Merge remote-tracking branch 'origin/issue-6127' into issue-6126

Author: sharadsw

CHANGELOG.md

@@ -8,6 +8,35 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [7.10.2](https://github.com/specify/specify7/compare/v7.10.1...v7.10.2) (23 April 2025)
+
+## Added
+
+* **[Batch Editing](https://discourse.specifysoftware.org/t/batch-edit/2248)** for simple fields ([#5417](https://github.com/specify/specify7/pull/5417) – *Requested by many, many members*)
+* [**Added a 'Download' button** to record set and query results attachments](https://discourse.specifysoftware.org/t/bulk-download-attachments-from-a-query-result-or-record-set/2456) ([#6052](https://github.com/specify/specify7/pull/6052) – *Requested by The University of Michigan, Naturhistorisches Museum Bern, Beaty Biodiversity Museum, Agriculture and Agri-Food Canada, Muséum d'Histoire Naturelle Geneva, and Queensland Herbarium*)
+* The [Form Meta menu](https://discourse.specifysoftware.org/t/form-meta-menu/844) is now accessible when using "View in Forms" ([#5416](https://github.com/specify/specify7/pull/5416))
+* A default value can now be used for a query combo box ([#6037]([https://github.com/specify/specify7/pull/6037]) – *Requested by South African Institute for Aquatic Biodiversity and The Ohio State University Mollusk Division*)
+* Adds tooltip for required fields in bulk carry forward config ([#6202](https://github.com/specify/specify7/pull/6202))
+* Specify will use the default `TypeSearches` when a custom one is not defined for a table ([#6236](https://github.com/specify/specify7/pull/6236))
+* Adds a new `uniqueIdentifier` field to Storage ([#6249](https://github.com/specify/specify7/pull/6249))
+
+## Changed
+
+* Non-default Taxon trees can be deleted if they are not used ([#6186](https://github.com/specify/specify7/pull/6186))
+* Adds modern attachment placeholder icons for video, audio, text, and other attachment filetypes ([#6119](https://github.com/specify/specify7/pull/6119))
+
+## Fixed
+
+* Fixes an issue that caused some WorkBench data sets to match to the incorrect ranks ([#6322](https://github.com/specify/specify7/pull/6322))
+* Fixes an issue where the defaults for insect collections were missing ([#6383](https://github.com/specify/specify7/pull/6383))
+* Field formats in the Schema Config utility are selected automatically again ([#6255](https://github.com/specify/specify7/pull/6255))
+* Primary Collection Objects (COs) in a consolidated Collection Object Group (COG) can no longer be deleted unless another CO is marked as primary ([#6181](https://github.com/specify/specify7/pull/6181))
+* Fixes all cases where table aggregation separators were missing ([#6115](https://github.com/specify/specify7/pull/6115))
+* Fixes all cases where taxon tree structure is invalid due to accepted names not being designated as accepted ([#5366](https://github.com/specify/specify7/pull/5366))
+* Fixes all cases where coordinate text fields are empty but decimal coordinate fields contain values ([#5368](https://github.com/specify/specify7/pull/5368) – *Reported by The University of Michigan, College of Idaho, and several others*)
+* Fixes an issue where the Data Entry screen does not appear in the 'Geology' discipline ([#6365](https://github.com/specify/specify7/pull/6365))
+* Fixes an issue where unsaved changes would be lost when toggling the "Use Localized Field Labels" setting in the Form Meta menu
+
 ## [7.10.1](https://github.com/specify/specify7/compare/v7.10.0...v7.10.1) (10 March 2025)
 
 ## Added

Dockerfile

@@ -9,6 +9,7 @@ RUN apt-get update \
         libldap-2.4-2 \
         libmariadb3 \
         rsync \
+        tzdata \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 
@@ -42,6 +43,8 @@ RUN npx webpack --mode production
 
