From 58e2575c75a6ab787dc7c7618ffc41e0208b1d7a Mon Sep 17 00:00:00 2001 From: lenart Date: Fri, 7 Jul 2017 15:56:16 +0200 Subject: [PATCH 01/24] Truncate checklist items in activity modal [fixes SCI-1249] --- app/controllers/steps_controller.rb | 3 ++- app/helpers/activity_helper.rb | 16 ++++++++++++++-- .../my_modules/activities/_activity.html.erb | 2 +- .../_my_module_activity_element.html.erb | 2 +- 4 files changed, 18 insertions(+), 5 deletions(-) diff --git a/app/controllers/steps_controller.rb b/app/controllers/steps_controller.rb index 20ee1b81b..741d613ed 100644 --- a/app/controllers/steps_controller.rb +++ b/app/controllers/steps_controller.rb @@ -290,10 +290,11 @@ class StepsController < ApplicationController "activities.uncheck_step_checklist_item" completed_items = chkItem.checklist.checklist_items.where(checked: true).count all_items = chkItem.checklist.checklist_items.count + text_activity = chkItem.text.gsub(/\s+/, ' ') message = t( str, user: current_user.full_name, - checkbox: smart_annotation_parser(simple_format(chkItem.text)), + checkbox: text_activity, step: chkItem.checklist.step.position + 1, step_name: chkItem.checklist.step.name, completed: completed_items, diff --git a/app/helpers/activity_helper.rb b/app/helpers/activity_helper.rb index 83cf57023..d400abdb9 100644 --- a/app/helpers/activity_helper.rb +++ b/app/helpers/activity_helper.rb @@ -3,7 +3,19 @@ module ActivityHelper activity_titles = message.scan(/(.*?)<\/strong>/) activity_titles.each do |activity_title| activity_title = activity_title[0] - if activity_title.length > Constants::NAME_TRUNCATION_LENGTH + unless activity_title.length == smart_annotation_parser(activity_title) + .length + temp = activity_title.index('[') + while !temp.nil? && temp < len + if activity_title[temp + 1] == '#' || activity_title[temp + 1] == '@' + last_sa = activity_title.index(']', temp) + end + temp = activity_title.index('[', last_sa) + len = last_sa if last_sa > len + end + len += 4 + end + if activity_title.length > len title = "
#{truncate(activity_title, length: len)} @@ -13,7 +25,7 @@ module ActivityHelper else title = truncate(activity_title, length: len) end - message = message.gsub(/#{Regexp.escape(activity_title)}/, title) + message = smart_annotation_parser(message.gsub(/#{Regexp.escape(activity_title)}/, title)) end sanitize_input(message) if message end diff --git a/app/views/my_modules/activities/_activity.html.erb b/app/views/my_modules/activities/_activity.html.erb index 63a047b90..876dc74aa 100644 --- a/app/views/my_modules/activities/_activity.html.erb +++ b/app/views/my_modules/activities/_activity.html.erb @@ -2,6 +2,6 @@ <%= l activity.created_at, format: :full %> - <%= sanitize_input(activity.message) %> + <%= sanitize_input(smart_annotation_parser(activity.message)) %> diff --git a/app/views/reports/elements/_my_module_activity_element.html.erb b/app/views/reports/elements/_my_module_activity_element.html.erb index 8a709e931..e2b818de2 100644 --- a/app/views/reports/elements/_my_module_activity_element.html.erb +++ b/app/views/reports/elements/_my_module_activity_element.html.erb @@ -30,7 +30,7 @@   - <%= sanitize_input(activity.message) %> + <%= sanitize_input(smart_annotation_parser(activity.message)) %> <% end %> From e781dfc6a6cc4efdad1b8243f82e4c12b3844377 Mon Sep 17 00:00:00 2001 From: lenart Date: Wed, 2 Aug 2017 15:51:32 +0200 Subject: [PATCH 02/24] Truncate activity taking smart annotations into account fixes [SCI-1249] --- app/controllers/steps_controller.rb | 3 ++- app/helpers/activity_helper.rb | 39 ++++++++++++++++++----------- app/helpers/application_helper.rb | 16 ++++++------ 3 files changed, 35 insertions(+), 23 deletions(-) diff --git a/app/controllers/steps_controller.rb b/app/controllers/steps_controller.rb index 741d613ed..9b12b30b6 100644 --- a/app/controllers/steps_controller.rb +++ b/app/controllers/steps_controller.rb @@ -290,7 +290,8 @@ class StepsController < ApplicationController "activities.uncheck_step_checklist_item" completed_items = chkItem.checklist.checklist_items.where(checked: true).count all_items = chkItem.checklist.checklist_items.count - text_activity = chkItem.text.gsub(/\s+/, ' ') + text_activity = smart_annotation_parser(chkItem.text) + .gsub(/\s+/, ' ') message = t( str, user: current_user.full_name, diff --git a/app/helpers/activity_helper.rb b/app/helpers/activity_helper.rb index d400abdb9..35bdd3c64 100644 --- a/app/helpers/activity_helper.rb +++ b/app/helpers/activity_helper.rb @@ -1,31 +1,42 @@ module ActivityHelper + TAGS_LENGTH = 4 + TRUNCATE_OFFSET = 3 def activity_truncate(message, len = Constants::NAME_TRUNCATION_LENGTH) activity_titles = message.scan(/(.*?)<\/strong>/) activity_titles.each do |activity_title| activity_title = activity_title[0] - unless activity_title.length == smart_annotation_parser(activity_title) - .length - temp = activity_title.index('[') - while !temp.nil? && temp < len - if activity_title[temp + 1] == '#' || activity_title[temp + 1] == '@' - last_sa = activity_title.index(']', temp) - end - temp = activity_title.index('[', last_sa) - len = last_sa if last_sa > len - end - len += 4 + closing = activity_title.index('') + unless closing.nil? + ind = activity_title.index(' ind_temp end + temp = len + while !ind.nil? && !closing.nil? && ind < temp + stripped = strip_tags(activity_title[ind...closing]).length + temp += (activity_title[ind...closing + TAGS_LENGTH]).length - stripped + len = temp + TRUNCATE_OFFSET + TAGS_LENGTH if len <= closing + closing_temp = closing + 1 + closing = activity_title.index('', closing_temp) + unless closing.nil? + ind = activity_title.index(' ind_temp + end + end + len = activity_title.length if len > activity_title.length && + len != Constants::NAME_TRUNCATION_LENGTH if activity_title.length > len title = "
- #{truncate(activity_title, length: len)} + #{truncate(activity_title, length: len, escape: false)} #{activity_title}
" else - title = truncate(activity_title, length: len) + title = truncate(activity_title, length: len, escape: false) end - message = smart_annotation_parser(message.gsub(/#{Regexp.escape(activity_title)}/, title)) + message = message.gsub(/#{Regexp.escape(activity_title)}/, title) end sanitize_input(message) if message end diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 2c437a42c..82ad73da9 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -126,12 +126,12 @@ module ApplicationHelper next unless project if project.archived? "" \ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to project.name, projects_archive_path} #{I18n.t('atwho.res.archived')}" else "" \ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to project.name, project_path(project)}" end @@ -140,13 +140,13 @@ module ApplicationHelper next unless experiment if experiment.archived? "" \ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to experiment.name, experiment_archive_project_path(experiment.project)} " \ "#{I18n.t('atwho.res.archived')}" else ""\ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to experiment.name, canvas_experiment_path(experiment)}" end @@ -155,25 +155,25 @@ module ApplicationHelper next unless my_module if my_module.archived? "" \ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to my_module.name, module_archive_experiment_path(my_module.experiment)} " \ "#{I18n.t('atwho.res.archived')}" else "" \ - "#{sanitize_input(match[2])} " \ + "#{sanitize_input(match[2])}" \ "#{link_to my_module.name, protocols_my_module_path(my_module)}" end when 'sam' sample = Sample.find_by_id(match[3].base62_decode) if sample - " " \ + "" \ "#{link_to(sample.name, sample_path(sample.id), class: 'sample-info-link')}" else - " " \ + "" \ "#{match[1]} #{I18n.t('atwho.res.deleted')}" end end From 6c5bc32f24e35d1e0448eb22dafc8d32a1790cae Mon Sep 17 00:00:00 2001 From: lenart Date: Wed, 2 Aug 2017 16:00:23 +0200 Subject: [PATCH 03/24] Revert incorrect changes from previous commit [SCI-1249] --- app/views/my_modules/activities/_activity.html.erb | 2 +- app/views/reports/elements/_my_module_activity_element.html.erb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/app/views/my_modules/activities/_activity.html.erb b/app/views/my_modules/activities/_activity.html.erb index 876dc74aa..63a047b90 100644 --- a/app/views/my_modules/activities/_activity.html.erb +++ b/app/views/my_modules/activities/_activity.html.erb @@ -2,6 +2,6 @@ <%= l activity.created_at, format: :full %> - <%= sanitize_input(smart_annotation_parser(activity.message)) %> + <%= sanitize_input(activity.message) %> diff --git a/app/views/reports/elements/_my_module_activity_element.html.erb b/app/views/reports/elements/_my_module_activity_element.html.erb index e2b818de2..8a709e931 100644 --- a/app/views/reports/elements/_my_module_activity_element.html.erb +++ b/app/views/reports/elements/_my_module_activity_element.html.erb @@ -30,7 +30,7 @@   - <%= sanitize_input(smart_annotation_parser(activity.message)) %> + <%= sanitize_input(activity.message) %> <% end %> From a0f7030a70455e3fb77f6767e8ab1b34edf5d880 Mon Sep 17 00:00:00 2001 From: Mojca Lorber Date: Thu, 7 Sep 2017 14:54:12 +0200 Subject: [PATCH 04/24] fix bug with tinyMCE text validaton --- app/assets/javascripts/my_modules/results.js.erb | 5 +++-- app/assets/javascripts/protocols/steps.js.erb | 3 ++- app/assets/javascripts/sitewide/form_validators.js.erb | 6 +++--- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/app/assets/javascripts/my_modules/results.js.erb b/app/assets/javascripts/my_modules/results.js.erb index 079815e61..b56218e41 100644 --- a/app/assets/javascripts/my_modules/results.js.erb +++ b/app/assets/javascripts/my_modules/results.js.erb @@ -166,8 +166,9 @@ var $nameInput = $form.find('#result_name'); var nameValid = textValidator(ev, $nameInput, 0, <%= Constants::NAME_MAX_LENGTH %>); - var $textInput = TinyMCE.getContent(); - textValidator(ev, $textInput, 1, <%= Constants::TEXT_MAX_LENGTH %>, false, true); + var $descrTextarea = $form.find("#result_result_text_attributes_text"); + var $tinyMCEInput = TinyMCE.getContent(); + textValidator(ev, $descrTextarea, 1, <%= Constants::TEXT_MAX_LENGTH %>, false, $tinyMCEInput); break; case ResultTypeEnum.COMMENT: var $commentInput = $form.find('#comment_message'); diff --git a/app/assets/javascripts/protocols/steps.js.erb b/app/assets/javascripts/protocols/steps.js.erb index 3458fecb2..93ca6d6b2 100644 --- a/app/assets/javascripts/protocols/steps.js.erb +++ b/app/assets/javascripts/protocols/steps.js.erb @@ -540,8 +540,9 @@ var nameValid = textValidator(ev, $nameInput, 1, <%= Constants::NAME_MAX_LENGTH %>); var $descrTextarea = $form.find("#step_description"); + var $tinyMCEInput = TinyMCE.getContent(); var descriptionValid = textValidator(ev, $descrTextarea, 0, - <%= Constants::TEXT_MAX_LENGTH %>); + <%= Constants::TEXT_MAX_LENGTH %>, false, $tinyMCEInput); if (DragNDropSteps.filesStatus() && checklistsValid && diff --git a/app/assets/javascripts/sitewide/form_validators.js.erb b/app/assets/javascripts/sitewide/form_validators.js.erb index 323457e5d..aca5ef0f3 100644 --- a/app/assets/javascripts/sitewide/form_validators.js.erb +++ b/app/assets/javascripts/sitewide/form_validators.js.erb @@ -22,11 +22,11 @@ $.fn.onSubmitValidator = function(validatorCb) { * @param {boolean} clearErr Set clearErr to true if this is the only * error that can happen/show. */ -function textValidator(ev, textInput, textLimitMin, textLimitMax, clearErr, tinyMCE) { +function textValidator(ev, textInput, textLimitMin, textLimitMax, clearErr, tinyMCEInput) { clearErr = _.isUndefined(clearErr) ? false : clearErr; - if(tinyMCE){ - var text = textInput.length; + if(tinyMCEInput){ + var text = tinyMCEInput; } else { var text = $(textInput).val().trim(); $(textInput).val(text); From 05e627e97641550836cb7797ccec11f81b31e322 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Fri, 22 Sep 2017 17:10:53 +0200 Subject: [PATCH 05/24] Fix missing value in delayed_uploader_tutorial Closes OPENSCI-26. --- app/utilities/delayed_uploader_tutorial.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/app/utilities/delayed_uploader_tutorial.rb b/app/utilities/delayed_uploader_tutorial.rb index 993e519cb..87e349f1a 100644 --- a/app/utilities/delayed_uploader_tutorial.rb +++ b/app/utilities/delayed_uploader_tutorial.rb @@ -41,6 +41,7 @@ module DelayedUploaderTutorial my_module: my_module, user: current_user, created_at: temp_result.created_at, + updated_at: temp_result.created_at, message: I18n.t( 'activities.add_asset_result', user: current_user.full_name, From faaa016267aa48f6eb4498a4c71c53aa3342e326 Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Tue, 26 Sep 2017 13:41:53 +0200 Subject: [PATCH 06/24] Update AWS SDK v2 [SCI-1623] --- Gemfile | 2 +- Gemfile.lock | 16 +++++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/Gemfile b/Gemfile index 6754fde93..13b81f6d2 100644 --- a/Gemfile +++ b/Gemfile @@ -64,7 +64,7 @@ gem 'rubyzip' gem 'activerecord-import' gem 'paperclip', '~> 4.3' # File attachment, image attachment library -gem 'aws-sdk', '~> 2.2.8' +gem 'aws-sdk', '~> 2' gem 'aws-sdk-v1' gem 'delayed_job_active_record' gem 'devise-async' diff --git a/Gemfile.lock b/Gemfile.lock index aed66990c..9016ac2ef 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -69,15 +69,17 @@ GEM autosize-rails (1.18.17) rails (>= 3.1) awesome_print (1.7.0) - aws-sdk (2.2.8) - aws-sdk-resources (= 2.2.8) - aws-sdk-core (2.2.8) + aws-sdk (2.10.52) + aws-sdk-resources (= 2.10.52) + aws-sdk-core (2.10.52) + aws-sigv4 (~> 1.0) jmespath (~> 1.0) - aws-sdk-resources (2.2.8) - aws-sdk-core (= 2.2.8) + aws-sdk-resources (2.10.52) + aws-sdk-core (= 2.10.52) aws-sdk-v1 (1.66.0) json (~> 1.4) nokogiri (>= 1.4.4) + aws-sigv4 (1.0.2) babel-source (5.8.35) babel-transpiler (0.7.0) babel-source (>= 4.0, < 6) @@ -155,7 +157,7 @@ GEM introjs-rails (1.0.0) sass-rails (>= 3.2) thor (~> 0.14) - jmespath (1.1.3) + jmespath (1.3.1) jquery-rails (4.0.5) rails-dom-testing (~> 1.0) railties (>= 4.2.0) @@ -350,7 +352,7 @@ DEPENDENCIES auto_strip_attributes (~> 2.1) autosize-rails awesome_print - aws-sdk (~> 2.2.8) + aws-sdk (~> 2) aws-sdk-v1 base62 bcrypt (~> 3.1.10) From 7cc2136c744142276f227a635b4669516fe7c9ad Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Fri, 29 Sep 2017 13:32:31 +0200 Subject: [PATCH 07/24] Bump VERSION to 1.12.4 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 81f363239..89c881bc9 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.12.3 +1.12.4 From 6824f9a8bc28aca75a0c749fab0f76a39b6bb947 Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Mon, 2 Oct 2017 11:29:22 +0200 Subject: [PATCH 08/24] Improve memory utulization in PDF report generator [SCI-1482] --- app/controllers/reports_controller.rb | 3 ++- app/views/reports/report.pdf.erb | 4 +--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb index 524123e90..7a544e972 100644 --- a/app/controllers/reports_controller.rb +++ b/app/controllers/reports_controller.rb @@ -182,7 +182,8 @@ class ReportsController < ApplicationController @html = '

