added create variant shortcut and added no_login option

.env_example

@@ -7,6 +7,7 @@
 HOST=
 PORT=
 NO_PROXY=localhost
+LOGIN_REQUIRED=True
 
 ########## DB SETTINGS #########
 DB_HOST=

src/frontend_celery/config.py

@@ -30,6 +30,8 @@ class Config(object):
     HOST = os.environ.get('HOST')
     PORT = os.environ.get('PORT')
 
+    LOGIN_REQUIRED = os.environ.get('LOGIN_REQUIRED', "True").lower() in ["true"]
+
     ##### production config ####
     TESTING = False
     DEBUG = False

src/frontend_celery/webapp/auth/auth_routes.py

@@ -26,17 +26,42 @@
 
 @auth_blueprint.route('/login')
 def login():
+
+    next_url = request.args.get('next_login', url_for('main.index'))
+
+    if not current_app.config["LOGIN_REQUIRED"]:
+        return redirect(url_for("auth.auth", next_login=next_url))
+
     # construct redirect uri: first redirect to keycloak login page
     # then redirect to auth with the next param which defaults to the '/' route
     # auth itself redirects to next ie. the page which required a login
-    redirect_uri = url_for('auth.auth', _external=True, next_login=request.args.get('next_login', url_for('main.index')))
+    redirect_uri = url_for('auth.auth', _external=True, next_login=next_url)
 
     return oauth.keycloak.authorize_redirect(redirect_uri)
 
 
 @auth_blueprint.route('/auth')
 def auth():
-    token_response = oauth.keycloak.authorize_access_token()
+
+    if not current_app.config["LOGIN_REQUIRED"]:
+        token_response = {
+            "access_token": "xxx",
+            "expires_in": 300,
+            "refresh_expires_in": 1800,
+            "refresh_token": "xxx",
+            "token_type": "bearer",
+            "not-before-policy": 0,
+            "session_state": "xxx",
+            "userinfo": {
+                "preferred_username": "anonymous",
+                "given_name": "Arno",
+                "family_name": "Nym",
+                "affiliation": "Anonymous",
+                "roles": ["super_user", "user", "read_only"]
+            }
+        }
+    else:
+        token_response = oauth.keycloak.authorize_access_token()
 
     #userinfo = oauth.keycloak.userinfo(request)
     #idToken = oauth.keycloak.parse_id_token(tokenResponse)

src/frontend_celery/webapp/templates/index.html

@@ -93,6 +93,14 @@ <h4>Overview</h4>
 <div class="bst bsb">
     <h4>Changelog</h4>
 
+    <div class="underline">v 1.14.4 (03.11.2024)</div>
+    <div>
+        General changes:
+        <ul>
+            <li>Added shortcut to insert unknown variants from variant display page</li>
+        </ul>
+    </div>
+
     <div class="underline">v 1.14.3 (15.10.2024)</div>
     <div>
         General changes:

src/frontend_celery/webapp/templates/variant/create.html

@@ -31,7 +31,7 @@ <h1 class="bst">{% block title %} Create a new variant {% endblock %}</h1>
                      <label for="Chromosome" class="form-label">Chromosome</label>
                      <select class="form-select" name="chr" id="Chromosome" required>
                          {% for chr in chrs %}
-                            <option value="{{chr}}" {% if (chr == request.form['chr']) %} selected="selected" {% endif %}> {{chr}} </option>
+                            <option value="{{chr}}" {% if chr == request.form['chr'] or chr == request.args.get('chrom') %} selected="selected" {% endif %}> {{chr}} </option>
                          {% endfor %}
                     </select>
                     <div class="invalid-feedback">
@@ -43,7 +43,8 @@ <h1 class="bst">{% block title %} Create a new variant {% endblock %}</h1>
                     <label for="Position" class="form-label">Chromosomal position</label>
                     <input type="text" name="pos" pattern="[0-9 ]+" id="Position"
                            placeholder="pos" class="form-control validationreq"
-                           value="{{ request.form['pos'] }}" required>
+                           value={% if request.form.get('pos') is not none %}"{{ request.form.get('pos', '') }}"{% else %}"{{ request.args.get('pos', '') }}"{% endif %}
+                           required>
                     <div class="invalid-feedback">
                         Please provide a chromosomal position!
                     </div>
@@ -53,7 +54,8 @@ <h1 class="bst">{% block title %} Create a new variant {% endblock %}</h1>
                     <label for="Reference" class="form-label">Reference sequence</label>
                     <input type="text" name="ref"
                            placeholder="ref" class="form-control validationreq"
-                           value="{{ request.form['ref'] }}" id="Reference" required>
+                           value={% if request.form.get('ref') is not none %}"{{ request.form.get('ref', '') }}"{% else %}"{{ request.args.get('ref', '') }}"{% endif %}
+                           id="Reference" required>
                     <div class="invalid-feedback">
                         Please provide a reference sequence!
                     </div>
@@ -63,7 +65,8 @@ <h1 class="bst">{% block title %} Create a new variant {% endblock %}</h1>
                     <label for="Alternative" class="form-label">Alternative sequence</label>
                     <input type="text" name="alt"
                            placeholder="alt" class="form-control validationreq"
-                           value="{{ request.form['alt'] }}" id="Alternative" required>
+                           value={% if request.form.get('alt') is not none %}"{{ request.form.get('alt', '') }}"{% else %}"{{ request.args.get('alt', '') }}"{% endif %}
+                           id="Alternative" required>
                     <div class="invalid-feedback">
                         Please provide an alternative sequence!
                     </div>

src/frontend_celery/webapp/templates/variant/unknown_variant.html

@@ -0,0 +1,25 @@
+{% extends 'base.html' %}
+
+{% block content %}
+<div class="container">
+
+
+
+    <h1 class="bst">{% block title %} Unknown variant {% endblock %}</h1>
+
+
+    <div class="bst">
+        <div>The variant you are trying to access is unknown by HerediVar. Please click to following button to request a new variant:</div>
+        <div>
+            <a class="btn btn-primary" href="{{url_for('variant.create', **request.args)}}">create new variant</a>
+        </div>
+    </div>
+
+
+</div>
+
+{% endblock %}
+
+{% block special_scripts %}
+    <script src="/static/js/create.js"></script>
+{% endblock%}

src/frontend_celery/webapp/utils/decorators.py

@@ -74,34 +74,35 @@ def decorated_function(*args, **kwargs):
         if session.get('user') is None:
             return redirect(url_for('auth.login', next_login=request.url))
 
-        # user is logged in -> check if access token is still valid using introspect endpoint --> introspect endpoint can be omitted if token is validated locally using some jwt lib
+        if current_app.config["LOGIN_REQUIRED"]:
+            # user is logged in -> check if access token is still valid using introspect endpoint --> introspect endpoint can be omitted if token is validated locally using some jwt lib
 
-        token = session['tokenResponse']
+            token = session['tokenResponse']
 
-        #print(session['user'])
-        #print(token)
+            #print(session['user'])
+            #print(token)
 
-        # maybe also add: 
-        # state=5AzjFWCkQzjmh4YozUfuE8pHytJj3i
-        # nonce=fvdZHHR1mmAHBIbCQtgZ
-        # code_challenge=hoiDWU7Vf4tOreIeYyIi7IKcw2BseRW7j5wwXROJtPA
-        # code_challenge_method=S256
+            # maybe also add: 
+            # state=5AzjFWCkQzjmh4YozUfuE8pHytJj3i
+            # nonce=fvdZHHR1mmAHBIbCQtgZ
+            # code_challenge=hoiDWU7Vf4tOreIeYyIi7IKcw2BseRW7j5wwXROJtPA
+            # code_challenge_method=S256
 
