close #19 Support creating and editing groups of observations.

app/assets/javascripts/application.js

@@ -21,4 +21,5 @@
 //= require interleave.condition_occurrence
 //= require interleave.drug_exposure
 //= require interleave.measurement
+//= require interleave.observation
 //= require interleave.procedure_occurrence

app/assets/javascripts/interleave.observation.js.coffee

@@ -0,0 +1,68 @@
+class Interleave.Observation
+  constructor: () ->
+  render: (link) ->
+    $(link).on 'click', (e) ->
+      $modal = $('#observation_modal')
+      $observation = $('#observation_modal .observation')
+      $.ajax(this.href).done (response) ->
+        $observation.html(response)
+        $modal.foundation 'open'
+        $('.datepicker').datepicker
+          onClose: (dateText, inst) ->
+            $(inst.input).focusout()
+            return
+          changeMonth: true
+          changeYear: true
+        interleaveDatapointConceptsUrl = $('#concepts_interleave_datapoint_url').attr('href')
+        $('.observation_form').enableClientSideValidations()
+        if $('.observation_concept_id_select').length
+          $('#observation_observation_concept_id').select2
+            ajax:
+              url: interleaveDatapointConceptsUrl
+              dataType: 'json'
+              delay: 250
+              data: (params) ->
+                {
+                  q: params.term
+                  page: params.page
+                }
+              processResults: (data, params) ->
+                params.page = params.page or 1
+                results = $.map(data.concepts, (obj) ->
+                  obj.id = obj.concept_id
+                  obj.text = obj.text
+                  obj
+                )
+
+                {
+                  results: results
+                  pagination: more: params.page * 10 < data.total
+                }
+              cache: true
+            escapeMarkup: (markup) ->
+              markup
+            minimumInputLength: 2
+
+          $('#observation_condition_concept_id').on 'select2:select', (e) ->
+            $(this).blur()
+            return
+
+        $('.observation_form').on('ajax:success', (e, data, status, xhr) ->
+          $modal.foundation 'close'
+          Turbolinks.visit(location.toString())
+          $('.observations_list').fadeOut()
+        ).on 'ajax:error', (e, xhr, status, error) ->
+
+        $('.observation_form .cancel-link').on 'click', (e) ->
+          $modal.foundation 'close'
+          e.preventDefault()
+
+        return
+      e.preventDefault()
+      return
+    return
+
+$(document).on 'page:load ready', ->
+  return unless $('.observations.index').length > 0
+  ui = new Interleave.Observation
+  ui.render('.observation_link')

app/assets/stylesheets/application.scss

@@ -22,5 +22,6 @@
 @import "drug_exposures";
 @import "measurements";
 @import "procedure_occurrences";
+@import "observations";
 @import "jquery.ui.override";
 @import "select2";

app/assets/stylesheets/observations.scss

@@ -0,0 +1,129 @@
+#observations {
+  @include grid-row();
+
+  .interleave_datapoint {
+    @include grid-column(
+     $columns: 20
+    );
+  }
+
+  .observations_list {
+		@include grid-column(
+		  $columns: 24
+		);
+
+    th .current {
+      padding-right: 2em;
+      background-repeat: no-repeat;
+      background-position: right center;
+    }
+
+    th .asc {
+      background-image: asset_url("drop25.png");
+    }
+
+    th .desc {
+      background-image: asset_url("drop27.png");
+    }
+
+    table {
+      @include grid-column(
+       $columns: 24
+      );
+    }
+  }
+}
+
+#observation_modal {
+  position: fixed;
+  bottom: 0;
+  top: 30% !important;
+  right: 0;
+  left: 0;
+  width: 100%;
+}
+
+#observation {
+  @include grid-row();
+
+  .ui-autocomplete-input {
+    width: 90%;
+    height: 2.5rem;
+  }
+  .ui-button {
+    width: 5%;
+    height: 2.5rem;
+  }
+
+  .observation_date {
+    @include grid-column(
+     $columns: 12
+    );
+    input {
+      margin-bottom: 0;
+    }
+  }
+
+  .observation_type_concept_id {
+    label {
+      display: block;
+    }
+    @include grid-column(
+     $columns: 12
+    );
+    select {
+      margin-bottom: 0;
+    }
+
+    .select2 {
+      width: 100% !important;
+    }
+  }
+
+  .observation_value {
+    label {
+      display: block;
+    }
+    @include grid-column(
+     $columns: 12
+    );
+    input {
+      margin-bottom: 0;
+    }
+  }
+
+  .interleave_sub_datapoint {
+    label {
+      display: block;
+    }
+    @include grid-column(
+     $columns: 12
+    );
+    input {
+      margin-bottom: 0;
+    }
+  }
+
+  .interleave_sub_datapoints {
+    .left {
+      @include grid-column(
+       $columns: 12
+      );
+
+    }
+
+    .right {
+      @include grid-column(
+       $columns: 12
+      );
+    }
+  }
+
+  .navigation {
+    padding: 1rem;
+    @include grid-column-offset(12);
+    @include grid-column(
+     $columns: 12
+    );
+  }
+}

