Merge branch 'issue-5223' of https://github.com/specify/specify7 into…

… issue-5223

.env

@@ -3,11 +3,11 @@ DATABASE_PORT=3306
 MYSQL_ROOT_PASSWORD=password
 DATABASE_NAME=specify
 
-# When running Specify 7 for the first time or during updates that
-# require migrations, ensure that the MASTER_NAME and MASTER_PASSWORD
-# are set to the root username and password. This will ensure proper
-# execution of Django migrations during the initial setup.
-# After launching Specify and verifying the update is complete, you can
+# When running Specify 7 for the first time or during updates that 
+# require migrations, ensure that the MASTER_NAME and MASTER_PASSWORD 
+# are set to the root username and password. This will ensure proper 
+# execution of Django migrations during the ixnitial setup. 
+# After launching Specify and verifying the update is complete, you can 
 # safely replace these credentials with the master SQL user name and password.
 MASTER_NAME=root
 MASTER_PASSWORD=password
@@ -36,7 +36,7 @@ CELERY_RESULT_BACKEND=redis://redis/1
 LOG_LEVEL=WARNING
 
 # Set this variable to `true` to run Specify 7 in debug mode. This
-# should only be used during development and troubleshooting and not
-# during general use. Django applications leak memory when operated
+# should only be used during development and troubleshooting and not 
+# during general use. Django applications leak memory when operated 
 # continuously in debug mode.
 SP7_DEBUG=true

.github/workflows/docker.yml

@@ -37,7 +37,7 @@ jobs:
             # See https://github.com/specify/specify7-test-panel/issues/110#issuecomment-1943045253
             VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
             if [ "${{ github.event.repository.default_branch }}" = "$VERSION" ]; then
-              VERSION=edge
+              VERSION=production
             fi
           elif [[ $GITHUB_REF == refs/pull/* ]]; then
             VERSION=pr-${{ github.event.number }}
@@ -82,9 +82,9 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           platforms: ${{ matrix.platform }}
-          labels: ${{ steps.meta.outputs.labels }}
-          outputs: type=image,name=${{ env.REGISTRY_IMAGE }},push-by-digest=true,name-canonical=true,push=true
-      
+          tags: ${{ steps.prep.outputs.tags }}
+          push: true
+
       - name: Export digest
         run: |
           mkdir -p /tmp/digests
@@ -134,4 +134,4 @@ jobs:
       
       - name: Inspect image
         run: |
-          docker buildx imagetools inspect ${{ env.REGISTRY_IMAGE }}:${{ steps.meta.outputs.version }}
+          docker buildx imagetools inspect ${{ env.REGISTRY_IMAGE }}:${{ steps.meta.outputs.version }}

CHANGELOG.md

@@ -9,6 +9,26 @@ 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/).
 
+## [7.9.7](https://github.com/specify/specify7/compare/v7.9.6.2...v7.9.7) (1 October 2024)
+
+### Added
+* Added an all-new **Bulk Carry Forward** feature to enable series data entry in Specify 7 ([#4804](https://github.com/specify/specify7/pull/4804), [#5120](https://github.com/specify/specify7/pull/5120) – _Requested by University of Minnesota Entomology, Bulgarian Academy of Sciences, KU Entomology, and many others_)
+* Added support for Geography Code at any rank when building a query ([#5094](https://github.com/specify/specify7/pull/5094) – _Requested by Museu de Ciències Naturals de Barcelona, KU Ichthyology, and many others_)
+* Added a preference (enabled by default) to insert a [UTF-8 BOM](https://en.wikipedia.org/wiki/Byte_order_mark#:~:text=%5B3%5D-,UTF%2D8,-%5Bedit%5D) to CSV exports ([#5204](https://github.com/specify/specify7/pull/5204))
+* When enabled, you should be able to open exported CSV files in Excel without using the import utility.
+
+### Changed
+* Removed the limit on the number of results returned when searching a tree in the tree viewer ([#5125](https://github.com/specify/specify7/pull/5125))
+* Descriptions for User Preferences have been improved ([#5064](https://github.com/specify/specify7/pull/5064))
+* Specify in Docker is now built for both `x64_86` and `arm64` architectures, enabling native deployment on ARM-based servers ([#5235](https://github.com/specify/specify7/pull/5235))
+* Collection, Discipline, Division, and the Audit Log are now visible in the list of query tables by default ([#5133](https://github.com/specify/specify7/pull/5133))
+
+### Fixed
+* Fixed an issue that caused table aggregation separators to be cleared when set to the default separator (`; `) ([#5240](https://github.com/specify/specify7/pull/5240))
+* Fixed an issue that allowed users to carry forward preparations in an interaction when cloning or using carry forward ([#4905](https://github.com/specify/specify7/pull/4905))
+* Fixed an issue that would cause a crash if an `ExportFeed` was configured with an invalid Specify user ID ([#5042](https://github.com/specify/specify7/pull/5042))
+* Fixed an issue where a border would not appear for query items in the report query dialog ([#5159](https://github.com/specify/specify7/pull/5159))
+
 ## [7.9.6.2](https://github.com/specify/specify7/compare/v7.9.6.1...v7.9.6.2) (22 July 2024)
 