No content

' if @html.blank? render pdf: 'report', header: { right: '[page] of [topage]' }, - template: 'reports/report.pdf.erb' + template: 'reports/report.pdf.erb', + disable_javascript: true end end end diff --git a/app/views/reports/report.pdf.erb b/app/views/reports/report.pdf.erb index aaa96c774..6e96f962d 100644 --- a/app/views/reports/report.pdf.erb +++ b/app/views/reports/report.pdf.erb @@ -10,9 +10,7 @@
<% # Also whitelist and tags %> - <%= sanitize_input(fix_smart_annotation_image(@html), - ['img', 'input'], - ['type', 'disabled', 'checked']) %> + <%= @html.html_safe %>
From b26b963e54f4af429152b27df2af0b4676cc0946 Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Thu, 5 Oct 2017 16:19:25 +0200 Subject: [PATCH 09/24] Optimize update canvas SQL and remove module group name [SCI-1642] --- app/assets/javascripts/projects/canvas.js.erb | 113 ------- app/controllers/canvas_controller.rb | 212 ++++--------- app/controllers/my_modules_controller.rb | 4 +- app/controllers/search_controller.rb | 11 - app/helpers/permission_helper.rb | 6 - app/models/connection.rb | 6 +- app/models/experiment.rb | 288 +++++++----------- app/models/my_module.rb | 16 +- app/models/my_module_group.rb | 31 -- app/utilities/first_time_data_generator.rb | 5 +- app/views/canvas/_edit.html.erb | 7 - app/views/canvas/edit/_my_module.html.erb | 10 - .../edit/modal/_edit_module_group.html.erb | 19 -- app/views/search/index.html.erb | 16 - app/views/search/results/_workflows.html.erb | 33 -- config/locales/en.yml | 5 - ...171003082333_add_indexes_to_connections.rb | 6 + .../20171005135350_update_my_module_groups.rb | 5 + test/models/my_module_group_test.rb | 8 - 19 files changed, 198 insertions(+), 603 deletions(-) delete mode 100644 app/views/canvas/edit/modal/_edit_module_group.html.erb delete mode 100644 app/views/search/results/_workflows.html.erb create mode 100644 db/migrate/20171003082333_add_indexes_to_connections.rb create mode 100644 db/migrate/20171005135350_update_my_module_groups.rb diff --git a/app/assets/javascripts/projects/canvas.js.erb b/app/assets/javascripts/projects/canvas.js.erb index 65375ca2a..bd070ad7a 100644 --- a/app/assets/javascripts/projects/canvas.js.erb +++ b/app/assets/javascripts/projects/canvas.js.erb @@ -163,7 +163,6 @@ function initializeEdit() { // Read permissions from the data attributes of the form var canEditModules = _.isEqual($("#update-canvas").data("can-edit-modules"), "yes"); - var canEditModuleGroups = _.isEqual($("#update-canvas").data("can-edit-module-groups"), "yes"); var canCreateModules = _.isEqual($("#update-canvas").data("can-create-modules"), "yes"); var canCloneModules = _.isEqual($("#update-canvas").data("can-clone-modules"), "yes"); var canMoveModules = _.isEqual($("#update-canvas").data("can-move-modules"), "yes"); @@ -211,11 +210,6 @@ function initializeEdit() { $(".edit-module").on("click touchstart", editModuleHandler); } - if (canEditModuleGroups) { - initEditModuleGroups(); - $(".edit-module-group").on("click touchstart", editModuleGroupHandler); - } - if (canCloneModules) { bindCloneModuleAction( $(".module-options a.clone-module"), @@ -1220,22 +1214,6 @@ function updateModuleHtml(module, id, name, gridDistX, gridDistY) { // Add click handler for the edit module $(editModuleLink).on("click touchstart", editModuleHandler); } - if (_.isEqual($("#update-canvas").data("can-edit-module-groups"), "yes")) { - var editModuleGroupItem = document.createElement("li"); - $(editModuleGroupItem).appendTo(dropdownMenu); - $(editModuleGroupItem).hide(); - - var editModuleGroupLink = document.createElement("a"); - $(editModuleGroupLink) - .attr("href", "") - .attr("data-module-id", id) - .addClass("edit-module-group") - .html($("#edit-group-link-placeholder").text().trim()) - .appendTo(editModuleGroupItem); - - // Add click handler for the edit module group - $(editModuleGroupLink).on("click touchstart", editModuleGroupHandler); - } // Add clone links if neccesary if (_.isEqual($("#update-canvas").data("can-clone-modules"), "yes")) { @@ -1636,95 +1614,11 @@ editModuleHandler = function(ev) { /** * Initialize editing of module groups. */ -function initEditModuleGroups() { - function handleRenameConfirm(modal, ev) { - var input = modal.find("#edit-module-group-name-input"); - // Validate module group name - var moduleNameValid = textValidator(ev, input, 1, - <%= Constants::NAME_MAX_LENGTH %>, true); - if (moduleNameValid) { - var newModuleGroupName = input.val(); - var moduleId = modal.attr("data-module-id"); - var moduleEl = $("#" + moduleId); - // Update the module group name for all modules - // currently in the module group - var ids = connectedComponents(graph, moduleEl.attr("data-module-id")); - _.each(ids, function(id) { - $("#" + id).attr("data-module-group-name", newModuleGroupName); - }); - - // Hide modal - modal.modal("hide"); - } - } - - $("#modal-edit-module-group") - .on("show.bs.modal", function (event) { - var modal = $(this); - var moduleId = modal.attr("data-module-id"); - var moduleEl = $("#" + moduleId); - var input = modal.find("#edit-module-group-name-input"); - - // Set the input to the current module's name - input - .attr("value", moduleEl.attr("data-module-group-name")); - input.val(moduleEl.attr("data-module-group-name")); - - // Bind on enter button - input.keydown(function(ev) { - if (ev.keyCode == 13) { - // "Submit" modal - handleRenameConfirm(modal, ev); - - // In any case, prevent form submission - ev.preventDefault(); - ev.stopPropagation(); - return false; - } - }); - }) - .on("shown.bs.modal", function (event) { - $(this).find("#edit-module-group-name-input").focus(); - }) - .on("hide.bs.modal", function (event) { - // Remove potential error classes - $(this).find("#edit-module-group-name-input").parent().removeClass("has-error"); - $(this).find("span.help-block").remove(); - - $(this).find("#edit-module-group-name-input").off("keydown"); - - // When hiding modal, re-enable events - toggleCanvasEvents(true); - }); - - // Bind the confirm button on modal - $("#modal-edit-module-group").find("button[data-action='confirm']").on("click", function(ev) { - var modal = $(this).closest(".modal"); - handleRenameConfirm(modal, ev); - }); -} /** * Handler when editing a module group. */ -editModuleGroupHandler = function(ev) { - var modal = $("#modal-edit-module-group"); - var moduleEl = $(this).closest(".module"); - - // Set modal's module id - modal.attr("data-module-id", moduleEl.attr("data-module-id")); - - // Disable dragging & zooming events on canvas temporarily - toggleCanvasEvents(false); - - // Show modal - modal.modal("show"); - - ev.preventDefault(); - ev.stopPropagation(); - return false; -}; function initMoveModules() { function handleMoveConfirm(modal) { @@ -1978,7 +1872,6 @@ function deleteModule(id, linkConnections) { _.each (ins, function(inEdge) { if (graph.degree(inEdge[0]) === 0) { tempModuleEl = $("#" + inEdge[0]); - tempModuleEl.find(".edit-module-group").parents("li").hide(); tempModuleEl.find(".clone-module-group").parents("li").hide(); tempModuleEl.find(".move-module-group").parents("li").hide(); tempModuleEl.find(".delete-module-group").parents("li").hide(); @@ -1989,7 +1882,6 @@ function deleteModule(id, linkConnections) { _.each (outs, function(outEdge) { if (graph.degree(outEdge[1]) === 0) { tempModuleEl = $("#" + outEdge[1]); - tempModuleEl.find(".edit-module-group").parents("li").hide(); tempModuleEl.find(".clone-module-group").parents("li").hide(); tempModuleEl.find(".move-module-group").parents("li").hide(); tempModuleEl.find(".delete-module-group").parents("li").hide(); @@ -2361,7 +2253,6 @@ cloneModuleGroupHandler = function(moduleId, modulesSel, gridDistX, gridDistY) { var nm = cloneModule(m, gridDistX, gridDistY, elLeft(m), elTop(m) + height + offset - gridDistY); //Show module group options - nm.find(".edit-module-group").parents("li").show(); nm.find(".clone-module-group").parents("li").show(); nm.find(".move-module-group").parents("li").show(); nm.find(".delete-module-group").parents("li").show(); @@ -2963,12 +2854,10 @@ function initJsPlumb(containerSel, containerChildSel, modulesSel, params) { //Modules should belong to module group now //Show module group options for target and source - srcModuleEl.find(".edit-module-group").parents("li").show(); srcModuleEl.find(".clone-module-group").parents("li").show(); srcModuleEl.find(".move-module-group").parents("li").show(); srcModuleEl.find(".delete-module-group").parents("li").show(); - targetModuleEl.find(".edit-module-group").parents("li").show(); targetModuleEl.find(".clone-module-group").parents("li").show(); targetModuleEl.find(".move-module-group").parents("li").show(); targetModuleEl.find(".delete-module-group").parents("li").show(); @@ -3001,13 +2890,11 @@ function initJsPlumb(containerSel, containerChildSel, modulesSel, params) { var targetModuleEl = $("#" + c.targetId); //First source if (graph.degree(c.sourceId) === 0) { - srcModuleEl.find(".edit-module-group").parents("li").hide(); srcModuleEl.find(".clone-module-group").parents("li").hide(); srcModuleEl.find(".move-module-group").parents("li").hide(); srcModuleEl.find(".delete-module-group").parents("li").hide(); } if (graph.degree(c.targetId) === 0) { - targetModuleEl.find(".edit-module-group").parents("li").hide(); targetModuleEl.find(".clone-module-group").parents("li").hide(); targetModuleEl.find(".move-module-group").parents("li").hide(); targetModuleEl.find(".delete-module-group").parents("li").hide(); diff --git a/app/controllers/canvas_controller.rb b/app/controllers/canvas_controller.rb index 4f0291a64..14728cc92 100644 --- a/app/controllers/canvas_controller.rb +++ b/app/controllers/canvas_controller.rb @@ -29,58 +29,41 @@ class CanvasController < ApplicationController end def update - error = false - # Make sure that remove parameter is valid to_archive = [] - if can_archive_modules(@experiment) and - update_params[:remove].present? then - to_archive = update_params[:remove].split(",") - unless to_archive.all? { |id| is_int? id } - error = true + if can_archive_modules(@experiment) && update_params[:remove].present? + to_archive = update_params[:remove].split(',') + if to_archive.all? { |id| is_int? id } + to_archive.collect!(&:to_i) else - to_archive.collect! { |id| id.to_i } + return render_403 end end - if error then - render_403 and return - end - # Make sure connections parameter is valid connections = [] - if can_edit_connections(@experiment) and - update_params[:connections].present? then - conns = update_params[:connections].split(",") - unless conns.length % 2 == 0 and - conns.all? { |c| c.is_a? String } then - error = true - else + if can_edit_connections(@experiment) && update_params[:connections].present? + conns = update_params[:connections].split(',') + if conns.length.even? && conns.all? { |c| c.is_a? String } conns.each_slice(2).each do |c| connections << [c[0], c[1]] end + else + return render_403 end end - if error then - render_403 and return - end - # Make sure positions parameter is valid - positions = Hash.new - if can_reposition_modules(@experiment) and - update_params[:positions].present? then - poss = update_params[:positions].split(";") - center = "" - (poss.collect { |pos| pos.split(",") }).each_with_index do |pos, index| - unless pos.length == 3 && - pos[0].is_a?(String) && - float?(pos[1]) && - float?(pos[2]) - error = true - break + positions = {} + if can_reposition_modules(@experiment) && update_params[:positions].present? + poss = update_params[:positions].split(';') + center = '' + (poss.collect { |pos| pos.split(',') }).each_with_index do |pos, index| + unless pos.length == 3 && pos[0].is_a?(String) && + float?(pos[1]) && float?(pos[2]) + return render_403 end - if index == 0 + if index.zero? center = pos x = 0 y = 0 @@ -89,86 +72,59 @@ class CanvasController < ApplicationController y = pos[2].to_i - center[2].to_i end # Multiple modules cannot have same position - if positions.any? { |k,v| v[:x] == x and v[:y] == y} then - error = true - break - end + return render_403 if positions.any? { |_, v| v[:x] == x && v[:y] == y } positions[pos[0]] = { x: x, y: y } end end - if error then - render_403 and return - end - # Make sure that to_add is an array of strings, # as well as that positions for newly added modules exist to_add = [] - if can_create_modules(@experiment) and - update_params[:add].present? and - update_params["add-names"].present? then - ids = update_params[:add].split(",") - names = update_params["add-names"].split("|") - unless ids.length == names.length and - ids.all? { |id| id.is_a? String and positions.include? id } and - names.all? { |name| name.is_a? String } - error = true - else + if can_create_modules(@experiment) && update_params[:add].present? && + update_params['add-names'].present? + ids = update_params[:add].split(',') + names = update_params['add-names'].split('|') + if ids.length == names.length && + ids.all? { |id| id.is_a?(String) && positions.include?(id) } && + names.all? { |name| name.is_a? String } ids.each_with_index do |id, i| - to_add << { - id: id, - name: names[i], - x: positions[id][:x], - y: positions[id][:y] - } + to_add << { id: id, name: names[i], + x: positions[id][:x], y: positions[id][:y] } end + else + return render_403 end end - if error then - render_403 and return - end - # Make sure rename parameter is valid - to_rename = Hash.new - if can_edit_modules(@experiment) and - update_params[:rename].present? then + to_rename = {} + if can_edit_modules(@experiment) && update_params[:rename].present? begin to_rename = JSON.parse(update_params[:rename]) - # Okay, JSON parsed! - unless ( - to_rename.is_a? Hash and - to_rename.keys.all? { |k| k.is_a? String } and - to_rename.values.all? { |k| k.is_a? String } - ) - error = true + unless to_rename.is_a?(Hash) && + to_rename.keys.all? { |k| k.is_a? String } && + to_rename.values.all? { |k| k.is_a? String } + return render_403 end rescue - error = true + return render_403 end end - if error then - render_403 and return - end - # Make sure move parameter is valid to_move = {} if can_move_modules(@experiment) && update_params[:move].present? begin to_move = JSON.parse(update_params[:move]) - # Okay, JSON parsed! - unless ( - to_move.is_a? Hash and - to_move.keys.all? { |k| k.is_a? String } && - to_move.values.all? { |k| k.is_a? String } - ) - error = true + unless to_move.is_a?(Hash) && + to_move.keys.all? { |k| k.is_a? String } && + to_move.values.all? { |k| k.is_a? String } + return render_403 end rescue - error = true + return render_403 end end @@ -181,54 +137,21 @@ class CanvasController < ApplicationController end end - render_403 and return if error - # Make sure that to_clone is an array of pairs, # as well as that all IDs exist - to_clone = Hash.new - if can_clone_modules(@experiment) and - update_params[:cloned].present? then - clones = update_params[:cloned].split(";") - (clones.collect { |v| v.split(",") }).each do |val| - unless (val.length == 2 and - is_int? val[0] and - val[1].is_a? String and - to_add.any? { |m| m[:id] == val[1] }) - error = true - break - else + to_clone = {} + if can_clone_modules(@experiment) && update_params[:cloned].present? + clones = update_params[:cloned].split(';') + (clones.collect { |v| v.split(',') }).each do |val| + if val.length == 2 && is_int?(val[0]) && val[1].is_a?