Added some metadata to the trait export

2 files changed, 41 insertions, 13 deletions

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 1b27d7cb..4dc3e18c 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -350,12 +350,12 @@ class UserSession(object):
         Redis.delete(self.cookie_name)
         logger.debug("At end of delete_session")
 
-@app.before_request
+#@app.before_request
 def before_request():
     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)
@@ -537,7 +537,7 @@ 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)
@@ -551,7 +551,7 @@ 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)
@@ -575,7 +575,7 @@ 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)
@@ -619,7 +619,7 @@ 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")
@@ -629,7 +629,7 @@ 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")
@@ -660,7 +660,7 @@ 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
@@ -840,7 +840,7 @@ 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()
@@ -851,7 +851,7 @@ 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)
@@ -859,7 +859,7 @@ 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
@@ -944,7 +944,7 @@ 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