diff --git a/Gemfile b/Gemfile
index f8a685000..fa1a3f747 100644
--- a/Gemfile
+++ b/Gemfile
@@ -68,8 +68,6 @@ gem 'tinymce-rails' # Rich text editor
gem 'base62' # Used for smart annotations
-gem 'nokogiri' # XML parser
-
group :development, :test do
gem 'byebug'
gem 'better_errors'
diff --git a/app/assets/javascripts/application.js.erb b/app/assets/javascripts/application.js.erb
index 2ceb50997..56bf2fb5f 100644
--- a/app/assets/javascripts/application.js.erb
+++ b/app/assets/javascripts/application.js.erb
@@ -224,6 +224,32 @@ var HelperModule = (function(){
}
}
+ helpers.flashAlertMsg = function(message, type) {
+ var alertType;
+ var glyphSign;
+ $('#notifications').html('');
+ if (type === 'success') {
+ alertType = ' alert-success ';
+ glyphSign = ' glyphicon-ok-sign ';
+ } else if (type === 'danger') {
+ alertType = ' alert-danger ';
+ glyphSign = ' glyphicon-exclamation-sign ';
+ }
+ var htmlSnippet = '' +
+ '
' +
+ '' +
+ '' +
+ '' + message + '' +
+ '
' +
+ '
' + generateColumnNameTooltip(data.name) + ' | ');
@@ -1050,6 +1059,7 @@ function changeToEditMode() {
'data-position="' + colIndex + '" ' +
'data-id="' + $(el).attr('id') + '" ' +
'data-edit-url=' + $(el).attr('data-edit-url') + ' ' +
+ 'data-update-url=' + $(el).attr('data-update-url') + ' ' +
'data-destroy-html-url=' + $(el).attr('data-destroy-html-url') + ' ' +
'class="' + visLi + '"' +
'>' +
@@ -1151,7 +1161,7 @@ function changeToEditMode() {
var text = li.find('.text');
var textEdit = li.find('.text-edit');
var newName = textEdit.val().trim();
- var url = li.attr('data-edit-url');
+ var url = li.attr('data-update-url');
$.ajax({
url: url,
@@ -1193,34 +1203,57 @@ function changeToEditMode() {
cancelEditMode();
- var self = $(this);
- var li = self.closest('li');
- var text = li.find('.text');
- if ($(text).find('.modal-tooltiptext').length > 0) {
- text = $(text).find('.modal-tooltiptext');
+ var li = $(this).closest('li');
+ var url = li.attr('data-edit-url');
+ ajaxCallEvent();
+
+ function ajaxCallEvent(){
+ $.ajax({
+ url: url,
+ success: function() {
+ var text, textEdit, controls, controlsEdit;
+ text = li.find('.text');
+ if ($(text).find('.modal-tooltiptext').length > 0) {
+ text = $(text).find('.modal-tooltiptext');
+ }
+ textEdit = li.find('.text-edit');
+ controls = li.find('.controls .vis,.edit,.del');
+ controlsEdit = li.find('.controls .ok,.cancel');
+
+ // Toggle edit mode
+ columnEditMode = true;
+ li.addClass('editing');
+
+ // Set the text-edit's value
+ textEdit.val(text.text().trim());
+
+ // Toggle elements
+ text.hide();
+ controls.hide();
+ textEdit.css('display', ''); // show() doesn't work
+ controlsEdit.css('display', ''); // show() doesn't work
+ dropdownList.sortable('disable');
+ dropdownList.on('click', function(ev) {
+ ev.stopPropagation();
+ });
+ // Focus input
+ textEdit.focus();
+ },
+ error: function(e) {
+ $(li).clearFormErrors();
+ var msg = $.parseJSON(e.responseText);
+
+ renderFormError(undefined,
+ $(li).find('.text-edit'),
+ Object.keys(msg)[0] + ' ' + msg.name.toString());
+ var verticalHeight = $(li).offset().top;
+ dropdownList.scrollTo(verticalHeight,0);
+ setTimeout(function() {
+ $(li).clearFormErrors();
+ }, 5000);
+ }
+ });
}
- var textEdit = li.find('.text-edit');
- var controls = li.find('.controls .vis,.edit,.del');
- var controlsEdit = li.find('.controls .ok,.cancel');
-
- // Toggle edit mode
- columnEditMode = true;
- li.addClass('editing');
-
- // Set the text-edit's value
- textEdit.val(text.text().trim());
-
- // Toggle elements
- text.hide();
- controls.hide();
- textEdit.css('display', ''); // show() doesn't work
- controlsEdit.css('display', ''); // show() doesn't work
- dropdownList.sortable('disable');
- dropdownList.on('click', function(ev) {
- ev.stopPropagation();
- });
- // Focus input
- textEdit.focus();
});
// On hiding dropdown, cancel edit mode throughout dropdown
diff --git a/app/assets/javascripts/samples/sample_types_groups.js b/app/assets/javascripts/samples/sample_types_groups.js
index bf708d596..0a42fcce9 100644
--- a/app/assets/javascripts/samples/sample_types_groups.js
+++ b/app/assets/javascripts/samples/sample_types_groups.js
@@ -70,6 +70,17 @@
});
clearModal('#modal-delete');
+ },
+ error: function (e) {
+ $(li).clearFormErrors();
+ var msg = $.parseJSON(e.responseText);
+
+ renderFormError(undefined,
+ $(li).find('.text-edit'),
