Merge pull request #83 from ctreffe/develop

Develop

.gitignore

@@ -45,3 +45,4 @@ dist/
 mortimer_venv/
 .mortimer/
 .venv/
+.python-version

CHANGELOG.md

@@ -5,6 +5,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/), 
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Mortimer v0.8.13 (Released 2022-05-21)
+
+### Changed
+
+- (New) users are now allowed to remove documents in their own alfred3 
+  mongoDB collections.
+
+### Fixed
+
+- Fixed support for url-jumping support
+- Fixed #82
+
+### Added
+
+- Added logging capability (#78)
+- Added log calls for 412 server responses (#79)
+
 ## Mortimer v0.8.12 (Released 2021-10-28)
 
 ### Added

src/mortimer/__init__.py

@@ -27,7 +27,15 @@
 db = MongoEngine()  # mortimer database
 
 # application factory
-def create_app(instance_path=None):
+def create_app(instance_path=None, logfile: str = None):
+    logger = logging.getLogger("mortimer")
+    fh = logging.FileHandler(logfile)
+    formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
+    fh.setFormatter(formatter)
+
+    logger.addHandler(fh)
+    logger.setLevel(logging.INFO)
+
     app = Flask(__name__, instance_path=instance_path)
 
     # apply configuration

src/mortimer/_version.py

@@ -5,4 +5,4 @@
 
 
 
-__version__ = "0.8.12"
+__version__ = "0.8.13"

src/mortimer/config.py

@@ -84,7 +84,7 @@ class BaseConfig:
     MONGODB_SETTINGS["password"] = None
     MONGODB_SETTINGS["authentication_source"] = "admin"
     MONGODB_SETTINGS["ssl"] = False
-    MONGODB_SETTINGS["ssl_ca_certs"] = None
+    MONGODB_SETTINGS["tlsCAFile"] = None
 
     # Alfred settings
     ALFRED_DB = "alfred"

src/mortimer/models.py

@@ -89,7 +89,7 @@ def _prepare_db_role_privileges(self):
         c_unlinked = {**res, **{"collection": self.alfred_col_unlinked}}
         c_misc = {**res, **{"collection": self.alfred_col_misc}}
 
-        act = ["find", "insert", "update"]
+        act = ["find", "insert", "update", "remove"]
         priv = [{"resource": res_dict, "actions": act} for res_dict in [c_exp, c_unlinked, c_misc]]
         return priv
 
@@ -163,7 +163,7 @@ def mongo_saving_agent(self) -> dict:
             "user": self.alfred_user,
             "password": f.decrypt(self.alfred_pw).decode(),
             "use_ssl": str(appdb_config.get("ssl")).lower(),
-            "ca_file_path": str(appdb_config.get("ssl_ca_certs")),
+            "ca_file_path": str(appdb_config.get("tlsCAFile")),
             "activation_level": "1",
         }
         return {"mongo_saving_agent": mongo_config}
@@ -273,14 +273,6 @@ def parse_exp_secrets(self) -> ExperimentSecrets:
         try:
             secrets_string = f.decrypt(self.exp_secrets).decode()
         except TypeError:
-            logger = logging.getLogger(__name__)
-            logger.info(
-                (
-                    "Exception during secrets decryption. "
-                    "To proceed, the value of secrets.conf was set to an empty string."
-                    f" Exp id={str(self.id)}"
-                )
-            )
             secrets_string = ""
 
         exp_secrets = ExperimentSecrets(expdir=self.path)

src/mortimer/templates/experiment.html

@@ -146,15 +146,15 @@ <h1 class="card-text"><b>{{ n["fin"] }}</b> / <span class="text-muted">{{ n["tot
       </div>
       <div class="card-body border-info">
         <span class="text-muted">
-          {% if activity["last"] != 'none' %}
-          {{ activity["last"] }}
+          {% if activity["last_time"] != 'none' %}
+          {{ activity["last_time"] }}
           {% else %}
           - none -
           {% endif %}
         </span>
         <h3 class="card-text text-info">
-          {% if activity["last"] != 'none' %}
-          {{ activity["last"] }}
+          {% if activity["last_date"] != 'none' %}
+          {{ activity["last_date"] }}
           {% else %}
           - none -
           {% endif %}

src/mortimer/web_experiments/alfredo.py

@@ -26,12 +26,16 @@
     send_from_directory,
     session,
     url_for,
-    jsonify
+    jsonify,
 )
 from flask_login import current_user
 
 from mortimer.models import WebExperiment, User
-from mortimer.utils import create_fernet, is_social_media_preview, render_social_media_preview
+from mortimer.utils import (
+    create_fernet,
+    is_social_media_preview,
+    render_social_media_preview,
+)
 from alfred3 import alfredlog
 import alfred3.config
 
