Merge branch 'release-v0.29.0' into 'master'

Release v0.29.0

See merge request Scientific-IT-Systems/SampleDB!1137

README.md

@@ -63,7 +63,7 @@ docker run \
     --restart=always \
     --name sampledb \
     -p 8000:8000 \
-    sciapp/sampledb:0.28.2
+    sciapp/sampledb:0.29.0
 ```
 
 ### Once it's started

docker-compose.yml.dist

@@ -6,7 +6,7 @@ version: '3'
 
 services:
   web:
-    image: sciapp/sampledb:0.28.2
+    image: sciapp/sampledb:0.29.0
     restart: always
     container_name: sampledb
     # Note: this config option works with docker-compose version >1.27

docs/administrator_guide/getting_started.rst

@@ -42,7 +42,7 @@ Next, start the SampleDB container:
         --restart=always \
         --name sampledb \
         -p 8000:8000 \
-        sciapp/sampledb:0.28.2
+        sciapp/sampledb:0.29.0
 
 This will start a minimal SampleDB installation at ``http://localhost:8000`` and allow you to sign in with the username ``admin`` and the password ``password``.
 

docs/changelog.rst

@@ -1,6 +1,16 @@
 Changelog
 =========
 
+Version 0.29
+------------
+
+Released on August 19th, 2024.
+
+- Fixed simple search query escaping to support searching for special characters
+- Fixed handling of property named tags that contains an array or an object instead of tags
+- Fixed indentation level styling
+- Added support for flexible metadata in .eln imports
+
 Version 0.28.2
 --------------
 
@@ -30,7 +40,7 @@ Released on June 13th, 2024.
 - Added ``timeline`` array style for arrays of objects with a ``datetime`` property
 - Added search to text fields with more than 10 choices (configurable with ``SAMPLEDB_MIN_NUM_TEXT_CHOICES_FOR_SEARCH``)
 - Added support for ``"first"`` and ``"last"`` statistic for timeseries
-- Added badic and project groups to the HTTP API
+- Added basic and project groups to the HTTP API
 - Allow using dicts for the ``style`` attribute
 - Added support for ``"include"`` style for object reference properties
 - Allow referenced objects in search queries

requirements.txt

@@ -1,26 +1,26 @@
 appdirs==1.4.4
 APScheduler==3.10.4
 autocommand==2.2.2
-Babel==2.15.0
+babel==2.16.0
 backports.tarfile==1.2.0
-bcrypt==4.1.3
+bcrypt==4.2.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
 blinker==1.8.2
 Brotli==1.1.0
-certifi==2024.6.2
-cffi==1.16.0
+certifi==2024.7.4
+cffi==1.17.0
 chardet==5.2.0
 charset-normalizer==3.3.2
 cheroot==10.0.1
-CherryPy==18.9.0
+CherryPy==18.10.0
 click==8.1.7
 colorhash==2.0.0
-configparser==7.0.0
-cryptography==42.0.8
+configparser==7.1.0
+cryptography==43.0.0
 cssselect2==0.7.0
 dnspython==2.6.1
-email_validator==2.1.1
+email_validator==2.2.0
 fido2==1.1.3
 Flask==3.0.3
 flask-babel==4.0.0
@@ -32,52 +32,51 @@ Flask-SQLAlchemy==3.1.1
 Flask-WTF==1.2.1
 flexcache==0.3
 flexparser==0.3.1
-fonttools==4.53.0
+fonttools==4.53.1
 greenlet==3.0.3
 html5lib==1.1
 idna==3.7
-inflect==7.2.1
 itsdangerous==2.2.0
 jaraco.collections==5.0.1
 jaraco.context==5.3.0
-jaraco.functools==4.0.1
-jaraco.text==3.12.0
+jaraco.functools==4.0.2
+jaraco.text==4.0.0
 Jinja2==3.1.4
 kaleido==0.2.1
 ldap3==2.9.1
-Markdown==3.6
+Markdown==3.7
 MarkupSafe==2.1.5
-more-itertools==10.2.0
-numpy==1.26.4
+more-itertools==10.4.0
+numpy==2.1.0
 packaging==24.1
-pillow==10.3.0
-Pint==0.24
-plotly==5.22.0
+pillow==10.4.0
+Pint==0.24.3
+plotly==5.23.0
 portend==3.2.0
-psutil==5.9.8
+psutil==6.0.0
 psycopg2-binary==2.9.9
 pyasn1==0.6.0
 pycparser==2.22
-pydyf==0.10.0
+pydyf==0.11.0
 pyotp==2.9.0
-pyphen==0.15.0
+pyphen==0.16.0
 pypng==0.20220715.0
+python-dateutil==2.9.0.post0
 pytz==2024.1
 qrcode==7.4.2
-reportlab==4.2.0
+reportlab==4.2.2
 requests==2.31.0
-scipy==1.13.1
+scipy==1.14.0
 six==1.16.0
-soupsieve==2.5
-SQLAlchemy==2.0.30
-tempora==5.5.1
-tenacity==8.3.0
+soupsieve==2.6
+SQLAlchemy==2.0.32
+tempora==5.7.0
+tenacity==9.0.0
 tinycss2==1.3.0
-typeguard==4.3.0
 typing_extensions==4.12.2
 tzlocal==2.0.0
-urllib3==2.2.1
-weasyprint==62.2
+urllib3==2.2.2
+weasyprint==62.3
 webencodings==0.5.1
 Werkzeug==3.0.3
 WTForms==3.1.2

sampledb/__init__.py

@@ -33,11 +33,11 @@ def babel_locale_selector() -> str:
     if not current_user or not current_user.is_authenticated:
         return request_locale
 
-    auto_lc = sampledb.logic.settings.get_user_setting(current_user.id, 'AUTO_LC')
+    auto_lc = current_user.settings['AUTO_LC']
     if auto_lc:
         return request_locale
 
-    stored_locale = sampledb.logic.settings.get_user_setting(current_user.id, 'LOCALE')
+    stored_locale = current_user.settings['LOCALE']
     if stored_locale in sampledb.logic.locale.get_allowed_language_codes():
         return typing.cast(str, stored_locale)
 
@@ -48,10 +48,9 @@ def babel_timezone_selector() -> typing.Optional[str]:
     if flask.current_app.config['TIMEZONE']:
         return typing.cast(typing.Optional[str], flask.current_app.config['TIMEZONE'])
     if current_user.is_authenticated:
