def get(self):
db_session = sql_db_engine.create_session()
pools = OrmPooldbModel(db_session).get_query().filter(
OrmPooldbModel.PooldbMapper.USER_SUBMITTED == 'yes'
).all()
genom_count = 0
if pools:
query = OrmGdbModel(db_session).get_query()
query = query.filter(
OrmGdbModel.GdbMapper.REVIEWEDBY == None,
OrmGdbModel.GdbMapper.POOL_ID == pools[0].ID
)
genom_count = query.count()
form = SubmitForm()
rendered = render_template(
'submitView.html',
gen_num=genom_count,
form=form
)
db_session.commit()
db_session.close()
return Response(rendered, mimetype='text/html')
def get(self, res_id, page_id):
db_session = sql_db_engine.create_session()
self.pagination.current_page = page_id
pools_data = get_pools_data(db_session)
data = None
if 'sort' in request.args:
env_id = None
if 'env_id' in request.args:
env_id = request.args['env_id']
data = get_genoms_data(db_session, {
'pools[]': [res_id],
'sort': request.args['sort'],
'env_id': env_id
}, self.pagination)
else:
data = get_genoms_data(db_session, {'pools[]': [res_id]}, self.pagination)
data['pools'] = pools_data
data['pool_id'] = res_id
data['page_id'] = page_id
form = GenomForm()
rendered = render_template(
'poolDetailsView.html',
data=data,
app_data=self.app_settings,
pagination=self.pagination,
form=form
)
db_session.commit()
db_session.close()
return Response(rendered, mimetype='text/html')
def get(self):
db_session = sql_db_engine.create_session()
orm = OrmGdbModel(db_session)
rows_num = orm.get_num_of_rows()
rendered = render_template('mainView.html', rows_num=rows_num)
db_session.commit()
db_session.close()
return Response(rendered, mimetype='text/html')
def get(self, res_id):
directory = os.path.join(conf_manager.get_root_folder(), "download")
directory = os.path.join(directory, "genoms")
db_session = sql_db_engine.create_session()
orm = OrmGdbModel(db_session)
res = self.get_resource(orm, directory, res_id, "NAME")
db_session.commit()
db_session.close()
return res
def get(self, res_id):
db_session = sql_db_engine.create_session()
data = get_genoms_data(db_session, {'pools[]': [res_id]})
db_session.commit()
db_session.close()
if 'form' in request.args:
if request.args['form'] == 'json':
return self._as_json(data['genotypes'])
elif request.args['form'] == 'xml':
return self._as_xml(data['genotypes'])
return redirect('/')
def get(self, res_id):
db_session = sql_db_engine.create_session()
data = self._get_genom_data(db_session, res_id)
db_session.commit()
db_session.close()
if "form" in request.args:
if request.args["form"] == "json":
return self._as_json(data)
elif request.args["form"] == "xml":
return self._as_xml(data)
return self._as_html(data)
def get(self):
db_session = sql_db_engine.create_session()
data = dict()
data['pools'] = get_pools_data(db_session)
db_session.commit()
db_session.close()
if 'form' in request.args:
if request.args['form'] == 'json':
return self._as_json(data)
elif request.args['form'] == 'xml':
return self._as_xml(data)
return redirect('/')
def get(self, page_id):
db_session = sql_db_engine.create_session()
self.pagination.current_page = page_id
data = dict()
data['pools'] = get_pools_data(db_session, self.pagination)
data['page_id'] = page_id
db_session.commit()
db_session.close()
form = GenomForm()
rendered = render_template(
'browsePoolView.html',
data=data,
app_data=self.app_settings,
form=form,
pagination=self.pagination
)
return Response(rendered, mimetype='text/html')
def post(self):
db_session = sql_db_engine.create_session()
pools = OrmPooldbModel(db_session).get_query().filter(
OrmPooldbModel.PooldbMapper.USER_SUBMITTED == 'yes'
).all()
post_data = SubmitForm()
if not pools:
flash('Cannot add more genotypes')
return redirect(url_for('submitcontroller'))
if not post_data.validate_on_submit():
for key in post_data.errors:
for err in post_data.errors[key]:
flash('{0}'.format(err))
return redirect(url_for('submitcontroller'))
db_session.commit()
db_session.close()
flash('Genotype added successfully')
return redirect(url_for('submitcontroller'))
def get(self, page_id):
db_session = sql_db_engine.create_session()
self.pagination.current_page = page_id
if not "genom_filters" in session:
rendered = render_template("notFoundView.html")
return Response(rendered, mimetype="text/html")
if "sort" in request.args:
session["genom_filters"]["sort"] = request.args["sort"]
if "env_id" in request.args:
session["genom_filters"]["env_id"] = request.args["env_id"]
self.pagination.per_page = session["genom_filters"]["per_page"]
data = get_genoms_data(db_session, session["genom_filters"], self.pagination)
data["pools"] = get_pools_data(db_session)
data["pool_id"] = None
data["page_id"] = page_id
form = GenomForm()
rendered = render_template(
"poolDetailsView.html", data=data, app_data=self.app_settings, pagination=self.pagination, form=form
)
return Response(rendered, mimetype="text/html")
