Merge pull request #32 from ctreffe/develop

Mortimer v0.4.2

.gitignore

@@ -25,3 +25,5 @@ move_to_default_alfred.conf
 alfredo2_ca_chain.pem
 alfred.conf
 exp/
+.vscode/settings.json
+test.py

NEWS.md

@@ -1,17 +1,37 @@
+# Mortimer v0.4.2
+
+## Bugfixes
+
+* Fixed a bug introduced in v0.4.1, which led to a problem with new experiments. Their experiment ID did not get saved at the right time, which caused trouble with data export.
+
+## Smaller changes
+
+* Mortimer now displays its own version number and the alfred version currently running on the server.
+
+# Mortimer v0.4.1
+
+## Bugfixes
+
+* Fixed a bug in `alfredo.py` that caused trouble for videos implemented via `alfred.element.WebVideoElement` in Safari (wouldn't play at all) and Chrome (forward/backward wouldn't work)
+
 # Mortimer v0.4-beta
 
 ## Breaking changes
-- **Separation of web and local experiments**. Web experiments hosted via mortimer and local experiments now save their data into different collections in the Alfred database (`web` and `local`). This means that you can be completely sure that your web and local experiments don't interfere.
-- **`exp_id`** for local experiments. You need to specify a unique `exp_id` in the section `[metadata]` of your `config.conf` to be sure that you can retrieve your data from local experiments. Thankfully, Mortimer will always give you a new unique ID on its home page and on the page for local experiment creation.
+
+* **Separation of web and local experiments**. Web experiments hosted via mortimer and local experiments now save their data into different collections in the Alfred database ( `web` and `local` ). This means that you can be completely sure that your web and local experiments don't interfere.
+* **`exp_id`** for local experiments. You need to specify a unique `exp_id` in the section `[metadata]` of your `config.conf` to be sure that you can retrieve your data from local experiments. Thankfully, Mortimer will always give you a new unique ID on its home page and on the page for local experiment creation.
 
 ## New user interface
-- **Fully reworked user interface**. The new interface should be quite self-explanatory. Feel free to explore!
+
+* **Fully reworked user interface**. The new interface should be quite self-explanatory. Feel free to explore!
 
 ## New features
-- **File Management**
+
+* **File Management**
     - You can create directories and subdirectories belonging to your experiment
     - You can upload now multiple files at once
     - No one but you can access you files
-- **Configuration**. You can now configure your experiment from within Mortimer.
-- **Experiment Log**. You can now view your experiment's log file from within Mortimer.
-- **Futurize Scripts**. You can futurize an old script to help you port it to Alfred v1.0.
+* **Configuration**. You can now configure your experiment from within Mortimer.
+* **Experiment Log**. You can now view your experiment's log file from within Mortimer.
+* **Futurize Scripts**. You can futurize an old script to help you port it to Alfred v1.0.
+

mortimer/__init__.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 
 from flask import Flask
@@ -8,6 +8,9 @@
 from flask_mail import Mail
 from flask_dropzone import Dropzone
 import pymongo
+import alfred
+
+__version__ = '0.4.2'
 
 # the EnvironSetter sets enviroment variables for the current session
 # It is not included in the GitHub repository, because it contains sensitive
@@ -78,6 +81,13 @@ def create_app(config_class=Config):
     app.register_blueprint(local_experiments)
     app.register_blueprint(errors)
 
+    # global variables for use in templates
+    @app.context_processor
+    def version_processor():
+        mv = __version__
+        from alfred import __version__ as av
+        return {"v_mortimer": mv, "v_alfred": av}
+
     # bind extensions to app instance
     db.init_app(app)
     bcrypt.init_app(app)

mortimer/config.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 import os
@@ -14,29 +13,30 @@ class Config:
     if os.environ.get("MONGODB_SSL") == "True":
         mongodb_ssl = True
         ssl_ca_certs = os.environ.get("MONGODB_SSL_CAFILE")
-        ssl_ca_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), ssl_ca_certs)
+        ssl_ca_path = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), ssl_ca_certs
+        )
     else:
         mongodb_ssl = False
         ssl_ca_certs = None
         ssl_ca_path = None
 
-    SECRET_KEY = os.environ.get("SECRET_KEY")  # secret key of flask app (e.g. for encrypted session data)
-    PAROLE = os.environ.get("PAROLE")          # Parole/Passphrase for registration
-    EXP_PER_PAGE = 10                          # number of experiments displayed per page
+    SECRET_KEY = os.environ.get(
+        "SECRET_KEY"
+    )  # secret key of flask app (e.g. for encrypted session data)
+    PAROLE = os.environ.get("PAROLE")  # Parole/Passphrase for registration
+    EXP_PER_PAGE = 10  # number of experiments displayed per page
 
