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Link to flowcells on instrument type #909

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merged 2 commits into from
Jan 8, 2025
Merged

Link to flowcells on instrument type #909

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2abf4b7
Link to flowcells on instrument type
aanil Jan 7, 2025
0752c48
Update run note notfication email formatting on request from OC
aanil Jan 7, 2025
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8 changes: 7 additions & 1 deletion run_dir/design/deliveries.html
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,13 @@ <h3>
<td class="bioinfo-status-expand"><a href="#bioinfo-fc-{{ project_id }}-{{ flowcell_id }}" class="bioinfo-expand">
<span class="fa fa-chevron-right"></span></a></td>
<td></td>
<td class="bioinfo-granularity"><samp><a class="text-decoration-none" href="/flowcells/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
{% set url_addition = "" %}
{% if flowcell.get("instrument_type") == "element"%}
{% set url_addition = "_element" %}
{% elif flowcell.get("instrument_type") == "ont"%}
{% set url_addition = "_ont" %}
{% end %}
<td class="bioinfo-granularity"><samp><a class="text-decoration-none" href="/flowcells{{url_addition}}/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
<td><span class="bioinfo-status badge {{ status_css.get(flowcell['flowcell_status'], 'bg-primary') }}">{{ flowcell['flowcell_status'] }}</span></td>
<td class="bi-run-pwf hide-incoming {% if flowcell['checklist']['total'] == flowcell['checklist']['completed'] %} table-success {% else %} table-warning {% end %}">
<div class="progress">
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2 changes: 2 additions & 0 deletions status/deliveries.py
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Expand Up @@ -159,6 +159,7 @@ def get(self):

# define bioinfo checklist
sample_data = flowcells[flowcell_id][lane_id][sample_id]
instrument_type = sample_data.get("instrument_type")
checklist = self.__fill_checklist(sample_data)
if checklist["total"] and len(checklist["total"]) == len(
checklist["passed"]
Expand Down Expand Up @@ -233,6 +234,7 @@ def get(self):
flowcell_status = self.__aggregate_status(flowcell_statuses)
runs_bioinfo[flowcell_id]["flowcell_status"] = flowcell_status
runs_bioinfo[flowcell_id]["checklist"] = flowcell_checklists
runs_bioinfo[flowcell_id]["instrument_type"] = instrument_type

# add flowcell_status to the status_list (needed for filtering)
if flowcell_status not in status_list:
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2 changes: 1 addition & 1 deletion status/running_notes.py
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Expand Up @@ -328,7 +328,7 @@ def notify_tagged_user(
html = '<html>\
<body>\
<p> \
{} in the project <a href="{}/project/{}#{}">{}, {}</a>! The note is as follows</p>\
{} in the project <a href="{}/project/{}#{}">{}, {}</a><br>The note is as follows</p>\
<blockquote>\
<div class="panel panel-default" style="border: 1px solid #e4e0e0; border-radius: 4px;">\
<div class="panel-heading" style="background-color: #f5f5f5; padding: 10px 15px;">\
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