From b5551a452ab26df3027d314d190518744565b37e Mon Sep 17 00:00:00 2001 From: kedhammar Date: Wed, 4 Dec 2024 16:11:00 +0100 Subject: [PATCH] a single, absolutely flawless commit --- run_dir/design/ont_flowcell.html | 9 +++++++-- status/flowcell.py | 23 +++++++++++++++++++++-- status_app.py | 21 +++++++++++++++++---- 3 files changed, 45 insertions(+), 8 deletions(-) diff --git a/run_dir/design/ont_flowcell.html b/run_dir/design/ont_flowcell.html index 7cddd7a98..85fda4561 100644 --- a/run_dir/design/ont_flowcell.html +++ b/run_dir/design/ont_flowcell.html @@ -88,9 +88,14 @@

MinKNOW arguments

Barcode counts {% end %} - {% if flowcell.get('TACA_run_status') == "finished" %} + {% if has_minknow_report %}
  • - MinKNOW run report + MinKNOW report +
    • + {% end %} + {% if has_toulligqc_report %} +
  • + ToulligQC report
    • {% end %}
  • diff --git a/status/flowcell.py b/status/flowcell.py index 8981b1975..413a38992 100644 --- 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 index f5c899e62..18d76cabc 100644 --- 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(