Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div[class*="filterpanel-header"]',
- placement: 'left',
- arrowOffset: 'center',
- title: 'The Active filters pane tracks data during your session',
- content: 'The Active filters pane gives you a summary of the data being explored during your session and provides you with important context for selecting and interpreting the data.',
- yOffset: -17
- },{
- target: 'div[class*="status-row info_Subject hl-status-row nolink"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'When you begin a new session, you start off with all the subjects and data in DataSpace, so you\'ll need to filter down to the data you want to explore. Filters can be applied in the Active filters pane, and in any section of the DataSpace where you explore subject data (i.e. in Find subjects, Plot data, and View data grid).
Note the number of subjects in the data.',
- yOffset: 10
- },{
- target: 'div[class*="info_Species"]',
- placement: 'left',
- arrowOffset: 'center',
- title: 'Filtering data using the Active filters pane',
- content: 'In the Active filter pane, you can filter the data for subjects with specific subject characteristics (such as species), subjects from specific studies, or subjects who received specific products or treatments.',
- yOffset: -17,
- onNext: function(){
- checkTarget('div[class*="status-row info_Species"]');
- }
- },{
- target: 'div[class*="status-row info_Species"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'As an example, when we click on the species category \...',
- yOffset: -8,
- onNext: function(){
- document.querySelector('.info_Species > li:nth-child(1) > span:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('div[title="Human"]') !== null){
- document.querySelector('div[title="Human"]').click();
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'div[title="Human"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'We see the types of species represented in the data. We can select just one species and click the filter button to apply the filter.',
- xOffset: -30,
- yOffset: -55,
- onNext: function(){
- document.querySelector('a[class*="x-btn filterinfoaction x-unselectable"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('div[class="x-container filterstatus-content x-container-default"]') !== null){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'div[class*="x-container filterstatus-content x-container-default"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'We can see that our filter has been applied.',
- yOffset: -17
- },{
- target: '.info_Species > li:nth-child(1) > span:nth-child(1)',
- placement: 'left',
- arrowOffset: 'center',
- content: 'We can also see that the number of subjects, studies, products, and treatments has decreased.',
- yOffset: -17,
- onNext: function(){
- document.querySelector('.info_Species > li:nth-child(1) > span:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('span[class*="sorter-content"]') !== null){
- document.querySelector('span[class*="sorter-content"]').click();
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'span[class*="sorter-content"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'Each category has multiple related fields that can be filtered. To see the other fields available, click on the red arrow next to the category to expand the list. In this case, there are other subject characteristics to choose from.',
- yOffset: -17,
- onNext: function(){
- document.querySelector('a[class*="x-btn filterinfocancel x-unselectable"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('.info_Study > li:nth-child(1) > span:nth-child(1)') !== null){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: '.info_Study > li:nth-child(1) > span:nth-child(1)',
- placement: 'left',
- arrowOffset: 'center',
- content: 'Once you have applied one or more filters, if we click on the Studies row...',
- yOffset: -40,
- onNext: function(){
- document.querySelector('.info_Study > li:nth-child(1)').click();
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="x-grid-group-title"]'), "Has data in active filters");
- if(document.querySelector('span[class*="sorter-content"]') !== null &&
- isVisCoords(document.querySelector('span[class*="sorter-content"]')) &&
- nodes.length > 0){
- nodes[0].classList.add("has-data-header");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('div[class*="has-data-header"]') !== null){
- clearInterval(checkExist2);
- checkTarget('div[class*="has-data-header"]');
- }
- }, 100);
-
- },
- multipage: true
- },{
- target: 'div[class*="has-data-header"]',
- placement: 'left',
- arrowOffset: 'center',
- yOffset: -60,
- content: 'The studies will be listed under \'Has data in active filters\' and \'No data in active filters\' to indicate if any subjects in that study meet the filter criteria.',
- onNext: function(){
- // Need to handle what if there are two of these?
- // document.querySelectorAll('div[class*="infopane"]')
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- },{
- target: 'div[title*="CAVD 256"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'Hover over one of the studies to see the red info link to the study page.',
- xOffset: -30,
- onNext: function(){
- document.querySelector('a[class*="x-btn filterinfocancel x-unselectable"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('span[class*="closeitem"]') !== null){
- document.querySelector('span[class*="closeitem"]').style.display = 'block';
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'span[class*="closeitem"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'You can remove a filter by clicking the red ❌ in the corner of the filter box. The Clear button removes all filters. Click the Save button to save your filters for further exploration in a future session.',
- xOffset: -200,
- yOffset: -50,
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- var node = document.querySelector('h3[class*="tour-section-title"]');
- if(node !== null && isVisCoords(node)){
- checkTarget('h3[class*="tour-section-title"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_find_subjects.js b/resources/cds-tours/definitions/tour_find_subjects.js
deleted file mode 100644
index f6df9f6e8..000000000
--- a/resources/cds-tours/definitions/tour_find_subjects.js
+++ /dev/null
@@ -1,336 +0,0 @@
-var tour_find_subjects = {
- title: 'Find-subjects',
- description: 'A tour for the "Find subjects" section.',
- id: 'tour-find-subjects',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 0){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
- var nodes = null;
- var promise = new Promise(function(resolve, reject){
- nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear"));
- if(nodes.length > 0){
- resolve();
- } else {
- document.querySelector('div.nav-label:nth-child(1)').click();
- reject();
- }
- }).then(function(result){
- nodes[0].click();
- }).then(function(result){
- document.querySelector('div.nav-label:nth-child(1)').click();
- });
- },
-
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'Find subjects',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.
Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(3)',
- placement: 'left',
- title: 'Finding subjects and studies of interest',
- content: 'The Find subjects section helps you find subjects with common characteristics. You can also use it to profile the subject characteristics of a specific study or set of studies.',
- yOffset: -17,
- onNext: function() {
- document.querySelector('div.nav-label:nth-child(3) > span:nth-child(2)').click();
- var checkExist = setInterval(
- function() {
- if (
- nodeDisplaySearch(document.querySelectorAll('div[id*=summarydataview]')).length > 0 &&
- nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[class*="label"]'), " Subject characteristics")).length > 0
- ) {
- window.location = 'cds-app.view?#summary';
- checkTarget('div[id*=summarydataview]');
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'div[id*=summarydataview]',
- placement: 'top',
- arrowOffset: 'center',
- xOffset: 70,
- content: 'Here you see a set of parameters we can use to search for subjects and studies.',
- onNext: function(){
- document.querySelector('div[id*=summarydataview]').firstChild.nextSibling.classList.add("by-products-row");
- var checkExist = setInterval(
- function(){
- if(document.querySelector('div[class*="by-products-row"]') !== null){
- checkTarget('div.row:nth-child(2)');
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'div.row:nth-child(2)',
- placement: 'top',
- arrowOffset: 'center',
- xOffset: 70,
- content: 'Clicking the "Products" row will let you find the products for which there is data available in DataSpace.',
- onNext: function(){
- document.querySelector("div.row:nth-child(2)").click();
- var checkExist = setInterval(
- function(){
- if (document.querySelector('#sae-hierarchy-dropdown') !== null && document.querySelectorAll('span[class="parrow"]') !== null) {
- document.querySelector('#sae-hierarchy-dropdown').click();
- checkTarget('span[class="parrow"]');
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'span[class="parrow"]',
- placement: 'top',
- arrowOffset: 'left',
- xOffset: -20,
- content: 'Each category has other related categories that can be viewed. When you click on the red arrow next to the category, it expands the list',
- onNext: function(){
- document.querySelector('div[class*="x-container titlepanel secondary"]').click();
- checkTarget('.bargroup');
- }, multipage: true
-
- },{
- target: '.bargroup',
- placement: 'top',
- arrowOffset: 'left',
- xOffset: 70,
- content: 'This column shows the products by name.',
- onNext: function(){
- function nodeSearch(nodeList, strVal){
- for(i = 0; i < bars.length; i++){
- if(bars[i].innerHTML === strVal){
- bars[i].nextSibling.nextSibling.classList.add('index-selected', 'inactive');
- return(bars[i]);
- }
- }
- return("none found");
- }
- var bars = document.querySelectorAll('span[class="barlabel"]');
- var topElem = nodeSearch(bars, "AIDSVAX B/E");
- var botElem = nodeSearch(bars, "ALVAC (vCP1521)");
- nodeSearch(bars, "Alum");
- topElem.classList.add('bubblePoint');
- botElem.scrollIntoView(alignToTop = false);
- var checkExist = setInterval(
- function(){
- if(document.querySelector('span[class*="bubblePoint"]') !== null){
- checkTarget('span[class*="bubblePoint"]');
- clearInterval(checkExist);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="bubblePoint"]',
- placement: 'top',
- arrowOffset: 'left',
- xOffset: 70,
- content: 'Find a product of interest. When hovering over the text, teal indicates other products that have been administered with this product.',
- onNext: function(){
- var bars = document.querySelectorAll('span[class="barlabel"]');
- var botElem = nodeTextSearch(bars, "ALVAC (vCP1521)")[0];
- var checkExist = setInterval(
- function(){
- if(nodeTextSearch(bars, "ALVAC (vCP1521)").length > 0){
- nodeTextSearch(bars, "ALVAC (vCP1521)")[0].click();
- checkTarget('h2[class*="filterheader-text"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
- },{
- target: 'h2[class*="filterheader-text"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: 0,
- content: 'Clicking on a product will select that product. The Active filters show the impact of that selection on your data filters prior to applying the filter. The counts in teal show how many subjects received this product.',
- },{
- target: 'a[class="x-btn x-unselectable x-btn-toolbar x-box-item x-toolbar-item x-btn-rounded-inverted-accent-toolbar-small x-noicon x-btn-noicon x-btn-rounded-inverted-accent-toolbar-small-noicon"]',
- placement: 'bottom',
- arrowOffset: '250',
- xOffset: -250,
- content: 'Clicking the Filter button applies the filter to the data in your session.',
- onNext: function(){
- document.getElementsByClassName('x-btn x-unselectable x-btn-toolbar x-box-item x-toolbar-item x-btn-rounded-inverted-accent-toolbar-small x-noicon x-btn-noicon x-btn-rounded-inverted-accent-toolbar-small-noicon')[0].click();
- var checkExist = setInterval(
- function(){
- if (false){
- checkTarget('ul[class="detailstatus"]');
- }
- }, 100);
- }
- },{
- target: 'ul[class="detailstatus"]',
- placement: 'left',
- arrowOffset: '0',
- xOffset: 0,
- yOffset: 30,
- content: 'The total number of subjects has been reduced and a summary of those subjects is seen here.'
- },{
- target: 'h2[class*="filterheader-text"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: -45,
- content: 'You can save your filter or clear it by clicking the "clear" or "save" buttons.',
- onNext: function(){
-
- var hedr = document.querySelectorAll('h1[class*="lhdv"]');
- var shdr = nodeTextSearch(hedr, "Subject characteristics")[0];
- shdr.click();
- shdr.classList.add("find-subj-char");
-
- var checkExist = setInterval(
- function() {
- var node = document.querySelector('h1[class*="find-subj-char"]');
- if (
- node !== null &&
- node.className.match("active") !== null &&
- isVisCoords(node)
- ) {
- checkTarget('h1[class*="find-subj-char"]');
- clearInterval(checkExist);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'h1[class*="find-subj-char"]',
- placement: 'top',
- content: 'Looking at Subject characteristics...',
- yOffset: 20,
- onNext: function() {
- document.querySelector('span[class*="parrow"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('div[id*="boundlist"]').style.display !== "none") {
- var subj = document.querySelectorAll('li[class*="x-boundlist-item"]');
- var ages = nodeTextSearch(subj, "Age")[0];
- var spec = nodeTextSearch(subj, "Species")[0];
- ages.classList.add("x-boundlist-selected");
- spec.classList.remove("x-boundlist-selected");
- checkTarget('span[class*="parrow"]');
- clearInterval(checkExist);
- }
-
- }, 100);
- }, multipage: true
- },{
- target: 'span[class*="parrow"]',
- placement: 'top',
- content: 'Clicking Age...',
- yOffset: 0,
- xOffset: -20,
- onNext: function() {
- document.querySelector('span[class*="parrow"]').click();
- document.querySelector('li[class*="x-boundlist-selected"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelectorAll('div[class*="saeparent"]').length > 0) {
- document.querySelectorAll('div[class="saeparent"]')[3].firstChild.classList.add("age-elem");
- document.querySelector("div[class*='age-elem']").click();
- clearInterval(checkExist);
- checkTarget('div[class*="age-elem"]');
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'div[class*="age-elem"]',
- placement: 'top',
- arrowOffset: 'left',
- content: 'Now that you\'ve identified a group of subjects, we can look at their subject characteristics, e.g. by age category, by expanding with the plus sign.',
- xOffset: -20,
- onNext: function(){
-
- if(nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Hide empty")).length > 0) {
- var node = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Hide empty"))[0];
- } else {
- var node = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Show empty"))[0];
- }
- node.classList.add("hide-show-empty-btn");
- var checkExist = setInterval(
- function(){
- if(document.querySelector('span[class*="hide-show-empty-btn"]') !== null){
- checkTarget('span[class*="hide-show-empty-btn"]');
- clearInterval(checkExist);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="hide-show-empty-btn"]',
- placement: 'left',
- arrowOffset: 'center',
- yOffset: -53,
- content: 'Click on the Hide/Show empty button to remove categories that don\'t have subjects.',
- onNext: function(){
- document.querySelector('span[class*="hide-show-empty-btn"]').click();
- document.querySelector('div.nav-label:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- var node = document.querySelector('h3[class*="tour-section-title"]');
- if(node !== null && isVisCoords(node)){
- checkTarget('h3[class*="tour-section-title"]');
- clearInterval(checkExist);
- }
- }, 100);
-
- // document.querySelector('div.nav-label:nth-child(1)').click();
- // var checkExist = setInterval(
- // function(){
- // var node = document.querySelector('h3[class*="tour-section-title"]');
- // if(node !== null && isVisCoords(node)){
- // checkTarget('h3[class*="tour-section-title"]');
- // clearInterval(checkExist);
- // }
- // }, 100);
-
- }, multipage: true
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_get_oriented.js b/resources/cds-tours/definitions/tour_get_oriented.js
deleted file mode 100644
index 146873d68..000000000
--- a/resources/cds-tours/definitions/tour_get_oriented.js
+++ /dev/null
@@ -1,203 +0,0 @@
-var tour_get_oriented = {
- title: 'Get-oriented',
- description: 'A tour for getting oriented with DataSpace.',
- id: 'tour-get-oriented',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 1){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
- },
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'Get oriented to the DataSpace',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(1)',
- placement: 'left',
- title: 'Getting around the DataSpace',
- content: 'Let\'s take a look at the main areas of the DataSpace.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(2)',
- placement: 'left',
- title: 'Learn about',
- content: 'The Learn about section is where you\'ll find information about the studies conducted by the research networks, and the products, assays, and antibodies being evaluated in those studies. You can also search for publications and view reports from those studies.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(3)',
- placement: 'left',
- title: 'Subject data',
- content: 'The Find subjects, Plot data, and View data grid sections are where you can explore the study subject data.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(3)',
- placement: 'left',
- title: 'Find subjects',
- content: 'The Find subjects section helps you find subjects with common characteristics. You can also use it to profile the subject characteristics of a specific study or set of studies.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(4)',
- placement: 'left',
- title: 'Plot data',
- content: 'The Plot data section is where you can explore the subject data using simple plots that allow you to compare the data across studies and assays.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(5)',
- placement: 'left',
- title: 'View data grid',
- content: 'The View data grid section let\'s you explore the subject data in a spreadsheet format. From this section, you can export the subject data for further exploration in your own analysis tools.',
- yOffset: -17
- },{
- target: 'div.nav-label:nth-child(6)',
- placement: 'left',
- title: 'Monoclonal antibodies',
- content: 'The Monoclonal antibodies section is where you can explore data from monoclonal antibody characterization studies. In this section, you can search for antibodies and compare the neutralization curves and heatmaps for different antibody-virus combinations.',
- yOffset: -17
- },{
- target: 'div[class*="filterpanel-header"]',
- placement: 'left',
- title: 'Active filters',
- content: 'The Active filter pane gives you a summary of the data being explored during your session and provides you with important context for selecting and interpreting the data.',
- yOffset: -17,
- onNext: function(){
-
- function getScrollParent(node) {
- if (node == null) {
- return null;
- } else if (node.style.overflow == "hidden auto") {
- return node;
- } else {
- return getScrollParent(node.parentNode);
- }
- }
-
- nodeTextSearch(document.querySelectorAll('h2[class*="section-title"]'), "Groups and plots")[0].classList.add("groups-plots");
- getScrollParent(nodeTextSearch(document.querySelectorAll('h3'), "Explore relationships")[0]).classList.add("quick-link-scroll-frame");
- var smt = null;
-
- var checkExist_1 = setInterval(
- function(){
- var node = document.querySelector('h2[class*="groups-plots"]');
- if(node !== null){
- smt = Math.max(node.getBoundingClientRect().y - 200, 0);
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('div[class*="quick-link-scroll-frame"]');
- if(node !== null && smt !== null){
- node.scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="quick-link-scroll-frame"]');
- if(
- node !== null &&
- smt !== null &&
- (node.scrollTop === smt ||
- Math.abs((node.clientHeight + node.scrollTop) - node.scrollHeight) < 3)
- ){
- checkTarget('h2[class*="groups-plots"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'h2[class*="groups-plots"]',
- placement: 'top',
- arrowOffset: 'left',
- title: 'Curated groups and plots',
- content: 'This Saved groups and plots section on the Home page is where the DataSpace team shares plots and subject groups with all members. You can save your own groups here, too. Your groups will only be accessible to you.',
- yOffset: -17
- },{
- target: 'div[id*="cds-news"]',
- placement: 'top',
- arrowOffset: 'left',
- title: 'News',
- content: 'The News section on the Home page is where you\'ll find blogs about how other members have used the DataSpace. We\'ll also let you know about new data, new features, and collaboration opportunities.',
- yOffset: -17,
- onNext: function(){
-
- var smt = null;
-
- var checkExist_1 = setInterval(
- function(){
- var node = document.querySelector('h3[class*="tour-section-title"]');
- if(node !== null && smt === null){
- smt = Math.max(node.getBoundingClientRect().y - 300, 0);
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('div[class*="quick-link-scroll-frame"]');
- if(node !== null && smt !== null){
- node.scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="quick-link-scroll-frame"]');
- if(
- node !== null &&
- smt !== null &&
- (node.scrollTop === smt ||
- node.scrollTop === 0)
- ){
- checkTarget('h3[class*="tour-section-title"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_helpers.js b/resources/cds-tours/definitions/tour_helpers.js
deleted file mode 100644
index f0cdb7f8e..000000000
--- a/resources/cds-tours/definitions/tour_helpers.js
+++ /dev/null
@@ -1,98 +0,0 @@
-// Helper functions for DataSpace tours
-
-// searches innerHTML in node list for a given string
-//////////
-function nodeTextSearch(nodeList, strVal){
- if (nodeList.constructor.name === "String") {
- nodeList = document.querySelectorAll(nodeList);
- }
- var nodes = [];
- for(var i of nodeList){
- if(i.innerHTML === strVal){
- nodes.push(i);
- }
- }
- return(nodes);
-}
-// checks all nodes in a NodeList and return the first where display
-// does not equal none.
-//////////
-function nodeDisplaySearch(nodeList){
- var nodes = [];
- for(var i of nodeList){
- if(i.offsetParent !== null){
- nodes.push(i);
- }
- }
- return(nodes);
-}
-// checks which members of a node list have positive coordinates
-// would be nice if this was a part of display search
-//////////
-function nodePosCoordSearch(nodeList){
- var nodes = [];
- for(var i of nodeList){
- var bb = i.getBoundingClientRect();
- if(bb.x > 0 && bb.y > 0){
- nodes.push(i);
- }
- }
- return(nodes);
-}
-// checks if a given node has coordinates that are within the window.
-//////////
-function isVisCoords(node){
- var nod = node.getBoundingClientRect();
- var win = document.body.getBoundingClientRect();
- if(JSON.stringify(win) === JSON.stringify(nod) ||
- (nod.left >= win.left &&
- nod.top >= win.top &&
- nod.right < win.right &&
- nod.right > 0 &&
- nod.bottom < win.bottom &&
- nod.bottom > 0 &&
- node.offeseParent !== null)
- ){
- return(true);
- }
- return(false);
-}
-// returns how much to scroll by. will return values of zero when
-// scrolling not required.
-//////////
-function scrollAmount(node, amount = 60){
- var ndm = node.getBoundingClientRect();
- var bdm = document.body.getBoundingClientRect();
- var right = ndm.right + amount;
- var bottom = ndm.bottom + amount;
- var ret = { x: 0, y:0 };
-
- if( ndm.left < bdm.left ){
- ret.x = ndm.left - bdm.left;
- } else if( right > bdm.right ){
- ret.x = ndm.right - bdm.right;
- }
- if(ndm.top < bdm.top){
- ret.y = ndm.top - bdm.top;
- } else if( bottom > bdm.bottom ){
- ret.y = bottom - bdm.bottom;
- }
- return(ret);
-}
-
-// starts the next step of the tour if the next target is valid.
-//////////
-function checkTarget(target){
- var nod = document.querySelector(target);
- var xbd = window.innerWidth;
- var ybd = window.innerHeight;
-
- if ( nod !== null && nod.offsetParent !== null ) {
- var dim = nod.getBoundingClientRect();
- if ( dim.x >= 0 || dim.y >= 0 || dim.top > ybd || dim.left > xbd ) {
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- } else {
- window.hopscotch.endTour();
- }
-}
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_learn_about.js b/resources/cds-tours/definitions/tour_learn_about.js
deleted file mode 100644
index 8bb63891b..000000000
--- a/resources/cds-tours/definitions/tour_learn_about.js
+++ /dev/null
@@ -1,858 +0,0 @@
-var tour_learn_about = {
- title: 'Learn-about',
- description: 'A tour for the "Learn about" section.',
- id: 'tour-learn-about',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 0){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
- self.started = 0;
- document.querySelector('div.nav-label:nth-child(1)').click();
- var node = null;
- var promise = new Promise(function(resolve, reject) {
- node = document.querySelector('input[class*="search-studies"]');
- if(node !== null){
- resolve();
- }
- }).then(function(result) {
- node.value = "";
- if(node.value === ""){
-
- }
- }).then(function(result) {
- var event = new Event("change");
- node.dispatchEvent(event);
-
- });
-
- },
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'Learn about',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.
Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(2) > span:nth-child(2)',
- placement: 'left',
- title: 'Finding information in Learn about',
- content: 'The Learn about section is where you\'ll find information about the studies conducted by the research networks, and the products, assays, and antibodies being evaluated in those studies.',
- yOffset: -17,
- onNext: function() {
- document.querySelector('div.nav-label:nth-child(2) > span:nth-child(2)').click();
- var checkExist = setInterval(
- function() {
- if (document.querySelector('div[class*="learn-dim-selector"]') !== null &&
- document.querySelector('div[id*=learnheaderdataview]') !== null &&
- isVisCoords(document.querySelector('div[id*=learnheaderdataview]')) &&
- nodeDisplaySearch(document.querySelectorAll('td[class*=x-grid-cell]')).length > 0
- ) {
- window.location = 'cds-app.view?#learn/learn/Study';
- checkTarget('div[id*=learnheaderdataview]');
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'div[id*=learnheaderdataview]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: 64,
- yOffset: 25,
- title: 'Select a topic',
- content: 'In the Learn about section, there are 5 categories to explore -- Studies, Assays, Products, Monoclonal antibodies, Publications, and Reports.',
- onNext: function() {
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h1[class*="lhdv"]'), "Studies"));
- if(nodes.length > 0) {
- nodes[0].classList.add("learn-studies-tab");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('h1[class*="learn-studies-tab"]') !== null) {
- checkTarget('h1[class*="learn-studies-tab"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'h1[class*="learn-studies-tab"]',
- placement: 'bottom',
- arrowOffset: 'left',
- yOffset: 0,
- content: 'The Studies tab, contains a list of the studies conducted by the research networks contributing data and information to the DataSpace. Studies are listed by the network-assigned study number. Because not everyone is familiar with the study numbers, there are other ways to search for studies of interest. Each study in this view has a brief description and other summary information such as the study type, investigator, vaccine strategy used, products used, and study status.',
- onNext: function() {
- document.querySelector('div[id^="templatecolumn"][id*="-titleEl"]').classList.add("x-column-header-over");
- var checkExist = setInterval(
- function(){
- if(
- document.querySelector('div[id^="templatecolumn"][id*="-triggerEl"][class*="x-column-header-over"]') !== null
- ){
- checkTarget('div[id^="templatecolumn"][id*="-triggerEl"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
- },{
- target: 'div[id^="templatecolumn"][id*="-triggerEl"]',
- placement: 'top',
- title: 'Learn about - Studies',
- content: 'Use the column headers to sort and filter the list of studies.',
- xOffset: -20,
- onNext: function() {
- document.querySelector('div[id^="templatecolumn"][id*="-triggerEl"]').click();
- var checkExist = setInterval(
- function() {
- if (
- document.querySelector('a[class*="x-btn filter-btn x-unselectable x-box-item x-toolbar-item"]') !== null &&
- document.querySelectorAll('a[class*="x-btn filter-btn x-unselectable x-box-item x-toolbar-item"]').length === 3 &&
- document.querySelector('button[class*=sortDropdown][class*=ipdropdown]')
- ) {
- document.querySelector('div[id^="templatecolumn"][id*="-titleEl"]').classList.remove("x-column-header-over");
- document.querySelector('button[class*=sortDropdown][class*=ipdropdown]').click();
- checkTarget('button[class*=sortDropdown][class*=ipdropdown]');
- clearInterval(checkExist);
- }
- }, 100);
- },
- multipage: true
- },{
- target: 'button[class*=sortDropdown][class*=ipdropdown]',
- placement: 'top',
- content: 'Each column has 2 related fields that can be filtered. To see the other fields available, click on the red arrow next to the category to expand the list. In this case, you can choose to filter on study name or network.',
- placement: 'top',
- arrowOffset: 'right',
- yOffset: 0,
- xOffset: -15,
- onNext: function(){
-
- var checkExist_4 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[id*="menuitem"]'));
- if ( nodes.length > 0 ) {
- nodes[0].classList.add("search-by-menu-dropdown");
- clearInterval(checkExist_4);
- }
- }, 100);
-
- var checkExist_3 = setInterval(
- function(){
- var node = document.querySelector('div[class*="search-by-menu-dropdown"]');
- if ( node !== null ) {
- node.click();
- clearInterval(checkExist_3);
- }
- }, 100);
-
- var checkExist_2 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('a[class*="x-btn-custom-toolbar-small x-noicon x-btn-noicon"]'));
- if ( nodes.length > 0 ) {
- nodes[0].click();
- clearInterval(checkExist_2);
- }
- }, 100
- );
-
- var checkExist_1 = setInterval(
- function() {
- if(
- nodeDisplaySearch(document.querySelectorAll('div[class*=window-body-filterwindow]')).length === 0 &&
- nodeDisplaySearch(document.querySelectorAll('input')).length !== 0
- ){
- nodeDisplaySearch(document.querySelectorAll('input'))[0].classList.add("search-studies");
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('input[class*="search-studies"]');
- if(node !== null){
- node.value = "434";
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('input[class*="search-studies"]');
- var event = new Event("change");
- if(node !== null && node.value === "434"){
- node.dispatchEvent(event);
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var node1 = document.querySelector('tr[id*="gridview"][id*="record-cvd434"]');
- var node2 = document.querySelector('input[class*="search-studies"]');
- if(
- node1 !== null &&
- node2 !== null &&
- node1.nextSibling === null &&
- node1.previousSibling === null &&
- isVisCoords(node1) &&
- node2.value == "434"
- ){
- checkTarget('input[class*="search-studies"]');
- clearInterval(checkExist3);
- }
- },100);
-
- }, multipage: true
- },{
- target: 'input[class*="search-studies"]',
- placement: 'left',
- content: 'You can also use the search bar to find a specific study.',
- yOffset: -17,
- onNext: function(){
- var checkExist = setInterval(
- function() {
- if(
- document.querySelector('tr[id*="gridview"][id*="record-cvd434"]') !== null &&
- isVisCoords(document.querySelector('tr[id*="gridview"][id*="record-cvd434"]'))
- ){
- checkTarget('tr[id*="record-cvd434"]');
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
- },{
- target: 'tr[id*="record-cvd434"]',
- placement: 'top',
- arrowOffset: 'center',
- content: 'Clicking anywhere in the row takes you to the study page.',
- onNext: function(){
- document.querySelector('tr[id*="record-cvd434"]').click();
- var checkExist = setInterval(
- function() {
- if(document.querySelectorAll("div[class*='x-container modulecontainercolumn x-box-item']").length === 2){
- checkTarget('div[id*="app-module-studyheader"]');
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'div[id*="app-module-studyheader"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: -200,
- yOffset: -75,
- content: 'On the study pages, you\'ll find background information about the study, including the type of study, the species being studied, the grant under which it was conducted, as well as the study objectives, rationale, and methods. Treatment and assay schemas provide a summary view of vaccination administration and assay testing schedules.',
- onNext: function(){
-
- function getScrollParent(node) {
- if (node == null) {
- return null;
- }
- if (node.scrollHeight > node.clientHeight) {
- return node;
- } else {
- return getScrollParent(node.parentNode);
- }
- }
-
- var smt = null;
- var checkExist_2 = setInterval(
- function(){
- var nodes = nodeTextSearch('h3', "Findings");
- if(nodes.length > 0){
- nodes[0].classList.add("findings-header");
- clearInterval(checkExist_2);
- }
- }, 100);
-
- var checkExist_1 = setInterval(
- function(){
- var node = document.querySelector('h3[class*="findings-header"]');
- if(node !== null && smt === null){
- smt = Math.max(node.getBoundingClientRect().y - 300, 0);
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- if(document.querySelector('h3[class*="findings-header"]') !== null && smt !== null) {
- getScrollParent(document.querySelector('div[class="x-container auto-scroll-y x-container-default"]')).classList.add("find-scroll-frame");
- clearInterval(checkExist1);
- }
- }, 100);
-
- // if(smt + node.clientHeight > node.scrollHeight) smt = node.scrollHeight - node.clientHeight
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if(node !== null){
- node.scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if (
- node !== null && smt != null &&
- ( Math.abs(node.scrollTop - smt) < 3 ||
- Math.abs((node.clientHeight + node.scrollTop) - node.scrollHeight) < 3)
- ){
- checkTarget('h3[class*="findings-header"]');
- clearInterval(checkExist3);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'h3[class*="findings-header"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: -200,
- yOffset: -55,
- content: 'Completed studies include a summary of findings and links to publications.',
- onNext: function(){
-
- var snd = null;
- var smt = null;
- var checkExist1 = setInterval(
- function(){
- snd = document.querySelector('div[class*="find-scroll-frame"]');
- if( snd !== null ){
- smt = Math.max((snd.scrollTop + document.querySelector('div[id*="app-module-contactcds"]').getBoundingClientRect().y - 300), 0);
- document.querySelector('div[class*="find-scroll-frame"]').scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if (
- node !== null &&
- smt != null &&
- Math.abs(node.scrollTop - smt) < 3
- ) {
- checkTarget('div[id*="app-module-contactcds"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'div[id*="app-module-contactcds"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: -200,
- yOffset: -60,
- content: 'Additional resources and contact information are available for follow up questions.',
- },{
- target: 'div[id*="app-module-studyproducts"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: -200,
- yOffset: -60,
- content: 'Links to the Product pages in Learn about provide more information for the products tested in the study.',
- onNext: function(){
-
- var smt = Math.max(document.querySelector('div[id*="app-module-dataavailability"]').getBoundingClientRect().y - 300, 0);
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if(node !== null){
- document.querySelector('div[class*="find-scroll-frame"]').scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if(
- node !== null && smt != null &&
- ( Math.abs(node.scrollTop - smt) < 3 ||
- Math.floor(node.clientHeight + node.scrollTop) === Math.floor(node.scrollHeight) )
- ){
- checkTarget('div[id*="app-module-dataavailability"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[id*="app-module-dataavailability"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: -200,
- yOffset: -78,
- content: 'This section gives you a summary of the data collected during the study and whether the data is available via the DataSpace. Hover over the data type to get the status. Assays highlighted in red are links to the Assay pages in Learn about.',
- onNext: function(){
-
- var smt = null;
- var node = null;
- var checkExist1 = setInterval(
- function(){
- node = document.querySelector('div[class*="find-scroll-frame"]');
- smt = Math.max(document.querySelector('div[id*="app-module-studyreports"]').getBoundingClientRect().y - 100, 0);
- if(node !== null && smt !== null){
- node.scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if(
- node !== null && smt != null &&
- ( Math.abs(node.scrollTop - smt) < 3 ||
- Math.floor(node.clientHeight + node.scrollTop) === Math.floor(node.scrollHeight) )
- ){
- checkTarget('div[id*="app-module-studyreports"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'div[id*="app-module-studyreports"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: -200,
- yOffset: -60,
- content: 'Some studies have additional reports or presentations to summarize study findings.',
- onNext: function(){
-
- var smt = null;
- var node = null;
- var checkExist1 = setInterval(
- function(){
- node = document.querySelector('div[class*="find-scroll-frame"]');
- smt = Math.max(document.querySelector('.iarrow').getBoundingClientRect().y - 300, 0);
- if(node !== null && smt !== null){
- document.querySelector('div[class*="find-scroll-frame"]').scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="find-scroll-frame"]');
- if (
- node !== null && smt != null &&
- ( Math.abs(node.scrollTop - smt) < 3 ||
- Math.floor(node.clientHeight + node.scrollTop) === Math.floor(node.scrollHeight) )
- ){
- checkTarget('.iarrow');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: '.iarrow',
- placement: 'right',
- arrowOffset: 'top',
- content: 'Clicking this arrow sends the page back to Learn about.',
- onNext: function(){
-
- document.querySelector('.iarrow').click();
- var event = new Event("change");
-
- var ck1 = setInterval(
- function(){
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null){
- document.querySelector('input[id*=learn-search]').value = "";
- clearInterval(ck1);
- }
- }, 100);
-
- var ck2 = setInterval(
- function(){
- var event = new Event("change");
- var node = document.querySelector('input[id*="learn-search"]');
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null &&
- document.querySelector('input[id*=learn-search]').value === ""){
- document.querySelector('input[id*=learn-search]').dispatchEvent(event);
- clearInterval(ck2);
- }
- }, 100);
-
- var ck3 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('h1[class*="lhdv"][class*=active]'));
- if( nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h2'), 'CAVD 434')).length > 0 &&
- !isVisCoords(nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h2'), 'CAVD 434'))[0]) &&
- nodes.length > 0
- ){
- nodes[0].nextSibling.click();
- nodes[0].nextSibling.classList.add("learn-assay-tab");
- clearInterval(ck3);
- }
- }, 100);
-
- var ck5 = setInterval(
- function(){
- if(document.querySelector('h1[class*="learn-assay-tab"]') !== null){
- checkTarget('h1[class*="learn-assay-tab"]');
- clearInterval(ck5);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'h1[class*="learn-assay-tab"]',
- placement: 'right',
- arrowOffset: 'bottom',
- title: 'Learn about - Assays',
- content: 'Assay pages describe the assay methods and endpoints and show which studies have data for the assay. Each assay page contains assay dimensions and variable definitions to provide background on the assay data.',
- onNext: function(){
-
- var event = new Event("change");
- nodeDisplaySearch(document.querySelectorAll('h1[class*="lhdv"]'))[2].click();
-
- var checkExist1 = setInterval(
- function() {
- if(document.querySelector('input[placeholder*="Search products"]') !== null){
- var inbox = document.querySelector('input[placeholder*="Search products"]');
- inbox.value = "ALVAC";
- inbox.dispatchEvent(event);
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function() {
- if(nodeDisplaySearch(document.querySelectorAll('h2'))[1].innerHTML === "ALVAC (vCP1521)"){
- checkTarget('input[placeholder*="Search products"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
-
- }, multipage: true
-
- },{
- target: 'input[placeholder*="Search products"]',
- placement: 'left',
- arrowOffset: 'center',
- title: 'Learn about - Products',
- yOffset: -55,
- content: 'On the Products page, use the column filters or search bar to find specific products.',
- onNext: function(){
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('h2'), "ALVAC (vCP1521)");
- if(nodes.length > 0){
- nodes = nodeDisplaySearch(nodes);
- if(nodes.length > 0){
- nodes[0].classList.add("ALVACvCP15");
- clearInterval(checkExist1);
- }
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('h2[class*="ALVACvCP15"]') !== null &&
- isVisCoords(document.querySelector('h2[class*="ALVACvCP15"]'))){
- checkTarget('h2[class*="ALVACvCP15"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'h2[class*="ALVACvCP15"]',
- placement: 'top',
- arrowOffset: 'center',
- content: 'Clicking anywhere in the row takes you to the product page.',
- onNext: function(){
- document.querySelector('h2[class*="ALVACvCP15"]').click();
- var checkExist = setInterval(
- function() {
- if(document.querySelectorAll("div[class*='x-container modulecontainercolumn x-box-item']").length === 2){
- checkTarget('div[id*="app-module-productheader"]');
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
- },{
- target: 'div[id*="app-module-productheader"]',
- placement: 'top',
- arrowOffset: 'left',
- content: 'Get product details, see what studies used that product, and see what other products have been tested in combination with the product.',
- },{
- target: '.iarrow',
- placement: 'right',
- arrowOffset: 'top',
- content: 'Clicking this arrow sends the page back to Learn about.',
- onNext: function(){
-
- document.querySelector('.iarrow').click();
- var event = new Event("change");
-
- var ck1 = setInterval(
- function(){
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null){
- document.querySelector('input[id*=learn-search]').value = "";
- clearInterval(ck1);
- }
- }, 100);
-
- var ck2 = setInterval(
- function(){
- var event = new Event("change");
- var node = document.querySelector('input[id*="learn-search"]');
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null &&
- document.querySelector('input[id*=learn-search]').value === ""){
- document.querySelector('input[id*=learn-search]').dispatchEvent(event);
- clearInterval(ck2);
- }
- }, 100);
-
- var ck3 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('h1[class*="lhdv"][class*=active]'));
- if( nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h2'), 'ALVAC (vCP1521)')).length > 0 &&
- !isVisCoords(nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h2'), 'ALVAC (vCP1521)'))[0]) &&
- nodes.length > 0
- ){
- nodes[0].nextSibling.click();
- nodes[0].nextSibling.classList.add("learn-mab-tab");
- clearInterval(ck3);
- }
- }, 100);
-
- var ck5 = setInterval(
- function(){
- if(nodeDisplaySearch(document.querySelectorAll('input[id*="learn-search"]')).length > 0 &&
- document.querySelector('h1[class*="learn-mab-tab"][class*=active]') !== null &&
- document.querySelector('input[placeholder*="Search mabs"]') !== null){
- var inbox = document.querySelector('input[placeholder*="Search mabs"]');
- inbox.value = "PGT";
- inbox.dispatchEvent(event);
- clearInterval(ck5);
- }
- }, 100);
-
- var ck6 = setInterval(
- function(){
- if(document.querySelector('input[placeholder*="Search mabs"]') !== null &&
- document.querySelector('input[placeholder*="Search mabs"]').value === "PGT" &&
- nodeDisplaySearch(nodeTextSearch('h2', 'PGT121 + PGDM1400')).length > 0 &&
- isVisCoords(nodeDisplaySearch(nodeTextSearch('h2', 'PGT121 + PGDM1400'))[0])
- ){
- checkTarget('h1[class*="learn-mab-tab"]');
- clearInterval(ck6);
- }
- }, 100);
-
-
- }, multipage: true
-
- },{
- target: 'h1[class*="learn-mab-tab"]',
- placement: 'right',
- arrowOffset: 'top',
- title: 'Learn about - MAbs',
- content: 'On the MAbs page, use the column filters or search bar to find specific monoclonal antibodies.',
- onNext: function(){
-
- var promise = new Promise(function(resolve, reject){
- if(nodeDisplaySearch(nodeTextSearch('h2', 'PGT121 + PGDM1400')).length > 0){
- resolve();
- }
- }).then(function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('tr[id*="record-PGT121 + PGDM1400"]'));
- if( nodes.length > 0 &&
- isVisCoords(nodes[0])
- ){
- nodes[0].classList.add("record-pgt121-pgdm1400");
-
- }
- }).then(function(){
- if(document.querySelector('tr[class*="record-pgt121-pgdm1400"]') !== null){
- checkTarget('tr[class*="record-pgt121-pgdm1400"]');
-
- }
- });
-
- }, multipage: true
- },{
- target: 'tr[class*="record-pgt121-pgdm1400"]',
- placement: 'top',
- arrowOffset: 'center',
- title: 'Learn about - MAbs',
- content: 'Get details about monoclonal antibodies and see what studies tested them. For more details, follow the link to the Los Alamos National Lab antibody database.',
- onNext: function(){
-
- var event = new Event("change");
-
- var ck1 = setInterval(
- function(){
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null){
- document.querySelector('input[id*=learn-search]').value = "";
- clearInterval(ck1);
- }
- }, 100);
-
- var ck2 = setInterval(
- function(){
- var event = new Event("change");
- var node = document.querySelector('input[id*="learn-search"]');
- if(document.querySelector('input[id*=learn-search]').offsetParent !== null &&
- document.querySelector('div[id*="learnheader"]').offsetParent !== null &&
- document.querySelector('input[id*=learn-search]').value === ""){
- document.querySelector('input[id*=learn-search]').dispatchEvent(event);
- clearInterval(ck2);
- }
- }, 100);
-
- var ck3 = setInterval(
- function(){
- if( nodeDisplaySearch(document.querySelectorAll('tr[id*="record-PGT121 + PGDM1400"]')).length > 0 &&
- !isVisCoords(nodeDisplaySearch(document.querySelectorAll('tr[id*="record-PGT121 + PGDM1400"]'))[0])
- ){
- document.querySelector('h1[class*="learn-mab-tab"]').nextSibling.click();
- document.querySelector('h1[class*="learn-mab-tab"]').nextSibling.classList.add("learn-reports-tab");
- clearInterval(ck3);
- }
- }, 100);
-
- var checkExist = setInterval(
- function(){
- if(document.querySelector('h1[class*="learn-reports-tab"][class*=active]') !== null){
- checkTarget('h1[class*="learn-reports-tab"]');
- console.log("test");
- clearInterval(checkExist);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'h1[class*="learn-reports-tab"]',
- placement: 'right',
- arrowOffset: 'top',
- title: 'Learn about - Reports',
- content: 'On the Reports page, you\'ll find use cases describing how others have used the DataSpace and reports summarizing the studies and data in the DataSpace.',
- onNext: function(){
- nodeDisplaySearch(document.querySelectorAll('h1[class*="lhdv"]'))[5].click();
- var checkExist = setInterval(
- function(){
- if(nodeDisplaySearch(document.querySelectorAll('h1[class*="lhdv"]'))[5].className === 'lhdv active'){
- checkTarget('h1[class*="lhdv"][class*="lhdv active"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
-
- },{
- target: 'h1[class*="lhdv"][class*="lhdv active"]',
- placement: 'right',
- arrowOffset: 'top',
- title: 'Learn about - Publications',
- content: 'The Publications page combines publications across the contributing networks. Search publications by title, author, journal, and related studies.',
- onNext: function(){
-
- var node = null;
- var promise = new Promise(function(resolve, reject) {
- document.querySelector('h1[class*="learn-studies-tab"]').click();
- if(document.querySelector('h1[class*="learn-studies-tab"][class*="active"]') !== null){
- resolve();
- }
- }).then(function(result) {
- var nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('h2'), "CAVD 434"));
- if(nodes.length > 0){
-
- }
- }).then(function(result) {
- node = document.querySelector('input[class*="search-studies"]');
- if(node !== null){
- return;
- }
- }).then(function(result) {
- node.value = "";
- if(node.value === ""){
-
- }
- }).then(function(result) {
- var event = new Event("change");
- node.dispatchEvent(event);
- if(nodeTextSearch(document.querySelectorAll('h2'), "CAVD 434").length >= 0 &&
- isVisCoords(nodeTextSearch(document.querySelectorAll('h2'), "CAVD 434")[0])){
- checkTarget('div.nav-label:nth-child(1)');
-
- }
- });
-
- }
- },{
- target: 'div.nav-label:nth-child(1)',
- placement: 'left',
- yOffset: -17,
- content: 'The menu bar takes you back to the Home page',
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- checkTarget('h3[class*="tour-section-title"]');
- }
-
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_monoclonal_antibodies.js b/resources/cds-tours/definitions/tour_monoclonal_antibodies.js
deleted file mode 100644
index b1576eb4d..000000000
--- a/resources/cds-tours/definitions/tour_monoclonal_antibodies.js
+++ /dev/null
@@ -1,587 +0,0 @@
-var tour_monoclonal_antibodies = {
- title: 'Monoclonal Antibodies',
- description: 'A tour for the "Monoclonal antibodies" section.',
- id: 'tour-monoclonal-antibodies',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 0){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
-
- var nodes = null;
- var promise = new Promise(function(resolve, reject){
- nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear"));
- if(nodes.length > 0){
- resolve();
- }
- }).then(function(result){
- if(nodes[0] !== null){
- nodes[0].click();
-
- }
- }).then(function(result){
- document.querySelector('div.nav-label:nth-child(1)').click();
-
- });
- },
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'Monoclonal antibodies',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.
Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(6)',
- placement: 'left',
- title: 'Compare different antibody-virus combinations',
- content: 'The Monoclonal antibodies section is where you can explore data from monoclonal antibody (mAb) characterization studies. In this section, you can search for antibodies and compare the neutralization curves and heatmaps for different antibody-virus combinations.',
- yOffset: -17,
- onNext: function(){
-
- document.querySelector('div.nav-label:nth-child(6)').click();
- var event = new Event('mouseenter');
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[id*=gridcolumn][class*=x-column-header]'), "MAb/Mixture");
- if (nodes.length === 1) {
- var node = nodes[0];
- node.classList.add("mab-mix-column");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('span[class*="mab-mix-column"]');
- if (node !== null) {
- node.parentElement.dispatchEvent(event);
- node.nextSibling.classList.add("mab-mix-filter");
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- if (document.querySelector('span[class*="mab-mix-column"]') !== null &&
- document.querySelector('div[class*="mab-mix-filter"]') !== null) {
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist3);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'div[class*="mab-mix-filter"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: 10,
- yOffset: -25,
- title: 'The "mAb grid"',
- content: 'The mAb grid lists all the antibodies from the mAb characterization study data in DataSpace. The antibodies are listed by a standard name for the mAb or mixture of mAbs assigned by the DataSpace team.',
- },{
- target: 'h2[class*="mab-filterheader-text"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 20,
- yOffset: -40,
- content: 'The MAb Info pane gives you a summary of the mAbs available to plot and keeps track of the mAbs being explored in your session, similar to the Active filters for subject data.',
- onNext: function(){
-
- document.querySelector('div[class*="mab-mix-filter"]').click();
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[id*="tbtext"]'), "MAb/Mixture");
- if(nodes.length === 1 && isVisCoords(nodes[0])){
- nodes[0].classList.add("mab-mix-popup");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('div[class*="mab-mix-popup"]')){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist2);
- }
- },100);
-
- }, multipage: true
- },{
- target: 'div[class*="mab-mix-popup"]',
- placement: 'top',
- arrowOffset: 'center',
- xOffset: -110,
- yOffset: -10,
- title: 'Choosing mAb data to plot',
- content: 'The MAb/Mixture column can be sorted or filtered to specific mAbs.',
- onNext: function(){
-
- var event = new Event("click");
- nodeTextSearch(document.querySelectorAll('span[id*="templatecolumn"]'), "All")[0].
- parentElement.
- parentElement.
- previousSibling.
- dispatchEvent(event);
-
- var checkExist0 = setInterval(
- function(){
- var node = nodeTextSearch(document.querySelectorAll('span[id*="templatecolumn"]'), "All")[0].
- parentElement.
- parentElement.
- previousSibling;
- if(node.className.match("x-grid-hd-checker-on") === null){
- var event = new Event("change");
- var inbox = document.querySelector('input[placeholder*="Search MAb/Mixture"]');
- inbox.value = "PGT";
- inbox.dispatchEvent(event);
- clearInterval(checkExist0);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="x-grid-cell-inner"]'), "PGT121");
- var nodeIdx = null;
- for(var i = 0; i < nodes.length; i++){
- for(var j of Array(7)){
- nodes[i] = nodes[i].parentElement;
- }
- if(nodes[i].nodeName === "TBODY"){
- nodeIdx = i;
- }
- }
- if(nodeIdx !== null){
- nodeTextSearch(document.querySelectorAll('div[class*="x-grid-cell-inner"]'), "PGT121")[nodeIdx].click();
- nodes[nodeIdx].classList.add("top-of-table");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('tbody[class="top-of-table"]');
- if(node !== null){
- node.firstChild.nextSibling.classList.add("mab-mix-filter-select-row");
- node.firstChild.nextSibling.nextSibling.classList.add("mab-mix-filter-select-row");
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var nodes = document.querySelectorAll('tr[class*="mab-mix-filter-select-row"]');
- if(nodes.length === 2){
- for(var i of nodes){ i.firstChild.click(); }
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function(){
- var nodes = nodePosCoordSearch(document.querySelectorAll('tr[class*="mab-mix-filter-select-row"][class*="x-grid-row-selected"]'));
- if(nodes.length === 2){
- nodePosCoordSearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Filter"))[0].classList.add("mab-mix-popout-filter-button");
- clearInterval(checkExist4);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
- }, multipage: true
- },{
- target: 'span[class*="mab-mix-popout-filter-button"]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: -140,
- yOffset: 10,
- content: 'Clicking the Filter button will set the filter in the mAb grid.',
- onNext: function(){
- document.querySelector('span[class*="mab-mix-popout-filter-button"]').click();
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('span[class*="mab-mix-popout-filter-button"]');
- if (node === null) {
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist1);
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'div[class*="mab-mix-filter"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: 10,
- yOffset: -25,
- content: 'Now the list of mAbs only includes the mAbs selected.',
- onNext: function(){
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(
- nodeTextSearch(
- document.querySelectorAll('span[class*="x-column-header-text"]'), "Antibody binding type"
- )
- );
- if(nodes.length > 0){
- nodes[0].classList.add("antibody-binding-type-column");
- clearInterval(checkExist1);
- }
- }, 100);
-
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('span[class*="antibody-binding-type-column"]');
- if( node !== null){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'span[class*="antibody-binding-type-column"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: 10,
- yOffset: -25,
- content: 'We can also add filters to mAb metadata fields, such as the antibody binding type or filter by study.',
- onNext: function(){
-
- var event = new Event('mouseenter');
- var node = nodeTextSearch(document.querySelectorAll('span[id*="gridcolumn"]'), 'Viruses')[0];
-
- var checkExist1 = setInterval(
- function(){
- if(node !== null){
- node.classList.add("virus-column");
- node.nextSibling.classList.add("virus-filter");
- node.parentElement.dispatchEvent(event);
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('span[class*="virus-column"]') !== null &&
- document.querySelector('div[class*="virus-filter"]') !== null){
- clearInterval(checkExist2);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="virus-filter"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: 10,
- yOffset: -25,
- content: 'Clicking here we can now filter on viruses.',
- onNext: function(){
-
- document.querySelector('div[class*="virus-filter"]').click();
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('label[id*="checkboxfield"]'), "All"));
- if(nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('label[id*="checkboxfield"]'), "All")).length > 0){
- var node = nodes[0];
- node.classList.add("neut-tier-all-label");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('label[class*="neut-tier-all-label"]');
- if(node !== null){
- node.click();
-
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('label[id*="checkboxfield"]'), "1B");
- if(nodes.length > 0){
- nodes[0].classList.add("nt-1b-all-label");
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function(){
- var node = document.querySelector('label[class*="nt-1b-all-label"]');
- if(node !== null){
- node.click();
- clearInterval(checkExist4);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'label[class*="nt-1b-all-label"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -30,
- yOffset: 0,
- content: 'Many of the antibodies are tested against large panels of over 100 viruses, so you may also want to filter the viruses before you plot the data. In this case, we can select viruses that are in the neutralization tier category 1B. When looking for specific viruses, try CTRL + F to search for the virus name.',
- onNext: function(){
-
- var node = nodePosCoordSearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Done"))[0];
- node.classList.add('virus-filter-done');
- node.click();
-
- var checkExist = setInterval(
- function(){
- if(nodePosCoordSearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Done")).length === 0){
- clearInterval(checkExist);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'span[class*="mab-mix-column"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: -20,
- yOffset: -20,
- content: 'Now that we\'ve filtered the list of mAbs and viruses, we\'ll select the mAbs and mAb mixtures we want to view in the report. We put a check mark next to the mAbs we want to include in the report.',
- onNext: function(){
-
- var event = new Event("click");
- var node = document.querySelector('span[class*="mab-mix-column"]').
- parentElement.
- parentElement.
- previousSibling;
-
- if(node.className.match('x-grid-hd-checker-on') === null) node.dispatchEvent(event);
-
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('span[class*="mab-mix-column"]').
- parentElement.
- parentElement.
- previousSibling;
- if(node.className.match('x-grid-hd-checker-on') !== null ){
- document.querySelectorAll('a[class*=mabgridcolumnsbtn]')[0].classList.add("mab-report-button1");
- document.querySelectorAll('a[class*=mabgridcolumnsbtn]')[1].classList.add("mab-report-button2");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelectorAll('a[class*="mab-report-button"]').length === 2 ){
- clearInterval(checkExist2);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'a[class*="mab-report-button2"]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: -120,
- yOffset: 0,
- content: 'Now that we\'ve selected our mAbs and viruses we want to compare, we can view the data in 2 reports.',
- onNext: function(){
-
- document.querySelector('a[class*="mab-report-button2"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('div[class*="labkey-knitr"]') !== null &&
- nodeDisplaySearch(document.querySelectorAll('div[class*="labkey-knitr"]')).length > 0 &&
- nodeDisplaySearch(document.querySelectorAll('div[class*="svg-container"]')).length > 0 ){
- clearInterval(checkExist);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="svg-container"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: 0,
- content: 'The heatmap report shows the titer IC50 for each mAb-virus combination. The titer IC50 (50% maximal inhibitory concentration) is the concentration of the antibody required to achieve 50% neutralization of the virus. A low titer IC50 value indicates more efficient neutralization of the virus by the antibody. The geometric mean of the titer is plotted when the mAb-virus combination is tested in more than one study. Hover over the cell for each combination to see the titer value.
If you\'ve selected a large number of mAbs and viruses, the plot content might be very dense and hard to read. Hover over the plot to get the tool bar. Use the tool bar to zoom, pan, and resize the plot.',
- onNext: function(){
-
- document.querySelector('div[class*="iarrow"]').click();
- var checkExist = setInterval(
- function(){
- if(isVisCoords(document.querySelector('a[class*="mab-report-button1"]'))){
- clearInterval(checkExist);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'a[class*="mab-report-button1"]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: -115,
- yOffset: 0,
- content: 'The other report shows the neutralization curves of the mAbs and viruses selected.',
- onNext: function(){
-
- document.querySelector('a[class*="mab-report-button1"]').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector('button[onclick*="MAb Grid"]') !== null){
- document.querySelector('button[onclick*="MAb Grid"]').click();
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'button[onclick*="MAb Grid"]',
- placement: 'bottom',
- arrowOffset: 'left',
- xOffset: 45,
- yOffset: 0,
- content: 'The MAb Grid tab shows neutralization curves for all the mAb/mixture and virus combinations selected. There is also a tab for each of the mAbs/mixtures which shows the neutralization curves of all the viruses the mAb/mixture was tested against. Let\'s open the tab for one of the mAb mixtures and view the report.',
- onNext: function(){
- document.querySelector('button[onclick*="PGT121 + PGDM1400"]').click();
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }, multipage: true
- },{
- target: 'button[onclick*="PGT121 + PGDM1400"]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: 50,
- yOffset: 0,
- content: 'This tab shows the neutralization curves of all the viruses tested against one of the mAb mixtures. Scroll down to see the details of the curves.',
- onNext: function(){
- document.querySelector('button[onclick*="PGT121 + PGDM1400"]').click();
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }, multipage: true
- },{
- target: 'h2[class*="mab-filterheader-text"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: -68,
- content: 'You can save your filters for further exploration during another session. Saved data can also be accessed with our DataSpaceR API (see Tools & links for more details).',
- onNext: function(){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
-
- },{
- target: 'div[class*="iarrow"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: -24,
- content: 'Clicking this button takes you back to the MAb Grid.',
- onNext: function(){
- document.querySelector('div[class*="iarrow"]').click();
-
- var checkExist1 = setInterval(
- function(){
- var nodes1 = document.querySelectorAll('span[id*="button"]');
- if(nodes1.length > 0){
- var nodes2 = nodeTextSearch(nodes1, "Export CSV");
- if(nodes2.length > 0){
- var node = nodePosCoordSearch(nodes2)[0];
- if(node !== null){
- node.classList.add("export-mab-csv");
- clearInterval(checkExist1);
- }
- }
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('span[class*="export-mab-csv"]') !== null){
- clearInterval(checkExist2);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'span[class*="export-mab-csv"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -10,
- yOffset: -45,
- content: 'Data can also be exported as zipped CSV files or as an Excel workbook.',
- onNext: function(){
-
- var nodes = null;
- var promise = new Promise(function(resolve, reject){
- nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear"));
- if(nodes.length > 0){
- resolve();
- }
- }).then(function(result){
- if(nodes[0] !== null){
- nodes[0].click();
-
- }
- }).then(function(result){
- document.querySelector('div.nav-label:nth-child(1)').click();
-
- }).then(function(result){
- if(nodeDisplaySearch(document.querySelectorAll('h3[class*="tour-section-title"]')).length > 0){
- checkTarget('h3[class*="tour-section-title"]');
- }
- });
- }
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_plot_data.js b/resources/cds-tours/definitions/tour_plot_data.js
deleted file mode 100644
index dbb91f82e..000000000
--- a/resources/cds-tours/definitions/tour_plot_data.js
+++ /dev/null
@@ -1,802 +0,0 @@
-var tour_plot_data = {
- title: 'Plot-data',
- description: 'A tour for the "Plot data" section.',
- id: 'tour-plot-data',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 0){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- var nodes = null;
- var promise = new Promise(function(resolve, reject){
- nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear"));
- if(nodes.length > 0){
- resolve();
- }
- }).then(function(result){
- nodes[0].click();
- });
- },
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'Plot data',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.
Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(4)',
- placement: 'left',
- title: 'Creating subject data visualizations in Plot data',
- content: 'The Plot data section is where you can explore the subject data using simple plots that allow you to compare data across studies and assays.',
- yOffset: -17,
- onNext: function() {
-
- document.querySelector("div.nav-label:nth-child(4)").click();
-
- var checkExist1 = setInterval(
- function() {
- if (
- document.querySelector('div[id*=plot') !== null &&
- document.querySelector('div[id*=plot').style.display !== "none" &&
- document.querySelector('.info_Study') !== null
- ){
- document.querySelector('.info_Study').click();
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function() {
- if(document.querySelector('div[title*="CAVD 371"]') !== null &&
- document.querySelector('div[title*="CAVD 434"]') !== null){
- document.querySelector('div[title*="CAVD 371"]').click();
- document.querySelector('div[title*="CAVD 434"]').parentElement.parentElement.previousSibling.click();
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function() {
- if(nodeDisplaySearch(
- document.querySelectorAll('tr[class*="x-grid-row"][class*="x-grid-row-selected"][class*="x-grid-data-row"]')).length === 2
- ){
- document.querySelector('a[id*="button"][class*="x-btn filterinfoaction"]').click();
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function() {
- if(document.querySelector('div[class*="filterstatus-content"]') !== null &&
- document.querySelector('div[class="sel-list-item memberloc"]') !== null &&
- isVisCoords(document.querySelector('div[class*="filterstatus-content"]'))){
- clearInterval(checkExist4);
- checkTarget('div[class*="filterstatus-content"]');
- }
- }, 100);
-
- },
- multipage: true
- },{
- target: 'div[class*="filterstatus-content"]',
- placement: 'left',
- arrowOffset: 'top',
- content: 'Before you begin your plot, select the study or subject data you wish to explore. Use Learn about to identify studies of interest. Filter the data using the Active filters pane, Find subjects, or View data grid.',
- yOffset: -12,
- onNext: function(){
-
- var checkExist = setInterval(
- function(){
- if (
- document.querySelector('a[class*="yaxisbtn"]') !== null &&
- isVisCoords(document.querySelector('a[class*="yaxisbtn"]'))
- ) {
- clearInterval(checkExist);
- checkTarget('a[class*="yaxisbtn"]');
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'a[class*="yaxisbtn"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: -50,
- title: 'Choosing the y-axis for your plot',
- content: 'We start our plot by selecting what data we want on the y-axis.',
- onNext: function(){
-
- document.querySelector('a[class*="yaxisbtn"]').click();
- var checkExist1 = setInterval(
- function(){
- if (nodeDisplaySearch(nodePosCoordSearch(document.querySelectorAll('div[id*="dataview"]'))).length !== 0) {
- nodeDisplaySearch(nodePosCoordSearch(document.querySelectorAll('div[id*="dataview"]')))[0].classList.add("yaxis-sources");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if (document.querySelector('div[id*="dataview"][class*="yaxis-sources"]') !== null &&
- isVisCoords(document.querySelector('div[id*="dataview"][class*="yaxis-sources"]'))) {
- clearInterval(checkExist2);
- checkTarget('div[class*="yaxis-sources"]');
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="yaxis-sources"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -10,
- yOffset: 15,
- title: 'Choosing the type of data to plot',
- content: 'There are several different data sources that can be plotted. The number of subjects with data for that data source is shown next to the source.',
- onNext: function(){
-
- // var checkExist_05 = setInterval(
- // function(){
- // var nodes = nodeTextSearch(document.querySelectorAll('span[id*="button"]'), 'Cancel');
- // if(isVisible(nodes[0]) === 0){
- // window.hopscotch.endTour();
- // }
- // }, 100);
-
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), 'ICS (Intracellular Cytokine Staining)');
- if(nodes.length > 0){
- nodes[0].classList.add("ics-assay-label");
- nodes[0].click();
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[class*="section-title"]'), "ICS (Intracellular Cytokine Staining)");
- if ( nodes.length > 0 && isVisCoords(nodes[0]) ) {
- nodes[0].classList.add("ics-source-title");
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- if ( document.querySelector('span[class*="ics-source-title"]') !== null){
- checkTarget('span[class*="ics-source-title"]');
- clearInterval(checkExist3);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="ics-source-title"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -80,
- yOffset: -35,
- title: 'Choosing a measure to plot',
- content: 'Here we\'ve chosen the Intracellular Cytokine Staining assay. The recommended variables, highlighted in red, are the most commonly analyzed measures for this type of data. Additional measures are also available to plot. Hover over the variable name to get a definition. We\'ll use the default measure (background-subtracted magnitude).',
- onNext: function(){
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="dimension-header"]'), "Assay Dimensions");
- if(nodes.length > 0){
- nodes[0].classList.add("assay-dim-header");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var node = document.querySelector('div[class*="assay-dim-header"]');
- if(node !== null && isVisCoords(node)){
- checkTarget('div[class*="assay-dim-header"]');
- clearInterval(checkExist2);
- }
- },100);
- }, multipage: true
-
- },{
- target: 'div[class*="assay-dim-header"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -10,
- yOffset: -265,
- title: 'Choosing the assay dimensions',
- content: 'When plotting assay data, you will see an Assay Dimensions section which describes important elements specific to this data type. Many of the assay dimensions are also key fields that, when combined with other dimensions, are used to define unique records in the dataset.
Use this section to apply additional filters to the data for each of the assay dimensions. You\'ll want to review each dimension to make sure you haven\'t selected any values that are grayed out (i.e. not present in the filtered data). Selecting a value that is grayed out when that element can only have one value will result in a \"No data in the plot\" message. You can choose not to apply any filters to the assay dimensions, but your exploration will be more meaningful if your data is filtered with intention.
More information about the assay dimensions can be found on the assay pages in Learn about.',
- onNext: function(){
- var event = new Event('mouseleave');
- var dd = document.querySelectorAll('div[class*="field-display"]');
- dd[1].click();
- var checkExist1 = setInterval(
- function(){
- var node = nodeDisplaySearch(document.querySelectorAll('div[class*="functional_marker_name-dropdown"]'))[0];
- if(node !== null){
- node = nodeTextSearch(node.querySelectorAll('label[id*="radiofield"][id*="boxLabelEl"]'), "IFNg")[0];
- node.previousSibling.click();
- node.previousSibling.classList.add("tour-checked-fmn");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('input[class*="tour-checked-fmn"]') !== null){
- var node = nodeDisplaySearch(document.querySelectorAll('div[class*="functional_marker_name-dropdown"]'))[0];
- node.dispatchEvent(event);
- clearInterval(checkExist2);
- }
- }, 100);
-
- dd[2].click();
- var checkExist3 = setInterval(
- function(){
- var node = nodeDisplaySearch(document.querySelectorAll('div[class*="summary_level-dropdown"]'))[0];
- if(node !== null){
- node = nodeTextSearch(node.querySelectorAll('label[id*="radiofield"][id*="boxLabelEl"]'), "Protein")[0];
- node.previousSibling.click();
- node.previousSibling.classList.add("tour-checked-sl");
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function(){
- var event = new Event('mouseleave');
- if(document.querySelector('input[class*="tour-checked-sl"]') !== null){
- var node = nodeDisplaySearch(document.querySelectorAll('div[class*="summary_level-dropdown"]'))[0];
- node.dispatchEvent(event);
- clearInterval(checkExist4);
-
- }
- }, 100);
-
- var checkExist5 = setInterval(
- function(){
- if (document.querySelector('input[class*="tour-checked-sl"]') !== null &&
- document.querySelector('input[class*="tour-checked-fmn"]') !== null)
- {
-
- nodeTextSearch(document.querySelectorAll('span[id*="button"]'), 'Set y-axis')[0].classList.add("setYAxis");
-
- if(document.querySelector('span[class*="setYAxis"]') !== null){
- document.querySelector('input[class*="tour-checked-sl"]').classList.remove("tour-checked-sl");
- document.querySelector('input[class*="tour-checked-fmn"]').classList.remove("tour-checked-fmn");
- checkTarget('span[class*="setYAxis"]');
- clearInterval(checkExist5);
- }
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="setYAxis"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: 15,
- yOffset: -80,
- title: 'Set the y-axis',
- content: 'When finished making selections for the y-axis, click the button to set the axis.',
- onNext: function(){
-
- function getScrollParent(node) {
- if (node == null) {
- return null;
- }
- if (node.style.overflow === "hidden auto") {
- return node;
- } else {
- return getScrollParent(node.parentNode);
- }
- }
- document.querySelector('span[class*="setYAxis"]').click();
-
- var smt = null;
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[class*="AntigensInY"]'));
- if (
- nodes.length > 0 &&
- document.querySelector('div[class="x-mask"]') !== null &&
- !isVisCoords(document.querySelector('div[class="x-mask"]'))
- ) {
- getScrollParent(nodes[0]).classList.add("info-pane-scroll-frame");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(
- document.querySelector('div[class*="info-pane-scroll-frame"]') !== null &&
- !isVisCoords(document.querySelector('div[class="x-mask"]')) &&
- nodeDisplaySearch(
- nodeTextSearch(
- document.querySelectorAll('span[class*="statme status-label"]'),
- "Antigens in Y"
- )
- ).length > 0
- ){
- smt = Math.max(document.querySelector('div[class*="AntigensInY"]').getBoundingClientRect().y - 200, 0);
- document.querySelector('div[class*="info-pane-scroll-frame"]').scrollTo({left: 0, top: smt, behavior: 'smooth'});
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var node = document.querySelector('div[class*="info-pane-scroll-frame"]');
- if(
- isVisCoords(document.querySelector('div[class*="AntigensInY"]')) &&
- node !== null &&
- (node.scrollTop === smt ||
- Math.abs((node.clientHeight + node.scrollTop) - node.scrollHeight) < 3)
- ){
- checkTarget('div[class*="AntigensInY"]');
- clearInterval(checkExist3);
- }
- }, 100);
- }
- },{
- target: 'div[class*="AntigensInY"]',
- placement: 'left',
- arrowOffset: 220,
- yOffset: -225,
- content: 'We now have a one-dimensional plot. Hover over a single data point on the plot. The dark data points show data from the same subject. Click on a data point to see the details. Click outside the details to close the box.
In the Active Filters pane, we now have 2 new categories that describe the data in this plot. We see that the data is from 2 studies (CAVD 371 and 434) and includes 5 antigens across 11 time points. If we click on the \'Antigens in Y\'...',
- onNext: function(){
- document.querySelector('div[class*="AntigensInY"]').click();
-
- var checkExist = setInterval(
- function(){
- if(
- document.querySelector('span[class="section-title"]') !== null &&
- isVisCoords(document.querySelector('span[class="section-title"]')) &&
- nodeTextSearch(document.querySelectorAll('span[class="section-title"]'), "Magnitude (% cells) - Background subtracted")[0] !== "none found" &&
- document.querySelector('label[test-data-value="study_ICS_protein_panel-Any_Antigen"]') !== null &&
- document.querySelector('label[test-data-value="study_ICS_protein-Any_Antigen-Any_ENV"]') !== null
- ){
- document.querySelector('label[test-data-value="study_ICS_protein_panel-Any_Antigen"]').click();
- document.querySelector('label[test-data-value="study_ICS_protein-Any_Antigen-Any_ENV"]').click();
- clearInterval(checkExist);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('div[class*="antigen-selection-panel"]') !== null &&
- isVisCoords(document.querySelector('div[class*="antigen-selection-panel"]'))){
- checkTarget('div[class*="antigen-selection-panel"]');
- clearInterval(checkExist2);
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'div[class*="antigen-selection-panel"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 15,
- yOffset: 0,
- content: 'We see a list of the antigens (in this case, the proteins) included in the plot. Modifying the filters in this box will have the same effect as going back to the y-axis to modify the Protein filter in the assay dimensions. Let\'s filter to just ENV proteins.',
- onNext: function(){
-
- nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Done")[0].click();
- nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Set y-axis")[0].click();
-
- var checkExist = setInterval(
- function(){
- if (document.querySelectorAll('div[class="x-mask"]')[0].style.visibility === "hidden" ||
- document.querySelectorAll('div[class="x-mask"]')[0].style.display === "none") {
- checkTarget('div[id="xvarselector"]');
- clearInterval(checkExist);
- }
- }, 100);
-
- }
- },{
- target: 'div[id="xvarselector"]',
- placement: 'top',
- arrowOffset: 'center',
- title: 'Choosing the x-axis for your plot',
- xOffset: -60,
- yOffset: 0,
- content: 'Now let\'s select the type of data we want to plot on the x-axis. ',
- onNext: function(){
-
- document.querySelector('div[id="xvarselector"]').click();
- var checkExist = setInterval(
- function() {
- if (isVisCoords(nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Time points")[0])) {
- nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Time points")[0].classList.add("time-points-label");
- if(document.querySelector('div[class*="time-points-label"]') !== null &&
- isVisCoords(document.querySelector('div[class*="time-points-label"]'))){
- clearInterval(checkExist);
- checkTarget('div[class*="time-points-label"]');
- }
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="time-points-label"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'You\'ll notice there are a few other data types that can be plotted on the x-axis. Plotting the measure over time gives you a good overview of the data.',
- xOffset: -20,
- yOffset: -85,
- onNext: function() {
-
- nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Time points")[0].click();
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Study days");
- if (nodes.length > 0 && isVisCoords(nodes[0])) {
- nodes[0].classList.add("study-days-label");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('div[class*="study-days-label"]') !== null){
- checkTarget('div[class*="study-days-label"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="study-days-label"]',
- placement: 'left',
- arrowOffset: 'center',
- title: 'Plotting by time',
- content: 'The recommended time point is study days. By default, the study days are aligned by Day 0 (the study day when subjects received their first vaccination).',
- yOffset: -75,
- xOffset: -15,
- onNext: function() {
-
- var event = new Event("mousedown");
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[id*="button"][id*="btnInnerEl"]'), "Set x-axis");
- if(nodes.length > 0){
- nodes[0].click();
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="main-title"]'), "x-axis");
- if(
- nodes.length > 0 &&
- !isVisCoords(nodes[0]) &&
- document.querySelectorAll('g[class=study]').length === 2 ||
- document.querySelectorAll('g[class=study]').length === 12
- ) {
- checkTarget('g[class*="study"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'g[class*="study"]',
- placement: 'top',
- arrowOffset: 'left',
- content: 'Now the plot shows the background-subtracted magnitude over time. Below the plot, you can see the different studies and treatment groups, and when the study visits occurred.
Click on the "+" sign to expand the study groups.
The syringe icons indicate when the vaccinations were given to the subjects in each group. Hover over one of the icons to see what products were given. Notice that the study day at which the last vaccination is given is different for the different groups.
Collapse the study groups by clicking on the "-" sign.',
- yOffset: 0,
- xOffset: 0,
- onNext: function() {
- nodeTextSearch(document.querySelectorAll('h1[unselectable="on"]'), "x =")[0].click();
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[class*="section-title"]'), "Time points");
- if (nodes.length > 0 && isVisCoords(nodes[0])){
- nodeTextSearch(document.querySelectorAll('div[class*="main-label"]'), "Aligned by Day 0")[0].click();
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[class*="advanced-dropdown undefined-dropdown"]'));
- if(nodes.length !== 0){
- nodeTextSearch(nodes[0].querySelectorAll('label[id*="radiofield"][id*="boxLabelEl"]'), "Last Vaccination")[0].previousSibling.click();
- nodes[0].classList.add("aligned-by-dropdown");
- nodeTextSearch(document.querySelectorAll('div[class*="field-label"]'), "Aligned by:")[0].classList.add("aligned-by-label");
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- if(document.querySelector('div[class*="aligned-by-label"]') !== null &&
- document.querySelector("div[class*='aligned-by-dropdown']") !== null){
- checkTarget('div[class*="aligned-by-label"]');
- clearInterval(checkExist3);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="aligned-by-label"]',
- placement: 'left',
- arrowOffset: 'center',
- content: 'To make it easier to compare the immunogenicity measures at the \'peak time points\' across groups, we can re-align the study days by the last vaccination.',
- yOffset: -98,
- xOffset: -10,
- onNext: function(){
-
- var nodes = nodeDisplaySearch(document.querySelectorAll("div[class*='aligned-by-dropdown']"));
- if(nodes.length > 0){
- var event = new Event('mouseleave');
- nodes[0].dispatchEvent(event);
- }
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll("div[class*='aligned-by-dropdown']"));
- if(nodes.length === 0){
- nodeTextSearch(document.querySelectorAll('span[id*="button"][id*="btnInnerEl"]'), "Set x-axis")[0].click();
- clearInterval(checkExist1)
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="main-title"]'), "x-axis");
- if(nodes.length > 0 &&
- !isVisCoords(nodes[0]) &&
- document.querySelectorAll('g[class=study]').length === 2) {
- checkTarget('g[class*="study"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'g[class*="study"]',
- placement: 'top',
- arrowOffset: 'left',
- content: 'Now our plot shows time points aligned by last vaccination. We can select the time point 14 days after the last vaccination and add it to our filters. To select the time point either (1) click on the visit icons or (2) use a click and drag motion to highlight the plot in teal. Click the Filter button to apply the filter.',
- yOffset: 0,
- xOffset: 0,
- onNext: function() {
- nodeTextSearch(document.querySelectorAll('h1[unselectable="on"]'), "x =")[0].click();
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="main-title"]'), "x-axis");
- if(nodes.length > 0 && isVisCoords(nodes[0])) {
- for(var i of document.querySelectorAll('span[class*=arrow]')){
- if(isVisCoords(i)){
- i.classList.add("back-to-sources");
- }
- }
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('span[class="arrow back-to-sources"]') !== null){
- checkTarget('span[class="arrow back-to-sources"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true // multipage... This is really more about if the node identifier is generated during onNext or not...