(String) && + to_add.any? { |m| m[:id] == val[1] } to_clone[val[1]] = val[0] + else + return render_403 end end end - if error then - render_403 and return - end - - module_groups = Hash.new - if can_edit_module_groups(@experiment) and - update_params["module-groups"].present? then - begin - module_groups = JSON.parse(update_params["module-groups"]) - - # Okay, JSON parsed! - unless ( - module_groups.is_a? Hash and - module_groups.keys.all? { |k| k.is_a? String } and - module_groups.values.all? { |k| k.is_a? String } - ) - error = true - end - rescue - error = true - end - end - - if error then - render_403 and return - end - # Call the "master" function to do all the updating for us unless @experiment.update_canvas( to_archive, @@ -239,36 +162,29 @@ class CanvasController < ApplicationController to_clone, connections, positions, - current_user, - module_groups + current_user ) - render_403 and return + return render_403 end - #Save activities that modules were archived + # Save activities that modules were archived to_archive.each do |module_id| my_module = MyModule.find_by_id(module_id) - unless my_module.blank? - Activity.create( - type_of: :archive_module, - project: my_module.experiment.project, - experiment: my_module.experiment, - my_module: my_module, - user: current_user, - message: t( - 'activities.archive_module', - user: current_user.full_name, - module: my_module.name - ) - ) - end + next if my_module.blank? + Activity.create(type_of: :archive_module, + project: my_module.experiment.project, + experiment: my_module.experiment, + my_module: my_module, + user: current_user, + message: t('activities.archive_module', + user: current_user.full_name, + module: my_module.name)) end # Create workflow image @experiment.delay.generate_workflow_img - flash[:success] = t( - "experiments.canvas.update.success_flash") + flash[:success] = t('experiments.canvas.update.success_flash') redirect_to canvas_experiment_path(@experiment) end diff --git a/app/controllers/my_modules_controller.rb b/app/controllers/my_modules_controller.rb index be9eec021..c0457c635 100644 --- a/app/controllers/my_modules_controller.rb +++ b/app/controllers/my_modules_controller.rb @@ -291,7 +291,7 @@ class MyModulesController < ApplicationController task_names = [] new_samples = [] - @my_module.get_downstream_modules.each do |my_module| + @my_module.downstream_modules.each do |my_module| new_samples = samples.select { |el| my_module.samples.exclude?(el) } my_module.samples.push(*new_samples) task_names << my_module.name @@ -330,7 +330,7 @@ class MyModulesController < ApplicationController end task_names = [] - @my_module.get_downstream_modules.each do |my_module| + @my_module.downstream_modules.each do |my_module| task_names << my_module.name my_module.samples.destroy(samples & my_module.samples) end diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb index d809d39bd..2ff557292 100644 --- a/app/controllers/search_controller.rb +++ b/app/controllers/search_controller.rb @@ -8,7 +8,6 @@ class SearchController < ApplicationController search_projects if @search_category == :projects search_experiments if @search_category == :experiments - search_workflows if @search_category == :workflows search_modules if @search_category == :modules search_results if @search_category == :results search_tags if @search_category == :tags @@ -145,7 +144,6 @@ class SearchController < ApplicationController def count_search_results @project_search_count = count_by_name Project @experiment_search_count = count_by_name Experiment - @workflow_search_count = count_by_name MyModuleGroup @module_search_count = count_by_name MyModule @result_search_count = count_by_name Result @tag_search_count = count_by_name Tag @@ -161,7 +159,6 @@ class SearchController < ApplicationController @search_results_count = @project_search_count @search_results_count += @experiment_search_count - @search_results_count += @workflow_search_count @search_results_count += @module_search_count @search_results_count += @result_search_count @search_results_count += @tag_search_count @@ -190,14 +187,6 @@ class SearchController < ApplicationController @search_count = @experiment_search_count end - def search_workflows - @workflow_results = [] - if @workflow_search_count > 0 - @workflow_results = search_by_name(MyModuleGroup) - end - @search_count = @workflow_search_count - end - def search_modules @module_results = [] @module_results = search_by_name(MyModule) if @module_search_count > 0 diff --git a/app/helpers/permission_helper.rb b/app/helpers/permission_helper.rb index 907cb2ac8..ef403766f 100644 --- a/app/helpers/permission_helper.rb +++ b/app/helpers/permission_helper.rb @@ -64,7 +64,6 @@ module PermissionHelper :can_edit_connections, :can_create_modules, :can_edit_modules, - :can_edit_module_groups, :can_clone_modules, :can_archive_modules, :can_view_reports, @@ -149,7 +148,6 @@ module PermissionHelper :can_edit_connections, :can_create_modules, :can_edit_modules, - :can_edit_module_groups, :can_clone_modules, :can_archive_modules ] do |proxy, *args, &block| @@ -421,10 +419,6 @@ module PermissionHelper is_user_or_higher_of_project(experiment.project) end - def can_edit_module_groups(experiment) - is_user_or_higher_of_project(experiment.project) - end - def can_clone_modules(experiment) is_user_or_higher_of_project(experiment.project) end diff --git a/app/models/connection.rb b/app/models/connection.rb index e2c68652b..b6bcb7e68 100644 --- a/app/models/connection.rb +++ b/app/models/connection.rb @@ -1,4 +1,6 @@ class Connection < ActiveRecord::Base - belongs_to :to, :class_name => 'MyModule', :foreign_key => 'input_id', inverse_of: :inputs - belongs_to :from, :class_name => 'MyModule', :foreign_key => 'output_id', inverse_of: :outputs + belongs_to :to, class_name: 'MyModule', foreign_key: 'input_id', + inverse_of: :inputs + belongs_to :from, class_name: 'MyModule', foreign_key: 'output_id', + inverse_of: :outputs end diff --git a/app/models/experiment.rb b/app/models/experiment.rb index 3ad412694..9f2a7cfce 100644 --- a/app/models/experiment.rb +++ b/app/models/experiment.rb @@ -87,26 +87,27 @@ class Experiment < ActiveRecord::Base end def modules_without_group - MyModule.where(experiment_id: id).where(my_module_group: nil) - .where(archived: false) + MyModule.where(experiment_id: id) + .where(my_module_group: nil) + .where(archived: false) end def active_module_groups - self.my_module_groups.joins(:my_modules) - .where('my_modules.archived = ?', false) - .distinct + my_module_groups.joins(:my_modules) + .where('my_modules.archived = ?', false) + .distinct end def active_modules - my_modules.where(:archived => false) + my_modules.where(archived: false) end def archived_modules - my_modules.where(:archived => true) + my_modules.where(archived: true) end def assigned_samples - Sample.joins(:my_modules).where(my_modules: {id: my_modules} ) + Sample.joins(:my_modules).where(my_modules: { id: my_modules }) end def unassigned_samples(assigned_samples) @@ -122,15 +123,15 @@ class Experiment < ActiveRecord::Base to_clone, connections, positions, - current_user, - module_groups + current_user ) cloned_modules = [] begin - Experiment.transaction do + with_lock do # First, add new modules new_ids, cloned_pairs, originals = add_modules( - to_add, to_clone, current_user) + to_add, to_clone, current_user + ) cloned_modules = cloned_pairs.collect { |mn, _| mn } # Rename modules @@ -138,39 +139,31 @@ class Experiment < ActiveRecord::Base # Add activities that modules were created originals.each do |m| - Activity.create( - type_of: :create_module, + Activity.create(type_of: :create_module, user: current_user, - project: self.project, + project: project, experiment: m.experiment, my_module: m, - message: I18n.t( - "activities.create_module", - user: current_user.full_name, - module: m.name - ) - ) + message: I18n.t('activities.create_module', + user: current_user.full_name, + module: m.name)) end # Add activities that modules were cloned cloned_pairs.each do |mn, mo| - Activity.create( - type_of: :clone_module, + Activity.create(type_of: :clone_module, project: mn.experiment.project, experiment: mn.experiment, my_module: mn, user: current_user, - message: I18n.t( - "activities.clone_module", - user: current_user.full_name, - module_new: mn.name, - module_original: mo.name - ) - ) + message: I18n.t('activities.clone_module', + user: current_user.full_name, + module_new: mn.name, + module_original: mo.name)) end # Then, archive modules that need to be archived - archive_modules(to_archive, current_user) + archive_modules(to_archive, current_user) if to_archive.any? # Update connections, positions & module group variables # with actual IDs retrieved from the new modules creation @@ -187,17 +180,13 @@ class Experiment < ActiveRecord::Base updated_to_move_groups[mapped] = value end updated_connections = [] - connections.each do |a,b| + connections.each do |a, b| updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)] end - updated_positions = Hash.new + updated_positions = {} positions.each do |id, pos| updated_positions[new_ids.fetch(id, id)] = pos end - updated_module_groups = {} - module_groups.each do |id, name| - updated_module_groups[new_ids.fetch(id, id)] = name - end # Update connections update_module_connections(updated_connections) @@ -209,7 +198,7 @@ class Experiment < ActiveRecord::Base normalize_module_positions # Finally, update module groups - update_module_groups(updated_module_groups, current_user) + update_module_groups(current_user) # Finally move any modules to another experiment move_modules(updated_to_move) @@ -217,11 +206,12 @@ class Experiment < ActiveRecord::Base # Everyhing is set, now we can move any module groups move_module_groups(updated_to_move_groups) end - rescue ActiveRecord::ActiveRecordError, ArgumentError, ActiveRecord::RecordNotSaved + rescue ActiveRecord::ActiveRecordError, + ArgumentError, + ActiveRecord::RecordNotSaved return false end - - return true + true end # This method generate the workflow image and saves it as @@ -422,22 +412,15 @@ class Experiment < ActiveRecord::Base # Archive all modules. Receives an array of module integer IDs. def archive_modules(module_ids) - module_ids.each do |m_id| - my_module = self.my_modules.find_by_id(m_id) - unless my_module.blank? - my_module.archive! - end - end - modules.reload + my_modules.where(id: module_ids).each(&:archive!) + my_modules.reload end - # Archive all modules. Receives an array of module integer IDs and current user. + # Archive all modules. Receives an array of module integer IDs + # and current user. def archive_modules(module_ids, current_user) - module_ids.each do |m_id| - my_module = self.my_modules.find_by_id(m_id) - unless my_module.blank? - my_module.archive!(current_user) - end + my_modules.where(id: module_ids).each do |m| + m.archive!(current_user) end my_modules.reload end @@ -451,15 +434,14 @@ class Experiment < ActiveRecord::Base def add_modules(to_add, to_clone, current_user) originals = [] cloned_pairs = {} - ids_map = Hash.new + ids_map = {} to_add.each do |m| original = MyModule.find_by_id(to_clone.fetch(m[:id], nil)) - if original.present? then + if original.present? my_module = original.deep_clone(current_user) cloned_pairs[my_module] = original else - my_module = MyModule.new( - experiment: self) + my_module = MyModule.new(experiment: self) originals << my_module end @@ -528,7 +510,7 @@ class Experiment < ActiveRecord::Base # to bottom left corner. def move_module_groups(to_move) to_move.each do |ids, experiment_id| - modules = my_modules.where(id: ids) + modules = my_modules.find(ids) groups = Set.new(modules.map(&:my_module_group)) experiment = project.experiments.find_by_id(experiment_id) @@ -568,10 +550,8 @@ class Experiment < ActiveRecord::Base # Generates workflow img when the workflow or module is moved # to other experiment def generate_workflow_img_for_moved_modules(to_move) - to_move.values.uniq.each do |id| - experiment = Experiment.find_by_id(id) - next unless experiment - experiment.delay.generate_workflow_img + Experiment.where(id: to_move.values.uniq).each do |exp| + exp.delay.generate_workflow_img end end @@ -583,42 +563,39 @@ class Experiment < ActiveRecord::Base require 'rgl/base' require 'rgl/adjacency' require 'rgl/topsort' - dg = RGL::DirectedAdjacencyGraph.new - connections.each do |a,b| + connections.each do |a, b| # Check if both vertices exist - if (my_modules.find_all {|m| [a.to_i, b.to_i].include? m.id }).count == 2 + if (my_modules.find_all { |m| [a.to_i, b.to_i].include? m.id }).count == 2 dg.add_edge(a, b) end end # Check if cycles exist! topsort = dg.topsort_iterator.to_a - if topsort.length == 0 and dg.edges.size > 1 - raise ArgumentError, "Cycles exist." + if topsort.length.zero? && dg.edges.size > 1 + raise ArgumentError, 'Cycles exist.' end # First, delete existing connections # but keep a copy of previous state previous_sources = {} previous_sources.default = [] - my_modules.each do |m| + + my_modules.includes(inputs: { from: [:inputs, outputs: :to] }).each do |m| previous_sources[m.id] = [] m.inputs.each do |c| previous_sources[m.id] << c.from end end - self.my_modules.each do |m| - unless m.outputs.destroy_all - raise ActiveRecord::ActiveRecordError - end - end + # There are no callbacks in Connection, so delete_all should be safe + Connection.delete_all(output_id: my_modules) # Add new connections filtered_edges = dg.edges.collect { |e| [e.source, e.target] } filtered_edges.each do |a, b| - Connection.create!(:input_id => b, :output_id => a) + Connection.create!(input_id: b, output_id: a) end # Unassign samples from former downstream modules @@ -628,47 +605,49 @@ class Experiment < ActiveRecord::Base visited = [] # Assign samples to all new downstream modules filtered_edges.each do |a, b| - source = self.my_modules.find(a.to_i) - target = self.my_modules.find(b.to_i) + source = my_modules.includes({ inputs: :from }, :samples).find(a.to_i) + target = my_modules.find(b.to_i) # Do this only for new edges - if previous_sources[target.id].exclude?(source) - # Go as high upstream as new edges take us - # and then assign samples to all downsteam samples - assign_samples_to_new_downstream_modules(previous_sources, visited, source) - end + next unless previous_sources[target.id].exclude?(source) + # Go as high upstream as new edges take us + # and then assign samples to all downsteam samples + assign_samples_to_new_downstream_modules(previous_sources, + visited, + source) end # Save topological order of modules (for modules without workflow, # leave them unordered) - self.my_modules.each do |m| - if topsort.include? m.id.to_s - m.workflow_order = topsort.find_index(m.id.to_s) - else - m.workflow_order = -1 - end + my_modules.includes(:my_module_group).each do |m| + m.workflow_order = + if topsort.include? m.id.to_s + topsort.find_index(m.id.to_s) + else + -1 + end m.save! end - # Make sure to reload my modules, which now have updated connections and samples - self.my_modules.reload + # Make sure to reload my modules, which now have updated connections + # and samples + my_modules.reload true end # When connections are deleted, unassign samples that # are not inherited anymore def unassign_samples_from_old_downstream_modules(sources) - self.my_modules.each do |my_module| - sources[my_module.id].each do |s| + my_modules.each do |my_module| + sources[my_module.id].each do |src| # Only do this for newly deleted connections - if s.outputs.map{|i| i.to}.exclude? my_module - my_module.get_downstream_modules.each do |dm| - # Get unique samples for all upstream modules - um = dm.get_upstream_modules - um.shift # remove current module - ums = um.map{|m| m.samples}.flatten.uniq - s.samples.each do |sample| - dm.samples.destroy(sample) if ums.exclude? sample - end + next unless src.outputs.map(&:to).exclude? my_module + my_module.downstream_modules.each do |dm| + # Get unique samples for all upstream modules + um = dm.upstream_modules + um.shift # remove current module + ums = um.map(&:samples).flatten.uniq + src.samples.each do |sample| + dm.samples.destroy(sample) if ums.exclude? sample end end end @@ -678,24 +657,21 @@ class Experiment < ActiveRecord::Base # Assign samples to new connections recursively def assign_samples_to_new_downstream_modules(sources, visited, my_module) # If samples are already assigned for this module, stop going upstream - if visited.include? (my_module) - return - end + return if visited.include?(my_module) visited << my_module - # Edge case, when module is source or it doesn't have any new input connections - if my_module.inputs.blank? or ( - my_module.inputs.map{|c| c.from} - - sources[my_module.id] - ).empty? - my_module.get_downstream_modules.each do |dm| - new_samples = my_module.samples.select { |el| dm.samples.exclude?(el) } - dm.samples.push(*new_samples) + # Edge case, when module is source or it doesn't have any new input + # connections + if my_module.inputs.blank? || + (my_module.inputs.map(&:from) - sources[my_module.id]).empty? + my_module.downstream_modules.each do |dm| + new_samples = my_module.samples.where.not(id: dm.samples) + dm.samples << new_samples end else my_module.inputs.each do |input| # Go upstream for new in connections if sources[my_module.id].exclude?