From 30236049e0035556f6a8ae9294dcc38a22c9f9f8 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 6 Oct 2025 12:05:07 -0700
Subject: [PATCH 01/25] -> script updates

---
 shell/backup-solr.sh  | 2 +-
 shell/restore-solr.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/shell/backup-solr.sh b/shell/backup-solr.sh
index 692848be3..885437ce0 100644
--- a/shell/backup-solr.sh
+++ b/shell/backup-solr.sh
@@ -20,7 +20,7 @@ do
         echo "-h           This help."
         echo "-l <FILE>    Specifies a file which lists the cores to be backed up. Required if -c is not supplied."
         echo "-c <CORE>    Specifies a list of comma-separated cores to back up. Required if -l is not supplied."
-        echo "-f <FILE>    Specifies an output file name for the resulting TAR file. Optional. Default: solr_cores_backup_<datestamp>.tar"
+        echo "-f <FILE>    Specifies an output file name for the resulting TAR GZIP file. Optional. Default: solr_cores_backup_<datestamp>.tar.gz"
         echo "-d <BUCKET>  Specifies a destination bucket for storing the resulting TAR output. Optional."
         echo " "
         echo "You must store the Solr API password in SOLR_PWD before running this script!"
diff --git a/shell/restore-solr.sh b/shell/restore-solr.sh
index eafd796b0..a2961f5a3 100644
--- a/shell/restore-solr.sh
+++ b/shell/restore-solr.sh
@@ -73,7 +73,7 @@ for dirname in ${BACKUP_DIR}/*/; do
   fi
   if [ "$MAKE_CORE" = true ]; then
     echo "[STATUS] Core creation enabled - attempting creation of core \"${CORE}\"..."
-    sudo -u solr /opt/bitnami/solr/bin/solr create -c $CORE -s 2 -rf 2
+    sudo -u solr solr create -c $CORE
   else
     echo "[STATUS] Core creation disabled - this assumes core \"${CORE}\" exists already!"
     echo "  You'll see an error if it doesn't."

From 00ce70fdda1ed0a0cff82104a84ae4bb1a8aeb0a Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 7 Oct 2025 10:13:39 -0700
Subject: [PATCH 02/25] -> #1489

---
 idc/demo_views.py                    |  2 +-
 idc/views.py                         | 33 ++++++++++++++++++----------
 static/js/cartutils.js               | 33 ++++++++--------------------
 static/js/citations_modal.js         | 29 +++++++++++++++++++++---
 static/js/image_search.js            | 14 +++++-------
 templates/idc/explore_data_core.html | 12 +++++-----
 6 files changed, 70 insertions(+), 53 deletions(-)

diff --git a/idc/demo_views.py b/idc/demo_views.py
index 659d7966d..890ff0596 100644
--- a/idc/demo_views.py
+++ b/idc/demo_views.py
@@ -144,7 +144,7 @@ def explore_demo_page(request):
     is_json = False
 
     try:
-        req = request.GET if request.GET else request.POST
+        req = request.GET if request.method == 'GET' else request.POST
         is_dicofdic = (req.get('is_dicofdic', "False").lower() == "true")
         source = req.get('data_source_type', DataSource.SOLR)
         versions = json.loads(req.get('versions', '[]'))
diff --git a/idc/views.py b/idc/views.py
index 6e96af000..00e631e50 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -23,6 +23,7 @@
 import datetime
 import re
 import copy
+from xmlrpc.client import boolean
 
 from django.conf import settings
 from django.contrib.auth.decorators import login_required
@@ -226,7 +227,7 @@ def quota_page(request):
 def save_ui_hist(request):
     status = 200
     try:
-        req = request.POST or request.GET
+        req = request.GET if request.method == 'GET' else request.POST
         hist = req['his']
         try:
             user_data = User_Data.objects.get(user_id=request.user.id)
@@ -269,7 +270,7 @@ def studymp(request):
     ).distinct()
 
     try:
-       req = request.GET if request.GET else request.POST
+       req = request.GET if request.method == 'GET' else request.POST
        filters = json.loads(req.get('filters', '{}'))
 
        mxSeries = int(req.get('mxseries'))
@@ -534,7 +535,7 @@ def explore_data_page(request, filter_path=False, path_filters=None):
 
 def explorer_manifest(request):
     try:
-        req = request.GET or request.POST
+        req = request.GET if request.method == 'GET' else request.POST
         if req.get('manifest-type', 'file-manifest') == 'bq-manifest' :
             messages.error(request, "BigQuery export requires a cohort! Please save your filters as a cohort.")
             return JsonResponse({'msg': 'BigQuery export requires a cohort.'}, status=400)
@@ -549,7 +550,7 @@ def explorer_manifest(request):
 # by the explore_data_page method and forward it on to that view, returning its response.
 def parse_explore_filters(request):
     try:
-        if not request.GET:
+        if not request.GET or request.method != 'GET':
             raise Exception("This call only supports GET!")
         raw_filters = {x: request.GET.getlist(x) for x in request.GET.keys()}
         filters = {}
@@ -618,7 +619,7 @@ def cart_page(request):
         request.session.create()
 
     try:
-        req = request.GET if request.GET else request.POST
+        req = request.GET if request.method == 'GET' else request.POST
         carthist = json.loads(req.get('carthist', '{}'))
         mxseries = req.get('mxseries',0)
         mxstudies = req.get('mxstudies',0)
@@ -641,10 +642,11 @@ def cart_data(request):
     response = {}
     field_list = ['collection_id', 'PatientID', 'StudyInstanceUID', 'SeriesInstanceUID', 'aws_bucket', "source_DOI"]
     try:
-        req = request.GET if request.GET else request.POST
+        req = request.GET if request.method == 'GET' else request.POST
         filtergrp_list = json.loads(req.get('filtergrp_list', '{}'))
         aggregate_level = req.get('aggregate_level', 'StudyInstanceUID')
         results_level = req.get('results_level', 'StudyInstanceUID')
+        dois_only = bool(req.get('dois_only', 'false').lower() == 'true')
 
         partitions = json.loads(req.get('partitions', '{}'))
 
@@ -653,13 +655,22 @@ def cart_data(request):
         length = int(req.get('length', 100))
         mxseries = int(req.get('mxseries',1000))
 
-        if ((len(partitions)>0) and (aggregate_level == 'StudyInstanceUID')):
-            response = get_cart_data_studylvl(filtergrp_list, partitions, limit, offset, length, mxseries, results_lvl=results_level)
-        elif ((len(partitions)>0) and (aggregate_level == 'SeriesInstanceUID')):
-            response = get_cart_data_serieslvl(filtergrp_list, partitions, field_list, limit, offset)
-        else:
+        if len(partitions) <= 0 or aggregate_level not in ['SeriesInstanceUID', 'StudyInstanceUID']:
             response['numFound'] = 0
             response['docs'] = []
+        else:
+            if aggregate_level == 'StudyInstanceUID':
+                response = get_cart_data_studylvl(
+                    filtergrp_list, partitions, limit, offset, length, mxseries, with_records=(not dois_only),
+                    results_lvl=results_level, dois_only=dois_only
+                )
+            elif aggregate_level == 'SeriesInstanceUID':
+                response = get_cart_data_serieslvl(
+                    filtergrp_list, partitions, field_list if not dois_only else None, limit, offset,
+                    with_records=(not dois_only), dois_only=dois_only
+                )
+        if dois_only:
+            response = {'dois': response['dois']}
     except Exception as e:
         logger.error("[ERROR] While loading cart:")
         logger.exception(e)
diff --git a/static/js/cartutils.js b/static/js/cartutils.js
index f75bdcafb..6a8303316 100644
--- a/static/js/cartutils.js
+++ b/static/js/cartutils.js
@@ -124,9 +124,7 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
 
 
     const updateCartCounts =function(){
-
-        var buttonContents = '<button class="btn filter-type clear-cart" role="button" title="Clear the current filter set."><i class="fa fa-rotate-left"></i></button>';
-
+        var buttonContents = '<button class="btn filter-type clear-cart" role="button" title="Empty your cart."><i class="fa fa-rotate-left"></i></button>';
         if (Object.keys(window.proj_in_cart).length>0){
             var nmprojs = 0;
             var nmcases=0;
@@ -139,27 +137,17 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
                 nmseries=nmseries+window.proj_in_cart[projid]['series'];
             }
 
-
-            var content = buttonContents+'<span id ="#cart_stats">Cart contents: ' + nmseries.toString()+' series from '+nmprojs.toString()+
+            let content = buttonContents+'<span id ="#cart_stats">Cart contents: ' + nmseries.toString()+' series from '+nmprojs.toString()+
                 ' collections / '+nmcases.toString()+' cases / '+nmstudies.toString()+' studies</span>';
             localStorage.setItem('manifestSeriesCount',nmseries);
 
             $('#cart_stats_holder').html(content) ;
             $('#cart_stats').removeClass('empty-cart');
-            $('#export-manifest-cart').removeAttr('disabled');
-            $('.cart-view').removeAttr('disabled');
-            $('.clear-cart').removeAttr('disabled');
-            $('.clear-cart').on('click', function(){
-                 window.resetCart();
-            });
-
+            $('.cart-activated-controls').removeAttr('disabled');
         } else {
             $('#cart_stats_holder').html('<span id="#cart_stats">Your cart is currently empty</span>');
             $('#cart_stats').addClass('empty-cart');
-
-            $('#export-manifest-cart').attr('disabled', 'disabled');
-            $('.cart-view').attr('disabled', 'disabled');
-            $('.clear-cart').attr('disabled', 'disabled');
+            $('.cart-activated-controls').attr('disabled', 'disabled');
         }
 
     }
@@ -184,13 +172,9 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
 
          $('#cart_stats').addClass('empty-cart');
          $('#cart_stats').html("Your cart is currently empty.");
-         $('#export-manifest-cart').attr('disabled','disabled');
-         $('.cart-view').attr('disabled','disabled');
-         $('.clear-cart').attr('disabled','disabled');
+         $('.cart-activated-controls').attr('disabled','disabled');
     }
 
-
-
     //as user makes selections in the tables, record the selections in the cartHist object. Make new partitions from the selections
     const updateCartSelections = function(newSel){
 
@@ -198,11 +182,8 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
         var selections = window.cartHist[curInd]['selections'];
         selections.push(newSel);
         window.cartHist[curInd]['partitions'] = mkOrderedPartitions(window.cartHist[curInd]['selections']);
-
-
     }
 
-
     // make partitions from table selections
     const mkOrderedPartitions = function(selections){
         parts = new Array();
@@ -764,6 +745,10 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
         return newId;
     }
 
+    $('.shopping-cart-panel').on('click', '.clear-cart', function(){
+         window.resetCart();
+    });
+
     return {
         mkOrderedPartitions: mkOrderedPartitions,
         formcartdata: formcartdata,
diff --git a/static/js/citations_modal.js b/static/js/citations_modal.js
index cd99df381..57eebc075 100644
--- a/static/js/citations_modal.js
+++ b/static/js/citations_modal.js
@@ -70,12 +70,33 @@ require([
 
     $('#citations-modal').on('show.bs.modal', async function(event) {
         let button = $(event.relatedTarget);
-        let dois = button.attr('data-dois').split("||");
         let cites_list = $("#citations-modal .citations-list");
         let copy_cites = $("#citations-modal .copy-this");
+
+        let dois = null;
         cites_list.html(`
             Formatting citation(s)... <i class="fa fa-compass fa-spin"></i>
         `);
+        if(button.hasClass('for-cart')) {
+            let cart_result = await fetch(`${BASE_URL}/cart_data/`, {
+                    method: "POST",
+                    body: new URLSearchParams({
+                        'filtergrp_list': JSON.stringify(window.filtergrp_list),
+                        'partitions': JSON.stringify(window.partitions),
+                        'dois_only': 'true'
+                    }),
+                    headers: {"X-CSRFToken": csrftoken, "content-type": 'application/x-www-form-urlencoded'}
+            });
+            if(!cart_result.ok) {
+                cites_list.html("Failed to retrieve citations!");
+                throw new Error("Failed to retrieve citations!");
+            }
+            let data = await cart_result.json();
+            dois = data['dois'];
+        } else {
+            dois = button.attr('data-dois').split("||");
+        }
+
         let dois_to_get = dois.filter((d) => (DOI_CACHE[d] === null || DOI_CACHE[d] === undefined));
         if(dois_to_get.length > 0) {
             let resp = null;
@@ -85,8 +106,10 @@ require([
                     body: JSON.stringify({
                         'doi': dois_to_get
                     }),
-                    headers: {"X-CSRFToken": csrftoken},
-                    "content-type": "application/json"
+                    headers: {
+                        "X-CSRFToken": csrftoken,
+                        "content-type": "application/json"
+                    }
                 });
             } else {
                 let encoded_dois = dois_to_get.map(d => `doi=${encodeURIComponent(d)}`);
diff --git a/static/js/image_search.js b/static/js/image_search.js
index ec2687279..5a55b4ef7 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -177,9 +177,9 @@ require([
                         async_download ? "True" : "False"
                     );
                     if('dois' in data) {
-                        $('.citations-button').attr("data-dois", Object.keys(data['dois']).join("||"));
+                        $('.filter-display-panel .citations-button').attr("data-dois", Object.keys(data['dois']).join("||"));
                     } else {
-                        $('.citations-button').attr("data-dois", "");
+                        $('.filter-display-panel .citations-button').attr("data-dois", "");
                     }
                     if (('filtered_counts' in data) && ('origin_set' in data['filtered_counts']) &&
                         ('access' in data['filtered_counts']['origin_set']['All']['attributes']) &&
@@ -604,15 +604,11 @@ require([
 
             if (gtotals[0]>0){
                 $('#cart_stats').removeClass('empty-cart');
-                $('.cart-view').removeAttr('disabled');
-                $('.clear-cart').removeAttr('disabled');
-                $('#export-manifest-cart').removeAttr('disabled');
-            } else{
+                $('.cart-activated-controls').removeAttr('disabled');
+            } else {
                 $('#cart_stats').addClass('empty-cart');
                 $('#cart_stats').html('Your cart is currently empty.');
-                $('.cart-view').attr('disabled', 'disabled');
-                $('#export-manifest-cart').attr('disabled','disabled');
-                $('.clear-cart').attr('disabled','disabled');
+                $('.cart-activated-controls').attr('disabled','disabled');
             }
         }
         else if ("cartHist" in localStorage){
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index 005dee850..e5223c1c0 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -672,18 +672,20 @@ <h4>Cart</h4>
                     <div class="panel-body">
                         <p id="cart_stats_holder"><span id="cart_stats" class="empty-cart">Your cart is currently empty.</span></p>
                         <div class="cart-container space-top-10">
-                            <button id="export-manifest-cart" class="btn btn-primary cart-export btn-small" disabled data-toggle="modal"
+                            <button id="export-manifest-cart" class="btn btn-primary cart-export btn-small cart-activated-controls" disabled data-toggle="modal"
                                 data-target="#export-manifest-modal"
                                 title="Add items to the cart to enable this feature."
                             > Manifest <i class="fa fa-solid fa-download"></i>
                             </button>
-                            <button class="btn btn-small btn-default cart-view" role="button" title="Get cart details." disabled
+                            <button class="btn btn-small btn-special citations-button cart-activated-controls for-cart" disabled data-toggle="modal" data-target="#citations-modal" role="button"
+                                data-default-title="Display this cart's citation list in Vancouver format."
+                                title= "Add items to the cart to enable this feature."
+                            > Citations <i class="fa fa-list-numeric"></i>
+                            </button>
+                            <button class="btn btn-small btn-default cart-view cart-activated-controls" role="button" title="Get cart details." disabled
                                 onclick="viewcart()"
                             > View <i class="fa-solid fa-cart-shopping"></i>
                             </button>
-                            <!-- <button class="btn btn-small btn-special clear-cart" role="button" disabled
-                                    title="Empty your cart."> <i class="fa-solid fa-rotate-left"></i>
-                            </button> -->
                         </div>
                     </div>
                 </div>

From d7bab930a86cb4ae91b760a7030c669b9dfff005 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 7 Oct 2025 13:24:19 -0700
Subject: [PATCH 03/25] -> Clean up cart page buttons, add citations

---
 static/css/cart.css                           |  39 +++
 static/js/cart_page.js                        |  68 ++--
 static/js/citations_modal.js                  |   2 +-
 templates/cohorts/cart-description-modal.html |  21 +-
 templates/collections/cart_list.html          |  29 +-
 templates/idc/cart-details-modal.html         |   5 +-
 templates/idc/cart.html                       | 329 ------------------
 templates/idc/explore.html                    |   4 +-
 8 files changed, 99 insertions(+), 398 deletions(-)
 delete mode 100644 templates/idc/cart.html

diff --git a/static/css/cart.css b/static/css/cart.css
index 0f449cbe8..7b3b98dbc 100644
--- a/static/css/cart.css
+++ b/static/css/cart.css
@@ -19,3 +19,42 @@
 .export-button:hover, .btnGroupDropViewers:hover {
     cursor: pointer;
 }
+
+.cart-filter-display {
+    margin-bottom: 8px;
+}
+
+.filter-type, .adjustment-type {
+    color: #a66206;
+    font-weight: bold;
+    text-transform: uppercase;
+    display: inline-block;
+}
+
+.filter-att{
+    background-color: #2A537A;
+    border-radius: 3px;
+    display: inline-block;
+    color: #F8F8F8;
+    padding: 2px;
+    margin: 0 3px 3px 3px
+}
+
+.filter-title, .adjustments-op {
+    font-weight: bold;
+}
+
+.adjustment-att {
+    color: #2A537A;
+    font-weight: bold;
+    display: inline-block;
+}
+
+.cart-def-list {
+    margin-bottom: 15px;
+    padding-bottom: 9px;
+}
+
+.cart-def-list:not(:last-child) {
+    border-bottom: 2px solid black;
+}
diff --git a/static/js/cart_page.js b/static/js/cart_page.js
index 18455c748..39cf4b53d 100644
--- a/static/js/cart_page.js
+++ b/static/js/cart_page.js
@@ -32,8 +32,7 @@ require.config({
         cartutils: 'cartutils',
         tippy: 'libs/tippy-bundle.umd.min',
          '@popperjs/core': 'libs/popper.min',
-
-
+        citations_modal: 'citations_modal'
     },
     shim: {
         '@popperjs/core': {
@@ -50,7 +49,8 @@ require.config({
         'underscore': {exports: '_'},
         'session_security': ['jquery'],
         'cartutils': ['jquery'],
-        'export-manifest':['jquery']
+        'export-manifest':['jquery'],
+        'citations_modal': ['jquery']
     }
 });
 
@@ -64,17 +64,15 @@ require([
     'base', // This must ALWAYS be loaded!
     'jquerydt',
     'jqueryui',
-    'bootstrap'
+    'bootstrap',
+    'citations_modal'
 ], function(cartutils, tables, $, tippy, _, base) {
 
-     var ajaxtriggered = false;
+    var ajaxtriggered = false;
 
     window.resetCartPageView = function(){
-
-
         localStorage.setItem("cartcleared","yes");
         window.history.back();
-
     }
 
     tippy.delegate('#cart-table', {
@@ -97,40 +95,46 @@ require([
         var contentArray= [];
         for (var i=0;i< window.cartHist.length;i++){
             var cartDetail = window.cartHist[i];
-            var filter = JSON.stringify(cartDetail.filter);
+            var filter = cartDetail.filter;
+            let is_filtered = (Object.keys(filter).length > 0);
+            let filter_match = is_filtered ? " which match the filter" : "";
+            let filter_div = "", adjustment_div = "";
             var selections = cartDetail.selections;
             if (selections.length>0){
-                contentArray.push('Set filter definition set to: '+filter);
-                for (var j=0;j<selections.length;j++){
-                    var selectext=""
-                    var selec = selections[j]
-                    if (selec.sel.length ==4){
-                        if (selec.added) {
-                            selectext += "<li>Added the series " +selec.sel[3] +" from collection " + selec.sel[0] +", case "+selec.sel[1]+", study "+selec.sel[2];
-                        }
-                        else{
-                           selectext += "<li>Removed the series " +selec.sel[3] +" from collection " + selec.sel[0] +", case "+selec.sel[1]+", study "+selec.sel[2];
-                        }
-
+                if(is_filtered) {
+                    let filter_set = [];
+                    for(attr in filter) {
+                        filter_set.push(`<span class="filter-type">${attr}</span> in (${filter[attr].map(d => '<span class="filter-att">'+d+'</span>').join("")})`);
                     }
-                    else {
-                        if (selec.added) {
-                            selectext += "<li>Added series matching the filter from collection " + selec.sel[0]
-                        } else {
-                            selectext += "<li>Removed series matching the filter from collection " + selec.sel[0]
-                        }
+                    filter_div = `<div class="cart-filter-display"><span class="filter-title">Filter: </span>${filter_set.join(" AND ")}</div>`;
+                }
+                for (var j=0;j<selections.length;j++){
+                    var selectext= "";
+                    var selec = selections[j];
+                    let op = selec.added ? "Added" : "Removed";
+                    if (selec.sel.length == 4){
+                        selectext += `<span class="adjustments-op">${op}</span> series ${selec.sel[3]} from 
+                            <span class="adjustment-type">collection</span> <span class="adjustment-att">${selec.sel[0]}, 
+                            <span class="adjustment-type">case</span> <span class="adjustment-att">${selec.sel[1]}</span>, 
+                            <span class="adjustment-type">study</span> <span class="adjustment-att">${selec.sel[2]}</span>`;
+                    } else {
+                        selectext += `<span class="adjustments-op">${op}</span> series from 
+                            <span class="adjustment-type">collection</span> <span class="adjustment-att">${selec.sel[0]}</span>`
                         if (selec.sel.length > 1) {
-                            selectext += ", case " + selec.sel[1]
+                            selectext += `, <span class="adjustment-type">case </span> <span class="adjustment-att">${selec.sel[1]}</span>`
                         }
                         if (selec.sel.length > 2) {
-                            selectext += ", study " + selec.sel[2]
+                            selectext += `, <span class="adjustment-type">study</span> <span class="adjustment-att">${selec.sel[2]}</span>`
                         }
+                        selectext += filter_match
                     }
-                 contentArray.push(selectext);
+                    adjustment_div = `<div class="cart-adjustment-display">${selectext}</div>`;
                 }
             }
+            contentArray.push(`${filter_div}${adjustment_div}`)
         }
-        content = "<ol>"+contentArray.join('\n')+"</ol>";
+        let content = `<ul>${contentArray.map(d => `<li class="cart-def-list">${d}`).join("")}</ul>`;
+        console.log(content);
         $('#cart-description-modal').find('.modal-body').html(content);
     }
 
@@ -150,7 +154,7 @@ require([
          window.updatePartitionsFromScratch();
          var ret =cartutils.formcartdata();
          window.partitions = ret[0];
-         window.filtergrp_lst = ret[1];
+         window.filtergrp_list = ret[1];
 
 
          ajaxtriggered = true;
diff --git a/static/js/citations_modal.js b/static/js/citations_modal.js
index 57eebc075..7a3537466 100644
--- a/static/js/citations_modal.js
+++ b/static/js/citations_modal.js
@@ -81,7 +81,7 @@ require([
             let cart_result = await fetch(`${BASE_URL}/cart_data/`, {
                     method: "POST",
                     body: new URLSearchParams({
-                        'filtergrp_list': JSON.stringify(window.filtergrp_list),
+                        'filtergrp_list': JSON.stringify(window.filtergrp_list ? window.filtergrp_list : [{}]),
                         'partitions': JSON.stringify(window.partitions),
                         'dois_only': 'true'
                     }),
diff --git a/templates/cohorts/cart-description-modal.html b/templates/cohorts/cart-description-modal.html
index 30f0e7cfb..5470a0554 100644
--- a/templates/cohorts/cart-description-modal.html
+++ b/templates/cohorts/cart-description-modal.html
@@ -1,27 +1,14 @@
-<!-- Export Manifest Modal -->
+<!-- Cart Definition Modal -->
 <div class="modal fade" id="cart-description-modal" tabindex="-1" role="dialog"
-     aria-labelledby="exportManifestModal" aria-hidden="true" data-file-timestamp="{% now "Ymd_Gis" %}">
+     aria-labelledby="cartDefitionModal" aria-hidden="true" data-file-timestamp="{% now "Ymd_Gis" %}">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                <h4 class="modal-title" id="exportManifestModal">Cart Construction Details</h4>
-
-                <div class="form-group list-group">
-                        {% csrf_token %}
-                </div>
+                <h4 class="modal-title" id="cartDefitionModal">Cart Definition</h4>
             </div>
             <div class="modal-body">
-                  stuff here
-                </div>
-
-            <!--
-            <form id="export-manifest-form" method="GET" action="/explore/manifest/">
-                <div class="modal-body">
-                  stuff here
-                </div>
-
-            </form> -->
+            </div>
         </div>
     </div>
 </div>
diff --git a/templates/collections/cart_list.html b/templates/collections/cart_list.html
index 987c62732..8c42ed3a4 100644
--- a/templates/collections/cart_list.html
+++ b/templates/collections/cart_list.html
@@ -7,7 +7,6 @@
 
     <link type="text/css" rel="stylesheet" href="{% static 'css/spinner.css' %}">
     <link type="text/css" rel="stylesheet" href="{% static 'css/cart.css' %}">
-
     <link type="text/css" rel="stylesheet" href="{% static 'css/jquery-ui.min.css' %}">
 
