diff --git a/.gitignore b/.gitignore
index a150f57..b025de0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,6 @@ form_generator/.DS_Store
.DS_Store
.Rproj.user
.idea/
+Gemfile
+Gemfile.lock
+_site/
\ No newline at end of file
diff --git a/form_generator/Checklist.html b/form_generator/Checklist.html
index ade10c3..c3637ba 100644
--- a/form_generator/Checklist.html
+++ b/form_generator/Checklist.html
@@ -6,6 +6,15 @@
Empirical Standards
+
+
+
+
+
+
+
+
+
diff --git a/form_generator/js/DeviationHandler.js b/form_generator/js/DeviationHandler.js
new file mode 100644
index 0000000..64138ce
--- /dev/null
+++ b/form_generator/js/DeviationHandler.js
@@ -0,0 +1,318 @@
+// generate the deviation block for One Phase Reviewer Role
+// generate the deviation block for One Phase Reviewer Role
+function generate_one_phase_reviewer_deviation_block(checklistItem_id,data) {
+
+ // Create a question block with Yes-No radio answers
+ // 2nd Question
+ if(data!=null){
+ var deviation_block = generate_question_block_with_yes_no_radio_answers("deviation_block", "deviationRadio", "is the deviation reasonable?", checklistItem_id, 2.40, data.display1 == "False");
+
+ // Reviewer-specific deviation justification block
+ var deviation_justified = generate_message("deviation_justified:" + checklistItem_id, "", "message_style_2");
+
+ // Create a question block with type radio answers
+ // 3rd Question
+ var numbersArray = data.errortype.split(",").map(function(item) {
+ return parseInt(item, 10);
+ });
+
+ var deviation_not_justified = generate_question_block_with_type_radio_answers("deviation_not_justified", "justificationRadio", "Please indicate the type of unreasonable deviations. (Pick the largest number that applies.)", checklistItem_id, 2.06, numbersArray);
+
+ // (No-No-Yes)
+ var deviation_reasonable = generate_message("deviation_reasonable:" + checklistItem_id, "", "message_style_3");
+
+ // (No-No-No)
+ var deviation_unreasonable = generate_message("deviation_unreasonable:" + checklistItem_id, "", "message_style_3");
+
+ deviation_block.appendChild(deviation_justified);
+ deviation_block.appendChild(deviation_not_justified);
+ deviation_block.appendChild(deviation_reasonable);
+ deviation_block.appendChild(deviation_unreasonable);
+
+ if(data.displayfree == "True"){
+ var freeTextQuestion = generate_free_text_question("free_text_question", "freeText", data.freelabel, checklistItem_id);
+
+ deviation_block.appendChild(freeTextQuestion);
+ }
+ }else{
+ console.log("Data not fetched");
+ var deviation_block = generate_question_block_with_yes_no_radio_answers("deviation_block", "deviationRadio", "is the deviation reasonable?", checklistItem_id, 2.40);
+
+ // Reviewer-specific deviation justification block
+ var deviation_justified = generate_message("deviation_justified:" + checklistItem_id, "", "message_style_2");
+
+ // Create a question block with type radio answers
+ // 3rd Question
+ var deviation_not_justified = generate_question_block_with_type_radio_answers("deviation_not_justified", "justificationRadio", "Please indicate the type of unreasonable deviations. (Pick the largest number that applies.)", checklistItem_id, 2.06, type = [1,2,3,4]);
+
+ // (No-No-Yes)
+ var deviation_reasonable = generate_message("deviation_reasonable:" + checklistItem_id, "", "message_style_3");
+
+ // (No-No-No)
+ var deviation_unreasonable = generate_message("deviation_unreasonable:" + checklistItem_id, "", "message_style_3");
+
+ deviation_block.appendChild(deviation_justified);
+ deviation_block.appendChild(deviation_not_justified);
+
+ deviation_block.appendChild(deviation_reasonable);
+ deviation_block.appendChild(deviation_unreasonable);
+ var freeTextQuestion = generate_free_text_question("free_text_question", "freeText", 'How can this problem be addressed', checklistItem_id);
+
+ deviation_block.appendChild(freeTextQuestion);
+ }
+
+ console.log(deviation_block);
+ return deviation_block;
+}
+
+// generate the deviation block for Two Phase Reviewer Role
+function generate_two_phase_reviewer_deviation_block(checklistItem_id,data) {
+
+ // Create a question block with Yes-No radio answers
+ // 2nd Question
+ if(data!=null){
+ var deviation_block = generate_question_block_with_yes_no_radio_answers("deviation_block", "deviationRadio", "is the deviation reasonable?", checklistItem_id, 2.40, data.display1 == "False");
+
+ // Reviewer-specific deviation justification block
+ var deviation_justified = generate_message("deviation_justified:" + checklistItem_id, "", "message_style_2");
+
+ // Create a question block with type radio answers
+ // 3rd Question
+ var numbersArray = data.errortype.split(",").map(function(item) {
+ return parseInt(item, 10);
+ });
+
+ var deviation_not_justified = generate_question_block_with_type_radio_answers("deviation_not_justified", "justificationRadio", "Please indicate the type of unreasonable deviations. (Pick the largest number that applies.)", checklistItem_id, 2.06, numbersArray);
+
+ // (No-No-Yes)
+ var deviation_reasonable = generate_message("deviation_reasonable:" + checklistItem_id, "", "message_style_3");
+
+ // (No-No-No)
+ var deviation_unreasonable = generate_message("deviation_unreasonable:" + checklistItem_id, "", "message_style_3");
+
+ deviation_block.appendChild(deviation_justified);
+ deviation_block.appendChild(deviation_not_justified);
+ deviation_block.appendChild(deviation_reasonable);
+ deviation_block.appendChild(deviation_unreasonable);
+
+ if(data.displayfree == "True"){
+ var freeTextQuestion = generate_free_text_question("free_text_question", "freeText", data.freelabel, checklistItem_id);
+ console.log(data.freelabel);
+ deviation_block.appendChild(freeTextQuestion);
+ }
+ }else{
+ console.log("Data not fetched");
+
+ // new standard
+ var deviation_block = generate_question_block_with_yes_no_radio_answers("deviation_block", "deviationRadio", "is the deviation reasonable?", checklistItem_id, 2.40);
+
+ var deviation_justified = generate_message("deviation_justified:" + checklistItem_id, "", "message_style_2");
+ var deviation_not_justified = generate_question_block_with_type_radio_answers("deviation_not_justified", "justificationRadio", "Please indicate the type of unreasonable deviations. (Pick the largest number that applies.)", checklistItem_id, 2.06, [1,2,3,4]);
+
+ // (No-No-Yes)
+ var deviation_reasonable = generate_message("deviation_reasonable:" + checklistItem_id, "", "message_style_3");
+
+ // (No-No-No)
+ var deviation_unreasonable = generate_message("deviation_unreasonable:" + checklistItem_id, "", "message_style_3");
+
+ deviation_block.appendChild(deviation_justified);
+ deviation_block.appendChild(deviation_not_justified);
+ deviation_block.appendChild(deviation_reasonable);
+ deviation_block.appendChild(deviation_unreasonable);
+
+ var freeTextQuestion = generate_free_text_question("free_text_question", "freeText", "How can this problem be addressed", checklistItem_id);
+
+ deviation_block.appendChild(freeTextQuestion);
+ }
+
+ return deviation_block;
+}
+
+
+function generate_free_text_question(id, class_name, question, checklistItem_id) {
+ var question_block = document.createElement("div");
+ question_block.id = id + ":" + checklistItem_id;
+ question_block.className = "question_block_free_Text";
+
+ var questionText = document.createElement("div"); // Create a div for the question
+ questionText.innerHTML = " ↳ " + question;
+
+ var answerInput = document.createElement("div"); // Create a div for the input answer
+ answerInput.className = "freeTextContainer";
+
+ var answerInputField = document.createElement("textarea");
+ answerInputField.id = id + "-answer:" + checklistItem_id;
+ answerInputField.className = class_name + "Answer";
+ answerInputField.type = "text";
+
+ answerInput.appendChild(answerInputField);
+ question_block.appendChild(questionText);
+ question_block.appendChild(answerInput);
+
+ question_block.getAnswer = function () {
+ return answerInputField.value;
+ };
+
+ console.log(answerInputField.value);
+
+ return question_block;
+}
+
+
+// generate the deviation block for Author Role
+function generate_author_deviation_block(checklistItem_id) {
+ var deviation_block = generate_question_block_with_yes_no_radio_answers("deviation_block", "deviationRadio", "where does the manuscript justify the deviation?", checklistItem_id);
+
+ // Author-specific deviation justification message
+ var deviation_justified = generate_message("deviation_justified:" + checklistItem_id, "", "message_style_1");
+
+ deviation_block.appendChild(deviation_justified);
+
+ return deviation_block;
+}
+
+// generate the question block with the type radio buttons (type 1, type 2, type 3, type 4)
+function generate_question_block_with_type_radio_answers(id, class_name, question, checklistItem_id, padding, type) {
+ var question_block = document.createElement("div");
+
+ question_block.id = id + ":" + checklistItem_id;
+ question_block.className = "question_block type_block";
+ question_block.innerHTML = "↳ " + question;
+
+ var deviation_block_radios = document.createElement("div");
+ deviation_block_radios.innerHTML = " ";
+
+ // dictionary of tooltips text for each type of unreasonable deviation
+ var dict = {};
+
+ // type 1
+ dict[1] = "can be fixed by editing text only; e.g. clarifying text, adding references, changing a diagram, describing an additional limitation, copyediting.";
+
+ // type 2
+ dict[2] = "can be fixed by doing some new data analysis, redoing some existing data analysis, or collecting a small amount of additional data (e.g. going back to one interviewee, collecting some additional primary studies for a systematic review).";
+
+ // type 3
+ dict[3] = "can be fixed completely redoing data analysis, OR collecting additional data (e.g. conducting new or additional experiments or case studies; several new interviews, one or more additional rounds of questionnaire data collection).";
+
+ // type 4
+ dict[4] = "unacceptable conduct (e.g. plagiarism, p-hacking, HARKing, unethical data collection) OR problems the cannot be fixed without doing a brand new study (e.g. fundamentally invalid measures, data collection or analysis insufficient by an order of magnitude, no chain of evidence whatsoever from data to conclusions).";
+
+ for (let i in type) {
+ var deviationRadioType = document.createElement("input");
+ var deviationLabelType = document.createElement("label");
+
+ // Identify each radio button
+ deviationRadioType.id = id + "-radio:Type"+type[i]+":" + checklistItem_id;
+
+ // className - deal with all of them
+ deviationRadioType.className = class_name + "Type";
+
+ // These are the radio buttons of that element regardless of Type1 or Type2
+ // For Hiding Buttons
+ deviationRadioType.name = id + "-radio:" + checklistItem_id;
+
+ // deviation justification is a function
+ deviationRadioType.onclick = create_deviation_justification_block_and_show_hide_justification_location_textbox;
+
+ deviationRadioType.type = "radio";
+
+ // Value for comparisons
+ deviationRadioType.value = "type"+type[i];
+
+ // Actual Text of the Radio button
+ // Adding tooltip to type Radio button
+ deviationLabelType.innerHTML = "
type "+type[i]+ " "+dict[type[i]]+"
" + " ";
+
+ // For Labels
+ // Click on the label, click that radio button
+ deviationLabelType.htmlFor = deviationRadioType.id;
+
+ deviation_block_radios.appendChild(deviationRadioType);
+ deviation_block_radios.appendChild(deviationLabelType);
+ }
+
+ question_block.appendChild(deviation_block_radios);
+
+ return question_block;
+}
+
+function generate_question_block_with_yes_no_radio_answers(id, class_name, question, checklistItem_id, padding, display) {
+ var question_block = document.createElement("div");
+
+ question_block.id = id + ":" + checklistItem_id;
+ question_block.className = "question_block yes_no_block";
+
+ var deviation_block = document.createElement("div");
+ deviation_block.innerHTML = " ";
+
+ if (role == "\"author\"") {
+ var questiontext_container = document.createElement("span");
+ questiontext_container.innerHTML = "↳ " + question;
+ questiontext_container.className = "question_text_container";
+
+ // For authors, create location indicator + N/A checkbox
+ var justification_location_textbox = generate_location_textbox("justification_location_textbox", checklistItem_id);
+ var location_container = document.createElement("span");
+ location_container.className = "location_container";
+ location_container.appendChild(justification_location_textbox);
+
+ unjustified_checkbox = document.createElement("input");
+ unjustified_checkbox.type = "checkbox";
+ unjustified_checkbox.id = "unjustified_checkbox:" + checklistItem_id;
+ unjustified_checkbox.className = "unjustified_checkbox";
+ unjustified_checkbox.name = checklistItem_id;
+ unjustified_checkbox.onclick = create_deviation_justification_block_and_show_hide_justification_location_textbox;
+
+ var unjustified_container = document.createElement("span");
+ unjustified_container.appendChild(unjustified_checkbox);
+
+ question_block.appendChild(questiontext_container);
+ question_block.appendChild(location_container);
+ question_block.appendChild(unjustified_container);
+
+ var deviation_not_justified = generate_message("deviation_not_justified:" + checklistItem_id, " Your manuscript should justify any deviations from essential attributes.", "message_style_1 unjustified_warning");
+
+ question_block.appendChild(deviation_not_justified);
+ } else {
+ question_block.innerHTML = "↳ " + question;
+
+ // For reviewers, create yes-no radio buttons
+ var deviationRadioYes = document.createElement("input");
+ var deviationLabelYes = document.createElement("label");
+ deviationRadioYes.id = id + "-radio:Yes:" + checklistItem_id;
+ deviationRadioYes.className = class_name + "Yes";
+ deviationRadioYes.name = id + "-radio:" + checklistItem_id;
+ deviationRadioYes.onclick = create_deviation_justification_block_and_show_hide_justification_location_textbox;
+ deviationRadioYes.type = "radio";
+ deviationRadioYes.value = "yes";
+ deviationLabelYes.innerHTML = "yes ";
+ deviationLabelYes.htmlFor = deviationRadioYes.id;
+
+ var deviationRadioNo = document.createElement("input");
+ var deviationLabelNo = document.createElement("label");
+ deviationRadioNo.id = id + "-radio:No:" + checklistItem_id;
+ deviationRadioNo.className = class_name + "No";
+ deviationRadioNo.name = id + "-radio:" + checklistItem_id;
+ deviationRadioNo.onclick = create_deviation_justification_block_and_show_hide_justification_location_textbox;
+ deviationRadioNo.type = "radio";
+ deviationRadioNo.value = "no";
+ deviationLabelNo.innerHTML = "no";
+ deviationLabelNo.htmlFor = deviationRadioNo.id;
+
+ deviation_block.appendChild(deviationRadioYes);
+ deviation_block.appendChild(deviationLabelYes);
+ deviation_block.appendChild(deviationRadioNo);
+ deviation_block.appendChild(deviationLabelNo);
+ question_block.appendChild(deviation_block);
+ }
+
+ // if the deviation reasonable is fixed in the table
+ if (display) {
+ deviationRadioYes.disabled = true; // Disable 'Yes' radio button
+
+ // Cross out the label associated with the 'Yes' radio button
+ deviationLabelYes.innerHTML = "yes ";
+ }
+
+ return question_block;
+}
\ No newline at end of file
diff --git a/form_generator/js/FormValidity.js b/form_generator/js/FormValidity.js
new file mode 100644
index 0000000..0e4d923
--- /dev/null
+++ b/form_generator/js/FormValidity.js
@@ -0,0 +1,364 @@
+// Check if the completed checklist is valid (no missing items)
+function check_form_validity(event) {
+ event.preventDefault();
+ let validity = true;
+ let list = document.getElementById("Essential");
+
+ for (let ul of list.children) {
+ if (ul.tagName == 'UL') {
+ for (let li of ul.children) {
+ if (li.tagName != 'LI'){
+ continue;
+ }
+
+ // If yes-no is missing, the item is invalid
+ if (li.children[0].checked || li.children[1].checked) {
+ li.children[2].classList.remove("attention");
+ } else {
+ li.children[2].classList.add("attention");
+ validity = false;
+ }
+
+ let question_blocks = li.getElementsByClassName('question_block');
+
+ if (question_blocks[0].style.display != "none") {
+ let reasonable_yes = question_blocks[0].getElementsByClassName('deviationRadioYes')[0];
+ let reasonable_no = question_blocks[0].getElementsByClassName('deviationRadioNo')[0];
+
+ // If deviation reasonability missing, the item is invalid
+ if (reasonable_yes.checked || reasonable_no.checked) {
+ question_blocks[0].classList.remove("attention");
+ } else {
+ question_blocks[0].classList.add("attention");
+ validity = false;
+ }
+
+ if (question_blocks[1].style.display != "none") {
+ let types = question_blocks[1].getElementsByClassName('justificationRadioType');
+
+ // If deviation type missing, the item is invalid
+ if (types[0].checked || types[1] && types[1].checked || types[2] && types[2].checked || types[3] && types[3].checked) {
+ question_blocks[1].classList.remove("attention");
+ } else {
+ question_blocks[1].classList.add("attention");
+ validity = false;
+ }
+ }
+
+ let free_text = li.getElementsByClassName('question_block_free_Text')[0];
+
+ if (free_text.style.display != "none") {
+ let free_text_content = free_text.getElementsByClassName('freeTextAnswer')[0];
+
+ // If free text missing, the item is invalid
+ if (free_text_content.value == "") {
+ free_text.classList.add("attention");
+ validity = false;
+ } else {
+ free_text.classList.remove("attention");
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (!validity) {
+ document.getElementsByClassName("error_warning")[0].classList.remove("hide_display");
+ } else {
+ document.getElementsByClassName("error_warning")[0].classList.add("hide_display");
+ saveFile();
+ }
+}
+
+
+// Download the checklist with a specific format
+function saveFile() {
+ var checklists = document.getElementById('checklists');
+ var generated_text = '=================\n' +
+ 'Review Checklist\n' +
+ '=================\n';
+
+ var decision = document.getElementById("decision_msg");