(input.from) - assign_samples_to_new_downstream_modules(input.from) + assign_samples_to_new_downstream_modules(sources, visited, input.from) end end end @@ -705,104 +681,58 @@ class Experiment < ActiveRecord::Base # Input is a map where keys are module IDs, and values are # hashes like { x: , y: }. def update_module_positions(positions) - positions.each do |id, pos| - unless MyModule.update(id, x: pos[:x], y: pos[:y]) - raise ActiveRecord::ActiveRecordError - end + modules = my_modules.where(id: positions.keys) + modules.each do |m| + m.update_columns(x: positions[m.id.to_s][:x], y: positions[m.id.to_s][:y]) end - self.my_modules.reload + my_modules.reload end # Normalize module positions in this project. def normalize_module_positions # This method normalizes module positions so x-s and y-s # are all positive - x_diff = (self.my_modules.collect { |m| m.x }).min - y_diff = (self.my_modules.collect { |m| m.y }).min + x_diff = my_modules.collect(&:x).min + y_diff = my_modules.collect(&:y).min - self.my_modules.each do |m| - unless - m.update_attribute(:x, m.x - x_diff) and - m.update_attribute(:y, m.y - y_diff) - raise ActiveRecord::ActiveRecordError - end + my_modules.each do |m| + m.update_columns(x: m.x - x_diff, y: m.y - y_diff) end end # Recalculate module groups in this project. Input is # a hash of module ids and their corresponding module names. - def update_module_groups(module_groups, current_user) + def update_module_groups(current_user) require 'rgl/base' require 'rgl/adjacency' require 'rgl/connected_components' dg = RGL::DirectedAdjacencyGraph[] group_ids = Set.new - active_modules.each do |m| - unless m.my_module_group.blank? - group_ids << m.my_module_group.id - end - unless dg.has_vertex? m.id - dg.add_vertex m.id - end + active_modules.includes(:my_module_group, outputs: :to).each do |m| + group_ids << m.my_module_group.id unless m.my_module_group.blank? + dg.add_vertex m.id unless dg.has_vertex? m.id m.outputs.each do |o| dg.add_edge m.id, o.to.id end end workflows = [] - dg.to_undirected.each_connected_component { |w| workflows << w } - - # Retrieve maximum allowed module group name - max_length = (MyModuleGroup.validators_on(:name).select { |v| v.class == ActiveModel::Validations::LengthValidator }).first.options[:maximum] - # For each workflow, generate new names - new_index = 1 - wf_names = [] - suffix = I18n.t("my_module_groups.new.suffix") - cut_index = -(suffix.length + 1) - workflows.each do |w| - modules = MyModule.find(w) - - # Get an array of module names - names = [] - modules.each do |m| - names << module_groups.fetch(m.id.to_s, "") - end - names = names.uniq - name = (names.select { |v| v != "" }).join(", ") - - if w.length <= 1 - name = nil - elsif name.blank? - name = I18n.t("my_module_groups.new.name", index: new_index) - new_index += 1 - while MyModuleGroup.find_by(name: name).present? - name = I18n.t("my_module_groups.new.name", index: new_index) - new_index += 1 - end - elsif name.length > max_length - # If length is too long, shorten it - name = name[0..(max_length + cut_index)] + suffix - end - - wf_names << name + dg.to_undirected.each_connected_component do |w| + workflows << my_modules.find(w) end # Remove any existing module groups from modules - unless MyModuleGroup.destroy_all(:id => group_ids.to_a) + unless MyModuleGroup.destroy_all(id: group_ids.to_a) raise ActiveRecord::ActiveRecordError end # Second, create new groups - workflows.each_with_index do |w, i| + workflows.each do |modules| # Single modules are not considered part of any workflow - if w.length > 1 - group = MyModuleGroup.new( - name: wf_names[i], - experiment: self, - my_modules: MyModule.find(w)) - group.created_by = current_user - group.save! - end + next unless modules.length > 1 + MyModuleGroup.create!(experiment: self, + my_modules: modules, + created_by: current_user) end my_module_groups.reload diff --git a/app/models/my_module.rb b/app/models/my_module.rb index 27937bfeb..232dce7d2 100644 --- a/app/models/my_module.rb +++ b/app/models/my_module.rb @@ -252,28 +252,24 @@ class MyModule < ActiveRecord::Base end # Treat this module as root, get all modules of that subtree - def get_downstream_modules + def downstream_modules final = [] modules = [self] - while !modules.empty? + until modules.empty? my_module = modules.shift - if !final.include?(my_module) - final << my_module - end + final << my_module unless final.include?(my_module) modules.push(*my_module.my_modules.flatten) end final end # Treat this module as inversed root, get all modules of that inversed subtree - def get_upstream_modules + def upstream_modules final = [] modules = [self] - while !modules.empty? + until modules.empty? my_module = modules.shift - if !final.include?(my_module) - final << my_module - end + final << my_module unless final.include?(my_module) modules.push(*my_module.my_module_antecessors.flatten) end final diff --git a/app/models/my_module_group.rb b/app/models/my_module_group.rb index f965876c4..dc5b15ece 100644 --- a/app/models/my_module_group.rb +++ b/app/models/my_module_group.rb @@ -1,49 +1,18 @@ class MyModuleGroup < ActiveRecord::Base include SearchableModel - auto_strip_attributes :name, nullify: false - validates :name, - presence: true, - length: { maximum: Constants::NAME_MAX_LENGTH } validates :experiment, presence: true belongs_to :experiment, inverse_of: :my_module_groups belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User' has_many :my_modules, inverse_of: :my_module_group, dependent: :nullify - def self.search(user, - include_archived, - query = nil, - page = 1, - _current_team = nil, - options = {}) - exp_ids = - Experiment - .search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT) - .pluck(:id) - - new_query = MyModuleGroup - .distinct - .where('my_module_groups.experiment_id IN (?)', exp_ids) - .where_attributes_like('my_module_groups.name', query, options) - - # Show all results if needed - if page == Constants::SEARCH_NO_LIMIT - new_query - else - new_query - .limit(Constants::SEARCH_LIMIT) - .offset((page - 1) * Constants::SEARCH_LIMIT) - end - end - def ordered_modules my_modules.order(workflow_order: :asc) end def deep_clone_to_experiment(current_user, experiment) clone = MyModuleGroup.new( - name: name, created_by: created_by, experiment: experiment ) diff --git a/app/utilities/first_time_data_generator.rb b/app/utilities/first_time_data_generator.rb index c77cf8ca0..c3a7933d2 100644 --- a/app/utilities/first_time_data_generator.rb +++ b/app/utilities/first_time_data_generator.rb @@ -150,7 +150,6 @@ module FirstTimeDataGenerator # Create a module group my_module_group = MyModuleGroup.create( - name: 'Potato qPCR workflow', experiment: experiment ) @@ -317,7 +316,7 @@ module FirstTimeDataGenerator samples_to_assign << sample end - my_modules[1].get_downstream_modules.each do |mm| + my_modules[1].downstream_modules.each do |mm| samples_to_assign.each do |s| SampleMyModule.create( sample: s, @@ -881,7 +880,7 @@ module FirstTimeDataGenerator ).sneaky_save # create thumbnail - experiment.generate_workflow_img + experiment.delay.generate_workflow_img # Lastly, create cookie with according ids # so tutorial steps can be properly positioned diff --git a/app/views/canvas/_edit.html.erb b/app/views/canvas/_edit.html.erb index 45b44cb37..a362c5066 100644 --- a/app/views/canvas/_edit.html.erb +++ b/app/views/canvas/_edit.html.erb @@ -1,7 +1,6 @@
" data-can-edit-modules="<%= can_edit_modules(@experiment) ? "yes" : "no" %>" - data-can-edit-module-groups="<%= can_edit_module_groups(@experiment) ? "yes" : "no" %>" data-can-clone-modules="<%= can_clone_modules(@experiment) ? "yes" : "no" %>" data-can-move-modules="<%= can_move_modules(@experiment) ? "yes" : "no" %>" data-can-delete-modules="<%= can_archive_modules(@experiment) ? "yes" : "no" %>" @@ -49,9 +48,6 @@ - @@ -87,9 +83,6 @@ <% if can_edit_modules(@experiment) %> <%= render partial: "canvas/edit/modal/edit_module", locals: {experiment: @experiment } %> <% end %> -<% if can_edit_module_groups(@experiment) %> - <%= render partial: "canvas/edit/modal/edit_module_group", locals: {experiment: @experiment } %> -<% end %> <% if can_move_modules(@experiment) %> <%= render partial: "canvas/edit/modal/move_module", locals: {experiment: @experiment } %> <%= render partial: "canvas/edit/modal/move_module_group", locals: {experiment: @experiment } %> diff --git a/app/views/canvas/edit/_my_module.html.erb b/app/views/canvas/edit/_my_module.html.erb index 54ee90c4e..d0a876290 100644 --- a/app/views/canvas/edit/_my_module.html.erb +++ b/app/views/canvas/edit/_my_module.html.erb @@ -2,11 +2,6 @@ id="<%= my_module.id %>" data-module-id="<%= my_module.id %>" data-module-name="<%= my_module.name %>" - <% if my_module.my_module_group.present? %> - data-module-group-name="<%= my_module.my_module_group.name %>" - <% else %> - data-module-group-name="" - <% end %> data-module-x="<%= my_module.x %>" data-module-y="<%= my_module.y %>" data-module-conns="<%= construct_module_connections(my_module) %>"> @@ -26,11 +21,6 @@ <%=t "experiments.canvas.edit.edit_module" %> <% end %> - <% if can_edit_module_groups(my_module.experiment) %> -
  • > - <%=t "experiments.canvas.edit.edit_module_group" %> -
    • - <% end %> <% if can_clone_modules(my_module.experiment) %>
  • <%=t "experiments.canvas.edit.clone_module" %> diff --git a/app/views/canvas/edit/modal/_edit_module_group.html.erb b/app/views/canvas/edit/modal/_edit_module_group.html.erb deleted file mode 100644 index d2e14a628..000000000 --- a/app/views/canvas/edit/modal/_edit_module_group.html.erb +++ /dev/null @@ -1,19 +0,0 @@ - diff --git a/app/views/search/index.html.erb b/app/views/search/index.html.erb index 92bfaea45..b00a61fcb 100644 --- a/app/views/search/index.html.erb +++ b/app/views/search/index.html.erb @@ -70,19 +70,6 @@ <%= t'Experiments' %>
    • -
    - <%= render partial: 'canvas/full_zoom', locals: { experiment: @experiment, my_modules: @experiment.active_modules } %> + <%= render partial: 'canvas/full_zoom', locals: { experiment: @experiment, my_modules: @active_modules } %>
    diff --git a/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb b/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb new file mode 100644 index 000000000..29f1fb9a0 --- /dev/null +++ b/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb @@ -0,0 +1,7 @@ +class AddConnectionsAndSampleTasksIndexes < ActiveRecord::Migration + def change + add_index :connections, :input_id + add_index :connections, :output_id + add_index :sample_my_modules, :my_module_id + end +end diff --git a/db/migrate/20171003082333_add_indexes_to_connections.rb b/db/migrate/20171003082333_add_indexes_to_connections.rb deleted file mode 100644 index 861ae4d40..000000000 --- a/db/migrate/20171003082333_add_indexes_to_connections.rb +++ /dev/null @@ -1,6 +0,0 @@ -class AddIndexesToConnections < ActiveRecord::Migration - def change - add_index :connections, :input_id - add_index :connections, :output_id - end -end From de3c18509f24133b89380b70c4d4f82fee1e7f75 Mon Sep 17 00:00:00 2001 From: lenart Date: Fri, 6 Oct 2017 17:12:15 +0200 Subject: [PATCH 11/24] Variable name changes, added comments to code [fixes SCI-1249] --- app/helpers/activity_helper.rb | 44 +++++++++++++++++++++------------- 1 file changed, 28 insertions(+), 16 deletions(-) diff --git a/app/helpers/activity_helper.rb b/app/helpers/activity_helper.rb index 35bdd3c64..feb13115a 100644 --- a/app/helpers/activity_helper.rb +++ b/app/helpers/activity_helper.rb @@ -1,29 +1,41 @@ module ActivityHelper + # constants for correct truncation length TAGS_LENGTH = 4 TRUNCATE_OFFSET = 3 def activity_truncate(message, len = Constants::NAME_TRUNCATION_LENGTH) activity_titles = message.scan(/(.*?)<\/strong>/) activity_titles.each do |activity_title| activity_title = activity_title[0] - closing = activity_title.index('') - unless closing.nil? - ind = activity_title.index(' ind_temp + # find first closing tag of smart annotation + closing_tag_sa = activity_title.index('') + unless closing_tag_sa.nil? + opening_tag_sa = activity_title.index(' opening_temp end - temp = len - while !ind.nil? && !closing.nil? && ind < temp - stripped = strip_tags(activity_title[ind...closing]).length - temp += (activity_title[ind...closing + TAGS_LENGTH]).length - stripped - len = temp + TRUNCATE_OFFSET + TAGS_LENGTH if len <= closing - closing_temp = closing + 1 - closing = activity_title.index('', closing_temp) - unless closing.nil? - ind = activity_title.index(' ind_temp + len_temp = len + # check until we run out of smart annotations in message + while !opening_tag_sa.nil? && !closing_tag_sa.nil? && + opening_tag_sa < len_temp + stripped = strip_tags(activity_title[opening_tag_sa...closing_tag_sa]) + .length + len_temp += (activity_title[opening_tag_sa...closing_tag_sa + + TAGS_LENGTH]).length - stripped + len = len_temp + TRUNCATE_OFFSET + TAGS_LENGTH if len <= closing_tag_sa + closing_temp = closing_tag_sa + 1 + closing_tag_sa = activity_title.index('', closing_temp) + unless closing_tag_sa.nil? + # find next smart annotation + opening_tag_sa = activity_title.index(' opening_temp end end + # adjust truncation length according to smart annotations length len = activity_title.length if len > activity_title.length && len != Constants::NAME_TRUNCATION_LENGTH if activity_title.length > len From fe89b942e7c05f111582cfaedb2869d68ea17993 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Wed, 11 Oct 2017 14:15:37 +0200 Subject: [PATCH 12/24] Add Add-ons page to User -> Settings -> Account Closes SCI-1675. --- .../settings/account/addons_controller.rb | 8 +++++++ app/helpers/user_settings_helper.rb | 7 +++++- .../settings/account/_navigation.html.erb | 3 +++ .../settings/account/addons/index.html.erb | 22 +++++++++++++++++++ config/locales/en.yml | 5 +++++ config/routes.rb | 3 +++ 6 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 app/controllers/users/settings/account/addons_controller.rb create mode 100644 app/views/users/settings/account/addons/index.html.erb diff --git a/app/controllers/users/settings/account/addons_controller.rb b/app/controllers/users/settings/account/addons_controller.rb new file mode 100644 index 000000000..9b18d556a --- /dev/null +++ b/app/controllers/users/settings/account/addons_controller.rb @@ -0,0 +1,8 @@ +module Users + module Settings + module Account + class AddonsController < ApplicationController + end + end + end +end diff --git a/app/helpers/user_settings_helper.rb b/app/helpers/user_settings_helper.rb index ce06ccf60..448ef9b63 100644 --- a/app/helpers/user_settings_helper.rb +++ b/app/helpers/user_settings_helper.rb @@ -1,7 +1,8 @@ module UserSettingsHelper def on_settings_account_page? controller_name == 'registrations' && action_name == 'edit' || - controller_name == 'preferences' && action_name == 'index' + controller_name == 'preferences' && action_name == 'index' || + controller_name == 'addons' && action_name == 'index' end def on_settings_account_profile_page? @@ -12,6 +13,10 @@ module UserSettingsHelper controller_name == 'preferences' end + def on_settings_account_addons_page? + controller_name == 'addons' + end + def on_settings_team_page? controller_name.in?(%w(teams audits)) && action_name.in?(%w(index new create show audits_index)) diff --git a/app/views/users/settings/account/_navigation.html.erb b/app/views/users/settings/account/_navigation.html.erb index f890b5a5f..63993494d 100644 --- a/app/views/users/settings/account/_navigation.html.erb +++ b/app/views/users/settings/account/_navigation.html.erb @@ -5,4 +5,7 @@ + \ No newline at end of file diff --git a/app/views/users/settings/account/addons/index.html.erb b/app/views/users/settings/account/addons/index.html.erb new file mode 100644 index 000000000..de7c58a21 --- /dev/null +++ b/app/views/users/settings/account/addons/index.html.erb @@ -0,0 +1,22 @@ +<% provide(:head_title, t('users.settings.account.addons.head_title')) %> + +<%= render partial: 'users/settings/navigation.html.erb' %> +
    +
    + +
    +
    + <%= render partial: 'users/settings/account/navigation.html.erb' %> +
    +
    +