 {% endblock %}
@@ -19,22 +18,28 @@
 <div class="container-fluid">
 <div class="spinner" style="display: none;"><i class="fa-solid fa-spinner fa-spin spin"></i></div>
     <h3 class="pull-left">Cart - Study Level Summary</h3>
- <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal" data-target="#export-manifest-modal"
-
-                title="Make a cart selection to enable this feature."> Download Cart Images
-            </button>
-<button class="btn btn-special pull-right cart-modal-button" data-toggle="modal" data-target="#cart-description-modal" title="Get cart details.">Display Cart Construction Details</button>
-<button class="btn btn-default  pull-right cart-reset" title="Reset Cart." onclick="window.resetCartPageView()"> Clear Cart
-                             </button>
+    <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal"
+        data-target="#export-manifest-modal" title="Get the series manifest for this cart."
+    > Manifest <i class="fa fa-solid fa-download"></i>
+    </button>
+    <button class="btn pull-right btn-special citations-button filter-activated-controls for-cart" data-toggle="modal" data-target="#citations-modal" role="button"
+        title="Display this cohort's citation list in Vancouver format."
+    > Citations <i class="fa fa-list-numeric"></i>
+    </button>
+    <button class="btn btn-special pull-right cart-modal-button" data-toggle="modal"
+        data-target="#cart-description-modal" title="Display this cart's filter and selections."
+    > Definition <i class="fa fa-solid fa-magnifying-glass"></i>
+    </button>
+    <button class="btn btn-default  pull-right cart-reset" title="Reset Cart." onclick="window.resetCartPageView()"
+    > Clear <i class="fa fa-solid fa-trash-can"></i>
+    </button>
 </div>
 {% endblock %}
 {% block content %}
 <div class="container-fluid">
     <div class ="row">
-
         <div class="col-lg-12 col-md-12 collex-panel">
             <div class="cart-wrapper panel panel-default short-inner-content" role="panel panel-default" id="cart-list">
-
                 <div class="panel-body">
                     <div id="stats"> {{ stats }}</div>
                 <table id="cart-table" class="table collex-table sortable_table table-striped table-hover">
@@ -84,11 +89,11 @@ <h3 class="pull-left">Cart - Study Level Summary</h3>
 	{{ block.super }}
     <script type="text/javascript" src="{% static 'js/cart_page.js' %}?v={{ APP_VERSION }}"></script>
     <script type="text/javascript" src="{% static 'js/cohorts/export-manifest.js' %}?v={{ APP_VERSION }}"></script>
-
+    <script type="text/javascript" src="{% static 'js/citations_modal.js' %}?v={{ APP_VERSION }}"></script>
 {% endblock %}
 
 {% block modal_includes %}
-
+    {% include "idc/citations-modal.html" %}
     {% include "cohorts/cart-description-modal.html" %}
     {% include "cohorts/export-manifest-modal.html" %}
 {% endblock %}
\ No newline at end of file
diff --git a/templates/idc/cart-details-modal.html b/templates/idc/cart-details-modal.html
index 947ae1d44..1e2d1e53a 100644
--- a/templates/idc/cart-details-modal.html
+++ b/templates/idc/cart-details-modal.html
@@ -1,7 +1,6 @@
-    <!-- BigQuery String Modal -->
+    <!-- Cart Details Modal -->
     <div class="modal fade" id="cart-details-modal" tabindex="-1" role="dialog" aria-labelledby="bqStringDisplay"
          aria-hidden="true"
-
     >
         <div class="modal-dialog">
             <div class="modal-content" style="overflow-y:scroll">
@@ -11,9 +10,7 @@ <h4 class="modal-title" id="cartDetailsModal">Cart Details </h4>
                 </div>
                 <div class="modal-body">
                    <div id="cart_details">
-
                    </div>
-
                 </div>
             </div>
         </div>
diff --git a/templates/idc/cart.html b/templates/idc/cart.html
deleted file mode 100644
index 1582c228e..000000000
--- a/templates/idc/cart.html
+++ /dev/null
@@ -1,329 +0,0 @@
-<!--
-
- Copyright 2022, Institute for Systems Biology
-
- 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.
-
-
--->
-
-
-
-
-
-<!DOCTYPE html>
-<html lang="en" class="no-js">
-<head>
-    <meta charset="utf-8">
-    <meta http-equiv="x-ua-compatible" content="ie=edge">
-    <title>
-    IDC | About
-</title>
-    <meta name="description" content="
-    About IDC
-">
-    <meta name="viewport" content="width=device-width, initial-scale=1">
-
-    
-    <link type="text/css" rel="stylesheet" href="/static/css/select2.min.css" />
-    <link rel="icon" type="image/x-icon" href="/static/img/favicon.ico" />
-    <link type="text/css" rel="stylesheet" href="/static/css/style.css" />
-    <script type="text/javascript" src="/static/js/libs/modernizr.js"></script>
-
-    
-
-    
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=">
-        </script>
-        <script>
-          window.dataLayer = window.dataLayer || [];
-          function gtag(){dataLayer.push(arguments);}
-          gtag('js', new Date());
-
-          gtag('config', '');
-        </script>
-    
-    <script>
-        var STATIC_FILES_URL = '/static/';
-        var BASE_URL = 'http://localhost:8086' || "";
-        var STORAGE_URI = 'https://storage.googleapis.com/';
-        var OHIF_V2_PATH = 'https://dev-viewer.canceridc.dev/viewer/';
-        var OHIF_V3_PATH = 'https://dev-viewer.canceridc.dev/v3/viewer/?StudyInstanceUIDs';
-        var VOLVIEW_PATH = 'https://volview.kitware.app/?urls';
-        var SLIM_VIEWER_PATH = 'https://dev-viewer.canceridc.dev/slim/studies/';
-        var tmp = 'tmp';
-    </script>
-    <!-- Adobe User Research study -->
-
-    {% block js_file %}
-
-        {{ projcnts|json_script:"projcnts" }}
-        window.projcnts = JSON.parse(document.getElementById('projcnts').textContent);
-    {% endblock %}
-
-
-
-
-</head>
-<body class="content" id="body">
-<!--Include site main header-->
-
-
-
-
-
-
-<header class="site-header">
-
-    
-    <nav class="navbar navbar-default navbar-fixed-top idc-nav navbar-container">
-        <div class="container-fluid">
-            <div class="navbar-header">
-                <button type="button" class="navbar-toggle collapsed" data-toggle="collapse"
-                        data-target="#main-navbar-collapse" aria-expanded="false">
-                    <span class="sr-only">Toggle navigation</span>
-                    <span class="icon-bar"></span>
-                    <span class="icon-bar"></span>
-                    <span class="icon-bar"></span>
-                </button>
-                <a href="/" title="Home Page" >
-                    <img class="navbar-brand" src="/static/img/NIH_IDC_title.svg" alt="NIH IDC Logo"/>
-                </a>
-            </div>
-            <div class="collapse navbar-collapse" id="main-navbar-collapse">
-                <ul class="nav navbar-nav navbar-left">
-                    <li class="navbar-link navbar-item ">
-                        <a class="main-links" href="/explore/" title="Explore image data">Explore Images</a>
-                    </li>
-                    <li class="navbar-link navbar-item ">
-                        <a class="main-links" href="/collections/" title="View IDC collections">Collections</a>
-                    </li>
-                    <li class="navbar-link navbar-item">
-                        <a class="external-link" href=""
-                            url="https://learn.canceridc.dev/getting-started-with-idc"
-                            title="Getting Started with IDC"
-                            data-toggle="modal" data-target="#external-web-warning">
-                            Getting Started <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                            </a>
-                    </li>
-                    <li class="navbar-link navbar-item">
-                        <a class="external-link" href="" url="https://discourse.canceridc.dev"
-                           data-toggle="modal" data-target="#external-web-warning">
-                           User Forum <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                        </a>
-                    </li>
-                    <li class="navbar-link navbar-item">
-                        <a class="main-links" href="/news/" title="View news items">News</a>
-                    </li>
-                    <li class="navbar-link navbar-item">
-                        <a class="main-links" href="/about/" title="Information about IDC">About</a>
-                    </li>
-                    <li class="navbar-link navbar-item">
-                        <a class="external-link" href="" url="https://learn.canceridc.dev"
-                           data-toggle="modal" data-target="#external-web-warning" title="Documentation">
-                            Help <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                        </a>
-                    </li>
-                    
-                </ul>
-                <ul class="nav navbar-nav navbar-right">
-                    
-                    <li class="navbar-item inline-block navbar-signin">
-                        <a id="sign-in-dropdown" class="sign-in-dropdown dropdown-toggle navbar-item__text"
-                               href="/accounts/login/" title="Sign In"><i class="fa fa-solid fa-sign-in"></i>Sign In</a>
-                    </li>
-                
-                    </ul>
-                </div>
-        </div>
-    </nav>
-</header>
-
-<main id="about" class="main-content">
-    <div class="page-heading">
-        
-    <div class="container-fluid">
-        <h3 class="pull-left">About</h3>
-    </div>
-
-    </div>
-    <div class="container-fluid">
-        <!-- Site Messages -->
-        <div class="row">
-            <div class="col-lg-12 col-md-12 col-sm-12" style="z-index: 100;">
-                
-                <div id="js-messages"></div>
-            </div>
-        </div>
-        <!-- Page Content -->
-        <div class="row">
-            
-    <div class="container-fluid">
-        <div class ="row">
-            <div class="col-lg-12 col-md-12">
-                <div class="panel panel-default" role="panel panel-default">
-                    <div class="panel-body short-inner-content">
-                        <h5>About IDC</h5>
-                        <p>
-                            NCI Imaging Data Commons (IDC) is a cloud-based repository of publicly available cancer
-                            imaging data co-located with the analysis and exploration tools and resources. IDC is a node
-                            within the broader NCI <a href="https://datacommons.cancer.gov/"
-                            target="_blank" rel="noreferrer nofollow">Cancer Research Data Commons (CRDC)</a> infrastructure that provides
-                            secure access to a large, comprehensive, and expanding collection of cancer research data.
-                            All data hosted by IDC will be available publicly. The current content of IDC is populated
-                            using the radiology collections from <a class="external-link" href="" url="https://www.cancerimagingarchive.net/"
-                            data-toggle="modal" data-target="#external-web-warning">The Cancer Imaging Archive (TCIA) <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i></a>, as well as data
-                            collected by other major NCI initiatives, such as TCGA, CPTAC, NLST, and HTAN. IDC does not
-                            perform de-identification of images but will accept data de-identified by TCIA or other Data
-                            Coordinating Centers that are approved by NCI Security.
-                        </p>
-                        <p>
-                            IDC provides access to the data standardized using the <a class="external-link" href="" url="https://www.dicomstandard.org/"
-                            data-toggle="modal" data-target="#external-web-warning">Digital Imaging and Communication in Medicine (DICOM) <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i></a>
-                            standard. IDC collaborates with the projects generating the data to
-                            harmonize alternative formats into DICOM representation. Its content includes not only
-                            images, but also image annotations and analysis results, and is linked using common
-                            identifiers to the other types of cancer data, such as proteomics and genomics datasets in
-                            the <a href="https://datacommons.cancer.gov/" target="_blank" rel="noreferrer nofollow">
-                            Cancer Research Data Commons (CRDC)</a>. Access to the data is supported using standard
-                            interfaces. Given the IDC's role as an imaging data science platform, a major focus is on
-                            establishing best practices for imaging research. In this regard, a key role of IDC is in
-                            preparing and adapting commonly used tools for image analysis to be run on cloud
-                            environments with IDC-hosted datasets. Summarized derived data from analyses previously
-                            run will be associated with imaging data on IDC for ease of use by the research community.
-                        </p>
-                        <h5>Data Types</h5>
-                        <p>
-                            IDC contains various types of images and image-derived data harmonized using the DICOM standard.
-                            As of October 2022, IDC contains the following types of images:
-                            <ul>
-                                <li>Clinical and preclinical imaging</li>
-                                <li>Radiological images (e.g., CT, MRI, PET)</li>
-                                <li>Digital pathology images</li>
-                                <li>Multispectral microscopy images</li>
-                                <li>Image annotations (e.g., planar and volumetric, regions of interest)</li>
-                                <li>Parametric maps derived from images (e.g., perfusion and diffusion maps)</li>
-                                <li>Measurements derived from the images (e.g., radiomics features for the annotated regions of interest)</li>
-                                <li>Expert assessments of the image findings (e.g., qualitative characterizations of lesion appearance)</li>
-                            </ul>
-                        </p>
-                        <h5>Data Submission to IDC</h5>
-                        <p>
-                            Currently IDC will consider submissions from NCI-funded driving projects and data from special
-                            selected projects.
-                        </p>
-                        <p>
-                            IDC only hosts public datasets. It does not support access limitations,
-                            such as data embargoes or sequestration.
-                        </p>
-                        <p>
-                            Submitters of data to IDC must ensure that the data have been de-identified with respect to
-                            protected health information (PHI). Currently, IDC accepts data de-identified by
-                            <a class="external-link" href="" url="https://www.cancerimagingarchive.net/"
-                               data-toggle="modal" data-target="#external-web-warning">
-                               The Cancer Imaging Archive (TCIA) <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                            </a>. Datasets de-identified by other data coordinating centers
-                            (DCC) may be considered but in such cases further information will be required (see
-                            <a class="external-link" href=""
-                                url="https://docs.google.com/document/d/1gmGx3CiAV6w78VJtGJg22VyrtfjAFNYaPy3ebf0Mrl8/edit?usp=sharing"
-                                data-toggle="modal" data-target="#external-web-warning">
-                                Google Doc form <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                            </a>
-                            that will be used to collect information about how de-identification is done).
-                        </p>
-                        <p>
-                            If you are interested in making your data available within IDC, please contact us by sending
-                            email to <a href="mailto:support+submissions@canceridc.dev">support+submissions@canceridc.dev</a>.
-                        </p>
-                        <h5>Citing IDC</h5>
-                        <p>
-                            An overview of IDC is available in this open access publication. If you use IDC, please acknowledge us by citing it!
-                        </p>
-                        <p class="quote">
-                            Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S., Aerts, H. J. W. L.,
-                            Homeyer, A., Lewis, R., Akbarzadeh, A., Bontempi, D., Clifford, W., Herrmann, M. D., Höfener, H.,
-                            Octaviano, I., Osborne, C., Paquette, S., Petts, J., Punzo, D., Reyes, M., Schacherer, D. P.,
-                            Tian, M., White, G., Ziegler, E., Shmulevich, I., Pihl, T., Wagner, U., Farahani, K. & Kikinis, R.
-                            <br />
-                            NCI Imaging Data Commons. Cancer Res. 81, 4188–4193 (2021).
-                            <br />
-                            <a class="external-link" href="" url="http://dx.doi.org/10.1158/0008-5472.CAN-21-0950" data-toggle="modal" data-target="#external-web-warning">
-                                http://dx.doi.org/10.1158/0008-5472.CAN-21-0950 <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                            </a>
-                        </p>
-                        <p>
-                            You can also review the accompanying <a
-                                class="external-link" href="" url="https://www.youtube.com/playlist?list=PLhawVWNiPvwb2H0D9UTOIL23bc5DuDJRu"
-                                data-toggle="modal" data-target="#external-web-warning">demonstration videos <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                        </a> for a quick summary of some of the key features of the platform.
-                        </p>
-                    </div>
-                </div>
-            </div>
-        </div>
-    </div>
-
-        </div>
-    </div>
-    <!-- The landing page and collections page have a special layout, so they have their own footer include -->
-    
-        
-
-
-
-
-    <footer class="row container-fluid site-footer">
-        <div class="row">
-            <a href="/">Site Home</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="mailto:support@canceridc.dev">Contact Us</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="/privacy/" target="_blank" rel="noopener noreferrer">Privacy Policy</a>
-            &nbsp; &nbsp; | &nbsp;&nbsp;
-            <a href="https://www.cancer.gov/policies/accessibility" target="_blank" rel="noopener noreferrer">Accessibility</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="https://www.cancer.gov/policies/foia" target="_blank" rel="noopener noreferrer">FOIA</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" target="_blank" rel="noopener noreferrer">HHS Vulnerability Disclosure</a>
-        </div>
-        <div class="row">
-            <a href="https://www.hhs.gov/" target="_blank" rel="noopener noreferrer">U.S. Department of Health and Human Services</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="https://www.nih.gov/" target="_blank" rel="noopener noreferrer">National Institutes of Health</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="https://www.cancer.gov/" target="_blank" rel="noopener noreferrer">National Cancer Institute</a>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            <a href="https://www.usa.gov/" target="_blank" rel="noopener noreferrer">USA.gov</a>
-        </div>
-        <div class="row mat-toolbar-row">
-            NIH... Turning Discovery Into Health ®
-        </div>
-        <div class="row">
-            <i><b>Application Version:</b> local-dev.202311281501.98a8d5</i>
-            &nbsp; &nbsp; | &nbsp; &nbsp;
-            IDC Data Release Version 17.0 - November 17, 2023
-        </div>
-    </footer>
-
-
-    
-</main>
-
-
-
-
-
-</body>
-
-</html>
diff --git a/templates/idc/explore.html b/templates/idc/explore.html
index ade690533..6abf4d826 100644
--- a/templates/idc/explore.html
+++ b/templates/idc/explore.html
@@ -76,12 +76,12 @@ <h3 class="pull-left" role="heading" aria-level="1">Explore Image Data </h3>
 {% with user_is_social=request.user|has_social is_cohort=False %}
     {% include "cohorts/export-manifest-modal.html" with export_uri=export_uri user_is_social=user_is_social is_cohort=is_cohort %}
 {% endwith %}
-{% include "idc/citations-modal.html" %}
 {% include "idc/explore_data_core.html" %}
 
 {% endblock %}
 
 {% block modal_includes %}
+{% include "idc/citations-modal.html" %}
 {% include "cohorts/save-cohort-modal.html" %}
 {% include "cohorts/filter-alert.html" %}
 {% include "idc/download-modal.html" %}
@@ -144,6 +144,4 @@ <h3 class="pull-left" role="heading" aria-level="1">Explore Image Data </h3>
     <script type="text/javascript" src="{% static 'js/bq-string.js' %}?v={{ APP_VERSION }}"></script>
     <script type="text/javascript" src="{% static 'js/cohorts/export-manifest.js' %}?v={{ APP_VERSION }}"></script>
     <script type="text/javascript" src="{% static 'js/citations_modal.js' %}?v={{ APP_VERSION }}"></script>
-
-
 {% endblock %}
\ No newline at end of file

From 8eb8b5253c5c6504b9f2681c8196203c4e69a1fb Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 7 Oct 2025 16:05:09 -0700
Subject: [PATCH 04/25] -> dependabot

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 7a16bc5b7..ce4e899cb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 cryptography==44.0.2
-django==4.2.24
+django==4.2.25
 django-allauth==0.63.1
 django-anymail[mailgun]
 django-axes==5.40.0

From 4a48ae7dade833b60c1cc62d27e250a3780dc05f Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 7 Oct 2025 16:35:46 -0700
Subject: [PATCH 05/25] -> #1489

---
 static/js/cart_page.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/static/js/cart_page.js b/static/js/cart_page.js
index 39cf4b53d..40afc7efc 100644
--- a/static/js/cart_page.js
+++ b/static/js/cart_page.js
@@ -108,6 +108,7 @@ require([
                     }
                     filter_div = `<div class="cart-filter-display"><span class="filter-title">Filter: </span>${filter_set.join(" AND ")}</div>`;
                 }
+                let adjustments = [];
                 for (var j=0;j<selections.length;j++){
                     var selectext= "";
                     var selec = selections[j];
@@ -128,8 +129,9 @@ require([
                         }
                         selectext += filter_match
                     }
-                    adjustment_div = `<div class="cart-adjustment-display">${selectext}</div>`;
+                    adjustments.push(`<p>${selectext}</p>`);
                 }
+                adjustment_div = `<div class="cart-adjustment-display">${adjustments.join("\n")}</div>`;
             }
             contentArray.push(`${filter_div}${adjustment_div}`)
         }

From 7e07e89ff1e90307c0ef28ad0631aa66a10daf1b Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Thu, 9 Oct 2025 11:23:34 -0700
Subject: [PATCH 06/25] -> #1468

---
 static/js/tables.js                  |  6 +++++-
 templates/collections/cart_list.html | 18 +++++++++---------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/static/js/tables.js b/static/js/tables.js
index dabe05cd6..b19d3a45e 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -1538,7 +1538,11 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
 
         let refocus = function(){
             setTimeout(function(){
-                $(`#${input.attr('id')}`).focus();
+                let thisInput = $(`#${input.attr('id')}`);
+                thisInput.focus();
+                let val=thisInput.val();
+                thisInput.val("");
+                thisInput.val(val);
             }, 300);
         };
 
diff --git a/templates/collections/cart_list.html b/templates/collections/cart_list.html
index 8c42ed3a4..f86b5d96b 100644
--- a/templates/collections/cart_list.html
+++ b/templates/collections/cart_list.html
@@ -18,20 +18,20 @@
 <div class="container-fluid">
 <div class="spinner" style="display: none;"><i class="fa-solid fa-spinner fa-spin spin"></i></div>
     <h3 class="pull-left">Cart - Study Level Summary</h3>
-    <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal"
-        data-target="#export-manifest-modal" title="Get the series manifest for this cart."
-    > Manifest <i class="fa fa-solid fa-download"></i>
-    </button>
-    <button class="btn pull-right btn-special citations-button filter-activated-controls for-cart" data-toggle="modal" data-target="#citations-modal" role="button"
-        title="Display this cohort's citation list in Vancouver format."
-    > Citations <i class="fa fa-list-numeric"></i>
+    <button class="btn btn-default  pull-right cart-reset" title="Reset Cart." onclick="window.resetCartPageView()"
+    > Clear <i class="fa fa-solid fa-trash-can"></i>
     </button>
     <button class="btn btn-special pull-right cart-modal-button" data-toggle="modal"
         data-target="#cart-description-modal" title="Display this cart's filter and selections."
     > Definition <i class="fa fa-solid fa-magnifying-glass"></i>
     </button>
-    <button class="btn btn-default  pull-right cart-reset" title="Reset Cart." onclick="window.resetCartPageView()"
-    > Clear <i class="fa fa-solid fa-trash-can"></i>
+    <button class="btn pull-right btn-special citations-button filter-activated-controls for-cart" data-toggle="modal" data-target="#citations-modal" role="button"
+        title="Display this cohort's citation list in Vancouver format."
+    > Citations <i class="fa fa-list-numeric"></i>
+    </button>
+    <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal"
+        data-target="#export-manifest-modal" title="Get the series manifest for this cart."
+    > Manifest <i class="fa fa-solid fa-download"></i>
     </button>
 </div>
 {% endblock %}

From b9dc75c4540092eb3e199b34c722cfa41a1cba38 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Thu, 9 Oct 2025 11:26:45 -0700
Subject: [PATCH 07/25] -> Wording

---
 templates/collections/cart_list.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/collections/cart_list.html b/templates/collections/cart_list.html
index f86b5d96b..fd9942bc8 100644
--- a/templates/collections/cart_list.html
+++ b/templates/collections/cart_list.html
@@ -18,7 +18,7 @@
 <div class="container-fluid">
 <div class="spinner" style="display: none;"><i class="fa-solid fa-spinner fa-spin spin"></i></div>
     <h3 class="pull-left">Cart - Study Level Summary</h3>
-    <button class="btn btn-default  pull-right cart-reset" title="Reset Cart." onclick="window.resetCartPageView()"
+    <button class="btn btn-default  pull-right cart-reset" title="Empty the cart." onclick="window.resetCartPageView()"
     > Clear <i class="fa fa-solid fa-trash-can"></i>
     </button>
     <button class="btn btn-special pull-right cart-modal-button" data-toggle="modal"
@@ -26,7 +26,7 @@ <h3 class="pull-left">Cart - Study Level Summary</h3>
     > Definition <i class="fa fa-solid fa-magnifying-glass"></i>
     </button>
     <button class="btn pull-right btn-special citations-button filter-activated-controls for-cart" data-toggle="modal" data-target="#citations-modal" role="button"
-        title="Display this cohort's citation list in Vancouver format."
+        title="Display the cart's citation list in Vancouver format."
     > Citations <i class="fa fa-list-numeric"></i>
     </button>
     <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal"

From 00022fb425989bc4e2768cbca2f0a6e65172f164 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 13 Oct 2025 09:30:04 -0700
Subject: [PATCH 08/25] -> Citations icon to quotes

---
 static/css/cart.css                  | 15 +++++++++++++++
 static/css/search.css                | 15 ++++++++++++++-
 templates/collections/cart_list.html |  2 +-
 templates/idc/explore_data_core.html |  4 ++--
 4 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/static/css/cart.css b/static/css/cart.css
index 7b3b98dbc..619256ba8 100644
--- a/static/css/cart.css
+++ b/static/css/cart.css
@@ -58,3 +58,18 @@
 .cart-def-list:not(:last-child) {
     border-bottom: 2px solid black;
 }
+
+.citations-button .fa-quote-left,.citations-button .fa-quote-right {
+    position: relative;
+    font-size: xx-small;
+}
+
+.citations-button .fa-quote-left {
+    top: -5px;
+    margin-left: 2px;
+}
+
+.citations-button .fa-quote-right {
+    top: 2px;
+    margin-left: -1px;
+}
\ No newline at end of file
diff --git a/static/css/search.css b/static/css/search.css
index 91a3760e2..247c33b27 100644
--- a/static/css/search.css
+++ b/static/css/search.css
@@ -781,8 +781,21 @@ li.cartlist {
     }
 }
 
-
 #projects_table:hover, #cases_table:hover, #studies_table:hover{
     cursor:pointer;
+}
 