@@ -45,7 +49,7 @@ def __init__(self):
         self.config = None
 
     def generate_experiment(self, config=None):  # pylint: disable=method-hidden
-        """Hook for the ``generate_experiment`` function extracted from 
+        """Hook for the ``generate_experiment`` function extracted from
         the user's script.py. It is meant to be replaced in ``run.py``.
         """
 
@@ -75,7 +79,9 @@ def number_of_func_params(func):
 
 
 def import_script(experiment_id):
-    experiment = WebExperiment.objects.get_or_404(id=experiment_id)  # pylint: disable=no-member
+    experiment = WebExperiment.objects.get_or_404(
+        id=experiment_id
+    )  # pylint: disable=no-member
 
     # Fast path: see if the module has already been imported.
     try:
@@ -127,22 +133,23 @@ def get(self, key):
 
         self.lock.release()
         if rv is None:
-            try:
-                print("Tried to access experiment with key %s" % key)
-                print("Available Keys: %s" % list(self.experiments.keys()))
-            except Exception:
-                pass
+            molog = logging.getLogger("mortimer")
+            molog.warning(
+                f"Tried to access experiment with session id '{key}'. Available Keys:"
+                f" {list(self.experiments.keys())}"
+            )
             abort(412)
         self.save(key, rv)
         return rv
 
     def remove_outdated(self):
         self.lock.acquire()
         current_time = int(time())
+        molog = logging.getLogger("mortimer")
         for k in list(self.experiments.keys()):
             v = self.experiments[k]
             if current_time - v[0] > self.timeout:
-                print("delete exp with key %s and last access time %s" % (k, v[0]))
+                molog.warning(f"Delete exp with session id '{k}' and last access time {v[0]}")
                 del self.experiments[k]
         self.lock.release()
 
@@ -170,17 +177,21 @@ def start(expid):
     if is_social_media_preview(request.headers.get("User-Agent")):
         return render_social_media_preview(config)
 
-    if not experiment.public and experiment.password != request.form.get("password", None):
+    if not experiment.public and experiment.password != request.form.get(
+        "password", None
+    ):
         exp_url = url_for("alfredo.start", expid=str(experiment.id))
         return (
-            '<div align="center"><h1>Please enter the password</h1><form method="post" action="%s">\
-            <input type="password" name="password" /><button type="submit">Submit</button></form></div>'
-            % exp_url
+            '<div align="center"><h1>Please enter the password</h1><form method="post"'
+            ' action="%s">            <input type="password" name="password" /><button'
+            ' type="submit">Submit</button></form></div>' % exp_url
         )
-    
+
     args = request.args.to_dict()
     test_mode = args.get("test") in ["true", "True", "TRUE"]
-    debug_mode = args.get("debug") in ["true", "True", "TRUE"] or config.getboolean("general", "debug")
+    debug_mode = args.get("debug") in ["true", "True", "TRUE"] or config.getboolean(
+        "general", "debug"
+    )
     if not experiment.active and not test_mode and not debug_mode:
         return render_template("exp_inactive.html")
 
@@ -199,11 +210,8 @@ def start(expid):
     try:
         user_script = import_script(experiment.id)
         exp_session = user_script.exp.create_session(
-            session_id=sid, 
-            config=config, 
-            secrets=secrets, 
-            **request.args
-            )
+            session_id=sid, config=config, secrets=secrets, **request.args
+        )
 
     except Exception:
         msg = "Error during creation of experiment session."
@@ -215,10 +223,11 @@ def start(expid):
                     "web_experiments.experiment",
                     username=current_user.username,
                     exp_title=experiment.title,
-                ))
+                )
+            )
         else:
             abort(500)
-    
+
     try:
         exp_session._start()
         experiment_manager.save(sid, exp_session)
@@ -237,28 +246,38 @@ def start(expid):
         else:
             abort(500)
 
+    page = request.args.get("page", None)
+    if page:
+        return redirect(url_for("alfredo.experiment", page=page))
     return redirect(url_for("alfredo.experiment"))
 