+ Object.keys(msg)[0] + ' ' + msg.name.toString());
+ setTimeout(function() {
+ $(li).clearFormErrors();
+ }, 5000);
}
});
});
@@ -161,6 +172,17 @@
$(this).find('#sample_type_name'),
Object.keys(msg)[0] + ' '+ msg.name.toString());
});
+ },
+ error: function (e) {
+ $(li).clearFormErrors();
+ var msg = $.parseJSON(e.responseText);
+
+ renderFormError(undefined,
+ $(li).find('.text-edit'),
+ Object.keys(msg)[0] + ' ' + msg.name.toString());
+ setTimeout(function() {
+ $(li).clearFormErrors();
+ }, 5000);
}
});
});
@@ -202,6 +224,40 @@
$(this).find('#sample_group_name'),
Object.keys(msg)[0] + ' '+ msg.name.toString());
});
+ },
+ error: function (e) {
+ $(li).clearFormErrors();
+ var msg = $.parseJSON(e.responseText);
+
+ renderFormError(undefined,
+ $(li).find('.text-edit'),
+ Object.keys(msg)[0] + ' ' + msg.name.toString());
+ setTimeout(function() {
+ $(li).clearFormErrors();
+ }, 5000);
+ }
+ });
+ });
+ }
+
+ function editSampleGroupColor() {
+ $('.color-picker').on('click', function() {
+ var li = $(this).closest('li');
+ $.ajax({
+ url: li.attr('data-edit'),
+ success: function(data) {
+ },
+ error: function (e) {
+ $('.dropdown-colorselector.open').removeClass('open');
+ $(li).clearFormErrors();
+ var msg = $.parseJSON(e.responseText);
+
+ renderFormError(undefined,
+ $(li).find('.text-edit'),
+ Object.keys(msg)[0] + ' ' + msg.name.toString());
+ setTimeout(function() {
+ $(li).clearFormErrors();
+ }, 5000);
}
});
});
@@ -269,6 +325,7 @@
bindNewSampleGroupAction();
appendCarretToColorPickerDropdown();
sampleTypeGroupEditMode();
+ editSampleGroupColor();
}
// initialize sample types/groups actions
diff --git a/app/assets/javascripts/samples/samples.js b/app/assets/javascripts/samples/samples.js
index 1e5a3c7bc..5021f95eb 100644
--- a/app/assets/javascripts/samples/samples.js
+++ b/app/assets/javascripts/samples/samples.js
@@ -53,32 +53,6 @@ function updateSamplesTypesandGroups() {
});
}
-function sampleAlertMsg(message, type) {
- var alertType;
- var glyphSign;
- $('#notifications').html('');
- if (type === 'success') {
- alertType = ' alert-success ';
- glyphSign = ' glyphicon-ok-sign ';
- } else if (type === 'danger') {
- alertType = ' alert-danger ';
- glyphSign = ' glyphicon-exclamation-sign ';
- }
- var htmlSnippet = '' +
- '
' +
- '' +
- '' +
- '' + message + '' +
- '
' +
- '
No content
"
- end
- render pdf: "report",
+ @html = 'No content
' if @html.blank?
+ render pdf: 'report',
header: { right: '[page] of [topage]' },
- template: "reports/report.pdf.erb"
- }
+ template: 'reports/report.pdf.erb'
+ end
end
end
@@ -209,33 +202,32 @@ class ReportsController < ApplicationController
@url = project_report_path(@project, @report, format: :json)
end
- if !params.include? :contents
- render_403 and return
- end
+ render_403 and return unless params.include? :contents
+
@report_contents = params[:contents]
respond_to do |format|
- format.json {
+ format.json do
render json: {
- html: render_to_string({
- partial: "reports/new/modal/save.html.erb"
- })
+ html: render_to_string(
+ partial: 'reports/new/modal/save.html.erb'
+ )
}
- }
+ end
end
end
# Modal for adding contents into project element
def project_contents_modal
respond_to do |format|
- format.json {
+ format.json do
render json: {
- html: render_to_string({
- partial: "reports/new/modal/project_contents.html.erb",
+ html: render_to_string(
+ partial: 'reports/new/modal/project_contents.html.erb',
locals: { project: @project }
- })
+ )
}
- }
+ end
end
end
@@ -274,7 +266,7 @@ class ReportsController < ApplicationController
format.json do
render json: {
html: render_to_string(
- partial: "reports/new/modal/module_contents.html.erb",
+ partial: 'reports/new/modal/module_contents.html.erb',
locals: { project: @project, my_module: my_module }
)
}
@@ -289,18 +281,18 @@ class ReportsController < ApplicationController
respond_to do |format|
if step.blank?
- format.json {
+ format.json do
render json: {}, status: :not_found
- }
+ end
else
- format.json {
+ format.json do
render json: {
- html: render_to_string({
- partial: "reports/new/modal/step_contents.html.erb",
+ html: render_to_string(
+ partial: 'reports/new/modal/step_contents.html.erb',
locals: { project: @project, step: step }
- })
+ )
}
- }
+ end
end
end
end
@@ -311,18 +303,18 @@ class ReportsController < ApplicationController
respond_to do |format|
if result.blank?