+.citations-button .fa-quote-left,.citations-button .fa-quote-right {
+    position: relative;
+    font-size: xx-small;
 }
+
+.citations-button .fa-quote-left {
+    top: -5px;
+    margin-left: 2px;
+}
+
+.citations-button .fa-quote-right {
+    top: 2px;
+    margin-left: -1px;
+}
\ No newline at end of file
diff --git a/templates/collections/cart_list.html b/templates/collections/cart_list.html
index fd9942bc8..76e790ede 100644
--- a/templates/collections/cart_list.html
+++ b/templates/collections/cart_list.html
@@ -27,7 +27,7 @@ <h3 class="pull-left">Cart - Study Level Summary</h3>
     </button>
     <button class="btn pull-right btn-special citations-button filter-activated-controls for-cart" data-toggle="modal" data-target="#citations-modal" role="button"
         title="Display the cart's citation list in Vancouver format."
-    > Citations <i class="fa fa-list-numeric"></i>
+    > Citations <i class="smaller-icon fa fa-quote-left"></i><i class="smaller-icon fa fa-quote-right"></i>
     </button>
     <button id="export-manifest-cart" class="btn btn-special pull-right cart-export-from-cp"  data-toggle="modal"
         data-target="#export-manifest-modal" title="Get the series manifest for this cart."
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index e5223c1c0..c7bc43616 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -635,7 +635,7 @@ <h4>Cohort Filters</h4>
                             <button class="btn btn-small btn-special citations-button filter-activated-controls" disabled data-toggle="modal" data-target="#citations-modal" role="button"
                                 data-default-title="Display this cohort's citation list in Vancouver format."
                                 title= "Select a filter to enable this feature."
-                            > Citations <i class="fa fa-list-numeric"></i>
+                            > Citations <i class="smaller-icon fa fa-quote-left"></i><i class="smaller-icon fa fa-quote-right"></i>
                             </button>
                             <button class="btn btn-small btn-default bq-string-display filter-activated-controls" disabled data-toggle="modal"
                                 data-default-title="Display this cohort's filter as a BQ SQL string."
@@ -680,7 +680,7 @@ <h4>Cart</h4>
                             <button class="btn btn-small btn-special citations-button cart-activated-controls for-cart" disabled data-toggle="modal" data-target="#citations-modal" role="button"
                                 data-default-title="Display this cart's citation list in Vancouver format."
                                 title= "Add items to the cart to enable this feature."
-                            > Citations <i class="fa fa-list-numeric"></i>
+                            > Citations <i class="smaller-icon fa fa-quote-left"></i><i class="smaller-icon fa fa-quote-right"></i>
                             </button>
                             <button class="btn btn-small btn-default cart-view cart-activated-controls" role="button" title="Get cart details." disabled
                                 onclick="viewcart()"

From 342129fe36d35c409e59f6209118795271ed4096 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 14 Oct 2025 11:56:37 -0700
Subject: [PATCH 09/25] -> Download for collections (except NLST)

---
 idc/urls.py                          |  5 +--
 idc/views.py                         |  6 ++--
 static/js/downloader.js              | 20 +++++++-----
 static/js/tables.js                  | 46 +++++++++++++---------------
 templates/idc/explore_data_core.html |  1 +
 5 files changed, 42 insertions(+), 36 deletions(-)

diff --git a/idc/urls.py b/idc/urls.py
index c15d5ab00..3c009c734 100644
--- a/idc/urls.py
+++ b/idc/urls.py
@@ -60,8 +60,9 @@
     re_path(r'^cart/$', views.cart_page, name='cart'),
     re_path(r'^explore/cart/$', views.cart_page, name='get_explore_cart'),
     re_path(r'^cart_data/$', views.cart_data, name='get_cart_data'),
-    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
-    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_collex'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
+    re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
     re_path(r'^collaborators/$', views.collaborators, name='collaborators'),
     re_path(r'^collections/', include('idc_collections.urls')),
     re_path(r'^citations/', views.get_citations, name='get_citations'),
diff --git a/idc/views.py b/idc/views.py
index 00e631e50..28b946753 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -679,7 +679,7 @@ def cart_data(request):
     return JsonResponse(response, status=status)
 
 
-def get_series(request, patient_id, study_uid=None):
+def get_series(request, collection_id, patient_id=None, study_uid=None):
     try:
         status = 200
         response = { "result": [] }
@@ -688,8 +688,10 @@ def get_series(request, patient_id, study_uid=None):
             aggregate_level="SeriesInstanceUID"
         ).first()
         filters = {
-            "PatientID": [patient_id]
+            "collection_id": [collection_id]
         }
+        if patient_id:
+            filters['PaitnetID'] = [patient_id]
         if study_uid:
             filters["StudyInstanceUID"] = [study_uid]
         filter_query = build_solr_query(
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 0cb719be1..030b1d3bb 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -670,15 +670,21 @@ require([
         const patient_id = clicked.attr('data-patient');
 
         let series = [];
-        if(clicked.hasClass('download-study') || clicked.hasClass('download-case')) {
-            let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
-            let response = await fetch(`${BASE_URL}/series_ids/${patient_id}/${study_uri}`);
-            if (!response.ok) {
-                console.error(`[ERROR] Failed to retrieve series IDs for study ${study_id}: ${response.status}`);
+        if(clicked.hasClass('download-study') || clicked.hasClass('download-case') || clicked.hasClass('download-collection')) {
+            if(clicked.hasClass('download-collection') && parseInt(clicked.attr('data-total-series')) > 65000) {
+                console.debug("Saw more than 65k series, routing to BQ.");
                 return;
+            } else {
+                let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
+                let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
+                let response = await fetch(`${BASE_URL}/series_ids/${collection_id}/${patient_uri}${study_uri}`);
+                if (!response.ok) {
+                    console.error(`[ERROR] Failed to retrieve series IDs: ${response.status}`);
+                    return;
+                }
+                const series_data = await response.json();
+                series.push(...series_data['result']);
             }
-            const series_data = await response.json();
-            series.push(...series_data['result']);
         } else {
             series.push({
                 "bucket": clicked.attr('data-bucket'),
diff --git a/static/js/tables.js b/static/js/tables.js
index b19d3a45e..f8a8df7b5 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -242,7 +242,8 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 {className: "ckbx cartnumholder", "targets": [2]},
                 {className: "collex_name", "targets": [3]},
                 {className: "collex-case-count table-count", "targets": [4]},
-                {className: "projects_table_num_cohort table-count", "targets": [5]}];
+                {className: "projects_table_num_cohort table-count", "targets": [5]},
+                {className: "download-collection download-col", "targets": [6]}];
     }
 
     // project(collection) table column definitions
@@ -290,38 +291,39 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 return;
             }
         };
+        const download_col = {"type": "html", "orderable": false, data: 'collection_id', render: function(data, type, row) {
+                if ("showDirectoryPicker" in window) {
+                    return `<i class="fa fa-download download-all-instances download-collection"   
+                        data-collection="${row[0]}" 
+                        data-total-series="${row[6]['mxseries']}" 
+                        ></i>`;
+                }
+                return `<i class="fa fa-download download-all-disabled"></i>`;
+            }};
 
-        return [caret_col, cart_col, cartnum_col, collection_col, case_col, dyn_case_col];
+        return [caret_col, cart_col, cartnum_col, collection_col, case_col, dyn_case_col, download_col];
     }
 
      const setRowCartClasses = function(row){
-            if ( parseInt($(row).attr('series_in_cart'))>0)
-            {
+            if ( parseInt($(row).attr('series_in_cart'))>0) {
                 $(row).addClass('someInCart');
-            }
-            else{
+            } else{
                 $(row).removeClass('someInCart');
             }
 
-            if ( parseInt($(row).attr('series_in_cart'))<parseInt($(row).attr('mxseries')))
-            {
+            if ( parseInt($(row).attr('series_in_cart'))<parseInt($(row).attr('mxseries'))){
                 $(row).addClass('extraInItem');
-            }
-            else{
+            } else{
                 $(row).removeClass('extraInItem');
             }
 
             if ( parseInt($(row).attr('series_in_filter'))>parseInt($(row).attr('series_in_filter_and_cart'))){
                 $(row).addClass('extraInFilter');
-            }
-            else{
+            } else{
                 $(row).removeClass('extraInFilter');
             }
-
-
         }
 
-
     // creates the project or collection table  on document load and after filtering. Defines the chevron and cart selection actions
     window.updateProjectTable = function(collectionData,collectionStats, cartStats) {
         var newCollectionData = []
@@ -345,7 +347,6 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 lclstats['studies_in_filter']=0
             }
             if (('series_per_collec' in collectionStats) && (projid in collectionStats['series_per_collec'])) {
-                //stats['mxseries'] = collectionStats['series_per_collec'][projid]
                 lclstats['series_in_filter']=collectionStats['series_per_collec'][projid];
             } else {
                 lclstats['mxseries'] = 0
@@ -373,21 +374,16 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     } else {
                         lclstats[item + '_in_filter_and_cart'] = 0;
                     }
-
-                   }
-
-                  else{
+               } else{
                   lclstats[item + '_in_cart'] = 0;
                   lclstats[item + '_in_filter_and_cart'] = 0;
                   //stats[item + '_in_filter'] = 0;
-                  }
+              }
             }
-
             var ncur=[cur[0], lclstats["series_in_cart"], cur[0], cur[1],cur[2],cur[3],lclstats];
             newCollectionData.push(ncur);
         }
 
-
         $('#proj_table').DataTable().destroy();
         $("#proj_table_wrapper").find('.dataTables_controls').remove();
         var colDefs = projectTableColDefs();
@@ -404,6 +400,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     $(row).attr('data-projectid', data[0]);
                     $(row).data('totalcases', data[5]);
                     $(row).attr('totalcases', data[5]);
+                    $(row).attr('data-total-series', data[6]['mxseries'])
                     $(row).attr('id', 'project_row_' + data[0]);
                     var projid = data[0];
                     // stats is created from the explorer data page when the page is first created
@@ -419,7 +416,6 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
 
                     $(row).on('click', function(event) {
                         handleRowClick("collections", row, event, [projid])
-
                     });
 
                      $(row).find('.collection_info').on("mouseenter", function(e){
@@ -551,7 +547,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
         }};
         const study_col  = {"type": "num", "orderable": true, data: 'unique_studies'};
         const series_col =  {"type": "num", "orderable": true, data: 'unique_series'};
-        const download_col = {"type": "htlp", "orderable": false, data: 'patient_id', render: function(data, type, row) {
+        const download_col = {"type": "html", "orderable": false, data: 'patient_id', render: function(data, type, row) {
                 if ("showDirectoryPicker" in window) {
                     return `<i class="fa fa-download download-all-instances download-case"   
                         data-collection="${row['collection_id']}" 
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index c7bc43616..5a719c2d8 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -855,6 +855,7 @@ <h4 class="panel-title">
                                             <th class="collex_name sorting_1">Collection Name</th>
                                             <th class="numeric_data table-count">Total # of Cases</th>
                                             <th class="numeric_data table-count"># of Cases (filtered)</th>
+                                            <th class="download-col download-collex"></th>
                                         </tr>
                                         </thead>
                                     </table>

From c2b8c5215b1ec66f1359e61cd8ec85c2e97f4092 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Thu, 23 Oct 2025 18:44:49 -0700
Subject: [PATCH 10/25] -> Refuse downloads over 3TB, warn under that and over
 1TB

---
 etl/etl.py                           |  11 +-
 idc/urls.py                          |   3 +
 idc/views.py                         |   6 +-
 static/js/citations_modal.js         |   2 +-
 static/js/downloader.js              | 100 ++++++++---
 static/js/explore.js                 | 254 +++++++++------------------
 static/js/tables.js                  |  35 +++-
 templates/base.html                  |   5 +
 templates/idc/download-modal.html    |  24 ++-
 templates/idc/explore.html           |   1 +
 templates/idc/explore_data_core.html |   8 +-
 11 files changed, 220 insertions(+), 229 deletions(-)

diff --git a/etl/etl.py b/etl/etl.py
index 1476f813e..9c3b7ec3a 100644
--- a/etl/etl.py
+++ b/etl/etl.py
@@ -59,10 +59,10 @@
 COLLECTION_HEADER_CHK = "collection_uuid"
 
 FIELD_MAP = {x: i for i, x in enumerate([
-            "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
-            "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-            "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active"
-    ])}
+    "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
+    "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
+    "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active", "total_size"
+])}
 
 TOKENIZED_FIELDS = ["PatientID", "SeriesInstanceUID", "StudyInstanceUID"]
 
@@ -356,7 +356,7 @@ def load_collections(filename, data_version="8.0"):
         exact_collection_fields = [
             "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
             "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-            "access", "date_updated", "active"]
+            "access", "date_updated", "active", "total_size"]
         field_map = FIELD_MAP
         for line in csv_reader(collection_file):
             if COLLECTION_HEADER_CHK in line:
@@ -366,7 +366,6 @@ def load_collections(filename, data_version="8.0"):
                 for field in line:
                     field_map[field] = i
                     i += 1
-                print(field_map)
                 continue
             collex = {
                 'data': { x: line[field_map[x]] for x in exact_collection_fields },
diff --git a/idc/urls.py b/idc/urls.py
index 3c009c734..f89bcd6d9 100644
--- a/idc/urls.py
+++ b/idc/urls.py
@@ -49,6 +49,7 @@
     re_path(r'^explore/filters/', views.parse_explore_filters, name='parse_explore_filters'),
     re_path(r'^explore/bq_string/$', get_query_str_response, name='explore_bq_string'),
     re_path(r'^explore/manifest/$', views.explorer_manifest, name='get_explore_manifest'),
+    re_path(r'^explore/manifest/series/$', views.explorer_manifest, name='get_series_ids_manifest'),
     re_path(r'^tables/', views.populate_tables, name='populate_tables'),
     re_path(r'^studymp/', views.studymp, name='studymp'),
     re_path(r'^warning/', views.warn_page, name='warn'),
@@ -60,6 +61,8 @@
     re_path(r'^cart/$', views.cart_page, name='cart'),
     re_path(r'^explore/cart/$', views.cart_page, name='get_explore_cart'),
     re_path(r'^cart_data/$', views.cart_data, name='get_cart_data'),
+    re_path(r'^series_ids/$', views.get_series, name='get_series_ids_base'),
+    re_path(r'^series_ids_filter/$', views.get_series, name='get_series_ids_filter'),
     re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_collex'),
     re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
     re_path(r'^series_ids/(?P<collection_id>[A-Za-z0-9\.\-_]+)/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
diff --git a/idc/views.py b/idc/views.py
index 28b946753..d3098b111 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -450,7 +450,6 @@ def explore_data_page(request, filter_path=False, path_filters=None):
             collapse_on, is_json, uniques=uniques, totals=totals, with_stats=with_stats, disk_size=disk_size
         )
 
-        print(context.keys())
         if not('totals' in context):
           context['totals']={}
         if not('PatientID' in context['totals']):
@@ -702,7 +701,7 @@ def get_series(request, collection_id, patient_id=None, study_uid=None):
         result = query_solr_and_format_result(
             {
                 "collection": source.name,
-                "fields": ["PatientID", "StudyInstanceUID", "Modality", "crdc_series_uuid", "SeriesInstanceUID", "aws_bucket", "instance_size"],
+                "fields": ["collection_id", "PatientID", "StudyInstanceUID", "Modality", "crdc_series_uuid", "SeriesInstanceUID", "aws_bucket", "instance_size"],
                 "query_string": None,
                 "fqs": [filter_query['full_query_str']],
                 "facets": None, "sort": None, "counts_only": False, "limit": 2000
@@ -716,7 +715,8 @@ def get_series(request, collection_id, patient_id=None, study_uid=None):
                 "series_size": doc['instance_size'][0],
                 "modality": doc['Modality'][0],
                 "study_id": doc['StudyInstanceUID'],
-                "case": doc["PatientID"]
+                "patient_id": doc["PatientID"],
+                "collection_id": doc['collection_id']
             })
 
     except Exception as e:
diff --git a/static/js/citations_modal.js b/static/js/citations_modal.js
index 7a3537466..c7f4e6a59 100644
--- a/static/js/citations_modal.js
+++ b/static/js/citations_modal.js
@@ -66,7 +66,7 @@ require([
 
     A11y.Core();
 
-    let csrftoken = $.getCookie('csrftoken')
+    let csrftoken = $.getCookie('csrftoken');
 
     $('#citations-modal').on('show.bs.modal', async function(event) {
         let button = $(event.relatedTarget);
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 030b1d3bb..6b5e0624b 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -509,6 +509,17 @@ require([
             this.queues.bytes_downloaded += downloaded_amount;
         }
 
+        pendingfetchMessage(fetch_type) {
+            // Don't display if we already have pending downloads
+            if(this.in_progress > 0) {
+                return;
+            }
+            let messages = {
+                'content': `Fetching series IDs for ${fetch_type}...`
+            };
+            this.progressDisplay.show(null, messages, "seek", true, false);
+        }
+
         // Replaces the current floating message contents with a new message, including a new icon if provided
         statusMessage(message, type, icon, withClose, withCancel) {
             let messages = {
@@ -651,11 +662,61 @@ require([
 
     let downloader_manager = new DownloadManager();
 
+
+    async function handleLargeDownload(filter_and_cart) {
+        let series_job = await fetch(
+        `${SERIES_MANIFEST_URI}/`, {
+                method: "POST",
+                body: JSON.stringify(filter_and_cart),
+                headers: {
+                    "X-CSRFToken": csrftoken,
+                    "content-type": "application/json"
+                }
+            }
+        );
+        if(!series_job.ok) {
+            console.error("Unable to retrieve series IDs!");
+            return;
+        }
+        let job_result = await series_job.json();
+        downloader_manager.pendingfetchMessage("collection");
+        let polling = async function(file_name){
+            let check_res = await fetch(`${CHECK_MANIFEST_URL}${file_name}/`);
+            if(!check_res.ok) {
+                console.error("Unable to retrieve series IDs!");
+                return;
+            }
+            let result = await check_res.json();
+            if(result.manifest_ready) {
+                let results = await(`${FETCH_MANIFEST_URL}${file_name}`);
+                if(!results.ok) {
+                    console.error("Unable to retrieve series IDs!");
+                    return;
+                }
+                const series_data = await response.json();
+                series.push(...series_data['result']);
+            } else {
+                setTimeout(function(){
+                    polling();
+                },2000);
+            }
+        };
+    await polling(job_result.file_name);
+    }
+
+    $('.container-fluid').on('click', '.download-size-warning', function(){
+        const clicked = $(this);
+        let warning_button = $('#download-warning .download-all-instances');
+        warning_button.attr("data-collection", clicked.attr("data-collection"));
+        warning_button.attr("data-study", clicked.attr("data-study"));
+        warning_button.attr('data-patient', clicked.attr('data-patient'));
+    });
+
     $('.container-fluid').on('click', '.cancel-download', function () {
         downloader_manager.cancel();
     });
 
-    $('.container-fluid').on('click', '.download-all-instances', async function (event) {
+    $('body').on('click', '.download-all-instances', async function (event) {
         // Stop propagation to the other handlers or the showDirectoryPicker will complain.
         event.stopImmediatePropagation();
         event.preventDefault();
@@ -668,16 +729,22 @@ require([
         const collection_id = clicked.attr('data-collection');
         const study_id = clicked.attr('data-study');
         const patient_id = clicked.attr('data-patient');
+        const download_type = clicked.attr("data-download-type");
+        let csrftoken = $.getCookie('csrftoken');
 
         let series = [];
-        if(clicked.hasClass('download-study') || clicked.hasClass('download-case') || clicked.hasClass('download-collection')) {
-            if(clicked.hasClass('download-collection') && parseInt(clicked.attr('data-total-series')) > 65000) {
-                console.debug("Saw more than 65k series, routing to BQ.");
-                return;
+        if(download_type !== "series") {
+            if(parseInt(clicked.attr('data-total-series')) > 65000) {
+
             } else {
-                let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
-                let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
-                let response = await fetch(`${BASE_URL}/series_ids/${collection_id}/${patient_uri}${study_uri}`);
+                let response = null;
+                if(download_type in ["filter", "cart"]) {
+                    response = await fetch(`${BASE_URL}/${SERIES_IDS_FILTER_URL}`);
+                } else {
+                    let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
+                    let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
+                    response = await fetch(`${BASE_URL}/${SERIES_IDS_URL}${collection_id}/${patient_uri}${study_uri}`);
+                }
                 if (!response.ok) {
                     console.error(`[ERROR] Failed to retrieve series IDs: ${response.status}`);
                     return;
@@ -692,21 +759,14 @@ require([
                 "series_id": clicked.attr('data-series-id'),
                 "modality": clicked.attr('data-modality'),
                 "series_size": clicked.attr('data-series-size'),
-                "study_id": study_id
+                "study_id": study_id,
+                "patient_id": patient_id,
+                "collection_id": collection_id
             });
         }
         series.forEach(series_request => {
-            downloader_manager.addRequest({
-                'directory': directoryHandle,
-                'bucket': series_request['bucket'],
-                'crdc_series_id': series_request['crdc_series_id'],
-                'series_id': series_request['series_id'],
-                'collection_id': collection_id,
-                'study_id': series_request['study_id'],
-                'modality': series_request['modality'],
-                'patient_id': patient_id,
-                'series_size': series_request['series_size']
-            });
+            series_request['directory'] = directoryHandle;
+            downloader_manager.addRequest(series_request);
         });
         downloader_manager.beginDownloads();
     });
diff --git a/static/js/explore.js b/static/js/explore.js
index 97225d44f..2a6a3d478 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -84,10 +84,10 @@ require([
 
     for (program in window.programs) {
         for (project in window.programs[program]['projects']) {
-            var col = project;
-            var disp = window.programs[program]['projects'][project]['display'];
-            var val = window.programs[program]['projects'][project]['val'];
-            window.collectionData.push([col, disp, val, val]);
+            let id = project;
+            let disp = window.programs[program]['projects'][project]['display'];
+            let val = window.programs[program]['projects'][project]['val'];;
+            window.collectionData.push([id, disp, val, val]);
             window.selProjects[project]=new Object();
         }
     }
@@ -399,7 +399,7 @@ require([
         maxWidth: 130
     });
 
-    tippy('.bq-string-copy',{
+    const copy_tip = {
         content: 'Copied!',
         theme: 'blue',
         placement: 'right',
@@ -412,57 +412,17 @@ require([
             }, 1000);
         },
         maxWidth: 85
-    });
+    };
 
-    tippy.delegate('.series-table', {
-        content: 'Copied!',
-        theme: 'blue',
-        placement: 'right',
-        arrow: true,
-        interactive: true, // This is required for any table tooltip to show at the appropriate spot!
-        target: '.copy-this',
-        onShow(instance) {
-            setTimeout(function() {
-                instance.hide();
-            }, 1000);
-        },
-        trigger: "click",
-        maxWidth: 85
-    });
+    tippy('.bq-string-copy', copy_tip);
 
-    tippy.delegate('.studies-table', {
-        content: 'Copied!',
-        theme: 'blue',
-        placement: 'right',
-        arrow: true,
-        interactive: true, // This is required for any table tooltip to show at the appropriate spot!
-        target: '.copy-this',
-        onShow(instance) {
-            setTimeout(function() {
-                instance.hide();
-            }, 1000);
-        },
-        trigger: "click",
-        maxWidth: 85
-    });
+    tippy.delegate('.series-table', copy_tip);
 
-    tippy.delegate('.projects-table', {
-        content: 'Copied!',
-        theme: 'blue',
-        placement: 'right',
-        arrow: true,
-        interactive: true, // This is required for any table tooltip to show at the appropriate spot!
-        target: '.copy-this',
-        onShow(instance) {
-            setTimeout(function() {
-                instance.hide();
-            }, 1000);
-        },
-        trigger: "click",
-        maxWidth: 85
-    });
+    tippy.delegate('.studies-table', copy_tip);
+
+    tippy.delegate('.projects-table', copy_tip);
 
-    const dynamicCartTip = {
+    const dynamicTipFunc = {
         fn: (instance) => ({
             onShow() {
                 instance.setContent(instance.props.dynamicTip(instance.reference));
@@ -470,22 +430,25 @@ require([
         })
     };
 
-    tippy.delegate('.projects-table', {
+    const chromium_only = "Direct download is only available in Chromium browsers.";
+    const disabled_download_tooltip = {
+        plugins: [dynamicTipFunc],
         dynamicTip: function(ref){
-            if($(ref).parentsUntil('tbody').filter('tr').hasClass('extraInFilter') || !($(ref).parentsUntil('tbody').filter('tr').hasClass('someInCart'))) {
-                return "add series to cart"
+            if($(ref).hasClass('download-size-disabled')) {
+                return "This set of images is over 3TB in size. Please use manifest download to obtain these images.";
             }
-            return "remove series from cart"
+            return chromium_only;
         },
-        interactive: true,
-        allowHTML: true,
-        placement: 'right',
-        content: 'add series to cart', // placeholder text
-        target: '.shopping-cart-holder',
-        plugins: [dynamicCartTip]
-    });
+        content: chromium_only,
+        theme: 'dark',
+        placement: 'left',
+        arrow: false,
+        interactive:true,
+        target: '.download-all-disabled',
+        maxWidth: 200
+    };
 
-    tippy.delegate('.cases-table', {
+    const cart_tooltip = {
         dynamicTip: function(ref){
             if($(ref).parentsUntil('tbody').filter('tr').hasClass('extraInFilter') || !($(ref).parentsUntil('tbody').filter('tr').hasClass('someInCart'))) {
                 return "add series to cart"
@@ -497,55 +460,68 @@ require([
         placement: 'right',
         content: 'add series to cart', // placeholder text
         target: '.shopping-cart-holder',
-        plugins: [dynamicCartTip]
-    });
+        plugins: [dynamicTipFunc]
+    };
 
