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kedhammarkedhammar
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add running notes, homogenize js with illumina, remove undefined classes
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2 files changed

+34
-11
lines changed

2 files changed

+34
-11
lines changed

‎run_dir/design/ont_flowcells.html‎

Lines changed: 28 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -34,6 +34,7 @@ <h1>
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<th class="sort text-center" data-sort="basecalled_pass_bases_Gbp">Yield Passed (Gbp)</th>
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<th class="sort text-center" data-sort="basecalled_pass_read_count_M">Read Count Passed (M)</th>
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<th class="sort text-center" data-sort="n50_Kbp">N50 Passed (Kbp)</th>
37+
<th class="sort" data-sort="latest_running_note">Latest running note</th>
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</tr>
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</thead>
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<tfoot>
@@ -48,13 +49,14 @@ <h1>
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<th class="sort" data-sort="basecalled_pass_bases_Gbp"></th>
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<th class="sort" data-sort="basecalled_pass_read_count_M"></th>
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<th class="sort" data-sort="n50_Kbp"></th>
52+
<th class="sort" data-sort="latest_running_note"></th>
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</tr>
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</tfoot>
5355

5456
<tbody class="list">
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{% for onefc in ont_flowcells %}
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<tr>
57-
<td class = run_name>
59+
<td>
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<a class="text-decoration-none" href="/flowcells_ont/{{ onefc }}" target="_blank">{{ onefc }}</a>
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{% if ont_flowcells.get(onefc).get('TACA_run_status') == 'finished' %}
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<abbr title="Run completed"><span class="fa fa-check-circle"></span></abbr>
@@ -64,7 +66,7 @@ <h1>
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<abbr title="Run interrupted"><span class="fa fa-file-dashed-line"></span></abbr>
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{% end %}
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</td>
67-
<td class="library">
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<td>
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{% if ont_flowcells[onefc].get('library_id') %}
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<a class="text-decoration-none" href="
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https://ngi-lims-
@@ -82,7 +84,7 @@ <h1>
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{{ ont_flowcells[onefc].get("library_name","") }}
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{% end %}
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</td>
85-
<td class="lims_step">
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<td>
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{% if ont_flowcells[onefc].get('step_id') %}
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<a class="text-decoration-none" href="
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https://ngi-lims-
@@ -100,7 +102,7 @@ <h1>
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{{ ont_flowcells[onefc].get("step_id","") }}
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{% end %}
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</td>
103-
<td class="project">
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<td>
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{% if ont_flowcells[onefc].get('projects') %}
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{% for project_id, project_name in ont_flowcells[onefc]['projects'].items() %}
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<samp style="max-width:50px;">
@@ -109,26 +111,41 @@ <h1>
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{% end %}
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{% end %}
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</td>
112-
<td class="prep_kit">{{ ont_flowcells[onefc].get("prep_kit","") }}</td>
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<td class="flow_cell_qc text-center">
114+
<td>{{ ont_flowcells[onefc].get("prep_kit","") }}</td>
115+
<td class="text-center">
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{{ ont_flowcells[onefc].get("qc","") }}
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</td>
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117-
<td class="load_fmol text-center">
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<td class="text-center">
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{% try %}
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{{ ont_flowcells[onefc]["lims"]["loading"][-1]["load_fmol"] }}
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{% except %}
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{{ "" }}
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{% end %}
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</td>
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125-
<td class="basecalled_pass_bases_Gbp text-center">
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<td class="text-center">
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{{ ont_flowcells[onefc].get("basecalled_pass_bases_Gbp", "") }}
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</td>
128-
<td class="basecalled_pass_read_count_M text-center">{{ ont_flowcells[onefc].get("basecalled_pass_read_count_M", "") }}</td>
129-
<td class="n50_Kbp text-center">
130+
<td class="text-center">{{ ont_flowcells[onefc].get("basecalled_pass_read_count_M", "") }}</td>
131+
<td class="text-center">
130132
{{ ont_flowcells[onefc].get("n50_Kbp", "") }}
131133
</td>
134+
<td class="latest_running_note">
135+
{% if ont_flowcells[onefc].get('latest_running_note') %}
136+
{% set running_notes = ont_flowcells[onefc].get('latest_running_note') %}
137+
{% set latest_running_note_key = list(running_notes.keys())[0] %}
138+
<div class="card running-note-card">
139+
<div class='card-header'>
140+
<a class="text-decoration-none" href='mailto:{{ running_notes[latest_running_note_key]["email"].encode("ascii","ignore")}}'>{{ running_notes[latest_running_note_key]["user"]}}</a> - {{form_date(latest_running_note_key)}}
141+
{% if running_notes[latest_running_note_key]['categories'] %} - <span class="fillbadgecolour"> {{ running_notes[latest_running_note_key]['categories'] }} </span> {% end %}
142+
</div>
143+
<div class='card-body trunc-note-latest' style='white-space: pre-line'>
144+
{{running_notes[latest_running_note_key]['note']}}
145+
</div>
146+
</div>
147+
{% end %}
148+
</td>
132149
</tr>
133150
{% end %}
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</tbody>
@@ -152,7 +169,6 @@ <h1>
152169
"paging":false,
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"info":false,
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"order": [[ 0, "desc" ]],
155-
"autoWidth":true,
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dom: 'Bfrti',
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colReorder: true,
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buttons: [
@@ -173,6 +189,7 @@ <h1>
173189

174190
//Add the bootstrap classes to the search thingy
175191

192+
$('div.dataTables_filter input').addClass('form-control search search-query');
176193
$('#ont_fc_table_filter').addClass('form-inline float-right pt-1');
177194
$("#ont_fc_table_filter").appendTo($('#ont_page_title'));
178195
$('#ont_fc_table_filter label input').appendTo($('#ont_fc_table_filter'));

‎status/flowcells.py‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -178,6 +178,12 @@ def list_ont_flowcells(self, unfetched_runs):
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# Get step ID
179179
all_stats["step_id"] = all_stats["lims"]["loading"][-1]["step_id"]
180180

181+
all_stats["latest_running_note"] = (
182+
LatestRunningNoteHandler.get_latest_running_note(
183+
self.application, "flowcell", run_name
184+
)
185+
)
186+
181187
except Exception as e:
182188
application_log.warning(f"Error parsing {run_name}: {e}", exc_info=True)
183189
unfetched_runs.append(run_name)

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