- format.json {
+ format.json do
render json: {}, status: :not_found
- }
+ end
else
- format.json {
+ format.json do
render json: {
- html: render_to_string({
- partial: "reports/new/modal/result_contents.html.erb",
+ html: render_to_string(
+ partial: 'reports/new/modal/result_contents.html.erb',
locals: { project: @project, result: result }
- })
+ )
}
- }
+ end
end
end
end
@@ -384,12 +376,12 @@ class ReportsController < ApplicationController
if elements_empty? elements
format.json { render json: {}, status: :no_content }
else
- format.json {
+ format.json do
render json: {
status: :ok,
elements: elements
}
- }
+ end
end
end
end
@@ -442,242 +434,31 @@ class ReportsController < ApplicationController
private
- def in_params?(val)
- params.include? val and params[val] == "1"
- end
-
- def generate_new_el(hide)
- el = {}
- el[:html] = render_to_string({
- partial: "reports/elements/new_element.html.erb",
- locals: { hide: hide }
- })
- el[:children] = []
- el[:new_element] = true
- el
- end
-
- def generate_el(partial, locals)
- el = {}
- el[:html] = render_to_string({
- partial: partial,
- locals: locals
- })
- el[:children] = []
- el[:new_element] = false
- el
- end
-
- def generate_project_contents_json
- res = []
- if params.include? :modules
- modules = (params[:modules].select { |_, p| p == '1' })
- .keys
- .collect(&:to_i)
-
- # Get unique experiments from given modules
- experiments = MyModule.where(id: modules).map(&:experiment).uniq
- experiments.each do |experiment|
- res << generate_new_el(false)
- el = generate_el(
- 'reports/elements/experiment_element.html.erb',
- experiment: experiment
- )
- el[:children] = generate_experiment_contents_json(experiment, modules)
- res << el
- end
- end
- res << generate_new_el(false)
- res
- end
-
- def generate_experiment_contents_json(experiment, selected_modules)
- res = []
- experiment.my_modules.each do |my_module|
- next unless selected_modules.include?(my_module.id)
-
- res << generate_new_el(false)
- el = generate_el(
- 'reports/elements/my_module_element.html.erb',
- my_module: my_module
- )
- el[:children] = generate_module_contents_json(my_module)
- res << el
- end
- res << generate_new_el(false)
- res
- end
-
- def generate_module_contents_json(my_module)
- res = []
- if (in_params? :module_steps) && my_module.protocol.present? then
- my_module.protocol.completed_steps.each do |step|
- res << generate_new_el(false)
- el = generate_el(
- "reports/elements/step_element.html.erb",
- { step: step }
- )
- el[:children] = generate_step_contents_json(step)
- res << el
- end
- end
- if in_params? :module_result_assets then
- (my_module.results.select { |r| r.is_asset && r.active? }).each do |result_asset|
- res << generate_new_el(false)
- el = generate_el(
- "reports/elements/result_asset_element.html.erb",
- { result: result_asset }
- )
- el[:children] = generate_result_contents_json(result_asset)
- res << el
- end
- end
- if in_params? :module_result_tables then
- (my_module.results.select { |r| r.is_table && r.active? }).each do |result_table|
- res << generate_new_el(false)
- el = generate_el(
- "reports/elements/result_table_element.html.erb",
- { result: result_table }
- )
- el[:children] = generate_result_contents_json(result_table)
- res << el
- end
- end
- if in_params? :module_result_texts then
- (my_module.results.select { |r| r.is_text && r.active? }).each do |result_text|
- res << generate_new_el(false)
- el = generate_el(
- "reports/elements/result_text_element.html.erb",
- result: result_text
- )
- el[:children] = generate_result_contents_json(result_text)
- res << el
- end
- end
- if in_params? :module_activity then
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/my_module_activity_element.html.erb",
- { my_module: my_module, order: :asc }
- )
- end
- if in_params? :module_samples then
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/my_module_samples_element.html.erb",
- { my_module: my_module, order: :asc }
- )
- end
- res << generate_new_el(false)
- res
- end
-
- def generate_step_contents_json(step)
- res = []
- if in_params? :step_checklists then
- step.checklists.each do |checklist|
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/step_checklist_element.html.erb",
- { checklist: checklist }
- )
- end
- end
- if in_params? :step_assets then
- step.assets.each do |asset|
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/step_asset_element.html.erb",
- { asset: asset }
- )
- end
- end
- if in_params? :step_tables then
- step.tables.each do |table|
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/step_table_element.html.erb",
- { table: table }
- )
- end
- end
- if in_params? :step_comments then
- res << generate_new_el(false)
- res << generate_el(
- "reports/elements/step_comments_element.html.erb",
- { step: step, order: :asc }
- )
- end
- res << generate_new_el(false)
- res
- end
-
- def generate_result_contents_json(result)
- res = []
- if in_params? :result_comments then
- res << generate_new_el(true)
- res << generate_el(
- "reports/elements/result_comments_element.html.erb",
- { result: result, order: :asc }
- )
- else
- res << generate_new_el(false)
- end
- res
- end
-
- def elements_empty?(elements)
- if elements.blank?
- return true
- elsif elements.count == 0 then
- return true
- elsif elements.count == 1
- el = elements[0]
- if el.include? :new_element and el[:new_element]
- return true
- else
- return false
- end
- end
- return false
- end
-
def load_vars
@report = Report.find_by_id(params[:id])
-
- unless @report
- render_404
- end
+ render_404 unless @report
end
def load_vars_nested
@project = Project.find_by_id(params[:project_id])
-
- unless @project
- render_404
- end
+ render_404 unless @project
end
def check_view_permissions
- unless can_view_reports(@project)
- render_403
- end
+ render_403 unless can_view_reports(@project)
end
def check_create_permissions
- unless can_create_new_report(@project)
- render_403
- end
+ render_403 unless can_create_new_report(@project)
end
def check_destroy_permissions
- unless can_delete_reports(@project)
- render_403
- end
+ render_403 unless can_delete_reports(@project)
+ render_404 unless params.include? :report_ids
end
def report_params
- params.require(:report).permit(:name, :description, :grouped_by, :report_contents)
+ params.require(:report)
+ .permit(:name, :description, :grouped_by, :report_contents)
end
-
end
diff --git a/app/controllers/result_assets_controller.rb b/app/controllers/result_assets_controller.rb
index 6cdea4b86..3ce0b8745 100644
--- a/app/controllers/result_assets_controller.rb
+++ b/app/controllers/result_assets_controller.rb
@@ -29,6 +29,7 @@ class ResultAssetsController < ApplicationController
@asset = Asset.new(result_params[:asset_attributes])
@asset.created_by = current_user
@asset.last_modified_by = current_user
+ @asset.team = current_team
@result = Result.new(
user: current_user,
my_module: @my_module,
@@ -98,6 +99,7 @@ class ResultAssetsController < ApplicationController
asset = Asset.find_by_id(update_params[:asset_attributes][:id])
asset.created_by = current_user
asset.last_modified_by = current_user
+ asset.team = current_team
@result.asset = asset
end
diff --git a/app/controllers/result_tables_controller.rb b/app/controllers/result_tables_controller.rb
index c2e640474..7c3820625 100644
--- a/app/controllers/result_tables_controller.rb
+++ b/app/controllers/result_tables_controller.rb
@@ -31,6 +31,7 @@ class ResultTablesController < ApplicationController
def create
@table = Table.new(result_params[:table_attributes])
@table.created_by = current_user
+ @table.team = current_team
@table.last_modified_by = current_user
@result = Result.new(
user: current_user,
@@ -92,6 +93,7 @@ class ResultTablesController < ApplicationController
update_params = result_params
@result.last_modified_by = current_user
@result.table.last_modified_by = current_user
+ @result.table.team = current_team
@result.assign_attributes(update_params)
flash_success = t("result_tables.update.success_flash",
module: @my_module.name)
@@ -218,6 +220,4 @@ class ResultTablesController < ApplicationController
]
)
end
-
end
-
diff --git a/app/controllers/steps_controller.rb b/app/controllers/steps_controller.rb
index e057c2270..c781102c6 100644
--- a/app/controllers/steps_controller.rb
+++ b/app/controllers/steps_controller.rb
@@ -33,6 +33,14 @@ class StepsController < ApplicationController
@step.protocol = @protocol
@step.user = current_user
@step.last_modified_by = current_user
+ @step.assets.each do |asset|
+ asset.created_by = current_user
+ asset.team = current_team
+ end
+ @step.tables.each do |table|
+ table.created_by = current_user
+ table.team = current_team
+ end
# Update default checked state
@step.checklists.each do |checklist|
@@ -133,6 +141,18 @@ class StepsController < ApplicationController
@step.assign_attributes(step_params_all)
@step.last_modified_by = current_user
+ @step.assets.each do |asset|
+ asset.created_by = current_user if asset.new_record?
+ asset.last_modified_by = current_user unless asset.new_record?
+ asset.team = current_team
+ end
+
+ @step.tables.each do |table|
+ table.created_by = current_user if table.new_record?
+ table.last_modified_by = current_user unless table.new_record?
+ table.team = current_team
+ end
+
if @step.save
@step.reload
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 091fe00d8..9c15582b7 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -1,99 +1,95 @@
module ReportsHelper
+ def render_new_element(hide)
+ render partial: 'reports/elements/new_element.html.erb',
+ locals: { hide: hide }
+ end
-def render_new_element(hide)
- render partial: "reports/elements/new_element.html.erb",
- locals: { hide: hide }
-end
+ def render_report_element(element, provided_locals = nil)
+ children_html = ''.html_safe
-def render_report_element(element, provided_locals = nil)
- children_html = ''.html_safe
-
- # First, recursively render element's children
- if element.comments? || element.project_header?
- # Render no children
- elsif element.result?
- # Special handling for result comments
- if element.has_children?
- children_html.safe_concat render_new_element(true)
- element.children.each do |child|
- children_html.safe_concat render_report_element(child, provided_locals)
+ # First, recursively render element's children
+ if element.comments? || element.project_header?
+ # Render no children
+ elsif element.result?
+ # Special handling for result comments
+ if element.has_children?
+ children_html.safe_concat render_new_element(true)
+ element.children.each do |child|
+ children_html
+ .safe_concat render_report_element(child, provided_locals)
+ end
+ else
+ children_html.safe_concat render_new_element(false)
end
else
+ if element.has_children?
+ element.children.each do |child|
+ children_html.safe_concat render_new_element(false)
+ children_html
+ .safe_concat render_report_element(child, provided_locals)
+ end
+ end
children_html.safe_concat render_new_element(false)
end
- else
- if element.has_children?
- element.children.each do |child|
- children_html.safe_concat render_new_element(false)
- children_html.safe_concat render_report_element(child, provided_locals)
- end
+
+ file_name = element.type_of
+ if element.type_of.in? %w(step result_asset result_table result_text)
+ file_name = "my_module_#{element.type_of.singularize}"
end
- children_html.safe_concat render_new_element(false)
+ view = "reports/elements/#{file_name}_element.html.erb"
+
+ locals = provided_locals.nil? ? {} : provided_locals.clone
+ locals[:children] = children_html
+
+ # ReportExtends is located in config/initializers/extends/report_extends.rb
+
+ ReportElement.type_ofs.keys.each do |type|
+ next unless element.public_send("#{type}?")
+ local_sym = type.split('_').last.to_sym
+ local_sym = type
+ .split('_')
+ .first
+ .to_sym if type.in? ReportExtends::FIRST_PART_ELEMENTS
+ local_sym = :my_module if type.in? ReportExtends::MY_MODULE_ELEMENTS
+ locals[local_sym] = element.element_reference
+ locals[:order] = element
+ .sort_order if type.in? ReportExtends::SORTED_ELEMENTS
+ end
+
+ (render partial: view, locals: locals).html_safe
end
- view = "reports/elements/#{element.type_of}_element.html.erb"
-
- locals = provided_locals.nil? ? {} : provided_locals.clone
- locals[:children] = children_html
-
- if element.project_header?
- locals[:project] = element.element_reference
- elsif element.experiment?
- locals[:experiment] = element.element_reference
- elsif element.my_module?
- locals[:my_module] = element.element_reference
- elsif element.step?
- locals[:step] = element.element_reference
- elsif element.result_asset?
- locals[:result] = element.element_reference
- elsif element.result_table?
- locals[:result] = element.element_reference
- elsif element.result_text?
- locals[:result] = element.element_reference
- elsif element.my_module_activity?
- locals[:my_module] = element.element_reference
- locals[:order] = element.sort_order
- elsif element.my_module_samples?
- locals[:my_module] = element.element_reference
- locals[:order] = element.sort_order
- elsif element.step_checklist?
- locals[:checklist] = element.element_reference
- elsif element.step_asset?
- locals[:asset] = element.element_reference
- elsif element.step_table?
- locals[:table] = element.element_reference
- elsif element.step_comments?
- locals[:step] = element.element_reference
- locals[:order] = element.sort_order
- elsif element.result_comments?
- locals[:result] = element.element_reference
- locals[:order] = element.sort_order
- elsif element.project_activity?
- # TODO
- elsif element.project_samples?
- # TODO
+ # "Hack" to omit file preview URL because of WKHTML issues
+ def report_image_asset_url(asset)
+ prefix = ''
+ if ENV['PAPERCLIP_STORAGE'].present? &&
+ ENV['MAIL_SERVER_URL'].present? &&
+ ENV['PAPERCLIP_STORAGE'] == 'filesystem'
+ prefix = ENV['MAIL_SERVER_URL']
+ end
+ if !prefix.empty? &&
+ !prefix.include?('http://') &&
+ !prefix.include?('https://')
+ prefix = "http://#{prefix}"
+ end
+ url = prefix + asset.url(:medium, timeout: Constants::URL_LONG_EXPIRE_TIME)
+ image_tag(url)
end
- return (render partial: view, locals: locals).html_safe
-end
+ # "Hack" to load Glyphicons css directly from the CDN
+ # site so they work in report
+ def bootstrap_cdn_link_tag
+ specs = Gem.loaded_specs['bootstrap-sass']
+ return '' unless specs.present?
+ stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/" \
+ "#{specs.version.version}/css/bootstrap.min.css",
+ media: 'all')
+ end
-# "Hack" to omit file preview URL because of WKHTML issues
-def report_image_asset_url(asset)
- prefix = (ENV["PAPERCLIP_STORAGE"].present? && ENV["MAIL_SERVER_URL"].present? && ENV["PAPERCLIP_STORAGE"] == "filesystem") ? ENV["MAIL_SERVER_URL"] : ""
- prefix = (!prefix.empty? && !prefix.include?("http://") && !prefix.include?("https://")) ? "http://#{prefix}" : prefix
- url = prefix + asset.url(:medium, timeout: Constants::URL_LONG_EXPIRE_TIME)
- image_tag(url)
-end
-
-# "Hack" to load Glyphicons css directly from the CDN site so they work in report
-def bootstrap_cdn_link_tag
- specs = Gem.loaded_specs["bootstrap-sass"]
- specs.present? ? stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/#{specs.version.version}/css/bootstrap.min.css", media: "all") : ""
-end
-
-def font_awesome_cdn_link_tag
- stylesheet_link_tag(
- 'https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css'
- )
-end
+ def font_awesome_cdn_link_tag
+ stylesheet_link_tag(
+ 'https://maxcdn.bootstrapcdn.com/font-awesome' \
+ '/4.6.3/css/font-awesome.min.css'
+ )
+ end
end
diff --git a/app/models/asset.rb b/app/models/asset.rb
index dcce691a1..f31358cef 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -48,6 +48,7 @@ class Asset < ActiveRecord::Base
belongs_to :last_modified_by,
foreign_key: 'last_modified_by_id',
class_name: 'User'
+ belongs_to :team
has_one :step_asset,
inverse_of: :asset,
dependent: :destroy
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 17d658fb4..79efff5ad 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -291,8 +291,6 @@ class Protocol < ActiveRecord::Base
)
item2.created_by = current_user
item2.last_modified_by = current_user
- p item
- p item2
item2.save
end
@@ -306,6 +304,7 @@ class Protocol < ActiveRecord::Base
asset.file_file_size
)
asset2.created_by = current_user
+ asset2.team = dest.team
asset2.last_modified_by = current_user
asset2.file_processing = true if asset.is_image?