-    tippy.delegate('.series-table', {
+    const manifest_tooltip = {
         dynamicTip: function(ref){
-            if ($(ref).parentsUntil('tbody').filter('tr').hasClass('someInCart')) {
-                return "remove from cart"
+            let table_type = $(ref).parents('table').attr('data-table-type');
+            if(table_type === 'series') {
+                return 'Download a manifest file for this series.'
             }
-            return "add to cart"
+            return `Download a manifest file for all the series in this ${table_type}.`;
         },
-        interactive: true,
-        allowHTML: true,
-        placement: 'right',
-        content: 'add series to cart', // placeholder text
-        target: '.shopping-cart-holder',
-        plugins: [dynamicCartTip]
-    });
+        content: 'Download a manifest file.', // placeholder text
+        theme: 'dark',
+        placement: 'left',
+        arrow: false,
+        interactive:true,
+        target: '.export-button',
+        maxWidth: 200,
+        plugins: [dynamicTipFunc]
+    };
 
-    tippy.delegate('.studies-table', {
+    const download_tooltip = {
         dynamicTip: function(ref){
-            if($(ref).parentsUntil('tbody').filter('tr').hasClass('extraInFilter') || !($(ref).parentsUntil('tbody').filter('tr').hasClass('someInCart'))) {
-                return "add series to cart"
+            let table_type = $(ref).parents('table').attr('data-table-type');
+            return `Download all of the image instances in this ${table_type}.`;
+        },
+        content: 'Download all images.', // placeholder text
+        theme: 'dark',
+        placement: 'left',
+        arrow: false,
+        interactive:true,
+        target: '.download-all-instances',
+        maxWidth: 200,
+        plugins: [dynamicTipFunc]
+    };
+
+    tippy.delegate('.projects-table', disabled_download_tooltip);
+
+    tippy.delegate('.projects-table', download_tooltip);
+
+    tippy.delegate('.projects-table', cart_tooltip);
+
+    tippy.delegate('.cases-table', cart_tooltip);
+
+    tippy.delegate('.series-table', {
+        dynamicTip: function(ref){
+            if ($(ref).parentsUntil('tbody').filter('tr').hasClass('someInCart')) {
+                return "remove from cart"
             }
-            return "remove series from cart"
+            return "add to cart"
         },
         interactive: true,
         allowHTML: true,
         placement: 'right',
         content: 'add series to cart', // placeholder text
         target: '.shopping-cart-holder',
-        plugins: [dynamicCartTip]
+        plugins: [dynamicTipFunc]
     });
 
-    tippy.delegate('.cases-table', {
-        content: 'Copied!',
-        theme: 'blue',
-        placement: 'right',
-        arrow: true,
-        interactive: true, // This is required for any table tooltip to show at the appropriate spot!
-        target: '.copy-this',
-        onShow(instance) {
-            setTimeout(function() {
-                instance.hide();
-            }, 1000);
-        },
-        trigger: "click",
-        maxWidth: 85
-    });
+    tippy.delegate('.studies-table', cart_tooltip);
 
+    tippy.delegate('.cases-table', copy_tip);
 
     tippy.delegate('.filter-display-panel', {
         content: 'Get the citation list for this cohort.',
@@ -557,85 +533,21 @@ require([
         maxWidth: 200
     });
 
-    tippy.delegate('.cases-table', {
-        content: 'Download all of the image instances in this case.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-instances',
-        maxWidth: 200
-    });
+    tippy.delegate('.cases-table', download_tooltip);
 
-    tippy.delegate('.cases-table', {
-        content: 'Direct download is only available in Chromium browsers.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-disabled',
-        maxWidth: 200
-    });
+    tippy.delegate('.cases-table', disabled_download_tooltip);
 
-    tippy.delegate('.studies-table', {
-        content: 'Download all of the image instances in this study.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-instances',
-        maxWidth: 200
-    });
+    tippy.delegate('.studies-table', download_tooltip);
 
-    tippy.delegate('.studies-table', {
-        content: 'Download a manifest file for this study.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.export-button',
-        maxWidth: 200
-    });
+    tippy.delegate('.studies-table', manifest_tooltip);
 
-    tippy.delegate('.studies-table', {
-        content: 'Direct download is only available in Chromium browsers.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-disabled',
-        maxWidth: 200
-    });
+    tippy.delegate('.studies-table', disabled_download_tooltip);
 
-    tippy.delegate('.series-table', {
-        content: 'Download all of the image instances in this series.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-instances',
-        maxWidth: 200
-    });
+    tippy.delegate('.series-table', download_tooltip);
 
-    tippy.delegate('.series-table', {
-        content: 'Download a manifest file for this series.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.export-button',
-        maxWidth: 200
-    });
+    tippy.delegate('.series-table', manifest_tooltip);
 
-    tippy.delegate('.series-table', {
-        content: 'Direct download is only available in Chromium browsers.',
-        theme: 'dark',
-        placement: 'left',
-        arrow: false,
-        interactive:true,
-        target: '.download-all-disabled',
-        maxWidth: 200
-    });
+    tippy.delegate('.series-table', disabled_download_tooltip);
 
     tippy.delegate('.series-table', {
         content: 'Some or all of the images in this collection are not publicly available.',
@@ -677,10 +589,6 @@ require([
         maxWidth: 85
     });
 
-    $('.download-link').on('click', function(){
-        $('#download-images').modal("hide");
-    });
-
     $('.container-fluid').on('click', '.collapse-all', function(){
         let targets = $(this).hasClass('search-scope-toggle') ? '.search-scope-item' : '.search-config-item';
         $(targets).collapse('hide');
diff --git a/static/js/tables.js b/static/js/tables.js
index f8a8df7b5..d9b11272b 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -292,14 +292,27 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             }
         };
         const download_col = {"type": "html", "orderable": false, data: 'collection_id', render: function(data, type, row) {
-                if ("showDirectoryPicker" in window) {
-                    return `<i class="fa fa-download download-all-instances download-collection"   
-                        data-collection="${row[0]}" 
-                        data-total-series="${row[6]['mxseries']}" 
-                        ></i>`;
+            let download_size = window.collection[row[0]]['total_size'];
+            if ("showDirectoryPicker" in window && download_size < 3) {
+                let download_classes = "download-collection";
+                download_classes = (download_size > 1) ? `${download_classes} download-size-warning` : `${download_classes} download-all-instances`;
+                let modal_attr = "";
+                if(download_size > 1) {
+                    modal_attr = ` data-toggle="modal" data-target="#download-warning"`;
                 }
-                return `<i class="fa fa-download download-all-disabled"></i>`;
-            }};
+                return `<i class="fa fa-download ${download_classes}"   
+                    data-collection="${row[0]}" 
+                    data-total-series="${row[6]['mxseries']}" 
+                    data-download-type="collection"
+                    ${modal_attr}
+                    ></i>`;
+            }
+            let disabled_classes = "download-all-disabled";
+            if(download_size >= 3) {
+                disabled_classes = `${disabled_classes} download-size-disabled`;
+            }
+            return `<i class="fa fa-download ${disabled_classes}"></i>`;
+        }};
 
         return [caret_col, cart_col, cartnum_col, collection_col, case_col, dyn_case_col, download_col];
     }
@@ -551,7 +564,9 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 if ("showDirectoryPicker" in window) {
                     return `<i class="fa fa-download download-all-instances download-case"   
                         data-collection="${row['collection_id']}" 
-                        data-patient="${row['PatientID']}"                                       
+                        data-patient="${row['PatientID']}" 
+                        data-total-series="${row['unique_series']}"   
+                        data-download-type="case"                                 
                         ></i>`;
                 }
                 return `<i class="fa fa-download download-all-disabled"></i>`;
@@ -1002,7 +1017,9 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                 return `<i class="fa fa-download download-all-instances download-study"   
                                     data-collection="${row['collection_id']}" 
                                     data-study="${row['StudyInstanceUID']}" 
-                                    data-patient="${row['PatientID']}"                                       
+                                    data-patient="${row['PatientID']}" 
+                                    data-download-type="study" 
+                                    data-total-series="${row['unique_series']}"                         
                                     ></i>`;
                             }
                             return `<i class="fa fa-download download-all-disabled"></i>`;
diff --git a/templates/base.html b/templates/base.html
index 65e2de6ff..fdc451676 100755
--- a/templates/base.html
+++ b/templates/base.html
@@ -60,6 +60,8 @@
         const SLIM_VIEWER_PATH = '{{ SLIM_VIEWER_PATH }}';
         const FETCH_MANIFEST_URL = "{% url 'fetch_user_manifest_base' %}";
         const CHECK_MANIFEST_URL = "{% url 'check_user_manifest_base' %}";
+        const SERIES_IDS_URL = "{% url 'get_series_ids_base' %}";
+        const SERIES_IDS_FILTER_URL = "{% url 'get_series_ids_filter' %}";
     </script>
     <!-- OCPL Banner -->
     <script async src="https://assets.adobedtm.com/6a4249cd0a2c/785de09de161/launch-70d67a6a40a8.min.js"></script>
@@ -104,6 +106,9 @@
                                    style="display: none;"></i>
                                 <i class="floating-message-icon floating-message-icon-cancel fa-solid fa-circle-exclamation"
                                    style="display: none;"></i>
+                                <i class="floating-message-icon floating-message-icon-seek fa-solid fa-compass fa-spin"
+                                   style="display: none;"></i>
+
                             </p>
                             <p>
                                 <button type="button"
diff --git a/templates/idc/download-modal.html b/templates/idc/download-modal.html
index b6bb05cda..13f7c785b 100644
--- a/templates/idc/download-modal.html
+++ b/templates/idc/download-modal.html
@@ -1,29 +1,27 @@
 <!-- Warning Modal -->
-<div class="modal fade" id="download-images" tabindex="-1" role="dialog" data-backdrop="static"
-     aria-labelledby="download-header" aria-hidden="true">
+<div class="modal fade" id="download-warning" tabindex="-1" role="dialog" data-backdrop="static"
+     aria-labelledby="download-warning-header" aria-hidden="true">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">x</span>
                 </button>
-                <h4 class="modal-title" id="download-header">Download Images</h4>
+                <h4 class="modal-title" id="download-header">Large Download</h4>
             </div>
             <div class="modal-body">
                 <p>
-                    Instructions on how to download the files corresponding to the selection in the portal to either
-                    Google Colab VM, compute engine VM, or your computer are here:
-                    <b><a class="external-link download-link" href="" url="https://learn.canceridc.dev/data/downloading-data"
-                          title="Download IDC Images"
-                          data-toggle="modal" data-target="#external-web-warning"
-                    >
-                        https://learn.canceridc.dev/data/downloading-data <i class="fa-solid fa-external-link external-link-icon" aria-hidden="true"></i>
-                    </a></b>
+                    The total disk size of the images in this download exceeds 1TB (one terabyte), and may
+                    take a significant amount of time to transfer depending on your internet connection speed. Please do
+                    not refresh this browser tab/window during the download process or your progress may be lost.
                 </p>
             </div>
             <div class="modal-footer">
-                <button type="button" class="btn btn-primary btn-warn" data-dismiss="modal" aria-label="Close">
-                    Close
+                <button type="button" class="btn btn-primary download-all-instances" data-dismiss="modal" aria-label="Proceed with download">
+                    Proceed with download <i class="fa fa-download"></i>
+                </button>
+                <button type="button" class="btn btn-primary btn-warn" data-dismiss="modal" aria-label="Cancel">
+                    Cancel
                 </button>
             </div>
         </div>
diff --git a/templates/idc/explore.html b/templates/idc/explore.html
index 6abf4d826..0da43b545 100644
--- a/templates/idc/explore.html
+++ b/templates/idc/explore.html
@@ -111,6 +111,7 @@ <h3 class="pull-left" role="heading" aria-level="1">Explore Image Data </h3>
         const stats = JSON.parse(document.getElementById('stats').textContent)
         const set_attributes =JSON.parse(document.getElementById('set_attributes').textContent)
         const urlParams = new URLSearchParams(window.location.search);
+        const SERIES_MANIFEST_URI = "{% url 'get_series_ids_manifest' %}";
         window.attMap = {};
         window.openProjects = {};
         window.openCases = {};
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index 5a719c2d8..cc7426cb1 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -843,7 +843,7 @@ <h4 class="panel-title">
                                 </div>
                                 <div id="projects_panel" class="panel-body">
 
-                                    <table id="proj_table" class="table table-striped projects-table">
+                                    <table id="proj_table" class="table table-striped projects-table" data-table-type="collection">
                                         <thead id="projects_table_head">
                                         <tr>
                                             <th class="ckbx text_data viewbx" style="width:30px">
@@ -867,7 +867,7 @@ <h4 class="panel-title">
                                 <div class="panel-heading clearfix"><h4 class="panel-title">Selected Cases</h4></div>
                                 <div id="cases_panel" class="panel-body">
 
-                                    <table id="cases_tab" class="table table-striped cases-table">
+                                    <table id="cases_tab" class="table table-striped cases-table" data-table-type="case">
                                         <thead id="cases_table_head">
                                         <tr>
                                             <th class="ckbx text_data viewbx">
@@ -891,7 +891,7 @@ <h4 class="panel-title">
                             <div id="studies_panel_container" class="panel panel-default">
                                 <div class="panel-heading clearfix"><h4 class="panel-title">Selected Studies</h4></div>
                                 <div class="panel-body">
-                                    <table id="studies_tab" class="table table-striped studies-table">
+                                    <table id="studies_tab" class="table table-striped studies-table" data-table-type="study">
                                         <thead id="studies_table_head">
                                         <tr>
                                             <th class="ckbx text_data viewbx">
@@ -918,7 +918,7 @@ <h4 class="panel-title">
                             <div id="series_panel_container" class="panel panel-default">
                                 <div class="panel-heading clearfix"><h4 class="panel-title">Selected Series</h4></div>
                                 <div class="panel-body">
-                                    <table id="series_tab" class="table table-striped series-table">
+                                    <table id="series_tab" class="table table-striped series-table" data-table-type="series">
                                         <thead id="series_table_head">
                                         <tr>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>

From 18d379346d7d263921e7e51efa608394b07174e2 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 24 Oct 2025 14:43:21 -0700
Subject: [PATCH 11/25] -> Refuse downloads over 3TB, warn under that and over
 1TB

---
 Dockerfile              |  4 ++--
 static/js/downloader.js | 19 ++++++++++++++-----
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 532df627f..d8f859385 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -29,12 +29,12 @@ RUN apt-get update
 RUN apt-get install -y wget
 # TODO: we need to start using the keyring instead
 RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv A8D3785C
-RUN wget "http://repo.mysql.com/mysql-apt-config_0.8.30-1_all.deb" -P /tmp
+RUN wget "http://repo.mysql.com/mysql-apt-config_0.8.35-1_all.deb" -P /tmp
 
 # install lsb-release (a dependency of mysql-apt-config), since dpkg doesn't
 # do dependency resolution
 RUN apt-get install -y lsb-release
-RUN dpkg --install /tmp/mysql-apt-config_0.8.30-1_all.deb
+RUN dpkg --install /tmp/mysql-apt-config_0.8.35-1_all.deb
 
 # fetch the updated package metadata (in particular, mysql-server)
 RUN apt-get update
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 6b5e0624b..1d2222cd7 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -680,7 +680,18 @@ require([
         }
         let job_result = await series_job.json();
         downloader_manager.pendingfetchMessage("collection");
-        let polling = async function(file_name){
+
+        const MAX_ELAPSED_SERIES_IDS = 8000;
+        let polling = async function(file_name, check_start){
+            if(!check_start) {
+                check_start = Date.now();
+            }
+            let check_now = Date.now();
+            let elapsed_millis = check_now-check_start;
+            if((elapsed_millis) > MAX_ELAPSED_SERIES_IDS) {
+                console.error("Unable to retrieve series IDs!");
+                return;
+            }
             let check_res = await fetch(`${CHECK_MANIFEST_URL}${file_name}/`);
             if(!check_res.ok) {
                 console.error("Unable to retrieve series IDs!");
@@ -696,12 +707,10 @@ require([
                 const series_data = await response.json();
                 series.push(...series_data['result']);
             } else {
-                setTimeout(function(){
-                    polling();
-                },2000);
+                setTimeout(polling,2000, file_name, check_start);
             }
         };
-    await polling(job_result.file_name);
+        await polling(job_result.file_name);
     }
 
     $('.container-fluid').on('click', '.download-size-warning', function(){

From d31084789dd8c683bffd851268912ec27d0388c4 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 24 Oct 2025 14:48:37 -0700
Subject: [PATCH 12/25] -> Keys

---
 shell/install-deps.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/shell/install-deps.sh b/shell/install-deps.sh
index 639eedb88..c98a2e4dc 100755
--- a/shell/install-deps.sh
+++ b/shell/install-deps.sh
@@ -38,8 +38,8 @@ apt-get update -qq
 echo "[STATUS] Preparing System..."
 apt-get -y --force-yes install software-properties-common ca-certificates gnupg
 apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv B7B3B788A8D3785C
-wget "https://repo.mysql.com/mysql-apt-config_0.8.30-1_all.deb" -P /tmp
-dpkg --install /tmp/mysql-apt-config_0.8.30-1_all.deb
+wget "https://repo.mysql.com/mysql-apt-config_0.8.35-1_all.deb" -P /tmp
+dpkg --install /tmp/mysql-apt-config_0.8.35-1_all.deb
 
 apt-get update -qq
 

From abcbc752befd470c66de7e7309a9b8e7b5799f82 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 24 Oct 2025 17:19:28 -0700
Subject: [PATCH 13/25] -> Clean up error messaging for workers

---
 idc/views.py            |  2 +-
 static/js/downloader.js | 30 ++++++++++++++++--------------
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/idc/views.py b/idc/views.py
index d3098b111..34ce08355 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -690,7 +690,7 @@ def get_series(request, collection_id, patient_id=None, study_uid=None):
             "collection_id": [collection_id]
         }
         if patient_id:
-            filters['PaitnetID'] = [patient_id]
+            filters['PatientID'] = [patient_id]
         if study_uid:
             filters["StudyInstanceUID"] = [study_uid]
         filter_query = build_solr_query(
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 1d2222cd7..0d037014a 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -329,7 +329,8 @@ require([
         let true_error = event.data.message === 'error' && event.data.error.name !== "AbortError";
         let cancellation = downloader_manager.pending_cancellation || (event.data.message === 'error' && event.data.error.name === "AbortError");
         if (true_error) {
-            console.error(`Worker Error: ${JSON.stringify(event)}`);
+            console.error("Saw worker Error: ",event.data['error']);
+            console.error(event.data['text']);
             downloader_manager.statusMessage(`Encountered an error while downloading these files.`, 'error', "error", true, false);
         }
         if (event.data.message === 'done' || cancellation) {
@@ -410,19 +411,23 @@ require([
                 const studyInstanceUID = metadata['study'];
                 const seriesInstanceUID = metadata['series'];
                 const fileName = metadata['instance'];
+                let response = null;
+                let fileHandle = null;
+                const seriesDirectory = modality + "_" + seriesInstanceUID;
+                const filePath = [collection_id, patientID, studyInstanceUID, seriesDirectory].join("/");
                 try {
                     const directoryHandle = event.data['directoryHandle'];
-                    const seriesDirectory = modality + "_" + seriesInstanceUID;
-                    const filePath = [collection_id, patientID, studyInstanceUID, seriesDirectory].join("/");
                     const subDirectoryHandle = await createNestedDirectories(directoryHandle, filePath);
-                    const fileHandle = await subDirectoryHandle.getFileHandle(fileName, {create: true});
+                    fileHandle = await subDirectoryHandle.getFileHandle(fileName, {create: true});
                     const outputStream = await fileHandle.createWritable();
-                    let response = await fetch(s3_url, {
+                    response = await fetch(s3_url, {
                         signal: abort_controller.signal
                     });
+                    console.error("Checking response.");
                     if (!response.ok) {
+                        console.error("[Worker] Saw !ok response of ",response.status);
                         if(pending_abort) {
-                            console.log('User aborted downloads');
+                            console.log('[Worker] User aborted downloads!');
                         } else {
                             console.error('[Worker] Failed to fetch URL: '+s3_url, response.statusText);
                             self.postMessage({message: "error", error: "Failed to fetch URL"});
@@ -451,14 +456,11 @@ require([
                     if(error.name === "AbortError" || (error.name === undefined && pending_abort)) {
                         msg = "Fetch was aborted. The user may have cancelled their downloads.";
                     } else {
-                        console.error("[Worker Error]", error.name);
-                        console.error("[Worker Error]", error.message);
-                        if(error.message.indexOf("getFileHandle") >= 0) {
-                            console.error("[Worker Error] File name attempted: ",fileName);
+                        if((!fileHandle && error.name === "NotFoundError") || error.message.indexOf("getFileHandle") >= 0) {
+                            msg = "Encountered an error while trying to create the file '"+filePath+"/"+fileName+"'";
                         }
-                        console.error("[Worker Error] on S3 target ", s3_url);
                     }
-                    self.postMessage({message: 'error', path: s3_url, error: error, 'text': msg});
+                    self.postMessage({'message': 'error', 'path': s3_url, 'error': error, 'text': msg});
                 }
             }    
         `;
@@ -748,11 +750,11 @@ require([
             } else {
                 let response = null;
                 if(download_type in ["filter", "cart"]) {
-                    response = await fetch(`${BASE_URL}/${SERIES_IDS_FILTER_URL}`);
+                    response = await fetch(`${BASE_URL}${SERIES_IDS_FILTER_URL}`);
                 } else {
                     let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
                     let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
-                    response = await fetch(`${BASE_URL}/${SERIES_IDS_URL}${collection_id}/${patient_uri}${study_uri}`);
+                    response = await fetch(`${BASE_URL}${SERIES_IDS_URL}${collection_id}/${patient_uri}${study_uri}`);
                 }
                 if (!response.ok) {
                     console.error(`[ERROR] Failed to retrieve series IDs: ${response.status}`);

From 3aafb407cd52e626e8cff81ddd4c83295f44cfbf Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 27 Oct 2025 20:01:18 -0700
Subject: [PATCH 14/25] -> Downloads for cart and filters

---
 idc/views.py                         | 75 +++++++++++++++++-----------
 static/js/cohorts/export-manifest.js | 19 ++++---
 static/js/downloader.js              | 43 +++++++++++++---
 static/js/explore.js                 |  4 +-
 static/js/image_search.js            |  2 +-
 templates/idc/explore_data_core.html | 16 +++++-
 6 files changed, 108 insertions(+), 51 deletions(-)

diff --git a/idc/views.py b/idc/views.py
index 34ce08355..50a9c81cf 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -39,7 +39,9 @@
 from cohorts.models import Cohort, Cohort_Perms
 
 from idc_collections.models import Program, DataSource, Collection, ImagingDataCommonsVersion, Attribute, Attribute_Tooltips, DataSetType, Citation
-from idc_collections.collex_metadata_utils import build_explorer_context, get_collex_metadata, create_file_manifest, get_cart_data_serieslvl, get_cart_data_studylvl, get_table_data_with_cart_data
+from idc_collections.collex_metadata_utils import (build_explorer_context, get_collex_metadata, create_file_manifest,
+                                                   get_cart_data_serieslvl, get_cart_data_studylvl,
+                                                   get_table_data_with_cart_data, cart_manifest)
 from allauth.socialaccount.models import SocialAccount
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, JsonResponse
@@ -48,7 +50,7 @@
 from idc.models import User_Data
 from solr_helpers import build_solr_query, query_solr_and_format_result
 
-
+from idc.settings import MAX_FILE_LIST_REQUEST
 
 debug = settings.DEBUG
 logger = logging.getLogger(__name__)
@@ -678,35 +680,48 @@ def cart_data(request):
     return JsonResponse(response, status=status)
 
 
-def get_series(request, collection_id, patient_id=None, study_uid=None):
+def get_series(request, collection_id=None, patient_id=None, study_uid=None):
+    status = 200
+    response = {"result": []}
     try:
-        status = 200
-        response = { "result": [] }
-        source = ImagingDataCommonsVersion.objects.get(active=True).get_data_sources(
-            active=True, source_type=DataSource.SOLR,
-            aggregate_level="SeriesInstanceUID"
-        ).first()
-        filters = {
-            "collection_id": [collection_id]
-        }
-        if patient_id:
-            filters['PatientID'] = [patient_id]
-        if study_uid:
-            filters["StudyInstanceUID"] = [study_uid]
-        filter_query = build_solr_query(
-            filters,
-            with_tags_for_ex=False,
-            search_child_records_by=None, solr_default_op='AND'
-        )
-        result = query_solr_and_format_result(
-            {
-                "collection": source.name,
-                "fields": ["collection_id", "PatientID", "StudyInstanceUID", "Modality", "crdc_series_uuid", "SeriesInstanceUID", "aws_bucket", "instance_size"],
-                "query_string": None,
-                "fqs": [filter_query['full_query_str']],
-                "facets": None, "sort": None, "counts_only": False, "limit": 2000
+        fields = ["collection_id", "PatientID", "StudyInstanceUID", "Modality", "crdc_series_uuid", "SeriesInstanceUID", "aws_bucket", "instance_size"]
+        result = {}
+        if not collection_id:
+            # This is a request for filters and/or a cart
+            body_unicode = request.body.decode('utf-8')
+            body = json.loads(body_unicode)
+            partitions = body.get("partitions", {})
+            filtergrp_list = body.get("filtergrp_list", {})
+            if not(len(partitions) or len(filtergrp_list)):
+                raise Exception("You can only request series IDs based on a filter, collection ID, Patient ID, or study ID!")
+            result = cart_manifest(filtergrp_list, partitions, 0, fields, MAX_FILE_LIST_REQUEST)
+        else:
+            source = ImagingDataCommonsVersion.objects.get(active=True).get_data_sources(
+                active=True, source_type=DataSource.SOLR,
+                aggregate_level="SeriesInstanceUID"
+            ).first()
+            filters = {
+                "collection_id": [collection_id]
             }
-        )
+            if patient_id:
+                filters['PatientID'] = [patient_id]
+            if study_uid:
+                filters["StudyInstanceUID"] = [study_uid]
+            filter_query = build_solr_query(
+                filters,
+                with_tags_for_ex=False,
+                search_child_records_by=None, solr_default_op='AND'
+            )
+            result = query_solr_and_format_result(
+                {
+                    "collection": source.name,
+                    "fields": fields,
+                    "query_string": None,
+                    "fqs": [filter_query['full_query_str']],
+                    "facets": None, "sort": None, "counts_only": False, "limit": 2000
+                }
+            )
+
         for doc in result['docs']:
             response['result'].append({
                 "series_id": doc['SeriesInstanceUID'],
@@ -716,7 +731,7 @@ def get_series(request, collection_id, patient_id=None, study_uid=None):
                 "modality": doc['Modality'][0],
                 "study_id": doc['StudyInstanceUID'],
                 "patient_id": doc["PatientID"],
-                "collection_id": doc['collection_id']
+                "collection_id": doc['collection_id'][0]
             })
 
     except Exception as e:
diff --git a/static/js/cohorts/export-manifest.js b/static/js/cohorts/export-manifest.js
index e47415551..56f0d50fb 100644
--- a/static/js/cohorts/export-manifest.js
+++ b/static/js/cohorts/export-manifest.js
@@ -75,29 +75,28 @@ require([
         if (button.hasClass('series-export') || button.hasClass('study-export')){
             update_export_modal_for_mini(button);
         } else if (button.hasClass('cart-export')){
-            updatePartitionsFromScratch();
              window.updatePartitionsFromScratch();
-             var ret =cartutils.formcartdata();
+             let ret = cartutils.formcartdata();
              window.partitions = ret[0];
              window.filtergrp_lst = ret[1];
 