-        settings = sampledb.logic.settings.get_user_settings(current_user.id)
-        if settings['AUTO_TZ']:
-            return typing.cast(typing.Optional[str], flask.request.args.get('timezone', settings['TIMEZONE']))
-        return typing.cast(typing.Optional[str], settings['TIMEZONE'])
+        if current_user.settings['AUTO_TZ']:
+            return typing.cast(typing.Optional[str], flask.request.args.get('timezone', current_user.settings['TIMEZONE']))
+        return typing.cast(typing.Optional[str], current_user.settings['TIMEZONE'])
     return flask.request.args.get('timezone', None)
 
 

sampledb/config.py

@@ -479,7 +479,7 @@ def check_config(
     internal_config['PDFEXPORT_LOGO_WIDTH'] = min(200, max(0, config['PDFEXPORT_LOGO_WIDTH']))
     if config['PDFEXPORT_LOGO_URL'] is not None:
         logo_url = config['PDFEXPORT_LOGO_URL']
-        logo_image = None
+        logo_image: typing.Optional[Image.Image] = None
         if logo_url.startswith('file://'):
             logo_path = logo_url[7:]
             try:

sampledb/frontend/instruments.py

@@ -980,27 +980,38 @@ def instrument_log_file_attachment(instrument_id: int, log_entry_id: int, file_a
         file_attachment = get_instrument_log_file_attachment(file_attachment_id)
     except InstrumentLogFileAttachmentDoesNotExistError:
         return flask.abort(404)
-    file_extension = os.path.splitext(file_attachment.file_name)[1]
-    download = 'preview' not in flask.request.args
-    mime_type = flask.current_app.config.get('MIME_TYPES', {}).get(file_extension, '')
-    if not mime_type:
-        download = True
-    if download:
-        return flask.Response(
-            file_attachment.content,
-            200,
-            headers={
-                'Content-Disposition': f'attachment; filename="{file_attachment.file_name}"'
-            }
-        )
-    else:
-        return flask.Response(
-            file_attachment.content,
-            200,
-            headers={
-                'Content-Type': mime_type
-            }
-        )
+    return_preview = 'preview' in flask.request.args
+    return_thumbnail = 'thumbnail' in flask.request.args
+
+    if return_thumbnail:
+        if file_attachment.image_info:
+            return flask.Response(
+                file_attachment.image_info.thumbnail_content,
+                200,
+                headers={
+                    'Content-Type': file_attachment.image_info.thumbnail_mime_type
+                }
+            )
+        else:
+            return_preview = True
+    if return_preview:
+        file_extension = os.path.splitext(file_attachment.file_name)[1]
+        mime_type = flask.current_app.config.get('MIME_TYPES', {}).get(file_extension, '')
+        if mime_type:
+            return flask.Response(
+                file_attachment.content,
+                200,
+                headers={
+                    'Content-Type': mime_type
+                }
+            )
+    return flask.Response(
+        file_attachment.content,
+        200,
+        headers={
+            'Content-Disposition': f'attachment; filename="{file_attachment.file_name}"'
+        }
+    )
 
 
 @frontend.route('/instruments/<int:instrument_id>/log/mobile_upload/<token>', methods=['GET'])

sampledb/frontend/objects/object_form_parser.py

@@ -661,12 +661,14 @@ def parse_timeseries_form_data(
     timeseries_data_str = form_data.get(id_prefix + '__data', [''])[0]
     if not timeseries_data_str and not required:
         return None
+    timeseries_data: typing.List[typing.List[typing.Union[str, int, float]]]
     if not timeseries_data_str:
         timeseries_data = []
     else:
         csv_file = io.StringIO(timeseries_data_str)
         reader = csv.reader(csv_file, quoting=csv.QUOTE_NONNUMERIC)
-        timeseries_data = list(reader)
+        # csv.QUOTE_NONNUMERIC enables data conversion, however type annotations do not reflect this
+        timeseries_data = list(reader)  # type: ignore
         if timeseries_data and all(isinstance(value, str) for value in timeseries_data[0]):
             # skip header rows
             timeseries_data = timeseries_data[1:]
@@ -679,7 +681,7 @@ def parse_timeseries_form_data(
                 raise ValueError(_('invalid timeseries CSV data, expected datetime string or relative time in seconds, magnitude and (optional) magnitude in base units'))
             if not is_relative_time:
                 try:
-                    parsed_datetime = datetime.datetime.strptime(row[0], '%Y-%m-%d %H:%M:%S.%f')
+                    parsed_datetime = datetime.datetime.strptime(typing.cast(str, row[0]), '%Y-%m-%d %H:%M:%S.%f')
                 except ValueError as exc:
                     raise ValueError(_('invalid datetime in timeseries, expected format: YYYY-MM-DD hh:mm:ss.ffffff')) from exc
                 if user_timezone != pytz.utc: