From f9d5199a52929b81d0d5bc3f88f07b883bcc98ac Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 10:41:38 +0200
Subject: [PATCH 01/21] increased max_length for bioinfo analysis values

---
 core/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/core/models.py b/core/models.py
index 3ecbe12a..ed092c5b 100644
--- a/core/models.py
+++ b/core/models.py
@@ -413,7 +413,7 @@ def create_new_value(self, data):
 
 
 class BioinfoAnalysisValue(models.Model):
-    value = models.CharField(max_length=400, null=True, blank=True)
+    value = models.CharField(max_length=1000, null=True, blank=True)
     bioinfo_analysis_fieldID = models.ForeignKey(
         BioinfoAnalysisField, on_delete=models.CASCADE
     )

From 2a468139c7a965a1b1983086d1ec91f94794c115 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 12:46:47 +0200
Subject: [PATCH 02/21] Added multiple selection check box to Collecting
 Institution

---
 core/templates/core/searchSample.html | 161 +++++++++++++++++++++++++-
 core/views.py                         |  15 ++-
 2 files changed, 170 insertions(+), 6 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 6f90c5e5..723d7121 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -25,12 +25,83 @@
     #sample_list th:nth-child(2) input {
       white-space: nowrap;
     }
+    #sample_list thead tr.filter-row th {
+      vertical-align: top;
+    }
+    #sample_list thead tr.filter-row th input,
+    #sample_list thead tr.filter-row th select {
+      margin-top: 0;
+    }
     #sample_list th:last-child,
     #sample_list td:last-child {
       min-width: 260px;
+      white-space: normal;
+      overflow-wrap: anywhere;
+    }
+    #sample_list thead tr.filter-row th:last-child .institution-search-wrapper,
+    #sample_list thead tr.filter-row th:last-child button:not(.institution-search-clear),
+    #sample_list .institution-filter-options {
+      width: 100%;
+      max-width: 100%;
+      box-sizing: border-box;
+    }
+    #sample_list .institution-search-wrapper {
+      position: relative;
+    }
+    #sample_list .institution-search-wrapper input {
+      padding-right: 1.8rem;
+    }
+    #sample_list .institution-search-clear {
+      position: absolute;
+      top: 50%;
+      right: 0.45rem;
+      transform: translateY(-50%);
+      border: 0;
+      background: transparent;
+      color: #6c757d;
+      line-height: 1;
+      padding: 0;
+      width: 1rem;
+      height: 1rem;
     }
-    #sample_list thead tr.filter-row th:last-child select {
-      min-width: 220px;
+    #sample_list .institution-search-clear:hover,
+    #sample_list .institution-search-clear:focus {
+      color: var(--color-primary);
+      outline: none;
+    }
+    #sample_list thead tr.filter-row th:last-child button:not(.institution-search-clear) {
+      white-space: normal;
+    }
+    #sample_list .institution-filter-options {
+      max-height: 8rem;
+      overflow-x: hidden;
+      overflow-y: auto;
+      border: 1px solid #ced4da;
+      border-radius: 0.25rem;
+      background: #fff;
+      padding: 0.35rem 0.5rem;
+    }
+    #sample_list .institution-filter-option {
+      display: flex;
+      align-items: flex-start;
+      gap: 0.4rem;
+      font-size: 0.82rem;
+      font-weight: 400;
+      line-height: 1.15;
+      padding: 0.2rem 0;
+      white-space: normal;
+      overflow-wrap: anywhere;
+    }
+    #sample_list .institution-filter-option input {
+      flex: 0 0 auto;
+      margin-top: 0.15rem;
+    }
+    #sample_list .institution-filter-option span {
+      display: -webkit-box;
+      -webkit-box-orient: vertical;
+      -webkit-line-clamp: 3;
+      overflow: hidden;
+      overflow-wrap: anywhere;
     }
     #sample_list a.sample-browser-link {
       color: var(--color-blue);
@@ -207,7 +278,7 @@ <h1>Sample Browser</h1>
                                                     });
                                                 });
 
-                                                [2, 3].forEach(function(index) {
+                                                [2].forEach(function(index) {
                                                     var column = api.column(index);
                                                     var headerCell = $('.filter-row th').eq(index);  // Use the empty row for filters
                                                     var columnName = $('.dataTable thead tr:first th').eq(index).text().trim();
@@ -223,11 +294,91 @@ <h1>Sample Browser</h1>
                                                             column.search($(this).val(), false, false).draw();
                                                         });
 
-                                                    var options = index === 2 ? lineageOptions : institutionOptions;
-                                                    options.forEach(function (d) {
+                                                    lineageOptions.forEach(function (d) {
                                                         select.append('<option value="' + d + '">' + d + '</option>')
                                                     });
                                                 });
+
+                                                [3].forEach(function(index) {
+                                                    var column = api.column(index);
+                                                    var headerCell = $('.filter-row th').eq(index);
+                                                    var columnName = $('.dataTable thead tr:first th').eq(index).text().trim();
+                                                    var selectedInstitutions = [];
+                                                    headerCell.empty();
+                                                    var searchWrapper = $('<div class="institution-search-wrapper mb-1"></div>')
+                                                        .appendTo(headerCell)
+                                                        .on('click mousedown keydown touchstart', function (event) {
+                                                            event.stopPropagation();
+                                                        });
+                                                    var searchInput = $('<input type="text" class="form-control form-control-sm" placeholder="Search hospitals..." />')
+                                                        .appendTo(searchWrapper);
+                                                    $('<button type="button" class="institution-search-clear" aria-label="Clear hospital search">x</button>')
+                                                        .appendTo(searchWrapper)
+                                                        .on('click', function (event) {
+                                                            event.preventDefault();
+                                                            event.stopPropagation();
+                                                            searchInput.val('');
+                                                            renderInstitutionOptions('');
+                                                            searchInput.trigger('focus');
+                                                        });
+                                                    $('<button type="button" class="btn btn-outline-secondary btn-sm mb-1">Remove filter of ' + columnName + '</button>')
+                                                        .appendTo(headerCell)
+                                                        .on('click mousedown keydown touchstart', function (event) {
+                                                            event.stopPropagation();
+                                                        })
+                                                        .on('click', function () {
+                                                            selectedInstitutions = [];
+                                                            searchInput.val('');
+                                                            column.search('', false, false).draw();
+                                                            renderInstitutionOptions('');
+                                                        });
+                                                    var optionContainer = $('<div class="institution-filter-options"></div>')
+                                                        .appendTo(headerCell)
+                                                        .on('click mousedown keydown touchstart', function (event) {
+                                                            event.stopPropagation();
+                                                        });
+
+                                                    function updateInstitutionSearch() {
+                                                        column.search(selectedInstitutions.length ? JSON.stringify(selectedInstitutions) : '', false, false).draw();
+                                                    }
+
+                                                    function renderInstitutionOptions(searchText) {
+                                                        var orderedOptions = selectedInstitutions.concat(
+                                                            institutionOptions.filter(function (d) {
+                                                                return selectedInstitutions.indexOf(d) === -1;
+                                                            })
+                                                        );
+                                                        optionContainer.empty();
+                                                        orderedOptions.forEach(function (d) {
+                                                            if (searchText && d.toLowerCase().indexOf(searchText) === -1 && selectedInstitutions.indexOf(d) === -1) {
+                                                                return;
+                                                            }
+                                                            var optionId = 'institution-filter-' + Math.abs(d.split('').reduce(function (acc, char) {
+                                                                return ((acc << 5) - acc) + char.charCodeAt(0);
+                                                            }, 0));
+                                                            var label = $('<label class="institution-filter-option" for="' + optionId + '"></label>');
+                                                            var checkbox = $('<input type="checkbox" id="' + optionId + '" />')
+                                                                .prop('checked', selectedInstitutions.indexOf(d) !== -1)
+                                                                .on('change', function () {
+                                                                    if (this.checked && selectedInstitutions.indexOf(d) === -1) {
+                                                                        selectedInstitutions.push(d);
+                                                                    } else if (!this.checked) {
+                                                                        selectedInstitutions = selectedInstitutions.filter(function (value) {
+                                                                            return value !== d;
+                                                                        });
+                                                                    }
+                                                                    updateInstitutionSearch();
+                                                                    renderInstitutionOptions(searchInput.val().toLowerCase());
+                                                                });
+                                                            label.append(checkbox).append($('<span></span>').text(d));
+                                                            optionContainer.append(label);
+                                                        });
+                                                    }
+                                                    renderInstitutionOptions('');
+                                                    searchInput.on('keyup change clear', function () {
+                                                        renderInstitutionOptions($(this).val().toLowerCase());
+                                                    });
+                                                });
                                                 // Hide the loading message
                                                 $('#sample_loading_msg').hide();
                                                 // Now show the table
diff --git a/core/views.py b/core/views.py
index e7c4411c..2c168e23 100644
--- a/core/views.py
+++ b/core/views.py
@@ -1,5 +1,6 @@
 # Generic imports
 from datetime import datetime
+import json
 from collections import defaultdict, OrderedDict
 import re
 from django.shortcuts import render, redirect
@@ -65,10 +66,17 @@ def _get_search_sample_rows_for_user(user_obj):
     ]
 
 
-def _normalize_datatable_search_value(value, regex=False):
+def _normalize_datatable_search_value(value, regex=False, json_list=False):
     """Normalize DataTables search values, including escaped exact-match regexes."""
     if not value:
         return ""
+    if json_list and value.startswith("[") and value.endswith("]"):
+        try:
+            return [
+                str(item).strip() for item in json.loads(value) if str(item).strip()
+            ]
+        except (TypeError, ValueError, json.JSONDecodeError):
+            pass
     if regex and value.startswith("^") and value.endswith("$"):
         value = value[1:-1]
         # DataTables' escapeRegex() prefixes regex metacharacters with a
@@ -92,6 +100,10 @@ def _row_matches_search(row, global_search, column_filters):
         if not search_value:
             continue
         candidate = str(row[field_name] or "")
+        if isinstance(search_value, list):
+            if candidate not in search_value:
+                return False
+            continue
         if exact_match:
             if candidate != search_value:
                 return False
@@ -315,6 +327,7 @@ def search_sample_data(request):
             request.GET.get(f"columns[{index}][search][value]", ""),
             request.GET.get(f"columns[{index}][search][regex]", "false").lower()
             == "true",
+            index == 3,
         )
         exact_match = index in (2, 3)
         column_filters.append((field_name, search_value, exact_match))

From 72ab8a8274b0ada7a7a06cddbde8fe5fed3b308e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 13:14:27 +0200
Subject: [PATCH 03/21] Add Lineage and Institution filters refresh based on
 other filters

---
 core/templates/core/searchSample.html | 35 ++++++++++++++++++++++++---
 core/views.py                         | 30 +++++++++++++++++++++++
 2 files changed, 61 insertions(+), 4 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 723d7121..f7836d50 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -214,6 +214,8 @@ <h1>Sample Browser</h1>
                                     $(document).ready(function() {
                                         var lineageOptions = JSON.parse(document.getElementById('search-sample-lineage-options').textContent);
                                         var institutionOptions = JSON.parse(document.getElementById('search-sample-institution-options').textContent);
+                                        var refreshLineageOptions = null;
+                                        var refreshInstitutionOptions = null;
                                         var sampleUrlTemplate = "{% url 'sample_display' 0 %}";
 
                                         function escapeHtml(value) {
@@ -242,6 +244,18 @@ <h1>Sample Browser</h1>
                                                         );
                                                         return [];
                                                     }
+                                                    if (json.lineage_options) {
+                                                        lineageOptions = json.lineage_options;
+                                                        if (refreshLineageOptions) {
+                                                            refreshLineageOptions();
+                                                        }
+                                                    }
+                                                    if (json.collecting_institution_options) {
+                                                        institutionOptions = json.collecting_institution_options;
+                                                        if (refreshInstitutionOptions) {
+                                                            refreshInstitutionOptions();
+                                                        }
+                                                    }
                                                     return json.data || [];
                                                 }
                                             },
@@ -282,7 +296,7 @@ <h1>Sample Browser</h1>
                                                     var column = api.column(index);
                                                     var headerCell = $('.filter-row th').eq(index);  // Use the empty row for filters
                                                     var columnName = $('.dataTable thead tr:first th').eq(index).text().trim();
-                                                    var select = $('<select class="form-select form-select-sm"><option value="">Filter by ' + columnName + '</option></select>')
+                                                    var select = $('<select class="form-select form-select-sm"></select>')
                                                         .appendTo($(headerCell.empty()))
                                                         .on('click mousedown keydown touchstart', function (event) {
                                                             event.stopPropagation();
@@ -294,9 +308,19 @@ <h1>Sample Browser</h1>
                                                             column.search($(this).val(), false, false).draw();
                                                         });
 
-                                                    lineageOptions.forEach(function (d) {
-                                                        select.append('<option value="' + d + '">' + d + '</option>')
-                                                    });
+                                                    function renderLineageOptions() {
+                                                        var selectedLineage = select.val() || column.search();
+                                                        select.empty().append('<option value="">Filter by ' + columnName + '</option>');
+                                                        lineageOptions.forEach(function (d) {
+                                                            select.append($('<option></option>').val(d).text(d));
+                                                        });
+                                                        if (selectedLineage && lineageOptions.indexOf(selectedLineage) === -1) {
+                                                            select.append($('<option></option>').val(selectedLineage).text(selectedLineage));
+                                                        }
+                                                        select.val(selectedLineage);
+                                                    }
+                                                    refreshLineageOptions = renderLineageOptions;
+                                                    renderLineageOptions();
                                                 });
 
                                                 [3].forEach(function(index) {
@@ -374,6 +398,9 @@ <h1>Sample Browser</h1>
                                                             optionContainer.append(label);
                                                         });
                                                     }
+                                                    refreshInstitutionOptions = function () {
+                                                        renderInstitutionOptions(searchInput.val().toLowerCase());
+                                                    };
                                                     renderInstitutionOptions('');
                                                     searchInput.on('keyup change clear', function () {
                                                         renderInstitutionOptions($(this).val().toLowerCase());
diff --git a/core/views.py b/core/views.py
index 2c168e23..5e222379 100644
--- a/core/views.py
+++ b/core/views.py
@@ -338,6 +338,34 @@ def search_sample_data(request):
         if _row_matches_search(row, global_search, column_filters)
     ]
 
