Merge branch 'release-v0.25.3' into 'master'

Release v0.25.3

See merge request Scientific-IT-Systems/SampleDB!982

README.md

@@ -65,7 +65,7 @@ docker run \
     --restart=always \
     --name sampledb \
     -p 8000:8000 \
-    sciapp/sampledb:0.25.2
+    sciapp/sampledb:0.25.3
 ```
 
 ### Once it's started

docker-compose.yml.dist

@@ -6,7 +6,7 @@ version: '3'
 
 services:
   web:
-    image: sciapp/sampledb:0.25.2
+    image: sciapp/sampledb:0.25.3
     restart: always
     container_name: sampledb
     # Note: this config option works with docker-compose version >1.27

docs/administrator_guide/getting_started.rst

@@ -43,7 +43,7 @@ Next, start the SampleDB container:
         --restart=always \
         --name sampledb \
         -p 8000:8000 \
-        sciapp/sampledb:0.25.2
+        sciapp/sampledb:0.25.3
 
 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 0.25.3
+--------------
+
+Released on December 20th, 2023.
+
+- Fixed showing plotly plots on instrument page
+- Fixed datetime format in HTTP API
+- Fixed user interface issues related to admin-only action types
+- Fixed handling of defaults during complex schema upgrades
+
 Version 0.25.2
 --------------
 

sampledb/api/server/comments.py

@@ -20,7 +20,7 @@ def comment_to_json(comment: Comment) -> typing.Dict[str, typing.Any]:
         'object_id': comment.object_id,
         'comment_id': comment.id,
         'user_id': comment.user_id,
-        'utc_datetime': comment.utc_datetime.isoformat() if comment.utc_datetime is not None else None,
+        'utc_datetime': comment.utc_datetime.replace(tzinfo=None).isoformat() if comment.utc_datetime is not None else None,
         'content': comment.content
     }
     return comment_json

sampledb/api/server/instrument_log.py

@@ -37,7 +37,7 @@ def instrument_log_entry_version_to_json(version: instrument_log_entries.Instrum
     return {
         'log_entry_id': version.log_entry_id,
         'version_id': version.version_id,
-        'utc_datetime': version.utc_datetime.isoformat(),
+        'utc_datetime': version.utc_datetime.replace(tzinfo=None).isoformat(),
         'content': version.content,
         'categories': [
             category_to_json(category)

sampledb/frontend/index.py

@@ -24,8 +24,6 @@ def index() -> FlaskResponseT:
                 continue
             if action.admin_only and not flask_login.current_user.is_admin:
                 continue
-            if action.type.admin_only and not flask_login.current_user.is_admin:
-                continue
             if action.disable_create_objects:
                 continue
             if action.type.disable_create_objects:

sampledb/frontend/templates/actions/actions.html

@@ -5,7 +5,7 @@
 {% block content %}
   <h1>{% if action_type %}{{ _('%(action_type)s Actions', action_type=action_type.name | get_translated_text(default=_('Unnamed Action Type'))) }} {% else %}{{ _('Actions') }}{% endif %}</h1>
   <p class="text-muted">{% if action_type and action_type.description %}{{ action_type.description | get_translated_text(default='—') }}{% else %}{{ _('Actions represent processes like creating a sample or performing a measurement.') }}{% endif %} <a href="https://scientific-it-systems.iffgit.fz-juelich.de/SampleDB/user_guide/actions.html">{{ _("Read more.") }}</a></p>
-  {% if (current_user.is_admin or user_is_instrument_scientist) and not current_user.is_readonly %}
+  {% if (current_user.is_admin or user_is_instrument_scientist) and not current_user.is_readonly and (not action_type or not action_type.admin_only or current_user.is_admin) %}
     {% if action_type %}
     <a href="{{ url_for('.new_action', action_type_id=action_type.id) }}" class="btn btn-default">{{ _("Create Action") }} </a>
     {% else %}

sampledb/frontend/templates/instruments/instrument.html

@@ -589,6 +589,11 @@ <h4 class="modal-title" id="mobileFileLinkModalLabel">{{ _('Mobile File Upload')
       toggleShowMore
     } from "{{ fingerprinted_static('sampledb/js/view-object-data.js') }}";
     window.toggleShowMore = toggleShowMore;
+
+    import {
+      togglePlotlyChartDiv
+    } from "{{ fingerprinted_static('sampledb/js/sampledb-toggle.js') }}";
+    window.togglePlotlyChartDiv = togglePlotlyChartDiv;
   </script>
   <script type="text/javascript" nonce="{{ generate_inline_script_nonce() }}">
 