 - Fixed an issue that prevented `TimestampModified` from being captured upon saving a record since the `v7.9.6` release ([#5108](https://github.com/specify/specify7/issues/5108) – *Reported by the University of Kansas and Ohio State University*)

README.md

@@ -2,7 +2,7 @@
 # [Specify 7](https://www.specifysoftware.org/products/specify-7/)
 
 The [Specify Collections Consortium](https://www.specifysoftware.org) is pleased
-to offer Specify 7, a web implementation of our biological collections data
+to offer Specify 7, the web implementation of our biological collections data
 management platform.
 
 We encourage members to use
@@ -15,30 +15,27 @@ access to this repository.
 
 The new generation of Specify combines the interface design components and data
 management foundation of Specify 6 with the efficiency and ease-of-use of
-web-based data access and cloud computing. The Specify 7 web application uses
+web-based data access and cloud computing. Specify 7 uses
 the same interface layout language as Specify 6, so any user interface
-customization made in one product is mirrored in the other. Also Specify 6 and
-Specify 7 use the same data model and can work from the same Specify MySQL
-database, which means they can be run simultaneously with any Specify
-collection. By providing an easy migration path to the web, Specify 7 helps
+customization made in one platform is mirrored in the other. Also Specify 6 and
+Specify 7 use the same data model and can work from the same Specify MySQL or MariaDB
+database, which means 6 and 7 can be run simultaneously with any Specify
+collection. Specify 7 helps
 transition Specify 6 collections to cloud computing. It is also a great starting
-platform for collections which prefer zero workstation software installation and
+platform for institutions that prefer zero workstation software installation and
 ubiquitous web browser access.
 
-Specify 7’s server/browser architecture open the door for computing support of
-collaborative digitization projects and for remote hosting of institutional or
-project specimen databases. Without the need for a local area or campus network
+Specify 7’s architecture supports collaborative digitization projects and remote hosting of specimen databases. Without the need for a local area or campus network
 to connect to the MySQL data server, Specify 7 gives you and your collaborators
-access to a shared specimen database through any web browser. Without adequate
-IT support to maintain a secure database server? With the Specify 7 server
+access to a shared specimen database through any web browser. Finding it challenging to obtain IT support to maintain a local secure database server? With the Specify 7 server
 software supported on generic Linux servers, museums can utilize a server
 hosting service to provide support for the technical complexities of systems
 administration, security management, and backing-up. Want to create a joint
-database with remote collaborators for a collaborative digitizing effort? No
+database for a collaborative digitizing effort? No
 problem! Host, hire a hosting service or use
 our [Specify Cloud](https://www.specifysoftware.org/products/cloud/) service for
 your Specify database, set up accounts and go. We provide the same efficient
-user interface and printed reports and labels customization, and help desk
+user interface, report and labels customization and help desk
 support for Specify 7 as we do for Specify 6.
 
 **Secure.**
@@ -69,7 +66,7 @@ The Specify Collections Consortium is funded by its member
 institutions. The Consortium web site is:
 https://specifysoftware.org
 
-Specify 7 Copyright © 2023 Specify Collections Consortium. Specify
+Specify 7 Copyright © 2024 Specify Collections Consortium. Specify
 comes with ABSOLUTELY NO WARRANTY. This is free software licensed
 under GNU General Public License 2 (GPL2).
 