app/controllers/observations_controller.rb

@@ -0,0 +1,80 @@
+  class ObservationsController < ApplicationController
+  helper_method :sort_column, :sort_direction
+  before_filter :load_interleave_registry, only: [:index, :new, :create, :edit]
+  before_filter :load_interleave_person, only: [:index, :new, :create, :edit]
+  before_filter :load_observation, only: [:edit, :update]
+  before_filter :load_interleave_datapoint, only: [:new, :edit]
+
+  def index
+    @datapoint = @registry.interleave_datapoints.find(params[:datapoint_id])
+    params[:page]||= 1
+    options = {}
+    options[:sort_column] = sort_column
+    options[:sort_direction] = sort_direction
+    add_breadcrumbs(registry: @registry, interleave_person: @interleave_person, datapoint: @datapoint)
+    @observations = Observation.by_person(@interleave_person.person.person_id).by_interleave_data_point(@datapoint.id, options).paginate(per_page: 10, page: params[:page])
+  end
+
+  def new
+    @observation = Observation.new()
+    @observation.interleave_datapoint = @datapoint
+    @datapoint.initialize_defaults(@observation)
+    @concepts = []
+    @type_concepts = load_concepts('observation_type_concept_id')
+    @sub_datapoints = @datapoint.initialize_sub_datapoint_entities
+    respond_to do |format|
+      format.html { render :layout => false }
+    end
+  end
+
+  def create
+    @observation = Observation.new(observation_params)
+    interleave_registry_cdm_source =  @registry.interleave_registry_cdm_sources.where(cdm_source_name: InterleaveRegistryCdmSource::CDM_SOURCE_EX_NIHILO).first
+    @observation.person = @interleave_person.person
+
+    respond_to do |format|
+      if @observation.create_with_sub_datapoints!(interleave_registry_cdm_source, observations: params[:observations])
+        format.js { }
+      else
+        format.js { render json: { errors: @observation.errors.full_messages }, status: :unprocessable_entity }
+      end
+    end
+  end
+
+  def edit
+    @observation.interleave_datapoint = @datapoint
+    @concepts = [[@observation.observation_concept.concept_name, @observation.observation_concept_id]]
+    @type_concepts = load_concepts('observation_type_concept_id')
+    @sub_datapoints = @datapoint.initialize_sub_datapoint_entities(@observation.interleave_entity)
+    respond_to do |format|
+      format.html { render :layout => false }
+    end
+  end
+
+  def update
+    respond_to do |format|
+      if @observation.update_with_sub_datapoints!(observation_params, observations: params[:observations])
+        format.js { }
+      else
+        format.js { render json: { errors: @observation.errors.full_messages }, status: :unprocessable_entity }
+      end
+    end
+  end
+
+  private
+    def observation_params
+      params.require(:observation).permit(:interleave_datapoint_id, :observation_concept_id, :observation_date, :observation_time, :observation_type_concept_id, :value_as_number, :value_as_string, :value_as_concept_id, :qualifier_concept_id, :unit_concept_id)
+    end
+
+    def load_observation
+      @observation = Observation.find(params[:id])
+    end
+
+    def sort_column
+      ['observation_date'].concat(@datapoint.interleave_sub_datapoints.map { |interleave_sub_datapoint| interleave_sub_datapoint.id.to_s }).include?(params[:sort]) ? params[:sort] : "#{@datapoint.id}"
+    end
+
+    def sort_direction
+      %w[asc desc].include?(params[:direction]) ? params[:direction] : 'asc'
+    end
+end

app/helpers/application_helper.rb

@@ -47,6 +47,10 @@ def generate_datapoint_url(registry, interleave_person, datapoint, domain_id)
         haml_tag(:li, class: active?('active', 'measurements', 'index', 'datapoint_id' => datapoint.id.to_s)) do
           concat link_to datapoint.name, interleave_registry_interleave_person_measurements_url(registry, interleave_person, datapoint_id: datapoint.id), class: 'datapoint'
         end
+      when 'Observation'
+        haml_tag(:li, class: active?('active', 'observations', 'index', 'datapoint_id' => datapoint.id.to_s)) do
+          concat link_to datapoint.group_name, interleave_registry_interleave_person_observations_url(registry, interleave_person, datapoint_id: datapoint.id), class: 'datapoint'
+        end
       when 'Procedure'
         haml_tag(:li, class: active?('active', 'procedure_occurrences', 'index', 'datapoint_id' => datapoint.id.to_s)) do
           concat link_to datapoint.name, interleave_registry_interleave_person_procedure_occurrences_url(registry, interleave_person, datapoint_id: datapoint.id)