sampledb/logic/schemas/convert_to_schema.py

@@ -45,7 +45,7 @@ def convert_to_schema(
         if result:
             return result
     if previous_schema['type'] != new_schema['type']:
-        return generate_placeholder(new_schema), [_("Unable to convert property '%(title)s' from type '%(type1)s' to type '%(type2)s'.", title=get_translated_text(new_schema['title']), type1=previous_schema['type'], type2=new_schema['type'])]
+        return copy.deepcopy(generate_placeholder(new_schema)), [_("Unable to convert property '%(title)s' from type '%(type1)s' to type '%(type2)s'.", title=get_translated_text(new_schema['title']), type1=previous_schema['type'], type2=new_schema['type'])]
     if new_schema['type'] == 'text' and 'choices' in new_schema and isinstance(data, dict):
         result = _try_convert_text_to_choices(data, new_schema)
         if result:
@@ -72,7 +72,7 @@ def convert_to_schema(
         result = _try_convert_array_to_array(data, new_schema, previous_schema)
         if result:
             return result
-    return generate_placeholder(new_schema), [_("Unable to convert property '%(title)s' of type '%(type)s'.", title=get_translated_text(new_schema['title']), type=new_schema['type'])]
+    return copy.deepcopy(generate_placeholder(new_schema)), [_("Unable to convert property '%(title)s' of type '%(type)s'.", title=get_translated_text(new_schema['title']), type=new_schema['type'])]
 
 
 def _try_convert_text_to_tags(
@@ -111,7 +111,7 @@ def _try_convert_object_to_object(
         previous_schema: typing.Dict[str, typing.Any]
 ) -> typing.Optional[typing.Tuple[typing.Dict[str, typing.Any], typing.Sequence[str]]]:
     upgrade_warnings = []
-    new_data = generate_placeholder(new_schema)
+    new_data = copy.deepcopy(generate_placeholder(new_schema))
     if not isinstance(new_data, dict):
         return None
     for property_name, property_value in data.items():

sampledb/version.py

@@ -11,4 +11,4 @@
 
 import os
 
-__version__ = os.environ.get('SAMPLEDB_VERSION') or '0.25.2'
+__version__ = os.environ.get('SAMPLEDB_VERSION') or '0.25.3'

tests/api/server/test_comments.py

@@ -2,6 +2,7 @@
 """
 
 """
+import datetime
 
 import requests
 import pytest
@@ -164,13 +165,12 @@ def test_get_comments(flask_server, object, auth, user):
     assert r.status_code == 200
     result_json = r.json()
     assert len(result_json) == 1
-    assert 'utc_datetime' in result_json[0]
-    del result_json[0]['utc_datetime']
     assert result_json == [
         {
             'object_id': object.id,
             'comment_id': comment_id,
             'user_id': user.id,
+            'utc_datetime': sampledb.logic.comments.get_comment(comment_id).utc_datetime.strftime('%Y-%m-%dT%H:%M:%S.%f'),
             'content': content
         }
     ]

tests/api/server/test_instrument_log.py

@@ -77,7 +77,7 @@ def test_get_instrument_log_entries(flask_server, auth, user, app):
                 {
                     'version_id': 1,
                     'log_entry_id': log_entry.id,
-                    'utc_datetime': log_entry.versions[0].utc_datetime.isoformat(),
+                    'utc_datetime': log_entry.versions[0].utc_datetime.strftime('%Y-%m-%dT%H:%M:%S.%f'),
                     'content': "Example Log Entry",
                     'categories': []
                 }
@@ -108,7 +108,7 @@ def test_get_instrument_log_entries(flask_server, auth, user, app):
             {
                 'version_id': 1,
                 'log_entry_id': log_entry.id,
-                'utc_datetime': log_entry.versions[0].utc_datetime.isoformat(),
+                'utc_datetime': log_entry.versions[0].utc_datetime.strftime('%Y-%m-%dT%H:%M:%S.%f'),
                 'content': "Example Log Entry 2",
                 'categories': [
                     {
@@ -162,7 +162,7 @@ def test_get_instrument_log_entry(flask_server, auth, user):
             {
                 'version_id': 1,
                 'log_entry_id': log_entry.id,
-                'utc_datetime': log_entry.versions[0].utc_datetime.isoformat(),
+                'utc_datetime': log_entry.versions[0].utc_datetime.strftime('%Y-%m-%dT%H:%M:%S.%f'),
                 'content': "Example Log Entry",
                 'categories': []
             }