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

@@ -3,6 +3,7 @@
 exports[`fields are loaded 1`] = `
 [
   "[literalField CollectionObject.actualTotalCountAmt]",
+  "[literalField CollectionObject.age]",
   "[literalField CollectionObject.availability]",
   "[literalField CollectionObject.catalogNumber]",
   "[literalField CollectionObject.catalogedDate]",
@@ -104,6 +105,7 @@ exports[`fields are loaded 1`] = `
 exports[`literal fields are loaded 1`] = `
 [
   "[literalField CollectionObject.actualTotalCountAmt]",
+  "[literalField CollectionObject.age]",
   "[literalField CollectionObject.availability]",
   "[literalField CollectionObject.catalogNumber]",
   "[literalField CollectionObject.catalogedDate]",

specifyweb/frontend/js_src/lib/components/DataModel/__tests__/businessRules.test.ts

@@ -119,25 +119,6 @@ describe('Collection Object business rules', () => {
     expect(collectionObject.get('collectionObjectType')).toBeDefined();
   });
 
-  test('Save blocked when CollectionObjectType of a CollectionObject does not have same tree definition as its associated Determination -> taxon', async () => {
-    const collectionObject = getBaseCollectionObject();
-
-    const determination =
-      collectionObject.getDependentResource('determinations')?.models[0];
-
-    const { result } = renderHook(() =>
-      useSaveBlockers(determination, tables.Determination.getField('taxon'))
-    );
-
-    await act(async () => {
-      await determination?.businessRuleManager?.checkField('taxon');
-    });
-
-    expect(result.current[0]).toStrictEqual([
-      'Taxon does not belong to the same tree as this Object Type',
-    ]);
-  });
-
   const otherCollectionObjectTypeUrl = getResourceApiUrl(
     'CollectionObjectType',
     2

specifyweb/frontend/js_src/lib/components/DataModel/__tests__/resource.test.ts

@@ -291,6 +291,7 @@ test('getFieldsToNotClone', () => {
   });
   expect(getFieldsToNotClone(tables.CollectionObject, true, false)).toEqual([
     'actualTotalCountAmt',
+    'age',
     'catalogNumber',
     'timestampModified',
     'guid',
@@ -304,6 +305,7 @@ test('getFieldsToNotClone', () => {
   ]);
   expect(getFieldsToNotClone(tables.CollectionObject, false, false)).toEqual([
     'actualTotalCountAmt',
+    'age',
     'catalogNumber',
     'timestampModified',
     'guid',

specifyweb/frontend/js_src/lib/components/DataModel/__tests__/schemaBase.test.ts

@@ -24,5 +24,6 @@ test('domain data is fetched and parsed correctly', async () =>
     ],
     paleoContextChildTable: 'collectionobject',
     referenceSymbol: '#',
-    treeSymbol: '$',
+    treeRankSymbol: '$',
+    treeDefinitionSymbol: '%',
   }));

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

@@ -368,6 +368,7 @@ test('indexed fields are loaded', () =>
     {
       "accession": "[relationship CollectionObject.accession]",
       "actualTotalCountAmt": "[literalField CollectionObject.actualTotalCountAmt]",
+      "age": "[literalField CollectionObject.age]",
       "agent1": "[relationship CollectionObject.agent1]",
       "altCatalogNumber": "[literalField CollectionObject.altCatalogNumber]",
       "appraisal": "[relationship CollectionObject.appraisal]",

specifyweb/frontend/js_src/lib/components/DataModel/businessRuleDefs.ts

@@ -1,4 +1,3 @@
-import { formsText } from '../../localization/forms';
 import { resourcesText } from '../../localization/resources';
 import { f } from '../../utils/functools';
 import type { BusinessRuleResult } from './businessRules';
@@ -51,7 +50,6 @@ type MappedBusinessRuleDefs = {
 };
 
 const CURRENT_DETERMINATION_KEY = 'determination-isCurrent';
-const DETERMINATION_TAXON_KEY = 'determination-taxon';
 
 const hasNoCurrentDetermination = (collection: Collection<Determination>) =>
   collection.models.length > 0 &&
@@ -199,14 +197,8 @@ export const businessRuleDefs: MappedBusinessRuleDefs = {
               const taxonTreeDefinition = fetchedTaxon.definition;
               const COTypeTreeDefinition = fetchedCOType.taxonTreeDef;
 