 FROM common AS build-backend
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get update \
  && apt-get -y install --no-install-recommends \
         build-essential \
@@ -58,6 +61,7 @@ RUN apt-get update \
         python3.8-distutils \
         python3.8-dev \
         libmariadbclient-dev \
+        tzdata \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 
@@ -129,13 +133,15 @@ RUN echo \
         "\nREPORT_RUNNER_PORT = os.getenv('REPORT_RUNNER_PORT', '')" \
         "\nWEB_ATTACHMENT_URL = os.getenv('ASSET_SERVER_URL', None)" \
         "\nWEB_ATTACHMENT_KEY = os.getenv('ASSET_SERVER_KEY', None)" \
-        "\nWEB_ATTACHMENT_COLLECTION = os.getenv('ASSET_SERVER_COLLECTION', None)" \
+        "\nWEB_ATTACHMENT_COLLECTION = os.getenv('ASSET_SERVER_COLLECTION', DATABASE_NAME) or DATABASE_NAME" \
         "\nSEPARATE_WEB_ATTACHMENT_FOLDERS = os.getenv('SEPARATE_WEB_ATTACHMENT_FOLDERS', None)" \
         "\nCELERY_BROKER_URL = os.getenv('CELERY_BROKER_URL', None)" \
         "\nCELERY_RESULT_BACKEND = os.getenv('CELERY_RESULT_BACKEND', None)" \
         "\nCELERY_TASK_DEFAULT_QUEUE = os.getenv('CELERY_TASK_QUEUE', DATABASE_NAME)" \
         "\nANONYMOUS_USER = os.getenv('ANONYMOUS_USER', None)" \
         "\nSPECIFY_CONFIG_DIR = os.environ.get('SPECIFY_CONFIG_DIR', '/opt/Specify/config')" \
+        "\nhost = os.getenv('CSRF_TRUSTED_ORIGINS', None)" \
+        "\nCSRF_TRUSTED_ORIGINS = [origin.strip() for origin in host.split(',')] if host else []" \
         > settings/local_specify_settings.py
 
 RUN echo "import os \nDEBUG = os.getenv('SP7_DEBUG', '').lower() == 'true'\n" \

docker-entrypoint.sh

@@ -1,3 +1,4 @@
+#!/bin/bash
 set -e
 if [ -z "$(ls -A /volumes/static-files/specify-config)" ]; then
   mkdir -p /volumes/static-files/specify-config/config/

requirements.txt

@@ -1,6 +1,10 @@
+setuptools>=50.0.0
+tzdata
+wheel
+backports.zoneinfo==0.2.1
 kombu==5.2.4
 celery[redis]==5.2.7
-Django==3.2.15
+Django==4.2.18
 mysqlclient==2.1.1
 SQLAlchemy==1.2.11
 requests==2.32.2

specifyweb/accounts/views.py

@@ -16,7 +16,7 @@
 from django.shortcuts import render
 from django.template.response import TemplateResponse
 from django.utils import crypto
-from django.utils.http import is_safe_url, urlencode
+from django.utils.http import url_has_allowed_host_and_scheme, urlencode
 from django.views.decorators.cache import never_cache
 from typing import Union, Optional, Dict, cast
 from typing_extensions import TypedDict
@@ -362,7 +362,7 @@ def choose_collection(request) -> http.HttpResponse:
 
     redirect_to = (request.POST if request.method == "POST" else request.GET).get('next', '')
     redirect_resp = http.HttpResponseRedirect(
-        redirect_to if is_safe_url(url=redirect_to, allowed_hosts=request.get_host())
+        redirect_to if url_has_allowed_host_and_scheme(url=redirect_to, allowed_hosts=request.get_host())
         else settings.LOGIN_REDIRECT_URL
     )
 

specifyweb/attachment_gw/urls.py

@@ -1,14 +1,13 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    url(r'^get_settings/$', views.get_settings),
-    url(r'^get_upload_params/$', views.get_upload_params),
-    url(r'^get_token/$', views.get_token),
-    url(r'^proxy/$', views.proxy),
-    url(r'^download_all/$', views.download_all),
-    url(r'^dataset/$', views.datasets),
-    url(r'^dataset/(?P<ds_id>\d+)/$', views.dataset),
-
+    path('get_settings/', views.get_settings),
+    path('get_upload_params/', views.get_upload_params),
+    path('get_token/', views.get_token),
+    path('proxy/', views.proxy),
+    path('download_all/', views.download_all),
+    path('dataset/', views.datasets),
+    path('dataset/<int:ds_id>/', views.dataset),
 ]

specifyweb/attachment_gw/views.py

@@ -72,8 +72,11 @@ def get_collection(request=None):
     # do any better than using the first collection
     # and hoping that all the assets are in the same
     # folder.
-    from specifyweb.specify.models import Collection
-    return Collection.objects.all()[0].collectionname
+    # from specifyweb.specify.models import Collection
+    # return Collection.objects.all()[0].collectionname
+
+    # The default coll parameter to assets is the database name
+    return settings.DATABASE_NAME
 