- },{
- target: 'span[class="arrow back-to-sources"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 15,
- yOffset: -32,
- content: 'Clicking this back arrow, we can navigate back to select other sources for the x-axis.',
- onNext: function(){
- document.querySelector('span[class="arrow back-to-sources"]').click();
- var checkExist1 = setInterval(
- function(){
- if (nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Study and treatment variables")[0].parentElement.parentElement.style.display === ""){
- nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Study and treatment variables")[0].classList.add("study-treatment-vars");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if (document.querySelector('div[class*="study-treatment-vars"]') !== null &&
- isVisCoords(document.querySelector('div[class*="study-treatment-vars"]'))){
- clearInterval(checkExist2);
- checkTarget('div[class*="study-treatment-vars"]');
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="study-treatment-vars"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -10,
- yOffset: -48,
- content: 'Next, let\'s select a study and treatment variable to plot.',
- onNext: function(){
-
- document.querySelector('div[class*="study-treatment-vars"]').click();
- var checkExist1 = setInterval(
- function(){
- var nodes1 = nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Product Combination");
- var nodes2 = nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Study Name");
- if(nodes1.length !== 0 &&
- nodes2.length !== 0 &&
- nodes1[0].parentElement.parentElement.style.display === "" &&
- nodes2[0].parentElement.className === "content-item content-selected"){
- nodes1[0].classList.add("product-combination-label");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('div[class*="product-combination-label"]') !== null){
- document.querySelector('div[class*="product-combination-label"]').click();
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- if(document.querySelector('div[class*="product-combination-label"]') !== null &&
- document.querySelector('div[class*="product-combination-label"]').parentElement.className === "content-item content-selected"){
- checkTarget('div[class*="content-label"][class*="product-combination-label"]');
- clearInterval(checkExist3);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="content-label"][class*="product-combination-label"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: -10,
- yOffset: -70,
- content: 'Plotting product combination on the x-axis will help us compare responses to the ENV protein at those peak time points across treatment groups receiving different product combinations.',
- onNext: function(){
- nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Set x-axis")[0].click();
- var checkExist = setInterval(
- function(){
- if (document.querySelectorAll('div[class="x-mask"]')[0].style.display === "none" ||
- document.querySelectorAll('div[class="x-mask"]')[0].style.visibility === "hidden") {
- checkTarget('div[id="colorvarselector"]');
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'div[id="colorvarselector"]',
- placement: 'bottom',
- arrowOffset: 'center',
- xOffset: -35,
- title: 'Color as a third dimension',
- content: 'We can also add other variables as color.',
- onNext: function(){
- document.querySelector('div[id="colorvarselector"]').click();
- var checkExist1 = setInterval(
- function(){
- if(isVisCoords(nodeTextSearch(document.querySelectorAll('div[class*="main-title"]'), "color")[0])) {
- for(var i of nodeTextSearch(document.querySelectorAll('div[class*="content-label"]'), "Study and treatment variables")){
- if(i.parentElement.parentElement.style.display !== "none"){
- i.click();
- }
- }
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- for(var i of nodeTextSearch(document.querySelectorAll('div[class="content-label"]'), "Study Name")){
- if(isVisCoords(i)){
- i.classList.add("color-study-name");
- if(document.querySelector('div[class*="color-study-name"]') !== null){
- checkTarget('div[class*="color-study-name"]');
- clearInterval(checkExist2);
- }
- }
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'div[class*="color-study-name"]',
- placement: 'left',
- yOffset: -23,
- xOffset: -8,
- content: 'In this case, adding study name as color helps to also compare responses across studies.',
- onNext: function(){
- nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Set color")[0].click();
- var checkExist = setInterval(
- function(){
- if (document.querySelectorAll('div[class="x-mask"]')[0].style.display === "none" ||
- document.querySelectorAll('div[class="x-mask"]')[0].style.visibility === "hidden") {
- checkTarget('h2[class*="filterheader-text section-title-filtered"]');
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
- },{
- target: 'h2[class*="filterheader-text section-title-filtered"]',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 5,
- yOffset: -75,
- content: 'You can save your plot for further exploration during another session or go to View data grid to export the data. Saved data can also be accessed with our DataSpaceR API (see Tools & links for more details).',
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- var node = document.querySelector('h3[class*="tour-section-title"]');
- if(node !== null && isVisCoords(node)){
- checkTarget('h3[class*="tour-section-title"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
\ No newline at end of file
diff --git a/resources/cds-tours/definitions/tour_view_data_grid.js b/resources/cds-tours/definitions/tour_view_data_grid.js
deleted file mode 100644
index b4b2471db..000000000
--- a/resources/cds-tours/definitions/tour_view_data_grid.js
+++ /dev/null
@@ -1,459 +0,0 @@
-var tour_view_data_grid = {
- title: 'View-data-grid',
- description: 'A tour for the "View data grid" section.',
- id: 'tour-view-data-grid',
- winerror: 0,
- i18n: {
- skipBtn: 'Start the tour'
- },
- onStart: function(){
- window.onerror = function() { self.winerror = 1; hopscotch.endTour(); };
- if(self.winerror === 0){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- self.winerror = 0;
- }
- },
- onEnd: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- var nodes = null;
- var promise = new Promise(function(resolve, reject){
- nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear"));
- if(nodes.length > 0){
- resolve();
- }
- }).then(function(result){
- nodes[0].click();
- });
- },
- onClose: function(){
- hopscotch.endTour();
- },
- onError: function(){
- for(var i of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "clear")){
- i.click();
- }
- for(var j of nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Cancel")){
- j.click();
- }
- hopscotch.endTour();
- },
- steps:
- [
- {
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'DataSpace tours',
- content: 'This is a guided tour designed to take you on a specific path through the DataSpace. Clicking the \'Next\' button will advance you through the predefined steps of the tour. Please be aware that any additional clicking or scrolling during the tour (unless instructed) may cause the tour to terminate early. Some tours are not compatible with small screens. For best results, view tours in full screen mode.
Note: Taking this tour will change the filters in the Active filters pane. If you have applied filters during this session that you don\'t want to lose, save your data before proceeding on this tour. If you continue, your filters will be modified.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- },{
- target: 'div.nav-label:nth-child(5)',
- placement: 'left',
- title: 'View and export subject data in the data grid',
- content: 'The View data grid section let\'s you explore the subject data in a spreadsheet format. From this section, you can export the subject data for further exploration in your own analysis tools.',
- yOffset: -17,
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(5)').click();
- var checkExist = setInterval(
- function(){
- var node1 = nodeTextSearch(document.querySelectorAll('span[id*=button]'), "Add/Remove columns");
- var node2 = nodeTextSearch(document.querySelectorAll('span[class*="x-column-header-text"]'), "Study")[0];
- if (node1.length === 1){
- if(isVisCoords(node1[0]) && node2 !== null) {
- clearInterval(checkExist);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }
- }, 100);
- }
- },{
- target: '.info_Subject',
- placement: 'left',
- arrowOffset: 'center',
- content: 'Let\'s say you wanted to create a plot of the CAVD 434 study for Intracellular Cytokine Staining (ICS) data over time.
If Grid is your first stop during your session or you haven\'t applied any filters yet, the Active filters will contain all the subjects with data in the DataSpace.
You can filter to just CAVD 434 data by using the Active filters pane, Find subjects, or View data grid.',
- yOffset: -65,
- xOffset: 8,
- onNext: function(){
-
- var event = new Event('mouseenter');
- var checkExist1 = setInterval(
- function(){
- var node1 = nodeTextSearch(document.querySelectorAll('span[class*="x-column-header-text"]'), "Study");
- var node2 = nodeTextSearch(document.querySelectorAll('span[class*="gridtablhdv"]'), "Study and treatment");
- if( node1.length > 0 && node2.length > 0 && node1[0].nextSibling !== null ){
- node1[0].classList.add("study-column");
- node1[0].nextSibling.classList.add("study-filter");
- node2[0].classList.add("study-treatment-tab");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- if(document.querySelector('span[class*="study-treatment-tab"]') !== null){
- checkTarget('span[class*="study-treatment-tab"]');
- clearInterval(checkExist2);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="study-treatment-tab"]',
- placement: 'right',
- arrowOffset: 'center',
- xOffset: 10,
- yOffset: -85,
- content: 'In Grid, the tab called, \'Study and treatment\', contains subject data that will be included regardless of what other data is selected.
All columns in the grid can be sorted and filtered.',
- onNext: function(){
-
- var event = new Event('mouseenter');
- var checkExist1 = setInterval(
- function(){
- var node = document.querySelector('span[class*="study-column"]').parentElement;
- if(node !== null && isVisCoords(node)){
- node.dispatchEvent(event);
- clearInterval(checkExist1);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'div[class*="study-filter"]',
- placement: 'top',
- arrowOffset: 'left',
- xOffset: -20,
- yOffset: 0,
- content: 'You can use the study column to filter to CAVD 434 subjects.',
- onNext: function(){
- var event = new Event('mouseleave');
- document.querySelector('span[class*="study-column"]').parentElement.dispatchEvent(event);
- document.querySelector('div[class*="x-column"][class*="study-filter"]').click();
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[id*="tbtext"][class*="x-toolbar-text"]'), "Study");
- if(nodes.length === 1){
- var node = nodes[0];
- node.classList.add("data-grid-study-popup");
- if(isVisCoords(node) && document.querySelector('div[class*="data-grid-study-popup"]') !== null){
- clearInterval(checkExist1);
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- }
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div[class*="data-grid-study-popup"]',
- placement: 'top',
- arrowOffset: 'center',
- xOffset: -25,
- yOffset: 0,
- content: 'Here we select CAVD 434 and apply the filter.',
- onNext: function(){
-
- var checkExist_1 = setInterval(
- function() {
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[class*="x-window-filterwindow"]'));
- if( nodes.length > 0 ){
- nodeDisplaySearch(
- nodeTextSearch(
- nodes[0].querySelectorAll(
- 'div[class*="x-grid-cell-inner"]'), 'CAVD 434'
- )
- )[0].click();
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var nodes1 = nodePosCoordSearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), 'Filter'));
- var nodes2 = nodeDisplaySearch(document.querySelectorAll('div[class*="x-window-filterwindow"]'));
-
- if (
- nodes1.length > 0 &&
- nodes2.length > 0 &&
- nodes2[0].querySelectorAll('tr[class*="x-grid-row-selected"]').length === 1
- ) {
- nodes1[0].click();
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('div[class*="selitem"]'), 'Study: = CAVD 434');
- if ( nodes.length > 0 ) {
- var node = nodes[0];
- if (isVisCoords(node)) {
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist2);
- }
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div.nav-label:nth-child(4)',
- placement: 'left',
- arrowOffset: 'center',
- xOffset: 0,
- yOffset: -50,
- title: 'Grid keeps track of the data in your session',
- content: 'As you navigate through other areas of the DataSpace, Grid will keep track of the data explored in the session.
For example, if you go to Plot data...',
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(4) > span:nth-child(2)').click();
- var checkExist = setInterval(
- function(){
- if(document.querySelector("a[class*='yaxisbtn']") !== null &&
- isVisCoords(document.querySelector("a[class*='yaxisbtn']"))){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist);
- }
- }, 100);
- }, multipage: true
-
- },{
- target: 'a[class*="yaxisbtn"]',
- placement: 'right',
- arrowOffset: 'top',
- xOffset: 5,
- yOffset: -15,
- content: '...and create a plot of Intracellular Cytokine Staining (ICS) data over time for the CAVD 434 subjects selected...',
- onNext: function(){
-
- document.querySelector('a[class*="yaxisbtn"]').click();
- var checkExist_1 = setInterval(
- function(){
- var nodes = nodePosCoordSearch(nodeTextSearch(document.querySelectorAll('div[class="content-label"]'), 'ICS (Intracellular Cytokine Staining)'));
- if(nodes.length > 0){
- nodes[0].click();
- clearInterval(checkExist_1);
- }
- }, 100);
-
- var checkExist0 = setInterval(
- function(){
- var dd = document.querySelectorAll('div[class*="field-display"]');
- if(dd.length > 0){
- if(isVisCoords(dd[1])){
- dd[1].click();
- clearInterval(checkExist0);
- }
- }
- }, 100);
-
- var checkExist1 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[class*="functional_marker_name-dropdown"]'));
- if(nodes.length > 0 && isVisCoords(nodes[0])){
- var node = nodes[0];
- node = nodeTextSearch(node.querySelectorAll('label[id*="radiofield"][id*="boxLabelEl"]'), "IL2")[0];
- node.previousSibling.click();
- node.previousSibling.classList.add("tour-checked-il2");
- clearInterval(checkExist1);
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var event = new Event('mouseleave');
- if(document.querySelector('input[class*="tour-checked-il2"]') !== null){
- var nodes = nodeDisplaySearch(document.querySelectorAll('div[class*="functional_marker_name-dropdown"]'));
- if(nodes.length > 0){
- nodes[0].dispatchEvent(event);
- clearInterval(checkExist2);
- }
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var nodes1 = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Set y-axis"));
- var nodes2 = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('div[class*="main-label"]'), "IL2"));
- if ( nodes1.length > 0 && nodes2.length > 0 ) {
- nodes1[0].click();
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function(){
- var parNodes = [];
- for(var i of document.querySelectorAll('li[class=source-label]')){
- parNodes.push(i.parentElement);
- }
- if(nodeDisplaySearch(parNodes).length > 0){
- var node = nodeDisplaySearch(parNodes)[0];
- if(node !== null){
- node.classList.add("list-source-label-parent");
- clearInterval(checkExist4);
- }
- }
- }
- );
-
- var checkExist5 = setInterval(
- function(){
- if(
- document.querySelector('div[class*="AntigensInY"]') !== null &&
- nodeDisplaySearch(document.querySelectorAll('div[class*="AntigensInY"]')).length > 0 &&
- document.querySelector('ul[class*="list-source-label-parent"]') !== null
- ){
- window.hopscotch.startTour(window.hopscotch.getCurrTour(), window.hopscotch.getCurrStepNum());
- clearInterval(checkExist5);
- }
- }, 100);
-
- }, multipage: true
-
- },{
- target: 'div.nav-label:nth-child(5)',
- placement: 'left',
- content: '...the ICS data plotted will carry over to the data grid.
Going back to Grid...',
- yOffset: -17,
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(5)').click();
-
- var checkExist1 = setInterval(
- function(){
- if(document.querySelector('h1.lhdv:nth-child(2) > span:nth-child(1)') !== null){
- if(isVisCoords(document.querySelector('h1.lhdv:nth-child(2) > span:nth-child(1)'))){
- clearInterval(checkExist1);
- }
- }
- }, 100);
-
- var checkExist2 = setInterval(
- function(){
- var nodes = nodeDisplaySearch(nodeTextSearch(document.querySelectorAll('span[class*="gridtablhdv"]'), "ICS"));
- if(nodes.length > 0){
- nodes[0].classList.add("ics-data-tab");
- clearInterval(checkExist2);
- }
- }, 100);
-
- var checkExist3 = setInterval(
- function(){
- var node = document.querySelector('span[class*="ics-data-tab"]');
- if(node !== null){
- node.click();
- clearInterval(checkExist3);
- }
- }, 100);
-
- var checkExist4 = setInterval(
- function(){
- var node = document.querySelector('span[class*="ics-data-tab"]');
- if(node !== null && node.parentElement.className === "lhdv active"){
- node.click();
- checkTarget('span[class*="ics-data-tab"]');
- clearInterval(checkExist4);
- }
- }, 100);
-
-
- }, multipage: true
- },{
- target: 'span[class*="ics-data-tab"]',
- placement: 'right',
- arrowOffset: 'center',
- content: 'You now have a tab for the ICS assay data from Plot.
Clicking on the tab will let you see the data',
- xOffset: 15,
- yOffset: -65,
- onNext: function(){
-
- var ck1 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[class*="gridtablhdv"]'), "Study and treatment");
- if( nodes.length > 0 ){
- nodes[0].click();
- clearInterval(ck1);
- }
- }, 100);
-
- document.querySelector('div.nav-label:nth-child(5)').click();
-
- var ck2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Add/Remove columns");
- if(nodes.length > 0){
- nodes[0].classList.add("add-rm-col");
- clearInterval(ck2);
- }
- }, 100);
-
- var ck3 = setInterval(
- function(){
- if(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Add/Remove columns").length > 0 &&
- document.querySelector('span[class*="add-rm-col"]') !== null){
- checkTarget('span[class*="add-rm-col"]');
- clearInterval(ck3);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="add-rm-col"]',
- placement: 'left',
- content: 'You can also add additional columns or data types.',
- yOffset: -21,
- xOffset: -14,
- onNext: function(){
-
- var ck2 = setInterval(
- function(){
- var nodes = nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Export CSV");
- if(nodes.length > 0){
- nodes[0].classList.add("export-csv");
- clearInterval(ck2);
- }
- }, 100);
-
- var ck3 = setInterval(
- function(){
- if(nodeTextSearch(document.querySelectorAll('span[id*="button"]'), "Export CSV").length > 0 &&
- document.querySelector('span[class*="export-csv"]') !== null){
- checkTarget('span[class*="export-csv"]');
- clearInterval(ck3);
- }
- }, 100);
-
- }, multipage: true
- },{
- target: 'span[class*="export-csv"]',
- placement: 'left',
- content: 'You can save your data for further exploration during another session or export it as zipped CSV files or an Excel workbook. Saved data can also be accessed with our DataSpaceR API (see Tools & links for more details).',
- yOffset: -22,
- xOffset: -5,
- onNext: function(){
- document.querySelector('div.nav-label:nth-child(1)').click();
- var checkExist = setInterval(
- function(){
- var node = document.querySelector('h3[class*="tour-section-title"]');
- if(node !== null && isVisCoords(node)){
- checkTarget('h3[class*="tour-section-title"]');
- clearInterval(checkExist);
- }
- }, 100);
- }
- },{
- target: 'h3[class*="tour-section-title"]',
- placement: 'bottom',
- arrowOffset: 'center',
- title: 'This concludes the tour',
- content: 'We’re back on the Home page where we started. From here you can take another tour or try it out for yourself.
Have any questions? Click the Help section at the top of the page or contact us for more information.',
- xOffset: (window.innerWidth / 2) - 280,
- showSkip: true
- }
- ]
-};
diff --git a/resources/cds-tours/wikis/needtoknow-default-wiki b/resources/cds-tours/wikis/needtoknow-default-wiki
deleted file mode 100644
index 29c286cc2..000000000
--- a/resources/cds-tours/wikis/needtoknow-default-wiki
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/MAbMixMAbMeta.sql b/resources/queries/cds/MAbMixMAbMeta.sql
deleted file mode 100644
index 2bba4670a..000000000
--- a/resources/queries/cds/MAbMixMAbMeta.sql
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
--- mabmix
- mix.mab_mix_id,
- mix.mab_id,
--- mix meta
- mab_mix_label,
- mab_mix_name_std,
- mab_mix_type,
- mab_mix_name_other,
- mab_mix_lanlid,
--- mab meta
- mab_name_std,
- mabmeta.mab_lanl_id AS mab_lanlid,
- mab_hxb2_location,
- mab_ab_binding_type,
- mab_isotype,
- mabmeta.donor_id AS mab_donorid,
--- donor meta
- donormeta.donor_species AS mab_donor_species,
- donormeta.donor_clade AS mab_donor_clade,
- donormeta.donor_code AS mab_donor_code
-
-FROM MAbMix mix
-
-LEFT JOIN MAbMixMetadata mixmeta ON mix.mab_mix_id = mixmeta.mab_mix_id
-LEFT JOIN mab_metadata mabmeta ON mix.mab_id = mabmeta.mab_id
-LEFT JOIN donor_metadata donormeta ON mabmeta.donor_id = donormeta.donor_id
\ No newline at end of file
diff --git a/resources/queries/cds/MAbMixMAbMetaForLearnExport.query.xml b/resources/queries/cds/MAbMixMAbMetaForLearnExport.query.xml
deleted file mode 100644
index 603cd2116..000000000
--- a/resources/queries/cds/MAbMixMAbMetaForLearnExport.query.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-
-
-
-
-
-
- MAb ID
- Unique ID assigned to an individual mAb
-
-
- MAb Name
- A standardized name given to an individual mAb
-
-
- LANL ID
- Unique ID of the mAb assigned by LANL and used in the LANL database
-
-
- HXB2 Location
- Epitope position numbers in the HXB2 reference strain
-
-
- MAb Binding Type
- MAb classification indicating the binding site e.g., a region (like V3) or near a common functional domain (like the CD4 binding site, CD4BS)
-
-
- MAb Isotype
- MAb classification indicating the type of the antibody
-
-
- MAb Donor ID
- Unique ID assigned to the donor of the mab
-
-
- MAb Donor Species
- The species of the donor of the mab. The species in which the immune response was stimulated.