+ var unreasonable = document.getElementById("deviation_unreasonable");
+ var reasonable = document.getElementById("deviation_reasonable");
+
+ if (decision.style.display == "block") {
+ generated_text += "\nRecommended Decision: " + decision.innerText + "\n";
+ }
+
+ if (unreasonable.style.display == "block") {
+ generated_text += "\nUnreasonable Deviations\n";
+ }
+
+ if (reasonable.style.display == "block") {
+ generated_text += "\nUnreasonable Deviations Requiring Revision\n";
+ } else {
+ generated_text += "";
+ }
+
+ var essential_list = "\nEssential\r\n";
+
+ if (role == "\"author\""){
+ var location_type = document.getElementById('location_type');
+ location_type = location_type.options[location_type.selectedIndex].text;
+ generated_text += "\nNote: The numbers beside checklist items, if any, represent " + location_type.toLowerCase() + "\n";
+
+ essential_list += " Location" + "\t" + "Attribute\r\n\r\n";
+ }
+
+ var desirable_list = "\nDesirable\r\n";
+ var extraordinary_list = "\nExtraordinary\r\n";
+ var free_text_list = "\nFree Text Questions\r\n"
+
+ var include_desirable = false;
+ var include_extraordinary = false;
+
+ var type1_list = "";
+ var type2_list = "";
+ var type3_list = "";
+ var type4_list = "";
+
+ for (let list of checklists.children) {
+ if(list.tagName == 'UL' & list.style.display != 'none') {
+ for (let ul of list.children) {
+ if(ul.tagName == 'UL'){
+ var i = 0;
+ for (let li of ul.children) {
+ if (li.tagName != 'LI') {
+ continue;
+ }
+ i++;
+ var li_text = li.getAttribute("text").trim();
+ var regex = //g;
+ if (li_text.match(regex) != null)
+ li_text = li_text.replace(regex, "");
+
+ var regex2 = /\{sup\}.+\{\/sup\}/g;
+ var regex3 = //g;
+ var regex4 = /<\/b>/g;
+ var regex5 = //g;
+ var regex6 = /[\r\n]+/g;
+ var regex7 =/ \(.+?\)/g;
+ var regex8 = //g;
+ var regex9 = /<\/i>/g;
+
+ if (li_text.match(regex2) != null)
+ li_text = li_text.replace(regex2, "");
+ if (li_text.match(regex3) != null)
+ li_text = li_text.replace(regex3,"\n");
+ if (li_text.match(regex4) != null)
+ li_text = li_text.replace(regex4,"");
+ if (li_text.match(regex5) != null)
+ li_text = li_text.replace(regex5,"");
+ if (li_text.match(regex6) != null)
+ li_text = li_text.replace(regex6,"");
+ if (li_text.match(regex7) != null)
+ li_text = li_text.replace(regex7,"");
+ if (li_text.match(regex8) != null)
+ li_text = li_text.replace(regex8,"");
+ if (li_text.match(regex9) != null)
+ li_text = li_text.replace(regex9,"");
+
+ var location_value = "";
+ var location_textbox = li.getElementsByClassName('item_location_textbox');
+
+ if (list.id == 'Essential'){
+ if (role != "\"author\"" && li.children[0].checked) {
+ essential_list += 'Y' + '\t ' + li_text + '\r\n';
+ } else if (role == "\"author\"" && location_textbox[0].value != "") {
+ if (location_textbox.length == 1) {
+ location_value = location_textbox[0].value;
+ }
+
+ essential_list += " " + (location_value != "" ? location_value : "");
+
+ // Determine whether to push item text to new line based on location text length
+ if (location_value.length < 6) {
+ essential_list += '\t\t' + li_text + '\r\n';
+ } else if (location_value.length < 14) {
+ essential_list += '\t' + li_text + '\r\n';
+ } else {
+ essential_list += '\r\n\t\t' + li_text + '\r\n';
+ }
+
+ } else {
+ var reasonable_deviation = li.getElementsByClassName('deviationRadioYes')[0];
+ location_textbox = li.getElementsByClassName('justification_location_textbox');
+
+ // store for the free_text_question
+ var questionDiv = li.getElementsByClassName("question_block_free_Text");
+
+ if (questionDiv[0]) {
+ var question_text = questionDiv[0].querySelector('div:first-child').textContent.trim().replace(/^\W+/g, '');
+ console.log(question_text)
+ var inputCollection = li.getElementsByClassName('freeTextAnswer');
+ console.log(inputCollection);
+
+ if (inputCollection[0]) {
+ var input_text = inputCollection[0].value;
+ }
+ }
+
+ if (location_textbox[0] && location_textbox[0].value != "" || reasonable_deviation && reasonable_deviation.checked) {
+ if (location_textbox.length == 1) {
+ location_value = location_textbox[0].value;
+ }
+
+ if (role == "\"author\"") {
+ essential_list += " " + (location_value != "" ? location_value : "");
+
+ // Determine whether to push item text to new line based on location text length
+ if (location_value.length < 6) {
+ essential_list += '\t\t' + li_text + ' (justified deviation)\r\n';
+ } else if (location_value.length < 14) {
+ essential_list += '\t' + li_text + ' (justified deviation)\r\n';
+ } else {
+ essential_list += '\r\n\t\t' + li_text + ' (justified deviation)\r\n';
+ }
+
+ } else {
+ essential_list += 'R' + '\t ' + li_text + '\r\n';
+ }
+
+ } else {
+ var fixable_deviation = li.getElementsByClassName('justificationRadioType');
+
+ if (fixable_deviation.length != 0){
+ if (fixable_deviation[0].checked) {
+ type1_list += '1\t ' + li_text + '\r\n';
+ if(input_text !== ""){
+ type1_list += ' \t ' + question_text + '\r\n';
+ type1_list += ' \t \t ' + input_text + '\r\n';
+ }
+ } else if (fixable_deviation[1].checked) {
+ type2_list += '2\t ' + li_text + '\r\n';
+ if(input_text !== ""){
+ type2_list += ' \t ' + question_text + '\r\n';
+ type2_list += ' \t \t ' + input_text + '\r\n';
+ }
+ } else if (fixable_deviation[2].checked) {
+ type3_list += '3\t ' + li_text + '\r\n';
+ if(input_text !== ""){
+ type3_list += ' \t ' + question_text + '\r\n';
+ type3_list += ' \t \t ' + input_text + '\r\n';
+ }
+ } else if (fixable_deviation[3].checked) {
+ type4_list += '4\t ' + li_text + '\r\n';
+ if(input_text !== ""){
+ type4_list += ' \t ' + question_text + '\r\n';
+ type4_list += ' \t \t ' + input_text + '\r\n';
+ }
+ }
+ } else {
+ essential_list += (role == "\"author\"" ? ' *' : ' ') + '\t\t' + li_text;
+ essential_list += (role == "\"author\"" ? ' (unjustified deviation)\r\n' : '\r\n');
+ }
+ }
+ }
+ }
+ else if (list.id == 'Desirable') {
+ if (li.children[0].checked || role == "\"author\"" && location_textbox[0].value != "") {
+ include_desirable = true;
+
+ if (location_textbox.length == 1) {
+ location_value = location_textbox[0].value;
+ desirable_list += " " + (location_value != "" ? location_value : "");
+
+ // Determine whether to push item text to new line based on location text length
+ if (location_value.length < 6) {
+ desirable_list += '\t\t' + li_text + '\r\n';
+ } else if (location_value.length < 14) {
+ desirable_list += '\t' + li_text + '\r\n';
+ } else {
+ desirable_list += '\r\n\t\t' + li_text + '\r\n';
+ }
+ } else {
+ desirable_list += 'Y' + '\t ' + li_text + '\r\n';
+ }
+ }
+ } else if (li.children[0].checked || role == "\"author\"" && location_textbox[0].value != "") {
+ include_extraordinary = true;
+
+ if (location_textbox.length == 1) {
+ location_value = location_textbox[0].value;
+ extraordinary_list += " " + (location_value != "" ? location_value : "");
+
+ // Determine whether to push item text to new line based on location text length
+ if (location_value.length < 6) {
+ extraordinary_list += '\t\t' + li_text + '\r\n';
+ } else if (location_value.length < 14) {
+ extraordinary_list += '\t' + li_text + '\r\n';
+ } else {
+ extraordinary_list += '\r\n\t\t' + li_text + '\r\n';
+ }
+ } else {
+ extraordinary_list += 'Y' + '\t ' + li_text + '\r\n';
+ }
+ }
+
+ }
+
+ }
+ }
+ }
+ }
+
+ generated_text += type4_list + type3_list + type2_list + type1_list;
+
+ generated_text += essential_list;
+
+ if (include_desirable) {
+ generated_text += desirable_list;
+ }
+ if (include_extraordinary) {
+ generated_text += extraordinary_list;
+ }
+
+ generated_text += "\n";
+
+ let date_generated = new Date();
+ let date_string = date_generated.toLocaleDateString("en-CA", {timeZone: "-12:00"});
+ let time_string = date_generated.toLocaleTimeString("en-US", {timeZone: "-12:00"});
+
+ let date_formatted = new Date(date_string);
+ generated_text += '\nGenerated: ' + date_generated.toDateString() + ', ';
+ generated_text += time_string.slice(0, -6) + time_string.substr(8,3) + ' AoE\n\n';
+
+ if (role != "\"author\"") {
+ generated_text += "=======\n" +
+ "Legend\n" +
+ "=======\n" +
+ "Y = yes, the paper has this attribute\n" +
+ "R = a reasonable, acceptable deviation from the standards\n" +
+ "1 = a deviation that can be fixed by editing text only\n" +
+ "2 = a deviation that can be fixed by doing some new data analysis, redoing some existing data analysis, or collecting a small amount of additional data\n" +
+ "3 = a deviation that can be fixed by completely redoing data analysis, or collecting additional data\n" +
+ "4 = a deviation that cannot be fixed, or at least not without doing a brand new study\n\n\n";
+ }
+
+ generated_text+= "=================\n" +
+ "Standards Used\n" +
+ "=================\n";
+
+ var elms = document.querySelectorAll(".standard_links");
+ for (var i = 0; i < elms.length; i++) {
+ generated_text += elms[i].innerHTML + '\n';
+ }
+
+ pageURL = window.location.href;
+ generated_text += "\nURL: " + pageURL;
+
+ var newLink = document.createElement('a');