asset2.save
@@ -323,6 +322,7 @@ class Protocol < ActiveRecord::Base
table2 = Table.new(name: table.name, contents: table.contents)
table2.created_by = current_user
table2.last_modified_by = current_user
+ table2.team = dest.team
step2.tables << table2
end
end
diff --git a/app/models/report.rb b/app/models/report.rb
index 3cd7aa376..5d1b5e599 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -105,12 +105,13 @@ class Report < ActiveRecord::Base
el.position = index
el.report = self
el.parent = parent
- el.type_of = json_element["type_of"]
- el.sort_order = json_element["sort_order"]
- el.set_element_reference(json_element["id"])
+ el.type_of = json_element['type_of']
+ el.sort_order = json_element['sort_order']
+ el.set_element_reference(json_element['id'])
el.save!
- if json_element["children"].present?
- json_element["children"].each_with_index do |child, i|
+
+ if json_element['children'].present?
+ json_element['children'].each_with_index do |child, i|
save_json_element(child, i, el)
end
end
diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index 131d3d528..398a69883 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -1,22 +1,5 @@
class ReportElement < ActiveRecord::Base
- enum type_of: {
- project_header: 0,
- my_module: 1,
- step: 2,
- result_asset: 3,
- result_table: 4,
- result_text: 5,
- my_module_activity: 6,
- my_module_samples: 7,
- step_checklist: 8,
- step_asset: 9,
- step_table: 10,
- step_comments: 11,
- result_comments: 12,
- project_activity: 13, # TODO
- project_samples: 14, # TODO
- experiment: 15
- }
+ enum type_of: Extends::REPORT_ELEMENT_TYPES
# This is only used by certain elements
enum sort_order: {
@@ -32,8 +15,12 @@ class ReportElement < ActiveRecord::Base
belongs_to :report, inverse_of: :report_elements
# Hierarchical structure representation
- has_many :children, -> { order(:position) }, class_name: "ReportElement", foreign_key: "parent_id", dependent: :destroy
- belongs_to :parent, class_name: "ReportElement"
+ has_many :children,
+ -> { order(:position) },
+ class_name: 'ReportElement',
+ foreign_key: 'parent_id',
+ dependent: :destroy
+ belongs_to :parent, class_name: 'ReportElement'
# References to various report entities
belongs_to :project, inverse_of: :report_elements
@@ -59,44 +46,18 @@ class ReportElement < ActiveRecord::Base
# Get the referenced element (previously, element's type_of must be set)
def element_reference
- if project_header? or project_activity? or project_samples?
- return project
- elsif experiment?
- return experiment
- elsif my_module? or my_module_activity? or my_module_samples?
- return my_module
- elsif step? or step_comments?
- return step
- elsif result_asset? or result_table? or result_text? or result_comments?
- return result
- elsif step_checklist?
- return checklist
- elsif step_asset?
- return asset
- elsif step_table?
- return table
+ ReportExtends::ELEMENT_REFERENCES.each do |el_ref|
+ return eval(el_ref.element.gsub('_id', '')) if el_ref.check(self)
end
end
-
# Set the element reference (previously, element's type_of must be set)
def set_element_reference(ref_id)
- if project_header? or project_activity? or project_samples?
- self.project_id = ref_id
- elsif experiment?
- self.experiment_id = ref_id
- elsif my_module? or my_module_activity? or my_module_samples?
- self.my_module_id = ref_id
- elsif step? or step_comments?
- self.step_id = ref_id
- elsif result_asset? or result_table? or result_text? or result_comments?
- self.result_id = ref_id
- elsif step_checklist?
- self.checklist_id = ref_id
- elsif step_asset?
- self.asset_id = ref_id
- elsif step_table?
- self.table_id = ref_id
+ ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
+ check = el_ref.check(self)
+ next unless check
+ public_send("#{el_ref.element}=", ref_id)
+ break
end
end
@@ -120,18 +81,17 @@ class ReportElement < ActiveRecord::Base
private
def has_one_of_referenced_elements
- num_of_refs = [
- project,
- experiment,
- my_module,
- step,
- result,
- checklist,
- asset,
- table
- ].count { |r| r.present? }
+ num_of_refs = [project,
+ experiment,
+ my_module,
+ step,
+ result,
+ checklist,
+ asset,
+ table].count { |r| r.present? }
if num_of_refs != 1
- errors.add(:base, "Report element must have exactly one element reference.")