-
-
- MAb Donor Clade
- The clade of the virus strain (subtype) that infected the donor
-
-
- MAb Mixture ID
- Unique ID assigned to an individual mAb or mixture of mAbs
-
-
- MAb or Mixture Standardized Name
- A standardized name assigned to an individual mAb or a mixture of mAbs
-
-
- MAb Label
- A label (MAb name) assigned to an individual mAb or a mixture of mAbs to distinguish them from MAbs/mixtures with the same standardized name, e.g., when mAbs with the same standardized name are compared within a study
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/MAbMixMAbMetaForLearnExport.sql b/resources/queries/cds/MAbMixMAbMetaForLearnExport.sql
deleted file mode 100644
index e031a8ebc..000000000
--- a/resources/queries/cds/MAbMixMAbMetaForLearnExport.sql
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
--- This script is the same as MAbMixMAbMeta.sql, creating this script specifically for the Learn > MAbs Export so that the captions/column titles defined in query.xml don't clash with expected captions for Monoclonal Antibodies grid Export
-
-SELECT
--- mabmix
- mix.mab_mix_id,
- mix.mab_id,
--- mix meta
- mab_mix_label,
- mab_mix_name_std,
- mab_mix_type,
- mab_mix_name_other,
- mab_mix_lanlid,
--- mab meta
- mab_name_std,
- mabmeta.mab_lanl_id AS mab_lanlid,
- mab_hxb2_location,
- mab_ab_binding_type,
- mab_isotype,
- mabmeta.donor_id AS mab_donorid,
--- donor meta
- donormeta.donor_species AS mab_donor_species,
- donormeta.donor_clade AS mab_donor_clade
-
-FROM MAbMix mix
-
-LEFT JOIN MAbMixMetadata mixmeta ON mix.mab_mix_id = mixmeta.mab_mix_id
-LEFT JOIN mab_metadata mabmeta ON mix.mab_id = mabmeta.mab_id
-LEFT JOIN donor_metadata donormeta ON mabmeta.donor_id = donormeta.donor_id
\ No newline at end of file
diff --git a/resources/queries/cds/MAbMixMAbMetaForLearnExport/LearnGridExportView.qview.xml b/resources/queries/cds/MAbMixMAbMetaForLearnExport/LearnGridExportView.qview.xml
deleted file mode 100644
index a1606b817..000000000
--- a/resources/queries/cds/MAbMixMAbMetaForLearnExport/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/StudyVisitTagInfo.sql b/resources/queries/cds/StudyVisitTagInfo.sql
deleted file mode 100644
index bb2cee3d3..000000000
--- a/resources/queries/cds/StudyVisitTagInfo.sql
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-s.container.entityid AS container_id,
-s.label AS study_label,
-s.description AS study_description,
-
-sp.TimepointType AS timepoint_type,
-
-vtm.study_group_id.group_name,
-vtm.visit_row_id,
-vtm.is_vaccination,
-vtm.is_challenge,
-vtm.visit_tag_label,
-vtm.detail_label,
-
-v.ProtocolDay AS protocol_day,
-v.Label AS visit_label,
-v.SequenceNumMin AS sequence_num_min,
-v.SequenceNumMax AS sequence_num_max,
-
-vt.name AS visit_tag_name,
-vt.caption AS visit_tag_caption,
-vt.singleuse AS single_use,
-
-ta.coded_label AS group_label
-
-FROM visittagmap vtm
-FULL JOIN study.StudyProperties sp ON sp.container = vtm.container
-LEFT JOIN cds.Study s ON s.study_name = sp.Label
-LEFT JOIN study.Visit v ON v.rowid = vtm.visit_row_id
-LEFT JOIN study.VisitTag vt ON vtm.visit_tag = vt.name
-LEFT JOIN cds.treatmentarm ta ON ta.container = vtm.container AND ta.arm_id = vtm.arm_id
-WHERE s.label IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/cds/UserStudyAccess.sql b/resources/queries/cds/UserStudyAccess.sql
deleted file mode 100644
index 63df46c7e..000000000
--- a/resources/queries/cds/UserStudyAccess.sql
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- studies that have data added
-SELECT
- allStudy.study_name AS "StudyWithData",
- study.study_name IS NOT NULL AS "accessible"
-FROM
-cds.metadata.study allStudy
-LEFT JOIN cds.study study
-ON allStudy.study_name=study.study_name
-INNER JOIN
-(
- SELECT DISTINCT
- sa.prot
- FROM cds.metadata.studyassay sa
- WHERE sa.has_data = true
-) noEmptyStudy
-ON allStudy.study_name = noEmptyStudy.prot
\ No newline at end of file
diff --git a/resources/queries/cds/alignment_mab_metadata.sql b/resources/queries/cds/alignment_mab_metadata.sql
deleted file mode 100644
index be830c46c..000000000
--- a/resources/queries/cds/alignment_mab_metadata.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-SELECT *
-FROM cds.alignment a
- INNER JOIN cds.donor_mab_sequence dseq ON a.sequence_id = dseq.sequence_id
- INNER JOIN cds.mab_metadata mm ON dseq.mab_id = mm.mab_id
\ No newline at end of file
diff --git a/resources/queries/cds/assayCombinedAntigenPanel.sql b/resources/queries/cds/assayCombinedAntigenPanel.sql
deleted file mode 100644
index f3d668b0a..000000000
--- a/resources/queries/cds/assayCombinedAntigenPanel.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-SELECT apm.panel_name, ac.antigen_cds_id, ap.cds_panel_id FROM cds.assay_combined_antigen_metadata ac
-INNER JOIN cds.antigenPanel ap ON ac.antigen_cds_id = ap.cds_ag_id
-INNER JOIN cds.antigenPanelMeta apm ON apm.cds_panel_id = ap.cds_panel_id
\ No newline at end of file
diff --git a/resources/queries/cds/assay_combined_antigen_metadata/LearnGridExportView.qview.xml b/resources/queries/cds/assay_combined_antigen_metadata/LearnGridExportView.qview.xml
deleted file mode 100644
index 754882e67..000000000
--- a/resources/queries/cds/assay_combined_antigen_metadata/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/bamaAntigenWithPanelMeta.sql b/resources/queries/cds/bamaAntigenWithPanelMeta.sql
deleted file mode 100644
index 2bd689e3b..000000000
--- a/resources/queries/cds/bamaAntigenWithPanelMeta.sql
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- bama.assay_identifier,
- bama.cds_ag_id,
- bama.antigen_full_name,
- bama.antigen_short_name,
- bama.antigen_plot_label,
- bama.antigen_name_other,
- bama.dna_construct_id,
- bama.antigen_type_component,
- bama.antigen_category,
- bama.antigen_type_region,
- bama.antigen_type_scaffold,
- bama.antigen_type_modifiers,
- bama.antigen_type_tags,
- bama.antigen_type_differentiate,
- bama.antigen_control,
- bama.isolate_name_component,
- bama.isolate_species,
- bama.isolate_donor_id,
- bama.isolate_differentiate,
- bama.isolate_clade,
- bama.isolate_clone,
- bama.isolate_mutations,
- bama.isolate_cloner_pi,
- bama.isolate_country_origin,
- bama.isolate_yr_isolated,
- bama.isolate_fiebig_stage,
- bama.isolate_accession_num,
- bama.production_component,
- bama.production_host_cell,
- bama.production_purification_method,
- bama.production_special_reagent,
- bama.production_manufacturer,
- bama.production_codon_optimization,
- bama.transfection_method,
- bama.transmitter_founder_status,
- GROUP_CONCAT(DISTINCT apm.panel_name, '|') AS panel_names
-FROM cds.bamaantigen bama
- LEFT JOIN cds.antigenPanel ap ON ap.cds_ag_id = bama.cds_ag_id
- LEFT JOIN cds.antigenPanelMeta apm ON apm.cds_panel_id = ap.cds_panel_id
-
-GROUP BY
- bama.assay_identifier,
- bama.cds_ag_id,
- bama.antigen_full_name,
- bama.antigen_short_name,
- bama.antigen_plot_label,
- bama.antigen_name_other,
- bama.dna_construct_id,
- bama.antigen_type_component,
- bama.antigen_category,
- bama.antigen_type_region,
- bama.antigen_type_scaffold,
- bama.antigen_type_modifiers,
- bama.antigen_type_tags,
- bama.antigen_type_differentiate,
- bama.antigen_control,
- bama.isolate_name_component,
- bama.isolate_species,
- bama.isolate_donor_id,
- bama.isolate_differentiate,
- bama.isolate_clade,
- bama.isolate_clone,
- bama.isolate_mutations,
- bama.isolate_cloner_pi,
- bama.isolate_country_origin,
- bama.isolate_yr_isolated,
- bama.isolate_fiebig_stage,
- bama.isolate_accession_num,
- bama.production_component,
- bama.production_host_cell,
- bama.production_purification_method,
- bama.production_special_reagent,
- bama.production_manufacturer,
- bama.production_codon_optimization,
- bama.transfection_method,
- bama.transmitter_founder_status
\ No newline at end of file
diff --git a/resources/queries/cds/bamaantigen/AssayAntigenExportView.qview.xml b/resources/queries/cds/bamaantigen/AssayAntigenExportView.qview.xml
deleted file mode 100644
index ee4ad79be..000000000
--- a/resources/queries/cds/bamaantigen/AssayAntigenExportView.qview.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/donor_mab.sql b/resources/queries/cds/donor_mab.sql
deleted file mode 100644
index 42a4dc421..000000000
--- a/resources/queries/cds/donor_mab.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-SELECT DISTINCT dms.mab_id,
- dms.donor_id
-FROM donor_mab_sequence AS dms
-WHERE dms.donor_id IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/cds/donor_mab_sequence_alignment.sql b/resources/queries/cds/donor_mab_sequence_alignment.sql
deleted file mode 100644
index 495faa2e3..000000000
--- a/resources/queries/cds/donor_mab_sequence_alignment.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-SELECT *
-FROM alignment ali
- JOIN donor_mab_sequence AS dms ON dms.sequence_id = ali.sequence_id
\ No newline at end of file
diff --git a/resources/queries/cds/donor_mab_sequence_germline.sql b/resources/queries/cds/donor_mab_sequence_germline.sql
deleted file mode 100644
index 211f4d235..000000000
--- a/resources/queries/cds/donor_mab_sequence_germline.sql
+++ /dev/null
@@ -1,12 +0,0 @@
-SELECT dms.mab_id,
- dms.donor_id,
- sgl.sequence_id,
- sgl.allele,
- sgl.percent_identity,
- sgl.matches,
- sgl.alignment_length,
- sgl.score,
- sgl.container,
- sgl.run_application
-FROM sequence_germline AS sgl
- JOIN donor_mab_sequence AS dms ON dms.sequence_id = sgl.sequence_id
\ No newline at end of file
diff --git a/resources/queries/cds/donor_mab_sequence_header_source.sql b/resources/queries/cds/donor_mab_sequence_header_source.sql
deleted file mode 100644
index f02db4edf..000000000
--- a/resources/queries/cds/donor_mab_sequence_header_source.sql
+++ /dev/null
@@ -1,15 +0,0 @@
-SELECT seq.sequence_id,
- dms.mab_id,
- dms.donor_id,
- mab.mab_name_std,
- don.donor_code,
- sqh.header,
- src.source,
- seq.sequence_aa,
- seq.sequence_nt
-FROM sequence seq
- JOIN donor_mab_sequence AS dms ON dms.sequence_id = seq.sequence_id
- JOIN sequence_header AS sqh ON sqh.sequence_id = seq.sequence_id
- JOIN header_source AS src ON src.source_id = sqh.source_id
- LEFT JOIN mab_metadata AS mab ON mab.mab_id = dms.mab_id
- LEFT JOIN donor_metadata AS don ON don.donor_id = dms.donor_id
\ No newline at end of file
diff --git a/resources/queries/cds/ds_assay.sql b/resources/queries/cds/ds_assay.sql
deleted file mode 100644
index 62a8f1bdf..000000000
--- a/resources/queries/cds/ds_assay.sql
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- IA.assay_identifier,
- assay_type,
- assay_label,
- assay_short_name,
- assay_category,
- assay_detection_platform,
- assay_body_system_type,
- assay_body_system_target,
- assay_general_specimen_type,
- assay_description,
- assay_method_description,
- assay_endpoint_description,
- assay_endpoint_statistical_analysis
- FROM cds.import_assay as IA
- INNER JOIN (
- SELECT DISTINCT
- assay_identifier,
- assay_type
- FROM cds.ds_subjectassay
-
- UNION
- SELECT DISTINCT
- assay_identifier,
- 'NABMAb' AS assay_type
- FROM cds.ds_nabmab
-
- ) AS SA ON IA.assay_identifier=SA.assay_identifier
-
-UNION
-
-SELECT
- IA.assay_identifier,
- NULL AS assay_type, --Note: this may need to be updated, it is not yet clear what assay_type values will be for Non-Integrated Assay. Updating this would also require updating learn_assay.sql.
- assay_label,
- assay_short_name,
- assay_category,
- assay_detection_platform,
- assay_body_system_type,
- assay_body_system_target,
- assay_general_specimen_type,
- assay_description,
- assay_method_description,
- assay_endpoint_description,
- assay_endpoint_statistical_analysis
- FROM cds.import_assay as IA
- INNER JOIN cds.import_document ID ON IA.assay_identifier=ID.assay_identifier WHERE ID.document_type='Non-Integrated Assay'
\ No newline at end of file
diff --git a/resources/queries/cds/ds_bama.sql b/resources/queries/cds/ds_bama.sql
deleted file mode 100644
index d8ce67d06..000000000
--- a/resources/queries/cds/ds_bama.sql
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-subject_id AS participantid,
-CAST(study_day AS DOUBLE) AS sequencenum,
-study_day AS visit_day,
-prot AS study_prot,
-prot,
-
--- DIMENSIONS
-assay_identifier,
-exp_assayid,
-specimen_type,
-antigen,
-antigen_type,
-antibody_isotype,
-summary_level,
-protein,
-protein_panel,
-clade,
-vaccine_matched,
-detection_ligand,
-instrument_code,
-lab_code,
-bama_lab_source_key,
-dilution,
-
--- MEASURES
-bama_response AS response_call,
-mfi_delta,
-mfi_delta_baseline,
-mfi_raw,
-mfi_raw_baseline,
-mfi_blank,
-mfi_blank_baseline,
-mfi_bkgd,
-mfi_bkgd_blank,
-auc
-
-FROM cds.import_bama
\ No newline at end of file
diff --git a/resources/queries/cds/ds_bamaantigen.sql b/resources/queries/cds/ds_bamaantigen.sql
deleted file mode 100644
index d3a53265d..000000000
--- a/resources/queries/cds/ds_bamaantigen.sql
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- bama.assay_identifier,
- bama.cds_ag_id,
- bama.antigen_full_name,
- bama.antigen_short_name,
- bama.antigen_plot_label,
- bama.antigen_name_other,
- bama.dna_construct_id,
- bama.antigen_type_component,
- bama.antigen_category,
- bama.antigen_type_region,
- bama.antigen_type_scaffold,
- bama.antigen_type_modifiers,
- bama.antigen_type_tags,
- bama.antigen_type_differentiate,
- bama.antigen_control,
- bama.isolate_name_component,
- bama.isolate_species,
- bama.isolate_donor_id,
- bama.isolate_differentiate,
- bama.isolate_clade,
- bama.isolate_clone,
- bama.isolate_mutations,
- bama.isolate_cloner_pi,
- bama.isolate_country_origin,
- bama.isolate_yr_isolated,
- bama.isolate_fiebig_stage,
- bama.isolate_accession_num,
- bama.production_component,
- bama.production_host_cell,
- bama.production_purification_method,
- bama.production_special_reagent,
- bama.production_manufacturer,
- bama.production_codon_optimization,
- bama.transfection_method,
- bama.transmitter_founder_status
-FROM cds.import_BAMAAntigen bama
\ No newline at end of file
diff --git a/resources/queries/cds/ds_bcr_sequence_study.sql b/resources/queries/cds/ds_bcr_sequence_study.sql
deleted file mode 100644
index 86ad79ca3..000000000
--- a/resources/queries/cds/ds_bcr_sequence_study.sql
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright (c) 2015-2025 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- subject_id AS participantid,
- CAST(study_day AS DOUBLE) AS sequencenum,
- study_day AS visit_day,
- prot AS study_prot,
- prot,
- specimen_type,
- bcr_study_seq_id,
- lab_code,
- seq_method,
- assay_identifier,
- plate,
- well
-
-FROM cds.import_bcr_sequence_study
\ No newline at end of file
diff --git a/resources/queries/cds/ds_demographics.sql b/resources/queries/cds/ds_demographics.sql
deleted file mode 100644
index b7236aa93..000000000
--- a/resources/queries/cds/ds_demographics.sql
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- -- KEYS
- dd.prot AS study_prot,
- dd.prot,
- dd.subject_id AS participantid,
-
- -- VARCHAR
- dd.subject_species AS species,
- dd.subject_subspecies AS subspecies,
- dd.subject_sex_at_birth AS sexatbirth,
- dd.subject_gender_identity AS genderidentity,
- dd.subject_race_nih AS race,
- dd.subject_hispanic AS ethnicity,
- dd.subject_country_enrollment AS country_enrollment,
- dd.subject_circumcised_enrollment AS circumcised_enrollment,
- dd.subject_study_cohort AS studycohort,
-
- -- INTEGER
- CAST(ROUND(10 * Floor(dd.subject_age_enrollment_years / 10.0)) AS VARCHAR) || '-' || CAST(ROUND((10 * Floor(dd.subject_age_enrollment_years / 10.0)) + 9) AS VARCHAR) AS agegroup_range,
- CAST(ROUND(10 * Floor(dd.subject_age_enrollment_years / 10.0)) AS INTEGER) AS agegroup_enrollment,
- dd.subject_age_enrollment_years AS age_enrollment,
-
- dd.subject_bmi_enrollment AS bmi_enrollment,
- (CASE WHEN dd.subject_bmi_enrollment IS NULL THEN NULL
- WHEN dd.subject_bmi_enrollment < 18.5 THEN 'Underweight'
- WHEN dd.subject_bmi_enrollment < 24.9 THEN 'Normal Weight'
- WHEN dd.subject_bmi_enrollment < 29.9 THEN 'Overweight'
- ELSE 'Obese'
- END)
- AS bmi_category,
-
- -- import_demographics.subject_bmi_enrollment AS bmi,
-
- -- STUDY RELATED
- istudy.study_label,
- istudy.study_short_name,
- istudy.study_start_date,
- istudy.study_first_enr_date,
- istudy.study_fu_complete_date,
- istudy.study_public_date,
- istudy.network AS study_network,
- istudy.study_grant_pi_name AS study_grant_pi_name,
- istudy.study_strategy AS study_strategy,
- it.study_arm_last_exp_vacc_day AS study_last_vaccination_day,
- istudy.study_type,
-
- -- TREATMENT RELATED
- it.study_part,
- it.study_group,
- it.study_arm,
- -- NOTE: this is duplicated from ds_treatmentarm.sql with the exception of including the study label prefix (issue 24492)
- CASE WHEN (it.study_group = it.study_arm) THEN (istudy.study_label || ' Group ' || it.study_group || ' ' || it.study_randomization) -- e.g. Group 1 Vaccine
- ELSE
- CASE WHEN (it.study_group LIKE 'Group%' OR it.study_group LIKE 'group%')
- THEN (istudy.study_label || ' ' || it.study_group || ' Arm ' || it.study_arm || ' ' || it.study_randomization) -- e.g. Group 1 Arm 2 Vaccine
- ELSE (istudy.study_label || ' Group ' || it.study_group || ' Arm ' || it.study_arm || ' ' || it.study_randomization) -- e.g. Group 1 Arm 2 Vaccine
- END
- END AS study_arm_summary,
- it.study_arm_description_coded_label AS study_arm_coded_label,
- it.study_randomization,
- it.product_class_combination_label AS study_product_class_combination,
- it.product_combination_label AS study_product_combination
-
-FROM cds.import_studysubject AS dd
-LEFT JOIN cds.import_study AS istudy
- ON istudy.prot = dd.prot
-LEFT JOIN cds.import_studypartgrouparmsubject AS its
- ON its.prot = dd.prot AND its.subject_id = dd.subject_id
-LEFT JOIN cds.import_studypartgrouparm it
- ON it.prot = dd.prot AND it.study_part = its.study_part
- AND it.study_group = its.study_group AND it.study_arm = its.study_arm
diff --git a/resources/queries/cds/ds_document.sql b/resources/queries/cds/ds_document.sql
deleted file mode 100644
index 44acb3b8a..000000000
--- a/resources/queries/cds/ds_document.sql
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright (c) 2016 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT *
-FROM cds.import_document
diff --git a/resources/queries/cds/ds_elispot.sql b/resources/queries/cds/ds_elispot.sql
deleted file mode 100644
index e943db353..000000000
--- a/resources/queries/cds/ds_elispot.sql
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-subject_id AS participantid,
-CAST(study_day AS DOUBLE) AS sequencenum,
-study_day AS visit_day,
-prot AS study_prot,
-prot,
-
--- DIMENSIONS
-summary_level,
-specimen_type,
-assay_identifier,
-antigen,
-antigen_type,
-cell_type,
-cell_name,
-clade,
-protein_panel,
-protein,
-peptide_pool,
--- Delimiter has to match ChartUtil.ANTIGEN_LEVEL_DELIMITER
-(CASE WHEN protein_panel IS NULL THEN 'null' ELSE protein_panel END)
- || '|||' || (CASE WHEN protein IS NULL THEN 'null' ELSE protein END)
- AS protein_panel_protein,
-(CASE WHEN protein_panel IS NULL THEN 'null' ELSE protein_panel END)
- || '|||' || (CASE WHEN protein IS NULL THEN 'null' ELSE protein END)
- || '|||' || (CASE WHEN peptide_pool IS NULL THEN 'null' ELSE peptide_pool END)
- AS protein_panel_protein_peptide_pool,
-vaccine_matched,
-functional_marker_name,
-functional_marker_type,
-
--- LOOKUPS
-els_ifng_lab_source_key,
-lab_code,
-exp_assayid,
-
--- MEASURES
-els_ifng_response AS response_call,
-mean_sfc,
-mean_sfc_neg,
-mean_sfc_raw
-
-FROM cds.import_ELS_IFNg
\ No newline at end of file
diff --git a/resources/queries/cds/ds_elispotantigen.sql b/resources/queries/cds/ds_elispotantigen.sql
deleted file mode 100644
index 3e96c9f90..000000000
--- a/resources/queries/cds/ds_elispotantigen.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- assay_identifier,
- antigen_name,
- antigen_type,
- protein_panel,
- protein,
- peptide_pool,
- clade,
- antigen_description,
- antigen_control
-FROM cds.import_ELISpotAntigen
\ No newline at end of file
diff --git a/resources/queries/cds/ds_facts.sql b/resources/queries/cds/ds_facts.sql
deleted file mode 100644
index 28223888a..000000000
--- a/resources/queries/cds/ds_facts.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DD.participantid,
-DD.folder.entityid as container,
-DD.container as study,
-S.label AS study_label,
-TA.coded_label AS treatment_arm,
-DD.participantid || '-product' AS product_group
-FROM study.demographics AS DD
-LEFT JOIN cds.treatmentarmsubjectmap AS TSM ON (DD.participantid = TSM.participantid AND DD.container = TSM.container)
-LEFT JOIN cds.treatmentarm AS TA ON (TSM.arm_id = TA.arm_id)
-LEFT JOIN cds.study AS S ON (DD.container = S.container)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_ics.sql b/resources/queries/cds/ds_ics.sql
deleted file mode 100644
index 779fb4da6..000000000
--- a/resources/queries/cds/ds_ics.sql
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-subject_id AS participantid,
-CAST(study_day AS DOUBLE) AS sequencenum,
-study_day AS visit_day,
-prot AS study_prot,
-prot,
-assay_identifier,
-
--- DIMENSIONS
-summary_level,
-specimen_type,
-cell_type,
-cell_name,
-antigen,
-antigen_type,
-protein_panel,
-protein,
-peptide_pool,
--- Delimiter has to match ChartUtil.ANTIGEN_LEVEL_DELIMITER
-(CASE WHEN protein_panel IS NULL THEN 'null' ELSE protein_panel END)
- || '|||' || (CASE WHEN protein IS NULL THEN 'null' ELSE protein END)
- AS protein_panel_protein,
-(CASE WHEN protein_panel IS NULL THEN 'null' ELSE protein_panel END)
- || '|||' || (CASE WHEN protein IS NULL THEN 'null' ELSE protein END)
- || '|||' || (CASE WHEN peptide_pool IS NULL THEN 'null' ELSE peptide_pool END)
- AS protein_panel_protein_peptide_pool,
-functional_marker_name,
-functional_marker_type,
-clade,
-vaccine_matched,
-
--- LOOKUPS
-ics_lab_source_key,
-exp_assayid,
-lab_code,
-
--- MEASURES
-ics_response AS response_call,
-pctpos,
-pctpos_adj,
-pctpos_neg,
-control,
-pooled_info,
-response_method,
-functionality_score,
-polyfunctionality_score
-
-FROM cds.import_ics
\ No newline at end of file
diff --git a/resources/queries/cds/ds_icsantigen.sql b/resources/queries/cds/ds_icsantigen.sql
deleted file mode 100644
index 89dcc4d3f..000000000
--- a/resources/queries/cds/ds_icsantigen.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- assay_identifier,
- antigen_name,
- antigen_type,
- protein_panel,
- protein,
- peptide_pool,
- clade,
- antigen_description,
- antigen_control
-FROM cds.import_ICSAntigen
\ No newline at end of file
diff --git a/resources/queries/cds/ds_lab.sql b/resources/queries/cds/ds_lab.sql
deleted file mode 100644
index c0d26534f..000000000
--- a/resources/queries/cds/ds_lab.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- lab_code,
- lab_name,
- lab_pi_name
-FROM cds.import_lab
\ No newline at end of file
diff --git a/resources/queries/cds/ds_mabmetasummary.sql b/resources/queries/cds/ds_mabmetasummary.sql
deleted file mode 100644
index f18346a78..000000000
--- a/resources/queries/cds/ds_mabmetasummary.sql
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- mixmeta.mab_mix_name_std,
- mixmeta.mab_mix_id,
- mixmeta.mab_mix_type,
- mix.mab_id,
- mixmeta.container,
- mabmeta.mab_hxb2_location,
- mabmeta.mab_ab_binding_type,
- mabmeta.mab_isotype,
- donormeta.donor_species AS mab_donor_species
-
-FROM cds.MAbMix mix
-JOIN cds.MAbMixMetadata mixmeta ON (mixmeta.container = mix.container AND mixmeta.mab_mix_id = mix.mab_mix_id)
-JOIN cds.mab_metadata mabmeta ON (mabmeta.container = mix.container AND mabmeta.mab_id = mix.mab_id)
-LEFT JOIN cds.donor_metadata donormeta ON (donormeta.container = mix.container AND donormeta.donor_id = mabmeta.donor_id)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_mixlabels.sql b/resources/queries/cds/ds_mixlabels.sql
deleted file mode 100644
index c6ee5973a..000000000
--- a/resources/queries/cds/ds_mixlabels.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT tidy_mix.mab_mix_name_std, GROUP_CONCAT(DISTINCT tidy_mix.mab_mix_label, '; ') as mab_label
-FROM (
- SELECT * FROM cds.MAbMixMetadata raw_mix WHERE raw_mix.mab_mix_name_std <> raw_mix.mab_mix_label
- ) tidy_mix
-GROUP BY tidy_mix.mab_mix_name_std
\ No newline at end of file
diff --git a/resources/queries/cds/ds_nab.sql b/resources/queries/cds/ds_nab.sql
deleted file mode 100644
index 2f96a3366..000000000
--- a/resources/queries/cds/ds_nab.sql
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-nab.subject_id AS participantid,
-CAST(nab.study_day AS DOUBLE) AS sequencenum,
-nab.study_day AS visit_day,
-nab.prot AS study_prot,
-nab.prot,
-nab.assay_identifier,
-
--- DIMENSIONS
-nab.summary_level,
-nab.specimen_type,
-na.antigen_name as antigen,
-na.antigen_type,
-na.neutralization_tier,
-na.clade,
--- Delimiter has to match ChartUtil.ANTIGEN_LEVEL_DELIMITER
-(CASE WHEN na.neutralization_tier IS NULL THEN 'null' ELSE na.neutralization_tier END)
- || '|||' || (CASE WHEN na.clade IS NULL THEN 'null' ELSE na.clade END)
- || '|||' || (CASE WHEN na.virus IS NULL THEN 'null' ELSE na.virus END)
- AS tier_clade_virus,
-nab.vaccine_matched,
-nab.target_cell,
-nab.initial_dilution,
-na.virus,
-na.virus_type,
-na.virus_full_name,
-na.virus_species,
-na.virus_host_cell,
-na.virus_backbone,
-na.virus_insert_name,
-
--- LOOKUPS
-nab.nab_lab_source_key,
-nab.exp_assayid,
-nab.lab_code,
-
--- MEASURES
-nab.nab_response AS response_call,
-nab.titer_ic50,
-nab.titer_ic80,
-nab.nab_response_ID50,
-nab.nab_response_ID80,
-nab.titer_ID50,
-nab.titer_ID80,
-nab.slope
-
-FROM cds.import_nab nab left join cds.import_nabantigen na on na.cds_virus_id = nab.cds_virus_id AND na.assay_identifier = nab.assay_identifier
