Merge pull request #898 from aanil/queues_update

Link and search for element FCs
NationalGenomicsInfrastructure · Nov 14, 2024 · a14b77e · a14b77e
2 parents f84f6e2 + 4aab030
commit a14b77e
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Showing 4 changed files with 39 additions and 4 deletions.
diff --git a/run_dir/design/bioinfo_tab/run_lane_sample_view.html b/run_dir/design/bioinfo_tab/run_lane_sample_view.html
@@ -69,12 +69,16 @@
   <tbody class="text-center">
       {% for flowcell_id, flowcell in sorted(bioinfo['run_lane_sample_view'].items()) %}
         {% set disabled = True if flowcell.get('flowcell_status') in ['Demultiplexing', 'Transferring', 'Sequencing', 'ERROR', 'Failed', 'Delivered'] else False %}
+        {% set url_addition = "" %}
+        {% if flowcell.get("instrument_type") == "element"%}
+          {% set url_addition = "_element" %}
+        {% end %}
         <tr class="bioinfo-fc  {% if disabled %} bioinfo-status-disabled {% end %}"
             id="bioinfo-fc-{{ flowcell_id }}" data-parent="#bioinfo-project-{{ project_id }}">
           <td class="bioinfo-status-expand"><a class="bioinfo-expand text-decoration-none" href="#bioinfo-fc-{{ flowcell_id }}">
             <span class="fa fa-chevron-right"></span></a></td>
           <td></td>
-          <td><samp><a class="text-decoration-none" href="/flowcells/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
+          <td><samp><a class="text-decoration-none" href="/flowcells{{url_addition}}/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
           <td class="bioinfo-status-runstate"><span class="badge {{ status_css.get(flowcell['flowcell_status'], 'bg-secondary') }}">{{ flowcell['flowcell_status'] }}</span></td>
           <td class="bioinfo-status-row ?"><span class="fa fa-arrow-alt-right"></span></td>
           <td class="bioinfo-status-qc undemultiplexedreads unknown">?</td>

diff --git a/run_dir/design/bioinfo_tab/sample_run_lane_view.html b/run_dir/design/bioinfo_tab/sample_run_lane_view.html
@@ -113,13 +113,17 @@
             </td>
         </tr>
         {% for flowcell_id, flowcell in sorted(sample['flowcells'].items()) %}
+          {% set url_addition = "" %}
+          {% if flowcell.get("instrument_type") == "element"%}
+            {% set url_addition = "_element" %}
+          {% end %}
           <tr class="bioinfo-fc  {% if flowcell.get('flowcell_status') in ['Demultiplexing', 'Transferring', 'Sequencing', 'ERROR', 'Failed', 'Delivered'] %} bioinfo-status-disabled {% end %}"
               id="bioinfo-fc-{{ sample_id }}-{{ flowcell_id }}"
               data-parent="#bioinfo-sample-{{ sample_id }}" style="display:none;">
             <td></td>
             <td class="bioinfo-status-expand"><a href="#bioinfo-fc-{{ sample_id }}-{{ flowcell_id }}" class="bioinfo-expand">
               <span class="fa fa-chevron-right"></span></a></td>
-            <td><samp><a class="text-decoration-none" href="/flowcells/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
+            <td><samp><a class="text-decoration-none" href="/flowcells{{url_addition}}/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
             <td class="bioinfo-status-runstate"><span class="badge {{ status_css.get(flowcell['flowcell_status'], 'bg-secondary') }}">{{ flowcell['flowcell_status'] }}</span></td>
             <td class="bioinfo-status-row ?"><span class="fa fa-arrow-alt-right"></span></td>
             <td class="bioinfo-status-qc undemultiplexedreads unknown">?</td>

diff --git a/status/bioinfo_analysis.py b/status/bioinfo_analysis.py
@@ -100,17 +100,24 @@ def get(self, project_id):
         edit_history = {}
         for row in view[project_id].rows:
             flowcell_id = row.value.get("run_id")
+            instrument_type = row.value.get("instrument_type", "illumina")
             lane_id = row.value.get("lane")
             sample_id = row.value.get("sample")
             changes = row.value.get("values", {})
             last_timestamp = max(list(changes))
             bioinfo_qc = changes.get(last_timestamp, {})
+            bioinfo_data["instrument_type"] = instrument_type
 
             # building first view
             bioinfo1 = bioinfo_data["sample_run_lane_view"]
             if sample_id not in bioinfo1:
                 bioinfo1[sample_id] = {
-                    "flowcells": {flowcell_id: {"lanes": {lane_id: bioinfo_qc}}}
+                    "flowcells": {
+                        flowcell_id: {
+                            "lanes": {lane_id: bioinfo_qc},
+                            "instrument_type": instrument_type,
+                        }
+                    }
                 }
             elif flowcell_id not in bioinfo1[sample_id]["flowcells"]:
                 bioinfo1[sample_id]["flowcells"][flowcell_id] = {
@@ -129,7 +136,8 @@ def get(self, project_id):
             bioinfo2 = bioinfo_data["run_lane_sample_view"]
             if flowcell_id not in bioinfo2:
                 bioinfo2[flowcell_id] = {
-                    "lanes": {lane_id: {"samples": {sample_id: bioinfo_qc}}}
+                    "lanes": {lane_id: {"samples": {sample_id: bioinfo_qc}}},
+                    "instrument_type": instrument_type,
                 }
             elif lane_id not in bioinfo2[flowcell_id]["lanes"]:
                 bioinfo2[flowcell_id]["lanes"][lane_id] = {

diff --git a/status/flowcells.py b/status/flowcells.py
@@ -259,6 +259,7 @@ class FlowcellSearchHandler(SafeHandler):
     cached_fc_list = None
     cached_xfc_list = None
     cached_ont_fc_list = None
+    cached_element_fc_list = None
     last_fetched = None
 
     def get(self, search_string):
@@ -287,6 +288,13 @@ def search_flowcell_names(self, search_string=""):
             )
             FlowcellSearchHandler.cached_ont_fc_list = [row.key for row in ont_fc_view]
 
+            element_fc_view = self.application.element_runs_db.view(
+                "info/name", descending=True
+            )
+            FlowcellSearchHandler.cached_element_fc_list = [
+                row.key for row in element_fc_view
+            ]
+
             FlowcellSearchHandler.last_fetched = datetime.datetime.now()
 
         search_string = search_string.lower()
@@ -314,6 +322,17 @@ def search_flowcell_names(self, search_string=""):
             except AttributeError:
                 pass
 
+        for row_key in FlowcellSearchHandler.cached_element_fc_list:
+            try:
+                if search_string in row_key.lower():
+                    fc = {
+                        "url": f"/flowcells_element/{row_key}",
+                        "name": row_key,
+                    }
+                    flowcells.append(fc)
+            except AttributeError:
+                pass
+
         for row_key in FlowcellSearchHandler.cached_fc_list:
             try:
                 if search_string in row_key.lower():