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

lib/geardb.py

@@ -1728,6 +1728,38 @@ def save(self):
             cursor.close()
             conn.close()
 
+    def remove(self):
+        """
+        Deletes the current display from the database.
+        """
+        conn = Connection()
+        cursor = conn.get_cursor()
+
+        # first remove any layout_display entries
+        qry = """
+                DELETE FROM layout_displays
+                WHERE display_id = %s
+        """
+        cursor.execute(qry, (self.id,))
+
+        # Then remove from anly dataset_preference entries
+        qry = """
+                DELETE FROM dataset_preference
+                WHERE display_id = %s
+        """
+        cursor.execute(qry, (self.id,))
+
+        # Then remove the display itself
+        qry = """
+                DELETE FROM dataset_display
+                WHERE id = %s
+        """
+        cursor.execute(qry, (self.id,))
+
+        cursor.close()
+        conn.commit()
+        conn.close()
+
 @dataclass
 class Dataset:
     id: str

www/api/resources/multigene_dash_data.py

@@ -142,15 +142,16 @@ def post(self, dataset_id):
 
         try:
             ana = geardb.get_analysis(analysis, dataset_id, session_id)
+            # Using adata with "backed" mode does not work with volcano plot
+            adata = ana.get_adata(backed=False)
         except Exception as e:
+            import traceback
+            traceback.print_exc()
             return {
                 'success': -1,
                 'message': str(e),
             }
 
-        # Using adata with "backed" mode does not work with volcano plot
-        adata = ana.get_adata(backed=False)
-
         adata.obs = order_by_time_point(adata.obs)
 
         # get a map of all levels for each column

www/api/resources/plotly_data.py

@@ -119,13 +119,14 @@ def post(self, dataset_id):
 
         try:
             ana = geardb.get_analysis(analysis, dataset_id, session_id)
+            adata = ana.get_adata(backed=True)
         except Exception as e:
+            import traceback
+            traceback.print_exc()
             return_dict["success"] = -1
             return_dict["message"] = str(e)
             return return_dict
 
-        adata = ana.get_adata(backed=True)
-
         if projection_id:
             try:
                 adata = create_projection_adata(adata, dataset_id, projection_id)

www/api/resources/tsne_data.py

@@ -211,13 +211,15 @@ def post(self, dataset_id):
 
         try:
             ana = geardb.get_analysis(analysis, dataset_id, session_id)
+            adata = ana.get_adata(backed=True)
         except Exception as e:
+            import traceback
+            traceback.print_exc()
             return {
                 "success": -1,
                 "message": str(e)
             }
 
-        adata = ana.get_adata(backed=True)
 
         if projection_id:
             try:

www/cgi/delete_dataset_analysis.cgi

@@ -23,18 +23,59 @@ def main():
     session_id = form.getvalue('session_id')
     user = geardb.get_user_from_session_id(session_id)
 
+    if not user:
+        print('Content-Type: application/json\n\n')
+        print(json.dumps({'success': 0, 'error': 'User not found'}))
+        return
+
     source_ana = geardb.Analysis(id=analysis_id, type=analysis_type,
                                  dataset_id=dataset_id, session_id=session_id, user_id=user.id)
     source_pipeline_base = source_ana.base_path()
 
     result = {'success': 0}
 
+    # verify this analysis belongs to the user
+    if not os.path.exists(source_pipeline_base):
+        result = {'success': 0, 'error': 'Analysis not found'}
+        sys.stdout = original_stdout
+        print('Content-Type: application/json\n\n')
+        print(json.dumps(result))
+        return
+    if not source_ana.user_id == user.id:
+        result = {'success': 0, 'error': 'Analysis does not belong to user'}
+        sys.stdout = original_stdout
+        print('Content-Type: application/json\n\n')
+        print(json.dumps(result))
+        return
+
     try:
-        # TODO: need to verify ownership here in the future before deleting
-        #print("DEBUG: would rmtree this:{0}".format(source_pipeline_base), file=sys.stderr)
+        # move directory to a backup in case of failures
+        #shutil.move(source_pipeline_base, source_pipeline_base + '.deleted')
+
+        # find any dataset displays with this analysis id in the plotly_config
+        """
+        conn = Connection()
+        cursor = conn.get_cursor()
+        qry = "SELECT * from dataset_display where plotly_config like '%\"id\":\"{}\"%'".format(analysis_id)
+        cursor.execute(qry, (self.id,))
+        for (display_id, user_id, label, plot_type, plotly_config) in cursor:
+            display = DatasetDisplay(
+                id=display_id,
+                dataset_id=self.id,
+                user_id=user_id,
+                label=label,
+                plot_type=plot_type,
+                plotly_config=plotly_config
+            )
+            display.remove()
+        """
+
+        #shutil.rmtree(source_pipeline_base + '.deleted')
         shutil.rmtree(source_pipeline_base)
         result = {'success': 1}
     except:
+        # restore the backup
+        #shutil.move(source_pipeline_base + '.deleted', source_pipeline_base)
         result = {'success': 0, 'error': 'Unable to delete dataset'}
 
     sys.stdout = original_stdout

www/dataset_explorer.html

@@ -438,7 +438,7 @@
                                                             <div class="field">
                                                                 <label class="label">Pubmed ID</label>
                                                                 <div class="control">
-                                                                    <input class="input" readonly>
+                                                                    <input class="input">
                                                                 </div>
                                                             </div>
                                                         </div>
@@ -451,7 +451,7 @@
                                                             <div class="field">
                                                                 <label class="label">GEO ID</label>
                                                                 <div class="control">
-                                                                    <input class="input" readonly>
+                                                                    <input class="input">
                                                                 </div>
                                                             </div>
                                                         </div>

www/js/classes/analysis.js

@@ -170,6 +170,7 @@ class Analysis {
             document.querySelector(UI.newAnalysisOptionElt).setAttribute("selected", "selected");
             document.querySelector(UI.analysisSelect).dispatchEvent(new Event("change"));
             await this.getSavedAnalysesList(this.dataset.id, 0);
+            resetStepperWithHrefs(UI.primaryFilterSection);
 
         } catch (error) {
             createToast(`Error deleting analysis: ${error.message}`);

www/js/dataset_explorer.js

@@ -349,6 +349,15 @@ const addDatasetListEventListeners = () => {
             const title = document.querySelector(`${selectorBase}-editable-title`).dataset.originalVal;
             document.querySelector(`${selectorBase}-editable-title`).value = title;
 
+            const ldesc = document.querySelector(`${selectorBase}-editable-ldesc`).dataset.originalVal;
+            document.querySelector(`${selectorBase}-editable-ldesc`).value = ldesc;
+
+            const pubmedId = document.querySelector(`${selectorBase}-editable-pubmed-id`).dataset.originalVal;
+            document.querySelector(`${selectorBase}-editable-pubmed-id`).value = pubmedId;
+
+            const geoId = document.querySelector(`${selectorBase}-editable-geo-id`).dataset.originalVal;
+            document.querySelector(`${selectorBase}-editable-geo-id`).value = geoId;
+
             document.querySelector(`${selectorBase} .js-action-links`).classList.remove("is-hidden");
 
         });