\ No newline at end of file
diff --git a/resources/queries/cds/ds_nabantigen.sql b/resources/queries/cds/ds_nabantigen.sql
deleted file mode 100644
index 502eb8bb2..000000000
--- a/resources/queries/cds/ds_nabantigen.sql
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- assay_identifier,
- antigen_name,
- antigen_type,
- virus,
- virus_type,
- virus_insert_name,
- neutralization_tier,
- clade,
- antigen_description,
- antigen_control,
- virus_full_name,
- virus_name_other,
- virus_species,
- virus_host_cell,
- virus_backbone,
- cds_virus_id
-
-FROM cds.import_NAbAntigen
\ No newline at end of file
diff --git a/resources/queries/cds/ds_nabmab.sql b/resources/queries/cds/ds_nabmab.sql
deleted file mode 100644
index 80a96a76b..000000000
--- a/resources/queries/cds/ds_nabmab.sql
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- dd.prot,
- 0 AS sequencenum,
- dd.mab_mix_id AS participantid,
- dd.mab_mix_id,
- dd.mab_name_source,
- dd.summary_level,
- dd.target_cell,
- dd.assay_identifier,
- dd.mab_concentration,
- dd.mab_concentration_units,
- dd.specimen_concentration_id,
- dd.curve_id,
- dd.specimen_type,
- dd.lab_code,
- na.virus,
- dd.initial_concentration,
- dd.min_concentration,
- dd.max_concentration,
- dd.percent_neutralization,
- dd.neutralization_plus_minus,
- dd.min_well_value,
- dd.max_well_value,
- dd.mean_well_value,
- dd.well_std_dev,
- dd.titer_curve_ic50,
- dd.titer_curve_ic80,
- dd.nab_response_ic50,
- dd.nab_response_ic80,
- dd.titer_point_ic50,
- dd.titer_point_ic80,
- dd.slope,
- na.virus_type,
- na.virus_full_name,
- na.virus_species,
- na.virus_host_cell,
- na.virus_backbone,
- dd.virus_dilution,
- na.clade,
- na.neutralization_tier,
- -- Delimiter has to match ChartUtil.ANTIGEN_LEVEL_DELIMITER
- (CASE WHEN na.neutralization_tier IS NULL THEN 'null' ELSE na.neutralization_tier END)
- || '|||' || (CASE WHEN na.clade IS NULL THEN 'null' ELSE na.clade END)
- || '|||' || (CASE WHEN na.virus IS NULL THEN 'null' ELSE na.virus END)
- AS tier_clade_virus,
- dd.fit_min,
- dd.fit_max,
- dd.fit_asymmetry,
- dd.fit_slope,
- dd.fit_inflection,
- dd.fit_error,
- dd.vaccine_matched,
- dd.virus_control_mean,
- dd.cell_control_mean
-
-FROM cds.import_NABMAb AS dd left join cds.import_nabantigen na on na.cds_virus_id = dd.cds_virus_id AND na.assay_identifier = dd.assay_identifier
\ No newline at end of file
diff --git a/resources/queries/cds/ds_pkmab.sql b/resources/queries/cds/ds_pkmab.sql
deleted file mode 100644
index 258f85f9c..000000000
--- a/resources/queries/cds/ds_pkmab.sql
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright (c) 2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- dd.subject_id AS participantid,
- CAST(dd.study_day AS DOUBLE) AS sequencenum,
-
- dd.study_day AS visit_day,
- dd.prot AS study_prot,
- dd.prot,
-
- dd.visit_code,
- VT.visit_time_label,
- VT.hours_post_initial_infusion,
- VT.hours_post_recent_infusion,
- dd.source_assay,
-
- dd.assay_identifier,
- dd.summary_level,
- dd.specimen_type,
- dd.lab_code,
-
- dd.mab_mix_id,
- mixmeta.mab_mix_name_std,
- mixmeta.mab_mix_label,
- dd.mab_name_source,
- dd.mab_concentration,
- dd.mab_concentration_units,
- dd.lloq,
- dd.lloq_units
-
-FROM cds.import_PKMAb AS dd
-LEFT JOIN MAbMixMetadata mixmeta ON dd.mab_mix_id = mixmeta.mab_mix_id and dd.container = mixmeta.container
-LEFT JOIN (
- SELECT subjectvisit.subject_id,
- subjectvisit.visit_code,
- subjectvisit.container,
- visittime.visit_time_label,
- visittime.hours_post_initial_infusion,
- visittime.hours_post_recent_infusion
- FROM
- (SELECT DISTINCT subject_id, visit_code, container FROM import_pkmab) AS subjectvisit
- LEFT JOIN
- import_studypartgrouparmsubject AS subjectgroup
- ON subjectgroup.subject_id = subjectvisit.subject_id
- AND subjectgroup.container = subjectvisit.container
- LEFT JOIN
- import_studypartgrouparmvisittime AS visittime
- ON subjectgroup.prot = visittime.prot
- AND subjectgroup.study_arm = visittime.study_arm
- AND subjectgroup.study_group = visittime.study_group
- AND subjectvisit.visit_code = visittime.visit_code
- AND subjectgroup.container = visittime.container
- ) AS VT ON dd.container = VT.container AND dd.subject_id = VT.subject_id AND dd.visit_code = VT.visit_code
-
diff --git a/resources/queries/cds/ds_product.sql b/resources/queries/cds/ds_product.sql
deleted file mode 100644
index 6284671d3..000000000
--- a/resources/queries/cds/ds_product.sql
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT *
-FROM cds.import_product
\ No newline at end of file
diff --git a/resources/queries/cds/ds_properties.sql b/resources/queries/cds/ds_properties.sql
deleted file mode 100644
index e6c5acb74..000000000
--- a/resources/queries/cds/ds_properties.sql
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-CAST(SUM(assays) AS INTEGER) AS assays,
-CAST(SUM(studies) AS INTEGER) AS studies,
-CAST(SUM(subjects) AS INTEGER) AS subjects,
-CAST(SUM(products) AS INTEGER) AS products,
-CAST(SUM(datacount) AS INTEGER) AS datacount,
-CAST(SUM(subjectlevelstudies) AS INTEGER) AS subjectlevelstudies
-FROM (
- -- assays
- SELECT
- COUNT(assay.assay_identifier) AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- 0 AS datacount,
- 0 AS subjectlevelstudies
- FROM cds.assay AS assay
-
- UNION
-
- -- studies
- SELECT
- 0 AS assays,
- COUNT(study.study_name) AS studies,
- 0 AS subjects,
- 0 AS products,
- 0 AS datacount,
- 0 AS subjectlevelstudies
- FROM cds.study AS study
-
- UNION
-
- -- studies with subject-level data
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- 0 AS datacount,
- COUNT(DISTINCT demographics.study_label) AS subjectlevelstudies
- FROM study.Demographics AS demographics
-
- UNION
- -- subjects
- SELECT
- 0 AS assays,
- 0 AS studies,
- COUNT(*) AS subjects,
- 0 AS products,
- 0 AS datacount,
- 0 AS subjectlevelstudies
- FROM study.Demographics
-
- UNION
-
- -- products
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- COUNT(*) AS products,
- 0 AS datacount,
- 0 AS subjectlevelstudies
- FROM cds.Product
-
- UNION
-
- -- datacount
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- COUNT(*) AS datacount,
- 0 AS subjectlevelstudies
- FROM study.ICS
-
- UNION
-
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- COUNT(*) AS datacount,
- 0 AS subjectlevelstudies
- FROM study.ELISPOT
-
- UNION
-
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- COUNT(*) AS datacount,
- 0 AS subjectlevelstudies
- FROM study.NAb
-
- UNION
-
- SELECT
- 0 AS assays,
- 0 AS studies,
- 0 AS subjects,
- 0 AS products,
- COUNT(*) AS datacount,
- 0 AS subjectlevelstudies
- FROM study.BAMA
-) _union_
\ No newline at end of file
diff --git a/resources/queries/cds/ds_publication.sql b/resources/queries/cds/ds_publication.sql
deleted file mode 100644
index 9d5a67b6b..000000000
--- a/resources/queries/cds/ds_publication.sql
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Copyright (c) 2016-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- publication_id AS id,
- publication_title AS title,
- publication_author_all AS author_all,
- publication_journal_short AS journal_short,
- publication_date AS date,
- publication_volume AS volume,
- publication_issue AS issue,
- publication_location AS location,
- publication_pmid AS pmid,
- publication_link AS link,
- publication_author_first AS author_first,
- publication_label AS publication_label,
- publication_abstract AS publication_abstract
-FROM cds.import_Publication
\ No newline at end of file
diff --git a/resources/queries/cds/ds_study.sql b/resources/queries/cds/ds_study.sql
deleted file mode 100644
index 36bad53c3..000000000
--- a/resources/queries/cds/ds_study.sql
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
--- KEYS
-import_study.prot AS study_name,
-containers.EntityId AS container,
-
--- VARCHAR
-import_study.network,
-import_study.study_label AS label,
-import_study.study_short_name AS short_name,
-import_study.study_title AS title,
-import_study.study_type AS type,
-import_study.study_status AS status,
-import_study.study_stage AS stage,
-import_study.study_species AS species,
-import_study.study_population AS population,
-import_study.study_primary_poc_name AS primary_poc_name,
-import_study.study_primary_poc_email AS primary_poc_email,
-import_study.study_grant_pi_name AS grant_pi_name,
-import_study.study_grant_pi_email AS grant_pi_email,
-import_study.study_grant_pm_name AS grant_pm_name,
-import_study.study_grant_pm_email AS grant_pm_email,
-import_study.study_investigator_name AS investigator_name,
-import_study.study_investigator_email AS investigator_email,
-import_study.study_strategy AS strategy,
-
--- DATE
-import_study.study_first_enr_date AS first_enr_date,
-import_study.study_fu_complete_date AS followup_complete_date,
-import_study.study_start_date AS start_date,
-import_study.study_public_date AS public_date,
-
--- TEXT
-import_study.study_rationale AS rationale,
-import_study.study_description AS description,
-import_study.study_hypothesis AS hypothesis,
-import_study.study_objectives AS objectives,
-import_study.study_methods AS methods,
-import_study.study_findings AS findings,
-import_study.study_discussion AS discussion,
-import_study.study_context AS context,
-import_study.cavd_affiliation AS cavd_affiliation,
-import_study.treatment_schema_link AS treatment_schema_link,
-import_study.assay_schema_link AS assay_schema_link,
-import_study.study_groups AS groups,
-import_study.study_conclusions AS conclusions,
-import_study.study_publications AS publications,
-import_study.study_executive_summary AS executive_summary,
-import_study.study_data_availability AS data_availability,
-import_study.atlas_link AS atlas_link,
-import_study.cavd_link AS cavd_link,
-import_study.study_clintrials_id AS clintrials_id,
-import_study.study_specimen_repository AS specimen_repository_label
-
-FROM cds.import_study AS import_study
-JOIN core.containers AS containers ON (containers.name = import_study.prot)
diff --git a/resources/queries/cds/ds_studyassay.sql b/resources/queries/cds/ds_studyassay.sql
deleted file mode 100644
index 3293b212c..000000000
--- a/resources/queries/cds/ds_studyassay.sql
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright (c) 2016-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT
- md.prot,
- md.assay_identifier,
- md.assay_status,
- md.provenance_source,
- md.provenance_summary,
- d.prot IS NOT NULL AND d.assay_identifier IS NOT NULL AS "has_data"
-FROM import_studyassay md --metadataTable
-LEFT JOIN (
- -- Could use ds_subjectassay, but then we must ensure this is run after that in the ETL
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_ICS
-
- UNION
-
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_nab
-
- UNION
-
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_els_ifng
-
- UNION
-
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_bama
-
- UNION
-
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_nabmab
-
- UNION
-
- SELECT DISTINCT
- prot,
- assay_identifier
- FROM cds.import_pkmab
-) d --dataTable
-ON d.prot=md.prot AND d.assay_identifier=md.assay_identifier
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studydocument.sql b/resources/queries/cds/ds_studydocument.sql
deleted file mode 100644
index 4a5a05105..000000000
--- a/resources/queries/cds/ds_studydocument.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * Copyright (c) 2016-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- imsd.prot AS prot,
- imsd.document_id AS document_id,
- imsd.study_document_order AS document_order,
- imsd.access_level AS access_level
-FROM cds.import_studydocument imsd
diff --git a/resources/queries/cds/ds_studygroup.sql b/resources/queries/cds/ds_studygroup.sql
deleted file mode 100644
index 76af74904..000000000
--- a/resources/queries/cds/ds_studygroup.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DISTINCT study_group AS group_name,
-prot
-FROM
-cds.import_studypartgrouparm
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studygroupvisit.sql b/resources/queries/cds/ds_studygroupvisit.sql
deleted file mode 100644
index 6e0f071fc..000000000
--- a/resources/queries/cds/ds_studygroupvisit.sql
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DISTINCT studygroup.row_id AS group_id,
-visit.rowid AS visit_row_id,
-arm_visit.prot
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-JOIN ( SELECT * FROM cds.studygroup ) AS studygroup ON (studygroup.container.name = arm_visit.prot AND studygroup.group_name = arm_visit.study_group)
-JOIN ( SELECT * FROM study.visit ) AS visit ON (visit.Folder.name = arm_visit.prot AND visit.sequencenummin = CAST(arm_visit.study_day AS DOUBLE))
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studymab.sql b/resources/queries/cds/ds_studymab.sql
deleted file mode 100644
index 20a364c52..000000000
--- a/resources/queries/cds/ds_studymab.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT
- import_nabmab.prot,
- import_nabmab.mab_mix_id
-FROM import_nabmab
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studypartgrouparmproduct.sql b/resources/queries/cds/ds_studypartgrouparmproduct.sql
deleted file mode 100644
index 46069f31a..000000000
--- a/resources/queries/cds/ds_studypartgrouparmproduct.sql
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * Copyright (c) 2016-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT prot,
- study_part,
- study_group,
- study_arm,
- product_id,
- container AS projectContainer
-FROM cds.import_studypartgrouparmproduct
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studyproduct.sql b/resources/queries/cds/ds_studyproduct.sql
deleted file mode 100644
index ca2e9f508..000000000
--- a/resources/queries/cds/ds_studyproduct.sql
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT
- md.prot AS study_name,
- md.prot,
- md.product_id,
- md.container AS projectContainer,
- d.product_id IS NOT NULL AND d.prot IS NOT NULL AS has_data
-FROM import_studyproduct md --metadataTable
---Pulls in real data for each metadata relationship if it exists.
-LEFT JOIN ds_subjectproduct d --dataTable
-ON (
- md.prot=d.prot
- AND md.product_id=d.product_id
-)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_studypublication.sql b/resources/queries/cds/ds_studypublication.sql
deleted file mode 100644
index 3d57c4696..000000000
--- a/resources/queries/cds/ds_studypublication.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * Copyright (c) 2016-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- prot AS prot,
- publication_id AS publication_id,
- study_publication_order AS publication_order
-FROM cds.import_StudyPublication
\ No newline at end of file
diff --git a/resources/queries/cds/ds_subjectassay.sql b/resources/queries/cds/ds_subjectassay.sql
deleted file mode 100644
index 9957e9b74..000000000
--- a/resources/queries/cds/ds_subjectassay.sql
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright (c) 2015-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-participantid,
-assay_identifier,
-assay_type,
-SS.study_name,
-lab_code,
-label
-FROM (
- SELECT
- DISTINCT participantid,
- 'ICS' AS assay_type,
- assay_identifier,
- container,
- lab_code
- FROM study.ICS
-
- UNION
-
- SELECT
- DISTINCT participantid,
- 'NAb' AS assay_type,
- assay_identifier,
- container,
- lab_code
- FROM study.NAb
-
- UNION
-
- SELECT
- DISTINCT participantid,
- 'ELISPOT' AS assay_type,
- assay_identifier,
- container,
- lab_code
- FROM study.ELISpot
-
- UNION
-
- SELECT
- DISTINCT participantid,
- 'BAMA' AS assay_type,
- assay_identifier,
- container,
- lab_code
- FROM study.BAMA
-
- UNION
-
- SELECT
- DISTINCT participantid,
- 'PKMAb' AS assay_type,
- assay_identifier,
- container,
- lab_code
- FROM study.PKMAb
-
-) AS DD
-INNER JOIN cds.study AS SS ON SS.container = DD.container
diff --git a/resources/queries/cds/ds_subjectproduct.sql b/resources/queries/cds/ds_subjectproduct.sql
deleted file mode 100644
index 53a627167..000000000
--- a/resources/queries/cds/ds_subjectproduct.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-ArmProduct.product_id,
-ArmSubject.subject_id AS participantid,
-ProductInsert.insert_name,
-ProductInsert.clade_name,
-ArmProduct.prot,
-ArmProduct.container AS projectContainer
-
-FROM cds.import_studypartgrouparmproduct AS ArmProduct
-JOIN cds.import_studypartgrouparmsubject AS ArmSubject ON (
- ArmSubject.prot = ArmProduct.prot AND
- ArmSubject.study_part = ArmProduct.study_part AND
- ArmSubject.study_group = ArmProduct.study_group AND
- ArmSubject.study_arm = ArmProduct.study_arm
-)
-LEFT JOIN cds.import_productinsert AS ProductInsert ON (
- ProductInsert.product_id = ArmProduct.product_id
-)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_treatmentarm.sql b/resources/queries/cds/ds_treatmentarm.sql
deleted file mode 100644
index a6dd0f6d7..000000000
--- a/resources/queries/cds/ds_treatmentarm.sql
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-(prot || '-' || study_part || '-' || study_group || '-' || study_arm) AS arm_id,
-subCont.EntityId AS container,
-study_part AS arm_part,
-study_group AS arm_group,
-study_arm AS arm_name,
-study_randomization AS randomization,
-study_arm_description AS description,
--- Ignoring study_part for now
-CASE WHEN (study_group = study_arm)
-THEN ('Group ' || study_group || ' ' || study_randomization) -- e.g. Group 1 Vaccine
-ELSE
- CASE WHEN (study_group LIKE 'Group%' OR study_group LIKE 'group%')
- THEN (study_group || ' Arm ' || study_arm || ' ' || study_randomization) -- e.g. Group 1 Arm 2 Vaccine
- ELSE ('Group ' || study_group || ' Arm ' || study_arm || ' ' || study_randomization) -- e.g. Group 1 Arm 2 Vaccine
- END
-END AS coded_label,
--- study_arm_description_coded_label AS coded_label,
-study_arm_last_exp_vacc_day AS last_day,
-prot
-FROM
-cds.import_studypartgrouparm AS arm
-JOIN core.containers AS subCont ON (subCont.name = arm.prot AND arm.container = subCont.parent)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_treatmentarmsubject.sql b/resources/queries/cds/ds_treatmentarmsubject.sql
deleted file mode 100644
index 56ffaa5a6..000000000
--- a/resources/queries/cds/ds_treatmentarmsubject.sql
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-TA.arm_id,
-ITS.subject_id AS participantId,
-ITS.prot
-FROM cds.treatmentarm AS TA
-JOIN cds.import_studypartgrouparmsubject AS ITS
-ON (TA.container.name = ITS.prot AND
- TA.arm_part = ITS.study_part AND
- TA.arm_group = ITS.study_group AND
- TA.arm_name = ITS.study_arm)
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validateDatasetSubjects.sql b/resources/queries/cds/ds_validateDatasetSubjects.sql
deleted file mode 100644
index b68b26fde..000000000
--- a/resources/queries/cds/ds_validateDatasetSubjects.sql
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright (c) 2015-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
---Returns all the subjects that appear in the datasets that do not appear in the demographics table.
---Expected to return 0 rows.
-SELECT
-datasets.subjects_in_datasets as "prot subject",
-study,
-id
-FROM(
- SELECT
- prot||' '||subject_id as subjects_in_datasets,
- prot as study,
- subject_id as id
- FROM (
- SELECT
- DISTINCT subject_id,
- prot
- FROM import_ics
-
- UNION
-
- SELECT
- DISTINCT subject_id,
- prot
- FROM import_nab
-
- UNION
-
- SELECT
- DISTINCT subject_id,
- prot
- FROM import_els_ifng
-
- UNION
-
- SELECT
- DISTINCT subject_id,
- prot
- FROM import_bama
-
- UNION
-
- SELECT
- DISTINCT subject_id,
- prot
- FROM import_pkmab
- ) _union_
-) as datasets
-LEFT JOIN(
- SELECT
- prot||' '||subject_id as subjects_in_demographics
- FROM import_studysubject
-) as demographics on demographics.subjects_in_demographics = datasets.subjects_in_datasets
-WHERE demographics.subjects_in_demographics IS NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validateDatasetVisitTime.sql b/resources/queries/cds/ds_validateDatasetVisitTime.sql
deleted file mode 100644
index 01ee6c51c..000000000
--- a/resources/queries/cds/ds_validateDatasetVisitTime.sql
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright (c) 2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
---Returns all the visits that appear in the datasets that do not appear in the studypartgrouparmvisit table.
---Expected to return 0 rows.
-SELECT
- subject_id,
- 'PKMAB' as assay_type,
- study_day,
- visit_code,
- possible_visittimes.visit
-FROM (
- SELECT DISTINCT
- MQ.subject_id,
- MQ.prot || '-' || IQ.study_arm || '-' || IQ.study_group || '-' || MQ.study_day || '-' || MQ.visit_code AS visit,
- MQ.study_day,
- MQ.visit_code
- FROM import_pkmab AS MQ
- LEFT JOIN
- import_studypartgrouparmsubject AS IQ
- ON MQ.subject_id = IQ.subject_id AND MQ.container = IQ.container
- ) AS recorded_visittimes
- LEFT JOIN (
- SELECT DISTINCT
- prot || '-' || study_arm || '-' || study_group || '-' || study_day || '-' || visit_code visit
- FROM import_studypartgrouparmvisittime
- ) AS possible_visittimes
- ON recorded_visittimes.visit=possible_visittimes.visit
-WHERE possible_visittimes.visit IS NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validateDatasetVisits.sql b/resources/queries/cds/ds_validateDatasetVisits.sql
deleted file mode 100644
index ca2b83501..000000000
--- a/resources/queries/cds/ds_validateDatasetVisits.sql
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright (c) 2015-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
---Returns all the visits that appear in the datasets that do not appear in the studypartgrouparmvisit table.
---Expected to return 0 rows.
-SELECT
-subject_id,
-assay_type,
-study_day
-FROM (
- SELECT
- MQ.subject_id,
- MQ.assay_type,
- MQ.prot || '-' || IQ.study_arm || '-' || IQ.study_group || '-' || MQ.study_day AS visit,
- MQ.study_day
- FROM
- (SELECT DISTINCT
- subject_id,
- prot,
- study_day,
- 'BAMA' as assay_type
- FROM import_bama
-
- UNION
-
- SELECT DISTINCT
- subject_id,
- prot,
- study_day,
- 'ELISPOT' as assay_type
- FROM import_els_ifng
-
- UNION
-
- SELECT DISTINCT
- subject_id,
- prot,
- study_day,
- 'ICS' as assay_type
- FROM import_ics
-
- UNION
-
- SELECT DISTINCT
- subject_id,
- prot,
- study_day,
- 'NAB' as assay_type
- FROM import_nab
-
- UNION
-
- SELECT DISTINCT
- subject_id,
- prot,
- study_day,
- 'PKMAB' as assay_type
- FROM import_pkmab
- ) AS MQ
- LEFT JOIN
- import_studypartgrouparmsubject AS IQ
- ON MQ.subject_id = IQ.subject_id
-) AS recorded_visits
-LEFT JOIN (
- SELECT DISTINCT
- prot || '-' || study_arm || '-' || study_group || '-' || study_day AS visit
- FROM import_studypartgrouparmvisit
-) AS possible_visits
-ON recorded_visits.visit=possible_visits.visit
-WHERE possible_visits.visit IS NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validateVisitTagAssignment.sql b/resources/queries/cds/ds_validateVisitTagAssignment.sql
deleted file mode 100644
index 93d9eafbe..000000000
--- a/resources/queries/cds/ds_validateVisitTagAssignment.sql
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
---Returns all the study arms that have the same single-use visit tag defined for more than one visit.
---Expected to return 0 rows.
-SELECT * FROM (
- SELECT prot, study_group, study_arm,
- 'Enrollment' AS visit_tag,
- count(*) AS assignment_count
- FROM cds.import_studypartgrouparmvisit
- WHERE enrollment
- GROUP BY prot, study_group, study_arm
-
- UNION
-
- SELECT prot, study_group, study_arm,
- 'Last Vaccination' AS visit_tag,
- count(*) AS assignment_count
- FROM cds.import_studypartgrouparmvisit
- WHERE lastvacc
- GROUP BY prot, study_group, study_arm
-
- UNION
-
- SELECT prot, study_group, study_arm,
- 'First Vaccination' AS visit_tag,
- count(*) AS assignment_count
- FROM cds.import_studypartgrouparmvisit
- WHERE firstvacc
- GROUP BY prot, study_group, study_arm
-) X
-WHERE assignment_count > 1
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validatestudyassay.sql b/resources/queries/cds/ds_validatestudyassay.sql
deleted file mode 100644
index b11951549..000000000
--- a/resources/queries/cds/ds_validatestudyassay.sql
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright (c) 2016-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
---Returns all the subjects assays pairs that appear in the datasets where the corresponding study assay pair is not
---enumerated in the studyassay table.
---Expected to return 0 rows
-SELECT DISTINCT
- d.prot,
- d.subject_id,
- d.assay_identifier
-FROM import_studyassay md --metadataTable
-FULL JOIN (
- SELECT DISTINCT
- prot,
- subject_id,
- assay_identifier
- FROM cds.import_ICS
-
- UNION
-
- SELECT DISTINCT
- prot,
- subject_id,
- assay_identifier
- FROM cds.import_nab
-
- UNION
-
- SELECT DISTINCT
- prot,
- subject_id,
- assay_identifier
- FROM cds.import_els_ifng
-
- UNION
-
- SELECT DISTINCT
- prot,
- subject_id,
- assay_identifier
- FROM cds.import_bama
-
- UNION
-
- SELECT DISTINCT
- prot,
- subject_id,
- assay_identifier
- FROM cds.import_pkmab
-) d --dataTable
-ON d.prot=md.prot AND d.assay_identifier=md.assay_identifier
-WHERE md.prot IS NULL AND md.assay_identifier IS NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_validatestudyproduct.sql b/resources/queries/cds/ds_validatestudyproduct.sql
deleted file mode 100644
index 08b099e6a..000000000
--- a/resources/queries/cds/ds_validatestudyproduct.sql
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * Copyright (c) 2016 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
---Returns all the subjects products pairs that appear in the data that are not represented in the studyproduct table.