-             var projS = new Set();
+             let projS = new Set();
              for (var i=0;i<partitions.length;i++){
                 projS.add(partitions[i].id[0]);
              }
-            var mxstudies=0;
-            var mxseries=0;
-            var projl = [...projS]
-            for (var i=0;i<projl.length;i++){
-               var proj = projl[i]
+            let mxstudies=0;
+            let mxseries=0;
+            let projl = [...projS]
+            for (let i=0;i<projl.length;i++){
+               let proj = projl[i]
                mxseries+= window.selProjects[proj].mxseries;
                mxstudies+= window.selProjects[proj].mxstudies;
             }
-            var filterSets = new Array();
+            let filterSets = [];
             for(let i=0; i< window.cartHist.length;i++) {
                filterSets.push(window.cartHist[i]['filter'])
             }
-            update_export_modal_for_cart(partitions, filterSets);
+            update_export_modal_for_cart(window.partitions, filterSets);
         } else if (button.hasClass('cart-export-from-cp')){
             update_export_modal_for_cart(window.partitions, window.filtergrp_list);
         } else if(button.hasClass('export-cohort-manifest')) {
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 0d037014a..ae15139b6 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -21,13 +21,19 @@ require.config({
     baseUrl: STATIC_FILES_URL + 'js/',
     paths: {
         jquery: 'libs/jquery-3.7.1.min',
-        base: 'base'
+        base: 'base',
+        cartutils: 'cartutils',
+        filterutils: 'filterutils'
+    },
+    shim: {
+        'cartutils': ['jquery'],
+        'filterutils': ['jquery']
     }
 });
 
 require([
-    'base', 'jquery'
-], function (base, $) {
+    'base', 'jquery', 'cartutils', 'filterutils',
+], function (base, $, cartutils, filterutils) {
 
     const byte_level = Object.freeze({
         1: "KB",
@@ -423,7 +429,6 @@ require([
                     response = await fetch(s3_url, {
                         signal: abort_controller.signal
                     });
-                    console.error("Checking response.");
                     if (!response.ok) {
                         console.error("[Worker] Saw !ok response of ",response.status);
                         if(pending_abort) {
@@ -749,8 +754,34 @@ require([
 
             } else {
                 let response = null;
-                if(download_type in ["filter", "cart"]) {
-                    response = await fetch(`${BASE_URL}${SERIES_IDS_FILTER_URL}`);
+                if(["cohort", "cart"].includes(download_type)) {
+                    let filter_and_cart = {};
+                    if (download_type === "cohort") {
+                        let filtergrp_list = [];
+                        for(const [attr, vals] of Object.entries(filterutils.parseFilterObj())) {
+                            filtergrp_list.push({[attr]: vals});
+                        }
+                        filter_and_cart["filtergrp_list"] = filtergrp_list;
+                    } else {
+                         window.updatePartitionsFromScratch();
+                         let ret = cartutils.formcartdata();
+                         window.partitions = ret[0];
+                         window.filtergrp_lst = ret[1];
+                        let filterSets = [];
+                        for(let i=0; i< window.cartHist.length;i++) {
+                           filterSets.push(window.cartHist[i]['filter']);
+                        }
+                        filter_and_cart['partitions'] = window.partitions;
+                        filter_and_cart['filtergrp_list'] = filterSets;
+                    }
+                    response = await fetch(`${BASE_URL}${SERIES_IDS_FILTER_URL}`, {
+                            method: "POST",
+                            body: JSON.stringify(filter_and_cart),
+                            headers: {
+                                "X-CSRFToken": csrftoken,
+                                "content-type": "application/json"
+                            }
+                        });
                 } else {
                     let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
                     let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
diff --git a/static/js/explore.js b/static/js/explore.js
index 2a6a3d478..a3dbed147 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -483,8 +483,8 @@ require([
 
     const download_tooltip = {
         dynamicTip: function(ref){
-            let table_type = $(ref).parents('table').attr('data-table-type');
-            return `Download all of the image instances in this ${table_type}.`;
+            let download_type = $(ref).attr('data-download-type');
+            return `Download all of the image instances in this ${download_type}.`;
         },
         content: 'Download all images.', // placeholder text
         theme: 'dark',
diff --git a/static/js/image_search.js b/static/js/image_search.js
index 5a55b4ef7..aaf98868d 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -141,7 +141,7 @@ require([
             success: function (data) {
                 try {
                     let curInd = window.cartHist.length-1;
-                    let tmp=filterutils.parseFilterObj()
+                    let tmp=filterutils.parseFilterObj();
                     let filtObj=JSON.parse(JSON.stringify(tmp));
                     if (cartHist[curInd].selections.length>0){
                         let cartSel = new Object();
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index cc7426cb1..03d315af7 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -630,7 +630,13 @@ <h4>Cohort Filters</h4>
                                 data-default-title="Export this cohort's series as a manifest for download."
                                 data-target="#export-manifest-modal"
                                 title="Select a filter to enable this feature."
-                            > Manifest <i class="fa fa-solid fa-download"></i>
+                            > Manifest <i class="fa fa-solid fa-list"></i>
+                            </button>
+                            <button id="download-cohort-images" class="btn btn-primary btn-small filter-activated-controls download-all-instances" disabled
+                                data-default-title="Download the instance image files for this cohort."
+                                title="Select a filter to enable this feature."
+                                data-download-type="cohort"
+                            > Download <i class="fa fa-solid fa-download"></i>
                             </button>
                             <button class="btn btn-small btn-special citations-button filter-activated-controls" disabled data-toggle="modal" data-target="#citations-modal" role="button"
                                 data-default-title="Display this cohort's citation list in Vancouver format."
@@ -675,7 +681,13 @@ <h4>Cart</h4>
                             <button id="export-manifest-cart" class="btn btn-primary cart-export btn-small cart-activated-controls" disabled data-toggle="modal"
                                 data-target="#export-manifest-modal"
                                 title="Add items to the cart to enable this feature."
-                            > Manifest <i class="fa fa-solid fa-download"></i>
+                            > Manifest <i class="fa fa-solid fa-list"></i>
+                            </button>
+                            <button id="download-cart-images" class="btn btn-primary btn-small cart-activated-controls download-all-instances" disabled
+                                data-default-title="Download the instance image files for this cart."
+                                title="Select a filter to enable this feature."
+                                data-download-type="cart"
+                            > Download <i class="fa fa-solid fa-download"></i>
                             </button>
                             <button class="btn btn-small btn-special citations-button cart-activated-controls for-cart" disabled data-toggle="modal" data-target="#citations-modal" role="button"
                                 data-default-title="Display this cart's citation list in Vancouver format."

From d2e6226db17e791f8377e3aad560b17505405e25 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 28 Oct 2025 11:58:22 -0700
Subject: [PATCH 15/25] -> Downloads for cart and filters

---
 idc/views.py            | 34 +++++++++++++++++++++++++++++--
 static/js/downloader.js | 44 ++++++++++++++++++++++++++++++++++-------
 2 files changed, 69 insertions(+), 9 deletions(-)

diff --git a/idc/views.py b/idc/views.py
index 50a9c81cf..7a43a0267 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -694,7 +694,29 @@ def get_series(request, collection_id=None, patient_id=None, study_uid=None):
             filtergrp_list = body.get("filtergrp_list", {})
             if not(len(partitions) or len(filtergrp_list)):
                 raise Exception("You can only request series IDs based on a filter, collection ID, Patient ID, or study ID!")
-            result = cart_manifest(filtergrp_list, partitions, 0, fields, MAX_FILE_LIST_REQUEST)
+            if len(partitions):
+                result = cart_manifest(filtergrp_list, partitions, 0, fields, MAX_FILE_LIST_REQUEST)
+            else:
+                source = ImagingDataCommonsVersion.objects.get(active=True).get_data_sources(
+                    active=True, source_type=DataSource.SOLR,
+                    aggregate_level="SeriesInstanceUID"
+                ).first()
+                filter_query = build_solr_query(
+                    { w: v for x in filtergrp_list for w, v in list(x.items())},
+                    with_tags_for_ex=False,
+                    search_child_records_by=None, solr_default_op='AND'
+                )
+                result = query_solr_and_format_result(
+                    {
+                        "collection": source.name,
+                        "fields": fields,
+                        "query_string": None,
+                        "fqs": [filter_query['full_query_str']],
+                        "facets": {'instance_size': 'sum(instance_size)'}, "sort": None, "counts_only": False, "limit": MAX_FILE_LIST_REQUEST,
+                        "totals": ['SeriesInstanceUID', 'collection_id', 'PatientID', 'StudyInstanceUID']
+                    },
+                    normalize_facets=False
+                )
         else:
             source = ImagingDataCommonsVersion.objects.get(active=True).get_data_sources(
                 active=True, source_type=DataSource.SOLR,
@@ -718,7 +740,7 @@ def get_series(request, collection_id=None, patient_id=None, study_uid=None):
                     "fields": fields,
                     "query_string": None,
                     "fqs": [filter_query['full_query_str']],
-                    "facets": None, "sort": None, "counts_only": False, "limit": 2000
+                    "facets": None, "sort": None, "counts_only": False, "limit": MAX_FILE_LIST_REQUEST
                 }
             )
 
@@ -733,6 +755,14 @@ def get_series(request, collection_id=None, patient_id=None, study_uid=None):
                 "patient_id": doc["PatientID"],
                 "collection_id": doc['collection_id'][0]
             })
+        if 'facets' in result:
+            response['download_stats'] = {
+                'series_count': result['facets']['total_SeriesInstanceUID'],
+                'study_count': result['facets']['total_StudyInstanceUID'],
+                'collection_count': result['facets']['total_collection_id'],
+                'case_count': result['facets']['total_PatientID'],
+                'queue_byte_size': result['facets']['instance_size'],
+            }
 
     except Exception as e:
         logger.error("[ERROR] While fetching series per study ID:")
diff --git a/static/js/downloader.js b/static/js/downloader.js
index ae15139b6..1bdca69dc 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -56,9 +56,9 @@ require([
         }
         let byte_count = 0;
         let converted_size = size;
-        while(converted_size > 1024) {
+        while(converted_size > 1000) {
             byte_count += 1;
-            converted_size /= 1024;
+            converted_size /= 1000;
         }
         let bytes = (Math.round(converted_size*1000)/1000).toFixed(3);
         return `${bytes} ${byte_level[byte_count]}` ;
@@ -219,10 +219,14 @@ require([
         queue_byte_size = 0;
         bytes_downloaded = 0;
         series_count = 0;
+        study_count = 0;
+        case_count = 0;
+        collection_count = 0;
         start_time = -1;
         collections = new Set([]);
         cases = new Set([]);
         studies = new Set([]);
+        preset_totals = false;
 
         cancellation_underway = false;
 
@@ -257,12 +261,24 @@ require([
             this.bytes_downloaded = 0;
             this.series_count = 0;
             this.collections = new Set([]);
+            this.collection_count = 0;
             this.cases = new Set([]);
+            this.case_count = 0;
             this.studies = new Set([]);
+            this.study_count = 0;
             this.cancellation_underway = false;
             this.start_time = -1;
         }
 
+        set_download_totals(queue_byte_size, collection_count, case_count, study_count, series_count) {
+            this.queue_byte_size = queue_byte_size;
+            this.collection_count = collection_count;
+            this.case_count = case_count;
+            this.study_count = study_count;
+            this.series_count = series_count;
+            this.preset_totals = true;
+        }
+
         get active_requests() {
             return (this.working_queue.length > 0);
         }
@@ -294,11 +310,16 @@ require([
             let request_success = false;
             if(this.hopper.length < this.HOPPER_LIMIT && !this.cancellation_underway) {
                 this.hopper.push(new DownloadRequest(request));
-                this.queue_byte_size += parseFloat(request['series_size']);
-                this.series_count += 1;
                 this.studies.add(request['study_id']);
                 this.collections.add(request['collection_id']);
                 this.cases.add(request['patient_id']);
+                if(!this.preset_totals) {
+                    this.queue_byte_size += parseFloat(request['series_size']);
+                    this.series_count += 1;
+                    this.collection_count = this.collections.size;
+                    this.study_count = this.studies.size;
+                    this.case_count = this.cases.size;
+                }
                 request_success = true;
             }
             return request_success;
@@ -494,9 +515,9 @@ require([
 
         get all_requested() {
             return `${this.queues.total_downloads_requested} requested in ` +
-                `${this.queues.collections.size} collection(s) / ` +
-                `${this.queues.cases.size} case(s) / ` +
-                `${this.queues.studies.size} ${this.queues.studies.size <= 1 ? "study" : "studies"} / ` +
+                `${this.queues.collection_count} collection(s) / ` +
+                `${this.queues.case_count} case(s) / ` +
+                `${this.queues.study_count} ${this.queues.study_count <= 1 ? "study" : "studies"} / ` +
                 `${this.queues.series_count} series`;
         }
 
@@ -655,6 +676,12 @@ require([
             });
         }
 
+        set_download_stats(stats) {
+            this.queues.set_download_totals(
+                stats.queue_byte_size, stats.collection_count, stats.case_count, stats.study_count, stats.series_count
+            );
+        }
+
         beginDownloads() {
             if(!this.queues.isEmpty()) {
                 if(this.in_progress <= 0) {
@@ -793,6 +820,9 @@ require([
                 }
                 const series_data = await response.json();
                 series.push(...series_data['result']);
+                if('download_stats' in series_data){
+                    downloader_manager.set_download_stats(series_data['download_stats']);
+                }
             }
         } else {
             series.push({

From 287a42f52d5da3fb2aa27b25c14a5e83c313d7ee Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 28 Oct 2025 18:03:06 -0700
Subject: [PATCH 16/25] -> Ensure proper cancellation

---
 static/js/downloader.js | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/static/js/downloader.js b/static/js/downloader.js
index 1bdca69dc..2e5fe9b1b 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -537,7 +537,7 @@ require([
             this.queues.bytes_downloaded += downloaded_amount;
         }
 
-        pendingfetchMessage(fetch_type) {
+        pendingFetchMessage(fetch_type) {
             // Don't display if we already have pending downloads
             if(this.in_progress > 0) {
                 return;
@@ -674,6 +674,14 @@ require([
             this.downloadWorkers.forEach(worker => {
                 worker.postMessage({'abort': true, 'reason': 'User cancelled download.'});
             });
+            // Sometimes worker latency can cause a race condition between final cleanup and resetting the download
+            // manager's state. Run trigger a final time after waiting a couple of seconds to be totally sure
+            // we've cleaned up after ourselves.
+            setTimeout(2000, function(){
+                if(downloader_manager.pending_cancellation) {
+                    downloader_manager.triggerWorkerDownloads();
+                }
+            });
         }
 
         set_download_stats(stats) {
@@ -713,7 +721,7 @@ require([
             return;
         }
         let job_result = await series_job.json();
-        downloader_manager.pendingfetchMessage("collection");
+        downloader_manager.pendingFetchMessage("collection");
 
         const MAX_ELAPSED_SERIES_IDS = 8000;
         let polling = async function(file_name, check_start){
@@ -782,6 +790,7 @@ require([
             } else {
                 let response = null;
                 if(["cohort", "cart"].includes(download_type)) {
+                    downloader_manager.pendingFetchMessage(download_type);
                     let filter_and_cart = {};
                     if (download_type === "cohort") {
                         let filtergrp_list = [];

From 85303a27f06d728eddfcbc31fd62b194fb5049c7 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 31 Oct 2025 17:26:30 -0700
Subject: [PATCH 17/25] -> Tooltip fixes/improvements -> Cart size reinstated,
 will disable over 3TB for JS download

---
 etl/etl.py                           |  8 +--
 idc/urls.py                          |  1 -
 idc/views.py                         | 99 ++++------------------------
 static/css/style.css                 |  7 +-
 static/css/vendor.css                |  2 +-
 static/js/base.js                    |  3 +-
 static/js/cartutils.js               | 58 ++++++++--------
 static/js/explore.js                 | 33 ++++------
 static/js/filterutils.js             |  4 +-
 static/js/image_search.js            | 69 ++-----------------
 static/js/tables.js                  | 33 +++++-----
 static/js/utils.js                   | 33 +++++++++-
 templates/idc/explore_data_core.html | 31 +++++----
 13 files changed, 137 insertions(+), 244 deletions(-)

diff --git a/etl/etl.py b/etl/etl.py
index 9c3b7ec3a..343a95560 100644
--- a/etl/etl.py
+++ b/etl/etl.py
@@ -61,7 +61,7 @@
 FIELD_MAP = {x: i for i, x in enumerate([
     "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
     "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-    "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active", "total_size"
+    "program", "access", "date_updated", "tcia_wiki_collection_id", "license_short_name", "active", "total_size", "total_size_with_ar"
 ])}
 
 TOKENIZED_FIELDS = ["PatientID", "SeriesInstanceUID", "StudyInstanceUID"]
@@ -146,8 +146,8 @@
 }
 
 SOLR_SINGLE_VAL = {
-    "StudyInstanceUID": ["PatientID", "StudyInstanceUID", "crdc_study_uuid"],
-    "SeriesInstanceUID": ["PatientID", "StudyInstanceUID", "SeriesInstanceUID", "crdc_study_uuid", "crdc_series_uuid"]
+    "StudyInstanceUID": ["PatientID", "StudyInstanceUID", "crdc_study_uuid","instance_size"],
+    "SeriesInstanceUID": ["PatientID", "StudyInstanceUID", "SeriesInstanceUID", "crdc_study_uuid", "crdc_series_uuid", "instance_size"]
 }
 
 ETL_CONFIG = {}
@@ -356,7 +356,7 @@ def load_collections(filename, data_version="8.0"):
         exact_collection_fields = [
             "collection_id", "collection_uuid", "name", "collections", "image_types", "supporting_data", "subject_count", "doi",
             "source_url", "cancer_type", "species", "location", "analysis_artifacts", "description", "collection_type",
-            "access", "date_updated", "active", "total_size"]
+            "access", "date_updated", "active", "total_size", "total_size_with_ar"]
         field_map = FIELD_MAP
         for line in csv_reader(collection_file):
             if COLLECTION_HEADER_CHK in line:
diff --git a/idc/urls.py b/idc/urls.py
index f89bcd6d9..8b419509c 100644
--- a/idc/urls.py
+++ b/idc/urls.py
@@ -51,7 +51,6 @@
     re_path(r'^explore/manifest/$', views.explorer_manifest, name='get_explore_manifest'),
     re_path(r'^explore/manifest/series/$', views.explorer_manifest, name='get_series_ids_manifest'),
     re_path(r'^tables/', views.populate_tables, name='populate_tables'),
-    re_path(r'^studymp/', views.studymp, name='studymp'),
     re_path(r'^warning/', views.warn_page, name='warn'),
     re_path(r'^about/$', views.about_page, name='about_page'),
     re_path(r'^dashboard/', views.dashboard_page, name='dashboard'),
diff --git a/idc/views.py b/idc/views.py
index 7a43a0267..dfba7d712 100644
--- a/idc/views.py
+++ b/idc/views.py
@@ -51,6 +51,7 @@
 from solr_helpers import build_solr_query, query_solr_and_format_result
 
 from idc.settings import MAX_FILE_LIST_REQUEST
+from idc_collections.collex_metadata_utils import convert_disk_size
 
 debug = settings.DEBUG
 logger = logging.getLogger(__name__)
@@ -247,86 +248,6 @@ def save_ui_hist(request):
     return JsonResponse({}, status=status)
 
 
-# returns various metadata mappings for selected projects used in calculating cart selection
-# counts 'on the fly' client side
-def studymp(request):
-    response = {}
-    status = 200
-    sources = ImagingDataCommonsVersion.objects.get(active=True).get_data_sources(
-            active=True, source_type=DataSource.SOLR,
-            aggregate_level="StudyInstanceUID"
-        )
-    data_types = [DataSetType.IMAGE_DATA, DataSetType.ANCILLARY_DATA, DataSetType.DERIVED_DATA]
-    data_sets = DataSetType.objects.filter(data_type__in=data_types)
-    aggregate_level='StudyInstanceUID'
-    versions=[]
-    versions = ImagingDataCommonsVersion.objects.filter(
-        version_number__in=versions
-    ).get_data_versions(active=True) if len(versions) else ImagingDataCommonsVersion.objects.filter(
-        active=True
-    ).get_data_versions(active=True)
-    aux_sources = data_sets.get_data_sources().filter(
-        source_type=DataSource.SOLR,
-        aggregate_level__in=["case_barcode", "sample_barcode", aggregate_level],
-        id__in=versions.get_data_sources().filter(source_type=DataSource.SOLR).values_list("id", flat=True)
-    ).distinct()
-
-    try:
-       req = request.GET if request.method == 'GET' else request.POST
-       filters = json.loads(req.get('filters', '{}'))
-
-       mxSeries = int(req.get('mxseries'))
-       mxStudies= int(req.get('mxstudies'))
-       limit = int(req.get('limit', mxStudies))
-       offset = int(req.get('offset',0))
-
-       casestudymp = dict()
-       studymp = dict()
-       projstudymp = dict()
-
-       idsEx = get_collex_metadata(
-            filters, ['collection_id', 'PatientID','StudyInstanceUID', 'SeriesInstanceUID'], record_limit=limit,
-            sources=sources, offset=offset, records_only=True, custom_facets={}, aux_sources=aux_sources,
-            collapse_on='StudyInstanceUID', counts_only=False, filtered_needed=False,
-            raw_format=True, default_facets=False, sort=None
-        )
-
-       logger.debug("[STATUS] records pulled: {}".format(len(idsEx['docs'])))
-
-       for doc in idsEx['docs']:
-          proj=doc['collection_id'][0]
-          patientid=doc['PatientID']
-          studyid= doc['StudyInstanceUID']
-          cnt = len(doc['SeriesInstanceUID'])
-
-          if not patientid in casestudymp:
-              casestudymp[patientid]={}
-          if not proj in projstudymp:
-              projstudymp[proj] = {}
-          studymp[studyid]={}
-          studymp[studyid]['cnt'] = cnt
-          studymp[studyid]['proj'] = proj
-          studymp[studyid]['PatientID'] = patientid
-          studymp[studyid]['val'] = []
-          projstudymp[proj][studyid] = cnt
-          casestudymp[patientid][studyid] = cnt
-
-       response["studymp"] = studymp
-       response['casestudymp'] = casestudymp
-       response['projstudymp'] = projstudymp
-
-    except Exception as e:
-        logger.error("[ERROR] While attempting to get studymp:")
-        logger.exception(e)
-        messages.error(
-           request,
-           "Encountered an error when attempting to get the studymp - please contact the administrator."
-        )
-        status = 400
-
-    return JsonResponse(response, status=status)
-
-
 def populate_tables(request):
     response = {}
     status = 200
@@ -648,6 +569,7 @@ def cart_data(request):
         aggregate_level = req.get('aggregate_level', 'StudyInstanceUID')
         results_level = req.get('results_level', 'StudyInstanceUID')
         dois_only = bool(req.get('dois_only', 'false').lower() == 'true')
+        size_only = bool(req.get('size_only', 'false').lower() == 'true')
 
         partitions = json.loads(req.get('partitions', '{}'))
 
@@ -656,22 +578,29 @@ def cart_data(request):
         length = int(req.get('length', 100))
         mxseries = int(req.get('mxseries',1000))
 
