Specify 7.10 Release Announcement

[Grant]

Specify 7.10

Specify 7.10 is a major update to the Specify 7 collections management platform.

Specify 6 Compatibility

Starting with the Specify 7.10 update, catalog number uniqueness will not be enforced in Specify 6. If you need to reinstate this functionality, please contact us.

New fields, tables, and features introduced in this update will not be available in Specify 6, including the ‘Geology’ discipline.

If you need to add a new collection, discipline, or division to your database, please let our team know. We can assist you with this until this functionality is added to Specify 7 later this year!

Update Instructions

Specify Cloud users will receive this update upon request for now. It will be rolled out more widely later unless otherwise requested.

Before you pull the latest changes, please note that you must update the version of the docker-compositions repository you are using if you deploy via Docker.

If you do not already have access, click here to request access to this repository or email support@specifysoftware.org with your GitHub username, member institution or collection, and any additional questions or notes for us!

If you have not already logged into your GitHub account with the appropriate permission to access the docker-compositions GitHub repository, you will need to do so first, otherwise you will receive a permission error:

Could not resolve to a Repository with the name 'specify/docker-compositions'. (repository)

If you are not logged in or do not have the appropriate permissions on GitHub, you will see a 404 when you go to this link. If your account is logged in and has read permission, you should see the appropriate repository.

From our development team:

The production branch of docker-compositions as been updated for Specify 7.10! See GitHub commit here.

The main update for docker-compositions in Specify v7.10 is that the Specify 6 container is no longer necessary. The static files that Specify 7 relied on from Specify 6 have been relocated to the config directory in Specify 7. Setting up the new location for static files in Specify 7.10 required changes to the nginx configuration and the docker-compose file. The usage of specifycloud can manage Specify instances of both older versions and v7.10, dynamically configuring the static files for both scenarios.

The following changes have been made, so the user will not need to edit themselves:

• docker-compose.yml changes:

  • for the sp7 production docker containers, remove the sp6 volume mount - "specify6803:/opt/Specify:ro"
  • add - SPECIFY_CONFIG_DIR=/opt/specify7/config to environment
  • remove the Specify 6 container

• nginx.conf changes:

  • replace
    • this rewrite ^/static/config/(.*)$ /specify6803/config/$1 break;
    • with this rewrite ^/static/config/(.*)$ /static-files-sp7demofish/specify-config/config/$1 break;

When using the ‘just-specify-7’, ‘all-in-one’, or ‘multiple-databases’, pull the latest changes from the production branch of docker-compositions.

It’s best to not pull these changes until you start using Specify 7.10.

Edit the nginx config and docker-compose environment variables normally for your specific deployment.

Users who are managing a local installation (not using Docker) can pull the latest changes and deploy right away.

Once this is up to date, you or an IT administrator will need to pull the Docker tag “production” for the specify7-service.

docker pull specifyconsortium/specify7-service:production

After this, you can start the container(s) for Specify 7!

docker compose up -d

Major Features:

All features not marked with an asterisk below will be accessible for all disciplines, not just geology and paleontology.

• Introduction of ‘Geology’*: We have introduced a new Geology discipline. It can now be added to databases upon request by our team.
  • New Tree:* Tectonic Unit
• Collection Object Groups (COGs): Capture two or more Collection Objects (COs) that share common information based on physical integrity. This serves as a fully featured replacement for containers.
• Independent Subviews: Add COs to an Accession from the Accession form, include COs in Collecting Events, and much more.
• Collection Object Types (COTs): A significant change allows for more effective management of different types of Collection Objects within a single collection.
• Tree Creation Utility: New taxon trees can be created for use with COTs.
• Catalog Number Uniqueness: Catalog number uniqueness is now configurable.
• Extended Age Queries*: Improved queries for records with chronostratigraphic, relative, and absolute age data.
• Bulk Carry Forward: Users can now carry forward hundreds of records at a time.
• Merging Record Sets: Record sets can be easily merged.
• Extended Batch Attachment Uploader: Added support for Agent, Preparation, Storage, Reference Work, Locality, and many other tables.
• Updated Defaults: New defaults have been added, eliminating the need for files from Specify 6.

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Release Announcement

7.10.1 (10 March 2025)

Added

• A Catalog Number format can now be linked to a specific Collection Object Type (COT)! (#6277)
• Added a uniqueIdentifier field to the Storage table (#6249)

Fixed

• Fixed an issue where Specify would not auto-select a field format in Schema Config (#6255)

7.10.0 (5 March 2025)

This release of Specify 7 now falls under the GPL-3.0 license.

