Merge branch 'ui-v2' of github.com:IGS/gEAR into ui-v2

lib/geardb.py

@@ -108,15 +108,15 @@ 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)
         h5_path = ds.get_file_path()
 
         # 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
 

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

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">

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) {

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">