 @openapi(schema={
     "get": {

specifyweb/barvis/urls.py

@@ -1,7 +1,7 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    url(r'^taxon_bar/$', views.taxon_bar),
+    path('taxon_bar/', views.taxon_bar),
 ]

specifyweb/businessrules/__init__.py

@@ -1 +0,0 @@
-default_app_config = 'specifyweb.businessrules.apps.BussinessRuleConfig'

specifyweb/businessrules/urls.py

@@ -1,8 +1,8 @@
-from django.conf.urls import include, url
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    url(r'^uniqueness_rules/(?P<discipline_id>\d+)/$', views.uniqueness_rule),
-    url(r'^uniqueness_rules/validate/$', views.validate_uniqueness),
+    path('uniqueness_rules/<int:discipline_id>/', views.uniqueness_rule),
+    path('uniqueness_rules/validate/', views.validate_uniqueness),
 ]

specifyweb/context/remote_prefs.py

@@ -1,4 +1,4 @@
-from django.utils.encoding import force_text
+from django.utils.encoding import force_str
 
 from specifyweb.specify.models import Spappresourcedata
 
@@ -11,10 +11,10 @@ def get_remote_prefs() -> str:
     # Spappresource.data is stored in a blob field even though we treat
     # it as a TextField. Starting in django 2.2 it doesn't automatically
     # get decoded from bytes to str.
-    return '\n'.join(force_text(r.data) for r in res)
+    return '\n'.join(force_str(r.data) for r in res)
 
 def get_global_prefs() -> str:
     res = Spappresourcedata.objects.filter(
         spappresource__name='preferences',
         spappresource__spappresourcedir__usertype='Global Prefs')
-    return '\n'.join(force_text(r.data) for r in res)
+    return '\n'.join(force_str(r.data) for r in res)

specifyweb/context/testurls.py

@@ -2,15 +2,15 @@
 Provides urls to access the mocked views
 """
 
-from django.conf.urls import url
+from django.urls import path, re_path
 
 from . import testsviews as views
 
 urlpatterns = [
-    url(r'^collection/$', views.collection),
-    url(r'^domain.json$', views.domain),
-    url(r'^viewsets/(?P<level>\d+).xml$', views.viewsets),
-    url(r'^schema_localization.json$', views.schema_localization),
-    url(r'^app.resource$', views.app_resource),
-    url(r'^available_related_searches.json$', views.available_related_searches),
+    path('collection/', views.collection),
+    re_path(r'^domain.json$', views.domain),
+    re_path(r'^viewsets/(?P<level>\d+).xml$', views.viewsets),
+    re_path(r'^schema_localization.json$', views.schema_localization),
+    re_path(r'^app.resource$', views.app_resource),
+    re_path(r'^available_related_searches.json$', views.available_related_searches),
 ]

specifyweb/context/urls.py

@@ -2,36 +2,36 @@
 Defines the urls for the app context subsystem
 """
 
-from django.conf.urls import url
+from django.urls import path, re_path
 from django.urls import path
 
 from . import views, user_resources, collection_resources
 from ..attachment_gw.views import get_settings as attachment_settings
 from ..report_runner.views import get_status as report_runner_status
 