+        doi_or_size_only = (dois_only or size_only)
+
         if len(partitions) <= 0 or aggregate_level not in ['SeriesInstanceUID', 'StudyInstanceUID']:
             response['numFound'] = 0
             response['docs'] = []
         else:
             if aggregate_level == 'StudyInstanceUID':
                 response = get_cart_data_studylvl(
-                    filtergrp_list, partitions, limit, offset, length, mxseries, with_records=(not dois_only),
-                    results_lvl=results_level, dois_only=dois_only
+                    filtergrp_list, partitions, limit, offset, length, mxseries, with_records=(not doi_or_size_only),
+                    results_lvl=results_level, dois_only=dois_only, size_only=size_only
                 )
             elif aggregate_level == 'SeriesInstanceUID':
                 response = get_cart_data_serieslvl(
-                    filtergrp_list, partitions, field_list if not dois_only else None, limit, offset,
-                    with_records=(not dois_only), dois_only=dois_only
+                    filtergrp_list, partitions, field_list if (not doi_or_size_only) else None, limit, offset,
+                    with_records=(not doi_or_size_only), dois_only=dois_only, size_only=size_only
                 )
         if dois_only:
             response = {'dois': response['dois']}
+        if size_only:
+            response = {
+                "total_size": response['total_size'],
+                "display_size": convert_disk_size(response['total_size'])
+            }
     except Exception as e:
         logger.error("[ERROR] While loading cart:")
         logger.exception(e)
@@ -704,7 +633,7 @@ def get_series(request, collection_id=None, patient_id=None, study_uid=None):
                 filter_query = build_solr_query(
                     { w: v for x in filtergrp_list for w, v in list(x.items())},
                     with_tags_for_ex=False,
-                    search_child_records_by=None, solr_default_op='AND'
+                    search_child_records_by={w: "StudyInstanceUID" for x in filtergrp_list for w in x}, solr_default_op='AND'
                 )
                 result = query_solr_and_format_result(
                     {
diff --git a/static/css/style.css b/static/css/style.css
index f496e6ec0..2c9ece912 100755
--- a/static/css/style.css
+++ b/static/css/style.css
@@ -4524,8 +4524,11 @@ d-topics-list iframe {
 }
 
 .download-all-disabled {
-  cursor: not-allowed;
-  color: gray;
+  cursor: not-allowed !important;
+}
+
+.fa.download-all-disabled {
+    color: gray;
 }
 
 #floating-message {
diff --git a/static/css/vendor.css b/static/css/vendor.css
index 7ed5c0d04..2a31d172f 100644
--- a/static/css/vendor.css
+++ b/static/css/vendor.css
@@ -2832,7 +2832,7 @@ select[multiple].input-lg,
     box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125); }
   .btn.disabled, .btn[disabled],
   fieldset[disabled] .btn {
-    cursor: not-allowed;
+    cursor: not-allowed !important;
     opacity: 0.65;
     filter: alpha(opacity=65);
     -webkit-box-shadow: none;
diff --git a/static/js/base.js b/static/js/base.js
index 9719b1079..61dfe4ede 100644
--- a/static/js/base.js
+++ b/static/js/base.js
@@ -276,6 +276,7 @@ define(['jquery', 'utils'], function($, utils) {
             utils.removeCookie(name, path);
         },
         blockResubmit: utils.blockResubmit,
-        checkManifestReady: utils.checkManifestReady
+        checkManifestReady: utils.checkManifestReady,
+        updateDownloadBtns: utils.updateDownloadBtns
     };
 });
diff --git a/static/js/cartutils.js b/static/js/cartutils.js
index 6a8303316..64d913e37 100644
--- a/static/js/cartutils.js
+++ b/static/js/cartutils.js
@@ -122,10 +122,10 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
         return deferred.promise();
     };
 
-
-    const updateCartCounts =function(){
+    const updateCartCounts = async function(){
         var buttonContents = '<button class="btn filter-type clear-cart" role="button" title="Empty your cart."><i class="fa fa-rotate-left"></i></button>';
-        if (Object.keys(window.proj_in_cart).length>0){
+        let cart_has_contents = Boolean(Object.keys(window.proj_in_cart).length>0);
+        if (cart_has_contents){
             var nmprojs = 0;
             var nmcases=0;
             var nmstudies=0;
@@ -138,7 +138,7 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
             }
 
             let content = buttonContents+'<span id ="#cart_stats">Cart contents: ' + nmseries.toString()+' series from '+nmprojs.toString()+
-                ' collections / '+nmcases.toString()+' cases / '+nmstudies.toString()+' studies</span>';
+                ' collections / '+nmcases.toString()+' cases / '+nmstudies.toString()+' studies</span> <span class="cart_disk_size">(Calculating size...)</span>';
             localStorage.setItem('manifestSeriesCount',nmseries);
 
             $('#cart_stats_holder').html(content) ;
@@ -149,6 +149,28 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
             $('#cart_stats').addClass('empty-cart');
             $('.cart-activated-controls').attr('disabled', 'disabled');
         }
+        let cart_disk_size = 0;
+        let cart_disk_display_size = "(Calculating...)";
+        let cart_disk_resp = await fetch(`${BASE_URL}/cart_data/`, {
+                method: "POST",
+                body: new URLSearchParams({
+                    'filtergrp_list': JSON.stringify(window.filtergrp_list ? window.filtergrp_list : [{}]),
+                    'partitions': JSON.stringify(window.partitions),
+                    'size_only': 'true'
+                }),
+                headers: {"X-CSRFToken": $.getCookie('csrftoken'), "content-type": 'application/x-www-form-urlencoded'}
+        });
+        if(!cart_disk_resp.ok) {
+            console.error("Unable to fetch cart size!");
+            cart_disk_size = 4;
+            cart_disk_display_size = "(Unable to retrieve size.)";
+        } else {
+            let cart_disk_res = await cart_disk_resp.json();
+            cart_disk_size = cart_disk_res['total_size']/Math.pow(1000,4);
+            cart_disk_display_size = cart_disk_res['display_size'];
+        }
+        $('.cart_disk_size').html(cart_disk_display_size);
+        base.updateDownloadBtns('cart', cart_has_contents, cart_disk_size);
 
     }
 
@@ -298,7 +320,6 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
 
      window.updatePartitionsFromScratch = function(){
         window.partitions = new Array();
-
         for (var i=0;i<window.cartHist.length;i++){
            var cartHist=window.cartHist[i];
            updateGlobalPartitions(cartHist.partitions);
@@ -308,10 +329,6 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
            refilterGlobalPartitions(cartHist,i);
         }
         fixpartitions();
-        var filtStrings = createFiltStrings();
-        var solrStr = createSolrString(filtStrings);
-        window.solrStr = solrStr;
-        var ii=1;
     };
 
     //looking across the history of cart selections, create one set of exclusive partitions of the imaging data
@@ -490,29 +507,6 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
         return(filtStrings);
     }
 
-    // not really needed, but used to creating the solr string in on the client side
-    const createSolrString = function(filtStringA){
-        var solrStr=''
-        var solrA=[]
-        for (var i=0;i< window.partitions.length;i++){
-            var curPart = window.partitions[i];
-            if (!curPart['null']) {
-                var curPartAttStrA = parsePartitionAttStrings(filtStringA, curPart);
-                var curPartStr = parsePartitionStrings(curPart);
-                for (var j = 0; j < curPartAttStrA.length; j++) {
-                    if (curPartAttStrA[j].length > 0) {
-                        solrA.push('(' + curPartStr + ')(' + curPartAttStrA[j] + ')')
-                    } else{
-                        solrA.push(curPartStr);
-                    }
-                }
-            }
-        }
-        solrA = solrA.map(x => '('+x+')');
-        var solrStr = solrA.join(' OR ')
-        return solrStr
-    }
-
     const parsePartitionAttStrings = function(filtStringA, partition){
         var attStrA =[];
         var filt2D = partition['filt'];
diff --git a/static/js/explore.js b/static/js/explore.js
index a3dbed147..eea8bfe2d 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -73,9 +73,6 @@ require([
     //sesssionStorage.setItem("cartHist",JSON.stringify(window.cartHist));
     window.partitions = new Array();
 
-    window.studymp=new Object();
-    window.projstudymp = new Object();
-    window.casestudymp = new Object();
     window.collection = JSON.parse(document.getElementById('collections').textContent);
     var lst = Object.keys(window.collection).sort();
     window.collectionData = new Array();
@@ -481,8 +478,17 @@ require([
         plugins: [dynamicTipFunc]
     };
 
+    let disabled_messages = {
+        'download-all-disabled': chromium_only,
+        'download-size-disabled': "This set of images is over 3TB in size. Please use manifest download to obtain these images.",
+        'download-cart-disabled': "Add items to the cart to enable this feature.",
+        'download-cohort-disabled': "Select a filter to enable this feature."
+    };
     const download_tooltip = {
         dynamicTip: function(ref){
+            if($(ref).hasClass('is-disabled')){
+                return disabled_messages[$(ref).attr('data-disabled-type')];
+            }
             let download_type = $(ref).attr('data-download-type');
             return `Download all of the image instances in this ${download_type}.`;
         },
@@ -491,15 +497,11 @@ require([
         placement: 'left',
         arrow: false,
         interactive:true,
-        target: '.download-all-instances',
+        target: '.download-instances',
         maxWidth: 200,
         plugins: [dynamicTipFunc]
     };
 
-    tippy.delegate('.projects-table', disabled_download_tooltip);
-
-    tippy.delegate('.projects-table', download_tooltip);
-
     tippy.delegate('.projects-table', cart_tooltip);
 
     tippy.delegate('.cases-table', cart_tooltip);
@@ -533,22 +535,10 @@ require([
         maxWidth: 200
     });
 
-    tippy.delegate('.cases-table', download_tooltip);
-
-    tippy.delegate('.cases-table', disabled_download_tooltip);
-
-    tippy.delegate('.studies-table', download_tooltip);
-
     tippy.delegate('.studies-table', manifest_tooltip);
 
-    tippy.delegate('.studies-table', disabled_download_tooltip);
-
-    tippy.delegate('.series-table', download_tooltip);
-
     tippy.delegate('.series-table', manifest_tooltip);
 
-    tippy.delegate('.series-table', disabled_download_tooltip);
-
     tippy.delegate('.series-table', {
         content: 'Some or all of the images in this collection are not publicly available.',
         theme: 'dark',
@@ -571,6 +561,9 @@ require([
         maxWidth: 800
     });
 
+    tippy.delegate('#body', disabled_download_tooltip);
+    tippy.delegate('#body', download_tooltip);
+
     tippy.delegate('#body', {
         content: function(reference) {
             return "Copied!";
diff --git a/static/js/filterutils.js b/static/js/filterutils.js
index 226a3b754..583e9c069 100644
--- a/static/js/filterutils.js
+++ b/static/js/filterutils.js
@@ -69,7 +69,7 @@ define(['jquery', 'base'], function($, base) {
             $('.filter-activated-controls').each(function(){
                 if(!$(this).attr('data-pending-manifest')) {
                     $(this).attr("disabled","disabled");
-                    $(this).attr("title","Select a filter to enable this feature.");
+                    !$(this).hasClass('tip-titled') && $(this).attr("title","Select a filter to enable this feature.");
                 }
             })
             $('.bq-string, .citations-list').html("");
@@ -89,7 +89,7 @@ define(['jquery', 'base'], function($, base) {
             $('.filter-placeholder').hide();
             $('.filter-activated-controls').each((function(){
                 if(!$(this).attr('data-pending-manifest')) {
-                    $(this).attr("title", $(this).attr("data-default-title"));
+                     !$(this).hasClass('tip-titled') && $(this).attr("title", $(this).attr("data-default-title"));
                     $(this).removeAttr("disabled");
                 }
             }));
diff --git a/static/js/image_search.js b/static/js/image_search.js
index aaf98868d..820070ebc 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -86,13 +86,7 @@ require([
     window.filterObj = {};
     window.projIdSel = [];
     window.studyIdSel = [];
-    //window.tcgaColls = ["tcga_blca", "tcga_brca", "tcga_cesc", "tcga_coad", "tcga_esca", "tcga_gbm", "tcga_hnsc", "tcga_kich", "tcga_kirc", "tcga_kirp", "tcga_lgg", "tcga_lihc", "tcga_luad", "tcga_lusc", "tcga_ov", "tcga_prad", "tcga_read", "tcga_sarc", "tcga_stad", "tcga_thca", "tcga_ucec"];
     window.projSets = new Object();
-    window.projSets['tcga']=["tcga_blca", "tcga_brca", "tcga_cesc", "tcga_coad", "tcga_esca", "tcga_gbm", "tcga_hnsc", "tcga_kich", "tcga_kirc", "tcga_kirp", "tcga_lgg", "tcga_lihc", "tcga_luad", "tcga_lusc", "tcga_ov", "tcga_prad", "tcga_read", "tcga_sarc", "tcga_stad", "tcga_thca", "tcga_ucec"];
-    window.projSets['rider']=["rider_lung_ct", "rider_phantom_pet_ct","rider_breast_mri", "rider_neuro_mri","rider_phantom_mri", "rider_lung_pet_ct"];
-    window.projSets['qin'] = ["qin_headneck","qin_lung_ct","qin_pet_phantom","qin_breast_dce_mri"];
-
-
 
     window.hidePanel=function(){
         $('#lh_panel').hide();
@@ -103,7 +97,6 @@ require([
         $('#rh_panel').addClass('col-lg-12');
         $('#rh_panel').addClass('col-md-12');
     };
-
     window.showPanel=function(){
         $('#lh_panel').show();
         $('#show_lh').hide();
@@ -191,6 +184,8 @@ require([
                         $('#search_def_access').addClass('is-hidden');
                         $('.access_warn').addClass('is-hidden');
                     }
+                    let download_btn = $('#download-cohort-images');
+                    let download_btn_tips = $('#download-cohort-images-tooltips');
                     if(isFiltered && data.total > 0) {
                         $('#search_def_stats').html("Cohort filter contents: " +
                             data.totals.SeriesInstanceUID.toString() + " series from " +
@@ -198,10 +193,13 @@ require([
                             data.totals.StudyInstanceUID.toString() + " studies (Size on disk: " +
                             data.totals.disk_size + ")"
                         );
+                        base.updateDownloadBtns("cohort", true, parseFloat(data.totals.disk_size.split(" ")[0]));
+
                     } else if(isFiltered && data.total <= 0) {
                         $('#search_def_stats').html('<span style="color:red">There are no cases matching the selected set of filters</span>');
                     } else {
                         $('#search_def_stats').html("&nbsp;");
+                        base.updateDownloadBtns("cohort", false, 0);
                     }
 
                     filterutils.updateCollectionTotals('Program', data.programs);
@@ -568,63 +566,6 @@ require([
         }, 0);
     }
 
-    updatecartedits = function(){
-        if (("cartedits" in localStorage) && (localStorage.getItem("cartedits") == "true")) {
-            var edits = window.cartHist[window.cartHist.length - 1]['selections'];
-
-            var filt = Object();
-            filt['StudyInstanceUID'] = new Array();
-            var studymp = {};
-            for (var i = 0; i < edits.length; i++) {
-                var sel = edits[i]['sel'];
-                var studyid = sel[2];
-                filt['StudyInstanceUID'].push(studyid);
-                var seriesid = sel[3];
-                if (!(studyid in studymp)) {
-                    studymp[studyid] = []
-                }
-                studymp[studyid].push(seriesid)
-            }
-            if ("studymp" in sessionStorage) {
-                var studymp = JSON.parse(sessionStorage.getItem("studymp"));
-                for (studyid in studymp) {
-                    window.studymp[studyid]['val'] = studymp[studyid]
-                }
-            }
-            if ("seriesdel" in sessionStorage) {
-                window.seriesdel = JSON.parse(sessionStorage.getItem("seriesdel"));
-            }
-
-            cartutils.updateGlobalCart(false, studymp, 'series')
-            window.updateTableCounts(1);
-            var gtotals = cartutils.getGlobalCounts();
-            var content = "Cart contents: " + gtotals[3]+" series from "+gtotals[0]+" collections / "+ gtotals[1]+" cases / "+gtotals[2]+ " studies";
-
-            $('#cart_stats').html(content) ;
-
-            if (gtotals[0]>0){
-                $('#cart_stats').removeClass('empty-cart');
-                $('.cart-activated-controls').removeAttr('disabled');
-            } else {
-                $('#cart_stats').addClass('empty-cart');
-                $('#cart_stats').html('Your cart is currently empty.');
-                $('.cart-activated-controls').attr('disabled','disabled');
-            }
-        }
-        else if ("cartHist" in localStorage){
-            localStorage.removeItem("cartHist");
-        }
-        if ("cartedits" in sessionStorage){
-            sessionStorage.removeItem("cartedits");
-        }
-        if ("studymp" in sessionStorage){
-            sessionStorage.removeItem("studymp");
-        }
-        if ("seriesdel" in sessionStorage) {
-            sessionStorage.removeItem("seriesdel");
-        }
-    }
-
      $(document).ready(async function () {
 
         tables.initializeTableCacheData();
diff --git a/static/js/tables.js b/static/js/tables.js
index d9b11272b..59a4d5370 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -292,9 +292,9 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             }
         };
         const download_col = {"type": "html", "orderable": false, data: 'collection_id', render: function(data, type, row) {
-            let download_size = window.collection[row[0]]['total_size'];
+            let download_size = window.collection[row[0]]['total_size_with_ar'];
             if ("showDirectoryPicker" in window && download_size < 3) {
-                let download_classes = "download-collection";
+                let download_classes = "download-collection download-instances";
                 download_classes = (download_size > 1) ? `${download_classes} download-size-warning` : `${download_classes} download-all-instances`;
                 let modal_attr = "";
                 if(download_size > 1) {
@@ -306,12 +306,10 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     data-download-type="collection"
                     ${modal_attr}
                     ></i>`;
+            } else {
+                let disabled_type = ("showDirectoryPicker" in window) ? "dowbload-size-disabled" : "download_all_disabled";
+                return `<i class="fa fa-download is-disabled download-instances" data-disabled-type="${disabled_type}"></i>`;
             }
-            let disabled_classes = "download-all-disabled";
-            if(download_size >= 3) {
-                disabled_classes = `${disabled_classes} download-size-disabled`;
-            }
-            return `<i class="fa fa-download ${disabled_classes}"></i>`;
         }};
 
         return [caret_col, cart_col, cartnum_col, collection_col, case_col, dyn_case_col, download_col];
@@ -562,14 +560,14 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
         const series_col =  {"type": "num", "orderable": true, data: 'unique_series'};
         const download_col = {"type": "html", "orderable": false, data: 'patient_id', render: function(data, type, row) {
                 if ("showDirectoryPicker" in window) {
-                    return `<i class="fa fa-download download-all-instances download-case"   
+                    return `<i class="fa fa-download download-instances download-all-instances download-case"   
                         data-collection="${row['collection_id']}" 
                         data-patient="${row['PatientID']}" 
                         data-total-series="${row['unique_series']}"   
                         data-download-type="case"                                 
                         ></i>`;
                 }
-                return `<i class="fa fa-download download-all-disabled"></i>`;
+                return `<i class="fa fa-download  download-instances is-disabled" data-disabled-type="download-all-disabled"></i>`;
         }};
         return [caret_col, cart_col, cartnum_col, collection_col, case_col, study_col, series_col, download_col];
     };
@@ -1014,7 +1012,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                           "orderable": false,
                           data: 'StudyInstanceUID', render: function (data, type, row) {
                             if ("showDirectoryPicker" in window) {
-                                return `<i class="fa fa-download download-all-instances download-study"   
+                                return `<i class="fa fa-download download-all-instances download-instances download-study"   
                                     data-collection="${row['collection_id']}" 
                                     data-study="${row['StudyInstanceUID']}" 
                                     data-patient="${row['PatientID']}" 
@@ -1022,7 +1020,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                     data-total-series="${row['unique_series']}"                         
                                     ></i>`;
                             }
-                            return `<i class="fa fa-download download-all-disabled"></i>`;
+                            return `<i class="fa fa-download download-instances is-disabled" data-disabled-type="download-all-disabled"></i>`;
                         }
                     }
                 ],
@@ -1368,7 +1366,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                       "orderable": false,
                       data: 'SeriesInstanceUID', render: function (data, type, row){
                           if("showDirectoryPicker" in window) {
-                            return `<i class="fa fa-download download-all-instances" data-bucket="${row['aws_bucket']}" 
+                            return `<i class="fa fa-download download-all-instances download-instances" data-bucket="${row['aws_bucket']}" 
                                 data-series="${row['crdc_series_uuid']}" 
                                 data-series-id="${row['SeriesInstanceUID']}" 
                                 data-modality="${row['Modality']}" 
@@ -1378,7 +1376,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                 data-series-size="${row['instance_size']}"                                                 
                                 ></i>`
                           }
-                          return `<i class="fa fa-download download-all-disabled"></i>`
+                          return `<i class="fa fa-download is-disabled download-instances" data-disabled-type="download-all-disabled"></i>`
                       }
                   }
             ],
@@ -1957,10 +1955,9 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
     }
 
     const handleCartClick = function(tabletype, row, elem, ids){
-         var updateElems =["series", "studies","cases"]
-        //$(row).find('.shopping-cart-holder').trigger('shopping-cart:update-started');
-         var addingToCart = true;
-         if (tabletype=="series") {
+         let updateElems =["series", "studies","cases"];
+         let addingToCart = true;
+         if (tabletype==="series") {
              if ($(elem).parentsUntil('tr').parent().hasClass('someInCart')) {
                  addingToCart = false;
              } else {
@@ -1975,7 +1972,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
          }
 
          // record new selection
-         var newSel={}
+         let newSel={};
          newSel['added'] = addingToCart;
          newSel['sel'] = ids;
          cartutils.updateCartSelections(newSel);
diff --git a/static/js/utils.js b/static/js/utils.js
index fbbbf0605..070fbc7d8 100644
--- a/static/js/utils.js
+++ b/static/js/utils.js
@@ -142,6 +142,36 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
         _hideFloatingMessage(true);
     });
 
+
+        // Enabled is equivalent to 'is there a filter' or 'is something in the cart'
+    function _updateDownloadBtns(type, enabled, disk_size) {
+        let btn = $(`#download-${type}-images`);
+        let btn_tip = $(`#download-${type}-images-tooltips`);
+        let btn_and_tips = $(`#download-${type}-images-tooltips, #download-${type}-images-tooltips`);
+        if(!enabled){
+            btn_tip.addClass('is-disabled');
+            btn_tip.attr('data-disabled-type', `download-${type}-disabled`);
+            btn.attr("disabled", "disabled");
+            return;
+        }
+        if ("showDirectoryPicker" in window) {
+            btn_and_tips.removeClass('is-disabled download-all-instances download-size-warning');
+            if (disk_size > 3) {
+                btn_tip.addClass('is-disabled');
+                btn_tip.attr('data-disabled-type', "download-size-disabled");
+                btn.attr("disabled", "disabled");
+            } else {
+                btn.removeAttr("disabled");
+                btn_tip.attr('data-disabled-type', "");
+                (disk_size > 2) ? btn.addClass('download-size-warning') : btn.addClass('download-all-instances');
+            }
+        } else {
+            btn_tip.addClass('is-disabled');
+            btn_tip.attr('data-disabled-type', "download-all-disabled");
+            btn.attr("disabled", "disabled");
+        }
+    }
+
     const MAX_ELAPSED = 240000;
     function _checkManifestReady(file_name, check_start) {
         if(!check_start) {
@@ -226,6 +256,7 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
         getCookie: _getCookie,
         removeCookie: _removeCookie,
         checkManifestReady: _checkManifestReady,
-        checkForManifest: _checkForManifest
+        checkForManifest: _checkForManifest,
+        updateDownloadBtns: _updateDownloadBtns
     };
 });
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index 03d315af7..74bd06359 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -632,15 +632,16 @@ <h4>Cohort Filters</h4>
                                 title="Select a filter to enable this feature."
                             > Manifest <i class="fa fa-solid fa-list"></i>
                             </button>
-                            <button id="download-cohort-images" class="btn btn-primary btn-small filter-activated-controls download-all-instances" disabled
-                                data-default-title="Download the instance image files for this cohort."
-                                title="Select a filter to enable this feature."
+                            <span id="download-cohort-images-tooltips" class="download-instances is-disabled" data-download-type="cohort" data-disabled-type="download-cohort-disabled">
+                            <button id="download-cohort-images" class="btn btn-primary btn-small filter-activated-controls download-all-instances tip-titled" disabled
                                 data-download-type="cohort"
                             > Download <i class="fa fa-solid fa-download"></i>
                             </button>
-                            <button class="btn btn-small btn-special citations-button filter-activated-controls" disabled data-toggle="modal" data-target="#citations-modal" role="button"
-                                data-default-title="Display this cohort's citation list in Vancouver format."
-                                title= "Select a filter to enable this feature."
+                            </span>
+                            <button class="btn btn-small btn-special citations-button filter-activated-controls" disabled
+                                data-toggle="modal" data-target="#citations-modal" role="button"
+                                data-default-title=""
+                                title="Select a filter to enable this feature."
                             > Citations <i class="smaller-icon fa fa-quote-left"></i><i class="smaller-icon fa fa-quote-right"></i>
                             </button>
                             <button class="btn btn-small btn-default bq-string-display filter-activated-controls" disabled data-toggle="modal"
@@ -680,21 +681,25 @@ <h4>Cart</h4>
                         <div class="cart-container space-top-10">
                             <button id="export-manifest-cart" class="btn btn-primary cart-export btn-small cart-activated-controls" disabled data-toggle="modal"
                                 data-target="#export-manifest-modal"
+                                data-default-title="Download a manifest of this cart's series."
                                 title="Add items to the cart to enable this feature."
                             > Manifest <i class="fa fa-solid fa-list"></i>
                             </button>
-                            <button id="download-cart-images" class="btn btn-primary btn-small cart-activated-controls download-all-instances" disabled
-                                data-default-title="Download the instance image files for this cart."
-                                title="Select a filter to enable this feature."
+                            <span id="download-cart-images-tooltips" class="download-instances is-disabled" data-download-type="cart" data-disabled-type="download-cart-disabled">
+                            <button id="download-cart-images" class="btn btn-primary btn-small cart-activated-controls tip-titled" disabled
                                 data-download-type="cart"
                             > Download <i class="fa fa-solid fa-download"></i>
                             </button>
-                            <button class="btn btn-small btn-special citations-button cart-activated-controls for-cart" disabled data-toggle="modal" data-target="#citations-modal" role="button"
-                                data-default-title="Display this cart's citation list in Vancouver format."
-                                title= "Add items to the cart to enable this feature."
+                            </span>
+                            <button class="btn btn-small btn-special citations-button cart-activated-controls for-cart"
+                                disabled data-toggle="modal" data-target="#citations-modal" role="button"
+                                data-default-title=""
+                                title="Add items to the cart to enable this feature."
                             > Citations <i class="smaller-icon fa fa-quote-left"></i><i class="smaller-icon fa fa-quote-right"></i>
                             </button>
-                            <button class="btn btn-small btn-default cart-view cart-activated-controls" role="button" title="Get cart details." disabled
+                            <button class="btn btn-small btn-default cart-view cart-activated-controls" role="button"
+                                data-default-title="View this cart's complete contents."
+                                title="Add items to the cart to enable this feature." disabled
                                 onclick="viewcart()"
                             > View <i class="fa-solid fa-cart-shopping"></i>
                             </button>