+ newLink.href = 'data:text/plain;charset=utf-8,' + encodeURIComponent(generated_text);
+ newLink.download = 'reviewChecklist.txt';
+
+ if (document.createEvent) {
+ var event = document.createEvent('MouseEvents');
+ event.initEvent('click', true, true);
+ newLink.dispatchEvent(event);
+ } else {
+ newLink.click();
+ }
+ return false;
+}
\ No newline at end of file
diff --git a/form_generator/js/HashMap.js b/form_generator/js/HashMap.js
new file mode 100644
index 0000000..bd3ab26
--- /dev/null
+++ b/form_generator/js/HashMap.js
@@ -0,0 +1,61 @@
+class HashMap {
+ constructor() {
+ this._buckets = [];
+ }
+
+ _hash(key) {
+ let hash = 0;
+ for (let i = 0; i < key.length; i++) {
+ hash = (hash + key.charCodeAt(i)) % this._buckets.length;
+ }
+ return hash;
+ }
+
+ set(key, value) {
+ const index = this._hash(key);
+ if (!this._buckets[index]) {
+ this._buckets[index] = [];
+ }
+
+ const bucket = this._buckets[index];
+ for (let i = 0; i < bucket.length; i++) {
+ if (bucket[i][0] === key) {
+ bucket[i][1] = value;
+ return;
+ }
+ }
+
+ bucket.push([key, value]);
+ }
+
+ get(key) {
+ const index = this._hash(key);
+ const bucket = this._buckets[index];
+ if (!bucket) {
+ return undefined;
+ }
+
+ for (let i = 0; i < bucket.length; i++) {
+ if (bucket[i][0] === key) {
+ return bucket[i][1];
+ }
+ }
+
+ return undefined;
+ }
+
+ remove(key) {
+ const index = this._hash(key);
+ const bucket = this._buckets[index];
+ if (!bucket) {
+ return;
+ }
+
+ for (let i = 0; i < bucket.length; i++) {
+ if (bucket[i][0] === key) {
+ bucket.splice(i, 1);
+ return;
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/form_generator/js/PopulateChecklist.js b/form_generator/js/PopulateChecklist.js
new file mode 100644
index 0000000..5fb3ad3
--- /dev/null
+++ b/form_generator/js/PopulateChecklist.js
@@ -0,0 +1,88 @@
+function populate_checklist() {
+ console.log("Populating " + role + " checklist");
+
+ // Clear all stored items for this checklist
+ let keys = Object.keys(localStorage);
+
+ // Move nonessential keys to last
+ let nonessential = keys.filter(check_nonessential_keys);
+ for (let key of nonessential) {
+ let index = keys.indexOf(key);
+ keys.push(keys.splice(index, 1)[0]);
+ }
+
+ for (let key of keys) {
+
+ if (key != role && key.includes(role)) {
+ let listClass = key.replace(role + "-", "");
+ let item = document.getElementsByClassName(listClass)[0];
+ let state = JSON.parse(localStorage.getItem(key));
+
+ if (item != null) {
+ if (role != "\"author\"") {
+ if (state.checked) {
+ item.children[0].click();
+
+ } else if (!state.checked) {
+ item.children[1].click();
+
+ let question_blocks = item.getElementsByClassName('question_block');
+ let reasonable_yes = question_blocks[0].getElementsByClassName('deviationRadioYes')[0];
+ let reasonable_no = question_blocks[0].getElementsByClassName('deviationRadioNo')[0];
+
+ if (state.reasonable) {
+ reasonable_yes.click();
+
+ } else if (!state.reasonable) {
+ reasonable_no.click();
+
+ let types = question_blocks[1].getElementsByClassName('justificationRadioType');
+
+ if (state.deviationType == 1) {
+ types[0].click();
+ } else if (state.deviationType == 2) {
+ types[1].click();
+ } else if (state.deviationType == 3) {
+ types[2].click();
+ } else if (state.deviationType == 4) {
+ types[3].click();
+ }
+
+ let free_text_box = item.getElementsByClassName('question_block_free_Text')[0];
+ let free_text_content = free_text_box.getElementsByClassName('freeTextAnswer')[0];
+
+ if (Object.hasOwn(state, "freeText") && state.freeText != "") {
+ free_text_content.value = state.freeText;
+ }
+ }
+ }
+ } else {
+ let location_box = item.getElementsByClassName('item_location_textbox')[0];
+ let missing_button = item.getElementsByClassName('missing_checkbox')[0];
+
+ if (state.location != "") {
+ location_box.value = state.location;
+
+ } else if (!state.location) {
+ missing_button.click();
+
+ let justification_box = item.getElementsByClassName('justification_location_textbox')[0];
+ let justification_button = item.getElementsByClassName('unjustified_checkbox')[0];
+
+ if (Object.hasOwn(state, "justified") && state.justified != "") {
+ justification_box.value = state.justified;
+
+ } else if (!state.justified) {
+ justification_button.click();
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+// Check if the key is nonessential
+function check_nonessential_keys(key) {
+ return key.includes("Desirable") || key.includes("Extraordinary");
+}
\ No newline at end of file
diff --git a/form_generator/js/ReadEmpiricalStandards.js b/form_generator/js/ReadEmpiricalStandards.js
new file mode 100644
index 0000000..0664e0f
--- /dev/null
+++ b/form_generator/js/ReadEmpiricalStandards.js
@@ -0,0 +1,52 @@
+// Generate relative path for each standard document
+function readSpecificEmpiricalStandard(standard_name) {
+ var mdFile = new XMLHttpRequest();
+ var loc = window.location.pathname;
+ var dir = loc.substring(0, loc.lastIndexOf('/'));
+ var dir = dir.substring(0, dir.lastIndexOf('/'));
+ var standard_file_name = standard_name.replaceAll("\"", "").replace(" ", "");
+ var standard_file_path = dir + "/docs/standards/" + standard_file_name + ".md";
+ var empirical_standard = "";
+ mdFile.open("GET", standard_file_path, false);
+ mdFile.onreadystatechange = function () {
+ if (mdFile.readyState === 4) {
+ if (mdFile.status === 200 || mdFile.status == 0) {
+ empirical_standard = mdFile.responseText;
+ } else {
+ alert("Can't read " + standard_file_path);
+ }
+ } else {
+ alert("Can't read " + standard_file_path);
+ }
+ }
+ mdFile.send(null);
+ return empirical_standard;
+}
+
+// Load the table file for the customization of the checklist
+function readSpecificEmpiricalStandard_table(standard_name) {
+ //loadConfiguration();
+ var mdFile = new XMLHttpRequest();
+ var loc = window.location.pathname;
+ var dir = loc.substring(0, loc.lastIndexOf('/'));
+ var dir = dir.substring(0, dir.lastIndexOf('/'));
+ var standard_file_name = standard_name.replaceAll("\"", "").replace(" ", "");
+ console.log(standard_file_name);
+ var standard_file_path = dir + "/docs/attribute_customizations/" + standard_file_name + "_table.md";
+ console.log(standard_file_path);
+ var empirical_standard = "";
+ mdFile.open("GET", standard_file_path, false);
+ mdFile.onreadystatechange = function () {
+ if (mdFile.readyState === 4) {
+ if (mdFile.status === 200 || mdFile.status == 0) {
+ empirical_standard = mdFile.responseText;
+ } else {
+ alert("Can't read " + standard_file_path);
+ }
+ } else {
+ alert("Can't read " + standard_file_path);
+ }
+ }
+ mdFile.send(null);
+ return empirical_standard;
+}
\ No newline at end of file
diff --git a/form_generator/js/RequirementsChecklist.js b/form_generator/js/RequirementsChecklist.js
new file mode 100644
index 0000000..3aba2e2
--- /dev/null
+++ b/form_generator/js/RequirementsChecklist.js
@@ -0,0 +1,780 @@
+var dataStructure = new HashMap();
+var footnotes = {};
+var imrad_order = [];
+
+function create_requirements_checklist(file) {
+
+ // Create Element "FORM"
+ var form = document.createElement("FORM");
+ form.id = "checklists";
+ form.name = "checklists";
+
+ let clear_button = create_clear_checklist_button();
+ form.appendChild(clear_button);
+
+ // create Header for Essential Requirements with an unordered list
+ var EssentialUL = create_requirements_heading_with_UL("Essential");
+
+ // create Header for Desirable Requirements with an unordered list
+ var DesirableUL = create_requirements_heading_with_UL("Desirable");
+
+ // create Header for Extraordinary Requirements with an unordered list
+ var ExtraordinaryUL = create_requirements_heading_with_UL("Extraordinary");
+
+ if (role != "\"author\"") {
+ DesirableUL.className = "hide_display";
+ ExtraordinaryUL.className = "hide_display";
+ }
+
+ // unshift() method adds new items to the beginning of an array, and returns the new length
+ if (!standard_keys.includes("\"General Standard\"")) {
+ standard_keys.unshift("\"General Standard\"");
+ }
+
+ create_requirements_checklist_table(file);
+
+ let standards_list = [];
+
+ var i = 0;
+ for (let key of standard_keys) {
+ i++;
+
+ // Obtain all the information for a Standard
+ empirical_standard = readSpecificEmpiricalStandard(key);
+
+ var dom = document.createElement("div");
+ dom.innerHTML = empirical_standard;
+ var standardTag = dom.getElementsByTagName("standard")[0];
+
+ // collect all the footnotes
+ collect_footnotes(dom, standardTag);
+
+ let standardName = "\"" + standardTag.getAttribute('name') + "\"";
+ standardName = standardName.replaceAll("\"", "");
+ standards_list.push(standardName.replaceAll(/\s/g, ""));
+
+ var checklistTags = standardTag.getElementsByTagName("checklist");
+ for (let checklistTag of checklistTags) {
+
+ let checklistType = checklistTag.getAttribute('name');
+
+ // dealing with footnotes
+ checklistHTML = checklistTag.innerHTML.replaceAll("", "" + standardName + "--footnote--") // To make footnotes belong to their standards
+
+ // Add all information for "all_intro_items", etc.