    <%= t('users.settings.account.addons.title') %>

    +
    + + <%= t('users.settings.account.addons.no_addons') %> + +
    +
    +
    +
    +
    +
    diff --git a/config/locales/en.yml b/config/locales/en.yml index 24498ed3c..cb1a4a473 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -1292,6 +1292,7 @@ en: navigation: profile: "Profile" preferences: "Preferences" + addons: "Add-ons" preferences: head_title: "Settings | My preferences" edit: @@ -1307,6 +1308,10 @@ en: select_team: "Select team" tutorial_reset_flash: "Tutorial can now be repeated." tutorial_reset_error: "Tutorial could not be repeated." + addons: + head_title: "Settings | Add-ons" + title: "Add-ons" + no_addons: "You have no add-ons." teams: head_title: "Settings | Teams" breadcrumbs: diff --git a/config/routes.rb b/config/routes.rb index 7aed6b3f9..c6b412da4 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -28,6 +28,9 @@ Rails.application.routes.draw do get 'users/settings/account/preferences', to: 'users/settings/account/preferences#index', as: 'preferences' + get 'users/settings/account/addons', + to: 'users/settings/account/addons#index', + as: 'addons' put 'users/settings/account/preferences', to: 'users/settings/account/preferences#update', as: 'update_preferences' From 9a8e33c6d7bd71d159a2162ecd0b427dd8183d2b Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Wed, 11 Oct 2017 17:24:31 +0200 Subject: [PATCH 13/24] Small fixes [SCI-1642] --- app/models/experiment.rb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/app/models/experiment.rb b/app/models/experiment.rb index 60d94beb6..23fa3640a 100644 --- a/app/models/experiment.rb +++ b/app/models/experiment.rb @@ -647,7 +647,7 @@ class Experiment < ActiveRecord::Base um = dm.upstream_modules um.shift # remove current module ums = um.map(&:samples).flatten.uniq - src.samples.each do |sample| + src.samples.find_each do |sample| dm.samples.destroy(sample) if ums.exclude? sample end end @@ -693,8 +693,8 @@ class Experiment < ActiveRecord::Base def normalize_module_positions # This method normalizes module positions so x-s and y-s # are all positive - x_diff = my_modules.collect(&:x).min - y_diff = my_modules.collect(&:y).min + x_diff = my_modules.pluck(:x).min + y_diff = my_modules.pluck(:y).min my_modules.each do |m| m.update_columns(x: m.x - x_diff, y: m.y - y_diff) From 56f52ebfa7fa18ec6a9a1a39fe33ba7df30034bc Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Thu, 12 Oct 2017 14:43:25 +0200 Subject: [PATCH 14/24] Optimize memory usage in samples/repositories import [SCI-1665] --- Gemfile | 3 +- Gemfile.lock | 4 + app/controllers/repositories_controller.rb | 11 +- app/controllers/teams_controller.rb | 177 ++++++++---------- app/models/repository.rb | 107 ++++++----- app/models/team.rb | 30 ++- .../import_repository/parse_repository.rb | 44 +++-- .../_parse_records_modal.html.erb | 2 +- 8 files changed, 213 insertions(+), 165 deletions(-) diff --git a/Gemfile b/Gemfile index 6754fde93..65740b8d7 100644 --- a/Gemfile +++ b/Gemfile @@ -47,6 +47,7 @@ gem 'commit_param_routing' # Enables different submit actions in the same form t gem 'kaminari' gem "i18n-js", ">= 3.0.0.rc11" # Localization in javascript files gem 'roo', '~> 2.7.1' # Spreadsheet parser +gem 'creek' gem 'wicked_pdf' gem 'silencer' # Silence certain Rails logs gem 'wkhtmltopdf-heroku' @@ -72,7 +73,6 @@ gem 'ruby-graphviz', '~> 1.2' # Graphviz for rails gem 'tinymce-rails', '~> 4.5.7' # Rich text editor gem 'base62' # Used for smart annotations -gem 'newrelic_rpm' group :development, :test do gem 'byebug' @@ -85,6 +85,7 @@ group :development, :test do end group :production do + gem 'newrelic_rpm' gem 'puma' gem 'rails_12factor' end diff --git a/Gemfile.lock b/Gemfile.lock index aed66990c..be92e9091 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -115,6 +115,9 @@ GEM commit_param_routing (0.0.1) concurrent-ruby (1.0.0) crass (1.0.2) + creek (1.1.2) + nokogiri (~> 1.6.0) + rubyzip (>= 1.0.0) debug_inspector (0.0.2) deface (1.0.2) colorize (>= 0.5.8) @@ -362,6 +365,7 @@ DEPENDENCIES bootstrap_form byebug commit_param_routing + creek deface (~> 1.0) delayed_job_active_record delayed_paperclip! diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb index bb56e7938..6b638589c 100644 --- a/app/controllers/repositories_controller.rb +++ b/app/controllers/repositories_controller.rb @@ -198,12 +198,15 @@ class RepositoriesController < ApplicationController if parsed_file.too_large? repository_response(t('general.file.size_exceeded', file_size: Constants::FILE_MAX_SIZE_MB)) - elsif parsed_file.empty? - flash[:notice] = t('teams.parse_sheet.errors.empty_file') - redirect_to back and return else @import_data = parsed_file.data - if parsed_file.generated_temp_file? + + unless @import_data.header.any? && @import_data.columns.any? + return repository_response(t('teams.parse_sheet.errors.empty_file')) + end + + @temp_file = parsed_file.generate_temp_file + if @temp_file respond_to do |format| format.json do render json: { diff --git a/app/controllers/teams_controller.rb b/app/controllers/teams_controller.rb index 622cff038..32bd3d1d8 100644 --- a/app/controllers/teams_controller.rb +++ b/app/controllers/teams_controller.rb @@ -7,106 +7,77 @@ class TeamsController < ApplicationController def parse_sheet session[:return_to] ||= request.referer - respond_to do |format| - if params[:file] - begin + unless params[:file] + return parse_sheet_error(t('teams.parse_sheet.errors.no_file_selected')) + end + if params[:file].size > Constants::FILE_MAX_SIZE_MB.megabytes + error = t('general.file.size_exceeded', + file_size: Constants::FILE_MAX_SIZE_MB) + return parse_sheet_error(error) + end - if params[:file].size > Constants::FILE_MAX_SIZE_MB.megabytes - error = t 'general.file.size_exceeded', - file_size: Constants::FILE_MAX_SIZE_MB - - format.html { - flash[:alert] = error - redirect_to session.delete(:return_to) - } - format.json { - render json: {message: error}, - status: :unprocessable_entity - } - - else - sheet = Team.open_spreadsheet(params[:file]) - - # Check if we actually have any rows (last_row > 1) - if sheet.last_row.between?(0, 1) - flash[:notice] = t( - "teams.parse_sheet.errors.empty_file") - redirect_to session.delete(:return_to) and return - end - - # Get data (it will trigger any errors as well) - @header = sheet.row(1) - @columns = sheet.row(2) - - # Fill in fields for dropdown - @available_fields = @team.get_available_sample_fields - # Truncate long fields - @available_fields.update(@available_fields) do |_k, v| - v.truncate(Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) - end - - # Save file for next step (importing) - @temp_file = TempFile.new( - session_id: session.id, - file: params[:file] - ) - - if @temp_file.save - @temp_file.destroy_obsolete - # format.html - format.json { - render :json => { - :html => render_to_string({ - :partial => "samples/parse_samples_modal.html.erb" - }) - } - } - else - error = t("teams.parse_sheet.errors.temp_file_failure") - format.html { - flash[:alert] = error - redirect_to session.delete(:return_to) - } - format.json { - render json: {message: error}, - status: :unprocessable_entity - } - end - end - rescue ArgumentError, CSV::MalformedCSVError - error = t('teams.parse_sheet.errors.invalid_file', - encoding: ''.encoding) - format.html { - flash[:alert] = error - redirect_to session.delete(:return_to) - } - format.json { - render json: {message: error}, - status: :unprocessable_entity - } - rescue TypeError - error = t("teams.parse_sheet.errors.invalid_extension") - format.html { - flash[:alert] = error - redirect_to session.delete(:return_to) - } - format.json { - render json: {message: error}, - status: :unprocessable_entity - } + begin + sheet = Team.open_spreadsheet(params[:file]) + # Get data (it will trigger any errors as well) + if sheet.is_a?(Roo::CSV) + @header = sheet.row(1) + @columns = sheet.row(2) + elsif sheet.is_a?(Roo::Excelx) + i = 1 + sheet.each_row_streaming do |row| + @header = row.map(&:cell_value) if i == 1 + @columns = row.map(&:cell_value) if i == 2 + i += 1 + break if i > 2 end else - error = t("teams.parse_sheet.errors.no_file_selected") - format.html { - flash[:alert] = error - session[:return_to] ||= request.referer - redirect_to session.delete(:return_to) - } - format.json { - render json: {message: error}, - status: :unprocessable_entity - } + i = 1 + sheet.rows.each do |row| + @header = row.values if i == 1 + @columns = row.values if i == 2 + i += 1 + break if i > 2 + end end + + unless @header && @header.any? && @columns && @columns.any? + return parse_sheet_error(t('teams.parse_sheet.errors.empty_file')) + end + + # Fill in fields for dropdown + @available_fields = @team.get_available_sample_fields + # Truncate long fields + @available_fields.update(@available_fields) do |_k, v| + v.truncate(Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) + end + + # Save file for next step (importing) + @temp_file = TempFile.new( + session_id: session.id, + file: params[:file] + ) + + if @temp_file.save + @temp_file.destroy_obsolete + respond_to do |format| + format.json do + render json: { + html: render_to_string( + partial: 'samples/parse_samples_modal.html.erb' + ) + } + end + end + else + return parse_sheet_error( + t('teams.parse_sheet.errors.temp_file_failure') + ) + end + rescue ArgumentError, CSV::MalformedCSVError + return parse_sheet_error(t('teams.parse_sheet.errors.invalid_file', + encoding: ''.encoding)) + rescue TypeError + return parse_sheet_error(t('teams.parse_sheet.errors.invalid_extension')) end end @@ -275,6 +246,20 @@ class TeamsController < ApplicationController private + def parse_sheet_error(error) + respond_to do |format| + format.html do + flash[:alert] = error + session[:return_to] ||= request.referer + redirect_to session.delete(:return_to) + end + format.json do + render json: { message: error }, + status: :unprocessable_entity + end + end + end + def load_vars @team = Team.find_by_id(params[:id]) diff --git a/app/models/repository.rb b/app/models/repository.rb index 64058833b..93b5a30e4 100644 --- a/app/models/repository.rb +++ b/app/models/repository.rb @@ -114,6 +114,7 @@ class Repository < ActiveRecord::Base name_index = -1 total_nr = 0 nr_of_added = 0 + header_skipped = false mappings.each.with_index do |(_k, value), index| if value == '-1' @@ -130,54 +131,69 @@ class Repository < ActiveRecord::Base unless col_compact.map(&:id).uniq.length == col_compact.length return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr } end + rows = if sheet.is_a?(Roo::CSV) + sheet + elsif sheet.is_a?(Roo::Excelx) + sheet.each_row_streaming + else + sheet.rows + end # Now we can iterate through record data and save stuff into db - transaction do - (2..sheet.last_row).each do |i| - total_nr += 1 - record_row = RepositoryRow.new(name: sheet.row(i)[name_index], - repository: self, - created_by: user, - last_modified_by: user) - record_row.transaction(requires_new: true) do - unless record_row.save - errors = true - raise ActiveRecord::Rollback - end + rows.each do |row| + # Skip empty rows + next if row.empty? + unless header_skipped + header_skipped = true + next + end + total_nr += 1 - row_cell_values = [] + # Creek XLSX parser returns Hash of the row, Roo - Array + row = row.is_a?