 
 @alfredo.route("/experiment", methods=["GET", "POST"])
 def experiment():
+    molog = logging.getLogger("mortimer")
     try:
         sid = session["sid"]
     except KeyError:
+        molog.warning(
+            "Experiment route called, but there was no session id in the session"
+            " cookie."
+        )
         abort(412)
 
     experiment = experiment_manager.get(sid)
     tkey = experiment.current_page.name + sid
 
     try:
         if request.method == "GET":
-            url_pagename = request.args.get("page", None) # https://basepath.de/experiment?page=name
+            url_pagename = request.args.get(
+                "page", None
+            )  # https://basepath.de/experiment?page=name
             if url_pagename:
-                experiment.movement_manager.jump_by_name(name=url_pagename)
+                experiment.movement_manager.move(direction=f"jump>{url_pagename}")
 
             token = session["page_tokens"].get(tkey, uuid4().hex)
             session["page_tokens"][tkey] = token
-            session.modified = True # because the dict is mutable
+            session.modified = True  # because the dict is mutable
 
             current_page_html = make_response(experiment.ui.render_html(token))
             current_page_html.cache_control.no_cache = True
@@ -269,11 +288,10 @@ def experiment():
             submitted_token = request.values.get("page_token", None)
 
             token = session["page_tokens"].pop(tkey, None)
-            session.modified = True # because the dict is mutable
+            session.modified = True  # because the dict is mutable
             if not token or not token == submitted_token:
                 return redirect(url_for("alfredo.experiment"))
 
-
             data = request.values.to_dict()
             data.pop("move", None)
             data.pop("directjump", None)
@@ -287,9 +305,11 @@ def experiment():
             else:
                 abort(400)
             return redirect(url_for("alfredo.experiment"))
-        
+
     except Exception:
-        log = alfredlog.QueuedLoggingInterface("alfred3", f"exp.{str(experiment.exp_id)}")
+        log = alfredlog.QueuedLoggingInterface(
+            "alfred3", f"exp.{str(experiment.exp_id)}"
+        )
         log.session_id = sid
         msg = "Exception during experiment execution."
         log.exception(msg)
@@ -311,9 +331,13 @@ def staticfile(identifier):
     try:
         sid = session["sid"]
         experiment = experiment_manager.get(sid)
-        path, content_type = experiment.user_interface_controller.get_static_file(identifier)
+        path, content_type = experiment.user_interface_controller.get_static_file(
+            identifier
+        )
         dirname, filename = os.path.split(path)
-        resp = make_response(send_from_directory(dirname, filename, mimetype=content_type))
+        resp = make_response(
+            send_from_directory(dirname, filename, mimetype=content_type)
+        )
         # resp.cache_control.no_cache = True
         return resp
 
@@ -326,13 +350,16 @@ def dynamicfile(identifier):
     try:
         sid = session["sid"]
         experiment = experiment_manager.get(sid)
-        strIO, content_type = experiment.user_interface_controller.get_dynamic_file(identifier)
+        strIO, content_type = experiment.user_interface_controller.get_dynamic_file(
+            identifier
+        )
     except KeyError:
         abort(404)
     resp = make_response(send_file(strIO, mimetype=content_type))
     resp.cache_control.no_cache = True
     return resp
 
+
 @alfredo.route("/callable/<identifier>", methods=["GET", "POST"])
 def callable(identifier):
     try:
@@ -341,19 +368,18 @@ def callable(identifier):
         f = experiment.user_interface_controller.get_callable(identifier)
     except KeyError:
         abort(404)
-    
+
     if request.content_type == "application/json":
         values = request.get_json()
     else:
         values = request.values.to_dict()
-    
-    values.pop("_", None) # remove argument with name "_"
-    
+
+    values.pop("_", None)  # remove argument with name "_"
+
     rv = f(**values)
     if rv is not None:
         resp = jsonify(rv)
         resp.cache_control.no_cache = True
         return resp
     else:
         return (" ", 204)
-

src/mortimer/web_experiments/routes.py

@@ -192,13 +192,16 @@ def experiment(username, exp_title):
     if times:
         try:
             activity["first"] = datetime.fromtimestamp(times[0]["first"]).strftime('%Y-%m-%d, %H:%M')
-            activity["last"] = datetime.fromtimestamp(times[0]["last"]).strftime('%H:%M')
+            activity["last_time"] = datetime.fromtimestamp(times[0]["last"]).strftime('%H:%M')
+            activity["last_date"] = datetime.fromtimestamp(times[0]["last"]).strftime('%Y-%m-%d')
         except TypeError:
             activity["first"] = times[0]["first"]
-            activity["last"] = times[0]["last"]
+            activity["last_time"] = times[0]["last"]
+            activity["last_date"] = "none"
     else:
         activity["first"] = "none"
-        activity["last"] = "none"
+        activity["last_time"] = "none"
+        activity["last_date"] = "none"
 
     # Form for script.py upload
     form = NewScriptForm()