---Expected to return 0 rows
-SELECT DISTINCT
- d.participantid,
- d.product_id,
- d.prot
-FROM import_studyproduct md --metadataTable
-RIGHT JOIN ds_subjectproduct d --dataTable
-ON (
- md.prot=d.prot
- AND md.product_id=d.product_id
-)
-WHERE md.prot IS NULL AND md.product_id IS NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_visit.sql b/resources/queries/cds/ds_visit.sql
deleted file mode 100644
index 909267a8d..000000000
--- a/resources/queries/cds/ds_visit.sql
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DISTINCT study_day,
-'Day ' || study_day AS label,
-CAST(study_day AS DOUBLE) AS protocolday,
-CAST(study_day AS DOUBLE) AS sequencenummin,
-CAST(study_day AS DOUBLE) AS sequencenummax,
--- TRUE AS showbydefault,
--- 0 AS displayorder,
--- 0 AS chronologicalorder,
-'normal' AS sequencenumhandling,
-prot
-FROM cds.import_studypartgrouparmvisit
\ No newline at end of file
diff --git a/resources/queries/cds/ds_visittag.sql b/resources/queries/cds/ds_visittag.sql
deleted file mode 100644
index 33b00edf4..000000000
--- a/resources/queries/cds/ds_visittag.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DISTINCT arm_visit.study_arm_visit_type AS Name,
-arm_visit.study_arm_visit_type AS caption,
-FALSE AS SingleUse
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-WHERE study_arm_visit_type IS NOT NULL AND study_arm_visit_type != 'Placeholder'
-
--- add the pre-defined alignment visits tags
-UNION ALL SELECT 'Enrollment' AS Name, 'Enrollment' AS caption, TRUE AS SingleUse
-UNION ALL SELECT 'First Vaccination' AS Name, 'First Vaccination' AS caption, TRUE AS SingleUse
-UNION ALL SELECT 'Last Vaccination' AS Name, 'Last Vaccination' AS caption, TRUE AS SingleUse
\ No newline at end of file
diff --git a/resources/queries/cds/ds_visittagalignment.sql b/resources/queries/cds/ds_visittagalignment.sql
deleted file mode 100644
index 6df2a4878..000000000
--- a/resources/queries/cds/ds_visittagalignment.sql
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-SELECT tasm.Container AS container,
-tasm.ParticipantId AS participantid,
-vtm.visit_row_id AS visitid,
-v.ProtocolDay AS protocolday,
-vtm.visit_tag AS visittagname
-FROM cds.treatmentarmsubjectmap tasm
-LEFT JOIN cds.visittagmap vtm ON tasm.arm_id = vtm.arm_id AND tasm.container = vtm.container AND vtm.single_use
-LEFT JOIN study.visit v ON vtm.visit_row_id = v.RowId
-WHERE vtm.visit_tag IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/cds/ds_visittagmap.sql b/resources/queries/cds/ds_visittagmap.sql
deleted file mode 100644
index db51efcf7..000000000
--- a/resources/queries/cds/ds_visittagmap.sql
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * Copyright (c) 2015-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DISTINCT arm_visit.study_arm_visit_type AS visit_tag,
-visit.rowid AS visit_row_id,
-studygroup.row_id AS study_group_id,
-arm_visit.study_arm,
-arm_visit.prot || '-' || arm_visit.study_part || '-' || arm_visit.study_group || '-' || arm_visit.study_arm AS arm_id,
-arm_visit.prot,
-arm_visit.study_arm_visit_label AS visit_tag_label,
-FALSE AS single_use,
-arm_visit.isvaccvis AS is_vaccination,
-arm_visit.ischallvis AS is_challenge,
-arm_visit.study_arm_visit_detail_label AS detail_label
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-JOIN (SELECT * FROM cds.studygroup) AS studygroup ON (studygroup.container.name = arm_visit.prot AND studygroup.group_name = arm_visit.study_group)
-JOIN (SELECT * FROM study.visit) AS visit ON (visit.Folder.Name = arm_visit.prot AND visit.sequencenummin = CAST(arm_visit.study_day AS DOUBLE))
-WHERE arm_visit.study_arm_visit_type IS NOT NULL AND arm_visit.study_arm_visit_type != 'Placeholder'
-
-UNION
-
-SELECT
-DISTINCT 'Enrollment' AS visit_tag,
-visit.rowid AS visit_row_id,
-studygroup.row_id AS study_group_id,
-arm_visit.study_arm,
-arm_visit.prot || '-' || arm_visit.study_part || '-' || arm_visit.study_group || '-' || arm_visit.study_arm AS arm_id,
-arm_visit.prot,
-arm_visit.study_arm_visit_label AS visit_tag_label,
-TRUE AS single_use,
-arm_visit.isvaccvis AS is_vaccination,
-arm_visit.ischallvis AS is_challenge,
-arm_visit.study_arm_visit_detail_label AS detail_label
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-JOIN (SELECT * FROM cds.studygroup) AS studygroup ON (studygroup.container.name = arm_visit.prot AND studygroup.group_name = arm_visit.study_group)
-JOIN (SELECT * FROM study.visit) AS visit ON (visit.Folder.Name = arm_visit.prot AND visit.sequencenummin = CAST(arm_visit.study_day AS DOUBLE))
-WHERE arm_visit.enrollment
-
-UNION
-
-SELECT
-DISTINCT 'Last Vaccination' AS visit_tag,
-visit.rowid AS visit_row_id,
-studygroup.row_id AS study_group_id,
-arm_visit.study_arm,
-arm_visit.prot || '-' || arm_visit.study_part || '-' || arm_visit.study_group || '-' || arm_visit.study_arm AS arm_id,
-arm_visit.prot,
-arm_visit.study_arm_visit_label AS visit_tag_label,
-TRUE AS single_use,
-arm_visit.isvaccvis AS is_vaccination,
-arm_visit.ischallvis AS is_challenge,
-arm_visit.study_arm_visit_detail_label AS detail_label
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-JOIN (SELECT * FROM cds.studygroup) AS studygroup ON (studygroup.container.name = arm_visit.prot AND studygroup.group_name = arm_visit.study_group)
-JOIN (SELECT * FROM study.visit) AS visit ON (visit.Folder.Name = arm_visit.prot AND visit.sequencenummin = CAST(arm_visit.study_day AS DOUBLE))
-WHERE arm_visit.lastvacc
-
-UNION
-
-SELECT
-DISTINCT 'First Vaccination' AS visit_tag,
-visit.rowid AS visit_row_id,
-studygroup.row_id AS study_group_id,
-arm_visit.study_arm,
-arm_visit.prot || '-' || arm_visit.study_part || '-' || arm_visit.study_group || '-' || arm_visit.study_arm AS arm_id,
-arm_visit.prot,
-arm_visit.study_arm_visit_label AS visit_tag_label,
-TRUE AS single_use,
-arm_visit.isvaccvis AS is_vaccination,
-arm_visit.ischallvis AS is_challenge,
-arm_visit.study_arm_visit_detail_label AS detail_label
-FROM cds.import_studypartgrouparmvisit AS arm_visit
-JOIN (SELECT * FROM cds.studygroup) AS studygroup ON (studygroup.container.name = arm_visit.prot AND studygroup.group_name = arm_visit.study_group)
-JOIN (SELECT * FROM study.visit) AS visit ON (visit.Folder.Name = arm_visit.prot AND visit.sequencenummin = CAST(arm_visit.study_day AS DOUBLE))
-WHERE arm_visit.firstvacc
diff --git a/resources/queries/cds/import_assay/LearnGridExportView.qview.xml b/resources/queries/cds/import_assay/LearnGridExportView.qview.xml
deleted file mode 100644
index 28535abe5..000000000
--- a/resources/queries/cds/import_assay/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/import_product/LearnGridExportView.qview.xml b/resources/queries/cds/import_product/LearnGridExportView.qview.xml
deleted file mode 100644
index 18ac39768..000000000
--- a/resources/queries/cds/import_product/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/import_publication/LearnGridExportView.qview.xml b/resources/queries/cds/import_publication/LearnGridExportView.qview.xml
deleted file mode 100644
index be179b96b..000000000
--- a/resources/queries/cds/import_publication/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/import_study/LearnGridExportView.qview.xml b/resources/queries/cds/import_study/LearnGridExportView.qview.xml
deleted file mode 100644
index f3170633e..000000000
--- a/resources/queries/cds/import_study/LearnGridExportView.qview.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/learn_assay.sql b/resources/queries/cds/learn_assay.sql
deleted file mode 100644
index c1789a723..000000000
--- a/resources/queries/cds/learn_assay.sql
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright (c) 2015-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT *,
- (CASE WHEN (AA.assay_identifier = 'PK MAB' OR AA.assay_type IS NULL) THEN false -- assay_type is null for Non-Integrated assay, at least for now, see ds_assay query.
- ELSE true
- END) AS hasAntigen
-FROM cds.assay AS AA
-LEFT JOIN (
- SELECT assay_identifier AS id,
- COUNT(assay_identifier) AS study_count
- FROM (
- SELECT DISTINCT assay_identifier,
- study_name
- FROM ds_subjectassay
- ) _x_
- GROUP BY assay_identifier
-)
-AS BB ON AA.assay_identifier = BB.id
\ No newline at end of file
diff --git a/resources/queries/cds/learn_assaydocuments.sql b/resources/queries/cds/learn_assaydocuments.sql
deleted file mode 100644
index 39956bc22..000000000
--- a/resources/queries/cds/learn_assaydocuments.sql
+++ /dev/null
@@ -1,10 +0,0 @@
-SELECT
-ad.document_id,
-d.label,
-d.filename,
-d.document_type,
-ad.assay_identifier,
-d.video_link,
-d.video_thumbnail_label
-FROM cds.assaydocument ad
-LEFT JOIN cds.document d ON ad.document_id = d.document_id
\ No newline at end of file
diff --git a/resources/queries/cds/learn_assaysforstudies.sql b/resources/queries/cds/learn_assaysforstudies.sql
deleted file mode 100644
index 9e5dceb62..000000000
--- a/resources/queries/cds/learn_assaysforstudies.sql
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each assay.
-SELECT
- sa.prot,
- sa.has_data,
- sa.assay_identifier AS "study_assay_id",
- sa.assay_status,
- amd.*
-FROM cds.metadata.studyassay sa
-LEFT JOIN assay amd
-ON amd.assay_identifier=sa.assay_identifier
diff --git a/resources/queries/cds/learn_documentsforstudies.sql b/resources/queries/cds/learn_documentsforstudies.sql
deleted file mode 100644
index 84e7998f4..000000000
--- a/resources/queries/cds/learn_documentsforstudies.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each document.
-SELECT
- sd.prot,
- sd.document_order,
- (sd.access_level = 'members' AND sd.access_level IS NOT NULL) OR study.study_name IS NOT NULL AS "accessible",
- doc.*
-FROM cds.ds_studydocument sd
-LEFT JOIN document doc
-ON doc.document_id=sd.document_id
-LEFT JOIN study study
-ON study.study_name=sd.prot
diff --git a/resources/queries/cds/learn_elispot_antigens.sql b/resources/queries/cds/learn_elispot_antigens.sql
deleted file mode 100644
index f3384f83c..000000000
--- a/resources/queries/cds/learn_elispot_antigens.sql
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT
- assay_identifier,
- protein_panel as antigen_name,
- protein,
- pools,
- description as antigen_description,
- antigen_control,
- clades
-FROM elispotantigen AS MAIN
-JOIN (
- SELECT
- protein_panel as pp,
- protein as p,
- GROUP_CONCAT(DISTINCT peptide_pool, ', ') AS pools,
- GROUP_CONCAT(DISTINCT antigen_description, ', ') AS description
- FROM cds.elispotantigen
- GROUP BY elispotantigen.protein_panel, elispotantigen.protein) AS pool_query
-ON MAIN.protein_panel = pool_query.pp AND MAIN.protein = pool_query.p
-JOIN (
- SELECT
- protein_panel AS pp,
- GROUP_CONCAT(DISTINCT clade, ', ') AS clades
- FROM cds.elispotantigen
- GROUP BY elispotantigen.protein_panel) AS clade_query
-ON MAIN.protein_panel = clade_query.pp
-ORDER BY MAIN.protein_panel
\ No newline at end of file
diff --git a/resources/queries/cds/learn_ics_antigens.sql b/resources/queries/cds/learn_ics_antigens.sql
deleted file mode 100644
index 72d160c98..000000000
--- a/resources/queries/cds/learn_ics_antigens.sql
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT DISTINCT
- assay_identifier,
- protein_panel as antigen_name,
- protein,
- pools,
- description as antigen_description,
- antigen_control,
- clades
-FROM icsantigen AS MAIN
-JOIN (
- SELECT
- protein_panel as pp,
- protein as p,
- GROUP_CONCAT(DISTINCT peptide_pool, ', ') AS pools,
- GROUP_CONCAT(DISTINCT antigen_description, ', ') AS description
- FROM cds.icsantigen
- GROUP BY icsantigen.protein_panel, icsantigen.protein) AS pool_query
-ON MAIN.protein_panel = pool_query.pp AND MAIN.protein = pool_query.p
-JOIN (
- SELECT
- protein_panel AS pp,
- GROUP_CONCAT(DISTINCT clade, ', ') AS clades
- FROM cds.icsantigen
- GROUP BY icsantigen.protein_panel) AS clade_query
-ON MAIN.protein_panel = clade_query.pp
-ORDER BY MAIN.protein_panel
\ No newline at end of file
diff --git a/resources/queries/cds/learn_mabStudies.sql b/resources/queries/cds/learn_mabStudies.sql
deleted file mode 100644
index 020f20e7b..000000000
--- a/resources/queries/cds/learn_mabStudies.sql
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright (c) 2018-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
--- mab as subject
-SELECT mabwithstudy.prot as prot, mabwithstudy.mab_mix_name_std, mabwithstudy.mab_label as mix_labels,
- studyassay.label, studyassay.description, studyassay.has_data, studyassay.assay_status, 'MAb Characterization Studies' as study_type,
- 'Go to Monoclonal antibodies to visualize or export mAb data' as subheader_instr
-FROM cds.learn_mab_mix_forstudies mabwithstudy
-LEFT JOIN cds.learn_studiesforassays studyassay
- ON mabwithstudy.prot = studyassay.prot
- AND studyassay.assay_identifier = 'NAB MAB'
-
-UNION
-
--- mab as product
-SELECT s.study_name as prot, mab.mab_mix_name_std, null as mix_labels,
- s.label, s.description, spm.has_data, studyassay.assay_status, 'MAb Administration Studies' as study_type,
- 'Visualize subject-level data in Plot or export from Grid. Additional data may be available. See study page.' as subheader_instr
-FROM cds.metadata.studyproductmap spm
- JOIN cds.product p ON (spm.product_id = p.product_id AND spm.projectContainer = p.container)
- JOIN cds.MabMixMetadata mab ON (mab.mab_mix_id = p.mab_mix_id AND mab.container = p.container)
- LEFT JOIN cds.metadata.study s ON (spm.study_name=s.study_name AND spm.container = s.container)
- LEFT JOIN cds.learn_studiesforassays studyassay
- ON (s.study_name = studyassay.prot AND s.container = studyassay.container
- AND studyassay.assay_identifier = 'PK MAB')
-
diff --git a/resources/queries/cds/learn_mab_mix_forstudies.sql b/resources/queries/cds/learn_mab_mix_forstudies.sql
deleted file mode 100644
index 1fc5ffc1f..000000000
--- a/resources/queries/cds/learn_mab_mix_forstudies.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT studymabmix.*, labels.mab_label
-FROM
- (SELECT DISTINCT smab.prot, mixmeta.mab_mix_name_std
- FROM cds.studymab smab
- JOIN cds.MAbMixMetadata mixmeta
- ON smab.mab_mix_id = mixmeta.mab_mix_id) studymabmix
- LEFT JOIN cds.ds_mixlabels labels
- ON studymabmix.mab_mix_name_std = labels.mab_mix_name_std
-
diff --git a/resources/queries/cds/learn_mab_mix_meta.sql b/resources/queries/cds/learn_mab_mix_meta.sql
deleted file mode 100644
index 006d0692f..000000000
--- a/resources/queries/cds/learn_mab_mix_meta.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- meta.*,
- labels.mab_label as mix_labels
-FROM cds.MAbMixMAbMeta meta
-LEFT JOIN cds.ds_mixlabels labels
- ON meta.mab_mix_name_std = labels.mab_mix_name_std
diff --git a/resources/queries/cds/learn_product.sql b/resources/queries/cds/learn_product.sql
deleted file mode 100644
index 903868741..000000000
--- a/resources/queries/cds/learn_product.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * Copyright (c) 2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each product.
-SELECT
- prod.*,
- mab.mab_mix_name_std
-FROM cds.product prod
-LEFT JOIN cds.MAbMixMetadata mab ON prod.mab_mix_id = mab.mab_mix_id AND prod.container = mab.container
\ No newline at end of file
diff --git a/resources/queries/cds/learn_productsforstudies.sql b/resources/queries/cds/learn_productsforstudies.sql
deleted file mode 100644
index 9889fe6d3..000000000
--- a/resources/queries/cds/learn_productsforstudies.sql
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * Copyright (c) 2017-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each product.
-SELECT
-spm.study_name,
-spm.has_data,
-p.*
-FROM cds.metadata.studyproductmap spm
-JOIN cds.product p ON spm.product_id = p.product_id AND spm.projectContainer = p.container
\ No newline at end of file
diff --git a/resources/queries/cds/learn_publicationExternalLinks.sql b/resources/queries/cds/learn_publicationExternalLinks.sql
deleted file mode 100644
index 8ea469501..000000000
--- a/resources/queries/cds/learn_publicationExternalLinks.sql
+++ /dev/null
@@ -1,6 +0,0 @@
-SELECT
- elm.protocol_id,
- el.*
-FROM cds.external_link el
- LEFT JOIN cds.external_link_map elm ON el.cds_link_id = elm.cds_link_id
-WHERE elm.type = 'publication'
diff --git a/resources/queries/cds/learn_publicationdata.sql b/resources/queries/cds/learn_publicationdata.sql
deleted file mode 100644
index f3cb72e0f..000000000
--- a/resources/queries/cds/learn_publicationdata.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- pd.publication_id,
- pd.display_order,
- doc.*
-FROM cds.publicationDocument pd
- LEFT JOIN document doc ON pd.document_id = doc.document_id
diff --git a/resources/queries/cds/learn_publicationsforstudies.sql b/resources/queries/cds/learn_publicationsforstudies.sql
deleted file mode 100644
index 181c51eaa..000000000
--- a/resources/queries/cds/learn_publicationsforstudies.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (c) 2017-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each publication.
-SELECT
- sp.prot,
- sp.publication_order,
- s.label AS "study_label",
- s.short_name AS "study_short_name",
- s.description,
- pub.*,
- COUNT(pd.document_id) AS available_data_count
-FROM cds.ds_studypublication sp
-LEFT JOIN publication pub
-ON pub.id=sp.publication_id
-LEFT JOIN cds.metadata.study s ON sp.prot=s.study_name
-LEFT JOIN cds.publicationDocument pd ON sp.publication_id = pd.publication_id
-GROUP BY sp.prot, sp.publication_order, s.label, s.short_name, s.description,
- pub.id, pub.container, pub.title, pub.author_all, pub.journal_short,
- pub.date, pub.volume, pub.issue, pub.location, pub.pmid, pub.link,
- pub.author_first, pub.publication_label, pub.publication_abstract
diff --git a/resources/queries/cds/learn_relationshipsforstudies.sql b/resources/queries/cds/learn_relationshipsforstudies.sql
deleted file mode 100644
index 38f6cc1ff..000000000
--- a/resources/queries/cds/learn_relationshipsforstudies.sql
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Study.js. Grabs all metadata for each publication.
-SELECT
- sr.prot,
- sr.rel_prot,
- sr.relationship
-FROM cds.import_studyrelationship sr
-
diff --git a/resources/queries/cds/learn_studiesforassays.sql b/resources/queries/cds/learn_studiesforassays.sql
deleted file mode 100644
index 8af72293c..000000000
--- a/resources/queries/cds/learn_studiesforassays.sql
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\Assay.js. Grabs all metadata for each study.
-SELECT
- sa.assay_identifier,
- sa.has_data,
- sa.assay_status,
- sa.prot,
- smd.*
-FROM cds.metadata.studyassay sa
-LEFT JOIN cds.metadata.study smd
-ON smd.study_name=sa.prot
diff --git a/resources/queries/cds/learn_studiesforgroups.sql b/resources/queries/cds/learn_studiesforgroups.sql
deleted file mode 100644
index 7730f0645..000000000
--- a/resources/queries/cds/learn_studiesforgroups.sql
+++ /dev/null
@@ -1,23 +0,0 @@
--- Query for studies with either product or assay data associated with it, used by the learn group store
--- to get the list of studies for the group summary pages
-
-SELECT DISTINCT g.study_name,
- g.study_label,
- g.description,
- g.has_data
-FROM (SELECT s.study_name,
- s.label AS study_label,
- s.description,
- CASE
- WHEN (afs.has_data IS NULL AND pfs.has_data IS NULL) THEN false
- WHEN (afs.has_data IS NULL) THEN pfs.has_data
- WHEN (pfs.has_data IS NULL) THEN afs.has_data
- ELSE (afs.has_data OR pfs.has_data)
- END AS has_data
-
- FROM cds.study s
- LEFT JOIN cds.learn_productsforstudies pfs
- ON s.study_name = pfs.study_name
- LEFT JOIN cds.learn_assaysforstudies afs ON s.study_name = afs.prot) g
-
-GROUP BY g.study_name, g.study_label, g.description, g.has_data
diff --git a/resources/queries/cds/learn_studiesforproducts.sql b/resources/queries/cds/learn_studiesforproducts.sql
deleted file mode 100644
index ac7623245..000000000
--- a/resources/queries/cds/learn_studiesforproducts.sql
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- Helper query for store\StudyProduct.js. Grabs all metadata for each study.