+ if (checklistType == "Essential") {
+ separate_essential_attributes_based_on_IMRaD_tags(standardTag.getAttribute('name'), checklistHTML);
+ }
+
+ // Reformat the checklists from MD to HTML
+ var Yes_No = document.createElement("div");
+ Yes_No.className = "checklist_labels"
+
+ if (role == "\"author\"") {
+ Yes_No.classList.add("author_labels");
+
+ var attribute_label = document.createElement("span");
+ attribute_label.innerHTML = "Attribute";
+ attribute_label.className = "attribute_label";
+
+ var location_label = document.createElement("span");
+ var location_types_combobox = document.createElement("select");
+ location_types_combobox.id = 'location_type';
+
+ var location_types = [
+ { value: 'line_no', text: 'Line Number(s)' },
+ { value: 'page_no', text: 'Page #, Line #' },
+ { value: 'page_with_paragraph_no', text: 'Page #, Paragraph #' },
+ { value: 'section_no', text: 'Section #, Line #' },
+ { value: 'section_with_paragraph_no', text: 'Section #, Paragraph #' },
+ ];
+
+ location_types.forEach(function (option) {
+ var location = document.createElement('option');
+ location.value = option.value;
+ location.text = option.text;
+ location_types_combobox.appendChild(location);
+ });
+
+ location_types_combobox.selectedIndex = 0;
+ location_label.className = "location_container";
+ location_label.appendChild(location_types_combobox);
+
+ var missing_label = document.createElement("span");
+ missing_label.innerHTML = "N/A";
+
+ Yes_No.appendChild(attribute_label);
+ Yes_No.appendChild(location_label);
+ Yes_No.appendChild(missing_label);
+ } else {
+ Yes_No.innerHTML = " yes no";
+ }
+
+ if (checklistType == "Essential") {
+ if (i == 1) {
+ EssentialUL.appendChild(Yes_No);
+ }
+ }
+ else if (checklistType == "Desirable") {
+
+ // Change from Markdown to HTML elements
+ checklists = preparation_to_convert_MD_to_HTML(standardTag.getAttribute('name'), checklistTag.getAttribute('name'), checklistHTML, footnotes);
+ DesirableUL.appendChild(checklists);
+ }
+ else if (checklistType == "Extraordinary") {
+
+ // Change from Markdown to HTML elements
+ checklists = preparation_to_convert_MD_to_HTML(standardTag.getAttribute('name'), checklistTag.getAttribute('name'), checklistHTML, footnotes);
+ ExtraordinaryUL.appendChild(checklists);
+ }
+ }
+ }
+
+ all_essential_IMRaD_items_innerHTML = "" + all_intro_items + "\n_hr_" + all_method_items + "\n_hr_" + all_results_items + "\n_hr_" + all_discussion_items + "\n_hr_" + all_other_items;
+
+ all_essential_IMRaD_items_innerHTML = all_essential_IMRaD_items_innerHTML.replaceAll("\n_hr_", "").length > 0 ? all_essential_IMRaD_items_innerHTML : "";
+
+ // Notify testers in the case of unrecognized tags, no tags at all, or untagged attributes
+ notify_testers();
+
+ // Change from Markdown to HTML elements
+ checklists = preparation_to_convert_MD_to_HTML(standards_list, 'Essential', all_essential_IMRaD_items_innerHTML, footnotes);
+ EssentialUL.appendChild(checklists);
+
+ // Add Essential Attributes to the form
+ form.appendChild(EssentialUL);
+
+ // Create download button
+ var download = create_download_button();
+
+ var error_warning = document.createElement("div");
+ error_warning.className = "error_warning attention hide_display";
+ error_warning.innerHTML = "Some required items are missing.";
+
+ var download_test = create_download_configuration_button();
+
+ // (All 'Yes' -> accept manuscript)
+ var decision_msg = generate_message("decision_msg", (role != "\"author\"" ? "The manuscript meets all essential criteria: ACCEPT." : ""), "message_style_4");
+ form.appendChild(decision_msg);
+
+ if (role == "\"author\"") {
+ // (At least one 'No-No-No' -> reject manuscript)
+ var deviation_unreasonable = generate_message("deviation_unreasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable.", "message_style_4");
+ form.appendChild(deviation_unreasonable);
+ // (At least one 'No-No-Yes' -> explain fix)
+ var deviation_reasonable = generate_message("deviation_reasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable. Please give specific suggestions for how each deviation can be addressed.", "message_style_4");
+ form.appendChild(deviation_reasonable);
+
+ } else if (role == "\"one-phase-reviewer\"") {
+ // (At least one 'No-No-No' -> reject manuscript)
+ var deviation_unreasonable = generate_message("deviation_unreasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable.", "message_style_4");
+ form.appendChild(deviation_unreasonable);
+ // (At least one 'No-No-Yes' -> explain fix)
+ var deviation_reasonable = generate_message("deviation_reasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable. Please give specific suggestions for how each deviation can be addressed.", "message_style_4");
+ form.appendChild(deviation_reasonable);
+
+ } else if (role == "\"two-phase-reviewer\"") {
+ // (At least one 'No-No-No' -> reject manuscript)
+ var deviation_unreasonable = generate_message("deviation_unreasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable.", 2, 0);
+ form.appendChild(deviation_unreasonable);
+
+ // (At least one 'No-No-Yes' -> explain fix)
+ var deviation_reasonable = generate_message("deviation_reasonable", "In the free-text part of your review, please explain the deviation(s) and why they are not reasonable. Please give specific suggestions for how each deviation can be addressed.", "message_style_4");
+ form.appendChild(deviation_reasonable);
+
+ }
+
+ // Add Desirable and Extraordinary Unordered List to Form
+ form.appendChild(DesirableUL);
+ form.appendChild(ExtraordinaryUL);
+ form.appendChild(download);
+ form.appendChild(error_warning);
+
+ return form;
+}
+
+function create_requirements_checklist_table(file) {
+ // Create Element "FORM"
+ var form = document.createElement("FORM");
+ form.id = "checklists";
+ form.name = "checklists";
+
+ // unshift() method adds new items to the beginning of an array, and returns the new length
+ if (!standard_keys.includes("\"General Standard\"")) {
+ standard_keys.unshift("\"General Standard\"");
+ }
+
+ if (file == null) {
+ var i = 0;
+ const Essentail_dataStructure = new HashMap();
+ const Desirable_dataStructure = new HashMap();
+ const Extraordinary_dataStructure = new HashMap();
+ for (let key of standard_keys) {
+ i++;
+ // Obtain all the information for a Standard
+ empirical_standard1 = readSpecificEmpiricalStandard_table(key);
+ // Convert Markdown to HTML
+ var htmlTable = convertMarkdownToHTML(empirical_standard1);
+
+ // Get a reference to the container element where you want to display the table
+ var dom1 = document.createElement("div");
+ // Append the HTML table to the container
+ dom1.innerHTML = htmlTable;
+
+ var checklists1 = dom1.getElementsByTagName('checklist')[2];
+ for (let checks of checklists1.getElementsByTagName('row')) {
+ var content0 = checks.getElementsByTagName('Type')[0].innerHTML;
+ var content1 = checks.getElementsByTagName('content')[0].innerHTML;
+ var content2 = checks.getElementsByTagName('display1')[0].innerHTML;
+ var content3 = checks.getElementsByTagName('errortype')[0].innerHTML;
+ var content4 = checks.getElementsByTagName('displayfree')[0].innerHTML;
+ var content5 = checks.getElementsByTagName('freelabel')[0].innerHTML;
+ var rowData = {
+ type: content0,
+ content: content1,
+ display1: content2,
+ errortype: content3,
+ displayfree: content4,
+ freelabel: content5
+ };
+
+ // update the encoding method to get the key for the contents
+ const key = Encode_key(content1);
+ dataStructure.set(key, rowData)
+ }
+ }
+ } else {
+ console.log(file);
+
+ // Parse the JSON string to an object
+ const jsonObject = JSON.parse(file);
+
+ // Loop through the keys in the parsed JSON object
+ Object.keys(jsonObject).forEach(key => {
+ dataStructure.set(jsonObject[key][0], jsonObject[key][1]);
+ });
+ }
+ return;
+}
+
+// create Header with Unordered List (Essential, Desirable, Extraordinary)
+function create_requirements_heading_with_UL(title) {
+ var H3_ = document.createElement("H3");
+ var UL_ = document.createElement("UL");
+
+ H3_.className = "checklist_heading";
+ H3_.innerHTML = title;
+ UL_.id = title;
+ UL_.appendChild(H3_);
+
+ return UL_;
+}
+
+function create_download_configuration_button() {
+ var download = document.createElement("button");
+ download.innerHTML = "Download_Configuration";
+ download.id = "checklist_download_config";
+ download.name = "checklist_download_config";
+ download.disabled = false;
+ download.onclick = saveConfig;
+ return download;
+}
+
+function saveConfig() {
+ // Convert HashMap to JSON string
+ console.log(dataStructure._buckets)
+ // Loop through the _buckets array in yourHashMap
+ const extractedData = {};
+
+ // Loop through the _buckets array in dataStructure
+ dataStructure._buckets.NaN.forEach((value, index) => {
+ console.log(value);
+ console.log(index);
+ extractedData[index] = value;
+ });
+ console.log(extractedData)
+ const jsonContent = JSON.stringify(extractedData);
+
+ // Parse the JSON string to an object
+ const jsonObject = JSON.parse(jsonContent);
+
+ // Convert the object back to a formatted JSON string with indentation
+ const formattedJsonContent = JSON.stringify(jsonObject, null, 2);
+
+ // Create a Blob from the formatted JSON content
+ const blob = new Blob([formattedJsonContent], { type: 'application/json' });
+
+ // Create a temporary URL for the Blob
+ const url = URL.createObjectURL(blob);
+
+ // Create a download link
+ const downloadLink = document.createElement('a');
+ downloadLink.href = url;
+ downloadLink.download = 'reviewConfig.json'; // Set the file name here
+
+ // Append the download link to the body (or any other part of the DOM)
+ document.body.appendChild(downloadLink);
+
+ // Programmatically trigger the click event on the download link
+ downloadLink.click();
+
+ // Clean up by revoking the Blob URL
+ URL.revokeObjectURL(url);
+ return false;
+}
+
+// Notify testers in the case of unrecognized tags, no tags at all, or untagged attributes
+function notify_testers() {
+ tester = getParameterByName('y')[0] == 'noval' ? true : false;
+ if (tester) {
+ alert_msg = "";
+ if (unrecognized_tags != "") {
+ alert_msg += "Warning — unrecognized tag(s):\n" + unrecognized_tags;
+ }
+ if (standards_with_no_tags != "") {
+ alert_msg += "\nWarning — there are no tags at:\n" + standards_with_no_tags;
+ }
+ if (standards_with_untagged_attributes != "") {
+ alert_msg += "\nWarning — there are untagged attributes at:\n" + standards_with_untagged_attributes;
+ }
+ if (alert_msg != "") {
+ alert(alert_msg);
+ }
+ }
+}
+
+// Create download button to download text file
+function create_download_button() {
+ var download = document.createElement("button");
+ download.innerHTML = "Download";
+ download.id = "checklist_download";
+ download.name = "checklist_download";
+
+ if (role == "\"author\"") {
+ download.onclick = saveFile;
+ } else {
+ download.addEventListener("click", check_form_validity, false);
+ }
+ return download;
+}
+
+// Prepare unordered lists
+function preparation_to_convert_MD_to_HTML(standardTagName, checklistTagName, checklistInnerHTML, footnotes) {
