Merge pull request #901 from kedhammar/toulligqc

Add ToulligQC reports to ONT
NationalGenomicsInfrastructure · Dec 9, 2024 · 519f685 · 519f685
2 parents f011208 + b5551a4
commit 519f685
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Showing 3 changed files with 45 additions and 8 deletions.
diff --git a/run_dir/design/ont_flowcell.html b/run_dir/design/ont_flowcell.html
@@ -88,9 +88,14 @@ <h4 class = "mt-3 mb-2">MinKNOW arguments</h4>
             <a class="nav-link {{ 'active' if not sample_data else '' }}" href="#tab_barcode_information" role="tab" data-toggle="tab">Barcode counts</a>
           </li>
         {% end %}
-        {% if flowcell.get('TACA_run_status') == "finished" %}
+        {% if has_minknow_report %}
           <li class="nav-item">
-            <a class="nav-link" href="/flowcells_ont/{{ flowcell.get('run_name') }}/report" target="_blank">MinKNOW run report</a>
+            <a class="nav-link" href="/flowcells_ont/{{ flowcell.get('run_name') }}/minknow_report" target="_blank">MinKNOW report</a>
+          </li>
+        {% end %}
+        {% if has_toulligqc_report %}
+          <li class="nav-item">
+            <a class="nav-link" href="/flowcells_ont/{{ flowcell.get('run_name') }}/toulligqc_report" target="_blank">ToulligQC report</a>
           </li>
         {% end %}
         <li class="nav-item">

diff --git a/status/flowcell.py b/status/flowcell.py
@@ -463,14 +463,27 @@ def fetch_ont_run_stats(
     return run_dict
 
 
-class ONTReportHandler(SafeHandler):
+class ONTMinKNOWReportHandler(SafeHandler):
     """Serves a page showing the MinKNOW .html report of a given run"""
 
     def __init__(self, application, request, **kwargs):
         super(SafeHandler, self).__init__(application, request, **kwargs)
 
     def get(self, name):
-        reports_dir = self.application.minknow_path
+        reports_dir = self.application.minknow_reports_path
+        report_path = os.path.join(reports_dir, f"report_{name}.html")
+
+        self.write(open(report_path).read())
+
+
+class ONTToulligQCReportHandler(SafeHandler):
+    """Serves a page showing the ToulligQC .html report of a given run"""
+
+    def __init__(self, application, request, **kwargs):
+        super(SafeHandler, self).__init__(application, request, **kwargs)
+
+    def get(self, name):
+        reports_dir = self.application.toulligqc_reports_path
         report_path = os.path.join(reports_dir, f"report_{name}.html")
 
         self.write(open(report_path).read())
@@ -744,6 +757,12 @@ def get(self, name):
                 flowcell=self.fetch_ont_flowcell(name),
                 barcodes=self.fetch_barcodes(name),
                 args=self.fetch_args(name),
+                has_minknow_report=os.path.exists(
+                    f"{self.application.minknow_reports_path}/report_{name}.html"
+                ),
+                has_toulligqc_report=os.path.exists(
+                    f"{self.application.toulligqc_reports_path}/report_{name}.html"
+                ),
                 user=self.get_current_user(),
             )
         )

diff --git a/status_app.py b/status_app.py
@@ -38,7 +38,8 @@
     ElementFlowcellHandler,
     FlowcellHandler,
     ONTFlowcellHandler,
-    ONTReportHandler,
+    ONTMinKNOWReportHandler,
+    ONTToulligQCReportHandler,
 )
 from status.flowcells import (
     FlowcellDemultiplexHandler,
@@ -182,6 +183,8 @@
     WorksetsHandler,
 )
 
+ONT_RUN_PATTERN = r"\d{8}_\d{4}_[0-9a-zA-Z]+_[0-9a-zA-Z]+_[0-9a-zA-Z]+"
+
 
 class Application(tornado.web.Application):
     def __init__(self, settings):
@@ -354,8 +357,15 @@ def __init__(self, settings):
             ("/flowcells", FlowcellsHandler),
             (r"/flowcells/(\d{6,8}_[^/]*)$", FlowcellHandler),
             (r"/flowcells_element/([^/]*)$", ElementFlowcellHandler),
-            (r"/flowcells_ont/(\d{8}_[^/]*)$", ONTFlowcellHandler),
-            (r"/flowcells_ont/(\d{8}_[^/]*)/[^/]*$", ONTReportHandler),
+            (rf"/flowcells_ont/({ONT_RUN_PATTERN})$", ONTFlowcellHandler),
+            (
+                rf"/flowcells_ont/({ONT_RUN_PATTERN})/minknow_report$",
+                ONTMinKNOWReportHandler,
+            ),
+            (
+                rf"/flowcells_ont/({ONT_RUN_PATTERN})/toulligqc_report$",
+                ONTToulligQCReportHandler,
+            ),
             ("/flowcells_plot", FlowcellPlotHandler),
             ("/ont_flowcells_plot", ONTFlowcellPlotHandler),
             ("/data_delivered_plot", DeliveryPlotHandler),
@@ -518,7 +528,10 @@ def __init__(self, settings):
         self.multiqc_path = settings.get("multiqc_path")
 
         # MinKNOW reports
-        self.minknow_path = settings.get("minknow_path")
+        self.minknow_reports_path = settings.get("minknow_reports_path")
+
+        # ToulligQC reports
+        self.toulligqc_reports_path = settings.get("toulligqc_reports_path")
 
         # lims backend credentials
         limsbackend_cred_loc = Path(