-        issuer = current_app.config['ISSUER']
-        url = f'{issuer}/protocol/openid-connect/token/introspect'
-        data = {'token': token.get("access_token"), 'token_type_hint': 'access_token', 'username': session['user']['preferred_username'], 'client_secret': current_app.config['CLIENTSECRET'], 'client_id': current_app.config['CLIENTID']}
-        header = {'Authorization': f'Bearer {token.get("access_token")}'}
-        resp = requests.post(url, data=data, headers=header)
-        resp.raise_for_status()
-        resp = resp.json()
-
-        # if access token is not valid request a new one using the refresh token
-        if not resp['active']:
-            print('access token invalid refreshing token')
-            refresh_status_code = refresh_token()
-            # if the refresh token is expired as well promt a new login by invalidating the client session
-            if refresh_status_code != 200:
-                return redirect(url_for('auth.logout', auto_logout='True', next_logout=url_for('auth.login', next_login=request.url))) # logout and return to login page! with next= page which you wanted to access in the first place
+            issuer = current_app.config['ISSUER']
+            url = f'{issuer}/protocol/openid-connect/token/introspect'
+            data = {'token': token.get("access_token"), 'token_type_hint': 'access_token', 'username': session['user']['preferred_username'], 'client_secret': current_app.config['CLIENTSECRET'], 'client_id': current_app.config['CLIENTID']}
+            header = {'Authorization': f'Bearer {token.get("access_token")}'}
+            resp = requests.post(url, data=data, headers=header)
+            resp.raise_for_status()
+            resp = resp.json()
+
+            # if access token is not valid request a new one using the refresh token
+            if not resp['active']:
+                print('access token invalid refreshing token')
+                refresh_status_code = refresh_token()
+                # if the refresh token is expired as well promt a new login by invalidating the client session
+                if refresh_status_code != 200:
+                    return redirect(url_for('auth.logout', auto_logout='True', next_logout=url_for('auth.login', next_login=request.url))) # logout and return to login page! with next= page which you wanted to access in the first place
 
         return f(*args, **kwargs)
     return decorated_function
@@ -113,9 +114,10 @@ def decorator(f):
         @require_login
         @wraps(f)
         def wrapper(*args, **kwargs):
-            grant_access, status_code = request_uma_ticket(resources)
-            if not grant_access:
-                abort(status_code)
+            if current_app.config["LOGIN_REQUIRED"]:
+                grant_access, status_code = request_uma_ticket(resources)
+                if not grant_access:
+                    abort(status_code)
             return f(*args, **kwargs)
         return wrapper
     return decorator

src/frontend_celery/webapp/variant/variant_routes.py

@@ -75,7 +75,7 @@ def create():
 
     if do_redirect:
         return redirect(url_for('variant.create'))
-    return render_template('variant/create.html', chrs=chroms, vcf_file_import_active=current_app.config["VCF_FILE_IMPORT_ACTIVE"])
+    return render_template('variant/create.html', chrs=chroms, vcf_file_import_active=current_app.config["VCF_FILE_IMPORT_ACTIVE"], **request.args)
 
 
 
@@ -125,12 +125,15 @@ def create_sv():
 @variant_blueprint.route('/display/chr=<string:chr>&pos=<int:pos>&ref=<string:ref>&alt=<string:alt>', methods=['GET']) # alternative url using vcf information
 @require_permission(['read_resources'])
 def display(variant_id=None, chr=None, pos=None, ref=None, alt=None):
+
     conn = get_connection()
 
     # get variant id from parameters or pull from genomic coordinates
     if variant_id is None:
         require_set(chr, pos, ref, alt)
         variant_id = conn.get_variant_id(chr, pos, ref, alt)
+    if variant_id is None and any([e is not None for e in [chr, pos, ref, alt]]):
+        return redirect(url_for('variant.unknown_variant', chrom=chr, pos=pos, ref=ref, alt=alt))
     require_valid(variant_id, "variant", conn)
 
     # get available lists for user
@@ -146,6 +149,12 @@ def display(variant_id=None, chr=None, pos=None, ref=None, alt=None):
                         )
 
 
+@variant_blueprint.route('/unknown_variant', methods=["GET"])
+@require_permission(['read_resources'])
+def unknown_variant():
+    return render_template('variant/unknown_variant.html', **request.args)
+
+
 @variant_blueprint.route('/get_clinvar_upload_status', methods=['GET'])
 @require_permission(['read_resources'])
 def get_clinvar_upload_status():