     # Mortimer database login settings
     MONGODB_SETTINGS = {
         "host": os.environ.get("MONGODB_HOST"),
         "port": int(os.environ.get("MONGODB_PORT")),
-
         "db": os.environ.get("MONGODB_MORTIMER_DB"),
         "username": os.environ.get("MONGODB_MORTIMER_USER"),
         "password": os.environ.get("MONGODB_MORTIMER_PW"),
         "authentication_source": os.environ.get("MONGODB_MORTIMER_AUTHDB"),
-
-        "ssl": mongodb_ssl,                     # True / False
+        "ssl": mongodb_ssl,  # True / False
         "ssl_ca_certs": ssl_ca_certs
-
         # "ssl": False,
         # "ssl_ca_certs": "mongodb_ca_file.pem"  # filepath must be relative to the directory that contains config.py and __init__.py
     }
@@ -45,21 +45,18 @@ class Config:
     MONGODB_ALFRED_SETTINGS = {
         "host": os.environ.get("MONGODB_HOST"),
         "port": int(os.environ.get("MONGODB_PORT")),
-
         "db": os.environ.get("MONGODB_ALFRED_DB"),
         "username": os.environ.get("MONGODB_ALFRED_USER"),
         "password": os.environ.get("MONGODB_ALFRED_PW"),
         "authentication_source": os.environ.get("MONGODB_ALFRED_AUTHDB"),
-
         "ssl": mongodb_ssl,
         "ssl_ca_certs": ssl_ca_certs
-
         # "ssl": False,
         # "ssl_ca_certs": "mongodb_ca_file.pem"  # filepath must be relative to the directory that contains config.py and __init__.py
     }
 
     # Mail settings
-    MAIL_USE = True     # enable or disable password reset emails
+    MAIL_USE = True  # enable or disable password reset emails
     MAIL_SERVER = os.environ.get("MAIL_SERVER")
     MAIL_PORT = os.environ.get("MAIL_PORT")
     MAIL_USE_TLS = True
@@ -68,8 +65,8 @@ class Config:
 
     # Flask-Dropzone settings:
     DROPZONE_ALLOWED_FILE_CUSTOM = True
-    DROPZONE_ALLOWED_FILE_TYPE = '.pdf, image/*, .txt, .xml, .pem, .mp3, .mp4, .ogg'
+    DROPZONE_ALLOWED_FILE_TYPE = ".pdf, image/*, .txt, .xml, .pem, .mp3, .mp4, .ogg"
     DROPZONE_MAX_FILE_SIZE = 10
     DROPZONE_MAX_FILES = 100
     DROPZONE_UPLOAD_ON_CLICK = True
-    DROPZONE_UPLOAD_BTN_ID = 'upload'
+    DROPZONE_UPLOAD_BTN_ID = "upload"

mortimer/errors/handlers.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 
 from flask import Blueprint, render_template

mortimer/export.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 from __future__ import print_function
@@ -14,7 +13,7 @@
 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'))
+    bytes_f.write(f.getvalue().encode("utf-8"))
     # seeking was necessary. Python 3.5.2, Flask 0.12.2
     bytes_f.seek(0)
     f.close()
@@ -29,13 +28,15 @@ def to_json(cursor):
     return sIO
 
 
-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)):
             for j in range(len(rows[i])):
                 if isinstance(rows[i][j], str) or isinstance(rows[i][j], str):
-                    rows[i][j].replace('\n', '')
+                    rows[i][j].replace("\n", "")
     csvfile = io.StringIO()
     writer = csv.writer(csvfile, dialect=dialect, **writerparams)
     for row in rows:
@@ -44,35 +45,42 @@ def to_csv(cursor, none_value=None, remove_linebreaks=False, dialect='excel', **
 
