From ffd827d8ab5a544437e13c4001157954257a5921 Mon Sep 17 00:00:00 2001
From: adkinsrs <sadkins@som.umaryland.edu>
Date: Fri, 30 Aug 2024 11:27:10 -0400
Subject: [PATCH 1/2] Resolving #880

---
 lib/geardb.py                    |  4 ++--
 www/cgi/save_dataset_display.cgi | 16 +++++++++++++---
 www/dataset_curator.html         |  8 ++++++++
 www/js/curator_common.js         | 23 ++++++++++++++++++++---
 www/multigene_curator.html       |  8 ++++++++
 5 files changed, 51 insertions(+), 8 deletions(-)

diff --git a/lib/geardb.py b/lib/geardb.py
index ca452698..bc273a50 100644
--- a/lib/geardb.py
+++ b/lib/geardb.py
@@ -108,7 +108,7 @@ def get_analysis(analysis, dataset_id, session_id):
 
         # Check that the h5ad file exists
         if not os.path.exists(ana.dataset_path()):
-            raise FileNotFoundError("No h5 file found for the passed in analysis")
+            raise FileNotFoundError("No h5 file found for the passed in analysis {}".format(ana.dataset_path()))
 
     else:
         ds = Dataset(id=dataset_id, has_h5ad=1)
@@ -116,7 +116,7 @@ def get_analysis(analysis, dataset_id, session_id):
 
         # Let's not fail if the file isn't there
         if not os.path.exists(h5_path):
-            raise FileNotFoundError("No h5 file found for this dataset")
+            raise FileNotFoundError("No h5 file found for this dataset {}".format(h5_path))
         ana = Analysis(type='primary', dataset_id=dataset_id)
     return ana
 
diff --git a/www/cgi/save_dataset_display.cgi b/www/cgi/save_dataset_display.cgi
index e799819f..330cff80 100755
--- a/www/cgi/save_dataset_display.cgi
+++ b/www/cgi/save_dataset_display.cgi
@@ -93,6 +93,14 @@ def main():
     cursor = cnx.get_cursor()
 
     user = geardb.get_user_from_session_id(session_id=session_id)
+
+    if not user:
+        print('User not found for session_id {}'.format(session_id), file=sys.stderr)
+        sys.stdout = original_stdout
+        print('Content-Type: application/json\n\n')
+        print(json.dumps(dict(display_id=None, success=False)))
+        return
+
     user_id = user.id
 
     if display_id:
@@ -113,10 +121,10 @@ def main():
                 WHERE id = %s;
             """
             cursor.execute(query, (label, plot_type, plotly_config, display_id))
-            result = dict(success=True)
+            result = dict(display_id=display_id, success=True)
         else:
             print('UPDATE DIDNT HAPPEN?', file=sys.stderr)
-            result = dict(success=False)
+            result = dict(display_id=display_id, success=False)
     else:
         # Display doesn't exist yet, insert new
 
@@ -155,7 +163,8 @@ def main():
         print("Invalid filename: {}".format(filename), file=sys.stderr)
         sys.stdout = original_stdout
         print('Content-Type: application/json\n\n')
-        print(json.dumps(dict(success=False)))
+        result["success"] = False
+        print(json.dumps(result))
         return
 
     # Add plot_type to config so it can be passed in the POST cmd as well
@@ -167,6 +176,7 @@ def main():
     image_success = False
     url = "https://localhost/api/plot/{}".format(dataset_id)
 
+    is_local = True
     if is_local:
         url = alt_url
 
diff --git a/www/dataset_curator.html b/www/dataset_curator.html
index abb47257..3f284e1b 100644
--- a/www/dataset_curator.html
+++ b/www/dataset_curator.html
@@ -360,6 +360,14 @@ <h5 class="title is-5 is-clickable js-collapsable-trigger">
                   <input id="new-display-label" class="input" type="text" placeholder="Enter name of display" />
                 </div>
               </div>
+              <div class="field">
+                <div class="control">
+                  <label class="checkbox" disabled>
+                    <input type="checkbox" id="overwrite-display-check" disabled>
+                    Overwrite existing display instead
+                  </label>
+                </div>
+              </div>
               <div class="field">
                 <div class="control">
                   <label class="checkbox">
diff --git a/www/js/curator_common.js b/www/js/curator_common.js
index f27a6ccc..137139b1 100644
--- a/www/js/curator_common.js
+++ b/www/js/curator_common.js
@@ -12,6 +12,7 @@ let catColumns = [];
 let levels = {};    // categorical columns as keys + groups as values
 
 let datasetId = null;
+let chosenDisplayId = null;
 let organismId = null;
 let analysisObj = null;
 
@@ -344,8 +345,8 @@ const curatorApiCallsMixin = {
                 throw new Error("Could not save this new display. Please contact the gEAR team.");
             }
 
-            // Make new display card and make it the default display
-            renderUserDisplayCard({id: display_id, label, plot_type: plotType, plotly_config: plotConfig}, display_id);
+            // Ensure the display is not a default display (the user must choose to make it default)
+            renderUserDisplayCard({id: display_id, label, plot_type: plotType, plotly_config: plotConfig}, -1);
 
             return display_id;
         } catch (error) {
@@ -535,6 +536,12 @@ const chooseNewDisplay = async () => {
     document.getElementById("plot-type-select-c-failed").classList.remove("is-hidden");
     document.getElementById("plot-options-s-success").classList.add("is-hidden");
 
+    // Ensure display saves as a new display
+    chosenDisplayId = null;
+    document.getElementById("overwrite-display-check").checked = false;
+    document.getElementById("overwrite-display-check").disabled = true;
+    disableCheckboxLabel(document.getElementById("overwrite-display-check"), true);
+
     // update genes, analysis, and plot type selects in parallel
     await Promise.all([
         updateDatasetGenes(),
@@ -602,6 +609,11 @@ const cloneDisplay = async (event, display) => {
     const cloneElt = event.currentTarget;
     cloneElt.classList.add("is-loading");
 
+    // Give user option to overwrite display
+    chosenDisplayId = display.id;
+    document.getElementById("overwrite-display-check").disabled = false;
+    disableCheckboxLabel(document.getElementById("overwrite-display-check"), false);
+
     await updateDatasetGenes(),
 
     document.getElementById("analysis-select").disabled = false;
@@ -1585,7 +1597,12 @@ document.getElementById("save-display-btn").addEventListener("click", async (eve
     const label = document.getElementById("new-display-label").value;
     event.target.classList.add("is-loading");
     try {
-        const displayId = await curatorApiCallsMixin.saveDatasetDisplay(datasetId, null, label, plotStyle.plotType, plotStyle.plotConfig);
+        let displayIdToUse = null;
+        if (document.getElementById("overwrite-display-check").checked) {
+            displayIdToUse = chosenDisplayId;
+        }
+
+        const displayId = await curatorApiCallsMixin.saveDatasetDisplay(datasetId, displayIdToUse, label, plotStyle.plotType, plotStyle.plotConfig);
         createToast("Display saved.", "is-success");
 
         if (document.getElementById("make-default-display-check").checked) {
diff --git a/www/multigene_curator.html b/www/multigene_curator.html
index 72d50dfc..d17c1fd2 100644
--- a/www/multigene_curator.html
+++ b/www/multigene_curator.html
@@ -378,6 +378,14 @@ <h5 class="title is-5 is-clickable js-collapsable-trigger">
                   <input id="new-display-label" class="input" type="text" placeholder="Enter name of display" />
                 </div>
               </div>
+              <div class="field">
+                <div class="control">
+                  <label class="checkbox" disabled>
+                    <input type="checkbox" id="overwrite-display-check" disabled>
+                    Overwrite existing display instead
+                  </label>
+                </div>
+              </div>
               <div class="field">
                 <div class="control">
                   <label class="checkbox">

From f8766711fc5c9c92d5ca7dc8fb24050e82a83bdc Mon Sep 17 00:00:00 2001
From: adkinsrs <sadkins@som.umaryland.edu>
Date: Fri, 30 Aug 2024 11:27:58 -0400
Subject: [PATCH 2/2] need to remove devel variable

---
 www/cgi/save_dataset_display.cgi | 1 -
 1 file changed, 1 deletion(-)

diff --git a/www/cgi/save_dataset_display.cgi b/www/cgi/save_dataset_display.cgi
index 330cff80..57a27677 100755
--- a/www/cgi/save_dataset_display.cgi
+++ b/www/cgi/save_dataset_display.cgi
@@ -176,7 +176,6 @@ def main():
     image_success = False
     url = "https://localhost/api/plot/{}".format(dataset_id)
 
-    is_local = True
     if is_local:
         url = alt_url