+    lineage_option_filters = [
+        column_filter
+        for column_filter in column_filters
+        if column_filter[0] != "lineage"
+    ]
+    lineage_options = sorted(
+        {
+            row["lineage"]
+            for row in sample_rows
+            if row["lineage"]
+            and _row_matches_search(row, global_search, lineage_option_filters)
+        }
+    )
+
+    institution_option_filters = [
+        column_filter
+        for column_filter in column_filters
+        if column_filter[0] != "collecting_institution"
+    ]
+    collecting_institution_options = sorted(
+        {
+            row["collecting_institution"]
+            for row in sample_rows
+            if row["collecting_institution"]
+            and _row_matches_search(row, global_search, institution_option_filters)
+        }
+    )
+
     order_column = request.GET.get("order[0][column]")
     order_direction = request.GET.get("order[0][dir]", "asc")
     if order_column is not None:
@@ -362,6 +390,8 @@ def search_sample_data(request):
             "recordsTotal": len(sample_rows),
             "recordsFiltered": len(filtered_rows),
             "data": paginated_rows,
+            "lineage_options": lineage_options,
+            "collecting_institution_options": collecting_institution_options,
         }
     )
 

From 9eaefdc8d8195c894c18fa78e40b6a5414b359cb Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 13:24:38 +0200
Subject: [PATCH 04/21] Added button to clear sample filter

---
 core/templates/core/searchSample.html | 34 +++++++++++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index f7836d50..93897cbf 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -17,6 +17,12 @@
     #sample_list th:first-child input {
       white-space: nowrap;
     }
+    #sample_list .sample-id-search-wrapper {
+      position: relative;
+    }
+    #sample_list .sample-id-search-wrapper input {
+      padding-right: 1.8rem;
+    }
     #sample_list th:nth-child(2),
     #sample_list td:nth-child(2) {
       min-width: 135px;
@@ -51,6 +57,7 @@
     #sample_list .institution-search-wrapper input {
       padding-right: 1.8rem;
     }
+    #sample_list .sample-id-search-clear,
     #sample_list .institution-search-clear {
       position: absolute;
       top: 50%;
@@ -64,6 +71,8 @@
       width: 1rem;
       height: 1rem;
     }
+    #sample_list .sample-id-search-clear:hover,
+    #sample_list .sample-id-search-clear:focus,
     #sample_list .institution-search-clear:hover,
     #sample_list .institution-search-clear:focus {
       color: var(--color-primary);
@@ -280,8 +289,16 @@ <h1>Sample Browser</h1>
                                                 [0, 1].forEach(function(index) {
                                                   var column = api.column(index);
                                                   var headerCell = $('.filter-row th').eq(index);
+                                                  var inputContainer = headerCell.empty();
+                                                  if (index === 0) {
+                                                    inputContainer = $('<div class="sample-id-search-wrapper"></div>')
+                                                      .appendTo(headerCell)
+                                                      .on('click mousedown keydown touchstart', function (event) {
+                                                        event.stopPropagation();
+                                                      });
+                                                  }
                                                   var input = $('<input type="text" class="form-control form-control-sm" placeholder="Type to search..." />')
-                                                    .appendTo(headerCell.empty())
+                                                    .appendTo(inputContainer)
                                                     .on('click mousedown keydown touchstart', function (event) {
                                                       event.stopPropagation();
                                                     })
@@ -290,6 +307,19 @@ <h1>Sample Browser</h1>
                                                         column.search(this.value).draw();
                                                       }
                                                     });
+                                                  if (index === 0) {
+                                                    $('<button type="button" class="sample-id-search-clear" aria-label="Clear sample sequencing ID search">x</button>')
+                                                      .appendTo(inputContainer)
+                                                      .on('click', function (event) {
+                                                        event.preventDefault();
+                                                        event.stopPropagation();
+                                                        input.val('');
+                                                        if (column.search()) {
+                                                          column.search('').draw();
+                                                        }
+                                                        input.trigger('focus');
+                                                      });
+                                                  }
                                                 });
 
                                                 [2].forEach(function(index) {
@@ -310,7 +340,7 @@ <h1>Sample Browser</h1>
 
                                                     function renderLineageOptions() {
                                                         var selectedLineage = select.val() || column.search();
-                                                        select.empty().append('<option value="">Filter by ' + columnName + '</option>');
+                                                        select.empty().append('<option value="">Clear ' + columnName + 'filter </option>');
                                                         lineageOptions.forEach(function (d) {
                                                             select.append($('<option></option>').val(d).text(d));
                                                         });

From d4629f199b8dfb7ad034dbe84a8c89b318526ddf Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 13:40:50 +0200
Subject: [PATCH 05/21] Added a date range filter

---
 core/templates/core/searchSample.html | 72 +++++++++++++++++++--------
 core/views.py                         | 24 ++++++++-
 2 files changed, 73 insertions(+), 23 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 93897cbf..c18c6785 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -25,12 +25,17 @@
     }
     #sample_list th:nth-child(2),
     #sample_list td:nth-child(2) {
-      min-width: 135px;
+      min-width: 170px;
     }
     #sample_list th:nth-child(2) .dt-column-title,
     #sample_list th:nth-child(2) input {
       white-space: nowrap;
     }
+    #sample_list .date-range-filter {
+      display: flex;
+      flex-direction: column;
+      gap: 0.25rem;
+    }
     #sample_list thead tr.filter-row th {
       vertical-align: top;
     }
@@ -286,17 +291,14 @@ <h1>Sample Browser</h1>
                                             initComplete: function () {
                                                 var api = this.api();
 
-                                                [0, 1].forEach(function(index) {
+                                                [0].forEach(function(index) {
                                                   var column = api.column(index);
                                                   var headerCell = $('.filter-row th').eq(index);
-                                                  var inputContainer = headerCell.empty();
-                                                  if (index === 0) {
-                                                    inputContainer = $('<div class="sample-id-search-wrapper"></div>')
-                                                      .appendTo(headerCell)
-                                                      .on('click mousedown keydown touchstart', function (event) {
-                                                        event.stopPropagation();
-                                                      });
-                                                  }
+                                                  var inputContainer = $('<div class="sample-id-search-wrapper"></div>')
+                                                    .appendTo(headerCell.empty())
+                                                    .on('click mousedown keydown touchstart', function (event) {
+                                                      event.stopPropagation();
+                                                    });
                                                   var input = $('<input type="text" class="form-control form-control-sm" placeholder="Type to search..." />')
                                                     .appendTo(inputContainer)
                                                     .on('click mousedown keydown touchstart', function (event) {
@@ -307,19 +309,45 @@ <h1>Sample Browser</h1>
                                                         column.search(this.value).draw();
                                                       }
                                                     });
-                                                  if (index === 0) {
-                                                    $('<button type="button" class="sample-id-search-clear" aria-label="Clear sample sequencing ID search">x</button>')
-                                                      .appendTo(inputContainer)
-                                                      .on('click', function (event) {
-                                                        event.preventDefault();
-                                                        event.stopPropagation();
-                                                        input.val('');
-                                                        if (column.search()) {
-                                                          column.search('').draw();
-                                                        }
-                                                        input.trigger('focus');
+                                                  $('<button type="button" class="sample-id-search-clear" aria-label="Clear sample sequencing ID search">x</button>')
+                                                    .appendTo(inputContainer)
+                                                    .on('click', function (event) {
+                                                      event.preventDefault();
+                                                      event.stopPropagation();
+                                                      input.val('');
+                                                      if (column.search()) {
+                                                        column.search('').draw();
+                                                      }
+                                                      input.trigger('focus');
+                                                    });
+                                                });
+
+                                                [1].forEach(function(index) {
+                                                  var column = api.column(index);
+                                                  var headerCell = $('.filter-row th').eq(index);
+                                                  var dateContainer = $('<div class="date-range-filter"></div>')
+                                                    .appendTo(headerCell.empty())
+                                                    .on('click mousedown keydown touchstart', function (event) {
+                                                      event.stopPropagation();
+                                                    });
+                                                  var startInput = $('<input type="date" class="form-control form-control-sm" aria-label="Collection date from" />')
+                                                    .appendTo(dateContainer);
+                                                  var endInput = $('<input type="date" class="form-control form-control-sm" aria-label="Collection date to" />')
+                                                    .appendTo(dateContainer);
+
+                                                  function updateDateRangeSearch() {
+                                                    var searchValue = '';
+                                                    if (startInput.val() || endInput.val()) {
+                                                      searchValue = JSON.stringify({
+                                                        from: startInput.val(),
+                                                        to: endInput.val()
                                                       });
+                                                    }
+                                                    if (column.search() !== searchValue) {
+                                                      column.search(searchValue, false, false).draw();
+                                                    }
                                                   }
+                                                  startInput.add(endInput).on('change clear', updateDateRangeSearch);
                                                 });
 
                                                 [2].forEach(function(index) {
@@ -340,7 +368,7 @@ <h1>Sample Browser</h1>
 
                                                     function renderLineageOptions() {
                                                         var selectedLineage = select.val() || column.search();
-                                                        select.empty().append('<option value="">Clear ' + columnName + 'filter </option>');
+                                                        select.empty().append('<option value="">Clear ' + columnName + ' filter </option>');
                                                         lineageOptions.forEach(function (d) {
                                                             select.append($('<option></option>').val(d).text(d));
                                                         });
diff --git a/core/views.py b/core/views.py
index 5e222379..9ed1299e 100644
--- a/core/views.py
+++ b/core/views.py
@@ -66,7 +66,9 @@ def _get_search_sample_rows_for_user(user_obj):
     ]
 
 
-def _normalize_datatable_search_value(value, regex=False, json_list=False):
+def _normalize_datatable_search_value(
+    value, regex=False, json_list=False, json_object=False
+):
     """Normalize DataTables search values, including escaped exact-match regexes."""
     if not value:
         return ""
@@ -77,6 +79,15 @@ def _normalize_datatable_search_value(value, regex=False, json_list=False):
             ]
         except (TypeError, ValueError, json.JSONDecodeError):
             pass
+    if json_object and value.startswith("{") and value.endswith("}"):
+        try:
+            return {
+                key: str(item).strip()
+                for key, item in json.loads(value).items()
+                if str(item).strip()
+            }
+        except (AttributeError, TypeError, ValueError, json.JSONDecodeError):
+            pass
     if regex and value.startswith("^") and value.endswith("$"):
         value = value[1:-1]
         # DataTables' escapeRegex() prefixes regex metacharacters with a
@@ -104,6 +115,16 @@ def _row_matches_search(row, global_search, column_filters):
             if candidate not in search_value:
                 return False
             continue
+        if isinstance(search_value, dict):
+            start_date = search_value.get("from")
+            end_date = search_value.get("to")
+            if not candidate:
+                return False
+            if start_date and candidate < start_date:
+                return False
+            if end_date and candidate > end_date:
+                return False
+            continue
         if exact_match:
             if candidate != search_value:
                 return False
@@ -328,6 +349,7 @@ def search_sample_data(request):
             request.GET.get(f"columns[{index}][search][regex]", "false").lower()
             == "true",
             index == 3,
+            index == 1,
         )
         exact_match = index in (2, 3)
         column_filters.append((field_name, search_value, exact_match))

From 5afdaa782f991ab87d2706c7d0a27dafd6929825 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 29 Jun 2026 14:52:12 +0200
Subject: [PATCH 06/21] added date range filter

---
 core/templates/core/searchSample.html | 71 +++++++++++++++++++++++++--
 1 file changed, 67 insertions(+), 4 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index c18c6785..22c8f5ad 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -10,7 +10,7 @@
     }
     #sample_list th:first-child,
     #sample_list td:first-child {
-      min-width: 210px;
+      min-width: 190px;
       white-space: nowrap;
     }
     #sample_list th:first-child .dt-column-title,
@@ -25,7 +25,7 @@
     }
     #sample_list th:nth-child(2),
     #sample_list td:nth-child(2) {
-      min-width: 170px;
+      min-width: 150px;
     }
     #sample_list th:nth-child(2) .dt-column-title,
     #sample_list th:nth-child(2) input {
@@ -34,7 +34,25 @@
     #sample_list .date-range-filter {
       display: flex;
       flex-direction: column;
-      gap: 0.25rem;
+      gap: 0.35rem;
+    }
+    #sample_list .date-range-filter label {
+      display: block;
+      font-size: 0.78rem;
+      font-weight: 400;
+      line-height: 1.1;
+      margin-bottom: 0.15rem;
+      white-space: normal;
+    }
+    #sample_list .date-range-input-wrapper {
+      position: relative;
+    }
+    #sample_list .date-range-input-wrapper input {
+      box-sizing: border-box;
+      font-size: 0.82rem;
+      padding-left: 0.35rem;
+      padding-right: 1.45rem;
+      width: 100%;
     }
     #sample_list thead tr.filter-row th {
       vertical-align: top;
@@ -76,8 +94,23 @@
       width: 1rem;
       height: 1rem;
     }
+    #sample_list .date-range-clear {
+      position: absolute;
+      top: 50%;
+      right: 0.3rem;
+      transform: translateY(-50%);
+      border: 0;
+      background: transparent;
+      color: #6c757d;
+      line-height: 1;
+      padding: 0;
+      width: 0.9rem;
+      height: 0.9rem;
+    }
     #sample_list .sample-id-search-clear:hover,
     #sample_list .sample-id-search-clear:focus,
+    #sample_list .date-range-clear:hover,
+    #sample_list .date-range-clear:focus,
     #sample_list .institution-search-clear:hover,
     #sample_list .institution-search-clear:focus {
       color: var(--color-primary);
@@ -330,10 +363,22 @@ <h1>Sample Browser</h1>
                                                     .on('click mousedown keydown touchstart', function (event) {
                                                       event.stopPropagation();
                                                     });
+                                                  var startField = $('<div class="date-range-field"></div>')
+                                                    .appendTo(dateContainer);
+                                                  $('<label>Start date filter</label>')
+                                                    .appendTo(startField);
+                                                  var startWrapper = $('<div class="date-range-input-wrapper"></div>')
+                                                    .appendTo(startField);
                                                   var startInput = $('<input type="date" class="form-control form-control-sm" aria-label="Collection date from" />')
+                                                    .appendTo(startWrapper);
+                                                  var endField = $('<div class="date-range-field"></div>')
                                                     .appendTo(dateContainer);
+                                                  $('<label>End date filter</label>')
+                                                    .appendTo(endField);
+                                                  var endWrapper = $('<div class="date-range-input-wrapper"></div>')
+                                                    .appendTo(endField);
                                                   var endInput = $('<input type="date" class="form-control form-control-sm" aria-label="Collection date to" />')
-                                                    .appendTo(dateContainer);
+                                                    .appendTo(endWrapper);
 
