rails generate model JointsInfo --no-migration
+bin/rails generate model SpecialTest --no-migration
+
+
+# Setup the views
+
+bin/rails generate controller dashboard
+

app/controllers/dashboard_controller.rb

@@ -0,0 +1,78 @@
+require 'yaml'
+
+
+## Debugging:
+# If the response should be filtered and it is not being filtered **and** you
+# are geting all the values for that column, check to make sure that you are
+# selecting from the allowed tables and columns.
+
+
+ALLOWED_TABLES = {
+  "JointInfo" => ["Joint", "Osteokinematics"],
+  "Joint"     => ["Common Name", "Joint"]
+}
+
+
+class DashboardController < ApplicationController
+  before_action :load_manifest
+
+  def index
+    # Renders the main page
+    respond_to do |format|
+      format.html
+      format.json { render json: @manifest }
+    end
+  end
+
+  # GET /dashboard/options?table=Joint&filter_col=joint_id&value=1
+  def options
+    # 1. Define what is allowed to be accessed
+
+    table_name = params[:table]
+    col_name = params[:pluck_column]
+
+    # 2. Validate that the table and column exist in your allowlist
+    if ALLOWED_TABLES.key?(table_name) && ALLOWED_TABLES[table_name].include?(col_name)
+      table = table_name.constantize
+      quoted_col = ActiveRecord::Base.connection.quote_column_name(col_name)
+
+      if params[:filter_column].present? && ALLOWED_TABLES[table_name].include?(params[:filter_column])
+        puts "Filtering with 'filter_column'"
+        options = table.select(Arel.sql(quoted_col)).where(params[:filter_column] => params[:value]).pluck(Arel.sql(quoted_col))
+      else
+        puts "***NO FILTERING***"
+        options = table.distinct.pluck(Arel.sql(quoted_col))
+      end
+      
+      render json: options
+    else
+      render json: { error: "Invalid table or column requested" }, status: :bad_request
+    end
+  end
+
+  # GET /dashboard/data?joint=Acromioclavicular&sub_joint=X
+  def data
+    results = {}
+    
+    # Use the data_sources from YAML to aggregate data
+    @manifest['data_sources'].each do |source|
+      debugger
+      table = source['table'].constantize
+      # Find the filter value from the params that matches the filter_column
+      # We assume the filter_column name in DB matches the filter ID in YAML
+      filter_val = params[source['filter_column']]
+      
+      record = table.find_by(source['filter_column'] => filter_val)
+      results[source['key']] = record ? record.attributes : {}
+    end
+    
+    #debugger
+    render json: results
+  end
+
+  private
+
+  def load_manifest
+    @manifest = YAML.load_file(Rails.root.join('config', 'dashboard_manifest.yml'))
+  end
+end

app/helpers/dashboard_helper.rb

@@ -0,0 +1,2 @@
+module DashboardHelper
+end

app/models/joint.rb

@@ -0,0 +1,5 @@
+class Joint < ApplicationRecord
+  def readonly?
+    true
+  end
+end

app/models/joint_info.rb

@@ -0,0 +1,5 @@
+class JointInfo < ApplicationRecord
+  def readonly?
+    true
+  end
+end

app/models/special_test.rb

@@ -0,0 +1,5 @@
+class SpecialTest < ApplicationRecord
+  def readonly?
+    true
+  end
+end