+
+ // superscript tags
+ checklistInnerHTML = checklistInnerHTML.replaceAll("", "{sup}").replaceAll("", "{/sup}");
+
+ var tempDivElement = document.createElement("div");
+ tempDivElement.innerHTML = checklistInnerHTML;
+ checklistInnerText = tempDivElement.innerText;
+
+ checklistText = checklistInnerText.replaceAll(">", "").replaceAll(/\n\s*\n/g, '\n').replaceAll("\n", " ");
+
+ // Transform Markdown tags to HTMLtags
+ checklistText = convert_MD_tags_to_HTML_tags(checklistText);
+
+ // Standard Files - Change from docs to link, change from .md file to nothing
+ checklistText = checklistText.replaceAll('https://github.com/acmsigsoft/EmpiricalStandards/blob/master/docs/standards/', '../docs/standards?standard=').replaceAll('.md', '');
+
+ // Supplement Files - Change from docs to link, change from .md file to nothing
+ checklistText = checklistText.replaceAll('https://github.com/acmsigsoft/EmpiricalStandards/blob/master/docs/supplements/', '../docs/supplements?supplement=').replaceAll('.md', '');
+
+ // Convert Markdown Checklists to HTML checklists
+ checklists = convert_MD_standard_checklists_to_html_standard_checklists(standardTagName, checklistTagName, checklistText, footnotes)
+
+ return checklists;
+}
+
+// Create a button for clearing the current checklist
+function create_clear_checklist_button() {
+ let clear_button = document.createElement("input");
+ clear_button.type = "reset";
+ clear_button.value = "Clear checklist";
+ clear_button.id = "clear_checklist";
+
+ clear_button.addEventListener("click", clear_checklist, false);
+
+ return clear_button;
+}
+
+// Clear the current checklist
+function clear_checklist(event) {
+ let clear_check = confirm("This will erase all progress on the current checklist. Are you sure?");
+
+ if (!clear_check) {
+ event.preventDefault();
+ } else {
+ console.log("Clearing " + role + " checklist");
+ localStorage.setItem(role, "");
+
+ // Clear all stored items for this checklist
+ let keys = Object.keys(localStorage);
+ for (let key of keys) {
+ if (key != role && key.includes(role)) {
+ localStorage.removeItem(key, "");
+ }
+ }
+
+ // If author, hide deviation blocks and display primary location boxes
+ if (role == "\"author\"") {
+ primary_locations = document.getElementsByClassName("item_location_textbox");
+ deviation_boxes = document.getElementsByClassName("question_block");
+
+ for (let location_box of primary_locations) {
+ location_box.style.visibility = "visible";
+ }
+
+ for (let deviation_box of deviation_boxes) {
+ deviation_box.style.display = "none";
+ }
+ }
+ }
+}
+
+
+function separate_essential_attributes_based_on_IMRaD_tags(standardName, checklistHTML) {
+ const IMRaD_tags = ["", "", "", "", ""]; // Known IMRaD tags
+ let imrad_counts = [];
+
+ // Attributes of each IMRaD tag
+ var intro = checklistHTML.includes("") ? checklistHTML.match(/([\s\S]*?)\n\s*<\/?\w+>/i)[1] : "";
+ var method = checklistHTML.includes("") ? checklistHTML.match(/([\s\S]*?)\n\s*<\/?\w+>/i)[1] : "";
+ var results = checklistHTML.includes("") ? checklistHTML.match(/([\s\S]*?)\n\s*<\/?\w+>/i)[1] : "";
+ var discussion = checklistHTML.includes("") ? checklistHTML.match(/([\s\S]*?)\n\s*<\/?\w+>/i)[1] : "";
+ var other = checklistHTML.includes("") ? checklistHTML.match(/([\s\S]*?)\n\s*<\/?\w+>/i)[1] : "";
+
+ tags = checklistHTML.match(/\n\s*<\w+>/g);
+ // No tags at all => treat as ''
+ if (tags === null) {
+ other = checklistHTML;
+ standards_with_no_tags += "[" + standardName + "]\n";
+ }
+ // Unrecognized tags => treat as ''
+ else for (const tag of tags) {
+ if (!IMRaD_tags.includes(tag.trim())) {
+ unrecognized_tags += "[" + tag.trim() + " @ " + standardName + "]\n";
+ var unrecognized = checklistHTML.match(new RegExp(tag.trim() + "([\\s\\S]*?)<\\/?\\w+>", "i"))[1];
+ other = unrecognized + other;
+ }
+ }
+
+ // Attributes that do not belong under any tag => treat as ''
+ untaged = checklistHTML.match(/^[\s\r\n]+-([\s\S]*?)\n(<\w+>)/i);
+ if (untaged != null) {
+ other = "-" + untaged[1] + other;
+ standards_with_untagged_attributes += "[" + standardName + "]\n";
+ }
+
+ // Count IMRaD items
+ let intro_items = intro.match(/(\[\s\])/img);
+ let intro_count = intro_items != null ? imrad_counts.push(intro_items.length) : imrad_counts.push(0);
+
+ let method_items = method.match(/(\[\s\])/img);
+ let method_count = method_items != null ? imrad_counts.push(method_items.length) : imrad_counts.push(0);
+
+ let results_items = results.match(/(\[\s\])/img);
+ let results_count = results_items != null ? imrad_counts.push(results_items.length) : imrad_counts.push(0);
+
+ let discussion_items = discussion.match(/(\[\s\])/img);
+ let discussion_count = discussion_items != null ? imrad_counts.push(discussion_items.length) : imrad_counts.push(0);
+
+ let other_items = other.match(/(\[\s\])/img);
+ let other_count = other_items != null ? imrad_counts.push(other_items.length) : imrad_counts.push(0);
+
+ imrad_order.push(imrad_counts);
+
+ // Combine IMRaD tags of all standards
+ all_intro_items = all_intro_items + intro;
+ all_method_items = all_method_items + method;
+ all_results_items = all_results_items + results;
+ all_discussion_items = all_discussion_items + discussion;
+ all_other_items = all_other_items + other;
+}
+
+// convert from Markdown to HTML checklists
+function convert_MD_standard_checklists_to_html_standard_checklists(standardName, checklistName, checklistText, footnotes) {
+
+ tester = getParameterByName('y')[0] == 'noval' ? true : false;
+
+ // Create Unordered List
+ var checklists = document.createElement("UL");
+
+ // Positioning Essential, Desirable, Extraordinary lines on page
+ // Essential needs more room for radio buttons
+ if (role == "\"author\"") {
+ checklists.className = "author_items item_list";
+ } else if (checklistName == "Essential") {
+ checklists.className = "reviewer_essential_items item_list";
+ } else {
+ checklists.className = "reviewer_nonessential_items item_list";
+ }
+
+ // splitting lines on bullet points from markdown file
+ lines = checklistText.includes("- [ ]") ? checklistText.split("- [ ]") : checklistText.includes("- ") ? checklistText.split("- ") : checklistText.split("");
+ console.log("Lines: " + lines);
+
+ var i = 0;
+
+ var imrad_count_index = 0;
+ var attribute_numbers = Array(standardName.length).fill(0);
+ console.log(attribute_numbers);
+
+ // IMRaD line break flag is set to equal false
+ var IMRaD_line_break = false;
+
+ for(let line of lines){
+
+ // removes whitespace, replace all line breaks ( ) and tab character(\t)
+ line_text = line.trim().replaceAll(" ", "").replaceAll(" ", "").replaceAll(" ", "").replaceAll("\t", "");
+
+ if (line_text != ""){
+ i++;
+
+ line_text = line.trim().replace("---", "—");
+
+ // Trim and remove line breaks in markdown text
+ while (line_text.match(/$/)) {
+ line_text = line_text.replace(/$/, "");
+ line_text = line_text.trim();
+ }
+
+ var checklistItemLI = document.createElement("LI");
+ var checklistItemText = document.createElement("span");
+
+ if (role == "\"author\"") {
+ checklistItemLI.classList.add("author_list_item");
+ checklistItemText.classList.add("item_text");
+ }
+
+ if(IMRaD_line_break) {
+ checklists.appendChild(document.createElement("br"));
+ }
+
+ // !!!!!!!!!!!!!!!! we dont need this part in the checklist
+ if(line_text.includes("complies with all applicable empirical standards")) {
+ continue;
+ }
+
+ // if line_text includes a specific regex set to true ( line break with horizontal rule)
+ IMRaD_line_break = line_text.includes('_hr_') ? true : false;
+
+ // Replace line break and horizontal rule with empty string
+ line_text = line_text.replace(/(_hr_)+/g, '');
+
+ let checklistItem_class = "";
+ var checklistItem_id = "";
+
+ // Determine which standard to use for the current essential item
+ if (checklistName == "Essential") {
+ let imrad_counts = imrad_order[imrad_count_index];
+ let tag_count = imrad_counts[0];
+
+ let found = false;
+ let num = attribute_numbers[imrad_count_index];
+
+ // Find the current count
+ while (found == false) {
+ if (tag_count == 0) {
+ imrad_counts.shift();
+ imrad_order[imrad_count_index] = imrad_counts;
+
+ // If this isn't the last array of counts, move to the next one
+ if (imrad_count_index + 1 < standardName.length) {
+ imrad_count_index++;
+
+ imrad_counts = imrad_order[imrad_count_index];
+ tag_count = imrad_counts[0];
+ num = attribute_numbers[imrad_count_index];
+
+ // If this is the last array of counts, reset to the first
+ } else {
+ imrad_count_index = 0;
+
+ imrad_counts = imrad_order[imrad_count_index];
+ tag_count = imrad_counts[0];
+ num = attribute_numbers[imrad_count_index];
+ }
+ } else {
+ found = true;
+ num++;
+ attribute_numbers[imrad_count_index] = num;
+ }
+ }
+
+ checklistItem_class = standardName[imrad_count_index] + "-" + checklistName + ":" + num;
+ tag_count--;
+ imrad_counts[0] = tag_count;
+ imrad_order[imrad_count_index] = imrad_counts;
+
+ checklistItem_id = "-" + checklistName + ":" + i;
+ } else {
+ checklistItem_class = standardName.replaceAll(/\s/g, "") + "-" + checklistName + ":" + i;
+ checklistItem_id = standardName + "-" + checklistName + ":" + i;
+ }
+
+ checklistItemLI.classList.add(checklistItem_class);
+
+ // Change the text to the string held in line_text
+ checklistItemLI.setAttribute("text", line_text);
+
+ console.log("Line text: " + line_text);
+
+ if(line_text.replaceAll("
", "") == "") {
+ continue;
+ }
+
+ if(line_text.includes("footnote")) {
+ checklistItemText = createTooltip(checklistItemText, line_text, footnotes);
+ } else {
+ checklistItemText.innerHTML = " " + line_text;
+ }
+
+ //locate the current checklist into the table
+ data = dataStructure.get(Encode_key(line_text));
+
+ if (checklistName == "Essential"){
+ // create Input Elements
+
+ var userInputYes;
+ var userInputNo;
+ var location_container;
+ var missing_container;
+
+ if (role == "\"author\"") {
+
+ location_container = document.createElement("span");
+ location_container.className = "location_container";
+
+ userInputYes = generate_location_textbox("item_location_textbox", checklistItem_id);
+ userInputYes.onfocus = hide_deviation_block_and_show_location_textbox;
+
+ missing_container = document.createElement("span");
+
+ userInputNo = document.createElement("input");
+ userInputNo.type = "checkbox";
+ userInputNo.id = "missing_checkbox:" + checklistItem_id;
+ userInputNo.className = "missing_checkbox";
+ userInputNo.name = checklistItem_id;
+ userInputNo.onclick = show_hide_location_textbox;
+
+ } else {
+ userInputYes = document.createElement("input");
+ userInputYes.id = "checklist-radio:Yes:" + checklistItem_id;
+ userInputYes.className = "checklistRadioYes";
+ userInputYes.name = "checklist-radio:" + checklistItem_id;
+
+ // in the case of YES, hide the deviation block
+ userInputYes.onclick = hide_deviation_block_and_show_location_textbox;
+
+ userInputYes.type = "radio";
+ userInputYes.value = "yes";
+ userInputYes.checked = tester;
+
+ userInputNo = document.createElement("input");
+ userInputNo.id = "checklist-radio:No:" + checklistItem_id;