 
 def to_excel_csv(cursor, none_value=None, **writerparams):
-    return to_csv(cursor, none_value=none_value, remove_linebreaks=True,
-                  delimiter=';', dialect='excel', **writerparams)
-
-
-def to_excel(cursor, none_value=None):
-    from openpyxl import Workbook
-    wb = Workbook(encoding='utf-8')
-    sheet = wb.get_active_sheet()
-    docs = cursor_to_rows(cursor, none_value)
-    for i in range(len(docs)):
-        for j in range(len(docs[i])):
-            tmp = docs[i][j]
-            if not(isinstance(tmp, str) and isinstance(tmp, str) and
-                    isinstance(tmp, float) and isinstance(tmp, int)):
-                tmp = str(tmp)
-            sheet.cell(row=i, column=j).value = tmp
-    # f = TemporaryFile()
-    f = io.StringIO()
-    wb.save(f)
-    f.seek(0)
-    return f
+    return to_csv(
+        cursor,
+        none_value=none_value,
+        remove_linebreaks=True,
+        delimiter=";",
+        dialect="excel",
+        **writerparams
+    )
+
+
+# def to_excel(cursor, none_value=None):
+#     from openpyxl import Workbook
+#     wb = Workbook(encoding='utf-8')
+#     sheet = wb.get_active_sheet()
+#     docs = cursor_to_rows(cursor, none_value)
+#     for i in range(len(docs)):
+#         for j in range(len(docs[i])):
+#             tmp = docs[i][j]
+#             if not(isinstance(tmp, str) and isinstance(tmp, str) and
+#                     isinstance(tmp, float) and isinstance(tmp, int)):
+#                 tmp = str(tmp)
+#             sheet.cell(row=i, column=j).value = tmp
+#     # f = TemporaryFile()
+#     f = io.StringIO()
+#     wb.save(f)
+#     f.seek(0)
+#     return f
 
 
 def natural_sort(l):
     def convert(text):
         return int(text) if text.isdigit() else text.lower()
 
     def alphanum_key(key):
-        return [convert(c) for c in re.split('([0-9]+)', key[0])]
+        return [convert(c) for c in re.split("([0-9]+)", key[0])]
+
     return sorted(l, key=alphanum_key)
 
 
@@ -90,7 +98,7 @@ def cursor_to_rows(cursor, none_value=None):
 
 class Header(object):
     def __init__(self, *docs):
-        self.tag = docs[0]['tag']
+        self.tag = docs[0]["tag"]
         self.parent = None
         self.names = []
         self.children = []
@@ -104,24 +112,24 @@ def setParent(self, p):
         return self
 
     def addDoc(self, doc):
-        assert(self.tag == doc['tag'])
+        assert self.tag == doc["tag"]
         for k, v in natural_sort(list(doc.items())):
-            if k in ['_id', 'tag', 'uid']:
+            if k in ["_id", "tag", "uid"]:
                 pass
-            elif k == 'subtree_data':
+            elif k == "subtree_data":
                 for subDoc in v:
                     if subDoc == {}:
                         continue
                     found = False
                     for child in self.children:
-                        if subDoc['tag'] == child.tag:
+                        if subDoc["tag"] == child.tag:
                             child.addDoc(subDoc)
                             found = True
                             break
                     if not found:
                         self.children.append(Header(subDoc).setParent(self))
-            elif k == 'additional_data':
-                v['tag'] = 'additional_data'
+            elif k == "additional_data":
+                v["tag"] = "additional_data"
                 if self.additional_data is None:
                     self.additional_data = Header(v)
                 else:
@@ -131,7 +139,7 @@ def addDoc(self, doc):
 
     def getFlatHeaders(self, with_root=True, deep=True, additional_data=True):
         rl = []
-        pre = self.tag + '.' if with_root else ''
+        pre = self.tag + "." if with_root else ""
         for name in self.names:
             rl.append(pre + name)
         if deep:
@@ -145,23 +153,25 @@ def getFlatHeaders(self, with_root=True, deep=True, additional_data=True):
 
     def getDataFromDoc(self, doc):
         rv = []
-        assert(doc == {} or doc['tag'] == self.tag)
+        assert doc == {} or doc["tag"] == self.tag
         headers = self.getFlatHeaders(False, False, False)
         for header in headers:
             rv.append(doc.get(header, None))
         for child in self.children:
             found = False
-            for subDoc in doc.get('subtree_data', []):
+            for subDoc in doc.get("subtree_data", []):
                 try:
-                    if subDoc['tag'] == child.tag:
+                    if subDoc["tag"] == child.tag:
                         found = True
                         break
-                except KeyError as e:
+                except KeyError:
                     print(subDoc)
                     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):
@@ -172,8 +182,8 @@ def getDataFromDocs(self, docs):
 
     def __unicode__(self):
         if self.parent:
-            return str(self.parent) + '.' + self.tag
+            return str(self.parent) + "." + self.tag
         return str(self.tag)
 
     def __str__(self):
-        return str(self).encode('utf-8')
+        return str(self).encode("utf-8")

mortimer/forms.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 
 from flask_wtf import FlaskForm

mortimer/local_experiments/routes.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 
 from mortimer import export
@@ -99,7 +99,7 @@ def experiments():
 @login_required
 def user_experiments(username):
 
-    page = request.args.get("page", 1, type=int)
+    # page = request.args.get("page", 1, type=int)
     user = User.objects.get_or_404(username=username)
 
     if user.username != current_user.username: