def upload_phenotypes(proj_id):
pheno_file = request.files['phenotypes']
filename = secure_filename(pheno_file.filename)
# TODO: Also test the file is a CSV
if pheno_file:
error, result = file_to_obj_list("PHENOTYPES", pheno_file, proj_id)
if error:
headers, error_list = result
return render_template('upload_error_report.html',
title="Phenotypes Upload Error Report",
filename=filename,
headers=headers,
errors=error_list)
for pheno in result:
db.session.add(pheno)
# Project log entry
log = ProjectLog(proj_id, request.remote_addr, current_user.email,
"Uploaded Phenotypes File: '{}'".format(filename))
db.session.add(log)
db.session.commit()
flash("Successfully uploaded phenotypes file: '{}'".format(filename),
"success")
else:
flash("No phenotypes file", "danger")
return redirect(url_for('project', id=proj_id))
def upload_genotypes(proj_id):
geno_file = request.files['genotypes']
filename = secure_filename(geno_file.filename)
# TODO: Also test the file is a CSV
if geno_file:
error, result = file_to_obj_list("GENOTYPES", geno_file, proj_id)
if error:
return render_template(
'upload_error_report.html',
title="Genotypes Upload Error Report",
filename=filename,
headers=["ID", "Marker", "Allele 1", "Allele 2"],
errors=result)
for geno in result:
db.session.add(geno)
# Project log entry
log = ProjectLog(proj_id, request.remote_addr, current_user.email,
"Uploaded Genotypes File: '{}'".format(filename))
db.session.add(log)
db.session.commit()
flash("Successfully uploaded genotypes file: '{}'".format(filename),
"success")
else:
flash("No genotypes file", "danger")
return redirect(url_for('project', id=proj_id))
def upload_individuals(proj_id):
ind_file = request.files['individuals']
filename = secure_filename(ind_file.filename)
# TODO Also test the file is a CSV
if ind_file:
error, result = file_to_obj_list("INDIVIDUALS", ind_file, proj_id)
if error:
return render_template('upload_error_report.html',
title="Individuals Upload Error Report",
filename=filename,
headers=["ID", "Gender"],
errors=result)
for ind in result:
# TODO Test the individual does not already exist
# TODO Create dummy parents?
db.session.add(ind)
# Project log entry
log = ProjectLog(proj_id, request.remote_addr, current_user.email,
"Uploaded Individuals File: '{}'".format(filename))
db.session.add(log)
db.session.commit()
flash("Successfully uploaded individuals file: '{}'".format(filename),
"success")
else:
flash("No individuals file", "danger")
return redirect(url_for('project', id=proj_id))
def remove_member(user_email, proj_id):
num_admins = ProjectMemship.query.filter_by(project_id=proj_id,
is_project_admin=True).count()
if num_admins == 1 and current_user.email == user_email:
flash(
"Cannot delete oneself if there is no other project administrator",
"danger")
return redirect(url_for('project', id=proj_id))
ProjectMemship.query.filter(
ProjectMemship.user_email == user_email
and ProjectMemship.project_id == proj_id).delete()
# Project log entry
log = ProjectLog(proj_id, request.remote_addr, current_user.email,
("Removed user " + user_email))
db.session.add(log)
db.session.commit()
flash("User removed successfully", "success")
if current_user.email == user_email:
return redirect(url_for('index'))
else:
return redirect(url_for('project', id=proj_id))
def add_member(proj_id):
project_memship = ProjectMemship(
user_email=request.form.get('email'),
project_id=proj_id,
is_project_admin=(request.form.get('is_project_admin') == 'on'))
db.session.add(project_memship)
# Project log entry
message = "Added user " + project_memship.user_email + " as "
if project_memship.is_project_admin:
message += "administrator"
else:
message += "contributor"
log = ProjectLog(proj_id, request.remote_addr, current_user.email, message)
db.session.add(log)
db.session.commit()
flash("Member added to project", "success")
return redirect(url_for('project', id=proj_id))
def delete_project(id):
# Delete all members
ProjectMemship.query.filter_by(project_id=id).delete()
# TODO Delete all geno, pheno, group, indv
Genotype.query_by_project(id).delete(synchronize_session=False)
Phenotype.query_by_project(id).delete(synchronize_session=False)
Individual.query.filter_by(project_id=id).\
delete()
# Delete the project itself
Project.query.filter_by(id=id).delete()
# Project log entry
log = ProjectLog(id, request.remote_addr, current_user.email,
"Deleted project {}".format(id))
db.session.add(log)
db.session.commit()
flash("Project deleted successfully", "success")
return redirect(url_for('index'))
def add_project():
form = AddProjectForm()
if form.validate_on_submit():
project = Project(title=form.title.data, desc=form.desc.data)
memship = ProjectMemship(user=current_user,
project=project,
is_project_admin=True)
db.session.add(project)
db.session.add(memship)
# Need to commit to give the project an id
db.session.commit()
# Project log entry
log = ProjectLog(project.id, request.remote_addr, current_user.email,
("Created project " + str(project)))
db.session.add(log)
db.session.commit()
flash("Added new project", "success")
return redirect(url_for('project', id=project.id))
return render_template('add_project.html', title='Add Project', form=form)