Added

• Geology has been added as a new discipline to Specify! (#5032)
• Subviews now have borders to make it easier to distinguish where a subview starts and ends (#6031)
• Added bulk carry forward (#4804, #5120)– Requested by University of Minnesota Entomology, Bulgarian Academy of Sciences, KU Entomology, and many others)
• Added support for Geography Code at any level in queries (#5094 – Requested by Museu de Ciències Naturals de Barcelona, KU Ichthyology, and many others)
• Added preference to add UTF-8 BOM to CSV exports (For Excel) (#5204 – Requested by Natural History Museum of Denmark and many others)
• Added support for Independent Subviews on data entry forms (#5253 – Requested by The University of Kansas, The University of Michigan, and many others)
  • For example, this enables adding:
    • Collection Objects to an Accession from the Accession form
    • Collection Objects to a Collecting Event from the Collecting Event form
    • Treatment Events to an Accession from the Accession form
    • and much more
  • Independent relationships (e.g. Collecting Event to Locality) can now be displayed as a subview rather than a query combo box
• Added Collection Object Types (COTs)
  • The Taxon Tree can be based on the COT (#5248, #5127)
  • Added the ability to create new Taxon trees (#5080, #5372)
  • Multiple Taxon trees can be viewed in the tree viewer (#5036)
  • Added COT pick list (#5170)
  • Added a feature to choose type of Taxon tree in WB (#5091)
• Extended Paleo Context to Geologic Context, Relative Age, and Absolute Age
  • Added Extended Age Query functionality (#5272, #5411)
  • Added a dialog with the chrono chart image for geologic table (#5262)
  • Add Absolute and Relative Age Citations (#5341)
• Added a new Tectonic Unit Tree (#5178, #5316, #5345 – Requested for Geology)
• Added Collection Object Groups (COGs) (#5032)
  • Added COG related business rules (#5442, #5449, #5275, #5374, #5403, #5406)
  • Added 3 types of COG: Consolidated, Discrete, and Drill Core
    • Consolidated COG preparations are transacted together when used with interactions (#5445)
• Record Sets can now be merged together (#5405 – Requested by The University of Kansas, Museum of Natural History of Geneva, The University of Texas, Museum für Naturkunde Berlin, Natural History Museum Basel, and many others)
• Record Sets can now be selected when adding new items to a record (e.g. Collection Objects to an Accession or COG) (#5263, #5498)
• Added a tool to remove unmapped lines in WorkBench data sets (#5265 – _Requested by Royal Botanic Gardens Edinburgh)
• Batch Attachment Uploader now supports more tables (#5332)
  • Storage (Full Name)
  • Preparation (Barcode, GUID)
  • Treatment Event (FieldNumber)
  • Exchange In (ExchangeInNumber)
  • Exchange Out (ExchangeOutNumber)
  • Reference Work (Title, GUID)
  • Locality (UniqueIdentifier, GUID)
  • Permit (PermitNumber)
  • Agent (GUID)
  • Collecting Trip (CollectingTripName)
  • Deaccession (DeaccessionNumber)

Changed

• Catalog numbers are no longer required by Specify to be unique, although they are set to be unique by default (#5400)
• Tree nodes can now be deleted along with all their unused children, making tree cleaning much easier (#5324)
• Tree searches now return more than 20 results (#5125)
• The Audit Log is now accessible via the query menu (#5133)
• A new white space sensitivity attribute has been added for form fields (#5086)
• The Specify interface schema has been updated to include new Geology fields and pick lists (#5257)
• Added new default app resources and form definitions (#5367)
  • Added the ability to transfer the ownership of Record Sets and Queries.
  • When using the default form definitions and app resources:
    • Collection Relationships can now be created
    • Agents will default to “Person” instead of “Organization”
    • Agent “Members” will only appear when the Agent is a “Group”
    • Agent Identifiers for ORCID, WikiData, and other IDs is now included by default
    • Taxon “Hybrid” fields only display if the Taxon is marked as a hybrid
    • Tree Definition tables now allow the user to customize and see all ranks in a single subview
    • Tree full name direction can now be customized
    • Preparation count can no longer be set to a negative number–antimatter will no longer be cataloged.

Fixed

• Fixed an issue that caused table/grid view results to not show more than 20 items at a time (#5298 – Reported by CSIRO and OSU)
• Fixed an issue preventing non-loanable Preparations from being used in other interactions
  (#5271)
• Cloning an interaction no longer clones the interaction preparations (#4905)
• Fixed an issue that removed any table aggregation separator if it matches the default ("; ") (#5240)
• A tool has been added to create a root node in trees if one is not already present (#5394)
• Saving an ExportFeed with an invalid user is no longer possible (#5042)
• Fixed cases where “Deselect All” did not disable the “Select” button (#5270)
• Fixed an issue with the Specify 7 version being missing (#5397)
• Workbench column headers now use the new table icons (#5176)

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The full changelog is available on GitHub

For source code go to the GitHub Specify 7 repository

For more information about Specify 7, or about this release, see Specify 7 | Specify Collections Consortium, or email support@specifysoftware.org.

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New Documentation

These articles are still a work-in-progress, but feel free to leave a comment with any clarifying questions in the meantime so we can expand and cover areas of interest!

Collection Object Types

Collection Object Types

Overview The introduction of Collection Object Types (COT) in Specify 7 significantly enhances the management of diverse collection objects within a single collection. This feature allows users to define multiple types of collection objects, each with its own unique attributes and taxonomic trees. This capability overcomes previous limitations in managing various materials within a single collection. It also provides new opportunities for collections that include diverse materials cataloged toge…

Add New Taxon Trees

Adding a New Taxon Tree to the Same Collection

Starting with Specify 7.10, you can add a new Taxon tree to an existing collection for use with the Collection Object Groups mechanism to enable the concurrent management of different “object types” within the same collection. Important Note: Taxon trees created using this mechanism are only available within a single discipline. No default data is loaded into the tree upon initialization. However, you can obtain source tree data from our website (Taxon Files), GBIF, WoRMs, or other sources. A…

Collection Object Groups

Collection Object Groups

Introduction When research specimens and samples are itemized in a Specify database, they are represented as Specify “Collection Objects” or “COs”. It is not uncommon in collections to have discrete Collection Objects that have, or have had, some type of physical relationship that needs to be recorded in data. For example, two different Collection Objects might have been part of the same physical object or biological organism in the field. Or perhaps specimens that were independent entities in …

Paleo Context / Geologic Context

Paleo Context / Geologic Context

The Paleo/Geo Context in Specify allows users to link their specimens to their paleontological or geological context. This functionality can be configured to display as either Paleo Context (PC) or Geologic Context (GC), depending on the user’s discipline, ensuring that the information is relevant and accessible. Specify offers several fields and relationships that can be used in ways that best align with your conceptualization and linking preferences. The essential fields for Paleo/Geo Contex…

Extended Age Queries

Extended Age Queries

Overview The Extended Age Query (EAQ) feature enhances the querying capabilities for the Collection Object (CO) table within the Query Builder by allowing users to filter collections based on geological ages. It is a powerful tool for researchers and curators in the geological and paleontological fields to accurately filter and analyze collection objects. By using both named periods and numerical ranges, users can improve their data queries and gain a deeper understanding of their collections. T…

Independent Subviews

Independent Subviews

Starting in version 7.10, Specify supports independent subviews. This enhancement allows users to efficiently search, add, and remove records to a one-to-many subview. These can be displayed both as a traditional embedded subview or as a button. An Independent Subview can be distinguished from its dependent counterpart (for both button/non-button subviews) by a magnifying glass which is used to search existing related records, or a link icon. Unlike dependent records, because the records can e…

Bulk Carry Forward

Bulk Carry Forward

Bulk Carry Forward is an enhancement of the Carry Forward button that enables users to carry forward multiple records simultaneously. This functionality allows the creation of several collection objects with sequential catalog numbers and prefilled values derived from the initial record. Currently, bulk carry forward can only be utilized to generate a predetermined number of records through auto-numbering, and no range can be selected among existing catalog numbers. This option is exclusively a…

Updated Documentation

Merge Record Sets

Record Sets in Specify 7

Record Sets A record set is an easy way to group records together that can be easily revisited and used for things like interactions The default permissions that Specify ships with allow Guest users to View the record sets, but not modify, add or delete them. All other users can use record sets in their entirety. Creating a Record Set To create a blank record set click on Record Sets in the navigation bar, then select New and then there will be a list of differe…