app/views/dashboard/index.html.erb

@@ -0,0 +1,219 @@
+<h1 style="font-family: Arial, sans-serif;">Dynamic Dashboard</h1>
+
+<div id="filter-area" style="margin-bottom: 20px; display: flex; gap: 15px; font-family: Arial, sans-serif;">
+  <!-- Dropdowns injected here by JS -->
+</div>
+
+<div id="results-area" style="display: flex; gap: 20px;">
+  <!-- Grids injected here by JS -->
+</div>
+
+<style>
+  .dyn-grid { border-collapse: collapse; border: 2px solid #000; font-family: Arial; font-size: 12px; }
+  .dyn-grid td { border: 1px solid #000; padding: 4px 8px; text-align: center; }
+  .bg-dark-blue { background-color: #002060; color: white; font-weight: bold; }
+  .bg-light-blue { background-color: #D9E1F2; font-weight: bold; }
+  .bg-pale-yellow { background-color: #FFFFCC; }
+  .bg-pale-green { background-color: #E2EFDA; }
+  .bg-pale-orange { background-color: #FCE4D6; }
+</style>
+
+
+<script>
+document.addEventListener("DOMContentLoaded", () => {
+  let manifest = {};
+  let currentSelections = {};
+
+  async function init() {
+    const resp = await fetch(
+      '/dashboard',
+      {
+        headers: {
+          'Accept': 'application/json'
+        }
+      });
+    manifest = await resp.json();
+    await renderRootFilters();
+  }
+
+  async function renderRootFilters() {
+    const rootFilters = manifest.filters.filter(f => f.depends_on === null);
+    for (const f of rootFilters) {
+      await createDropdown(f);
+    }
+    //rootFilters.forEach(f => await createDropdown(f));
+  }
+
+  async function createDropdown(config) {
+    const container = document.createElement("div");
+    container.id = `container_${config.id}`;
+    
+    const label = document.createElement("label");
+    label.textContent = config.label + ": ";
+    label.style.fontWeight = "bold";
+
+    const select = document.createElement("select");
+    select.id = config.id;
+    select.innerHTML = `<option value="">Select...</option>`;
+    
+    // Marked callback as async
+    select.addEventListener("change", async (e) => {
+      const val = e.target.value;
+      currentSelections[config.id] = val;
+      
+      // 1. Clear dependent filters and data
+      clearDependents(config.id);
+      
+      // 2. Load options for children (Fixed with for...of)
+      const children = manifest.filters.filter(f => f.depends_on === config.id);
+      for (const child of children) {
+        const options = await fetchOptions(child, val);
+        populateDropdown(child.id, options);
+      }
+
+      // 3. Update data grid
+      updateGrid();
+    });
+
+    container.appendChild(label);
+    container.appendChild(select);
+    document.getElementById("filter-area").appendChild(container);
+    // Special handling for parent items:
+    if (config.depends_on === null) {
+      var options = await fetchOptions(config);
+      populateDropdown(select.id, options)
+    }
+  }
+
+  async function fetchOptions(config, value) {
+    var params
+    if (config.filter_column == undefined) {
+      console.log(config + "Undefined filter col");
+      params = new URLSearchParams({
+        table: config.table, 
+        pluck_column: config.pluck_column,
+      });
+    } else {
+       params = new URLSearchParams({
+        table: config.table,
+        pluck_column: config.pluck_column,
+        filter_column: config.filter_column,
+        value: value
+      });
+    }
+    const resp = await fetch(`/dashboard/options?${params.toString()}`);
+    return await resp.json();
+  }
+
+  function populateDropdown(id, options) {
+    const select = document.getElementById(id) || createMissingDropdown(id);
+    select.innerHTML = `<option value="">Select...</option>`;
+    options.forEach(opt => {
+      select.innerHTML += `<option value="${opt}">${opt}</option>`;
+    });
+    // If this is the last dropdown, it should be visible now
+    const container = document.getElementById(`container_${id}`);
+    if(container) container.style.display = "block";
+  }
+
+  function createMissingDropdown(id) {
+    const config = manifest.filters.find(f => f.id === id);
+    const container = document.createElement("div");
+    container.id = `container_${id}`;
+    container.style.display = "none"; // Hidden until parent is selected
+    
+    const label = document.createElement("label");
+    label.textContent = config.label + ": ";
+    
+    const select = document.createElement("select");
+    select.id = id;
+    
+    // Marked callback as async
+    select.addEventListener("change", async (e) => {
+      currentSelections[id] = e.target.value;
+      clearDependents(id);
+      const children = manifest.filters.filter(f => f.depends_on === id);
+      
+      // Fixed with for...of loop
+      for (const child of children) {
+        const opts = await fetchOptions(child, e.target.value);
+        populateDropdown(child.id, opts);
+      }
+      updateGrid();
+    });
+
+    container.appendChild(label);
+    container.appendChild(select);
+    document.getElementById("filter-area").appendChild(container);
+    return select;
+  }
+
+  function clearDependents(id) {
+    // Recursively find all filters that depend on this ID and reset them
+    manifest.filters.forEach(f => {
+      if (f.depends_on === id) {
+        const select = document.getElementById(f.id);
+        if (select) select.innerHTML = `<option value="">Select...</option>`;
+        const container = document.getElementById(`container_${f.id}`);
+        if (container) container.style.display = "none";
+        delete currentSelections[f.id];
+        clearDependents(f.id);
+      }
+    });
+  }
+
+  async function updateGrid() {
+    const params = new URLSearchParams(currentSelections);
+    const resp = await fetch(`/dashboard/data?${params.toString()}`);
+    const data = await resp.json();
+    renderLayout(data);
+  }
+
+  function renderLayout(data) {
+    const area = document.getElementById("results-area");
+    area.innerHTML = "";
+
+    // Group layout by grid name (defaults to 'main')
+    const grids = {};
+    manifest.layout.forEach(item => {
+      const gridId = item.grid || 'main';
+      if (!grids[gridId]) grids[gridId] = [];
+      grids[gridId].push(item);
+    });
+
+    Object.keys(grids).forEach(gridId => {
+      const table = document.createElement("table");
+      table.className = "dyn-grid";
+      
+      const layoutItems = grids[gridId];
+      const maxRow = Math.max(...layoutItems.map(i => i.row));
+      
+      for (let r = 0; r <= maxRow; r++) {
+        const tr = document.createElement("tr");
+        const rowItems = layoutItems.filter(i => i.row === r);
+        
+        rowItems.forEach(item => {
+          const td = document.createElement("td");
+          td.className = item.class;
+          td.colSpan = item.colspan || 1;
+          td.rowSpan = item.rowspan || 1;
+          
+          if (item.text) {
+            td.textContent = item.text;
+          } else if (item.value) {
+            // Resolve nested JSON path (e.g., "main_info.joint")
+            const parts = item.value.split('.');
+            const val = parts.reduce((obj, key) => (obj && obj[key] !== undefined) ? obj[key] : '', data);
+            td.textContent = val;
+          }
+          tr.appendChild(td);
+        });
+        table.appendChild(tr);
+      }
+      area.appendChild(table);
+    });
+  }
+
+  init();
+});
+</script>

config/dashboard_manifest.yml

@@ -0,0 +1,48 @@
+# Filter Hierarchy: Defines the dropdowns and their dependencies
+filters:
+  - id: "joint"
+    label: "Select Joint"
+    table: "Joint"
+    pluck_column: "Joint"
+    depends_on: null # Root level
+  - id: "joint_info"
+    label: "Select kinematics"
+    table: "JointInfo" # A separate table in SQLite
+    pluck_column: "Osteokinematics"
+    depends_on: "joint" # Only appears after 'joint' is selected
+    filter_column: "Joint" # Filter SubJoint where joint_id == selected joint value
+
+# Data Mapping: Defines which tables to hit for the final grid
+data_sources:
+  - table: "Joint"
+    key: "main_info" # Nested JSON key
+    filter_column: "joint" 
+  - table: "JointInfo" # MUST MATCH DATABASE TABLE
+    key: "joint_details"
+    filter_column: "Osteokinematics"
+
+# Layout: Defines the visual grid
+# colors: dark_blue, light_blue, pale_yellow, pale_green, pale_orange
+layout:
+  - { row: 0, col: 0, colspan: 3, rowspan: 1, text: "Joint Information", class: "bg-dark-blue" }
+  - { row: 1, col: 0, colspan: 2, rowspan: 1, text: "Anatomical Name", class: "bg-light-blue" }
+  - { row: 2, col: 0, colspan: 2, rowspan: 1, value: "main_info.Joint", class: "bg-pale-yellow" }
+  - { row: 1, col: 2, colspan: 1, rowspan: 1, text: "Common Name", class: "bg-light-blue" }
+  - { row: 2, col: 2, colspan: 1, rowspan: 1, value: "main_info.Common Name", class: "bg-pale-yellow" }
+  - { row: 3, col: 0, colspan: 1, rowspan: 1, text: "Diarthrodial Joint Type", class: "bg-light-blue" }
+  - { row: 4, col: 0, colspan: 1, rowspan: 1, value: "main_info.Diarthrodial joint", class: "bg-pale-yellow" }
+  - { row: 3, col: 1, colspan: 1, rowspan: 1, text: "Alternate Name", class: "bg-light-blue" }
+  - { row: 4, col: 1, colspan: 1, rowspan: 1, value: "main_info.Alternate Name", class: "bg-pale-yellow" }
+  - { row: 3, col: 2, colspan: 1, rowspan: 1, text: "Planes of Freedom", class: "bg-light-blue" }
+  - { row: 4, col: 2, colspan: 1, rowspan: 1, value: "main_info.# of Plains", class: "bg-pale-yellow" }
+  - { row: 5, col: 0, colspan: 1, rowspan: 1, text: "Arthrokinematic Rule", class: "bg-light-blue"}
+  - { row: 6, col: 0, colspan: 1, rowspan: 1, value: "joint_details.Arthrokinematic Rule", class: "bg-pale-yellow"}
+  #- { row: 5, col: 0, colspan: 4, rowspan: 1, value: "main_info.notes", class: "bg-pale-green" }
+  
+  # Ligaments Table (separate grid)
+  #- { grid: "ligaments", row: 0, col: 0, colspan: 1, rowspan: 1, text: "Ligaments", class: "bg-dark-blue" }
+  #- { grid: "ligaments", row: 0, col: 1, colspan: 1, rowspan: 1, value: ".list", class: "bg-pale-orange" }
+
+
+# http://localhost:3000/dashboard/options?table=JointInfo&pluck_column=Osteokinematics&filter_col=undefined&value=Glenohumeral
+# http://localhost:3000/dashboard/options?table=JointInfo&pluck_column=Osteokinematics&filter_col=Common%20Joint%20Name&value=Shoulder

