diff options
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/export_trait_data.py | 30 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 22 |
3 files changed, 44 insertions, 13 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 3d9b508a..04e3d578 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -75,7 +75,10 @@ class GSearch(object): this_trait['group'] = line[1] this_trait['tissue'] = line[2] this_trait['symbol'] = line[6] - this_trait['description'] = line[7].decode('utf-8', 'replace') + if line[7]: + this_trait['description'] = line[7].decode('utf-8', 'replace') + else: + this_trait['description'] = "N/A" this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9])) diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 7ca4a4c0..107f87c6 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -4,11 +4,17 @@ import simplejson as json from pprint import pformat as pf +from base.trait import GeneralTrait +from base import data_set + def export_sample_table(targs): sample_data = json.loads(targs['export_data']) trait_name = targs['trait_display_name'] - final_sample_data = [] + + meta_data = get_export_metadata(targs['trait_id'], targs['dataset']) + + final_sample_data = meta_data for sample_group in ['primary_samples', 'other_samples']: for row in sample_data[sample_group]: @@ -18,6 +24,28 @@ def export_sample_table(targs): return trait_name, final_sample_data +def get_export_metadata(trait_id, dataset_name): + dataset = data_set.create_dataset(dataset_name) + this_trait = GeneralTrait(dataset=dataset, + name=trait_id, + cellid=None, + get_qtl_info=False) + + metadata = [] + if dataset.type == "Publish": + metadata.append(["Phenotype ID: " + trait_id]) + metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + metadata.append(["Group: " + dataset.group.name]) + metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) + metadata.append(["Authors: " + this_trait.authors]) + metadata.append(["Title: " + this_trait.title]) + metadata.append(["Journal: " + this_trait.journal]) + metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) + metadata.append([]) + + return metadata + + def dict_to_sorted_list(dictionary): sorted_list = [item for item in dictionary.iteritems()] sorted_list = sorted(sorted_list, cmp=cmp_samples) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index ce76e0e8..a871e91a 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -356,7 +356,7 @@ def get_cookie(): g.user_session = UserSession() g.cookie_session = AnonUser() -@app.after_request +#@app.after_request def set_cookie(response): if not request.cookies.get(g.cookie_session.cookie_name): response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) @@ -538,7 +538,7 @@ def basic_info(): ip_address = request.remote_addr, user_agent = request.headers.get('User-Agent')) -@app.route("/manage/verify_email") +#@app.route("/manage/verify_email") def verify_email(): user = DecodeUser(VerificationEmail.key_prefix).user user.confirmed = json.dumps(basic_info(), sort_keys=True) @@ -552,7 +552,7 @@ def verify_email(): response.set_cookie(UserSession.cookie_name, session_id_signed) return response -@app.route("/n/password_reset", methods=['GET']) +#@app.route("/n/password_reset", methods=['GET']) def password_reset(): """Entry point after user clicks link in E-mail""" logger.debug("in password_reset request.url is:", request.url) @@ -576,7 +576,7 @@ def password_reset(): else: return redirect(url_for("login")) -@app.route("/n/password_reset_step2", methods=('POST',)) +#@app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): """Handle confirmation E-mail for password reset""" logger.debug("in password_reset request.url is:", request.url) @@ -620,7 +620,7 @@ class DecodeUser(object): logger.debug("data is:", data) return model.User.query.get(data['id']) -@app.route("/n/login", methods=('GET', 'POST')) +#@app.route("/n/login", methods=('GET', 'POST')) def login(): lu = LoginUser() login_type = request.args.get("type") @@ -630,7 +630,7 @@ def login(): else: return lu.standard_login() -@app.route("/n/login/github_oauth2", methods=('GET', 'POST')) +#@app.route("/n/login/github_oauth2", methods=('GET', 'POST')) def github_oauth2(): from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET code = request.args.get("code") @@ -661,7 +661,7 @@ def github_oauth2(): url = "/n/login?type=github&uid="+user_details["user_id"] return redirect(url) -@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) +#@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) def orcid_oauth2(): from uuid import uuid4 from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL @@ -841,7 +841,7 @@ class LoginUser(object): db_session.add(login_rec) db_session.commit() -@app.route("/n/logout") +#@app.route("/n/logout") def logout(): logger.debug("Logging out...") UserSession().delete_session() @@ -852,7 +852,7 @@ def logout(): return response -@app.route("/n/forgot_password", methods=['GET']) +#@app.route("/n/forgot_password", methods=['GET']) def forgot_password(): """Entry point for forgotten password""" print("ARGS: ", request.args) @@ -860,7 +860,7 @@ def forgot_password(): print("ERRORS: ", errors) return render_template("new_security/forgot_password.html", errors=errors) -@app.route("/n/forgot_password_submit", methods=('POST',)) +#@app.route("/n/forgot_password_submit", methods=('POST',)) def forgot_password_submit(): """When a forgotten password form is submitted we get here""" params = request.form @@ -945,7 +945,7 @@ def is_redis_available(): # return LoginUser().actual_login(user, assumed_by=assumed_by) -@app.route("/n/register", methods=('GET', 'POST')) +#@app.route("/n/register", methods=('GET', 'POST')) def register(): params = None errors = None |