From 3f92d9c7c3f398c9fc0c92fa0338d24315381b41 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 31 Oct 2025 17:38:32 -0700
Subject: [PATCH 18/25] -> Tooltip updates

---
 static/js/cartutils.js | 12 +++++++++---
 static/js/explore.js   |  2 +-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/static/js/cartutils.js b/static/js/cartutils.js
index 64d913e37..7cec9580e 100644
--- a/static/js/cartutils.js
+++ b/static/js/cartutils.js
@@ -125,6 +125,7 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
     const updateCartCounts = async function(){
         var buttonContents = '<button class="btn filter-type clear-cart" role="button" title="Empty your cart."><i class="fa fa-rotate-left"></i></button>';
         let cart_has_contents = Boolean(Object.keys(window.proj_in_cart).length>0);
+        let cart_controls = $('.cart-activated-controls');
         if (cart_has_contents){
             var nmprojs = 0;
             var nmcases=0;
@@ -136,18 +137,23 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
                 nmstudies=nmstudies+window.proj_in_cart[projid]['studies'];
                 nmseries=nmseries+window.proj_in_cart[projid]['series'];
             }
-
             let content = buttonContents+'<span id ="#cart_stats">Cart contents: ' + nmseries.toString()+' series from '+nmprojs.toString()+
                 ' collections / '+nmcases.toString()+' cases / '+nmstudies.toString()+' studies</span> <span class="cart_disk_size">(Calculating size...)</span>';
             localStorage.setItem('manifestSeriesCount',nmseries);
 
             $('#cart_stats_holder').html(content) ;
             $('#cart_stats').removeClass('empty-cart');
-            $('.cart-activated-controls').removeAttr('disabled');
+            cart_controls.each(function(){
+                $(this).removeAttr('disabled');
+                !$(this).hasClass('tip-titled') && $(this).attr("title",$(this).attr("data-default-title"));
+            });
         } else {
             $('#cart_stats_holder').html('<span id="#cart_stats">Your cart is currently empty</span>');
             $('#cart_stats').addClass('empty-cart');
-            $('.cart-activated-controls').attr('disabled', 'disabled');
+            cart_controls.each(function(){
+                $(this).attr('disabled', 'disabled');
+                !$(this).hasClass('tip-titled') && $(this).attr("title","Add items to the cart to enable this feature.");
+            });
         }
         let cart_disk_size = 0;
         let cart_disk_display_size = "(Calculating...)";
diff --git a/static/js/explore.js b/static/js/explore.js
index eea8bfe2d..42d150c0a 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -525,7 +525,7 @@ require([
 
     tippy.delegate('.cases-table', copy_tip);
 
-    tippy.delegate('.filter-display-panel', {
+    tippy.delegate('#body', {
         content: 'Get the citation list for this cohort.',
         theme: 'dark',
         placement: 'left',

From 9e109f22c2857187837f04f76ecceaaf267c19e7 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Tue, 4 Nov 2025 10:57:31 -0800
Subject: [PATCH 19/25] -> Tooltip fixes

---
 static/css/style.css | 4 ++--
 static/js/tables.js  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/static/css/style.css b/static/css/style.css
index 2c9ece912..ed48d0590 100755
--- a/static/css/style.css
+++ b/static/css/style.css
@@ -4523,11 +4523,11 @@ d-topics-list iframe {
   cursor: pointer;
 }
 
-.download-all-disabled {
+.download-all-disabled, .is-disabled.download-instances {
   cursor: not-allowed !important;
 }
 
-.fa.download-all-disabled {
+.fa.download-all-disabled, .fa.is-disabled {
     color: gray;
 }
 
diff --git a/static/js/tables.js b/static/js/tables.js
index 59a4d5370..fa7b491df 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -307,7 +307,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     ${modal_attr}
                     ></i>`;
             } else {
-                let disabled_type = ("showDirectoryPicker" in window) ? "dowbload-size-disabled" : "download_all_disabled";
+                let disabled_type = ("showDirectoryPicker" in window) ? "download-size-disabled" : "download_all_disabled";
                 return `<i class="fa fa-download is-disabled download-instances" data-disabled-type="${disabled_type}"></i>`;
             }
         }};

From 2f7b73f410d772f0745856303d2a062124cf9503 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Wed, 5 Nov 2025 18:52:07 -0800
Subject: [PATCH 20/25] -> expansion table changes

---
 static/css/search.css | 14 +++++++--
 static/js/tables.js   | 72 ++++++++++++++++++++++++-------------------
 2 files changed, 51 insertions(+), 35 deletions(-)

diff --git a/static/css/search.css b/static/css/search.css
index 247c33b27..e42ec0305 100644
--- a/static/css/search.css
+++ b/static/css/search.css
@@ -382,17 +382,25 @@ tr {
     display: table;
     width: 100%; }
 
-.expansion-toggle i {
+.table-striped > tbody > tr.entity-table-row.open {
+    background-color: #ffebce; !important
+}
+
+.expansion-toggle {
+    text-align: center;
     font-size: larger;
 }
 
 .expansion-toggle.open {
-    background-color: #c5b9d5;
+    background-color: #ffebce;
+}
+
+.table-striped > tbody > tr.entity-table-row:hover {
+    background-color: #b7cfe5;
 }
 
 .expansion-toggle:hover {
     cursor: pointer;
-    background-color: #b7cfe5;
 }
 
 .export-button:hover, .citations-button:hover, .btnGroupDropViewers:hover {
diff --git a/static/js/tables.js b/static/js/tables.js
index fa7b491df..19d549bdb 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -251,18 +251,18 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
         var caret_col= { "type": "html", "orderable": false, render: function (data) {
             if (('state' in window.selProjects[data]) && ('view' in window.selProjects[data]['state']) && (window.selProjects[data]['state']['view'] )) {
                 return '<a role="button" title="Display cases in this collection below.">'+
-                    '<i class="fa fa-solid fa-caret-right is-hidden"></i>' +
-                    '<i class="fa fa-solid fa-caret-down"></i></a>'
+                    '<i class="fa fa-solid fa-folder is-hidden"></i>' +
+                    '<i class="fa fa-solid fa-folder-open"></i></a>'
             } else {
                 return '<a role="button" title="Display cases in this collection below.">'+
-                    '<i class="fa fa-solid fa-caret-right"></i>' +
-                    '<i class="fa fa-solid fa-caret-down is-hidden"></i></a>'
+                    '<i class="fa fa-solid fa-folder"></i>' +
+                    '<i class="fa fa-solid fa-folder-open is-hidden"></i></a>'
             }
        },
             createdCell: function(td) {
                 $(td).attr("title", "Display cases in this collection below.");
                 $(td).addClass('expansion-toggle');
-                if ($(td).find('.fa-caret-right.is-hidden').length > 0) {
+                if ($(td).find('.fa-folder.is-hidden').length > 0) {
                     $(td).addClass('open');
                 }
             }
@@ -407,6 +407,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 "order": ord,
                 "data": newCollectionData,
                 "createdRow": function (row, data, dataIndex) {
+                    $(row).addClass('entity-table-row');
                     $(row).data('projectid', data[0]);
                     $(row).attr('data-projectid', data[0]);
                     $(row).data('totalcases', data[5]);
@@ -510,19 +511,19 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 if ((collection_id in window.openCases) && (PatientID in window.openCases[collection_id]) ) {
                     //return '<input type="checkbox" checked>'
                    return '<a role="button">'+
-                        '<i class="fa fa-solid fa-caret-right is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
-                        '<i class="fa fa-solid fa-caret-down" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
+                        '<i class="fa fa-solid fa-folder is-hidden"></i>' +
+                        '<i class="fa fa-solid fa-folder-open"></i></a>'
 
                 } else {
                     return '<a role="button" title="Display studies in this case below.">'+
-                        '<i class="fa fa-solid fa-caret-right " style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
-                        '<i class="fa fa-solid fa-caret-down is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
+                        '<i class="fa fa-solid fa-folder"></i>' +
+                        '<i class="fa fa-solid fa-folder-open is-hidden"></i></a>'
                 }
             },
             createdCell: function(td) {
                 $(td).attr("title", "Display studies in this case below.");
                 $(td).addClass('expansion-toggle');
-                if ($(td).find('.fa-caret-right.is-hidden').length > 0) {
+                if ($(td).find('.fa-folder.is-hidden').length > 0) {
                     $(td).addClass('open');
                 }
             }
@@ -593,6 +594,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 "dom": '<"dataTables_controls"ilp>rt<"bottom"><"clear">',
                 "order": [[4, 'asc'],[3, 'asc']],
                 "createdRow": function (row, data, dataIndex) {
+                    $(row).addClass('entity-table-row');
                     $(row).attr('id', 'case_' + data['PatientID'])
                     $(row).attr('data-projectid', data['collection_id'][0]);
                     $(row).attr('data-caseid', data['PatientID']);
@@ -788,6 +790,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 "dom": '<"dataTables_controls"ilp>rt<"bottom"><"clear">',
                 "order": [[3, "asc"]],
                 "createdRow": function (row, data, dataIndex) {
+                    $(row).addClass('entity-table-row');
                     $(row).attr('id', 'study_' + data['StudyInstanceUID'])
                     $(row).attr('data-studyid', data['StudyInstanceUID']);
                     $(row).attr('data-caseid', data['PatientID']);
@@ -884,20 +887,20 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                             if ( (PatientID in window.openStudies) && (StudyInstanceUID in window.openStudies[PatientID])) {
                                 //return '<input type="checkbox" checked>'
                                return '<a role="button">'+
-                                    '<i class="fa fa-solid fa-caret-right is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
-                                    '<i class="fa fa-solid fa-caret-down" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
+                                    '<i class="fa fa-solid fa-folder is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
+                                    '<i class="fa fa-solid fa-folder-open" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
 
                             } else {
                                 return '<a role="button">'+
-                                    '<i class="fa fa-solid fa-caret-right " style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
-                                    '<i class="fa fa-solid fa-caret-down is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
+                                    '<i class="fa fa-solid fa-folder " style="font-family :\'Font Awesome 6 Free\' !important"></i>' +
+                                    '<i class="fa fa-solid fa-folder-open is-hidden" style="font-family :\'Font Awesome 6 Free\' !important"></i></a>'
 
                             }
                         },
                         createdCell: function(td) {
                             $(td).attr("title", "Display series in this study below.");
                             $(td).addClass('expansion-toggle');
-                            if ($(td).find('.fa-caret-right.is-hidden').length > 0) {
+                            if ($(td).find('.fa-folder.is-hidden').length > 0) {
                                 $(td).addClass('open');
                             }
                         }
@@ -989,7 +992,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                     }
                                     return '<a href="' + default_viewer + '" target="_blank" rel="noopener noreferrer"><i class="fa-solid fa-eye"></i>' +
                                         '<div class="dropdown viewer-toggle">' +
-                                        '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-caret-down"></i></a>' +
+                                        '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-folder-open"></i></a>' +
                                         '<ul class="dropdown-menu viewer-menu">' +
                                         '<li><a href="'+v3_link+'" target="_blank" rel="noopener noreferrer">OHIF v3</a></li>' +
                                         v2_element +
@@ -1163,6 +1166,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                  "order": [[0, "asc"]],
                  "createdRow": function (row, data, dataIndex) {
                     $(row).attr('id', 'series_' + data['SeriesInstanceUID']);
+                    $(row).addClass('entity-table-row');
                     $(row).attr('data-seriesid', data['SeriesInstanceUID']);
                     $(row).attr('data-studyid', data['StudyInstanceUID']);
                     $(row).attr('data-caseid', data['PatientID']);
@@ -1347,7 +1351,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
 
                             return '<a href="' + default_viewer + '" target="_blank" rel="noopener noreferrer"><i class="fa-solid fa-eye"></i>' +
                                 '<div class="dropdown viewer-toggle">' +
-                                '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-caret-down"></i></a>' +
+                                '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-folder-open"></i></a>' +
                                 '<ul class="dropdown-menu viewer-menu">' +
                                 '<li><a href="'+v3_link+'" target="_blank" rel="noopener noreferrer">OHIF v3</a></li>' +
                                 v2_element +
@@ -2062,8 +2066,8 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
     };
 
     $('.addMult').on('click', function() {
-        var idsattr=["data-projectid", "data-caseid", "data-studyid"]
-        var idsArr=[]
+        var idsattr= ["data-projectid", "data-caseid", "data-studyid"];
+        var idsArr= [];
         var tbl_head = $(this).parentsUntil('table').filter('thead');
         var tbl_head_id = tbl_head.attr('id');
         if ($(this).hasClass('fa-plus-circle')){
@@ -2095,12 +2099,14 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             idsArr.push(ids);
 
             if (rowsAdded) {
-                $(this).find('.expansion-toggle .fa-caret-right').addClass('is-hidden');
-                $(this).find('.expansion-toggle .fa-caret-down').removeClass('is-hidden');
+                $(this).addClass('open');
+                $(this).find('.expansion-toggle .fa-folder').addClass('is-hidden');
+                $(this).find('.expansion-toggle .fa-folder-open').removeClass('is-hidden');
                 $(this).find('.viewbx').addClass('open');
             } else{
-               $(this).find('.expansion-toggle .fa-caret-right').removeClass('is-hidden');
-                $(this).find('.expansion-toggle .fa-caret-down').addClass('is-hidden');
+                $(this).removeClass('open');
+               $(this).find('.expansion-toggle .fa-folder').removeClass('is-hidden');
+                $(this).find('.expansion-toggle .fa-folder-open').addClass('is-hidden');
                 $(this).find('.viewbx').removeClass('open');
             }
         });
@@ -2201,21 +2207,23 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
          }
          // click anywhere else, open tables below
          else {
-             let toggle_elem = $(row).find('.expansion-toggle')
+             let toggle_elem = $(row).find('.expansion-toggle');
+             let rowsAdded = null;
              if (toggle_elem.length>0) {
-                 var rowsAdded;
                  toggle_elem = toggle_elem[0];
                  $(toggle_elem).hasClass('open') ? $(toggle_elem).removeClass('open') : $(toggle_elem).addClass('open');
              }
-             if ($(row).find('.expansion-toggle .fa-caret-down.is-hidden').length>0){
-                 var rowsAdded = true;
-                 $(row).find('.expansion-toggle .fa-caret-right').addClass('is-hidden');
-                 $(row).find('.expansion-toggle .fa-caret-down').removeClass('is-hidden');
+             if ($(row).find('.expansion-toggle .fa-folder-open.is-hidden').length>0){
+                 rowsAdded = true;
+                 $(row).addClass('open');
+                 $(row).find('.expansion-toggle .fa-folder').addClass('is-hidden');
+                 $(row).find('.expansion-toggle .fa-folder-open').removeClass('is-hidden');
 
              } else {
-                 var rowsAdded = false;
-                 $(row).find('.expansion-toggle .fa-caret-right').removeClass('is-hidden');
-                 $(row).find('.expansion-toggle .fa-caret-down').addClass('is-hidden');
+                 rowsAdded = false;
+                 $(row).removeClass('open');
+                 $(row).find('.expansion-toggle .fa-folder').removeClass('is-hidden');
+                 $(row).find('.expansion-toggle .fa-folder-open').addClass('is-hidden');
              }
              changeViewStates(tabletype, [ids], rowsAdded);
          }

From 34a06442d2c9d7d108f2362cec8e956da627e043 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Thu, 6 Nov 2025 13:18:59 -0800
Subject: [PATCH 21/25] -> #1509

---
 static/css/search.css                |   7 +-
 static/js/explore.js                 |   1 +
 static/js/tables.js                  | 168 +++++++++++++--------------
 templates/idc/explore_data_core.html |  23 ++--
 4 files changed, 98 insertions(+), 101 deletions(-)

diff --git a/static/css/search.css b/static/css/search.css
index e42ec0305..2f345850b 100644
--- a/static/css/search.css
+++ b/static/css/search.css
@@ -418,13 +418,14 @@ tr {
 #studies_table_head th.ckbx:not(.cartnumholder), #studies_table td.ckbx:not(.cartnumholder),
 #series_table_head th.ckbx, #series_table td.ckbx {
     width: 5%;
+    text-align: left !important;
 }
 
 #search_def_stats {
     padding-top: 8px; }
 
 #projects_table td, #projects_table_head th {
-    width: 30%;
+    width: 40%;
     word-wrap: break-word; }
 
 #cases_table td, #cases_table_head th {
@@ -481,9 +482,9 @@ tr {
 #studies_table_head th.download-col,
 #studies_table td.download-col, #cases_table_head th.download-col,
 #cases_table td.download-col, #series_table_head th.download-col,
-#series_table td.download-col {
+#series_table td.download-col, #proj_table th.download-col, #proj_table td.download-col {
     width:6%;
-    min-width: 80px;
+    min-width: 60px;
 }
 
 #series_table_head th, #series_table td {
diff --git a/static/js/explore.js b/static/js/explore.js
index 42d150c0a..1441e3c5f 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -455,6 +455,7 @@ require([
         interactive: true,
         allowHTML: true,
         placement: 'right',
+        theme: 'dark',
         content: 'add series to cart', // placeholder text
         target: '.shopping-cart-holder',
         plugins: [dynamicTipFunc]
diff --git a/static/js/tables.js b/static/js/tables.js
index 19d549bdb..4dc9e1f49 100644
--- a/static/js/tables.js
+++ b/static/js/tables.js
@@ -213,7 +213,6 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             return cmp;
         }
 
-
         var dir = request.order[0]['dir'];
         var colId = parseInt(request.order[0]['column']);
         var col = cache.colOrder[colId];
@@ -237,13 +236,14 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
 
     // classes for project(collection) table columns
     var projectTableColDefs = function(){
-        return [{className: "ckbx text_data viewbx caseview", "targets": [0]},
-                {className: "ckbx shopping-cart-holder", "targets": [1]},
-                {className: "ckbx cartnumholder", "targets": [2]},
-                {className: "collex_name", "targets": [3]},
-                {className: "collex-case-count table-count", "targets": [4]},
-                {className: "projects_table_num_cohort table-count", "targets": [5]},
-                {className: "download-collection download-col", "targets": [6]}];
+        return [
+            {className: "ckbx text_data viewbx caseview", "targets": [0]},
+            {className: "download-collection download-col", "targets": [1]},
+            {className: "ckbx shopping-cart-holder", "targets": [2]},
+            {className: "ckbx cartnumholder", "targets": [3]},
+            {className: "collex_name", "targets": [4]},
+            {className: "collex-case-count projects_table_num_cohort table-count", "targets": [5]}
+        ];
     }
 
     // project(collection) table column definitions
@@ -282,15 +282,11 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                  ' <a class="copy-this" role="button" content="' + row[0] +
                  '" title="Copy the IDC collection_id to the clipboard"><i class="fa-solid fa-copy"></i></a>'
                }};
-        var case_col = { "type": "num", orderable: true };
-        var dyn_case_col = {
-            "type": "num",
-            orderable: true,
-            "createdCell": function (td, data, row) {
+        var case_col = { "type": "num", orderable: true, "createdCell": function (td, data, row) {
                 $(td).attr('id', 'patient_col_' + row[0]);
-                return;
-            }
-        };
+            }, render: function(td, data,row) {
+                return `${row[4]} / ${row[5]}`;
+            }};
         const download_col = {"type": "html", "orderable": false, data: 'collection_id', render: function(data, type, row) {
             let download_size = window.collection[row[0]]['total_size_with_ar'];
             if ("showDirectoryPicker" in window && download_size < 3) {
@@ -312,7 +308,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
             }
         }};
 
-        return [caret_col, cart_col, cartnum_col, collection_col, case_col, dyn_case_col, download_col];
+        return [caret_col, download_col, cart_col, cartnum_col, collection_col, case_col];
     }
 
      const setRowCartClasses = function(row){
@@ -399,7 +395,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
         $("#proj_table_wrapper").find('.dataTables_controls').remove();
         var colDefs = projectTableColDefs();
         var columns = projectTableColumns();
-        var ord = [[3, "asc"]]
+        var ord = [[4, "asc"]]
 
         $('#proj_table').DataTable(
             {
@@ -495,13 +491,14 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
     const caseTableColDefs = function(){
         return [
             {className: "ckbx studyview","targets": [0]},
-            {className: "ckbx shopping-cart-holder", "targets": [1]},
-            {className: "ckbx cartnumholder", "targets":[2]},
-            {className: "col1 project-name wide", "targets": [3]},
-            {className: "col1 case-id", "targets": [4]},
-            {className: "col1 numrows narrow", "targets": [5]},
-            {className: "col1 numseries narrow", "targets": [6]},
-            {className: "col1 download-case download-col", "targets": [7]}];
+            {className: "col1 download-case download-col", "targets": [1]},
+            {className: "ckbx shopping-cart-holder", "targets": [2]},
+            {className: "ckbx cartnumholder", "targets":[3]},
+            {className: "col1 project-name wide", "targets": [4]},
+            {className: "col1 case-id", "targets": [5]},
+            {className: "col1 numrows narrow", "targets": [6]},
+            {className: "col1 numseries narrow", "targets": [7]}
+        ];
     };
 
     const caseTableColumns = function() {
@@ -570,7 +567,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 }
                 return `<i class="fa fa-download  download-instances is-disabled" data-disabled-type="download-all-disabled"></i>`;
         }};
-        return [caret_col, cart_col, cartnum_col, collection_col, case_col, study_col, series_col, download_col];
+        return [caret_col, download_col, cart_col, cartnum_col, collection_col, case_col, study_col, series_col];
     };
 