config/database.yml

@@ -10,8 +10,11 @@ default: &default
   timeout: 5000
 
 development:
-  <<: *default
-  database: storage/development.sqlite3
+  adapter: sqlite3
+  max_connections: 5
+  timeout: 5000
+  database: storage/anat_proj.db
+  #readonly: true
 
 # Warning: The database defined as "test" will be erased and
 # re-generated from your development database when you run "rake".

config/routes.rb

@@ -11,4 +11,8 @@ Rails.application.routes.draw do
 
   # Defines the root path route ("/")
   # root "posts#index"
+  root "dashboard#index"
+  get "dashboard", to: "dashboard#index"
+  get "dashboard/options", to: "dashboard#options"
+  get "dashboard/data", to: "dashboard#data"
 end

test/controllers/dashboard_controller_test.rb

@@ -0,0 +1,14 @@
+require "test_helper"
+
+class DashboardControllerTest < ActionDispatch::IntegrationTest
+  test "options returns JSON" do
+    get "/dashboard/options",
+        params: {
+          table: 'Joint',
+          pluck_column: 'Joint'
+        }
+
+    assert_response :success
+    assert_equal "application/json", response.media_type
+  end
+end

test/fixtures/joints.yml

@@ -0,0 +1,11 @@
+# Read about fixtures at https://api.rubyonrails.org/classes/ActiveRecord/FixtureSet.html
+
+# This model initially had no columns defined. If you add columns to the
+# model remove the "{}" from the fixture names and add the columns immediately
+# below each fixture, per the syntax in the comments below
+#
+one: {}
+# column: value
+#
+two: {}
+# column: value

test/fixtures/joints_infos.yml

@@ -0,0 +1,11 @@
+# Read about fixtures at https://api.rubyonrails.org/classes/ActiveRecord/FixtureSet.html
+
+# This model initially had no columns defined. If you add columns to the
+# model remove the "{}" from the fixture names and add the columns immediately
+# below each fixture, per the syntax in the comments below
+#
+one: {}
+# column: value
+#
+two: {}
+# column: value

test/fixtures/special_tests.yml

@@ -0,0 +1,11 @@
+# Read about fixtures at https://api.rubyonrails.org/classes/ActiveRecord/FixtureSet.html
+
+# This model initially had no columns defined. If you add columns to the
+# model remove the "{}" from the fixture names and add the columns immediately
+# below each fixture, per the syntax in the comments below
+#
+one: {}
+# column: value
+#
+two: {}
+# column: value

test/models/joint_test.rb

@@ -0,0 +1,7 @@
+require "test_helper"
+
+class JointTest < ActiveSupport::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end

test/models/joints_info_test.rb

@@ -0,0 +1,7 @@
+require "test_helper"
+
+class JointsInfoTest < ActiveSupport::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end

test/models/special_test_test.rb

@@ -0,0 +1,7 @@
+require "test_helper"
+
+class SpecialTestTest < ActiveSupport::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end