 urlpatterns = [
-    url(r'^login/$', views.api_login),
-    url(r'^collection/$', views.collection),
-    url(r'^user_collection_access_for_sp6/(?P<userid>\d+)/$', views.user_collection_access_for_sp6),
-    url(r'^language/$', views.languages),
-    url(r'^schema/language/$', views.schema_language),
-
-    url(r'^api_endpoints.json$', views.api_endpoints),
-    url(r'^api_endpoints_all.json$', views.api_endpoints_all),
-    url(r'^user.json$', views.user),
-    url(r'^system_info.json$', views.system_info),
-    url(r'^domain.json$', views.domain),
-    url(r'^view.json$', views.view),
-    url(r'^views.json$', views.views),
-    url(r'^viewsets.json$', views.viewsets),
-    url(r'^datamodel.json$', views.datamodel),
-    url(r'^schema_localization.json$', views.schema_localization),
-    url(r'^app.resource$', views.app_resource),
-    url(r'^available_related_searches.json$', views.available_related_searches),
-    url(r'^remoteprefs.properties$', views.remote_prefs),
-
-    url(r'^attachment_settings.json$', attachment_settings),
-    url(r'^report_runner_status.json$', report_runner_status),
+    path('login/', views.api_login),
+    path('collection/', views.collection),
+    path('user_collection_access_for_sp6/<int:userid>/', views.user_collection_access_for_sp6),
+    path('language/', views.languages),
+    path('schema/language/', views.schema_language),
+
+    re_path(r'^api_endpoints.json$', views.api_endpoints),
+    re_path(r'^api_endpoints_all.json$', views.api_endpoints_all),
+    re_path(r'^user.json$', views.user),
+    re_path(r'^system_info.json$', views.system_info),
+    re_path(r'^domain.json$', views.domain),
+    re_path(r'^view.json$', views.view),
+    re_path(r'^views.json$', views.views),
+    re_path(r'^viewsets.json$', views.viewsets),
+    re_path(r'^datamodel.json$', views.datamodel),
+    re_path(r'^schema_localization.json$', views.schema_localization),
+    re_path(r'^app.resource$', views.app_resource),
+    re_path(r'^available_related_searches.json$', views.available_related_searches),
+    re_path(r'^remoteprefs.properties$', views.remote_prefs),
+
+    re_path(r'^attachment_settings.json$', attachment_settings),
+    re_path(r'^report_runner_status.json$', report_runner_status),
 
     path('user_resource/', user_resources.user_resources),
     path('user_resource/<int:resourceid>/', user_resources.user_resource),

specifyweb/export/urls.py

@@ -1,11 +1,11 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    url(r'^rss/$', views.rss_feed),
-    url(r'^extract_eml/(?P<filename>.+)$', views.extract_eml),
-    url(r'^make_dwca/$', views.export),
-    url(r'extract_query/(?P<query_id>\d+)/$', views.extract_query),
-    url(r'force_update/$', views.force_update),
+    path('rss/', views.rss_feed),
+    path('extract_eml/<path:filename>', views.extract_eml),
+    path('make_dwca/', views.export),
+    path('extract_query/<int:query_id>/', views.extract_query),
+    path('force_update/', views.force_update),
 ]

specifyweb/express_search/urls.py

@@ -1,8 +1,8 @@
-from django.conf.urls import url
+from django.urls import path, re_path
 
 from . import views
 urlpatterns = [
-    url(r'^$', views.search),
-    url(r'^related/$', views.related_search),
-    url(r'^querycbx/(?P<modelname>\w*)/$', views.querycbx_search),
+    path('', views.search),
+    path('related/', views.related_search),
+    re_path(r'^querycbx/(?P<modelname>\w*)/$', views.querycbx_search),
 ]

specifyweb/frontend/doc_urls.py

@@ -1,9 +1,9 @@
-from django.conf.urls import url
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    url(r'^api/tables/$', views.api_tables),
-    url(r'^api/operations/$', views.api_operations),
-    url(r'^api/operations/all/$', views.api_operations_all),
+    path('api/tables/', views.api_tables),
+    path('api/operations/', views.api_operations),
+    path('api/operations/all/', views.api_operations_all),
 ]

specifyweb/frontend/js_src/lib/components/Attachments/__tests__/__snapshots__/utils.test.ts.snap

@@ -31,6 +31,7 @@ exports[`allTablesWithAttachments 1`] = `
   "[table TreatmentEvent]",
   "[table AbsoluteAge]",
   "[table RelativeAge]",
+  "[table Spdataset]",
 ]
 `;
 
@@ -66,5 +67,6 @@ exports[`attachmentRelatedTables 1`] = `
   "TreatmentEventAttachment",
   "AbsoluteAgeAttachment",
   "RelativeAgeAttachment",
+  "SpDataSetAttachment",
 ]
 `;

specifyweb/frontend/js_src/lib/components/DataModel/__tests__/__snapshots__/specifyTable.test.ts.snap

@@ -1527,6 +1527,7 @@ exports[`tableScoping 1`] = `
   "SpAppResourceDir": "collection",
   "SpAuditLog": undefined,
   "SpAuditLogField": undefined,
+  "SpDataSetAttachment": "spdataset > collection",
   "SpExportSchema": "discipline",
   "SpExportSchemaItem": "spExportSchema > discipline",
   "SpExportSchemaItemMapping": "exportSchemaItem > spExportSchema > discipline",