app/models/concept.rb

@@ -10,6 +10,7 @@ class Concept < ActiveRecord::Base
   VOCABULARY_ID_GENDER = 'Gender'
   VOCABULARY_ID_LOINC = 'LOINC'
   VOCABULARY_ID_MEAS_TYPE = 'Meas Type'
+  VOCABULARY_ID_OBSERVATION_TYPE = 'Observation Type'
   VOCABULARY_ID_PROCEDURE_TYPE = 'Procedure Type'
   VOCABULARY_ID_RACE = 'Race'
   VOCABULARY_ID_RELATIONSHIP = 'Relationship'
@@ -25,13 +26,14 @@ class Concept < ActiveRecord::Base
   DOMAIN_ID_MEASUREMENT = 'Measurement'
   DOMAIN_ID_MEAS_VALUE = 'Meas Value'
   DOMAIN_ID_METADATA = 'Metadata'
+  DOMAIN_ID_OBSERVATION = 'Observation'
   DOMAIN_ID_PROCEDURE = 'Procedure'
   DOMAIN_ID_RACE = 'Race'
   DOMAIN_ID_RELATIONSHIP = 'Relationship'
   DOMAIN_ID_ROUTE = 'Route'
   DOMAIN_ID_TYPE_CONCEPT = 'Type Concept'
   DOMAIN_ID_UNIT = 'Unit'
-  DOMAIN_IDS = [DOMAIN_ID_CONDITION, DOMAIN_ID_GENDER, DOMAIN_ID_ETHNICITY, DOMAIN_ID_MEASUREMENT, DOMAIN_ID_METADATA, DOMAIN_ID_PROCEDURE, DOMAIN_ID_RACE, DOMAIN_ID_RELATIONSHIP, DOMAIN_ID_ROUTE, DOMAIN_ID_TYPE_CONCEPT, DOMAIN_ID_UNIT]
+  DOMAIN_IDS = [DOMAIN_ID_CONDITION, DOMAIN_ID_GENDER, DOMAIN_ID_ETHNICITY, DOMAIN_ID_MEASUREMENT, DOMAIN_ID_METADATA, DOMAIN_ID_OBSERVATION, DOMAIN_ID_PROCEDURE, DOMAIN_ID_RACE, DOMAIN_ID_RELATIONSHIP, DOMAIN_ID_ROUTE, DOMAIN_ID_TYPE_CONCEPT, DOMAIN_ID_UNIT]
 
   CONCEPT_CLASS_ANSWER = 'Answer'
   CONCEPT_CLASS_CLINICAL_FINDING = 'Clinical Finding'
@@ -45,10 +47,12 @@ class Concept < ActiveRecord::Base
   CONCEPT_CLASS_INGREDIENT = 'Ingredient'
   CONCEPT_CLASS_LAB_TEST = 'Lab Test'
   CONCEPT_CLASS_MEAS_TYPE = 'Meas Type'
+  CONCEPT_CLASS_OBSERVATION_TYPE = 'Observation Type'
   CONCEPT_CLASS_PROCEDURE_TYPE = 'Procedure Type'
   CONCEPT_CLASS_QUALIFIER_VALUE = 'Qualifier Value'
   CONCEPT_CLASS_RACE = 'Race'
   CONCEPT_CLASS_RELATIONSHIP = 'Relationship'
+  CONCEPT_CLASS_SURVEY = 'Survey'
   CONCEPT_CLASS_UNIT = 'Unit'
   CONCEPT_CLASSES = [CONCEPT_CLASS_ANSWER, CONCEPT_CLASS_CLINICAL_FINDING, CONCEPT_CLASS_CONDITION_TYPE, CONCEPT_CLASS_DRUG_TYPE, CONCEPT_CLASS_CPT4, CONCEPT_CLASS_DOMAIN, CONCEPT_CLASS_GENDER, CONCEPT_CLASS_ETHNICITY, CONCEPT_CLASS_LAB_TEST, CONCEPT_CLASS_MEAS_TYPE, CONCEPT_CLASS_PROCEDURE_TYPE, CONCEPT_CLASS_QUALIFIER_VALUE, CONCEPT_CLASS_RACE, CONCEPT_CLASS_RELATIONSHIP, CONCEPT_CLASS_UNIT]
 
@@ -76,6 +80,10 @@ def self.measurement_types
     valid.where(domain_id: Concept::DOMAIN_ID_TYPE_CONCEPT, vocabulary_id: Concept::VOCABULARY_ID_MEAS_TYPE , concept_class_id: Concept::CONCEPT_CLASS_MEAS_TYPE)
   end
 
+  def self.observation_types
+    valid.where(domain_id: Concept::DOMAIN_ID_TYPE_CONCEPT, vocabulary_id: Concept::VOCABULARY_ID_OBSERVATION_TYPE , concept_class_id: Concept::CONCEPT_CLASS_OBSERVATION_TYPE)
+  end
+
   def self.procedure_types
     valid.where(domain_id: Concept::DOMAIN_ID_TYPE_CONCEPT, vocabulary_id: Concept::VOCABULARY_ID_PROCEDURE_TYPE , concept_class_id: Concept::CONCEPT_CLASS_PROCEDURE_TYPE)
   end

app/models/concept_relationship.rb

@@ -0,0 +1,3 @@
+class ConceptRelationship < ActiveRecord::Base
+  self.table_name = 'concept_relationship'
+end