Merge pull request #51 from ctreffe/release-v0.8

Release v0.8

Author: jobrachem

.gitignore

@@ -42,3 +42,5 @@ tests/run_locally/run.py
 src/mortimer.egg-info
 build/
 dist/
+mortimer_venv/
+.mortimer/

CHANGELOG.md

@@ -5,7 +5,46 @@ 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).
 
-## [Unreleased]
+## Mortimer v0.8.4 (Released 2021-04-15)
+
+### Added v0.8.4
+
+- Added button for starting an experiment directly with url parameters
+
+### Changed v0.8.4
+- Participant registration route now works with experiment version. The version is required for registration and optional for checking.
+- Changed internal handling of page tokens
+- /callable route in alfredo.py does not automatically redirect to /experiment anymore. This prevents unnecessary redirects. Previously, those redirects happened every time the called function return `None`.
+- /callable route in alfredo.py now automatically jsonifies return values.
+
+## Mortimer v0.8.2
+
+### Added
+
+Starting from v0.8.2, Mortimer allows experimenters to check, whether partcipants have
+participated in a specific experiment through the route `/participation`.
+
+A guide on how to use it is available in the [wiki](https://github.com/ctreffe/mortimer/wiki/Check-participation)
+
+## Mortimer v0.8.0
+
+### Changed
+
+Mortimer was updated to be compatible with alfred3 v2.0. This included
+first and foremost an update to the data export handling and some small
+updates to configuration handling. Due to these changes, Mortimer v0.8.0
+is not compatible with older versions of alfred3.
+
+## Mortimer v0.7.0
+
+### Added
+
+* Added support for two additional collections in the alfred database.
+* Redesigned and enhanced data export. When used with alfred v1.4+, Mortimer now offers export of unlinked data and codebooks.
+
+### Fixed
+
+* Fixed a bug in the password reset email.
 
 ## Mortimer v0.6.1 (Released 2020-07-23)
 

src/mortimer/__init__.py

@@ -38,15 +38,13 @@ def create_app(instance_path=None):
     from mortimer.web_experiments.routes import web_experiments
     from mortimer.web_experiments.alfredo import alfredo
     from mortimer.main.routes import main
-    from mortimer.local_experiments.routes import local_experiments
     from mortimer.errors.handlers import errors
 
     # register blueprints
     app.register_blueprint(users)
     app.register_blueprint(web_experiments)
     app.register_blueprint(main)
     app.register_blueprint(alfredo)
-    app.register_blueprint(local_experiments)
     app.register_blueprint(errors)
 
     # global variables for use in templates

src/mortimer/_version.py

@@ -3,4 +3,4 @@
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
 
-__version__ = "0.6.1"
+__version__ = "0.8.4"

src/mortimer/config.py

@@ -96,6 +96,7 @@ class BaseConfig:
     MAIL_USE_TLS = None
     MAIL_USERNAME = None
     MAIL_PASSWORD = None
+    MAIL_SENDER_ADDRESS = None
 
     # Flask-Dropzone settings:
     DROPZONE_ALLOWED_FILE_CUSTOM = True

src/mortimer/export.py

@@ -7,29 +7,51 @@
 import csv
 import re
 import io
+import random
+
+from bson import json_util
 
 # this is necessary, because send_file requires bytes-like objects
 def make_str_bytes(f):
     # Creating the byteIO object from the StringIO Object
     bytes_f = io.BytesIO()
-    bytes_f.write(f.getvalue().encode("utf-8"))
+    try:
+        bytes_f.write(f.getvalue().encode("utf-8"))
+        f.close()
+    except AttributeError:
+        bytes_f.write(f.encode("utf-8"))
     # seeking was necessary. Python 3.5.2, Flask 0.12.2
+
     bytes_f.seek(0)
-    f.close()
     return bytes_f
 
 
-def to_json(cursor):
-    sIO = io.StringIO()
-    L = list(cursor)
-    json.dump(L, sIO)
-    sIO.seek(0)
-    return sIO
+def to_json(cursor, shuffle=False, decryptor=None):
+    """Turns a MongoDB Cursor into a JSON file.
+
+    Args:
+        shuffle: If *True*, the document order will be shuffled 
+            (useful e.g. for preventing a link of experiment and 
+            unlinked data).
+        decryptor: An alfred3.data_manager.Decryptor instance, which,
+            if provided, will be used to try decryption of the values
+            of all decouments.
+    """
+    data = list(cursor)
+
+    if decryptor:
+        decrypted_data = []
+        for doc in data:
+            decrypted_data.append(decryptor.decrypt(doc))
+        data = decrypted_data
+
+    if shuffle:
+        random.shuffle(data)
+    out = json_util.dumps(obj=data, indent=4)
+    return out
 
 
-def to_csv(
-    cursor, none_value=None, remove_linebreaks=False, dialect="excel", **writerparams
-):
+def to_csv(cursor, none_value=None, remove_linebreaks=False, dialect="excel", **writerparams):
     rows = cursor_to_rows(cursor, none_value)
     if remove_linebreaks:
         for i in range(1, len(rows)):
@@ -168,9 +190,7 @@ def getDataFromDoc(self, doc):
                     raise Exception("break")
             rv = rv + child.getDataFromDoc(subDoc if found else {})
         if self.additional_data:
-            rv = rv + self.additional_data.getDataFromDoc(
-                doc.get("additional_data", {})
-            )
+            rv = rv + self.additional_data.getDataFromDoc(doc.get("additional_data", {}))
         return rv
 
     def getDataFromDocs(self, docs):

src/mortimer/forms.py

@@ -11,9 +11,10 @@
     TextAreaField,
     SelectField,
     SelectMultipleField,
+    RadioField,
 )
 from wtforms.validators import DataRequired, Length, Email, EqualTo, ValidationError
-from mortimer.models import User, WebExperiment, LocalExperiment
+from mortimer.models import User, WebExperiment
 from flask import current_app
 import re
 
@@ -112,34 +113,6 @@ def validate_version(self, version):
     submit = SubmitField("Create")
 
 
-class LocalExperimentForm(FlaskForm):
-    title = StringField("Title", validators=[DataRequired()])
-    exp_id = StringField("Experiment ID", validators=[DataRequired()])
-    description = TextAreaField("Description")
-
-    def validate_title(self, title):
-        # , version=self.version
-        experiment = LocalExperiment.objects(
-            title__exact=title.data, author__exact=current_user.username
-        ).first()
-        if experiment is not None:
-            raise ValidationError(
-                "You already have a local experiment with this title. Please choose a unique title."
-            )
-
-    def validate_exp_id(self, exp_id):
-        experiment = LocalExperiment.objects(
-            exp_id__exact=exp_id.data, author__exact=current_user.username
-        ).first()
-        if experiment is not None:
-
-            raise ValidationError(
-                "There already exists an experiment with this ID in the database. Please choose a unique ID. If you already collected data using this ID, please contanct an administrator."
-            )
-
-    submit = SubmitField("Create")
-
-
 class ExperimentScriptForm(FlaskForm):
     script = TextAreaField("Script")
     version = StringField("Updated version", validators=[DataRequired()])
@@ -218,6 +191,32 @@ class ResetPasswordForm(FlaskForm):
     submit = SubmitField("Reset Password")
 
 
+class ExportCodebookForm(FlaskForm):
+    choices = [
+        ("csv1", "csv ( , )"),
+        ("csv2", "csv ( ; )"),
+        ("json", "json"),
+    ]
+    file_type = RadioField(default="csv2", choices=choices, validators=[DataRequired()])
+    version = SelectField("Version", validators=[DataRequired()], default="latest")
+
+
+class ExportExpDataForm(FlaskForm):
+    choices = [
+        ("csv1", "csv ( , )"),
+        ("csv2", "csv ( ; )"),
+        ("json", "json"),
+    ]
+    file_type = RadioField(default="csv2", choices=choices, validators=[DataRequired()])
+    data_type = RadioField(
+        default="exp_data",
+        choices=[("exp_data", "Experiment Data"), ("unlinked", "Unlinked Data")],
+        validators=[DataRequired()],
+    )
+    version = SelectMultipleField("Version", validators=[DataRequired()])
+    submit = SubmitField("Export Experiment Data")
+
+
 class ExperimentExportForm(FlaskForm):
 
     file_type = SelectField(
@@ -291,4 +290,3 @@ class ExperimentConfigurationForm(FlaskForm):
     minimum_display_time = StringField("Minimum display time")
 
     submit = SubmitField("Save")
-