-SELECT
-spm.study_name,
-spm.product_id,
-spm.has_data,
-s.label AS "study_label",
-s.description,
-s.short_name AS "study_short_name"
-FROM cds.metadata.studyproductmap spm
-LEFT JOIN cds.metadata.study s ON spm.study_name=s.study_name
\ No newline at end of file
diff --git a/resources/queries/cds/learn_studyExternalLinks.sql b/resources/queries/cds/learn_studyExternalLinks.sql
deleted file mode 100644
index c5a685e8c..000000000
--- a/resources/queries/cds/learn_studyExternalLinks.sql
+++ /dev/null
@@ -1,6 +0,0 @@
-SELECT
- elm.protocol_id,
- el.*
-FROM cds.external_link el
- LEFT JOIN cds.external_link_map elm ON el.cds_link_id = elm.cds_link_id
- WHERE elm.type = 'study'
diff --git a/resources/queries/cds/learn_studyrelationshiporder.sql b/resources/queries/cds/learn_studyrelationshiporder.sql
deleted file mode 100644
index 1cf3828ea..000000000
--- a/resources/queries/cds/learn_studyrelationshiporder.sql
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright (c) 2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT *
-FROM cds.import_studyrelationshiporder
\ No newline at end of file
diff --git a/resources/queries/cds/mAbGridBase.query.xml b/resources/queries/cds/mAbGridBase.query.xml
deleted file mode 100644
index 295f75d6e..000000000
--- a/resources/queries/cds/mAbGridBase.query.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-
-
-
-
-
-
-
- study_name
- study
- cds
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/nabAntigenWithPanelMeta.sql b/resources/queries/cds/nabAntigenWithPanelMeta.sql
deleted file mode 100644
index 3f1e44368..000000000
--- a/resources/queries/cds/nabAntigenWithPanelMeta.sql
+++ /dev/null
@@ -1,38 +0,0 @@
-SELECT
-ag.assay_identifier,
-ag.antigen_name,
-ag.antigen_type,
-ag.virus,
-ag.virus_type,
-ag.virus_insert_name,
-ag.neutralization_tier,
-ag.clade,
-ag.antigen_description,
-ag.antigen_control,
-ag.virus_full_name,
-ag.virus_name_other,
-ag.virus_species,
-ag.virus_host_cell,
-ag.virus_backbone,
-ag.cds_virus_id,
-GROUP_CONCAT(DISTINCT ap.panel_name, '|') AS panel_names
-FROM cds.nabantigen ag
-LEFT JOIN cds.virusPanel vp ON vp.cds_virus_id = ag.cds_virus_id
-LEFT JOIN cds.antigenPanelMeta ap ON ap.cds_panel_id = vp.cds_panel_id
-GROUP BY
-ag.assay_identifier,
-ag.antigen_name,
-ag.antigen_type,
-ag.virus,
-ag.virus_type,
-ag.virus_insert_name,
-ag.neutralization_tier,
-ag.clade,
-ag.antigen_description,
-ag.antigen_control,
-ag.virus_full_name,
-ag.virus_name_other,
-ag.virus_species,
-ag.virus_host_cell,
-ag.virus_backbone,
-ag.cds_virus_id
\ No newline at end of file
diff --git a/resources/queries/cds/nabantigen/AssayAntigenExportView.qview.xml b/resources/queries/cds/nabantigen/AssayAntigenExportView.qview.xml
deleted file mode 100644
index 5ae177510..000000000
--- a/resources/queries/cds/nabantigen/AssayAntigenExportView.qview.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/cds/pubCuratedGrpWithLabel.sql b/resources/queries/cds/pubCuratedGrpWithLabel.sql
deleted file mode 100644
index 1d7a3c36c..000000000
--- a/resources/queries/cds/pubCuratedGrpWithLabel.sql
+++ /dev/null
@@ -1,10 +0,0 @@
-SELECT
- sg.Label as label,
- pcg.cds_saved_group_id,
- pcg.publication_id
-FROM cds.publicationCuratedGroup pcg
-LEFT JOIN study.SubjectGroup sg
-ON pcg.cds_saved_group_id = sg.RowId
-LEFT JOIN study.SubjectCategory sc
- ON sc.RowId = sg.categoryId
-WHERE sc.ownerId = -1 --filter to only show curated/shared groups
\ No newline at end of file
diff --git a/resources/queries/cds/sequence_germline_mab_metadata.sql b/resources/queries/cds/sequence_germline_mab_metadata.sql
deleted file mode 100644
index 55b73c02e..000000000
--- a/resources/queries/cds/sequence_germline_mab_metadata.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-SELECT *
-FROM cds.sequence_germline sg
- INNER JOIN cds.donor_mab_sequence dseq ON sg.sequence_id = dseq.sequence_id
- INNER JOIN cds.mab_metadata mm ON dseq.mab_id = mm.mab_id
\ No newline at end of file
diff --git a/resources/queries/cds/studyCuratedGrpWithLabel.sql b/resources/queries/cds/studyCuratedGrpWithLabel.sql
deleted file mode 100644
index bf5a52e3a..000000000
--- a/resources/queries/cds/studyCuratedGrpWithLabel.sql
+++ /dev/null
@@ -1,6 +0,0 @@
-SELECT DISTINCT sgm.groupId.rowid AS cds_saved_group_id,
- sgm.GroupId.label,
- sgm.container.name AS prot -- each study protocol has a container of the same name as the study protocol
-FROM study.subjectgroupmap sgm
- LEFT JOIN study.subjectcategory sc ON sgm.groupId.CategoryId.RowId = sc.RowId
-WHERE sc.ownerId = -1 --filter to only show curated/shared groups
\ No newline at end of file
diff --git a/resources/queries/cds/subjectproduct_bridge.sql b/resources/queries/cds/subjectproduct_bridge.sql
deleted file mode 100644
index 503ecda78..000000000
--- a/resources/queries/cds/subjectproduct_bridge.sql
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
-DD.participantid,
-DD.folder.entityid as container,
-DD.participantid || '-product' AS product_group,
-P.product_name,
-SPM.insert_name,
-SPM.clade_name,
-P.product_type,
-P.product_developer,
-P.product_class_label
-FROM study.demographics AS DD
-LEFT JOIN cds.subjectproductmap AS SPM ON (DD.participantId = SPM.participantId AND DD.folder = SPM.container)
-LEFT JOIN cds.product AS P ON (SPM.product_id = P.product_id AND SPM.projectContainer = P.container)
\ No newline at end of file
diff --git a/resources/queries/study/BAMA/AssayExportView.qview.xml b/resources/queries/study/BAMA/AssayExportView.qview.xml
deleted file mode 100644
index 7f2dadffa..000000000
--- a/resources/queries/study/BAMA/AssayExportView.qview.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/study/NABMAb.query.xml b/resources/queries/study/NABMAb.query.xml
deleted file mode 100644
index 56dc29b5c..000000000
--- a/resources/queries/study/NABMAb.query.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-
-
-
-
-
-
- Visit
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/study/NABMAb/AssayExportView.qview.xml b/resources/queries/study/NABMAb/AssayExportView.qview.xml
deleted file mode 100644
index 0f846aefa..000000000
--- a/resources/queries/study/NABMAb/AssayExportView.qview.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/study/NAb/AssayExportView.qview.xml b/resources/queries/study/NAb/AssayExportView.qview.xml
deleted file mode 100644
index 166eb3f03..000000000
--- a/resources/queries/study/NAb/AssayExportView.qview.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/study/NAbMAbWithMixMeta.sql b/resources/queries/study/NAbMAbWithMixMeta.sql
deleted file mode 100644
index 0cedbdea7..000000000
--- a/resources/queries/study/NAbMAbWithMixMeta.sql
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- mab.prot,
- mab.mab_mix_id,
- MixMeta.mab_mix_name_std,
- MixMeta.mab_mix_label,
- mab.mab_name_source,
- mab.summary_level,
- mab.target_cell,
- mab.assay_identifier,
- mab.mab_concentration,
- mab.mab_concentration_units,
- mab.specimen_concentration_id,
- mab.curve_id,
- mab.specimen_type,
- mab.lab_code,
- mab.virus,
- mab.initial_concentration,
- mab.min_concentration,
- mab.max_concentration,
- mab.percent_neutralization,
- mab.neutralization_plus_minus,
- mab.min_well_value,
- mab.max_well_value,
- mab.mean_well_value,
- mab.well_std_dev,
- mab.titer_curve_ic50,
- mab.titer_curve_ic80,
- mab.nab_response_ic50,
- mab.nab_response_ic80,
- mab.titer_point_ic50,
- mab.titer_point_ic80,
- mab.slope,
- mab.virus_type,
- mab.virus_full_name,
- mab.virus_species,
- mab.virus_host_cell,
- mab.virus_backbone,
- mab.virus_dilution,
- mab.clade,
- mab.neutralization_tier,
- mab.tier_clade_virus,
- mab.fit_min,
- mab.fit_max,
- mab.fit_asymmetry,
- mab.fit_slope,
- mab.fit_inflection,
- mab.fit_error,
- mab.vaccine_matched,
- mab.virus_control_mean,
- mab.cell_control_mean
-
-FROM study.NABMAb as mab
- LEFT JOIN cds.MAbMixMetadata as MixMeta on (MixMeta.mab_mix_id = mab.mab_mix_id)
\ No newline at end of file
diff --git a/resources/queries/study/PKMAb/AssayExportView.qview.xml b/resources/queries/study/PKMAb/AssayExportView.qview.xml
deleted file mode 100644
index 9d0bc1798..000000000
--- a/resources/queries/study/PKMAb/AssayExportView.qview.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/resources/queries/study/ds_assayidentifier.sql b/resources/queries/study/ds_assayidentifier.sql
deleted file mode 100644
index 6633f7ece..000000000
--- a/resources/queries/study/ds_assayidentifier.sql
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright (c) 2017-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'BAMA' as dataset_name
-from study.BAMA as ds
-
-UNION
-
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'ELISPOT' as dataset_name
-from study.ELISPOT as ds
-
-UNION
-
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'ICS' as dataset_name
-from study.ICS as ds
-
-UNION
-
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'NAb' as dataset_name
-from study.NAb as ds
-
-UNION
-
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'PKMAb' as dataset_name
-from study.PKMAb as ds
-
-UNION
-
-SELECT
- DISTINCT ds.assay_identifier as assay_identifier,
- 'NABMAb' as dataset_name
-from study.NABMAb as ds
\ No newline at end of file
diff --git a/resources/queries/study/ds_gridbase.sql b/resources/queries/study/ds_gridbase.sql
deleted file mode 100644
index d77ce8ec8..000000000
--- a/resources/queries/study/ds_gridbase.sql
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright (c) 2015-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-SELECT
--- Display Columns
-SV.participantId.participantId AS SubjectId,
-STUDY.label AS Study,
-TS.coded_label AS TreatmentSummary,
-SV.Visit.RowId AS VisitRowId,
-
--- Join columns
-SV.participantsequencenum,
-SV.sequencenum,
-CAST(ROUND(Floor(SV.Visit.ProtocolDay)) AS INTEGER) AS ProtocolDay,
-SV.container,
-
--- single-use visit tag calculations for visit day alignment
-CAST(SV.Visit.ProtocolDay - visittagalignment_enrollment.ProtocolDay_Enrollment AS INTEGER) AS EnrollmentDay,
-CAST(SV.Visit.ProtocolDay - visittagalignment_last_vaccination.ProtocolDay_Last_Vaccination AS INTEGER) AS LastVaccinationDay,
-CAST(SV.Visit.ProtocolDay - visittagalignment_first_vaccination.ProtocolDay_First_Vaccination AS INTEGER) AS FirstVaccinationDay
-
-FROM study.ParticipantVisit AS SV
-LEFT JOIN cds.study AS STUDY ON (SV.container = study.container)
-LEFT JOIN cds.treatmentarmsubjectmap AS TASM ON (TASM.participantId = SV.participantId AND TASM.container = SV.container)
-LEFT JOIN cds.treatmentarm AS TS ON (TASM.arm_id = TS.arm_id)
-
--- Enrollment VisitTag
-LEFT JOIN (SELECT Container, ParticipantId, MIN(ProtocolDay) AS ProtocolDay_Enrollment FROM cds.visittagalignment
- WHERE visittagname='Enrollment' GROUP BY Container, ParticipantId) AS visittagalignment_enrollment
- ON SV.container=visittagalignment_enrollment.container
- AND SV.participantId.participantId=visittagalignment_enrollment.participantid
-
--- Last Vaccination VisitTag
-LEFT JOIN (SELECT Container, ParticipantId, MIN(ProtocolDay) AS ProtocolDay_Last_Vaccination FROM cds.visittagalignment
- WHERE visittagname='Last Vaccination' GROUP BY Container, ParticipantId) AS visittagalignment_last_vaccination
- ON SV.container=visittagalignment_last_vaccination.container
- AND SV.participantId.participantId=visittagalignment_last_vaccination.participantid
-
--- First Vaccination VisitTag
-LEFT JOIN (SELECT Container, ParticipantId, MIN(ProtocolDay) AS ProtocolDay_First_Vaccination FROM cds.visittagalignment
- WHERE visittagname='First Vaccination' GROUP BY Container, ParticipantId) AS visittagalignment_first_vaccination
- ON SV.container=visittagalignment_first_vaccination.container
- AND SV.participantId.participantId=visittagalignment_first_vaccination.participantid
-
-WHERE SV.participantId NOT IN
- (SELECT MAB.participantId FROM study.NABMAb AS MAB WHERE MAB.participantId = SV.participantId AND MAB.container = SV.container)
\ No newline at end of file
diff --git a/resources/queries/study/ds_mabgridbase.sql b/resources/queries/study/ds_mabgridbase.sql
deleted file mode 100644
index cf916445f..000000000
--- a/resources/queries/study/ds_mabgridbase.sql
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright (c) 2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-select
- MAB.mab_mix_id,
- MAB.container,
- prot as study,
- virus,
- virus_full_name,
- clade,
- neutralization_tier,
- tier_clade_virus,
- titer_curve_ic50,
-
- CASE WHEN titer_curve_ic50 < 0.1 OR titer_curve_ic50 = CAST('-Infinity' AS DOUBLE)
- THEN 'G0.1'
- WHEN titer_curve_ic50 >= -0.1 AND titer_curve_ic50 < 1
- THEN 'G1'
- WHEN titer_curve_ic50 >= 1 AND titer_curve_ic50 < 10
- THEN 'G10'
- WHEN titer_curve_ic50 >= 10 AND titer_curve_ic50 <= 50
- THEN 'G50'
- ELSE 'G50+'
- END AS titer_curve_ic50_group,
-
- target_cell,
- lab_code,
- summary_level,
-
- curve_id,
-
- MixMeta.mab_mix_name_std
-FROM study.NABMAb as MAB
- LEFT JOIN cds.MAbMixMetadata as MixMeta on (MixMeta.mab_mix_id = MAB.mab_mix_id)
-where MAB.specimen_concentration_id = 8
\ No newline at end of file
diff --git a/resources/queries/study/integratedAssays.sql b/resources/queries/study/integratedAssays.sql
deleted file mode 100644
index 3800644d0..000000000
--- a/resources/queries/study/integratedAssays.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-SELECT
-a.assay_identifier,
-a.assay_type AS datasetName
-FROM
-cds.assay a
-LEFT JOIN
-study.datasets ds
-ON a.assay_type = ds.name
-WHERE assay_type IS NOT NULL
\ No newline at end of file
diff --git a/resources/schemas/cds.xml b/resources/schemas/cds.xml
deleted file mode 100644
index 9d76e1074..000000000
--- a/resources/schemas/cds.xml
+++ /dev/null
@@ -1,2293 +0,0 @@
-
-
-
-
-
-
- Study ID
-
-
-
- Study Name
-
-
-
- Title
-
-
-
-
- Stage
-
-
-
-
- Description
-
-
-
- Groups
-
-
-
- Rationale
-
-
-
- Objectives
-
-
- Methods
-
-
-
- Findings
-
-
- Conclusions
-
-
-
- Date of Study Start
-
-
- Date Study Made Public
-
-
-
- CAVD Grantee
-
-
- Date First Subject Enrolled
-
-
- Date Follow-Up Complete
-
-
-
-
- Grant Principal Investigator
-
-
-
- Grant Project Manager
-
-
-
- Study Investigator
-
-
-
- Primary Point of Contact
-
-
-
- Vaccine Strategy
-
-
-
-
- Clinical Trials.gov ID
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- MAb Mixture ID
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Assay ID
-
-
- Assay Long Name
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Unique ID assigned to an individual mAb.
-
-
- A standardized name assigned to an individual mAb.
-
-
- Unique ID of the mAb assigned by LANL and used in the LANL database.
-
-
- Epitope position numbers in the HXB2 reference strain.
-
-
- A classification indicating the binding site e.g., a region (like V3) or near a common functional domain (like the CD4 binding site, CD4BS).
-
-
- A classification indicating the type of the antibody.
-
-
- Unique ID assigned to the donor of the mab.
-
- cds
- donor_metadata
- donor_id
-
-
-
- A reference ID to the `antibody_class` table, which indicates the class of the antibody.
-
- cds
- antibody_class
- mab_class_id
-
-
-
-
-
-
-
-
-
- A standardized name assigned to an individual mAb or a mixture of mAbs.
-
-
- A label (MAb name) assigned to an individual mAb or a mixture of mAbs to distinguish them from MAbs/mixtures with the same standardized name, e.g. when mAbs with the same standardized name are compared within a study.
-
-
-
-
-
-
- Metadata table for both NAb and NAb MAb
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Unique ID assigned to the assay for tracking purposes
-
-
-
- DataSpace antigen ID
- Unique ID assigned to antigen by DataSpace team
-
-
- Full virus name
- Standard, descriptive full name of antigen
-
-
- Short name
- Standard, abbreviated name of antigen
-
-
- Plot label
- Recommended label/name of antigen for use in plots and publications
-
-
- Aliases
- Alternate or common names (from submitted data, publications, etc.)
-
-
- DNA construct ID assigned for Montefiori Lab Plasmid Database.
-
-
- Concatenation of the elements of the antigen type
-
-
- Category
- Classification which indicates whether the antigen is a recombinant protein, synthetic peptide, or virus.
-
-
- Region
- Region of virus (or antibody) covered
-
-
- Scaffold
- Specific scaffolding applied to the protein
-
-
- Modifiers
- Deviation from natural protein
-
-
- Tags
- Specific peptide sequence attached to the protein
-
-
- Indicates additional distinctions needed to identify unique antigen type e.g. different provider of protein
-
-
- Control
- Indicates if antigen is a control
-
-
- Concatenation of the elements of the isolate name
-
-
- Species
- Classification for isolate species using informal taxonomy
-
-
- Donor ID
- Unique ID assigned to the isolate donor
-
-
- Indicates additional distinctions needed to identify unique isolates from the same donor, e.g. visits or specimen types
-
-
- Clade
- Clade (gene subtype) to which the isolate is most closely aligned
-
-
- Identifier assigned to indicate specific isolate clone
-
-
- Mutations
- Indicates specific mutations to the isolate
-
-
- Name of the investigator who cloned the isolate
-
-
- Country of origin of the isolate donor
-
-
- Year the isolate was isolated
-
-
- Classification for staging early HIV infection based on test results for markers of the virus and the immune response
-
-
- Unique identifier assigned to the amino acid sequence for the isolate
-
-
- Concatenation of production-related elements
-
-
- Host cell
- Host cell used to incubate the isolate stock during production process
-
-
- Purification methods
- Production process performed to purify the protein
-
-
- Special reagents
- Specific reagent used during production of protein
-
-
- Manufacturer
- Lab or commercial facility where antigen produced
-
-
- Indicates if codon optimization was performed during production
-
-
- Indicates stable transfection vs transient
-
-
- Classification of transmitter/founder status of the isolate
-
-
-
-
-
- DataSpace antigen ID
- Unique ID assigned to antigen by DataSpace team
-
-
- Full name
- Standard, descriptive full name of antigen
-
-
- Short name
- Standard, abbreviated name of antigen
-
-
- Plot label
- Recommended label/name of antigen for use in plots and publications
-
-
- Aliases
- Alternate or common names (from submitted data, publications, etc.)
-
-
- DNA construct ID
- DNA construct ID assigned for Montefiori Lab Plasmid Database
-
-
- Antigen category
- Classification which indicates whether the antigen is a recombinant protein, synthetic peptide, or virus
-
-
- Antigen type component
- Concatenation of the elements of the antigen type
-
-
- Region
- Region of virus (or antibody) covered
-
-
- Scaffold
- Specific scaffolding applied to the protein
-
-
- Modifiers
- Deviation from natural protein
-
-
- Tags
- Specific peptide sequence attached to the protein
-
-
- Virus type
- Classification which indicates the type of virus
-
-
- Backbone
- Virus backbone
-
-
- Reporter molecule
- Specific reporter molecule applied to the protein
-
-
- Antigen type differentiate
- Indicates additional distinctions needed to identify unique antigen type e.g. different provider of protein
-
-
- Antigen control
- Indicates if antigen is a control
-
-
- Isolate name component
- Concatenation of the elements of the isolate name
-
-
- Isolate species
- Classification for isolate species using informal taxonomy
-
-
- Isolate donor ID
- Unique ID assigned to the isolate donor
-
-
- Isolate differentiate
- Indicates additional distinctions needed to identify unique isolates from the same donor, e.g. visits or specimen types
-
-
- Isolate clade
- Clade (gene subtype) to which the isolate is most closely aligned
-
-
- Isolate clone designation
- Identifier assigned to indicate specific isolate clone
-
-
- Isolate mutations
- Indicates specific mutations to the isolate
-
-
- Neutralization tier
- Classification of neutralization of virus
-
-
- Isolate cloner/PI
- Name of the investigator who cloned the isolate
-
-
- Country of origin
- Country of origin of the isolate donor
-
-
- Year isolated
- Year the isolate was isolated
-
-
- Fiebig stage
- Classification for staging early HIV infection based on test results for markers of the virus and the immune response
-
-
- Accession #(s)
- Unique identifier assigned to the amino acid sequence for the isolate
-
-
- Amino acid sequence
- Specific string of amino acids for the isolate
-
-
- Production component
- Concatenation of production-related elements
-
-
- Host cell
- Host cell used to incubate the isolate stock during production process
-
-
- Purification methods
- Production process performed to purify the protein
-
-
- Special reagents
- Specific reagent used during production of protein
-
-
- Manufacturer
- Lab or commercial facility where antigen produced
-
-
- Codon Optimization
- Indicates if codon optimization was performed during production
-
-
- Source
- The lab/PI that originally made the reagent or published the sequence
-
-
- Transfection method
- Indicates stable transfection vs transient
-
-
- Transmitter/founder status
- Classification of transmitter/founder status of the isolate
-
-
- Pseudovirus backbone system
- Classification of pseudovirus system of the isolate backbone
-
-
-
-
-
-
-
- The unique CDS sequence ID.
-
-
- The sequence as nucleotides.
-
-
-
-
-
-
-
-
-
- The name of the alignment application.
-
-
- A JSON formatted string containing details about the alignment application and its inputs.
-
-
-
-
-
-
-
- The IMGT allele name.
-
-
- The IMGT allele sequence as nucleotides.
-
-
- The release date for the IMGT reference database version the sequence is from.
-
-
-
-
-
-
-
-
- The original fasta header list in the source.
-
-
- The CDS sequence ID associated with the header.
-
-
- Information about the sequence source.
-
-
-
-
-
-
-
-
- The IMGT allele name.
-
-
- The unique CDS sequence ID.
-
-
- The percent of matches in the alignment.
-
-
- The number of matches.
-
-
- The number of neucleotides in the alignment.
-
-
- The score given by the alignment algorithm.
-
-
- Which run number generated the alignment.
-
-
-
-
-
-
-
-
-
- The CDS mAb ID.
-
- cds
- mab_metadata
- mab_id
-
-
-
- The sequence ID associated with a given mAB ID and chain.
-
- cds
- sequence
- sequence_id
-
-
-
-
- cds
- donor_metadata
- donor_id
-
-
-
-
-
-
-
-
- The CDS sequence ID.
-
-
- True if the aligned sequence contains a stop codon.
-
-
- True if the V and J gene alignments are in-frame.
-
-
- True if the V(D)J sequence is predicted to be productive.
-
-
- True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'.
-
-
- True if the sequence alignment spans the entire V(D)J region. Meaning, sequence_alignment includes both the first V gene codon that encodes the mature polypeptide chain (i.e., after the leader sequence) and the last complete codon of the J gene (i.e., before the J-C splice site). This does not require an absence of deletions within the internal FWR and CDR regions of the alignment.
-
-
- V gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHV4-59*01 if using IMGT/GENE-DB).
-
-
- First or only D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB).
-
-
- J gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHJ4*02 if using IMGT/GENE-DB).
-
-
- Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement.
-
-
- Assembled, aligned, full-length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any).
-
-
- Amino acid translation of the aligned query sequence.
-
-
- Amino acid translation of the assembled germline sequence.
-
-
- Start position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- End position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- Start position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- End position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- Start position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- End position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
-
-
- Aligned portion of query sequence assigned to the V gene, including any indel corrections or numbering spacers.
-
-
- Amino acid translation of the v_sequence_alignment field.
-
-
- Aligned V gene germline sequence spanning the same region as the v_sequence_alignment field and including the same set of corrections and spacers (if any).
-
-
- Amino acid translation of the v_germline_alignment field.
-
-
- Aligned portion of query sequence assigned to the first or only D gene, including any indel corrections or numbering spacers.
-
-
- Amino acid translation of the d_sequence_alignment field.
-
-
- Aligned D gene germline sequence spanning the same region as the d_sequence_alignment field and including the same set of corrections and spacers (if any).
-
-
- Amino acid translation of the d_germline_alignment field.
-
-
- Aligned portion of query sequence assigned to the J gene, including any indel corrections or numbering spacers.
-
-
- Amino acid translation of the j_sequence_alignment field.
-
-
- Aligned J gene germline sequence spanning the same region as the j_sequence_alignment field and including the same set of corrections and spacers (if any).
-
-
- Amino acid translation of the j_germline_alignment field.
-
-
- Nucleotide sequence of the aligned FWR1 region.
-
-
- Amino acid translation of the fwr1 field.
-
-
- Nucleotide sequence of the aligned CDR1 region.
-
-
- Amino acid translation of the cdr1 field.
-
-
- Nucleotide sequence of the aligned FWR2 region.
-
-
- Amino acid translation of the fwr2 field.
-
-
- Nucleotide sequence of the aligned CDR2 region.
-
-
- Amino acid translation of the cdr2 field.
-
-
- Nucleotide sequence of the aligned FWR3 region.
-
-
- Amino acid translation of the fwr3 field.
-
-
- Nucleotide sequence of the aligned FWR4 region.
-
-
- Amino acid translation of the fwr4 field.
-
-
- Nucleotide sequence of the aligned CDR3 region.
-
-
- Amino acid translation of the cdr3 field.
-
-
- Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons.
-
-
- Number of nucleotides in the junction sequence.
-
-
- Amino acid translation of the junction.
-
-
- Number of amino acids in the junction sequence.
-
-
- Alignment score for the V gene.
-
-
- Alignment score for the first or only D gene alignment.
-
-
- Alignment score for the J gene alignment.
-
-
- CIGAR string for the V gene alignment.
-
-
- CIGAR string for the first or only D gene alignment.
-
-
- CIGAR string for the J gene alignment.
-
-
- V gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the V gene assignment as defined by the alignment tool.
-
-
- D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the first or only D gene as defined by the alignment tool.
-
-
- J gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the J gene assignment as defined by the alignment tool.
-
-
- Fractional identity for the V gene alignment.
-
-
- Fractional identity for the first or only D gene alignment.
-
-
- Fractional identity for the J gene alignment.
-
-
- Start position of the V gene in the query sequence (1-based closed interval).
-
-
- End position of the V gene in the query sequence (1-based closed interval).
-
-
- Alignment start position in the V gene reference sequence (1-based closed interval).
-
-
- Alignment end position in the V gene reference sequence (1-based closed interval).
-
-
- Start position of the first or only D gene in the query sequence. (1-based closed interval).
-
-
- End position of the first or only D gene in the query sequence. (1-based closed interval).
-
-
- Alignment start position in the D gene reference sequence for the first or only D gene (1-based closed interval).
-
-
- Alignment end position in the D gene reference sequence for the first or only D gene (1-based closed interval).
-
-
- Start position of the J gene in the query sequence (1-based closed interval).
-
-
- End position of the J gene in the query sequence (1-based closed interval).
-
-
- Alignment start position in the J gene reference sequence (1-based closed interval).
-
-
- Alignment end position in the J gene reference sequence (1-based closed interval).
-
-
- FWR1 start position in the query sequence (1-based closed interval).
-
-
- FWR1 end position in the query sequence (1-based closed interval).
-
-
- CDR1 start position in the query sequence (1-based closed interval).
-
-
- CDR1 end position in the query sequence (1-based closed interval).
-
-
- FWR2 start position in the query sequence (1-based closed interval).
-
-
- FWR2 end position in the query sequence (1-based closed interval).
-
-
- CDR2 start position in the query sequence (1-based closed interval).
-
-
- CDR2 end position in the query sequence (1-based closed interval).
-
-
- FWR3 start position in the query sequence (1-based closed interval).
-
-
- FWR3 end position in the query sequence (1-based closed interval).
-
-
- FWR4 start position in the query sequence (1-based closed interval).
-
-
- FWR4 end position in the query sequence (1-based closed interval).
-
-
- CDR3 start position in the query sequence (1-based closed interval).
-
-
- CDR3 end position in the query sequence (1-based closed interval).
-
-
- Nucleotide sequence of the combined N/P region between the V gene and first D gene alignment or between the V gene and J gene alignments.
-
-
- Number of nucleotides between the V gene and first D gene alignments or between the V gene and J gene alignments.
-
-
- Nucleotide sequence of the combined N/P region between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
-
-
- Number of nucleotides between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
-
-
- What application performed the alignment.
-
-
-
-
-
-
-
- A unique identifier of the mab class.
-
-
- A name for the mab class.
-
-
- A text description of the mab class.
-
-
-
-
-
-
-
-
- The CDS sequence ID associated with the lineage sequence
-
-
- The IMGT allele name
-
-
- If the allele sequence is preferred or not
-
-
- A note field that identifies how the preferred status was determined
-
-
-
-
-
-
-
- A unique ID value to reference the header source
-
-
- A short description of the source, e.g. PMID, DOI, short name
-
-
- A note for the source
-
-
-
-