def test_report_buttons():
all_runs = path_processing.get_all_runs_names()
run_id = all_runs[0]
samples_for_given_run = path_processing.get_samples_from_run_name(run_id)
sample_id = samples_for_given_run[0]
download_path = path_processing.get_fastq_fq1_download_path(
run_id, sample_id).replace(os.sep, '/')
path = urllib.parse.urljoin(DOWNLOAD_PATH, download_path)
assert check_status_code(path) == 200
download_path = path_processing.get_fastq_fq2_download_path(
run_id, sample_id).replace(os.sep, '/')
path = urllib.parse.urljoin(DOWNLOAD_PATH, download_path)
assert check_status_code(path) == 200
download_path = path_processing.get_fastqc_report_path(
run_id, sample_id, 1).replace(os.sep, '/')
path = urllib.parse.urljoin(DOWNLOAD_PATH, download_path)
assert check_status_code(path) == 200
download_path = path_processing.get_fastqc_report_path(
run_id, sample_id, 2).replace(os.sep, '/')
path = urllib.parse.urljoin(DOWNLOAD_PATH, download_path)
assert check_status_code(path) == 200
def test_specific_sample_page():
all_runs = path_processing.get_all_runs_names()
samples_for_given_run = path_processing.get_samples_from_run_name(
all_runs[0])
path = slash_join(BASE_LINK, 'runs', all_runs[0], samples_for_given_run[0])
status_code = check_status_code(path)
assert status_code == 200
def specific_run(run_id):
runs = pp.get_all_runs_names()
if run_id not in runs:
logger.info('Redirected for incorrect run_id {}'.format(run_id))
return redirect(url_for('runs'))
# target coverage
path = pp.get_sample_coverage_path(run_id)
if pp.check_existence(path):
sample_summary_table = data_preparation.get_summary(run_id)
else:
sample_summary_table = False
# presenting plot
path = pp.get_multisample_vcf_stats_path(run_id)
if pp.check_existence(path):
variants, variants_df = data_preparation.get_multisample_stats_df(run_id)
else:
variants, variants_df = False, False
# variants annotations
path = pp.get_annotated_variants_stats_path(run_id)
if pp.check_existence(path):
variants_annotations_df = pd.read_csv(path, delimiter='\t')
else:
variants_annotations_df = False
graphs = [
sample_summary_graph(sample_summary_table),
variants_graph(variants_df),
variants_annotations_graph(variants_annotations_df),
]
graphJSON = json.dumps(graphs, cls=plotly.utils.PlotlyJSONEncoder)
ids = ['graph-{}'.format(i) for i, _ in enumerate(graphs)]
data = {'sample_summary_table': data_preparation.prepare_sample_summary_html_table(sample_summary_table, run_id),
'graphJSON': graphJSON,
'ids': ids,
'variants': variants if variants else False,
'variants_annotations': variants_annotations_df if variants_annotations_df is False else True,
'coverage_sample_list': False,
'run_id': run_id,
'runs': runs,
}
# gene coverage
summary_path = pp.get_sample_gene_coverage_path(run_id)
if pp.check_existence(summary_path):
data['coverage_sample_list_exists'] = True
mean_cols_df = data_preparation.get_gene_summary(run_id)
df = data_preparation.prepare_mean_columns_df(mean_cols_df)
df.fillna(-1, inplace=True)
data['coverage_sample_list'] = df.round(2).values.tolist()[:100]
logger.info('Specific run_id page rendered correctly. {}'.format(run_id))
return render_template('runs/run.html', **data)
def specific_sample(run_id, sample_id):
if run_id not in pp.get_all_runs_names() or sample_id not in pp.get_samples_from_run_name(run_id):
logger.info('Invalid sample_id or run_id.')
return redirect(url_for('samples'))
data = {'run_id': run_id,
'sample_id': sample_id,
'samples': pp.samples_paths(pp.get_all_runs_names()),
'gene_coverage_exists': True,
'sample_variants_exists': True,
'coverage_sample_summary_exists': True}
# update data dict with tables and other data information
data.update(data_preparation.prepare_tables_for_sample_page(run_id, sample_id))
# update dict with links to download files and reports
data.update(data_preparation.links_to_external_download_data_and_reports(run_id, sample_id))
logger.info('Specific sample loaded correctly. {} {}'.format(run_id, sample_id))
return render_template('samples/sample.html', **data)
def runs():
runs = pp.get_all_runs_names()
logger.info("Runs page rendered.")
return render_template('runs/runs.html', runs=runs)
def samples():
runs = pp.get_all_runs_names()
samples = pp.samples_paths(runs)
logger.info('Samples page rendered.')
return render_template('samples/samples.html', samples=samples)
def test_specific_run_page():
all_runs = path_processing.get_all_runs_names()
path = urllib.parse.urljoin(BASE_LINK, 'runs', all_runs[0])
status_code = check_status_code(path)
assert status_code == 200