+ userInputNo.className = "checklistRadioNo";
+ userInputNo.name = "checklist-radio:" + checklistItem_id;
+ userInputNo.onclick = show_deviation_block_and_hide_location_textbox;
+ userInputNo.type = "radio";
+ userInputNo.value = "no";
+ }
+
+ // Generate a deviation block
+ var deviation_block;
+ if(role == "\"author\"") {
+ deviation_block = generate_author_deviation_block(checklistItem_id);
+
+ checklistItemLI.appendChild(checklistItemText);
+
+ location_container.appendChild(userInputYes);
+ missing_container.appendChild(userInputNo);
+
+ checklistItemLI.appendChild(location_container);
+ checklistItemLI.appendChild(missing_container);
+
+ checklistItemLI.appendChild(deviation_block);
+
+ } else if(role == "\"one-phase-reviewer\""){
+ // deviation_block = generate_reviewer_deviation_block(checklistItem_id);
+ if(data){
+ deviation_block = generate_one_phase_reviewer_deviation_block(checklistItem_id,data);
+ }else{
+ deviation_block = generate_one_phase_reviewer_deviation_block(checklistItem_id,null);
+ }
+
+ checklistItemLI.appendChild(userInputYes);
+ checklistItemLI.appendChild(userInputNo);
+
+ checklistItemText.appendChild(deviation_block);
+ checklistItemLI.appendChild(checklistItemText);
+
+ }
+ else if(role == "\"two-phase-reviewer\""){
+ if(data){
+ deviation_block = generate_two_phase_reviewer_deviation_block(checklistItem_id,data);
+ }else{
+ deviation_block = generate_two_phase_reviewer_deviation_block(checklistItem_id,null);
+ }
+
+ checklistItemLI.appendChild(userInputYes);
+ checklistItemLI.appendChild(userInputNo);
+
+ checklistItemText.appendChild(deviation_block);
+ checklistItemLI.appendChild(checklistItemText);
+ }
+
+ } else {
+ if (role == "\"author\"") {
+ var userInputYes;
+ location_container = document.createElement("span");
+ location_container.className = "location_container";
+
+ userInputYes = generate_location_textbox("item_location_textbox", checklistItem_id);
+
+ var userInputNo;
+ missing_container = document.createElement("span");
+
+ userInputNo = document.createElement("input");
+ userInputNo.type = "checkbox";
+ userInputNo.id = "missing_checkbox:" + checklistItem_id;
+ userInputNo.className = "missing_checkbox";
+ userInputNo.name = checklistItem_id;
+ userInputNo.onclick = show_hide_location_textbox;
+ userInputNo.value = line_text;
+
+ checklistItemLI.appendChild(checklistItemText);
+
+ location_container.appendChild(userInputYes);
+ checklistItemLI.appendChild(location_container);
+
+ missing_container.appendChild(userInputNo);
+ checklistItemLI.appendChild(missing_container);
+ } else {
+ var checkboxInput = document.createElement("input");
+ checkboxInput.type = "checkbox";
+ checkboxInput.id = checklistItem_id;
+ checkboxInput.className = "checkbox_attributes";
+ checkboxInput.name = checklistItem_id;
+ checkboxInput.value = line_text;
+ checklistItemLI.appendChild(checkboxInput);
+ checklistItemLI.appendChild(checklistItemText);
+ }
+ }
+
+ checklists.appendChild(checklistItemLI);
+ }
+ }
+ return checklists;
+}
+
+// A function to process the Encoding method of the contents to create a unique key for every single checklist
+function Encode_key(content) {
+ console.log(content);
+ // process the conentes within and
+ content = content.replace(/]*>|<\/a>/g, '');
+ // process the footnote issue
+ content = content.replace(/\{sup\}.*?\{\/sup\}/g, '');
+ // now remove all the non-alphabetic and non-numeric characters
+ content = content.replace(/[^a-zA-Z0-9]/g, '');
+ return content;
+}
\ No newline at end of file
diff --git a/form_generator/js/UIInteractionHandlers.js b/form_generator/js/UIInteractionHandlers.js
new file mode 100644
index 0000000..c1cb5a6
--- /dev/null
+++ b/form_generator/js/UIInteractionHandlers.js
@@ -0,0 +1,360 @@
+// This function is primarily responsible for controlling the displaying of the deviation blocks in the checklist.
+function generate_decision_message_block() {
+
+ var checklist_yes_not_checked_count;
+ var checklist_no_checked_count;
+
+ // Number of yes's that are not checked and nos checked
+ if (role != "\"author\"") {
+ checklist_yes_not_checked_count = $('input[class="checklistRadioYes"][type="radio"][value="yes"]').not(':checked').length;
+ checklist_no_checked_count = $('input[class="checklistRadioNo"][type="radio"][value="no"]:checked').length;
+ }
+
+ // Second level yes
+ deviation_yes_checked_count = $('input[class="deviationRadioYes"][type="radio"][value="yes"]:checked').length;
+
+ // Second level no
+ deviation_no_checked_count = $('input[class="deviationRadioNo"][type="radio"][value="no"]:checked').length;
+
+ console.log("Test: " + checklist_yes_not_checked_count + " yeses not counted; " + checklist_no_checked_count + " nos counted; " + deviation_yes_checked_count + " deviation yeses counted; " + deviation_no_checked_count + " deviation nos counted");
+
+ // Count the number of types (type1, type2, type3, type4)
+ justification_type1_checked_count = $('input[class="justificationRadioType"][type="radio"][value="type1"]:checked').length;
+ justification_type2_checked_count = $('input[class="justificationRadioType"][type="radio"][value="type2"]:checked').length;
+ justification_type3_checked_count = $('input[class="justificationRadioType"][type="radio"][value="type3"]:checked').length;
+ justification_type4_checked_count = $('input[class="justificationRadioType"][type="radio"][value="type4"]:checked').length;
+
+ var msg = "";
+
+ // FOR SAVING THE FILE
+ // Making sure every attribute has an option selected.
+ if (role == "\"one-phase-reviewer\"") {
+
+ document.getElementById("deviation_reasonable").style.display = "none";
+ document.getElementById("deviation_unreasonable").style.display = "none";
+ document.getElementById("Desirable").style.display = "none";
+ document.getElementById("Extraordinary").style.display = "none";
+ $('.checkbox_attributes').prop('checked', false);
+
+ console.log("checklist_yes_not_checked_count: ", checklist_yes_not_checked_count);
+ console.log("checklist_no_checked_count: ", checklist_no_checked_count);
+ console.log("deviation_yes_checked_count: ", deviation_yes_checked_count);
+ if (checklist_yes_not_checked_count == checklist_no_checked_count & checklist_no_checked_count == (deviation_yes_checked_count + justification_type1_checked_count + justification_type2_checked_count + justification_type3_checked_count + justification_type4_checked_count)) {
+
+ // if number of type 3 + type 4 is greater than 0
+ if (justification_type3_checked_count + justification_type4_checked_count + justification_type2_checked_count > 0) {
+ msg = "REJECT";
+ document.getElementById("deviation_unreasonable").style.display = "block";
+
+ // if number of type 1 is greater than 0
+ } else if (justification_type1_checked_count > 0) {
+ msg = "ACCEPT";
+ document.getElementById("deviation_reasonable").style.display = "block";
+ document.getElementById("Desirable").style.display = "block";
+ document.getElementById("Extraordinary").style.display = "block";
+ } else {
+ msg = "ACCEPT";
+ document.getElementById("Desirable").style.display = "block";
+ document.getElementById("Extraordinary").style.display = "block";
+ }
+
+ } else {
+ document.getElementById("decision_msg").style.display = "none";
+ }
+ } else if (role == "\"two-phase-reviewer\"") {
+ document.getElementById("deviation_reasonable").style.display = "none";
+ document.getElementById("deviation_unreasonable").style.display = "none";
+ document.getElementById("Desirable").style.display = "none";
+ document.getElementById("Extraordinary").style.display = "none";
+ $('.checkbox_attributes').prop('checked', false);
+
+ if (checklist_yes_not_checked_count == checklist_no_checked_count & checklist_no_checked_count == (deviation_yes_checked_count + justification_type1_checked_count + justification_type2_checked_count + justification_type3_checked_count + justification_type4_checked_count)) {
+
+ // if number of type 4 is greater than 0
+ if (justification_type4_checked_count > 0) {
+
+ msg = "REJECT";
+ document.getElementById("deviation_unreasonable").style.display = "block";
+
+ // if number of type 3 is greater than 0
+ } else if (justification_type3_checked_count > 0) {
+ msg = "REJECT BUT INVITE RESUBMISSION";
+ document.getElementById("deviation_unreasonable").style.display = "block";
+
+ // if number of type 2 is greater than 0
+ } else if (justification_type2_checked_count > 0) {
+ msg = "MAJOR REVISION";
+ document.getElementById("deviation_reasonable").style.display = "block";
+ document.getElementById("Desirable").style.display = "block";
+ document.getElementById("Extraordinary").style.display = "block";
+
+ // if number of type 1 is greater than 0
+ } else if (justification_type1_checked_count > 0) {
+ msg = "MINOR REVISION";
+ document.getElementById("deviation_reasonable").style.display = "block";
+ document.getElementById("Desirable").style.display = "block";
+ document.getElementById("Extraordinary").style.display = "block";
+
+ // ELSE: ACCEPT
+ } else {
+ msg = "ACCEPT";
+ document.getElementById("Desirable").style.display = "block";
+ document.getElementById("Extraordinary").style.display = "block";
+ }
+
+ document.getElementById("decision_msg").innerHTML = msg;
+ document.getElementById("decision_msg").style.display = "block";
+ } else {
+ document.getElementById("decision_msg").style.display = "none";
+ }
+
+ }
+}
+
+// Determine whether to show or hide the primary location textbox
+function show_hide_location_textbox() {
+ id = this.id;
+ console.log(id);
+
+ var missing_checkbox = document.getElementById(id);
+ console.log(missing_checkbox);
+
+ if (missing_checkbox.checked) {
+ console.log("Missing checked");
+ show_deviation_block_and_hide_location_textbox();
+ } else {
+ console.log("Missing unchecked");
+ hide_deviation_block_and_show_location_textbox();
+ }
+}
+
+//this function manages the display of the deviation block, which is dependent upon user input
+function show_deviation_block_and_hide_location_textbox() {
+
+ // Replace ID from Yes to an empty string
+ if (role == "\"author\"") {
+ id = this.id.replace("missing_checkbox:", "");
+
+ var item_location_textbox = document.getElementById("item_location_textbox:" + id);
+ item_location_textbox.style.visibility = "hidden";
+ item_location_textbox.value = "";
+
+ } else {
+ id = this.id.replace("checklist-radio:No:", "")
+ }
+
+ var deviation_block = document.getElementById("deviation_block:" + id);
+ if (deviation_block) {
+ deviation_block.style.display = (role == "\"author\"") ? "flex" : "block";
+ deviation_block.style.flexFlow = "wrap";
+ }
+
+ let deviationRadioYes = document.getElementById("deviation_block-radio:Yes:" + id);
+ if (deviationRadioYes && deviationRadioYes.disabled) {
+ let deviationRadioNo = document.getElementById("deviation_block-radio:No:" + id);
+ deviationRadioNo.click();
+ create_deviation_justification_block_and_show_hide_justification_location_textbox.call(deviationRadioNo);
+ }
+ //This function is primarily responsible for controlling the displaying of the deviation blocks in the checklist.