(Hash) ? row.values.map(&:to_s) : row.map(&:to_s) - sheet.row(i).each.with_index do |value, index| - if columns[index] && value - cell_value = RepositoryTextValue.new( - data: value, - created_by: user, - last_modified_by: user, - repository_cell_attributes: { - repository_row: record_row, - repository_column: columns[index] - } - ) - cell = RepositoryCell.new(repository_row: record_row, - repository_column: columns[index], - value: cell_value) - cell.skip_on_import = true - cell_value.repository_cell = cell - unless cell.valid? && cell_value.valid? - errors = true - raise ActiveRecord::Rollback - end - row_cell_values << cell_value - end - end - if RepositoryTextValue.import(row_cell_values, - recursive: true, - validate: false).failed_instances.any? - errors = true - raise ActiveRecord::Rollback - end - nr_of_added += 1 + record_row = RepositoryRow.new(name: row[name_index], + repository: self, + created_by: user, + last_modified_by: user) + record_row.transaction do + unless record_row.save + errors = true + raise ActiveRecord::Rollback end + + row_cell_values = [] + + row.each.with_index do |value, index| + if columns[index] && value + cell_value = RepositoryTextValue.new( + data: value, + created_by: user, + last_modified_by: user, + repository_cell_attributes: { + repository_row: record_row, + repository_column: columns[index] + } + ) + cell = RepositoryCell.new(repository_row: record_row, + repository_column: columns[index], + value: cell_value) + cell.skip_on_import = true + cell_value.repository_cell = cell + unless cell.valid? && cell_value.valid? + errors = true + raise ActiveRecord::Rollback + end + row_cell_values << cell_value + end + end + if RepositoryTextValue.import(row_cell_values, + recursive: true, + validate: false).failed_instances.any? + errors = true + raise ActiveRecord::Rollback + end + nr_of_added += 1 end end @@ -199,7 +215,10 @@ class Repository < ActiveRecord::Base # This assumption is based purely on biologist's habits Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) when '.xlsx' - Roo::Excelx.new(file_path) + # Roo Excel parcel was replaced with Creek, but it can be enabled back, + # just swap lines below. But only one can be enabled at the same time. + # Roo::Excelx.new(file_path) + Creek::Book.new(file_path).sheets[0] else raise TypeError end diff --git a/app/models/team.rb b/app/models/team.rb index 04a45375a..57284d2d1 100644 --- a/app/models/team.rb +++ b/app/models/team.rb @@ -45,7 +45,10 @@ class Team < ActiveRecord::Base # This assumption is based purely on biologist's habits Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) when '.xlsx' then - Roo::Excelx.new(file_path) + # Roo Excel parcel was replaced with Creek, but it can be enabled back, + # just swap lines below. But only one can be enabled at the same time. + # Roo::Excelx.new(file_path) + Creek::Book.new(file_path).sheets[0] else raise TypeError end @@ -66,6 +69,7 @@ class Team < ActiveRecord::Base errors = false nr_of_added = 0 total_nr = 0 + header_skipped = false # First let's query for all custom_fields we're refering to custom_fields = [] @@ -91,10 +95,28 @@ class Team < ActiveRecord::Base custom_fields << cf end end + + rows = if sheet.is_a?(Roo::CSV) + sheet + elsif sheet.is_a?(Roo::Excelx) + sheet.each_row_streaming + else + sheet.rows + end + # Now we can iterate through sample data and save stuff into db - (2..sheet.last_row).each do |i| + rows.each do |row| + # Skip empty rows + next if row.empty? + unless header_skipped + header_skipped = true + next + end total_nr += 1 - sample = Sample.new(name: sheet.row(i)[sname_index], + # Creek XLSX parser returns Hash of the row, Roo - Array + row = row.is_a?(Hash) ? row.values.map(&:to_s) : row.map(&:to_s) + + sample = Sample.new(name: row[sname_index], team: self, user: user) @@ -104,7 +126,7 @@ class Team < ActiveRecord::Base raise ActiveRecord::Rollback end - sheet.row(i).each.with_index do |value, index| + row.each.with_index do |value, index| if index == stype_index stype = SampleType.where(name: value.strip, team: self).take diff --git a/app/services/import_repository/parse_repository.rb b/app/services/import_repository/parse_repository.rb index 192f4b61e..23fe97b67 100644 --- a/app/services/import_repository/parse_repository.rb +++ b/app/services/import_repository/parse_repository.rb @@ -10,43 +10,57 @@ module ImportRepository def data # Get data (it will trigger any errors as well) - header = @sheet.row(1) - columns = @sheet.row(2) + if @sheet.is_a?(Roo::CSV) + header = @sheet.row(1) + columns = @sheet.row(2) + elsif @sheet.is_a?(Roo::Excelx) + i = 1 + @sheet.each_row_streaming do |row| + header = row.map(&:cell_value) if i == 1 + columns = row.map(&:cell_value) if i == 2 + i += 1 + break if i > 2 + end + else + i = 1 + @sheet.rows.each do |row| + header = row.values if i == 1 + columns = row.values if i == 2 + i += 1 + break if i > 2 + end + end # Fill in fields for dropdown @repository.available_repository_fields.transform_values! do |name| truncate(name, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) end - @temp_file = TempFile.create(session_id: @session.id, file: @file) + header ||= [] + columns ||= [] Data.new(header, columns, @repository.available_repository_fields, - @repository, - @temp_file) + @repository) end def too_large? @file.size > Constants::FILE_MAX_SIZE_MB.megabytes end - def empty? - @sheet.last_row.between?(0, 1) - end - - def generated_temp_file? + def generate_temp_file # Save file for next step (importing) - @temp_file = TempFile.new( + temp_file = TempFile.new( session_id: @session.id, file: @file ) - if @temp_file.save - @temp_file.destroy_obsolete - return true + if temp_file.save + temp_file.destroy_obsolete + return temp_file end end Data = Struct.new( - :header, :columns, :available_fields, :repository, :temp_file + :header, :columns, :available_fields, :repository ) end end diff --git a/app/views/repositories/_parse_records_modal.html.erb b/app/views/repositories/_parse_records_modal.html.erb index ccab285b1..7a15968ba 100644 --- a/app/views/repositories/_parse_records_modal.html.erb +++ b/app/views/repositories/_parse_records_modal.html.erb @@ -58,7 +58,7 @@
    - <%= hidden_field_tag 'file_id', @import_data.temp_file.id %> + <%= hidden_field_tag 'file_id', @temp_file.id %>
    From 38bce08b5abf341a0af005dcd863d78602e3fc33 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Fri, 13 Oct 2017 09:27:18 +0200 Subject: [PATCH 15/24] Minor wording change. --- config/locales/en.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/locales/en.yml b/config/locales/en.yml index cb1a4a473..402735557 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -1311,7 +1311,7 @@ en: addons: head_title: "Settings | Add-ons" title: "Add-ons" - no_addons: "You have no add-ons." + no_addons: "You have no sciNote Add-ons." teams: head_title: "Settings | Teams" breadcrumbs: From d2660344068f890a31ab57884bcda5ec04caf037 Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Fri, 13 Oct 2017 17:15:51 +0200 Subject: [PATCH 16/24] Use case insensitive sample types and groups in import [SCI-1689] --- app/models/team.rb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/app/models/team.rb b/app/models/team.rb index 04a45375a..88d29ffee 100644 --- a/app/models/team.rb +++ b/app/models/team.rb @@ -106,10 +106,12 @@ class Team < ActiveRecord::Base sheet.row(i).each.with_index do |value, index| if index == stype_index - stype = SampleType.where(name: value.strip, team: self).take + stype = SampleType.where(team: self) + .where('name ILIKE ?', value.strip) + .take unless stype - stype = SampleType.new(name: value, team: self) + stype = SampleType.new(name: value.strip, team: self) unless stype.save errors = true raise ActiveRecord::Rollback @@ -117,10 +119,12 @@ class Team < ActiveRecord::Base end sample.sample_type = stype elsif index == sgroup_index - sgroup = SampleGroup.where(name: value.strip, team: self).take + sgroup = SampleGroup.where(team: self) + .where('name ILIKE ?', value.strip) + .take unless sgroup - sgroup = SampleGroup.new(name: value, team: self) + sgroup = SampleGroup.new(name: value.strip, team: self) unless sgroup.save errors = true raise ActiveRecord::Rollback From 4d8f2665d340daf1ecf4bc67212060ad37963b47 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Tue, 17 Oct 2017 13:10:02 +0200 Subject: [PATCH 17/24] Revert "Add Add-ons page to User -> Settings -> Account [SCI-1675]" --- .../settings/account/addons_controller.rb | 8 ------- app/helpers/user_settings_helper.rb | 7 +----- .../settings/account/_navigation.html.erb | 3 --- .../settings/account/addons/index.html.erb | 22 ------------------- config/locales/en.yml | 5 ----- config/routes.rb | 3 --- 6 files changed, 1 insertion(+), 47 deletions(-) delete mode 100644 app/controllers/users/settings/account/addons_controller.rb delete mode 100644 app/views/users/settings/account/addons/index.html.erb diff --git a/app/controllers/users/settings/account/addons_controller.rb b/app/controllers/users/settings/account/addons_controller.rb deleted file mode 100644 index 9b18d556a..000000000 --- a/app/controllers/users/settings/account/addons_controller.rb +++ /dev/null @@ -1,8 +0,0 @@ -module Users - module Settings - module Account - class AddonsController < ApplicationController - end - end - end -end diff --git a/app/helpers/user_settings_helper.rb b/app/helpers/user_settings_helper.rb index 448ef9b63..ce06ccf60 100644 --- a/app/helpers/user_settings_helper.rb +++ b/app/helpers/user_settings_helper.rb @@ -1,8 +1,7 @@ module UserSettingsHelper def on_settings_account_page? controller_name == 'registrations' && action_name == 'edit' || - controller_name == 'preferences' && action_name == 'index' || - controller_name == 'addons' && action_name == 'index' + controller_name == 'preferences' && action_name == 'index' end def on_settings_account_profile_page? @@ -13,10 +12,6 @@ module UserSettingsHelper controller_name == 'preferences' end - def on_settings_account_addons_page? - controller_name == 'addons' - end - def on_settings_team_page? controller_name.in?(%w(teams audits)) && action_name.in?(%w(index new create show audits_index)) diff --git a/app/views/users/settings/account/_navigation.html.erb b/app/views/users/settings/account/_navigation.html.erb index 63993494d..f890b5a5f 100644 --- a/app/views/users/settings/account/_navigation.html.erb +++ b/app/views/users/settings/account/_navigation.html.erb @@ -5,7 +5,4 @@ - \ No newline at end of file diff --git a/app/views/users/settings/account/addons/index.html.erb b/app/views/users/settings/account/addons/index.html.erb deleted file mode 100644 index de7c58a21..000000000 --- a/app/views/users/settings/account/addons/index.html.erb +++ /dev/null @@ -1,22 +0,0 @@ -<% provide(:head_title, t('users.settings.account.addons.head_title')) %> - -<%= render partial: 'users/settings/navigation.html.erb' %> -
    -
    - -
    -
    - <%= render partial: 'users/settings/account/navigation.html.erb' %> -
    -
    -