     // recreates the cases table when a chevron is clicked in the projects table. Defines the chevron and cart selection actions.
@@ -865,16 +862,16 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                 },
                 "columnDefs": [
                     {className: "ckbx seriesview", "targets": [0]},
-                    {className: "ckbx shopping-cart-holder", "targets": [1]},
-                    {className: "ckbx cartnumholder", "targets": [2]},
-                    {className: "col1 case-id", "targets": [3]},
-                    {className: "col2 study-id study-id-col study-id-tltp", "targets": [4]},
-                    {className: "col1 study-date", "targets": [5]},
-                    {className: "col1 study-description", "targets": [6]},
-                    {className: "col1 numrows", "targets": [7]},
-                    {className: "ohif open-viewer", "targets": [8]},
-                    {className: "manifest-col", "targets": [9]},
-                    {className: "download-col download-study", "targets": [10]},
+                    {className: "download-col download-study", "targets": [1]},
+                    {className: "ckbx shopping-cart-holder", "targets": [2]},
+                    {className: "ckbx cartnumholder", "targets": [3]},
+                    {className: "col1 case-id", "targets": [4]},
+                    {className: "col2 study-id study-id-col study-id-tltp", "targets": [5]},
+                    {className: "col1 study-date", "targets": [6]},
+                    {className: "col1 study-description", "targets": [7]},
+                    {className: "col1 numrows", "targets": [8]},
+                    {className: "ohif open-viewer", "targets": [9]},
+                    {className: "manifest-col", "targets": [10]}
                 ],
                 "columns": [
                     {
@@ -904,8 +901,22 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                 $(td).addClass('open');
                             }
                         }
-                    },
-                   {
+                    },{
+                          "type":"html",
+                          "orderable": false,
+                          data: 'StudyInstanceUID', render: function (data, type, row) {
+                            if ("showDirectoryPicker" in window) {
+                                return `<i class="fa fa-download download-all-instances download-instances download-study"   
+                                    data-collection="${row['collection_id']}" 
+                                    data-study="${row['StudyInstanceUID']}" 
+                                    data-patient="${row['PatientID']}" 
+                                    data-download-type="study" 
+                                    data-total-series="${row['unique_series']}"                         
+                                    ></i>`;
+                            }
+                            return `<i class="fa fa-download download-instances is-disabled" data-disabled-type="download-all-disabled"></i>`;
+                        }
+                    },{
                        "type": "html",
                        "orderable": false,
                        render: function () {
@@ -992,7 +1003,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                                     }
                                     return '<a href="' + default_viewer + '" target="_blank" rel="noopener noreferrer"><i class="fa-solid fa-eye"></i>' +
                                         '<div class="dropdown viewer-toggle">' +
-                                        '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-folder-open"></i></a>' +
+                                        '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-caret-down"></i></a>' +
                                         '<ul class="dropdown-menu viewer-menu">' +
                                         '<li><a href="'+v3_link+'" target="_blank" rel="noopener noreferrer">OHIF v3</a></li>' +
                                         v2_element +
@@ -1009,23 +1020,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                               return '<i class="fa fa-list study-export export-button" data-series-count="'+row['unique_series']
                                   +'" data-uid="'+data+'"data-toggle="modal" data-target="#export-manifest-modal"></i>'
                           }
-                      },
-                    {
-                          "type":"html",
-                          "orderable": false,
-                          data: 'StudyInstanceUID', render: function (data, type, row) {
-                            if ("showDirectoryPicker" in window) {
-                                return `<i class="fa fa-download download-all-instances download-instances download-study"   
-                                    data-collection="${row['collection_id']}" 
-                                    data-study="${row['StudyInstanceUID']}" 
-                                    data-patient="${row['PatientID']}" 
-                                    data-download-type="study" 
-                                    data-total-series="${row['unique_series']}"                         
-                                    ></i>`;
-                            }
-                            return `<i class="fa fa-download download-instances is-disabled" data-disabled-type="download-all-disabled"></i>`;
-                        }
-                    }
+                      }
                 ],
                 "processing": true,
                 "serverSide": true,
@@ -1251,22 +1246,40 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                     });
                  },
                 "columnDefs": [
-                    {className: "ckbx shopping-cart-holder", "targets": [0]},
-                    {className: "col1 study-id study-id-col study-id-tltp", "targets": [1]},
-                    {className: "series-id series-id-tltp", "targets": [2]},
-                    {className: "series-number", "targets": [3]},
-                    {className: "col1 modality", "targets": [4]},
-                    {className: "col1 body-part-examined", "targets": [5]},
-                    {className: "series-description", "targets": [6]},
-                    {className: "ohif open-viewer", "targets": [7]},
-                    {className: "manifest-col", "targets": [8]},
-                    {className: "download-col download-series", "targets": [9]}
+                    {className: "download-col download-series", "targets": [0]},
+                    {className: "ckbx shopping-cart-holder", "targets": [1]},
+                    {className: "col1 study-id study-id-col study-id-tltp", "targets": [2]},
+                    {className: "series-id series-id-tltp", "targets": [3]},
+                    {className: "series-number", "targets": [4]},
+                    {className: "col1 modality", "targets": [5]},
+                    {className: "col1 body-part-examined", "targets": [6]},
+                    {className: "series-description", "targets": [7]},
+                    {className: "ohif open-viewer", "targets": [8]},
+                    {className: "manifest-col", "targets": [9]},
                  ],
                   "columns": [
-                      {"type": "html", "orderable": false, render: function () {
+                    {
+                      "type":"html",
+                      "orderable": false,
+                      data: 'SeriesInstanceUID', render: function (data, type, row){
+                          if("showDirectoryPicker" in window) {
+                            return `<i class="fa fa-download download-all-instances download-instances" data-bucket="${row['aws_bucket']}" 
+                                data-series="${row['crdc_series_uuid']}" 
+                                data-series-id="${row['SeriesInstanceUID']}" 
+                                data-modality="${row['Modality']}" 
+                                data-collection="${row['collection_id']}" 
+                                data-study="${row['StudyInstanceUID']}" 
+                                data-patient="${row['PatientID']}" 
+                                data-series-size="${row['instance_size']}"                                                 
+                                ></i>`
+                          }
+                          return `<i class="fa fa-download is-disabled download-instances" data-disabled-type="download-all-disabled"></i>`
+                      }
+                  }, {
+                    "type": "html", "orderable": false, render: function () {
                        return '<i class="fa-solid fa-cart-shopping shopping-cart"></i>'
                   }
-               }, {
+                }, {
                     "type": "text", "orderable": true, data: 'StudyInstanceUID', render: function (data) {
                         return pretty_print_id(data) +
                             ' <a class="copy-this" role="button" content="' + data +
@@ -1351,7 +1364,7 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
 
                             return '<a href="' + default_viewer + '" target="_blank" rel="noopener noreferrer"><i class="fa-solid fa-eye"></i>' +
                                 '<div class="dropdown viewer-toggle">' +
-                                '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-folder-open"></i></a>' +
+                                '<a class="dropdown-toggle btnGroupDropViewers" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true"><i class="fa-solid fa-caret-down"></i></a>' +
                                 '<ul class="dropdown-menu viewer-menu">' +
                                 '<li><a href="'+v3_link+'" target="_blank" rel="noopener noreferrer">OHIF v3</a></li>' +
                                 v2_element +
@@ -1365,23 +1378,6 @@ define(['cartutils','filterutils','tippy','jquery', 'base'], function(cartutils,
                       data: 'SeriesInstanceUID', render: function (data){
                           return '<i class="fa fa-list series-export export-button" data-uid="'+data+'"data-toggle="modal" data-target="#export-manifest-modal"></i>'
                       }
-                  }, {
-                      "type":"html",
-                      "orderable": false,
-                      data: 'SeriesInstanceUID', render: function (data, type, row){
-                          if("showDirectoryPicker" in window) {
-                            return `<i class="fa fa-download download-all-instances download-instances" data-bucket="${row['aws_bucket']}" 
-                                data-series="${row['crdc_series_uuid']}" 
-                                data-series-id="${row['SeriesInstanceUID']}" 
-                                data-modality="${row['Modality']}" 
-                                data-collection="${row['collection_id']}" 
-                                data-study="${row['StudyInstanceUID']}" 
-                                data-patient="${row['PatientID']}" 
-                                data-series-size="${row['instance_size']}"                                                 
-                                ></i>`
-                          }
-                          return `<i class="fa fa-download is-disabled download-instances" data-disabled-type="download-all-disabled"></i>`
-                      }
                   }
             ],
             "processing": true,
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
index 74bd06359..9144cf7ae 100644
--- a/templates/idc/explore_data_core.html
+++ b/templates/idc/explore_data_core.html
@@ -867,12 +867,11 @@ <h4 class="panel-title">
                                                 <i class="fa-solid fa-plus-circle fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                                 <i class="fa-solid fa-circle-minus fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                             </th>
+                                            <th class="download-col download-collex"></th>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>
-                                            <th class="ckbx cartnumholder"># of Series in Cart</th>
+                                            <th class="ckbx cartnumholder"># Series in Cart</th>
                                             <th class="collex_name sorting_1">Collection Name</th>
-                                            <th class="numeric_data table-count">Total # of Cases</th>
-                                            <th class="numeric_data table-count"># of Cases (filtered)</th>
-                                            <th class="download-col download-collex"></th>
+                                            <th class="numeric_data table-count">Cases (Total / Filtered)</th>
                                         </tr>
                                         </thead>
                                     </table>
@@ -891,13 +890,13 @@ <h4 class="panel-title">
                                                 <i class="fa-solid fa-plus-circle fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                                 <i class="fa-solid fa-circle-minus fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                             </th>
+                                            <th class="download-case download-col"></th>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>
-                                            <th class="ckbx cartnumholder"># of Series in Cart</th>
+                                            <th class="ckbx cartnumholder"># Series in Cart</th>
                                             <th class="text_data wide">Collection Name</th>
                                             <th class="text_data">Case ID <i class="fas fa-info-circle case-info"></i></th>
-                                            <th class="numeric_data narrow">Total # of Studies</th>
-                                            <th class="numeric_data narrow">Total # of Series</th>
-                                            <th class="download-case download-col"></th>
+                                            <th class="numeric_data narrow"># Studies</th>
+                                            <th class="numeric_data narrow"># Series</th>
                                         </tr>
                                         </thead>
                                     </table>
@@ -915,16 +914,16 @@ <h4 class="panel-title">
                                                  <i class="fa-solid fa-plus-circle fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                                 <i class="fa-solid fa-circle-minus fa-lg addMult" style="font-family :'Font Awesome 6 Free' !important"></i>
                                             </th>
+                                            <th class="download-col download-study"></th>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>
-                                            <th class="ckbx cartnumholder"># of Series in Cart</th>
+                                            <th class="ckbx cartnumholder"># Series in Cart</th>
                                             <th class="col1 text_data case-id has_aux" data-auxid="3">Case ID <i class="fas fa-info-circle case-info"></i></th>
                                             <th class="col2 text_data study-id study-id-col">Study Instance UID</th>
                                             <th class="col1 text_data study-date">Study Date</th>
                                             <th class="col1 text_data study-description">Study Description</th>
-                                            <th class="col1 numrows numeric_data table-count"># of Series</th>
+                                            <th class="col1 numrows numeric_data table-count"># Series</th>
                                             <th class="ohif text_data open-viewer">View</th>
                                             <th class="manifest-col"></th>
-                                            <th class="download-col download-study"></th>
                                         </tr>
                                         </thead>
                                     </table>
@@ -938,6 +937,7 @@ <h4 class="panel-title">
                                     <table id="series_tab" class="table table-striped series-table" data-table-type="series">
                                         <thead id="series_table_head">
                                         <tr>
+                                            <th class="download-files dowbload-series download-col"></th>
                                             <th class="ckbx cart-info"><i class="fa-solid fa-info-circle cart-info-icon"></i></th>
                                             <th class="study-id">Study Instance UID</th>
                                             <th class="series-id ">Series Instance UID</th>
@@ -947,7 +947,6 @@ <h4 class="panel-title">
                                             <th class="series-description">Series Description</th>
                                             <th class="open-viewer text_data">View</th>
                                             <th class="download-manifest"></th>
-                                            <th class="download-files dowbload-series download-col"></th>
                                         </tr>
                                         </thead>
                                     </table>

From f0d8bd173285a38554284bda8dd89f65dc8e00fa Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Fri, 7 Nov 2025 13:34:42 -0800
Subject: [PATCH 22/25] -> #1509

---
 static/css/search.css | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/static/css/search.css b/static/css/search.css
index 2f345850b..395e97bd7 100644
--- a/static/css/search.css
+++ b/static/css/search.css
@@ -417,15 +417,16 @@ tr {
 #cases_table_head th.ckbx:not(.cartnumholder), #cases_table td.ckbx:not(.cartnumholder),
 #studies_table_head th.ckbx:not(.cartnumholder), #studies_table td.ckbx:not(.cartnumholder),
 #series_table_head th.ckbx, #series_table td.ckbx {
-    width: 5%;
+    width: 3%;
     text-align: left !important;
+    min-width: 40px;
 }
 
 #search_def_stats {
     padding-top: 8px; }
 
 #projects_table td, #projects_table_head th {
-    width: 40%;
+    width: 45%;
     word-wrap: break-word; }
 
 #cases_table td, #cases_table_head th {
@@ -483,8 +484,8 @@ tr {
 #studies_table td.download-col, #cases_table_head th.download-col,
 #cases_table td.download-col, #series_table_head th.download-col,
 #series_table td.download-col, #proj_table th.download-col, #proj_table td.download-col {
-    width:6%;
-    min-width: 60px;
+    width:3%;
+    min-width: 40px;
 }
 
 #series_table_head th, #series_table td {

From b68b5ccff7fbd7fc5a86d1d7a970e285707459d9 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 10 Nov 2025 10:11:58 -0800
Subject: [PATCH 23/25] -> Bugfix for smaller filtered downloads

---
 static/js/image_search.js |  5 +----
 static/js/utils.js        | 13 +++++++++----
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/static/js/image_search.js b/static/js/image_search.js
index 820070ebc..4b6074f92 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -184,8 +184,6 @@ require([
                         $('#search_def_access').addClass('is-hidden');
                         $('.access_warn').addClass('is-hidden');
                     }
-                    let download_btn = $('#download-cohort-images');
-                    let download_btn_tips = $('#download-cohort-images-tooltips');
                     if(isFiltered && data.total > 0) {
                         $('#search_def_stats').html("Cohort filter contents: " +
                             data.totals.SeriesInstanceUID.toString() + " series from " +
@@ -193,8 +191,7 @@ require([
                             data.totals.StudyInstanceUID.toString() + " studies (Size on disk: " +
                             data.totals.disk_size + ")"
                         );
-                        base.updateDownloadBtns("cohort", true, parseFloat(data.totals.disk_size.split(" ")[0]));
-
+                        base.updateDownloadBtns("cohort", true, data.totals.disk_size_tb);
                     } else if(isFiltered && data.total <= 0) {
                         $('#search_def_stats').html('<span style="color:red">There are no cases matching the selected set of filters</span>');
                     } else {
diff --git a/static/js/utils.js b/static/js/utils.js
index 070fbc7d8..5d3a53b40 100644
--- a/static/js/utils.js
+++ b/static/js/utils.js
@@ -41,6 +41,9 @@ require.config({
 
 // Return an object for consts/methods used by most views
 define(['jquery', 'jqueryui'], function($, jqueryui) {
+    // Terabyte cutoffs for download button tooltips and enabling
+    let DOWNLOAD_SIZE_LIMIT = 3;
+    let DOWNLOAD_SIZE_WARN = 2;
 
     // Download block poll with cookie via StackOverflow:
     // https://stackoverflow.com/questions/1106377/detect-when-browser-receives-file-download
@@ -142,8 +145,10 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
         _hideFloatingMessage(true);
     });
 
-
-        // Enabled is equivalent to 'is there a filter' or 'is something in the cart'
+    // type - string, ID selector subtype for the buttons and tooltips to adjust
+    // enabled - bool, sets if the button is to be disabled or enabled
+    // disk_size - size for determining size limit enabling and tooltip message, is assumed to be in TB
+    // requires setting DOWNLOAD_SIZE_LIMIT and DOWNLOAD_SIZE_WARN
     function _updateDownloadBtns(type, enabled, disk_size) {
         let btn = $(`#download-${type}-images`);
         let btn_tip = $(`#download-${type}-images-tooltips`);
@@ -156,14 +161,14 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
         }
         if ("showDirectoryPicker" in window) {
             btn_and_tips.removeClass('is-disabled download-all-instances download-size-warning');
-            if (disk_size > 3) {
+            if (disk_size > DOWNLOAD_SIZE_LIMIT) {
                 btn_tip.addClass('is-disabled');
                 btn_tip.attr('data-disabled-type', "download-size-disabled");
                 btn.attr("disabled", "disabled");
             } else {
                 btn.removeAttr("disabled");
                 btn_tip.attr('data-disabled-type', "");
-                (disk_size > 2) ? btn.addClass('download-size-warning') : btn.addClass('download-all-instances');
+                (disk_size > DOWNLOAD_SIZE_WARN) ? btn.addClass('download-size-warning') : btn.addClass('download-all-instances');
             }
         } else {
             btn_tip.addClass('is-disabled');

From d33ff194d0caf05a80d4ca89aa277d0b87d32831 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 10 Nov 2025 10:36:07 -0800
Subject: [PATCH 24/25] -> >65k records, direct download shunts user to
 manifests/CLI

---
 static/js/cartutils.js    |  4 +-
 static/js/downloader.js   | 84 +++++++++++++++++++--------------------
 static/js/explore.js      |  1 +
 static/js/image_search.js |  4 +-
 static/js/utils.js        | 11 ++---
 5 files changed, 51 insertions(+), 53 deletions(-)

diff --git a/static/js/cartutils.js b/static/js/cartutils.js
index 7cec9580e..90065542c 100644
--- a/static/js/cartutils.js
+++ b/static/js/cartutils.js
@@ -126,11 +126,11 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
         var buttonContents = '<button class="btn filter-type clear-cart" role="button" title="Empty your cart."><i class="fa fa-rotate-left"></i></button>';
         let cart_has_contents = Boolean(Object.keys(window.proj_in_cart).length>0);
         let cart_controls = $('.cart-activated-controls');
+        var nmseries = 0;
         if (cart_has_contents){
             var nmprojs = 0;
             var nmcases=0;
             var nmstudies=0;
-            var nmseries =0;
             for (projid in window.proj_in_cart){
                 nmprojs++;
                 nmcases=nmcases+window.proj_in_cart[projid]['cases'];
@@ -176,7 +176,7 @@ define(['filterutils','jquery', 'tippy', 'base' ], function(filterutils, $,  tip
             cart_disk_display_size = cart_disk_res['display_size'];
         }
         $('.cart_disk_size').html(cart_disk_display_size);
-        base.updateDownloadBtns('cart', cart_has_contents, cart_disk_size);
+        base.updateDownloadBtns('cart', cart_has_contents, cart_disk_size, nmseries);
 
     }
 
diff --git a/static/js/downloader.js b/static/js/downloader.js
index 2e5fe9b1b..a550a3042 100644
--- a/static/js/downloader.js
+++ b/static/js/downloader.js
@@ -785,53 +785,49 @@ require([
 
         let series = [];
         if(download_type !== "series") {
-            if(parseInt(clicked.attr('data-total-series')) > 65000) {
-
-            } else {
-                let response = null;
-                if(["cohort", "cart"].includes(download_type)) {
-                    downloader_manager.pendingFetchMessage(download_type);
-                    let filter_and_cart = {};
-                    if (download_type === "cohort") {
-                        let filtergrp_list = [];
-                        for(const [attr, vals] of Object.entries(filterutils.parseFilterObj())) {
-                            filtergrp_list.push({[attr]: vals});
-                        }
-                        filter_and_cart["filtergrp_list"] = filtergrp_list;
-                    } else {
-                         window.updatePartitionsFromScratch();
-                         let ret = cartutils.formcartdata();
-                         window.partitions = ret[0];
-                         window.filtergrp_lst = ret[1];
-                        let filterSets = [];
-                        for(let i=0; i< window.cartHist.length;i++) {
-                           filterSets.push(window.cartHist[i]['filter']);
-                        }
-                        filter_and_cart['partitions'] = window.partitions;
-                        filter_and_cart['filtergrp_list'] = filterSets;
+            let response = null;
+            if(["cohort", "cart"].includes(download_type)) {
+                downloader_manager.pendingFetchMessage(download_type);
+                let filter_and_cart = {};
+                if (download_type === "cohort") {
+                    let filtergrp_list = [];
+                    for(const [attr, vals] of Object.entries(filterutils.parseFilterObj())) {
+                        filtergrp_list.push({[attr]: vals});
                     }
-                    response = await fetch(`${BASE_URL}${SERIES_IDS_FILTER_URL}`, {
-                            method: "POST",
-                            body: JSON.stringify(filter_and_cart),
-                            headers: {
-                                "X-CSRFToken": csrftoken,
-                                "content-type": "application/json"
-                            }
-                        });
+                    filter_and_cart["filtergrp_list"] = filtergrp_list;
                 } else {
-                    let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
-                    let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
-                    response = await fetch(`${BASE_URL}${SERIES_IDS_URL}${collection_id}/${patient_uri}${study_uri}`);
-                }
-                if (!response.ok) {
-                    console.error(`[ERROR] Failed to retrieve series IDs: ${response.status}`);
-                    return;
-                }
-                const series_data = await response.json();
-                series.push(...series_data['result']);
-                if('download_stats' in series_data){
-                    downloader_manager.set_download_stats(series_data['download_stats']);
+                     window.updatePartitionsFromScratch();
+                     let ret = cartutils.formcartdata();
+                     window.partitions = ret[0];
+                     window.filtergrp_lst = ret[1];
+                    let filterSets = [];
+                    for(let i=0; i< window.cartHist.length;i++) {
+                       filterSets.push(window.cartHist[i]['filter']);
+                    }
+                    filter_and_cart['partitions'] = window.partitions;
+                    filter_and_cart['filtergrp_list'] = filterSets;
                 }
+                response = await fetch(`${BASE_URL}${SERIES_IDS_FILTER_URL}`, {
+                        method: "POST",
+                        body: JSON.stringify(filter_and_cart),
+                        headers: {
+                            "X-CSRFToken": csrftoken,
+                            "content-type": "application/json"
+                        }
+                    });
+            } else {
+                let study_uri = (study_id !== undefined && study_id !== null) ? `${study_id}/` : "";
+                let patient_uri = (patient_id !== undefined && patient_id !== null) ? `${patient_id}/` : "";
+                response = await fetch(`${BASE_URL}${SERIES_IDS_URL}${collection_id}/${patient_uri}${study_uri}`);
+            }
+            if (!response.ok) {
+                console.error(`[ERROR] Failed to retrieve series IDs: ${response.status}`);
+                return;
+            }
+            const series_data = await response.json();
+            series.push(...series_data['result']);
+            if('download_stats' in series_data){
+                downloader_manager.set_download_stats(series_data['download_stats']);
             }
         } else {
             series.push({
diff --git a/static/js/explore.js b/static/js/explore.js
index 1441e3c5f..beb5d8724 100644
--- a/static/js/explore.js
+++ b/static/js/explore.js
@@ -482,6 +482,7 @@ require([
     let disabled_messages = {
         'download-all-disabled': chromium_only,
         'download-size-disabled': "This set of images is over 3TB in size. Please use manifest download to obtain these images.",
+        'download-count-disabled': "This set of images contains over 65000 records. Please use manifest download to obtain these images.",
         'download-cart-disabled': "Add items to the cart to enable this feature.",
         'download-cohort-disabled': "Select a filter to enable this feature."
     };
diff --git a/static/js/image_search.js b/static/js/image_search.js
index 4b6074f92..473aa7e80 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -191,12 +191,12 @@ require([
                             data.totals.StudyInstanceUID.toString() + " studies (Size on disk: " +
                             data.totals.disk_size + ")"
                         );
-                        base.updateDownloadBtns("cohort", true, data.totals.disk_size_tb);
+                        base.updateDownloadBtns("cohort", true, data.totals.disk_size_tb, data.totals.SeriesInstanceUID);
                     } else if(isFiltered && data.total <= 0) {
                         $('#search_def_stats').html('<span style="color:red">There are no cases matching the selected set of filters</span>');
                     } else {
                         $('#search_def_stats').html("&nbsp;");
-                        base.updateDownloadBtns("cohort", false, 0);
+                        base.updateDownloadBtns("cohort", false, 0, 0);
                     }
 
                     filterutils.updateCollectionTotals('Program', data.programs);
diff --git a/static/js/utils.js b/static/js/utils.js
index 5d3a53b40..4ddb5fb11 100644
--- a/static/js/utils.js
+++ b/static/js/utils.js
@@ -41,9 +41,10 @@ require.config({
 
 // Return an object for consts/methods used by most views
 define(['jquery', 'jqueryui'], function($, jqueryui) {
-    // Terabyte cutoffs for download button tooltips and enabling
+    // Terabyte and record count warning and cutoffs for download button tooltips and enabling
     let DOWNLOAD_SIZE_LIMIT = 3;
     let DOWNLOAD_SIZE_WARN = 2;
+    let DOWNLOAD_COUNT_LIMIT = 65000;
 
     // Download block poll with cookie via StackOverflow:
     // https://stackoverflow.com/questions/1106377/detect-when-browser-receives-file-download
@@ -148,8 +149,8 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
     // type - string, ID selector subtype for the buttons and tooltips to adjust
     // enabled - bool, sets if the button is to be disabled or enabled
     // disk_size - size for determining size limit enabling and tooltip message, is assumed to be in TB
-    // requires setting DOWNLOAD_SIZE_LIMIT and DOWNLOAD_SIZE_WARN
-    function _updateDownloadBtns(type, enabled, disk_size) {
+    // requires setting DOWNLOAD_COUNT_LIMIT, DOWNLOAD_SIZE_LIMIT, and DOWNLOAD_SIZE_WARN
+    function _updateDownloadBtns(type, enabled, disk_size, record_count) {
         let btn = $(`#download-${type}-images`);
         let btn_tip = $(`#download-${type}-images-tooltips`);
         let btn_and_tips = $(`#download-${type}-images-tooltips, #download-${type}-images-tooltips`);
@@ -161,10 +162,10 @@ define(['jquery', 'jqueryui'], function($, jqueryui) {
         }
         if ("showDirectoryPicker" in window) {
             btn_and_tips.removeClass('is-disabled download-all-instances download-size-warning');
-            if (disk_size > DOWNLOAD_SIZE_LIMIT) {
+            if (disk_size > DOWNLOAD_SIZE_LIMIT || record_count > DOWNLOAD_COUNT_LIMIT) {
                 btn_tip.addClass('is-disabled');
-                btn_tip.attr('data-disabled-type', "download-size-disabled");
                 btn.attr("disabled", "disabled");
+                btn_tip.attr('data-disabled-type', (disk_size > DOWNLOAD_SIZE_LIMIT ? "download-size-disabled" : "download-count-disabled"));
             } else {
                 btn.removeAttr("disabled");
                 btn_tip.attr('data-disabled-type', "");

From 82fa61df73a0cf07625954a69772cf0117c88863 Mon Sep 17 00:00:00 2001
From: "S. Paquette" <spaquett@systemsbiology.org>
Date: Mon, 10 Nov 2025 10:53:55 -0800
Subject: [PATCH 25/25] -> Properly disable the citations button if there are
 no records for the filter set.

---
 static/js/filterutils.js  | 1 -
 static/js/image_search.js | 3 +++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/static/js/filterutils.js b/static/js/filterutils.js
index 583e9c069..75f63e70a 100644
--- a/static/js/filterutils.js
+++ b/static/js/filterutils.js
@@ -643,7 +643,6 @@ define(['jquery', 'base'], function($, base) {
         window.handleFilterSelectionUpdate(null, true, true);
     }
 
-
     window.handleFilterSelectionUpdate = function(filterElem, mkFilt, doUpdate) {
         var promise =  null
         if (!(filterElem ===null)) {
diff --git a/static/js/image_search.js b/static/js/image_search.js
index 473aa7e80..556d2484e 100644
--- a/static/js/image_search.js
+++ b/static/js/image_search.js
@@ -194,6 +194,9 @@ require([
                         base.updateDownloadBtns("cohort", true, data.totals.disk_size_tb, data.totals.SeriesInstanceUID);
                     } else if(isFiltered && data.total <= 0) {
                         $('#search_def_stats').html('<span style="color:red">There are no cases matching the selected set of filters</span>');
+                        base.updateDownloadBtns("cohort", false, 0, 0);
+                        $('.citations-button').attr("disabled","disabled");
+                        $('.citations-button').attr("title", "There are no cases matching the selected set of filters");
                     } else {
                         $('#search_def_stats').html("&nbsp;");
                         base.updateDownloadBtns("cohort", false, 0, 0);