def file_view(project_id, document, sample = None):
projects = get_projects()
project = projects[project_id]
title = document
if sample: document = list_file('{}/{}/{}'.format(project['path'], sample, document))
else: document = list_file('{}/{}'.format(project['path'], document))
return render_template('file_view.html', title = title, document = document, sample = sample)
def sample(project_id, sample):
print('Sample:', sample)
projects = get_projects()
project = projects[project_id]
status = sample_status(project['path'], sample)
logs = list_ext(project['path'], sample, 'log')
return render_template('sample.html', title = 'Sample Dashboard', project = project, sample = status, logs = logs)
def archive_remove(project_id):
form = ArchiveRemove()
if form.validate_on_submit():
project = get_projects()[project_id]
if form.archive.data:
archive_project(project['path'])
flash('{} has been added to archived projects.'.format(project_id), 'info')
if form.remove.data:
remove_project(project_id)
flash('{} has been removed from active projects.'.format(project_id), 'info')
return redirect(url_for('home'))
return redirect(url_for('project', project_id = project_id))
return render_template('archive_remove.html', project_id = project_id, form = form)
def project(project_id):
form = StartStopProject()
project = get_projects()[project_id]
if request.method == 'POST':
if form.start.data:
if run_project(project['path']):
flash('Project Running', 'info')
time.sleep(2)
elif form.stop.data:
if stop_project(project):
flash('Project Stopped', 'info')
time.sleep(2)
return redirect(url_for('project', project_id = project_id))
processing = status_list(project)
return render_template('project.html', title = 'Project Dashboard', project = project, processing = processing, form = form)
def annotate_report(project_id):
form = AnnotateReport()
if request.method == 'POST':
project = get_projects()[project_id]
# print(request.form)
if 'annotate' in request.form:
# print('Annotating Project VCFs')
run_annotation(project['path'])
elif 'analyse' in request.form:
print('Analysing Quality Threshold Impact to Variant Spectrum')
run_analysis(project['path'])
elif 'filter' in request.form:
print('Filtering Variants at a Threshold of:', request.form['quality'])
print('Removing Common Variants')
run_subtraction(project['path'], request.form['quality'])
return render_template('annotate_report.html', project_id = project_id, form = form)
def home():
projects = get_projects()
return render_template('home.html', projects = projects)
def accession(project_id):
projects = get_projects()
project = projects[project_id]
title = '{} Samples'.format(project_id)
accession = list_file('{}/assets/{}'.format(project['path'], 'accession.txt'))
return render_template('accession.html', title = title, project_id = project_id, accession = accession)