-              return taxonTreeDefinition === COTypeTreeDefinition
-                ? void setSaveBlockers(
-                    currentDetermination as SpecifyResource<AnySchema>,
-                    currentDetermination.specifyTable.field.taxon,
-                    [],
-                    DETERMINATION_TAXON_KEY
-                  )
-                : resource.set('determinations', []);
+              if (taxonTreeDefinition !== COTypeTreeDefinition)
+                resource.set('determinations', []);
             })
             .catch((error) => {
               console.error('Error fetching resources:', error);
@@ -233,57 +225,6 @@ export const businessRuleDefs: MappedBusinessRuleDefs = {
                   accepted === null ? taxon : getLastAccepted(accepted)
                 );
 
-            const related = determination.collection?.related;
-            if (
-              related !== undefined &&
-              related.specifyTable.name === 'CollectionObject'
-            ) {
-              const collectionObject =
-                related as SpecifyResource<CollectionObject>;
-              void f
-                .all({
-                  defaultType:
-                    collectionObject.get('collectionObjectType') === undefined
-                      ? collectionObject
-                          .rgetPromise('collection')
-                          .then(async (collection) =>
-                            collection.rgetPromise('collectionObjectType')
-                          )
-                          .then((coType) => coType ?? undefined)
-                      : undefined,
-                  coType: collectionObject.rgetPromise(
-                    'collectionObjectType',
-                    true
-                  ),
-                })
-                .then(({ defaultType, coType }) => {
-                  const resolvedCoType = coType ?? defaultType;
-                  /*
-                   * Have to set save blockers directly here to get this working.
-                   * Since following code has to wait for above rgetPromise to resolve, returning a Promise<BusinessRuleResult> for validation here is too slow and
-                   * does not get captured by business rules.
-                   */
-                  if (
-                    resolvedCoType?.get('taxonTreeDef') ===
-                    (taxon?.get('definition') ?? '')
-                  ) {
-                    setSaveBlockers(
-                      determination as SpecifyResource<AnySchema>,
-                      determination.specifyTable.field.taxon,
-                      [],
-                      DETERMINATION_TAXON_KEY
-                    );
-                  } else {
-                    setSaveBlockers(
-                      determination as SpecifyResource<AnySchema>,
-                      determination.specifyTable.field.taxon,
-                      [formsText.invalidTree()],
-                      DETERMINATION_TAXON_KEY
-                    );
-                  }
-                });
-            }
-
             return taxon === null
               ? {
                   isValid: true,

specifyweb/frontend/js_src/lib/components/DataModel/schema.ts

@@ -30,7 +30,8 @@ type Schema = {
     'Institution'
   ];
   readonly referenceSymbol: string;
-  readonly treeSymbol: string;
+  readonly treeDefinitionSymbol: string;
+  readonly treeRankSymbol: string;
   readonly fieldPartSeparator: string;
 };
 
@@ -64,8 +65,10 @@ const schemaBase: Writable<Schema> = {
 
   // Prefix for -to-many indexes
   referenceSymbol: '#',
+  // Prefix for Tree Definitions
+  treeDefinitionSymbol: '%',
   // Prefix for tree ranks
-  treeSymbol: '$',
+  treeRankSymbol: '$',
   // Separator for partial fields (date parts in Query Builder)
   fieldPartSeparator: '-',
 };

specifyweb/frontend/js_src/lib/components/DataModel/schemaExtras.ts

@@ -83,6 +83,15 @@ export const schemaExtras: {
         indexed: false,
         unique: false,
       }),
+      new LiteralField(table, {
+        // TODO: LiteralField or Relationship?
+        name: 'age',
+        required: false,
+        readOnly: true,
+        type: 'java.lang.Integer',
+        indexed: false,
+        unique: false,
+      }),
     ],
     (): void => {
       const collection = getField(table, 'collection');