+ errors.add(:base,
+ 'Report element must have exactly one element reference.')
end
end
end
diff --git a/app/models/table.rb b/app/models/table.rb
index cf9874389..45ed3252e 100644
--- a/app/models/table.rb
+++ b/app/models/table.rb
@@ -10,6 +10,7 @@ class Table < ActiveRecord::Base
belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User'
belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User'
+ belongs_to :team
has_one :step_table, inverse_of: :table
has_one :step, through: :step_table
diff --git a/app/utilities/delayed_uploader_tutorial.rb b/app/utilities/delayed_uploader_tutorial.rb
index d7a7a58db..993e519cb 100644
--- a/app/utilities/delayed_uploader_tutorial.rb
+++ b/app/utilities/delayed_uploader_tutorial.rb
@@ -1,11 +1,12 @@
module DelayedUploaderTutorial
# Get asset from tutorial_files folder
- def self.get_asset(user, file_name)
+ def self.get_asset(user, team, file_name)
Asset.new(
file: File.open(
"#{Rails.root}/app/assets/tutorial_files/#{file_name}", 'r'
),
created_by: user,
+ team: team,
last_modified_by: user
)
end
@@ -15,11 +16,12 @@ module DelayedUploaderTutorial
def self.generate_result_asset(
my_module:,
current_user:,
+ current_team:,
result_name:,
created_at: Time.now,
file_name:
)
- temp_asset = get_asset(current_user, file_name)
+ temp_asset = get_asset(current_user, current_team, file_name)
temp_result = Result.new(
created_at: created_at,
user: current_user,
@@ -48,8 +50,9 @@ module DelayedUploaderTutorial
end
# Adds asset to existing step
- def self.add_step_asset(step:, current_user:, file_name:)
- temp_asset = DelayedUploaderTutorial.get_asset(current_user, file_name)
+ def self.add_step_asset(step:, current_user:, current_team:, file_name:)
+ temp_asset =
+ DelayedUploaderTutorial.get_asset(current_user, current_team, file_name)
step.assets << temp_asset
temp_asset.post_process_file(step.my_module.experiment.project.team)
end
diff --git a/app/utilities/first_time_data_generator.rb b/app/utilities/first_time_data_generator.rb
index 82a480e7f..5a30fed09 100644
--- a/app/utilities/first_time_data_generator.rb
+++ b/app/utilities/first_time_data_generator.rb
@@ -422,6 +422,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[0],
current_user: user,
+ current_team: team,
result_name: 'sF',
created_at: generate_random_time(my_modules[0].created_at, 2.days),
file_name: 'samples.txt'
@@ -440,6 +441,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
+ team: team,
contents: tab_content['module1']['experimental_design']
)
temp_result.save
@@ -467,6 +469,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[1].protocol.steps.where('position = 0').take,
current_user: user,
+ current_team: team,
file_name: 'sample-potatoe.txt'
)
@@ -474,6 +477,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
+ current_team: team,
result_name: 'PVY-inoculated plant, symptoms',
created_at: generate_random_time(my_modules[1].created_at, 1.days),
file_name: 'DSCN0660.JPG'
@@ -482,6 +486,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
+ current_team: team,
result_name: 'mock-inoculated plant',
created_at: generate_random_time(my_modules[1].created_at, 2.days),
file_name: 'DSCN0354.JPG'
@@ -490,6 +495,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
+ current_team: team,
result_name: 'Height of plants at 6dpi',
created_at: generate_random_time(my_modules[1].created_at, 3.days),
file_name: '6dpi_height.JPG'
@@ -541,6 +547,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[2].protocol.steps.where('position = 1').take,
current_user: user,
+ current_team: team,
file_name: 'RNeasy-Plant-Mini-Kit-EN.pdf'
)
@@ -559,6 +566,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
+ team: team,
contents: tab_content['module3']['nanodrop']
)
temp_result.save
@@ -581,6 +589,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[2],
current_user: user,
+ current_team: team,
result_name: 'Agarose gel electrophoresis of totRNA samples',
created_at: generate_random_time(my_modules[2].created_at, 3.days),
file_name: 'totRNA_gel.jpg'
@@ -599,6 +608,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[3].protocol.steps.where('position = 0').take,
current_user: user,
+ current_team: team,
file_name: 'G2938-90034_KitRNA6000Nano_ebook.pdf'
)
@@ -606,6 +616,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[3],
current_user: user,
+ current_team: team,
result_name: 'Result of RNA integrity',
created_at: generate_random_time(my_modules[3].created_at, 2.days),
file_name: 'Bioanalyser_result.JPG'
@@ -671,24 +682,28 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 0').take,
current_user: user,
+ current_team: team,
file_name: 'sample_preparation.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 1').take,
current_user: user,
+ current_team: team,
file_name: 'reaction_setup.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 2').take,
current_user: user,
+ current_team: team,
file_name: 'cycling_conditions.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 3').take,
current_user: user,
+ current_team: team,
file_name: '96plate.doc'
)
@@ -702,6 +717,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
+ team: team,
contents: tab_content['module6']['distribution'] % {
sample0: samples_to_assign[0].name,
sample1: samples_to_assign[1].name,
@@ -729,6 +745,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
+ current_team: team,
result_name: 'Mixtures and plate setup',
created_at: generate_random_time(my_modules[5].created_at, 2.days),
file_name: 'Mixes_Templats.xls'
@@ -737,6 +754,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
+ current_team: team,
result_name: 'Raw data from ABI 7300',
created_at: generate_random_time(my_modules[5].created_at, 3.days),
file_name: 'BootCamp-Experiment-results-20122.sds'
@@ -745,6 +763,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
+ current_team: team,
result_name: 'All results - curves',
created_at: generate_random_time(my_modules[5].created_at, 4.days),
file_name: 'curves.JPG'
@@ -791,6 +810,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[7].protocol.steps.where('position = 0').take,
current_user: user,
+ current_team: team,
file_name: 'ddCq-quantification_diagnostics-template.xls'
)
@@ -798,6 +818,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
+ current_team: team,
result_name: 'Results of ddCq method',
created_at: generate_random_time(my_modules[7].created_at, 1.days),
file_name: 'ddCq-quantification_diagnostics-results.xls'
@@ -806,6 +827,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
+ current_team: team,
result_name: 'Dilution curve and efficiency',
created_at: generate_random_time(my_modules[7].created_at, 2.days),
file_name: 'dilution_curve-efficiency.JPG'
@@ -814,6 +836,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
+ current_team: team,
result_name: 'Relative quantification results',
created_at: generate_random_time(my_modules[7].created_at, 3.days),
file_name: 'result-ddCq.JPG'
diff --git a/app/utilities/protocols_importer.rb b/app/utilities/protocols_importer.rb
index a44e8c897..0e0edddf1 100644
--- a/app/utilities/protocols_importer.rb
+++ b/app/utilities/protocols_importer.rb
@@ -22,18 +22,18 @@ module ProtocolsImporter
protocol.save!