                                                   function updateDateRangeSearch() {
                                                     var searchValue = '';
@@ -347,6 +392,24 @@ <h1>Sample Browser</h1>
                                                       column.search(searchValue, false, false).draw();
                                                     }
                                                   }
+                                                  $('<button type="button" class="date-range-clear" aria-label="Clear start date filter">x</button>')
+                                                    .appendTo(startWrapper)
+                                                    .on('click', function (event) {
+                                                      event.preventDefault();
+                                                      event.stopPropagation();
+                                                      startInput.val('');
+                                                      updateDateRangeSearch();
+                                                      startInput.trigger('focus');
+                                                    });
+                                                  $('<button type="button" class="date-range-clear" aria-label="Clear end date filter">x</button>')
+                                                    .appendTo(endWrapper)
+                                                    .on('click', function (event) {
+                                                      event.preventDefault();
+                                                      event.stopPropagation();
+                                                      endInput.val('');
+                                                      updateDateRangeSearch();
+                                                      endInput.trigger('focus');
+                                                    });
                                                   startInput.add(endInput).on('change clear', updateDateRangeSearch);
                                                 });
 

From 0311a91e0e12965931e52d4ab042114efb1e3e9b Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 30 Jun 2026 13:17:07 +0200
Subject: [PATCH 07/21] loosen the search of the submitting institution

---
 core/utils/samples.py | 8 +++++++-
 core/views.py         | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/core/utils/samples.py b/core/utils/samples.py
index 3093cdc2..1037c31f 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -703,7 +703,13 @@ def get_search_table_for_user(user_obj):
         return table_data
     if user_role == "Submitter":
         user_lab = core.utils.labs.get_lab_name_from_user(user_obj)
-        lab_entries = samples_to_search.get(user_lab, {})
+        lab_entries = {}
+        if user_lab:
+            user_lab_normalized = user_lab.lower()
+            for submitter_name, entries in samples_to_search.items():
+                if str(submitter_name or "").lower() == user_lab_normalized:
+                    lab_entries = entries
+                    break
         for info in lab_entries.values():
             table_data.extend(info.get("rows", []))
     else:
diff --git a/core/views.py b/core/views.py
index 9ed1299e..07109766 100644
--- a/core/views.py
+++ b/core/views.py
@@ -509,7 +509,7 @@ def intranet(request):
                 if not matches_lab:
                     continue
             else:
-                if value != lab_name:
+                if not value or not lab_name or value.lower() != lab_name.lower():
                     continue
             # Adapt YYYY-WNN to datetime format so it can be converted to date object
             converted_date = datetime.strptime(d["iso_yearweek"] + "-1", "%G-W%V-%u")

From 3f606704d60f4683cb7f37f7507751c6a89c1f36 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 30 Jun 2026 13:38:55 +0200
Subject: [PATCH 08/21] fixed Cauge percentage for submitting and collecting

---
 core/utils/bioinfo_analysis.py | 2 ++
 core/views.py                  | 5 ++++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/core/utils/bioinfo_analysis.py b/core/utils/bioinfo_analysis.py
index 511bffe7..8ff25152 100644
--- a/core/utils/bioinfo_analysis.py
+++ b/core/utils/bioinfo_analysis.py
@@ -41,6 +41,8 @@ def get_bio_analysis_stats_from_lab(
         bio_stats["analized"] = (
             core.models.DateUpdateState.objects.select_related("sampleID")
             .filter(sampleID__pk__in=lab_samples, stateID__state__iexact="Bioinfo")
+            .values("sampleID")
+            .distinct()
             .count()
         )
         bio_stats["received"] = (
diff --git a/core/views.py b/core/views.py
index 07109766..93f5eb9e 100644
--- a/core/views.py
+++ b/core/views.py
@@ -536,9 +536,12 @@ def intranet(request):
             start = time.time()
             sample_lab_objs = core.utils.samples.get_sample_objs_per_lab(lab_name)
             print(f"Took {start - time.time()} seconds for sample_lab_objs")
+            analysis_lab_name = (
+                lab_code if user_role == "Collector" and lab_code else lab_name
+            )
             analysis_percent = (
                 core.utils.bioinfo_analysis.get_bio_analysis_stats_from_lab(
-                    lab_name=(lab_code or lab_name), institution_type=lab_field
+                    lab_name=analysis_lab_name, institution_type=lab_field
                 )
             )
             print(f"Took {start - time.time()} seconds for analysis_percent")

From daf2419aafcde06808ab457e093adc681997dc59 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 30 Jun 2026 17:00:30 +0200
Subject: [PATCH 09/21] Added a "Download filtered table" button

---
 core/templates/core/searchSample.html |  21 ++++-
 core/urls.py                          |   5 ++
 core/views.py                         | 112 ++++++++++++++++++--------
 3 files changed, 104 insertions(+), 34 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 22c8f5ad..16cfbcfa 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -169,6 +169,18 @@
       width: 100%;
       max-width: 100%;
     }
+    .sample-browser-download .sample-browser-csv-button {
+      background-color: rgba(var(--color-green-rgb), 0.12);
+      border-color: var(--color-green);
+      color: var(--color-green);
+      font-weight: 500;
+    }
+    .sample-browser-download .sample-browser-csv-button:hover,
+    .sample-browser-download .sample-browser-csv-button:focus {
+      background-color: var(--color-green);
+      border-color: var(--color-green);
+      color: var(--color-white);
+    }
 </style>
 {% endblock %}
 
@@ -276,7 +288,7 @@ <h1>Sample Browser</h1>
                                             lengthMenu: [ [25, 50, 100, 200, -1], [25, 50, 100, 200, "All"] ],
                                             orderCellsTop: true,
                                             dom:
-                                                "<'row'<'col-md-3'l><'col-md-9'f>>" +
+                                                "<'row align-items-center'<'col-md-3'l><'col-md-4 sample-browser-download'><'col-md-5'f>>" +
                                                 "<'row'<'col-sm-12'tr>>" +
                                                 "<'row'<'col-sm-12 col-md-5'i><'col-sm-12 col-md-7'p>>",
                                             responsive: true,
@@ -323,6 +335,13 @@ <h1>Sample Browser</h1>
                                             ],
                                             initComplete: function () {
                                                 var api = this.api();
+                                                var csvUrl = "{% url 'search_sample_csv' %}";
+                                                $('<button type="button" class="btn btn-sm sample-browser-csv-button">Download filtered table</button>')
+                                                    .appendTo($('.sample-browser-download'))
+                                                    .on('click', function () {
+                                                        var params = $.param(table.ajax.params());
+                                                        window.location = csvUrl + (params ? '?' + params : '');
+                                                    });
 
                                                 [0].forEach(function(index) {
                                                   var column = api.column(index);
diff --git a/core/urls.py b/core/urls.py
index 5283bf00..7da10410 100644
--- a/core/urls.py
+++ b/core/urls.py
@@ -56,6 +56,11 @@
         core.views.search_sample_data,
         name="search_sample_data",
     ),
+    path(
+        "searchSample/csv",
+        core.views.search_sample_csv,
+        name="search_sample_csv",
+    ),
 ]
 if settings.DEBUG:
     urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
diff --git a/core/views.py b/core/views.py
index 93f5eb9e..622aac5f 100644
--- a/core/views.py
+++ b/core/views.py
@@ -1,10 +1,11 @@
 # Generic imports
 from datetime import datetime
+import csv
 import json
 from collections import defaultdict, OrderedDict
 import re
 from django.shortcuts import render, redirect
-from django.http import JsonResponse
+from django.http import HttpResponse, JsonResponse
 from django.contrib.auth.decorators import login_required
 from django.contrib.auth.models import Group
 from django.utils import timezone
@@ -305,38 +306,8 @@ def search_sample(request):
     )
 
 
-@login_required
-def search_sample_data(request):
-    """Return paginated sample browser data for DataTables server-side mode."""
-    sample_rows = _get_search_sample_rows_for_user(request.user)
-    if isinstance(sample_rows, dict) and "ERROR" in sample_rows:
-        try:
-            draw = int(request.GET.get("draw", 0) or 0)
-        except (TypeError, ValueError):
-            draw = 0
-        return JsonResponse(
-            {
-                "draw": draw,
-                "recordsTotal": 0,
-                "recordsFiltered": 0,
-                "data": [],
-                "error": sample_rows["ERROR"],
-            }
-        )
-
-    try:
-        draw = int(request.GET.get("draw", 0) or 0)
-    except (TypeError, ValueError):
-        draw = 0
-    try:
-        start = max(int(request.GET.get("start", 0) or 0), 0)
-    except (TypeError, ValueError):
-        start = 0
-    try:
-        length = int(request.GET.get("length", 25) or 25)
-    except (TypeError, ValueError):
-        length = 25
-
+def _get_filtered_search_sample_data(request, sample_rows):
+    """Apply DataTables search and ordering parameters to sample browser rows."""
     global_search = _normalize_datatable_search_value(
         request.GET.get("search[value]", ""),
         request.GET.get("search[regex]", "false").lower() == "true",
@@ -401,6 +372,47 @@ def search_sample_data(request):
         key=lambda row: _get_sort_value(row, field_name), reverse=reverse_order
     )
 
+    return filtered_rows, lineage_options, collecting_institution_options
+
+
+@login_required
+def search_sample_data(request):
+    """Return paginated sample browser data for DataTables server-side mode."""
+    sample_rows = _get_search_sample_rows_for_user(request.user)
+    if isinstance(sample_rows, dict) and "ERROR" in sample_rows:
+        try:
+            draw = int(request.GET.get("draw", 0) or 0)
+        except (TypeError, ValueError):
+            draw = 0
+        return JsonResponse(
+            {
+                "draw": draw,
+                "recordsTotal": 0,
+                "recordsFiltered": 0,
+                "data": [],
+                "error": sample_rows["ERROR"],
+            }
+        )
+
+    try:
+        draw = int(request.GET.get("draw", 0) or 0)
+    except (TypeError, ValueError):
+        draw = 0
+    try:
+        start = max(int(request.GET.get("start", 0) or 0), 0)
+    except (TypeError, ValueError):
+        start = 0
+    try:
+        length = int(request.GET.get("length", 25) or 25)
+    except (TypeError, ValueError):
+        length = 25
+
+    (
+        filtered_rows,
+        lineage_options,
+        collecting_institution_options,
+    ) = _get_filtered_search_sample_data(request, sample_rows)
+
     if length == -1:
         paginated_rows = filtered_rows[start:]
     else:
@@ -418,6 +430,40 @@ def search_sample_data(request):
     )
 
 
+@login_required
+def search_sample_csv(request):
+    """Download the currently filtered sample browser rows as CSV."""
+    sample_rows = _get_search_sample_rows_for_user(request.user)
+    response = HttpResponse(content_type="text/csv")
+    response["Content-Disposition"] = 'attachment; filename="relecov_samples.csv"'
+    writer = csv.writer(response)
+    writer.writerow(
+        [
+            "Sample Sequencing ID",
+            "Collection Date",
+            "Lineage",
+            "Collecting Institution",
+        ]
+    )
+
+    if isinstance(sample_rows, dict) and "ERROR" in sample_rows:
+        return response
+
+    filtered_rows, _lineage_options, _institution_options = (
+        _get_filtered_search_sample_data(request, sample_rows)
+    )
+    for row in filtered_rows:
+        writer.writerow(
+            [
+                row["sequencing_id"],
+                row["collection_date"],
+                row["lineage"],
+                row["collecting_institution"],
+            ]
+        )
+    return response
+
+
 @login_required
 def metadata_visualization(request):
     if request.user.username != "admin":

From 61d0bb12fcc5de76781d0b4bfabffc7b511e3564 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 1 Jul 2026 12:41:32 +0200
Subject: [PATCH 10/21] Added button to download surveillance data

---
 core/templates/core/searchSample.html |  27 +++-
 core/urls.py                          |   5 +
 core/utils/samples.py                 |  61 ++++++--
 core/views.py                         | 206 ++++++++++++++++++++++++++
 4 files changed, 277 insertions(+), 22 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 16cfbcfa..ce0c28ed 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -169,14 +169,20 @@
       width: 100%;
       max-width: 100%;
     }
-    .sample-browser-download .sample-browser-csv-button {
+    .sample-browser-download {
+      display: flex;
+      gap: 0.5rem;
+      justify-content: center;
+      flex-wrap: wrap;
+    }
+    .sample-browser-download .sample-browser-download-button {
       background-color: rgba(var(--color-green-rgb), 0.12);
       border-color: var(--color-green);
       color: var(--color-green);
       font-weight: 500;
     }
-    .sample-browser-download .sample-browser-csv-button:hover,
-    .sample-browser-download .sample-browser-csv-button:focus {
+    .sample-browser-download .sample-browser-download-button:hover,
+    .sample-browser-download .sample-browser-download-button:focus {
       background-color: var(--color-green);
       border-color: var(--color-green);
       color: var(--color-white);
@@ -336,11 +342,20 @@ <h1>Sample Browser</h1>
                                             initComplete: function () {
                                                 var api = this.api();
                                                 var csvUrl = "{% url 'search_sample_csv' %}";
-                                                $('<button type="button" class="btn btn-sm sample-browser-csv-button">Download filtered table</button>')
+                                                var surveillanceUrl = "{% url 'search_sample_surveillance_data' %}";
+                                                function downloadFilteredData(downloadUrl) {
+                                                    var params = $.param(table.ajax.params());
+                                                    window.location = downloadUrl + (params ? '?' + params : '');
+                                                }
+                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download filtered table</button>')
+                                                    .appendTo($('.sample-browser-download'))
+                                                    .on('click', function () {
+                                                        downloadFilteredData(csvUrl);
+                                                    });
+                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download surveillance data</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
-                                                        var params = $.param(table.ajax.params());
-                                                        window.location = csvUrl + (params ? '?' + params : '');
+                                                        downloadFilteredData(surveillanceUrl);
                                                     });
 
                                                 [0].forEach(function(index) {
diff --git a/core/urls.py b/core/urls.py
index 7da10410..835ca520 100644
--- a/core/urls.py
+++ b/core/urls.py
@@ -61,6 +61,11 @@
         core.views.search_sample_csv,
         name="search_sample_csv",
     ),
+    path(
+        "searchSample/surveillance-data",
+        core.views.search_sample_surveillance_data,
+        name="search_sample_surveillance_data",
+    ),
 ]
 if settings.DEBUG:
     urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
diff --git a/core/utils/samples.py b/core/utils/samples.py
index 1037c31f..57a0fd11 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -486,6 +486,49 @@ def get_public_database_fields(schema_obj, db_type):
     return None
 
 
+def get_iskylims_lookup_ids(sample_obj):
+    """Return iSkyLIMS lookup IDs for a sample, preferring unique sample id."""
+    lookup_ids = []
+    unique_id = (sample_obj.get_unique_id() or "").strip()
+    seq_id = (sample_obj.get_sequencing_sample_id() or "").strip()
+    if unique_id:
+        lookup_ids.append(unique_id)
+    if seq_id and seq_id not in lookup_ids:
+        lookup_ids.append(seq_id)
+    return lookup_ids
+
+
+def get_iskylims_sample_information(sample_obj):
+    """Return the first iSkyLIMS sample payload available for this sample."""
+    for sample_id in get_iskylims_lookup_ids(sample_obj):
+        iskylims_data = core.utils.rest_api.get_sample_information(sample_id)
+        if not iskylims_data or "ERROR" in iskylims_data:
+            continue
+        if not iskylims_data:
+            continue
+        return iskylims_data[0]
+    return None
+
+
+def get_iskylims_project_values(sample_obj):
+    """Return iSkyLIMS project values keyed by display label."""
+    iskylims_data = get_iskylims_sample_information(sample_obj)
+    if not iskylims_data:
+        return {}
+    project_field_display_map = core.utils.rest_api.get_sample_project_field_display_map(
+        iskylims_data.get("sample_project")
+    )
+    project_values = {}
+    for key, value in iskylims_data.get("Project values", {}).items():
+        project_values[project_field_display_map.get(key, key)] = value
+    return project_values
+
+
+def get_iskylims_project_value(sample_obj, label_name):
+    """Return one iSkyLIMS project value by display label."""
+    return get_iskylims_project_values(sample_obj).get(label_name, "")
+
+
 def get_sample_display_data(sample_id, user):
     """Check if user is allowed to see the data and if true collect all info
     from sample to display
@@ -552,23 +595,10 @@ def get_sample_display_data(sample_id, user):
     # Lab metadata in iSkyLIMS is keyed by the platform-wide unique sample id
     # (the value shown as Sample Name in iSky). Keep a fallback to the historical
     # sequencing_sample_id so legacy records can still resolve.
-    lookup_ids = []
-    unique_id = (sample_obj.get_unique_id() or "").strip()
-    seq_id = (sample_obj.get_sequencing_sample_id() or "").strip()
-    if unique_id:
-        lookup_ids.append(unique_id)
-    if seq_id and seq_id not in lookup_ids:
-        lookup_ids.append(seq_id)
-
-    # Fetch information from iSkyLIMS
-    for sample_id in lookup_ids:
-        iskylims_data = core.utils.rest_api.get_sample_information(sample_id)
-        if not iskylims_data or "ERROR" in iskylims_data:
-            continue
+    iskylims_data = get_iskylims_sample_information(sample_obj)
+    if iskylims_data:
         s_data["iskylims_basic"] = []
         s_data["iskylims_p_data"] = []
-        # iskylims_data is a list with one element. Then get the first element
-        iskylims_data = iskylims_data[0]
         project_field_display_map = (
             core.utils.rest_api.get_sample_project_field_display_map(
                 iskylims_data.get("sample_project")
@@ -586,7 +616,6 @@ def get_sample_display_data(sample_id, user):
             else:
                 s_data["iskylims_basic"].append([key, i_data])
         s_data["iskylims_project"] = iskylims_data.get("sample_project")
-        break
     return s_data
 
 
diff --git a/core/views.py b/core/views.py
index 622aac5f..513cf0e7 100644
--- a/core/views.py
+++ b/core/views.py
@@ -1,6 +1,7 @@
 # Generic imports
 from datetime import datetime
 import csv
+from io import BytesIO
 import json
 from collections import defaultdict, OrderedDict
 import re
@@ -8,9 +9,11 @@
 from django.http import HttpResponse, JsonResponse
 from django.contrib.auth.decorators import login_required
 from django.contrib.auth.models import Group
+from django.db.models import Prefetch
 from django.utils import timezone
 from django.utils.http import url_has_allowed_host_and_scheme
 from django.views.decorators.http import require_POST
+from openpyxl import Workbook
 
 # Local imports
 import core.models
@@ -464,6 +467,209 @@ def search_sample_csv(request):
     return response
 
 
+def _get_collection_iso_week(collection_date):
+    """Return ISO week in YYYY-WNN format from a collection date string."""
+    if not collection_date:
+        return ""
+    try:
+        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
+    except ValueError:
+        return ""
+    iso_year, iso_week, _ = parsed_date.isocalendar()
+    return f"{iso_year}-W{iso_week:02d}"
+
+
+def _get_epi_season(collection_date):
+    """Return epidemiological season in YYYY_YYYY format."""
+    if not collection_date:
+        return ""
+    try:
+        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
+    except ValueError:
+        return ""
+    year, week, _weekday = parsed_date.isocalendar()
+    if week >= 40:
+        season_start = year
+        season_end = year + 1
+    else:
+        season_start = year - 1
+        season_end = year
+    return f"{season_start}_{season_end}"
+
+
+
+def _get_sample_lineage_value(sample, property_name):
+    """Return a lineage value for the requested property name."""
+    if not sample:
+        return ""
+    lineage_values = getattr(sample, "surveillance_lineages", None)
+    if lineage_values is not None:
+        for lineage_value in lineage_values:
+            if lineage_value.lineage_fieldID.property_name == property_name:
+                return lineage_value.value or ""
+        return ""
+    lineage_value = sample.lineage_values.filter(
+        lineage_fieldID__property_name=property_name
+    ).last()
+    return lineage_value.value if lineage_value else ""
+
+
+def _get_sample_bioinfo_value(sample, property_name):
+    """Return a bioinfo analysis value for the requested property name."""
+    if not sample:
+        return ""
+    bioinfo_values = getattr(sample, "surveillance_bioinfo_values", None)
+    if bioinfo_values is not None:
+        for bioinfo_value in bioinfo_values:
+            if bioinfo_value.bioinfo_analysis_fieldID.property_name == property_name:
+                return bioinfo_value.value or ""
+        return ""
+    bioinfo_value = sample.bio_analysis_values.filter(
+        bioinfo_analysis_fieldID__property_name=property_name
+    ).last()
+    return bioinfo_value.value if bioinfo_value else ""
+
+
+def _get_sample_public_database_value(sample, property_name):
+    """Return a public database value for the requested property name."""
+    if not sample:
+        return ""
+    public_database_values = getattr(sample, "surveillance_public_database_values", None)
+    if public_database_values is not None:
+        for public_database_value in public_database_values:
+            if public_database_value.public_database_fieldID.property_name == property_name:
+                return public_database_value.value or ""
+        return ""
+    public_database_value = sample.publicdatabasevalues_set.filter(
+        public_database_fieldID__property_name=property_name
+    ).last()
+    return public_database_value.value if public_database_value else ""
+
+
+@login_required
+def search_sample_surveillance_data(request):
+    """Download surveillance data for the currently filtered sample browser rows."""
+    sample_rows = _get_search_sample_rows_for_user(request.user)
+    filtered_rows = []
+    if not (isinstance(sample_rows, dict) and "ERROR" in sample_rows):
+        filtered_rows, _lineage_options, _institution_options = (
+            _get_filtered_search_sample_data(request, sample_rows)
+        )
+
+    sequencing_ids = [row["sequencing_id"] for row in filtered_rows]
+    lineage_prefetch = Prefetch(
+        "lineage_values",
+        queryset=core.models.LineageValues.objects.filter(
+            lineage_fieldID__property_name__in=[
+                "lineage_assignment",
+                "lineage_assignment_software_version",
+                "lineage_assignment_database_version",
+            ]
+        ).select_related("lineage_fieldID"),
+        to_attr="surveillance_lineages",
+    )
+    bioinfo_prefetch = Prefetch(
+        "bio_analysis_values",
+        queryset=core.models.BioinfoAnalysisValue.objects.filter(
+            bioinfo_analysis_fieldID__property_name__in=[
+                "per_genome_greater_10x",
+                "bioinformatics_analysis_date",
+                "consensus_sequence_filename",
+                "qc_test",
+            ]
+        ).select_related("bioinfo_analysis_fieldID"),
+        to_attr="surveillance_bioinfo_values",
+    )
+    public_database_prefetch = Prefetch(
+        "publicdatabasevalues_set",
+        queryset=core.models.PublicDatabaseValues.objects.filter(
+            public_database_fieldID__property_name="gisaid_accession_id"
+        ).select_related("public_database_fieldID"),
+        to_attr="surveillance_public_database_values",
+    )
+    sample_lookup = {
+        sample.sequencing_sample_id: sample
+        for sample in core.models.Sample.objects.filter(
+            sequencing_sample_id__in=sequencing_ids
+        ).prefetch_related(
+            lineage_prefetch, bioinfo_prefetch, public_database_prefetch
+        )
+    }
+
+    workbook = Workbook()
+    worksheet = workbook.active
+    worksheet.title = "per_sample_data"
+    worksheet.append(
+        [
+            "COLLECTING_LAB_SAMPLE_ID",
+            "SEQUENCING_SAMPLE_ID",
+            "MICROBIOLOGY_LAB_SAMPLE_ID",
+            "UNIQUE_SAMPLE_ID",
+            "GISAID_ACCESSION_ID",
+            "COLLECTING_INSTITUTION",
+            "SUBMITTING_INSTITUTION",
+            "SUBMITTING_INSTITUTION_ID",
+            "CCAA",
+            "PROVINCE",
+            "SAMPLE_COLLECTION_DATE",
+            "WEEK",
+            "SEASON",
+            "LINEAGE",
+            "PANGOLIN_SOFTWARE_VERSION",
+            "PANGOLIN_DATABASE_VERSION",
+            "ANALYSIS_DATE",
+            "COVERAGE_10X",
+            "QC_TEST",
+            "CONSENSUS_SEQUENCE_FILENAME",
+        ]
+    )
+    for row in filtered_rows:
+        sample = sample_lookup.get(row["sequencing_id"])
+        iskylims_project_values = core.utils.samples.get_iskylims_project_values(
+            sample
+        )
+        worksheet.append(
+            [
+                sample.collecting_lab_sample_id if sample else "",
+                sample.sequencing_sample_id if sample else row["sequencing_id"],
+                sample.microbiology_lab_sample_id if sample else "",
+                sample.sample_unique_id if sample else "",
+                _get_sample_public_database_value(sample, "gisaid_accession_id"),
+                sample.collecting_institution if sample else "",
+                sample.submitting_institution if sample else "",
+                iskylims_project_values.get("Submitting Institution Identifier", ""),
+                iskylims_project_values.get("Autonomic Community", ""),
+                iskylims_project_values.get("Province", ""),
+                row["collection_date"],
+                _get_collection_iso_week(row["collection_date"]),
+                _get_epi_season(row["collection_date"]),
+                _get_sample_lineage_value(sample, "lineage_assignment"),
+                _get_sample_lineage_value(
+                    sample, "lineage_assignment_software_version"
+                ),
+                _get_sample_lineage_value(
+                    sample, "lineage_assignment_database_version"
+                ),
+                _get_sample_bioinfo_value(sample, "bioinformatics_analysis_date"),
+                _get_sample_bioinfo_value(sample, "per_genome_greater_10x"),
+                _get_sample_bioinfo_value(sample, "qc_test"),
+                _get_sample_bioinfo_value(sample, "consensus_sequence_filename"),
+            ]
+        )
+
+    output = BytesIO()
+    workbook.save(output)
+    output.seek(0)
+    response = HttpResponse(
+        output.getvalue(),
+        content_type=(
+            "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+        ),
+    )
+    response["Content-Disposition"] = 'attachment; filename="surveillance_data.xlsx"'
+    return response
+
+
 @login_required
 def metadata_visualization(request):
     if request.user.username != "admin":

From 7bb9bbcadee83d3f18343acef2fb67d751b1b65e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 1 Jul 2026 12:56:39 +0200
Subject: [PATCH 11/21] Added a time check to avoid long times of download

---
 core/templates/core/searchSample.html | 92 +++++++++++++++++++++++++--
 1 file changed, 86 insertions(+), 6 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index ce0c28ed..bc5d0f2e 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -173,13 +173,14 @@
       display: flex;
       gap: 0.5rem;
       justify-content: center;
-      flex-wrap: wrap;
+      flex-wrap: nowrap;
     }
     .sample-browser-download .sample-browser-download-button {
       background-color: rgba(var(--color-green-rgb), 0.12);
       border-color: var(--color-green);
       color: var(--color-green);
       font-weight: 500;
+      white-space: nowrap;
     }
     .sample-browser-download .sample-browser-download-button:hover,
     .sample-browser-download .sample-browser-download-button:focus {
@@ -294,7 +295,7 @@ <h1>Sample Browser</h1>
                                             lengthMenu: [ [25, 50, 100, 200, -1], [25, 50, 100, 200, "All"] ],
                                             orderCellsTop: true,
                                             dom:
-                                                "<'row align-items-center'<'col-md-3'l><'col-md-4 sample-browser-download'><'col-md-5'f>>" +
+                                                "<'row align-items-center'<'col-md-3'l><'col-md-5 sample-browser-download'><'col-md-4'f>>" +
                                                 "<'row'<'col-sm-12'tr>>" +
                                                 "<'row'<'col-sm-12 col-md-5'i><'col-sm-12 col-md-7'p>>",
                                             responsive: true,
@@ -343,19 +344,98 @@ <h1>Sample Browser</h1>
                                                 var api = this.api();
                                                 var csvUrl = "{% url 'search_sample_csv' %}";
                                                 var surveillanceUrl = "{% url 'search_sample_surveillance_data' %}";
-                                                function downloadFilteredData(downloadUrl) {
+                                                var surveillanceSecondsPerSample = 0.12;
+                                                var downloadWarningThresholdSeconds = 10;
+                                                function getFilteredSampleCount() {
+                                                    return table.page.info().recordsDisplay || 0;
+                                                }
+                                                function formatSampleCount(count) {
+                                                    return count.toLocaleString('en-US');
+                                                }
+                                                function getEstimatedDownloadSeconds(count) {
+                                                    return Math.ceil(count * surveillanceSecondsPerSample);
+                                                }
+                                                function formatEstimatedDuration(totalSeconds) {
+                                                    if (totalSeconds < 60) {
+                                                        return totalSeconds + ' seconds';
+                                                    }
+                                                    var minutes = Math.floor(totalSeconds / 60);
+                                                    var seconds = totalSeconds % 60;
+                                                    if (seconds === 0) {
+                                                        return minutes + ' min';
+                                                    }
+                                                    return minutes + ' min ' + seconds + ' sec';
+                                                }
+                                                function confirmLongDownload(count) {
+                                                    var estimatedSeconds = getEstimatedDownloadSeconds(count);
+                                                    if (estimatedSeconds <= downloadWarningThresholdSeconds) {
+                                                        return true;
+                                                    }
+                                                    return window.confirm(
+                                                        'You are about to generate a file for ' +
+                                                        formatSampleCount(count) +
+                                                        ' filtered samples. Estimated generation time: ' +
+                                                        formatEstimatedDuration(estimatedSeconds) +
+                                                        '. Consider applying more filters before continuing. Continue?'
+                                                    );
+                                                }
+                                                function getDownloadFilename(response, fallbackFilename) {
+                                                    var contentDisposition = response.headers.get('Content-Disposition') || '';
+                                                    var filenameMatch = contentDisposition.match(/filename="?([^";]+)"?/i);
+                                                    return filenameMatch ? filenameMatch[1] : fallbackFilename;
+                                                }
+                                                function setDownloadButtonsLoading(button, loadingText) {
+                                                    var originalText = button.text();
+                                                    $('.sample-browser-download-button').prop('disabled', true);
+                                                    button.text(loadingText);
+                                                    return function () {
+                                                        $('.sample-browser-download-button').prop('disabled', false);
+                                                        button.text(originalText);
+                                                    };
+                                                }
+                                                function startBlobDownload(blob, filename) {
+                                                    var objectUrl = window.URL.createObjectURL(blob);
+                                                    var downloadLink = document.createElement('a');
+                                                    downloadLink.href = objectUrl;
+                                                    downloadLink.download = filename;
+                                                    document.body.appendChild(downloadLink);
+                                                    downloadLink.click();
+                                                    document.body.removeChild(downloadLink);
+                                                    window.URL.revokeObjectURL(objectUrl);
+                                                }
+                                                function downloadFilteredData(downloadUrl, button, loadingText, fallbackFilename) {
+                                                    var filteredSampleCount = getFilteredSampleCount();
+                                                    if (!confirmLongDownload(filteredSampleCount)) {
+                                                        return;
+                                                    }
+                                                    var restoreButton = setDownloadButtonsLoading(button, loadingText);
                                                     var params = $.param(table.ajax.params());
-                                                    window.location = downloadUrl + (params ? '?' + params : '');
+                                                    fetch(downloadUrl + (params ? '?' + params : ''), {
+                                                        credentials: 'same-origin'
+                                                    })
+                                                        .then(function (response) {
+                                                            if (!response.ok) {
+                                                                throw new Error('Download request failed.');
+                                                            }
+                                                            var filename = getDownloadFilename(response, fallbackFilename);
+                                                            return response.blob().then(function (blob) {
+                                                                startBlobDownload(blob, filename);
+                                                            });
+                                                        })
+                                                        .catch(function () {
+                                                            window.alert('The file could not be generated. Please try again or apply more filters.');
+                                                        })
+                                                        .finally(restoreButton);
                                                 }
                                                 $('<button type="button" class="btn btn-sm sample-browser-download-button">Download filtered table</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
-                                                        downloadFilteredData(csvUrl);
+                                                        downloadFilteredData(csvUrl, $(this), 'Generating table...', 'relecov_samples.csv');
                                                     });
                                                 $('<button type="button" class="btn btn-sm sample-browser-download-button">Download surveillance data</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
-                                                        downloadFilteredData(surveillanceUrl);
+                                                        downloadFilteredData(surveillanceUrl, $(this), 'Generating surveillance data...', 'surveillance_data.xlsx');
                                                     });
 
                                                 [0].forEach(function(index) {

From 0d1489a551ff9e613b8139c1b0e3fc1d2dbaffb9 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 1 Jul 2026 12:56:56 +0200
Subject: [PATCH 12/21] re-arranged code

---
 core/utils/samples.py | 203 ++++++++++++++++++++++++++++++++++++++++++
 core/views.py         | 183 +------------------------------------
 2 files changed, 204 insertions(+), 182 deletions(-)

diff --git a/core/utils/samples.py b/core/utils/samples.py
index 57a0fd11..87b9eaeb 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -3,13 +3,16 @@
 import os
 import shutil
 import hashlib
+from datetime import datetime
 from collections import OrderedDict, defaultdict
 import pandas as pd
+from openpyxl import Workbook
 from django.contrib.auth.models import Group, User
 from django.core.files.storage import FileSystemStorage
 from django.conf import settings
 from django.db.models import Q
 from django.db.models import Count
+from django.db.models import Prefetch
 from django.db.models.functions import TruncDate
 import relecov_tools.utils
 from django.template.loader import render_to_string
@@ -529,6 +532,206 @@ def get_iskylims_project_value(sample_obj, label_name):
     return get_iskylims_project_values(sample_obj).get(label_name, "")
 
 
+SURVEILLANCE_LINEAGE_FIELDS = [
+    "lineage_assignment",
+    "lineage_assignment_software_version",
+    "lineage_assignment_database_version",
+]
+SURVEILLANCE_BIOINFO_FIELDS = [
+    "per_genome_greater_10x",
+    "bioinformatics_analysis_date",
+    "consensus_sequence_filename",
+    "qc_test",
+]
+SURVEILLANCE_PUBLIC_DATABASE_FIELDS = ["gisaid_accession_id"]
+SURVEILLANCE_COLUMNS = [
+    "COLLECTING_LAB_SAMPLE_ID",
+    "SEQUENCING_SAMPLE_ID",
+    "MICROBIOLOGY_LAB_SAMPLE_ID",
+    "UNIQUE_SAMPLE_ID",
+    "GISAID_ACCESSION_ID",
+    "COLLECTING_INSTITUTION",
+    "SUBMITTING_INSTITUTION",
+    "SUBMITTING_INSTITUTION_ID",
+    "CCAA",
+    "PROVINCE",
+    "SAMPLE_COLLECTION_DATE",
+    "WEEK",
+    "SEASON",
+    "LINEAGE",
+    "PANGOLIN_SOFTWARE_VERSION",
+    "PANGOLIN_DATABASE_VERSION",
+    "ANALYSIS_DATE",
+    "COVERAGE_10X",
+    "QC_TEST",
+    "CONSENSUS_SEQUENCE_FILENAME",
+]
+
+
+def get_collection_iso_week(collection_date):
+    """Return ISO week in YYYY-WNN format from a collection date string."""
+    if not collection_date:
+        return ""
+    try:
+        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
+    except ValueError:
+        return ""
+    iso_year, iso_week, _ = parsed_date.isocalendar()
+    return f"{iso_year}-W{iso_week:02d}"
+
+
+def get_epi_season(collection_date):
+    """Return epidemiological season in YYYY_YYYY format."""
+    if not collection_date:
+        return ""
+    try:
+        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
+    except ValueError:
+        return ""
+    year, week, _weekday = parsed_date.isocalendar()
+    if week >= 40:
+        season_start = year
+        season_end = year + 1
+    else:
+        season_start = year - 1
+        season_end = year
+    return f"{season_start}_{season_end}"
+
+
+def get_sample_lineage_value(sample_obj, property_name):
+    """Return a lineage value for the requested property name."""
+    if not sample_obj:
+        return ""
+    lineage_values = getattr(sample_obj, "surveillance_lineages", None)
+    if lineage_values is not None:
+        for lineage_value in lineage_values:
+            if lineage_value.lineage_fieldID.property_name == property_name:
+                return lineage_value.value or ""
+        return ""
+    lineage_value = sample_obj.lineage_values.filter(
+        lineage_fieldID__property_name=property_name
+    ).last()
+    return lineage_value.value if lineage_value else ""
+
+
+def get_sample_bioinfo_value(sample_obj, property_name):
+    """Return a bioinfo analysis value for the requested property name."""
+    if not sample_obj:
+        return ""
+    bioinfo_values = getattr(sample_obj, "surveillance_bioinfo_values", None)
+    if bioinfo_values is not None:
+        for bioinfo_value in bioinfo_values:
+            if bioinfo_value.bioinfo_analysis_fieldID.property_name == property_name:
+                return bioinfo_value.value or ""
+        return ""
+    bioinfo_value = sample_obj.bio_analysis_values.filter(
+        bioinfo_analysis_fieldID__property_name=property_name
+    ).last()
+    return bioinfo_value.value if bioinfo_value else ""
+
+
+def get_sample_public_database_value(sample_obj, property_name):
+    """Return a public database value for the requested property name."""
+    if not sample_obj:
+        return ""
+    public_database_values = getattr(
+        sample_obj, "surveillance_public_database_values", None
+    )
+    if public_database_values is not None:
+        for public_database_value in public_database_values:
+            if (
+                public_database_value.public_database_fieldID.property_name
+                == property_name
+            ):
+                return public_database_value.value or ""
+        return ""
+    public_database_value = sample_obj.publicdatabasevalues_set.filter(
+        public_database_fieldID__property_name=property_name
+    ).last()
+    return public_database_value.value if public_database_value else ""
+
+
+def get_surveillance_sample_lookup(sequencing_ids):
+    """Return samples keyed by sequencing sample ID with export values prefetched."""
+    lineage_prefetch = Prefetch(
+        "lineage_values",
+        queryset=core.models.LineageValues.objects.filter(
+            lineage_fieldID__property_name__in=SURVEILLANCE_LINEAGE_FIELDS
+        ).select_related("lineage_fieldID"),
+        to_attr="surveillance_lineages",
+    )
+    bioinfo_prefetch = Prefetch(
+        "bio_analysis_values",
+        queryset=core.models.BioinfoAnalysisValue.objects.filter(
+            bioinfo_analysis_fieldID__property_name__in=SURVEILLANCE_BIOINFO_FIELDS
+        ).select_related("bioinfo_analysis_fieldID"),
+        to_attr="surveillance_bioinfo_values",
+    )
+    public_database_prefetch = Prefetch(
+        "publicdatabasevalues_set",
+        queryset=core.models.PublicDatabaseValues.objects.filter(
+            public_database_fieldID__property_name__in=(
+                SURVEILLANCE_PUBLIC_DATABASE_FIELDS
+            )
+        ).select_related("public_database_fieldID"),
+        to_attr="surveillance_public_database_values",
+    )
+    return {
+        sample.sequencing_sample_id: sample
+        for sample in core.models.Sample.objects.filter(
+            sequencing_sample_id__in=sequencing_ids
+        ).prefetch_related(
+            lineage_prefetch, bioinfo_prefetch, public_database_prefetch
+        )
+    }
+
+
+def get_surveillance_sample_row(row, sample_obj):
+    """Return one per-sample surveillance export row."""
+    iskylims_project_values = get_iskylims_project_values(sample_obj)
+    collection_date = row["collection_date"]
+    return [
+        sample_obj.collecting_lab_sample_id if sample_obj else "",
+        sample_obj.sequencing_sample_id if sample_obj else row["sequencing_id"],
+        sample_obj.microbiology_lab_sample_id if sample_obj else "",
+        sample_obj.sample_unique_id if sample_obj else "",
+        get_sample_public_database_value(sample_obj, "gisaid_accession_id"),
+        sample_obj.collecting_institution if sample_obj else "",
+        sample_obj.submitting_institution if sample_obj else "",
+        iskylims_project_values.get("Submitting Institution Identifier", ""),
+        iskylims_project_values.get("Autonomic Community", ""),
+        iskylims_project_values.get("Province", ""),
+        collection_date,
+        get_collection_iso_week(collection_date),
+        get_epi_season(collection_date),
+        get_sample_lineage_value(sample_obj, "lineage_assignment"),
+        get_sample_lineage_value(
+            sample_obj, "lineage_assignment_software_version"
+        ),
+        get_sample_lineage_value(
+            sample_obj, "lineage_assignment_database_version"
+        ),
+        get_sample_bioinfo_value(sample_obj, "bioinformatics_analysis_date"),
+        get_sample_bioinfo_value(sample_obj, "per_genome_greater_10x"),
+        get_sample_bioinfo_value(sample_obj, "qc_test"),
+        get_sample_bioinfo_value(sample_obj, "consensus_sequence_filename"),
+    ]
+
+
+def build_surveillance_workbook(filtered_rows):
+    """Build the surveillance data workbook for filtered sample browser rows."""
+    sequencing_ids = [row["sequencing_id"] for row in filtered_rows]
+    sample_lookup = get_surveillance_sample_lookup(sequencing_ids)
+    workbook = Workbook()
+    worksheet = workbook.active
+    worksheet.title = "per_sample_data"
+    worksheet.append(SURVEILLANCE_COLUMNS)
+    for row in filtered_rows:
+        sample_obj = sample_lookup.get(row["sequencing_id"])
+        worksheet.append(get_surveillance_sample_row(row, sample_obj))
+    return workbook
+
+
 def get_sample_display_data(sample_id, user):
     """Check if user is allowed to see the data and if true collect all info
     from sample to display
diff --git a/core/views.py b/core/views.py
index 513cf0e7..a6564694 100644
--- a/core/views.py
+++ b/core/views.py
@@ -9,11 +9,9 @@
 from django.http import HttpResponse, JsonResponse
 from django.contrib.auth.decorators import login_required
 from django.contrib.auth.models import Group
-from django.db.models import Prefetch
 from django.utils import timezone
 from django.utils.http import url_has_allowed_host_and_scheme
 from django.views.decorators.http import require_POST
-from openpyxl import Workbook
 
 # Local imports
 import core.models
@@ -467,85 +465,6 @@ def search_sample_csv(request):
     return response
 
 
-def _get_collection_iso_week(collection_date):
-    """Return ISO week in YYYY-WNN format from a collection date string."""
-    if not collection_date:
-        return ""
-    try:
-        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
-    except ValueError:
-        return ""
-    iso_year, iso_week, _ = parsed_date.isocalendar()
-    return f"{iso_year}-W{iso_week:02d}"
-
-
-def _get_epi_season(collection_date):
-    """Return epidemiological season in YYYY_YYYY format."""
-    if not collection_date:
-        return ""
-    try:
-        parsed_date = datetime.strptime(collection_date, "%Y-%m-%d")
-    except ValueError:
-        return ""
-    year, week, _weekday = parsed_date.isocalendar()
-    if week >= 40:
-        season_start = year
-        season_end = year + 1
-    else:
-        season_start = year - 1
-        season_end = year
-    return f"{season_start}_{season_end}"
-
-
-
-def _get_sample_lineage_value(sample, property_name):
-    """Return a lineage value for the requested property name."""
-    if not sample:
-        return ""
-    lineage_values = getattr(sample, "surveillance_lineages", None)
-    if lineage_values is not None:
-        for lineage_value in lineage_values:
-            if lineage_value.lineage_fieldID.property_name == property_name:
-                return lineage_value.value or ""
-        return ""
-    lineage_value = sample.lineage_values.filter(
-        lineage_fieldID__property_name=property_name
-    ).last()
-    return lineage_value.value if lineage_value else ""
-
-
-def _get_sample_bioinfo_value(sample, property_name):
-    """Return a bioinfo analysis value for the requested property name."""
-    if not sample:
-        return ""
-    bioinfo_values = getattr(sample, "surveillance_bioinfo_values", None)
-    if bioinfo_values is not None:
-        for bioinfo_value in bioinfo_values:
-            if bioinfo_value.bioinfo_analysis_fieldID.property_name == property_name:
-                return bioinfo_value.value or ""
-        return ""
-    bioinfo_value = sample.bio_analysis_values.filter(
-        bioinfo_analysis_fieldID__property_name=property_name
-    ).last()
-    return bioinfo_value.value if bioinfo_value else ""
-
-
-def _get_sample_public_database_value(sample, property_name):
-    """Return a public database value for the requested property name."""
-    if not sample:
-        return ""
-    public_database_values = getattr(sample, "surveillance_public_database_values", None)
-    if public_database_values is not None:
-        for public_database_value in public_database_values:
-            if public_database_value.public_database_fieldID.property_name == property_name:
-                return public_database_value.value or ""
-        return ""
-    public_database_value = sample.publicdatabasevalues_set.filter(
-        public_database_fieldID__property_name=property_name
-    ).last()
-    return public_database_value.value if public_database_value else ""
-
-
 @login_required
 def search_sample_surveillance_data(request):
     """Download surveillance data for the currently filtered sample browser rows."""
@@ -556,107 +475,7 @@ def search_sample_surveillance_data(request):
             _get_filtered_search_sample_data(request, sample_rows)
         )
 
-    sequencing_ids = [row["sequencing_id"] for row in filtered_rows]
-    lineage_prefetch = Prefetch(
-        "lineage_values",
-        queryset=core.models.LineageValues.objects.filter(
-            lineage_fieldID__property_name__in=[
-                "lineage_assignment",
-                "lineage_assignment_software_version",
-                "lineage_assignment_database_version",
-            ]
-        ).select_related("lineage_fieldID"),
-        to_attr="surveillance_lineages",
-    )
-    bioinfo_prefetch = Prefetch(
-        "bio_analysis_values",
-        queryset=core.models.BioinfoAnalysisValue.objects.filter(
-            bioinfo_analysis_fieldID__property_name__in=[
-                "per_genome_greater_10x",
-                "bioinformatics_analysis_date",
-                "consensus_sequence_filename",
-                "qc_test",
-            ]
-        ).select_related("bioinfo_analysis_fieldID"),
-        to_attr="surveillance_bioinfo_values",
-    )
-    public_database_prefetch = Prefetch(
-        "publicdatabasevalues_set",
-        queryset=core.models.PublicDatabaseValues.objects.filter(
-            public_database_fieldID__property_name="gisaid_accession_id"
-        ).select_related("public_database_fieldID"),
-        to_attr="surveillance_public_database_values",
-    )
-    sample_lookup = {
-        sample.sequencing_sample_id: sample
-        for sample in core.models.Sample.objects.filter(
-            sequencing_sample_id__in=sequencing_ids
-        ).prefetch_related(
-            lineage_prefetch, bioinfo_prefetch, public_database_prefetch
-        )
-    }
-
-    workbook = Workbook()
-    worksheet = workbook.active
-    worksheet.title = "per_sample_data"
-    worksheet.append(
-        [
-            "COLLECTING_LAB_SAMPLE_ID",
-            "SEQUENCING_SAMPLE_ID",
-            "MICROBIOLOGY_LAB_SAMPLE_ID",
-            "UNIQUE_SAMPLE_ID",
-            "GISAID_ACCESSION_ID",
-            "COLLECTING_INSTITUTION",
-            "SUBMITTING_INSTITUTION",
-            "SUBMITTING_INSTITUTION_ID",
-            "CCAA",
-            "PROVINCE",
-            "SAMPLE_COLLECTION_DATE",
-            "WEEK",
-            "SEASON",
-            "LINEAGE",
-            "PANGOLIN_SOFTWARE_VERSION",
-            "PANGOLIN_DATABASE_VERSION",
-            "ANALYSIS_DATE",
-            "COVERAGE_10X",
-            "QC_TEST",
-            "CONSENSUS_SEQUENCE_FILENAME",
-        ]
-    )
-    for row in filtered_rows:
-        sample = sample_lookup.get(row["sequencing_id"])
-        iskylims_project_values = core.utils.samples.get_iskylims_project_values(
-            sample
-        )
-        worksheet.append(
-            [
-                sample.collecting_lab_sample_id if sample else "",
-                sample.sequencing_sample_id if sample else row["sequencing_id"],
-                sample.microbiology_lab_sample_id if sample else "",
-                sample.sample_unique_id if sample else "",
-                _get_sample_public_database_value(sample, "gisaid_accession_id"),
-                sample.collecting_institution if sample else "",
-                sample.submitting_institution if sample else "",
-                iskylims_project_values.get("Submitting Institution Identifier", ""),
-                iskylims_project_values.get("Autonomic Community", ""),
-                iskylims_project_values.get("Province", ""),
-                row["collection_date"],
-                _get_collection_iso_week(row["collection_date"]),
-                _get_epi_season(row["collection_date"]),
-                _get_sample_lineage_value(sample, "lineage_assignment"),
-                _get_sample_lineage_value(
-                    sample, "lineage_assignment_software_version"
-                ),
-                _get_sample_lineage_value(
-                    sample, "lineage_assignment_database_version"
-                ),
-                _get_sample_bioinfo_value(sample, "bioinformatics_analysis_date"),
-                _get_sample_bioinfo_value(sample, "per_genome_greater_10x"),
-                _get_sample_bioinfo_value(sample, "qc_test"),
-                _get_sample_bioinfo_value(sample, "consensus_sequence_filename"),
-            ]
-        )
-
+    workbook = core.utils.samples.build_surveillance_workbook(filtered_rows)
     output = BytesIO()
     workbook.save(output)
     output.seek(0)

From 04091c382058d797270a955df6234297d36b8298 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 10:56:54 +0200
Subject: [PATCH 13/21] Added button to download variant data

---
 core/templates/core/searchSample.html |  57 +++++++++---
 core/urls.py                          |   5 +
 core/utils/variants.py                | 129 ++++++++++++++++++++++++++
 core/views.py                         |  24 +++++
 4 files changed, 202 insertions(+), 13 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index bc5d0f2e..4e8d71e1 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -173,7 +173,11 @@
       display: flex;
       gap: 0.5rem;
       justify-content: center;
-      flex-wrap: nowrap;
+      flex-wrap: wrap;
+    }
+    .sample-browser-download-break {
+      flex-basis: 100%;
+      height: 0;
     }
     .sample-browser-download .sample-browser-download-button {
       background-color: rgba(var(--color-green-rgb), 0.12);
@@ -188,6 +192,11 @@
       border-color: var(--color-green);
       color: var(--color-white);
     }
+    #sample_card .card-body p.sample-browser-download-note {
+      font-size: 1.0rem !important;
+      line-height: 1.2;
+      margin-top: -0.5rem;
+    }
 </style>
 {% endblock %}
 
@@ -245,7 +254,8 @@ <h1>Sample Browser</h1>
                                 <div id="sample_card" class="d-none">
                                     <div class="card mx-3 my-3 w-auto p-3 border">
                                         <div class="card-body">
-                                            <p class="card-text">The following table shows the available samples to search</p>
+                                            <p class="card-text mb-1">The following table shows the available samples to search</p>
+                                            <p class="sample-browser-download-note">* All download buttons will download data only for the samples displayed after applying filters.</p>
                                             <div class="row row-space-2 margin-b-2">
                                                 <div class="col-sm-14">
                                                     <table id="sample_list" class="table table-striped table-bordered">
@@ -295,7 +305,7 @@ <h1>Sample Browser</h1>
                                             lengthMenu: [ [25, 50, 100, 200, -1], [25, 50, 100, 200, "All"] ],
                                             orderCellsTop: true,
                                             dom:
-                                                "<'row align-items-center'<'col-md-3'l><'col-md-5 sample-browser-download'><'col-md-4'f>>" +
+                                                "<'row align-items-center'<'col-md-2'l><'col-md-7 sample-browser-download'><'col-md-3'f>>" +
                                                 "<'row'<'col-sm-12'tr>>" +
                                                 "<'row'<'col-sm-12 col-md-5'i><'col-sm-12 col-md-7'p>>",
                                             responsive: true,
@@ -344,16 +354,27 @@ <h1>Sample Browser</h1>
                                                 var api = this.api();
                                                 var csvUrl = "{% url 'search_sample_csv' %}";
                                                 var surveillanceUrl = "{% url 'search_sample_surveillance_data' %}";
-                                                var surveillanceSecondsPerSample = 0.12;
+                                                var variantsLongTableUrl = "{% url 'search_sample_variants_long_table' %}";
                                                 var downloadWarningThresholdSeconds = 10;
+                                                var surveillanceDownloadEstimate = {
+                                                    baseSeconds: 0,
+                                                    secondsPerSample: 0.12
+                                                };
+                                                var variantsDownloadEstimate = {
+                                                    baseSeconds: 7,
+                                                    secondsPerSample: 0.0125
+                                                };
                                                 function getFilteredSampleCount() {
                                                     return table.page.info().recordsDisplay || 0;
                                                 }
                                                 function formatSampleCount(count) {
                                                     return count.toLocaleString('en-US');
                                                 }
-                                                function getEstimatedDownloadSeconds(count) {
-                                                    return Math.ceil(count * surveillanceSecondsPerSample);
+                                                function getEstimatedDownloadSeconds(count, estimate) {
+                                                    return Math.ceil(
+                                                        estimate.baseSeconds +
+                                                        count * estimate.secondsPerSample
+                                                    );
                                                 }
                                                 function formatEstimatedDuration(totalSeconds) {
                                                     if (totalSeconds < 60) {
@@ -366,8 +387,11 @@ <h1>Sample Browser</h1>
                                                     }
                                                     return minutes + ' min ' + seconds + ' sec';
                                                 }
-                                                function confirmLongDownload(count) {
-                                                    var estimatedSeconds = getEstimatedDownloadSeconds(count);
+                                                function confirmLongDownload(count, estimate) {
+                                                    if (!estimate) {
+                                                        return true;
+                                                    }
+                                                    var estimatedSeconds = getEstimatedDownloadSeconds(count, estimate);
                                                     if (estimatedSeconds <= downloadWarningThresholdSeconds) {
                                                         return true;
                                                     }
@@ -403,9 +427,9 @@ <h1>Sample Browser</h1>
                                                     document.body.removeChild(downloadLink);
                                                     window.URL.revokeObjectURL(objectUrl);
                                                 }
-                                                function downloadFilteredData(downloadUrl, button, loadingText, fallbackFilename) {
+                                                function downloadFilteredData(downloadUrl, button, loadingText, fallbackFilename, estimate) {
                                                     var filteredSampleCount = getFilteredSampleCount();
-                                                    if (!confirmLongDownload(filteredSampleCount)) {
+                                                    if (!confirmLongDownload(filteredSampleCount, estimate)) {
                                                         return;
                                                     }
                                                     var restoreButton = setDownloadButtonsLoading(button, loadingText);
@@ -427,15 +451,22 @@ <h1>Sample Browser</h1>
                                                         })
                                                         .finally(restoreButton);
                                                 }
-                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download filtered table</button>')
+                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download shown table *</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
                                                         downloadFilteredData(csvUrl, $(this), 'Generating table...', 'relecov_samples.csv');
                                                     });
-                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download surveillance data</button>')
+                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download surveillance data *</button>')
+                                                    .appendTo($('.sample-browser-download'))
+                                                    .on('click', function () {
+                                                        downloadFilteredData(surveillanceUrl, $(this), 'Generating surveillance data...', 'surveillance_data.xlsx', surveillanceDownloadEstimate);
+                                                    });
+                                                $('<span class="sample-browser-download-break" aria-hidden="true"></span>')
+                                                    .appendTo($('.sample-browser-download'));
+                                                $('<button type="button" class="btn btn-sm sample-browser-download-button">Download variants long table *</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
-                                                        downloadFilteredData(surveillanceUrl, $(this), 'Generating surveillance data...', 'surveillance_data.xlsx');
+                                                        downloadFilteredData(variantsLongTableUrl, $(this), 'Generating variants long table...', 'variants_long_table.xlsx', variantsDownloadEstimate);
                                                     });
 
                                                 [0].forEach(function(index) {
diff --git a/core/urls.py b/core/urls.py
index 835ca520..f09ff828 100644
--- a/core/urls.py
+++ b/core/urls.py
@@ -66,6 +66,11 @@
         core.views.search_sample_surveillance_data,
         name="search_sample_surveillance_data",
     ),
+    path(
+        "searchSample/variants-long-table",
+        core.views.search_sample_variants_long_table,
+        name="search_sample_variants_long_table",
+    ),
 ]
 if settings.DEBUG:
     urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
diff --git a/core/utils/variants.py b/core/utils/variants.py
index 25bb0718..de1be9ee 100644
--- a/core/utils/variants.py
+++ b/core/utils/variants.py
@@ -1,5 +1,7 @@
 # Generic imports
+from collections import defaultdict
 from django.db.models import F
+from openpyxl import Workbook
 
 # Local imports
 import core.models
@@ -97,6 +99,133 @@ def get_variant_data_from_sample(sample_id):
     return data
 
 
+VARIANTS_LONG_TABLE_COLUMNS = [
+    "sample",
+    "chrom",
+    "pos",
+    "ref",
+    "alt",
+    "dp",
+    "ref_dp",
+    "alt_dp",
+    "af",
+    "Gene ID",
+    "hgvs_c",
+    "hgvs_p",
+    "hgvs_p_1_letter",
+]
+
+
+def merge_variant_annotation_values(annotation_values):
+    """Merge annotation values following the SampleDisplay table style."""
+    if not annotation_values:
+        return ["-", "-", "-", "-"]
+    merged_values = []
+    for idx in range(len(annotation_values[0])):
+        column_values = [values[idx] for values in annotation_values]
+        unique_values = []
+        for value in column_values:
+            if value not in unique_values:
+                unique_values.append(value)
+        merged_values.append(" - ".join(unique_values))
+    return merged_values
+
+
+def get_variant_annotation_row(variant_obj, annotation_map=None):
+    """Return one merged annotation row fragment for one variant."""
+    if annotation_map is None:
+        variant_annotations = core.models.VariantAnnotation.objects.filter(
+            variantID_id=variant_obj
+        ).select_related("geneID_id")
+        annotations = list(variant_annotations)
+    else:
+        annotations = annotation_map.get(variant_obj.pk, [])
+    annotation_values = [
+        [
+            variant_annotation.get_geneID_id(),
+            variant_annotation.hgvs_c,
+            variant_annotation.hgvs_p,
+            variant_annotation.hgvs_p_1_letter,
+        ]
+        for variant_annotation in annotations
+    ]
+    return merge_variant_annotation_values(annotation_values)
+
+
+def get_variant_annotation_map(variant_ids):
+    """Return variant annotations grouped by variant ID."""
+    annotation_map = defaultdict(list)
+    variant_annotations = core.models.VariantAnnotation.objects.filter(
+        variantID_id__in=variant_ids
+    ).select_related("geneID_id")
+    for variant_annotation in variant_annotations:
+        annotation_map[variant_annotation.variantID_id_id].append(variant_annotation)
+    return annotation_map
+
+
+def get_variants_long_table_rows(filtered_rows):
+    """Return one row per sample variant annotation for filtered sample rows."""
+    sequencing_ids = [row["sequencing_id"] for row in filtered_rows]
+    variant_in_samples = list(
+        core.models.VariantInSample.objects.filter(
+            sampleID_id__sequencing_sample_id__in=sequencing_ids
+        )
+        .select_related(
+            "sampleID_id",
+            "variantID_id",
+            "variantID_id__chromosomeID_id",
+        )
+        .order_by("sampleID_id__sequencing_sample_id", "variantID_id__pos")
+    )
+    variant_ids = [
+        variant_in_sample.variantID_id_id
+        for variant_in_sample in variant_in_samples
+        if variant_in_sample.variantID_id_id
+    ]
+    annotation_map = get_variant_annotation_map(variant_ids)
+    rows = []
+    seen_sample_variants = set()
+    for variant_in_sample in variant_in_samples:
+        variant_obj = variant_in_sample.get_variantID_obj()
+        if variant_obj is None:
+            continue
+        sample_variant_key = (
+            variant_in_sample.sampleID_id_id,
+            variant_in_sample.variantID_id_id,
+        )
+        if sample_variant_key in seen_sample_variants:
+            continue
+        seen_sample_variants.add(sample_variant_key)
+        chromosome_obj = variant_obj.chromosomeID_id
+        variant_prefix = [
+            variant_in_sample.sampleID_id.get_sequencing_sample_id(),
+            chromosome_obj.get_chromosome_name() if chromosome_obj else "",
+            variant_obj.get_pos(),
+            variant_obj.get_ref(),
+            variant_obj.get_alt(),
+            variant_in_sample.get_dp(),
+            variant_in_sample.get_ref_dp(),
+            variant_in_sample.get_alt_dp(),
+            variant_in_sample.get_af(),
+        ]
+        annotation_row = get_variant_annotation_row(
+            variant_obj, annotation_map=annotation_map
+        )
+        rows.append(variant_prefix + annotation_row)
+    return rows
+
+
+def build_variants_long_table_workbook(filtered_rows):
+    """Build the variants long table workbook for filtered sample browser rows."""
+    workbook = Workbook()
+    worksheet = workbook.active
+    worksheet.title = "variants_long_table"
+    worksheet.append(VARIANTS_LONG_TABLE_COLUMNS)
+    for row in get_variants_long_table_rows(filtered_rows):
+        worksheet.append(row)
+    return workbook
+
+
 def get_variant_graphic_from_sample(sample_id):
     """Collect the variant information to send to create the plotly graphic"""
     v_data = {"x": [], "y": [], "v_id": []}
diff --git a/core/views.py b/core/views.py
index a6564694..7d098700 100644
--- a/core/views.py
+++ b/core/views.py
@@ -489,6 +489,30 @@ def search_sample_surveillance_data(request):
     return response
 
 
+@login_required
+def search_sample_variants_long_table(request):
+    """Download variants long table data for current sample browser filters."""
+    sample_rows = _get_search_sample_rows_for_user(request.user)
+    filtered_rows = []
+    if not (isinstance(sample_rows, dict) and "ERROR" in sample_rows):
+        filtered_rows, _lineage_options, _institution_options = (
+            _get_filtered_search_sample_data(request, sample_rows)
+        )
+
+    workbook = core.utils.variants.build_variants_long_table_workbook(filtered_rows)
+    output = BytesIO()
+    workbook.save(output)
+    output.seek(0)
+    response = HttpResponse(
+        output.getvalue(),
+        content_type=(
+            "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+        ),
+    )
+    response["Content-Disposition"] = 'attachment; filename="variants_long_table.xlsx"'
+    return response
+
+
 @login_required
 def metadata_visualization(request):
     if request.user.username != "admin":

From 811f48a32dc1ece371994d50c4c12b5e4d2aa98e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 11:30:39 +0200
Subject: [PATCH 14/21] Fixed buttons and table for smaller screens

---
 core/templates/core/searchSample.html | 33 ++++++++++++++++++++-------
 1 file changed, 25 insertions(+), 8 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 4e8d71e1..9386a9dc 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -4,8 +4,13 @@
 
 {% block extra_css %}
 <style>
+    .sample-browser-table-wrapper {
+      width: 100%;
+      overflow-x: auto;
+    }
     #sample_list {
       width: 100% !important;
+      min-width: 980px;
       table-layout: auto;
     }
     #sample_list th:first-child,
@@ -171,20 +176,29 @@
     }
     .sample-browser-download {
       display: flex;
-      gap: 0.5rem;
+      gap: 0.45rem;
       justify-content: center;
       flex-wrap: wrap;
+      margin: 0.35rem 0;
     }
     .sample-browser-download-break {
       flex-basis: 100%;
       height: 0;
     }
     .sample-browser-download .sample-browser-download-button {
+      align-items: center;
       background-color: rgba(var(--color-green-rgb), 0.12);
       border-color: var(--color-green);
       color: var(--color-green);
+      display: inline-flex;
       font-weight: 500;
-      white-space: nowrap;
+      justify-content: center;
+      line-height: 1.1;
+      min-height: 3rem;
+      padding: 0.35rem 0.55rem;
+      text-align: center;
+      white-space: normal;
+      width: 9.4rem;
     }
     .sample-browser-download .sample-browser-download-button:hover,
     .sample-browser-download .sample-browser-download-button:focus {
@@ -192,8 +206,8 @@
       border-color: var(--color-green);
       color: var(--color-white);
     }
-    #sample_card .card-body p.sample-browser-download-note {
-      font-size: 1.0rem !important;
+    #sample_card .card-body p.sample-browser-notes {
+      font-size: 0.9rem !important;
       line-height: 1.2;
       margin-top: -0.5rem;
     }
@@ -255,10 +269,12 @@ <h1>Sample Browser</h1>
                                     <div class="card mx-3 my-3 w-auto p-3 border">
                                         <div class="card-body">
                                             <p class="card-text mb-1">The following table shows the available samples to search</p>
-                                            <p class="sample-browser-download-note">* All download buttons will download data only for the samples displayed after applying filters.</p>
+                                            <p class="sample-browser-notes">* All download buttons will download data only for the samples displayed after applying filters.</p>
+                                            <p class="sample-browser-notes">** If your screen is small, you can scroll left and right to see whole table.</p>
                                             <div class="row row-space-2 margin-b-2">
-                                                <div class="col-sm-14">
-                                                    <table id="sample_list" class="table table-striped table-bordered">
+                                                <div class="col-12">
+                                                    <div class="table-responsive sample-browser-table-wrapper">
+                                                        <table id="sample_list" class="table table-striped table-bordered">
                                                         <colgroup>
                                                             <col style="width: 22%;">
                                                             <col style="width: 22%;">
@@ -280,7 +296,8 @@ <h1>Sample Browser</h1>
                                                             </tr>
                                                         </thead>
                                                         <tbody></tbody>
-                                                    </table>
+                                                        </table>
+                                                    </div>
                                                 </div>
                                             </div>
                                         </div>

From 7c4e6bf9e11214a42ae7c4c2c29b25745bff4467 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 11:31:46 +0200
Subject: [PATCH 15/21] made variants long table a CSV as it is easier to
 generate

---
 core/templates/core/searchSample.html |  2 +-
 core/views.py                         | 17 ++++++-----------
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 9386a9dc..189b04df 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -483,7 +483,7 @@ <h1>Sample Browser</h1>
                                                 $('<button type="button" class="btn btn-sm sample-browser-download-button">Download variants long table *</button>')
                                                     .appendTo($('.sample-browser-download'))
                                                     .on('click', function () {
-                                                        downloadFilteredData(variantsLongTableUrl, $(this), 'Generating variants long table...', 'variants_long_table.xlsx', variantsDownloadEstimate);
+                                                        downloadFilteredData(variantsLongTableUrl, $(this), 'Generating variants long table...', 'variants_long_table.csv', variantsDownloadEstimate);
                                                     });
 
                                                 [0].forEach(function(index) {
diff --git a/core/views.py b/core/views.py
index 7d098700..f9253cc6 100644
--- a/core/views.py
+++ b/core/views.py
@@ -499,17 +499,12 @@ def search_sample_variants_long_table(request):
             _get_filtered_search_sample_data(request, sample_rows)
         )
 
-    workbook = core.utils.variants.build_variants_long_table_workbook(filtered_rows)
-    output = BytesIO()
-    workbook.save(output)
-    output.seek(0)
-    response = HttpResponse(
-        output.getvalue(),
-        content_type=(
-            "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
-        ),
-    )
-    response["Content-Disposition"] = 'attachment; filename="variants_long_table.xlsx"'
+    response = HttpResponse(content_type="text/csv")
+    response["Content-Disposition"] = 'attachment; filename="variants_long_table.csv"'
+    writer = csv.writer(response)
+    writer.writerow(core.utils.variants.VARIANTS_LONG_TABLE_COLUMNS)
+    for row in core.utils.variants.get_variants_long_table_rows(filtered_rows):
+        writer.writerow(row)
     return response
 
 

From 2d02ba32179c9f308594ba8155c05cc35ee9f1a0 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 11:41:04 +0200
Subject: [PATCH 16/21] made the website slightly bigger

---
 core/static/core/main_style/css/main.css | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/core/static/core/main_style/css/main.css b/core/static/core/main_style/css/main.css
index 062f41ca..a8d88413 100644
--- a/core/static/core/main_style/css/main.css
+++ b/core/static/core/main_style/css/main.css
@@ -492,6 +492,10 @@ section {
   padding: 135px 0 0;
 }
 
+.hero-animated > .container.position-relative {
+  max-width: min(96vw, 1500px);
+}
+
 .hero-animated h1 {
   margin: 0 0 10px 0;
   font-size: 48px;

From 056eb7350f9adbfc2644dc975084b4ff4f9672a1 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 11:42:18 +0200
Subject: [PATCH 17/21] fixed black

---
 core/utils/samples.py | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/core/utils/samples.py b/core/utils/samples.py
index 87b9eaeb..f76f6f37 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -518,8 +518,10 @@ def get_iskylims_project_values(sample_obj):
     iskylims_data = get_iskylims_sample_information(sample_obj)
     if not iskylims_data:
         return {}
-    project_field_display_map = core.utils.rest_api.get_sample_project_field_display_map(
-        iskylims_data.get("sample_project")
+    project_field_display_map = (
+        core.utils.rest_api.get_sample_project_field_display_map(
+            iskylims_data.get("sample_project")
+        )
     )
     project_values = {}
     for key, value in iskylims_data.get("Project values", {}).items():
@@ -680,9 +682,7 @@ def get_surveillance_sample_lookup(sequencing_ids):
         sample.sequencing_sample_id: sample
         for sample in core.models.Sample.objects.filter(
             sequencing_sample_id__in=sequencing_ids
-        ).prefetch_related(
-            lineage_prefetch, bioinfo_prefetch, public_database_prefetch
-        )
+        ).prefetch_related(lineage_prefetch, bioinfo_prefetch, public_database_prefetch)
     }
 
 
@@ -705,12 +705,8 @@ def get_surveillance_sample_row(row, sample_obj):
         get_collection_iso_week(collection_date),
         get_epi_season(collection_date),
         get_sample_lineage_value(sample_obj, "lineage_assignment"),
-        get_sample_lineage_value(
-            sample_obj, "lineage_assignment_software_version"
-        ),
-        get_sample_lineage_value(
-            sample_obj, "lineage_assignment_database_version"
-        ),
+        get_sample_lineage_value(sample_obj, "lineage_assignment_software_version"),
+        get_sample_lineage_value(sample_obj, "lineage_assignment_database_version"),
         get_sample_bioinfo_value(sample_obj, "bioinformatics_analysis_date"),
         get_sample_bioinfo_value(sample_obj, "per_genome_greater_10x"),
         get_sample_bioinfo_value(sample_obj, "qc_test"),

From 29567ebd93eaa166cb639e4715aff568972c03db Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 13:22:50 +0200
Subject: [PATCH 18/21] Added bulk request to iSkyLIMS

---
 core/config.py                        |  1 +
 core/templates/core/searchSample.html |  2 +-
 core/utils/rest_api.py                | 13 ++++++
 core/utils/samples.py                 | 62 +++++++++++++++++++++++++--
 4 files changed, 74 insertions(+), 4 deletions(-)

diff --git a/core/config.py b/core/config.py
index 87404ccc..e574df0e 100644
--- a/core/config.py
+++ b/core/config.py
@@ -121,6 +121,7 @@
 ISKLIMS_PUT_LABORATORY_PARAMETER = "update-lab"
 ISKLIMS_GET_SAMPLE_FIELDS = "sample-fields"
 ISKLIMS_GET_SAMPLE_INFORMATION = ["sample-info", "sample"]
+ISKLIMS_GET_SAMPLE_PROJECT_VALUES_BULK = ["sample-project-values-bulk"]
 ISKLIMS_GET_SAMPLE_PARAMETER_INFORMATION = ["sample-info", "parameter"]
 ISKLIMS_GET_SAMPLE_PROJECT_PARAMETER_INFORMATION = ["sample-info"]
 ISKLIMS_GET_SAMPLE_PROJECT_FIELDS = ["projects-fields", "project"]
diff --git a/core/templates/core/searchSample.html b/core/templates/core/searchSample.html
index 189b04df..b3a1cdb6 100644
--- a/core/templates/core/searchSample.html
+++ b/core/templates/core/searchSample.html
@@ -375,7 +375,7 @@ <h1>Sample Browser</h1>
                                                 var downloadWarningThresholdSeconds = 10;
                                                 var surveillanceDownloadEstimate = {
                                                     baseSeconds: 0,
-                                                    secondsPerSample: 0.12
+                                                    secondsPerSample: 0.008
                                                 };
                                                 var variantsDownloadEstimate = {
                                                     baseSeconds: 7,
diff --git a/core/utils/rest_api.py b/core/utils/rest_api.py
index a47f0a9d..1000cd67 100644
--- a/core/utils/rest_api.py
+++ b/core/utils/rest_api.py
@@ -113,6 +113,19 @@ def get_sample_information(sample_name):
     return data["data"]
 
 
+def get_sample_project_values_bulk(sample_names, fields=None):
+    """Fetch selected iSkyLIMS project values for many samples in one request."""
+    query_data = {"samples": ",".join(sample_names)}
+    if fields:
+        query_data["fields"] = ",".join(fields)
+    data = create_get_api_instance(
+        core.config.ISKLIMS_GET_SAMPLE_PROJECT_VALUES_BULK, query_data
+    )
+    if "ERROR" in data:
+        return {"ERROR": data}
+    return data["data"]
+
+
 def get_sample_parameter_data(param_data):
     if isinstance(param_data, dict):
         data = create_get_api_instance(
diff --git a/core/utils/samples.py b/core/utils/samples.py
index f76f6f37..36ab431e 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -534,6 +534,47 @@ def get_iskylims_project_value(sample_obj, label_name):
     return get_iskylims_project_values(sample_obj).get(label_name, "")
 
 
+def get_iskylims_project_values_bulk(sample_objs):
+    """Return iSkyLIMS project values keyed by sequencing sample ID."""
+    sample_lookup_ids = OrderedDict()
+    request_ids = []
+    for sample_obj in sample_objs:
+        if sample_obj is None:
+            continue
+        lookup_ids = get_iskylims_lookup_ids(sample_obj)
+        if not lookup_ids:
+            continue
+        sample_lookup_ids[sample_obj.sequencing_sample_id] = lookup_ids
+        for lookup_id in lookup_ids:
+            if lookup_id not in request_ids:
+                request_ids.append(lookup_id)
+
+    if not request_ids:
+        return None
+
+    bulk_data = {}
+    for start in range(0, len(request_ids), SURVEILLANCE_ISKYLIMS_BULK_CHUNK_SIZE):
+        chunk_data = core.utils.rest_api.get_sample_project_values_bulk(
+            request_ids[start : start + SURVEILLANCE_ISKYLIMS_BULK_CHUNK_SIZE],
+            SURVEILLANCE_ISKYLIMS_FIELDS,
+        )
+        if not chunk_data or "ERROR" in chunk_data:
+            return None
+        bulk_data.update(chunk_data)
+
+    project_values_by_sample = {}
+    for sequencing_id, lookup_ids in sample_lookup_ids.items():
+        for lookup_id in lookup_ids:
+            sample_data = bulk_data.get(lookup_id)
+            if not sample_data:
+                continue
+            project_values_by_sample[sequencing_id] = sample_data.get(
+                "Project values", {}
+            )
+            break
+    return project_values_by_sample
+
+
 SURVEILLANCE_LINEAGE_FIELDS = [
     "lineage_assignment",
     "lineage_assignment_software_version",
@@ -546,6 +587,12 @@ def get_iskylims_project_value(sample_obj, label_name):
     "qc_test",
 ]
 SURVEILLANCE_PUBLIC_DATABASE_FIELDS = ["gisaid_accession_id"]
+SURVEILLANCE_ISKYLIMS_FIELDS = [
+    "Submitting Institution Identifier",
+    "Autonomic Community",
+    "Province",
+]
+SURVEILLANCE_ISKYLIMS_BULK_CHUNK_SIZE = 200
 SURVEILLANCE_COLUMNS = [
     "COLLECTING_LAB_SAMPLE_ID",
     "SEQUENCING_SAMPLE_ID",
@@ -686,9 +733,10 @@ def get_surveillance_sample_lookup(sequencing_ids):
     }
 
 
-def get_surveillance_sample_row(row, sample_obj):
+def get_surveillance_sample_row(row, sample_obj, iskylims_project_values=None):
     """Return one per-sample surveillance export row."""
-    iskylims_project_values = get_iskylims_project_values(sample_obj)
+    if iskylims_project_values is None:
+        iskylims_project_values = get_iskylims_project_values(sample_obj)
     collection_date = row["collection_date"]
     return [
         sample_obj.collecting_lab_sample_id if sample_obj else "",
@@ -718,13 +766,21 @@ def build_surveillance_workbook(filtered_rows):
     """Build the surveillance data workbook for filtered sample browser rows."""
     sequencing_ids = [row["sequencing_id"] for row in filtered_rows]
     sample_lookup = get_surveillance_sample_lookup(sequencing_ids)
+    iskylims_values_lookup = get_iskylims_project_values_bulk(sample_lookup.values())
     workbook = Workbook()
     worksheet = workbook.active
     worksheet.title = "per_sample_data"
     worksheet.append(SURVEILLANCE_COLUMNS)
     for row in filtered_rows:
         sample_obj = sample_lookup.get(row["sequencing_id"])
-        worksheet.append(get_surveillance_sample_row(row, sample_obj))
+        iskylims_project_values = None
+        if iskylims_values_lookup is not None:
+            iskylims_project_values = iskylims_values_lookup.get(
+                row["sequencing_id"], {}
+            )
+        worksheet.append(
+            get_surveillance_sample_row(row, sample_obj, iskylims_project_values)
+        )
     return workbook
 
 

From 53c9e2c5a746de6b04c3a515ac3b98ab104cc72e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 14:02:05 +0200
Subject: [PATCH 19/21] Fixed tittle upper distance

---
 core/static/core/custom/css/side_bar_menu.css | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/core/static/core/custom/css/side_bar_menu.css b/core/static/core/custom/css/side_bar_menu.css
index 1d62f1b7..9bb92edb 100644
--- a/core/static/core/custom/css/side_bar_menu.css
+++ b/core/static/core/custom/css/side_bar_menu.css
@@ -14,6 +14,10 @@
   flex: 1 0 auto;
 }
 
+#wrapper #content-wrapper #content > .container-fluid > .row:first-child {
+  padding-top: 1.5rem;
+}
+
 /* Clases auxiliares */
 .rounded-circle {
   border-radius: 50% !important;
@@ -209,4 +213,4 @@
   display: block;
   font-size: 0.6rem;
   margin-top: 0.25rem;
-}
\ No newline at end of file
+}

From 9986261a07f6994d8f19b78fd8459f9849261d71 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Thu, 2 Jul 2026 14:02:37 +0200
Subject: [PATCH 20/21] Fixed admin contact data error

---
 core/views.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/core/views.py b/core/views.py
index f9253cc6..f2dd8e94 100644
--- a/core/views.py
+++ b/core/views.py
@@ -939,6 +939,16 @@ def organism_annotation(request):
 def laboratory_contact(request):
     lab_data = core.utils.labs.get_lab_contact_details(request.user)
     user_lab = core.utils.labs.get_lab_name_from_user(request.user)
+    if not isinstance(lab_data, dict):
+        lab_label = user_lab or request.user.username
+        return render(
+            request,
+            "core/laboratoryContact.html",
+            {
+                "ERROR": f"No contact data found for your user {lab_label}",
+                "lab_data": {},
+            },
+        )
     proc_lab_data = {k.replace(" ", "_").lower(): v for k, v in lab_data.items()}
     if "ERROR" in lab_data:
         return render(

From 2bb7ae184bcc656c0ffd07bdb2ca45f031861a96 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Fri, 3 Jul 2026 10:11:46 +0200
Subject: [PATCH 21/21] added aggregated surveillance data

---
 core/utils/samples.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/core/utils/samples.py b/core/utils/samples.py
index 36ab431e..92b8039b 100644
--- a/core/utils/samples.py
+++ b/core/utils/samples.py
@@ -4,7 +4,7 @@
 import shutil
 import hashlib
 from datetime import datetime
-from collections import OrderedDict, defaultdict
+from collections import Counter, OrderedDict, defaultdict
 import pandas as pd
 from openpyxl import Workbook
 from django.contrib.auth.models import Group, User
@@ -615,6 +615,10 @@ def get_iskylims_project_values_bulk(sample_objs):
     "QC_TEST",
     "CONSENSUS_SEQUENCE_FILENAME",
 ]
+SURVEILLANCE_AGGREGATED_COLUMNS = [
+    "LINEAGE",
+    "NUMBER_SAMPLES",
+]
 
 
 def get_collection_iso_week(collection_date):
@@ -771,6 +775,7 @@ def build_surveillance_workbook(filtered_rows):
     worksheet = workbook.active
     worksheet.title = "per_sample_data"
     worksheet.append(SURVEILLANCE_COLUMNS)
+    lineage_counts = Counter()
     for row in filtered_rows:
         sample_obj = sample_lookup.get(row["sequencing_id"])
         iskylims_project_values = None
@@ -778,9 +783,17 @@ def build_surveillance_workbook(filtered_rows):
             iskylims_project_values = iskylims_values_lookup.get(
                 row["sequencing_id"], {}
             )
-        worksheet.append(
-            get_surveillance_sample_row(row, sample_obj, iskylims_project_values)
+        sample_row = get_surveillance_sample_row(
+            row, sample_obj, iskylims_project_values
         )
+        worksheet.append(sample_row)
+        lineage = sample_row[SURVEILLANCE_COLUMNS.index("LINEAGE")]
+        if lineage:
+            lineage_counts[lineage] += 1
+    aggregated_worksheet = workbook.create_sheet("aggregated_data")
+    aggregated_worksheet.append(SURVEILLANCE_AGGREGATED_COLUMNS)
+    for lineage, count in sorted(lineage_counts.items()):
+        aggregated_worksheet.append([lineage, count])
     return workbook