+ generate_decision_message_block();
+}
+
+//this function manages the display of the deviation block, which is dependent upon user input
+function hide_deviation_block_and_show_location_textbox() {
+
+ // Replace ID from Yes to an empty string
+ if (role == "\"author\"") {
+ id = this.id.replace("missing_checkbox:", "");
+ id = this.id.replace("item_location_textbox:", "");
+ console.log(id);
+
+ var item_location_textbox = document.getElementById("item_location_textbox:" + id);
+ item_location_textbox.style.visibility = "visible";
+
+ } else {
+ id = this.id.replace("checklist-radio:Yes:", "");
+ }
+ hide_other_messages(id);
+
+ // Hide all Deviation Blocks
+ var block = document.getElementById("deviation_block:" + id);
+ block.style.display = "none";
+ var block = document.getElementById("deviation_justified:" + id);
+ block.style.display = "none";
+ var block = document.getElementById("deviation_not_justified:" + id);
+ block.style.display = "none";
+
+ if (role != "\"author\"") {
+ var msg_block = document.getElementById("free_text_question:" + id);
+ msg_block.style.display = "none";
+ var no_radio = document.getElementById("checklist-radio:No:" + id);
+ no_radio.checked = false;
+ } else {
+ var missing_checkbox = document.getElementById("missing_checkbox:" + id);
+ missing_checkbox.checked = false;
+
+ var justification_box = document.getElementById("justification_location_textbox:" + id);
+ justification_box.value = "";
+ }
+
+ // Uncheck all deviation-block-radio
+ for (let i = 0; i < document.getElementsByName("deviation_block-radio:" + id).length; i++) {
+ document.getElementsByName("deviation_block-radio:" + id)[i].checked = false;
+ }
+
+ // Uncheck all deviation-justified-radio
+ for (let i = 0; i < document.getElementsByName("deviation_block-radio:" + id).length; i++) {
+ document.getElementsByName("deviation_block-radio:" + id)[i].checked = false;
+ }
+
+ // Uncheck all deviation-not-justified-radio
+ for (let i = 0; i < document.getElementsByName("deviation_block-radio:" + id).length; i++) {
+ document.getElementsByName("deviation_block-radio:" + id)[i].checked = false;
+ }
+
+ //This function is primarily responsible for controlling the displaying of the deviation blocks in the checklist.
+ generate_decision_message_block();
+}
+
+
+//this function creates a deviation block for all Essential items in the standards
+function create_deviation_justification_block_and_show_hide_justification_location_textbox() {
+ // (No-Yes) deviation is justified
+ console.log(this);
+ if (this.id.includes("deviation_block-radio:Yes:")) {
+ id = this.id.replace("deviation_block-radio:Yes:", "")
+ hide_other_messages(id);
+ var block = document.getElementById("deviation_not_justified:" + id);
+ block.style.display = "none";
+ var block = document.getElementById("deviation_justified:" + id);
+ block.style.display = "block";
+
+ if (role != "\"author\"") {
+ var msg_block = document.getElementById("free_text_question:" + id);
+ msg_block.style.display = "none";
+ }
+
+ deviation_radio_name = this.name.replace("deviation_block-radio", "deviation_not_justified-radio");
+
+ for (let i = 0; i < document.getElementsByName(deviation_radio_name).length; i++) {
+ document.getElementsByName(deviation_radio_name)[i].checked = false;
+ }
+
+ }
+ // (No-No) deviation is unjustified (reviewer)
+ else if (this.id.includes("deviation_block-radio:No:")) {
+ id = this.id.replace("deviation_block-radio:No:", "")
+ hide_other_messages(id);
+ var empty_message = document.getElementById("deviation_justified:" + id);
+ empty_message.style.display = "none";
+ var message = document.getElementById("deviation_not_justified:" + id);
+ message.style.display = "block";
+ var msg_block = document.getElementById("free_text_question:" + id);
+ msg_block.style.display = "block";
+
+ deviation_radio_name = this.name.replace("deviation_block-radio", "deviation_justified-radio");
+
+ for (let i = 0; i < document.getElementsByName(deviation_radio_name).length; i++) {
+ document.getElementsByName(deviation_radio_name)[i].checked = false;
+ }
+
+ // (No-No) deviation is unjustified (author)
+ } else if (this.id.includes("unjustified_checkbox:")) {
+ id = this.id.replace("unjustified_checkbox:", "")
+ hide_other_messages(id);
+ var empty_message = document.getElementById("deviation_justified:" + id);
+ empty_message.style.display = "none";
+ var message = document.getElementById("deviation_not_justified:" + id);
+
+ var justification_box = document.getElementById("justification_location_textbox:" + id);
+ var unjustified_checkbox = document.getElementById("unjustified_checkbox:" + id);
+
+ if (unjustified_checkbox.checked) {
+ message.style.display = "inline";
+ justification_box.style.visibility = "hidden";
+ justification_box.value = "";
+ } else {
+ message.style.display = "none";
+ justification_box.style.visibility = "visible";
+ }
+
+ } else {
+ // (No-Yes-Yes) => deviation is justified and justification is reasonable
+ if (this.id.includes("deviation_justified-radio:Yes:")) {
+ id = this.id.replace("deviation_justified-radio:Yes:", "")
+ hide_other_messages(id);
+ var message = document.getElementById("justification_reasonable:" + id);
+ message.style.display = "block";
+ }
+ // (No-Yes-No) => deviation is justified but justification is unreasonable
+ else if (this.id.includes("deviation_justified-radio:No:")) {
+ id = this.id.replace("deviation_justified-radio:No:", "")
+ hide_other_messages(id);
+ var message = document.getElementById("justification_unreasonable:" + id);
+ message.style.display = "block";
+ }
+ // (No-No-Yes) => deviation is unjustified but reasonable
+ else if (this.id.includes("deviation_not_justified-radio:Yes:")) {
+ id = this.id.replace("deviation_not_justified-radio:Yes:", "")
+ hide_other_messages(id);
+ var message = document.getElementById("deviation_reasonable:" + id);
+ message.style.display = "block";
+ }
+ // (No-No-No) => deviation is unjustified and unreasonable
+ else if (this.id.includes("deviation_not_justified-radio:No:")) {
+ id = this.id.replace("deviation_not_justified-radio:No:", "")
+ hide_other_messages(id);
+ document.getElementById("deviation_unreasonable:" + id).style.display = "block";
+ }
+ }
+
+ //This function is primarily responsible for controlling the displaying of the deviation blocks in the checklist.
+ generate_decision_message_block();
+}
+
+//this function is responsible for hiding all messages displayed as a result of selecting 'No'
+function hide_other_messages(id) {
+ try {
+ document.getElementById("deviation_reasonable:" + id).style.display = "none";
+ document.getElementById("deviation_unreasonable:" + id).style.display = "none";
+ document.getElementById("justification_reasonable:" + id).style.display = "none";
+ document.getElementById("justification_unreasonable:" + id).style.display = "none";
+ document.getElementById("free_text_question:" + id).style.display = "none";
+ }
+ catch (err) { }
+}
+
+//This function creates tooltips for text
+//Anything between / and / is known as regular expressions
+function createTooltip(checklistItemText, line_text, footnotes) {
+ footnote_sups = line_text.match(/(.*?)\{sup\}(.+?)\{\/sup\}(.*?)/g);
+ if (footnote_sups) {
+ footnote_rest = line_text.match(/(?!.*\})(.*?)$/g);
+ footnote_rest = footnote_rest.filter(function (el) {
+ return el.trim() != "";
+ });
+ checklistItemText.innerHTML = checklistItemText.innerHTML.replace(" ", "");
+ var allTooltipsText = checklistItemText;
+ var i = 0;
+ for (let footnote_sup of footnote_sups) {
+ i++;
+ ftnt = footnote_sup.match(/(.*?)\{sup\}(.*?)\{\/sup\}(.*?)/);
+ var tooltip = document.createElement("span");
+ tooltip.className = "tooltip";
+ tooltip.innerHTML = ftnt[1].trim();
+
+ var tooltipText = document.createElement("span");
+ tooltipText.className = "tooltiptext";
+ tooltipText.innerHTML = convert_MD_tags_to_HTML_tags(footnotes[ftnt[2]]);
+ tooltip.appendChild(tooltipText);
+ allTooltipsText.appendChild(tooltip);
+ }
+ if (footnote_rest.length > 0) {
+ var tooltip = document.createElement("span");
+ tooltip.innerHTML = footnote_rest[0].trim();
+ allTooltipsText.appendChild(tooltip);
+ }
+ return allTooltipsText;
+ }
+ return checklistItemText;
+}
\ No newline at end of file
diff --git a/form_generator/js/Utilities.js b/form_generator/js/Utilities.js
new file mode 100644
index 0000000..a8b8038
--- /dev/null
+++ b/form_generator/js/Utilities.js
@@ -0,0 +1,107 @@
+// Function to convert Markdown tables to HTML tables
+function convertMarkdownToHTML(markdown) {
+ var lines = markdown.trim().split('\n');
+ var resultHTML = '