# Protocol is saved, populate it
- populate_protocol(protocol, protocol_json, user)
+ populate_protocol(protocol, protocol_json, user, team)
return protocol
end
- def import_into_existing(protocol, protocol_json, user)
+ def import_into_existing(protocol, protocol_json, user, team)
# Firstly, destroy existing protocol's contents
protocol.destroy_contents(user)
protocol.reload
# Alright, now populate the protocol
- populate_protocol(protocol, protocol_json, user)
+ populate_protocol(protocol, protocol_json, user, team)
protocol.reload
# Unlink the protocol
@@ -43,7 +43,7 @@ module ProtocolsImporter
private
- def populate_protocol(protocol, protocol_json, user)
+ def populate_protocol(protocol, protocol_json, user, team)
protocol.reload
asset_ids = []
@@ -93,7 +93,8 @@ module ProtocolsImporter
name: table_json['name'],
contents: Base64.decode64(table_json['contents']),
created_by: user,
- last_modified_by: user
+ last_modified_by: user,
+ team: team
)
StepTable.create!(
step: step,
@@ -106,7 +107,8 @@ module ProtocolsImporter
step_json["assets"].values.each do |asset_json|
asset = Asset.new(
created_by: user,
- last_modified_by: user
+ last_modified_by: user,
+ team: team
)
# Decode the file bytes
diff --git a/app/views/reports/elements/_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_asset_element.html.erb
rename to app/views/reports/elements/_my_module_result_asset_element.html.erb
diff --git a/app/views/reports/elements/_result_table_element.html.erb b/app/views/reports/elements/_my_module_result_table_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_table_element.html.erb
rename to app/views/reports/elements/_my_module_result_table_element.html.erb
diff --git a/app/views/reports/elements/_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_text_element.html.erb
rename to app/views/reports/elements/_my_module_result_text_element.html.erb
diff --git a/app/views/reports/elements/_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_step_element.html.erb
rename to app/views/reports/elements/_my_module_step_element.html.erb
diff --git a/app/views/reports/elements/_project_header_element.html.erb b/app/views/reports/elements/_project_header_element.html.erb
index c39d2a483..beb727530 100644
--- a/app/views/reports/elements/_project_header_element.html.erb
+++ b/app/views/reports/elements/_project_header_element.html.erb
@@ -18,4 +18,4 @@
<%= children if (defined? children and children.present?) %>
-
\ No newline at end of file
+
diff --git a/app/views/sample_groups/_sample_group.html.erb b/app/views/sample_groups/_sample_group.html.erb
index 18d702891..2e2a60a99 100644
--- a/app/views/sample_groups/_sample_group.html.erb
+++ b/app/views/sample_groups/_sample_group.html.erb
@@ -5,15 +5,18 @@
team_sample_group_destroy_confirmation_path(team, sample_group) %>"
data-color="<%= sample_group.color %>">
<%= sample_group.name %>
-
-
- <%= bootstrap_form_for [team, sample_group], remote: true do |f| %>
- <%= f.color_picker_select :color,
- Constants::TAG_COLORS,
- class: 'edit-sample-group-color' %>
- <% end %>
+
+
+
+
+ <%= bootstrap_form_for [team, sample_group], remote: true do |f| %>
+ <%= f.color_picker_select :color,
+ Constants::TAG_COLORS,
+ class: 'edit-sample-group-color' %>
+ <% end %>
+
+
+
-
-
diff --git a/app/views/sample_types/_sample_type.html.erb b/app/views/sample_types/_sample_type.html.erb
index 36c409bc8..8c6b90388 100644
--- a/app/views/sample_types/_sample_type.html.erb
+++ b/app/views/sample_types/_sample_type.html.erb
@@ -4,8 +4,11 @@
team_sample_type_destroy_confirmation_path(team, sample_type)
%>">
<%= sample_type.name %>
-
-
-
+
+
+
+
+
+
diff --git a/app/views/shared/_navigation.html.erb b/app/views/shared/_navigation.html.erb
index 3b4e97f2d..8870ad0a3 100644
--- a/app/views/shared/_navigation.html.erb
+++ b/app/views/shared/_navigation.html.erb
@@ -86,7 +86,8 @@
-