    <%= t('users.settings.account.addons.title') %>

    -
    - - <%= t('users.settings.account.addons.no_addons') %> - -
    -
    -
    -
    -
    -
    diff --git a/config/locales/en.yml b/config/locales/en.yml index 459367f3b..4241aba35 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -1287,7 +1287,6 @@ en: navigation: profile: "Profile" preferences: "Preferences" - addons: "Add-ons" preferences: head_title: "Settings | My preferences" edit: @@ -1303,10 +1302,6 @@ en: select_team: "Select team" tutorial_reset_flash: "Tutorial can now be repeated." tutorial_reset_error: "Tutorial could not be repeated." - addons: - head_title: "Settings | Add-ons" - title: "Add-ons" - no_addons: "You have no sciNote Add-ons." teams: head_title: "Settings | Teams" breadcrumbs: diff --git a/config/routes.rb b/config/routes.rb index c6b412da4..7aed6b3f9 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -28,9 +28,6 @@ Rails.application.routes.draw do get 'users/settings/account/preferences', to: 'users/settings/account/preferences#index', as: 'preferences' - get 'users/settings/account/addons', - to: 'users/settings/account/addons#index', - as: 'addons' put 'users/settings/account/preferences', to: 'users/settings/account/preferences#update', as: 'update_preferences' From 30d091dc65ccd11291d97520263d1908cf7617d0 Mon Sep 17 00:00:00 2001 From: zmagod Date: Tue, 17 Oct 2017 14:10:56 +0200 Subject: [PATCH 18/24] adds label under protocols keywords input [fixes SCI-1560] --- app/views/protocols/header/_edit_keywords_modal_body.html.erb | 3 ++- config/locales/en.yml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/app/views/protocols/header/_edit_keywords_modal_body.html.erb b/app/views/protocols/header/_edit_keywords_modal_body.html.erb index 51250f321..021e33ad1 100644 --- a/app/views/protocols/header/_edit_keywords_modal_body.html.erb +++ b/app/views/protocols/header/_edit_keywords_modal_body.html.erb @@ -4,4 +4,5 @@ <% end %> -<% end %> \ No newline at end of file + <%=t 'protocols.header.keywords_modal' %> +<% end %> diff --git a/config/locales/en.yml b/config/locales/en.yml index 4241aba35..5361ba628 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -1414,6 +1414,7 @@ en: no_authors: "No authors" description: "Description" no_description: "No description" + keywords_modal: "Input one or multiple keywords, confirm each keyword with ENTER key" edit_name_modal: title: "Edit name of protocol %{protocol}" label: "Name" From c8d2ae70fa40fb0fe1bbdf3dc2063015d5e9ef7e Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Tue, 17 Oct 2017 14:42:06 +0200 Subject: [PATCH 19/24] Move duplicated code to service [SCI-1665] --- Gemfile | 2 +- app/controllers/repositories_controller.rb | 3 +- app/controllers/teams_controller.rb | 28 ++-------- app/models/repository.rb | 40 +------------- app/models/team.rb | 35 +----------- .../import_repository/import_records.rb | 8 ++- .../import_repository/parse_repository.rb | 26 +-------- app/services/spreadsheet_parser.rb | 55 +++++++++++++++++++ 8 files changed, 70 insertions(+), 127 deletions(-) create mode 100644 app/services/spreadsheet_parser.rb diff --git a/Gemfile b/Gemfile index 65740b8d7..9a8576cd9 100644 --- a/Gemfile +++ b/Gemfile @@ -73,6 +73,7 @@ gem 'ruby-graphviz', '~> 1.2' # Graphviz for rails gem 'tinymce-rails', '~> 4.5.7' # Rich text editor gem 'base62' # Used for smart annotations +gem 'newrelic_rpm' group :development, :test do gem 'byebug' @@ -85,7 +86,6 @@ group :development, :test do end group :production do - gem 'newrelic_rpm' gem 'puma' gem 'rails_12factor' end diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb index 6b638589c..7454f1b81 100644 --- a/app/controllers/repositories_controller.rb +++ b/app/controllers/repositories_controller.rb @@ -205,8 +205,7 @@ class RepositoriesController < ApplicationController return repository_response(t('teams.parse_sheet.errors.empty_file')) end - @temp_file = parsed_file.generate_temp_file - if @temp_file + if (@temp_file = parsed_file.generate_temp_file) respond_to do |format| format.json do render json: { diff --git a/app/controllers/teams_controller.rb b/app/controllers/teams_controller.rb index 32bd3d1d8..c09e06389 100644 --- a/app/controllers/teams_controller.rb +++ b/app/controllers/teams_controller.rb @@ -17,30 +17,10 @@ class TeamsController < ApplicationController end begin - sheet = Team.open_spreadsheet(params[:file]) - # Get data (it will trigger any errors as well) - if sheet.is_a?(Roo::CSV) - @header = sheet.row(1) - @columns = sheet.row(2) - elsif sheet.is_a?(Roo::Excelx) - i = 1 - sheet.each_row_streaming do |row| - @header = row.map(&:cell_value) if i == 1 - @columns = row.map(&:cell_value) if i == 2 - i += 1 - break if i > 2 - end - else - i = 1 - sheet.rows.each do |row| - @header = row.values if i == 1 - @columns = row.values if i == 2 - i += 1 - break if i > 2 - end - end + sheet = SpreadsheetParser.open_spreadsheet(params[:file]) + @header, @columns = SpreadsheetParser.first_two_rows(sheet) - unless @header && @header.any? && @columns && @columns.any? + unless @header.any? && @columns.any? return parse_sheet_error(t('teams.parse_sheet.errors.empty_file')) end @@ -93,7 +73,7 @@ class TeamsController < ApplicationController if @temp_file.session_id == session.id # Check if mappings exists or else we don't have anything to parse if params[:mappings] - @sheet = Team.open_spreadsheet(@temp_file.file) + @sheet = SpreadsheetParser.open_spreadsheet(@temp_file.file) # Check for duplicated values h1 = params[:mappings].clone.delete_if { |k, v| v.empty? } diff --git a/app/models/repository.rb b/app/models/repository.rb index 93b5a30e4..349651882 100644 --- a/app/models/repository.rb +++ b/app/models/repository.rb @@ -58,17 +58,6 @@ class Repository < ActiveRecord::Base end end - def open_spreadsheet(file) - filename = file.original_filename - file_path = file.path - - if file.class == Paperclip::Attachment && file.is_stored_on_s3? - fa = file.fetch - file_path = fa.path - end - generate_file(filename, file_path) - end - def available_repository_fields fields = {} # First and foremost add record name @@ -131,13 +120,7 @@ class Repository < ActiveRecord::Base unless col_compact.map(&:id).uniq.length == col_compact.length return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr } end - rows = if sheet.is_a?(Roo::CSV) - sheet - elsif sheet.is_a?(Roo::Excelx) - sheet.each_row_streaming - else - sheet.rows - end + rows = SpreadsheetParser.spreadsheet_enumerator(sheet) # Now we can iterate through record data and save stuff into db rows.each do |row| @@ -202,25 +185,4 @@ class Repository < ActiveRecord::Base end { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr } end - - private - - def generate_file(filename, file_path) - case File.extname(filename) - when '.csv' - Roo::CSV.new(file_path, extension: :csv) - when '.tsv' - Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) - when '.txt' - # This assumption is based purely on biologist's habits - Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) - when '.xlsx' - # Roo Excel parcel was replaced with Creek, but it can be enabled back, - # just swap lines below. But only one can be enabled at the same time. - # Roo::Excelx.new(file_path) - Creek::Book.new(file_path).sheets[0] - else - raise TypeError - end - end end diff --git a/app/models/team.rb b/app/models/team.rb index 57284d2d1..ad22d7d42 100644 --- a/app/models/team.rb +++ b/app/models/team.rb @@ -26,33 +26,6 @@ class Team < ActiveRecord::Base has_many :protocol_keywords, inverse_of: :team, dependent: :destroy has_many :tiny_mce_assets, inverse_of: :team, dependent: :destroy has_many :repositories, dependent: :destroy - # Based on file's extension opens file (used for importing) - def self.open_spreadsheet(file) - filename = file.original_filename - file_path = file.path - - if file.class == Paperclip::Attachment and file.is_stored_on_s3? - fa = file.fetch - file_path = fa.path - end - - case File.extname(filename) - when '.csv' then - Roo::CSV.new(file_path, extension: :csv) - when '.tsv' then - Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) - when '.txt' then - # This assumption is based purely on biologist's habits - Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) - when '.xlsx' then - # Roo Excel parcel was replaced with Creek, but it can be enabled back, - # just swap lines below. But only one can be enabled at the same time. - # Roo::Excelx.new(file_path) - Creek::Book.new(file_path).sheets[0] - else - raise TypeError - end - end def search_users(query = nil) a_query = "%#{query}%" @@ -96,13 +69,7 @@ class Team < ActiveRecord::Base end end - rows = if sheet.is_a?(Roo::CSV) - sheet - elsif sheet.is_a?(Roo::Excelx) - sheet.each_row_streaming - else - sheet.rows - end + rows = SpreadsheetParser.spreadsheet_enumerator(sheet) # Now we can iterate through sample data and save stuff into db rows.each do |row| diff --git a/app/services/import_repository/import_records.rb b/app/services/import_repository/import_records.rb index e9deea8b4..ba80a4b0a 100644 --- a/app/services/import_repository/import_records.rb +++ b/app/services/import_repository/import_records.rb @@ -17,9 +17,11 @@ module ImportRepository private def run_import_actions - @repository.import_records(@repository.open_spreadsheet(@temp_file.file), - @mappings, - @user) + @repository.import_records( + SpreadsheetParser.open_spreadsheet(@temp_file.file), + @mappings, + @user + ) end def run_checks diff --git a/app/services/import_repository/parse_repository.rb b/app/services/import_repository/parse_repository.rb index 23fe97b67..222b71274 100644 --- a/app/services/import_repository/parse_repository.rb +++ b/app/services/import_repository/parse_repository.rb @@ -5,37 +5,15 @@ module ImportRepository @file = options.fetch(:file) @repository = options.fetch(:repository) @session = options.fetch(:session) - @sheet = @repository.open_spreadsheet(@file) + @sheet = SpreadsheetParser.open_spreadsheet(@file) end def data - # Get data (it will trigger any errors as well) - if @sheet.is_a?(Roo::CSV) - header = @sheet.row(1) - columns = @sheet.row(2) - elsif @sheet.is_a?(Roo::Excelx) - i = 1 - @sheet.each_row_streaming do |row| - header = row.map(&:cell_value) if i == 1 - columns = row.map(&:cell_value) if i == 2 - i += 1 - break if i > 2 - end - else - i = 1 - @sheet.rows.each do |row| - header = row.values if i == 1 - columns = row.values if i == 2 - i += 1 - break if i > 2 - end - end + header, columns = SpreadsheetParser.first_two_rows(@sheet) # Fill in fields for dropdown @repository.available_repository_fields.transform_values! do |name| truncate(name, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) end - header ||= [] - columns ||= [] Data.new(header, columns, @repository.available_repository_fields, diff --git a/app/services/spreadsheet_parser.rb b/app/services/spreadsheet_parser.rb new file mode 100644 index 000000000..3d5a64774 --- /dev/null +++ b/app/services/spreadsheet_parser.rb @@ -0,0 +1,55 @@ +class SpreadsheetParser + # Based on file's extension opens file (used for importing) + def self.open_spreadsheet(file) + filename = file.original_filename + file_path = file.path + + if file.class == Paperclip::Attachment && file.is_stored_on_s3? + fa = file.fetch + file_path = fa.path + end + + case File.extname(filename) + when '.csv' + Roo::CSV.new(file_path, extension: :csv) + when '.tsv' + Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) + when '.txt' + # This assumption is based purely on biologist's habits + Roo::CSV.new(file_path, csv_options: { col_sep: "\t" }) + when '.xlsx' + # Roo Excel parcel was replaced with Creek, but it can be enabled back, + # just swap lines below. But only one can be enabled at the same time. + # Roo::Excelx.new(file_path) + Creek::Book.new(file_path).sheets[0] + else + raise TypeError + end + end + + def self.spreadsheet_enumerator(sheet) + if sheet.is_a?(Roo::CSV) + sheet + elsif sheet.is_a?(Roo::Excelx) + sheet.each_row_streaming + else + sheet.rows + end + end + + def self.first_two_rows(sheet) + rows = spreadsheet_enumerator(sheet) + header = [] + columns = [] + i = 1 + rows.each do |row| + # Creek XLSX parser returns Hash of the row, Roo - Array + row = row.is_a?(Hash) ? row.values.map(&:to_s) : row.map(&:to_s) + header = row if i == 1 && row + columns = row if i == 2 && row + i += 1 + break if i > 2 + end + return header, columns + end +end From cd0aba1896f6d9b72246e09f03dbf94e1b003344 Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Tue, 17 Oct 2017 15:23:54 +0200 Subject: [PATCH 20/24] Change any? to empty? [SCI-1665] --- app/controllers/repositories_controller.rb | 2 +- app/controllers/teams_controller.rb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb index 7454f1b81..e356471e8 100644 --- a/app/controllers/repositories_controller.rb +++ b/app/controllers/repositories_controller.rb @@ -201,7 +201,7 @@ class RepositoriesController < ApplicationController else @import_data = parsed_file.data - unless @import_data.header.any? && @import_data.columns.any? + if @import_data.header.empty? || @import_data.columns.empty? return repository_response(t('teams.parse_sheet.errors.empty_file')) end diff --git a/app/controllers/teams_controller.rb b/app/controllers/teams_controller.rb index c09e06389..982b34d11 100644 --- a/app/controllers/teams_controller.rb +++ b/app/controllers/teams_controller.rb @@ -20,7 +20,7 @@ class TeamsController < ApplicationController sheet = SpreadsheetParser.open_spreadsheet(params[:file]) @header, @columns = SpreadsheetParser.first_two_rows(sheet) - unless @header.any? && @columns.any? + if @header.empty? || @columns.empty? return parse_sheet_error(t('teams.parse_sheet.errors.empty_file')) end From 631b41cdaaed7c9def70e6737b82b6e101a7119b Mon Sep 17 00:00:00 2001 From: Oleksii Kriuchykhin Date: Thu, 19 Oct 2017 11:38:23 +0200 Subject: [PATCH 21/24] Improve error handling in file uploads [SCI-1609][SCI-1612][SCI-1551] --- .../javascripts/sitewide/drag_n_drop.js.erb | 144 ++++++++++++------ app/assets/stylesheets/themes/scinote.scss | 3 +- app/controllers/result_assets_controller.rb | 62 ++++---- app/views/result_assets/_new.html.erb | 2 +- 4 files changed, 126 insertions(+), 85 deletions(-) diff --git a/app/assets/javascripts/sitewide/drag_n_drop.js.erb b/app/assets/javascripts/sitewide/drag_n_drop.js.erb index 0f1c62068..f585c3aaa 100644 --- a/app/assets/javascripts/sitewide/drag_n_drop.js.erb +++ b/app/assets/javascripts/sitewide/drag_n_drop.js.erb @@ -21,12 +21,13 @@ // loops through a list of files and display each file in a separate panel function listItems() { - droppedFiles = droppedFiles.filter(Boolean); + totalSize = 0; + _enableSubmitButton(); $('.panel-step-attachment-new').remove(); _dragNdropAssetsOff(); for(var i = 0; i < droppedFiles.length; i++) { $('#new-step-assets') - .append(_uploadedAseetPreview(droppedFiles[i], i)) + .append(_uploadedAssetPreview(droppedFiles[i], i)) .promise() .done(function() { _removeItemHandler(i); @@ -42,7 +43,6 @@ var prevEls = $('input').filter(function() { return this.name.match(regex); }); - droppedFiles = droppedFiles.filter(Boolean); var fd = new FormData($(ev.target).closest('form').get(0)); for(var i = 0; i < droppedFiles.length; i++) { var index = i + prevEls.length; @@ -56,30 +56,55 @@ return fd; } - function _validateFilesSize(file) { - var maxSize = file.size/1048576; - if(maxSize > <%= Constants::FILE_MAX_SIZE_MB %> && filesValid) { - return "

    <%= I18n.t 'general.file.size_exceeded', file_size: Constants::FILE_MAX_SIZE_MB %>

