Few fixes for the webviewer

Author: arteymix

rnaseq_pipeline/webviewer/__init__.py

@@ -69,7 +69,7 @@ def experiment_quantifications(experiment_id, mode, reference_id=None):
         mode_ix = ['counts', 'fpkm'].index(mode)
     except ValueError:
         abort(400, f'Unknown mode {mode} for quantifications, try either counts or fpkm.')
-    count_experiment_task = CountExperiment(experiment_id, reference_id=reference_id)
+    count_experiment_task = CountExperiment(experiment_id, reference_id=reference_id, taxon=None)
     if not count_experiment_task.complete():
         abort(404, f'No quantifications available for {experiment_id} in {reference_id}.')
     file_path = count_experiment_task.output()[mode_ix].path
@@ -81,7 +81,7 @@ def experiment_report(experiment_id, reference_id=None):
     if reference_id is None:
         gemma_task = GemmaTask(experiment_id)
         reference_id = gemma_task.reference_id
-    generate_report_task = GenerateReportForExperiment(experiment_id, reference_id=reference_id)
+    generate_report_task = GenerateReportForExperiment(experiment_id, reference_id=reference_id, taxon=None)
     if not generate_report_task.complete():
         abort(404, f'No report available for {experiment_id} in {reference_id}.')
     return send_file(generate_report_task.output().path)

rnaseq_pipeline/webviewer/templates/experiment-summary.html

@@ -20,29 +20,29 @@ <h2>{{ experiment_id }}</h2>
             </p>
             <dl class="row">
                 <dt class="col-sm-2">Gemma Dataset:</dt>
-                <dd class="col-sm-10"><a href="https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?shortName={{ experiment_id }}">{{ submit_data_task.dataset_short_name }}</a></dd>
+                <dd class="col-sm-10"><a target="_blank" href="https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?shortName={{ experiment_id }}">{{ submit_data_task.dataset_short_name }}</a></dd>
 
                 <dt class="col-sm-2">External Dataset:</dt>
-                <dd class="col-sm-10"><a href="{{ submit_data_task.external_uri }}">{{ submit_data_task.accession }} on {{ submit_data_task.external_database }}</a></dd>
+                <dd class="col-sm-10"><a target="_blank" rel="noopener noreferrer" href="{{ submit_data_task.external_uri }}">{{ submit_data_task.accession }} on {{ submit_data_task.external_database }}</a></dd>
 
                 <dt class="col-sm-2">Taxon:</dt>
                 <dd class="col-sm-10">{{ submit_data_task.taxon }}</dd>
 
                 <dt class="col-sm-2">Platform:</dt>
-                <dd class="col-sm-10"><a href="https://gemma.msl.ubc.ca/arrays/showArrayDesign.html?shortName={{ submit_data_task.platform_short_name }}">{{ submit_data_task.platform_short_name }}</a></dd>
+                <dd class="col-sm-10"><a href="https://gemma.msl.ubc.ca/arrays/showArrayDesign.html?name={{ submit_data_task.platform_short_name }}">{{ submit_data_task.platform_short_name }}</a></dd>
 
                 <dt class="col-sm-2">Reference:</dt>
                 <dd class="col-sm-10">{{ submit_data_task.reference_id }}</dd>
 
                 <dt class="col-sm-2">Quality Report:</dt>
-                <dd class="col-sm-10"><a href="{{ url_for('experiment_report', experiment_id=experiment_id) }}">MultiQC Report</a></dd>
+                <dd class="col-sm-10"><a href="{{ url_for('experiment_report', experiment_id=experiment_id, reference_id=submit_data_task.reference_id) }}">MultiQC Report</a></dd>
             </dl>
             <h3>Quantification Matrices</h3>
             <dl class="row">
                 <dt class="col-sm-2">Genes</dt>
                 <dd class="col-sm-10">
-                <a href="{{ url_for('experiment_quantifications', experiment_id=experiment_id, mode='counts', scope='genes') }}">Counts</a>,
-                <a href="{{ url_for('experiment_quantifications', experiment_id=experiment_id, mode='fpkm', scope='genes') }}">FPKM</a>
+                <a href="{{ url_for('experiment_quantifications', experiment_id=experiment_id, reference_id=submit_data_task.reference_id, mode='counts', scope='genes') }}">Counts</a>,
+                <a href="{{ url_for('experiment_quantifications', experiment_id=experiment_id, reference_id=submit_data_task.reference_id, mode='fpkm', scope='genes') }}">FPKM</a>
                 </dd>
                 <dt class="col-sm-2">Isoforms</dt>
                 <dd class="col-sm-10">Nothing, yet.</dd>