    "; + function _disableSubmitButton() { + $('.step-save').prop('disabled', true); + } + + function _enableSubmitButton() { + $('.step-save').prop('disabled', false); + } + + function _filerAndCheckFiles() { + for(var i = 0; i < droppedFiles.length; i++) { + if(droppedFiles[i].isValid == false) { + return false; + } + } + return (droppedFiles.length > 0); + } + + function _validateFilesSize(file) { + var fileSize = file.size; + totalSize += parseInt(fileSize); + if(fileSize > <%= Constants::FILE_MAX_SIZE_MB.megabyte %>) { + file.isValid = false; + _disableSubmitButton(); + return "

    <%= I18n.t 'general.file.size_exceeded', file_size: Constants::FILE_MAX_SIZE_MB %>

    "; } - totalSize += parseInt(maxSize); return ''; } function _validateTotalSize() { - if(totalSize > <%= Constants::FILE_MAX_SIZE_MB %>) { + if(totalSize > <%= Constants::FILE_MAX_SIZE_MB.megabyte %>) { filesValid = false; + _disableSubmitButton(); $.each($('.panel-step-attachment-new'), function() { - $(this) - .find('.panel-body') - .append("

    <%= I18n.t('general.file.total_size', size: Constants::FILE_MAX_SIZE_MB) %>

    "); + if(!$(this).find('p').hasClass('dnd-total-error')) { + $(this) + .find('.panel-body') + .append("

    <%= I18n.t('general.file.total_size', size: Constants::FILE_MAX_SIZE_MB) %>

    "); + } }); } else { - $('.dnd-error').remove(); - filesValid = true; + $('.dnd-total-error').remove(); + if(_filerAndCheckFiles()) { + filesValid = true; + _enableSubmitButton(); + } } } - function _uploadedAseetPreview(asset, i) { + function _uploadedAssetPreview(asset, i) { var html = '
    '; html += '
    '; html += ''; @@ -104,10 +129,9 @@ e.stopPropagation(); var $el = $(this); var index = $el.data('item-id'); - totalSize -= parseInt(droppedFiles[index]/1048576); - droppedFiles[index] = null; - $el.closest('.panel-step-attachment-new').remove(); - _validateTotalSize(); + totalSize -= parseInt(droppedFiles[index].size); + droppedFiles.splice(index, 1); + listItems(); }); } @@ -131,11 +155,10 @@ var totalSize = 0; function init(files) { - var filesPresent = droppedFiles.length; for(var i = 0; i < files.length; i++) { droppedFiles.push(files[i]); } - listItems(filesPresent); + listItems(); } // return the status of files if they are ready to submit @@ -144,18 +167,24 @@ } // loops through a list of files and display each file in a separate panel - function listItems(index) { - _dragNdropAssetsOff(); - for(var i = index; i < droppedFiles.length; i++) { - $('#new-result-assets-select') - .after(_uploadedAseetPreview(droppedFiles[i], i)) - .promise() - .done(function() { - _removeItemHandler(i); - }); + function listItems() { + totalSize = 0; + $('.panel-result-attachment-new').remove(); + if(droppedFiles.length < 1) { + _disableSubmitButton(); + } else { + _dragNdropAssetsOff(); + for(var i = 0; i < droppedFiles.length; i++) { + $('#new-result-assets-select') + .after(_uploadedAssetPreview(droppedFiles[i], i)) + .promise() + .done(function() { + _removeItemHandler(i); + }); + } + _validateTotalSize(); + dragNdropAssetsInit('results'); } - _validateTotalSize(); - dragNdropAssetsInit('results'); } // appent the files to the form before submit @@ -181,31 +210,51 @@ return fd; } + function _disableSubmitButton() { + $('.save-result').prop('disabled', true); + } + + function _enableSubmitButton() { + $('.save-result').prop('disabled', false); + } + function _filerAndCheckFiles() { - droppedFiles = droppedFiles.filter(Boolean); + for(var i = 0; i < droppedFiles.length; i++) { + if(droppedFiles[i].isValid == false) { + return false; + } + } return (droppedFiles.length > 0); } function _validateFilesSize(file) { - var maxSize = file.size/1048576; - if(maxSize > <%= Constants::FILE_MAX_SIZE_MB %> && isValid) { - return "

    <%= I18n.t 'general.file.size_exceeded', file_size: Constants::FILE_MAX_SIZE_MB %>

    "; + var fileSize = file.size; + totalSize += parseInt(fileSize); + if(fileSize > <%= Constants::FILE_MAX_SIZE_MB.megabyte %>) { + file.isValid = false; + _disableSubmitButton(); + return "

    <%= I18n.t 'general.file.size_exceeded', file_size: Constants::FILE_MAX_SIZE_MB %>

    "; } - totalSize += parseInt(maxSize); return ''; } function _validateTotalSize() { - if(totalSize > <%= Constants::FILE_MAX_SIZE_MB %>) { + if(totalSize > <%= Constants::FILE_MAX_SIZE_MB.megabyte %>) { isValid = false; + _disableSubmitButton(); $.each($('.panel-result-attachment-new'), function() { - $(this) - .find('.panel-body') - .append("

    <%= I18n.t('general.file.total_size', size: Constants::FILE_MAX_SIZE_MB) %>

    "); + if(!$(this).find('p').hasClass('dnd-total-error')) { + $(this) + .find('.panel-body') + .append("

    <%= I18n.t('general.file.total_size', size: Constants::FILE_MAX_SIZE_MB) %>

    "); + } }); } else { - $('.dnd-error').remove(); - isValid = true; + $('.dnd-total-error').remove(); + if(_filerAndCheckFiles()) { + isValid = true; + _enableSubmitButton(); + } } } @@ -220,7 +269,7 @@ } } - function _uploadedAseetPreview(asset, i) { + function _uploadedAssetPreview(asset, i) { var html = '
    '; html += '
    '; html += ''; @@ -249,10 +298,9 @@ e.stopPropagation(); var $el = $(this); var index = $el.data('item-id'); - totalSize -= parseInt(droppedFiles[index]/1048576); - droppedFiles[index] = null; - $el.closest('.panel-result-attachment-new').remove(); - _validateTotalSize(); + totalSize -= parseInt(droppedFiles[index].size); + droppedFiles.splice(index, 1); + listItems(); }); } diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss index e5a41a988..91a296e07 100644 --- a/app/assets/stylesheets/themes/scinote.scss +++ b/app/assets/stylesheets/themes/scinote.scss @@ -1288,7 +1288,8 @@ ul.content-module-activities { padding-top: 30px; } -.dnd-error { +.dnd-error, +.dnd-total-error { color: $color-milano-red; } diff --git a/app/controllers/result_assets_controller.rb b/app/controllers/result_assets_controller.rb index faeb069e2..e966bd731 100644 --- a/app/controllers/result_assets_controller.rb +++ b/app/controllers/result_assets_controller.rb @@ -76,23 +76,23 @@ class ResultAssetsController < ApplicationController @result.last_modified_by = current_user @result.assign_attributes(update_params) - success_flash = t("result_assets.update.success_flash", - module: @my_module.name) + success_flash = t('result_assets.update.success_flash', + module: @my_module.name) if @result.archived_changed?(from: false, to: true) if previous_asset.locked? respond_to do |format| - format.html { + format.html do flash[:error] = t('result_assets.archive.error_flash') redirect_to results_my_module_path(@my_module) return - } + end end end saved = @result.archive(current_user) - success_flash = t("result_assets.archive.success_flash", - module: @my_module.name) + success_flash = t('result_assets.archive.success_flash', + module: @my_module.name) if saved Activity.create( type_of: :archive_result, @@ -126,7 +126,7 @@ class ResultAssetsController < ApplicationController # Asset (file) and/or name has been changed saved = @result.save - if saved then + if saved # Release team's space taken due to # previous asset being removed team = @result.my_module.experiment.project.team @@ -134,9 +134,7 @@ class ResultAssetsController < ApplicationController team.save # Post process new file if neccesary - if @result.asset.present? - @result.asset.post_process_file(team) - end + @result.asset.post_process_file(team) if @result.asset.present? Activity.create( type_of: :edit_result, @@ -144,32 +142,33 @@ class ResultAssetsController < ApplicationController project: @my_module.experiment.project, experiment: @my_module.experiment, my_module: @my_module, - message: t( - "activities.edit_asset_result", - user: current_user.full_name, - result: @result.name - ) + message: t('activities.edit_asset_result', + user: current_user.full_name, + result: @result.name) ) end end respond_to do |format| if saved - format.html { + format.html do flash[:success] = success_flash redirect_to results_my_module_path(@my_module) - } - format.json { + end + format.json do render json: { - html: render_to_string({ - partial: "my_modules/result.html.erb", locals: {result: @result} - }) + html: render_to_string( + partial: 'my_modules/result.html.erb', locals: { result: @result } + ) }, status: :ok - } + end else - format.json { - render json: @result.errors, status: :bad_request - } + format.json do + render json: { + status: :error, + errors: @result.errors + }, status: :bad_request + end end end end @@ -189,22 +188,15 @@ class ResultAssetsController < ApplicationController def load_vars_nested @my_module = MyModule.find_by_id(params[:my_module_id]) - - unless @my_module - render_404 - end + render_404 unless @my_module end def check_create_permissions - unless can_create_result_asset_in_module(@my_module) - render_403 - end + render_403 unless can_create_result_asset_in_module(@my_module) end def check_edit_permissions - unless can_edit_result_asset_in_module(@my_module) - render_403 - end + render_403 unless can_edit_result_asset_in_module(@my_module) end def check_archive_permissions diff --git a/app/views/result_assets/_new.html.erb b/app/views/result_assets/_new.html.erb index fe28d123d..275e40cd9 100644 --- a/app/views/result_assets/_new.html.erb +++ b/app/views/result_assets/_new.html.erb @@ -11,6 +11,7 @@
    - <%# end %>
    From fa4c787c6ba0b1cd19fbd5dfc9786127e2c72e06 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Fri, 20 Oct 2017 14:13:58 +0200 Subject: [PATCH 22/24] Bump version to 1.12.5 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 89c881bc9..e0a6b34fb 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.12.4 +1.12.5 From 6c2c5aff17ff4ed88e715791f72fc6aca94c3762 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Mon, 23 Oct 2017 09:51:13 +0200 Subject: [PATCH 23/24] Additional fixes required by latest merge from master --- app/models/my_module.rb | 4 ++-- config/initializers/devise_async.rb | 3 --- ...20171003082333_add_connections_and_sample_tasks_indexes.rb | 2 +- db/migrate/20171005135350_update_my_module_groups.rb | 2 +- 4 files changed, 4 insertions(+), 7 deletions(-) diff --git a/app/models/my_module.rb b/app/models/my_module.rb index 4e01eee3a..e4677a97f 100644 --- a/app/models/my_module.rb +++ b/app/models/my_module.rb @@ -284,7 +284,7 @@ class MyModule < ApplicationRecord until modules.empty? my_module = modules.shift final << my_module unless final.include?(my_module) - modules.push(*my_module.my_modules.flatten) + modules.push(*my_module.my_modules) end final end @@ -296,7 +296,7 @@ class MyModule < ApplicationRecord until modules.empty? my_module = modules.shift final << my_module unless final.include?(my_module) - modules.push(*my_module.my_module_antecessors.flatten) + modules.push(*my_module.my_module_antecessors) end final end diff --git a/config/initializers/devise_async.rb b/config/initializers/devise_async.rb index ca94fa499..8f24c4a87 100644 --- a/config/initializers/devise_async.rb +++ b/config/initializers/devise_async.rb @@ -1,4 +1 @@ Devise::Async.enabled = true -Devise::Async.backend = :delayed_job -Devise::Async.queue = :devise_email -# Devise::Async.priority = 10 diff --git a/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb b/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb index 29f1fb9a0..78b40ca88 100644 --- a/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb +++ b/db/migrate/20171003082333_add_connections_and_sample_tasks_indexes.rb @@ -1,4 +1,4 @@ -class AddConnectionsAndSampleTasksIndexes < ActiveRecord::Migration +class AddConnectionsAndSampleTasksIndexes < ActiveRecord::Migration[4.2] def change add_index :connections, :input_id add_index :connections, :output_id diff --git a/db/migrate/20171005135350_update_my_module_groups.rb b/db/migrate/20171005135350_update_my_module_groups.rb index 99ad4de88..063ab784b 100644 --- a/db/migrate/20171005135350_update_my_module_groups.rb +++ b/db/migrate/20171005135350_update_my_module_groups.rb @@ -1,4 +1,4 @@ -class UpdateMyModuleGroups < ActiveRecord::Migration +class UpdateMyModuleGroups < ActiveRecord::Migration[4.2] def change remove_column :my_module_groups, :name, :string end From e740e586e8f4aa39b98989dd55e90fc217d5b622 Mon Sep 17 00:00:00 2001 From: Luka Murn Date: Mon, 23 Oct 2017 10:43:32 +0200 Subject: [PATCH 24/24] Additional fixes required by latest merge from master (nr. 2) --- Gemfile | 4 +++- Gemfile.lock | 13 +++++++++---- config/initializers/devise_async.rb | 3 +++ 3 files changed, 15 insertions(+), 5 deletions(-) diff --git a/Gemfile b/Gemfile index d4e9bd6a7..6937d6d89 100644 --- a/Gemfile +++ b/Gemfile @@ -71,7 +71,9 @@ gem 'aws-sdk', '~> 2' gem 'aws-sdk-v1' gem 'delayed_job_active_record' -gem 'devise-async' +gem 'devise-async', + git: 'https://github.com/mhfs/devise-async.git', + branch: 'devise-4.x' gem 'ruby-graphviz', '~> 1.2' # Graphviz for rails gem 'tinymce-rails', '~> 4.6.4' # Rich text editor diff --git a/Gemfile.lock b/Gemfile.lock index 90aab3ac9..c793aa1e6 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -21,6 +21,14 @@ GIT activejob (>= 4.2) paperclip (>= 3.3) +GIT + remote: https://github.com/mhfs/devise-async.git + revision: 177f6363a002f7ff28f1d289c8cab7ad8d9cb8c5 + branch: devise-4.x + specs: + devise-async (0.10.2) + devise (>= 4.0) + GIT remote: https://github.com/phatworx/devise_security_extension.git revision: b2ee978af7d49f0fb0e7271c6ac074dfb4d39353 @@ -185,9 +193,6 @@ GEM railties (>= 4.1.0, < 5.2) responders warden (~> 1.2.3) - devise-async (1.0.0) - activejob (>= 5.0) - devise (>= 4.0) devise_invitable (1.7.2) actionmailer (>= 4.1.0) devise (>= 4.0.0) @@ -498,7 +503,7 @@ DEPENDENCIES delayed_job_active_record delayed_paperclip! devise (~> 4.3.0) - devise-async + devise-async! devise_invitable devise_security_extension! factory_girl_rails diff --git a/config/initializers/devise_async.rb b/config/initializers/devise_async.rb index 8f24c4a87..0255b5671 100644 --- a/config/initializers/devise_async.rb +++ b/config/initializers/devise_async.rb @@ -1 +1,4 @@ Devise::Async.enabled = true +Devise::Async.backend = :delayed_job +Devise::Async.queue = :devise_email +# Devise::Async.priority = 10 \ No newline at end of file