2020-05-26 End of Sprint

• Updated permissions for the API so that users with a role of journal
  administrator can now submit content on behalf of a user, and can
  query the API for users.
• Allowed the userId string in API submissions to be either a Dryad user id or an ORCID.
• Added the internal_data to the API for new submissions, including
  publicationISSN and manuscriptNumber.
• Improved handling for author affiliations in the API. Affiliations
  may now be specified by ROR ID, ISNI ID, or textual name.
• Replicating published datasets to Zenodo
  • Adding dataset to Dryad community
  • Removing is-identical-to in metadata
  • Funders appear under the notes section
  • Re-enabled trigger to send to Zenodo when published
  • Documented delayed_job and queued/deferred publication procedures
• Zenodo software uploads (work in progress in other branches like zenodo-code)
  • Workflow for handling different dataset versioning states
  • Updating metadata
  • Uploading files
• Fixed dependency checks for OAI feed and Notifier
• Updated settings for OAI feed and notifier for new domain names in Merritt

2020-05-12 End of Sprint

• Added a help page to describe the benefits of, and requirements for,
  Journal Integration
• Added the peer-review sharingLink as a result field to more API
  calls.
• Metadata exported to Zenodo includes geolocation point and place names.
• Updated Merritt stage endpoints for OAI-PMH and Merritt-Sword.
• Updated gemfile versions that would update with bundler.
• Revised Travis tests to use Ubuntu 18.04 because older version of OS was now timing out with Chrome or webdriver updates and browser testing.

(Items below were merged into zenodo-code branch, but were accepted pull requests that will be merged as a large feature release at once later.)

• Rework of navigation for "upload directly" or "Upload by URL" to use links for accessibility.
• Page hiding when no files on upload page and logic to hide and show "Step 2" part of page
• Additional text around software uploads
• Refactor ZenodoCopy model to be a many relationship to Resource and code updates. (Needed for reusing table for software uploads to zenodo in addition to replication of data.)
• Software URLs download to local files before submission to Zenodo because they do not take links
  • Create unified exceptions for logging
  • Check digests for MD5 and SHA digest types if they are available in database.
  • Catch bad responses and timeouts
• More workflow validation and testing since replication of software to Zenodo requires submissions to be processed in order since changes build on each other.

2020-04-28 End-of-Sprint

• Updated references to GitHub throughout the website.
• Updated documentation about the journal module to reflect moving metadata into the main database.
• Expanded documetation about actions required for troubleshooting.
• Added JournalRole to represent privileges of journal staff, and updated permissions throughout the system to allow more functionality for users with a JournalRole of ‘admin’.
• Suppress individual file downloads for DataONE since only the full dataset download works because of Merritt storage implementation.
• NIOO-KNAW tenant enabled for partner login.

Items in feature branch zenodo_code

• New upload tab duplicates all functionality of existing dataset upload to new table and storage location.
  • Code modified to work with both pages and not be duplicated.
  • Slight text and other customizations on each page.
  • Both file and URL upload functionalities.
• New navigation to incorporate extra step.
• Review page
  • Icons for both Dryad and Zenodo.
  • New software section that shows only if software is uploaded.
  • List of software licenses and ways to choose and search within list.
• Workflow modifications for accessibility in file uploads by not using Radio buttons for navigation.
  • List both options (file and URL uploads) but hide step 2 until selection on initial page state.

2020-04-14 End of Sprint

• Updated the shopping-cart-report to guarantee that “submitted date” appears for all items.
• Added protection against users entering invalid DOIs.
• Moved journal metadata from the old Dryad journal module directly into the current Dryad database.
• Additional copy to Zenodo on publication
  • Additional API interactions to re-open published datasets for later versioning if published more than once.
  • Testing large submissions and file changes, replacements and deletions in subsequent versions.
  • Mechanism to defer jobs for processing later before restarts to avoid uncertain state except when necessary
  • Scripts for starting and stopping DelayedJob (Ruby queue processor) and for deferring tasks ahead of shutdown.
• Adding new tenant "Netherlands Institute of Ecology (NIOO-KNAW)," though it is not enabled for login yet.

2020-03-31 End of sprint

• Code to create duplicate copy that is submitted to Zenodo (not automated or triggered and waiting for changes on Zenodo end).
  • New database table to track status
  • Download files
  • Create Zenodo metadata
  • Check digests against known values and raise errors if incorrect
  • Upload files
  • Publish dataset
  • Error handling and logging of errors to database with status table
• Obtain and redirect to Amazon pre-signed S3 URLs for individual file downloads rather than mediating them through the Dryad service.
• Added documentation about the journal module and how it processes emails from journals.
• Added new fields to reports, including the CSV export on the Admin Dashboard and the Shopping Cart Report.
• Corrected problem with API that was preventing downloads when accessing datasets via the DOI.
• Added CurationStatus to the API results for versions of datasets.

2020-03-17 End of sprint

• Modified the system for handling expiration of peer_review status. Instead of automatically changing these items to submitted status, an email reminder is sent to the author. Followup reminders are sent monthly until the status has been changed.
• Updated shopping cart report to include the date on which each dataset was created.
• Corrected bug in API that was preventing download of data files and their associated metadata.
• Updated documentation, particularly regarding reporting and troubleshooting.
• Columbia University added as partner institution.

2020-03-03 End of sprint

• Added tenant for Stanford University.
• Moved some documentation from the old Dryad wiki into the documentation folder.
• Corrected several minor bugs that caused internal errors such as database constraint violations or null pointer errors.
• Configured and set up application to use delayed job/active job for future work.

2020-02-18 End of sprint

• Filtered out any whitespace that is added into the DOI lookup field on the submission form, so it doesn’t cause internal errors.
• Updated processing for autocomplete values associated with funders to include the same features as the other autocomplete fields, specifically “bubbling up” the best matches and adding an asterisk when non-controlled values are entered.
• Suppressed display of the asterisk for non-controlled affiliations and funders, when all users except ‘superusers’ are viewing dataset landing pages.
• Updated the listing of staff on the “Our Team” page.
• Improved alert messages that appear when deleting items in the submission system.
• Improved accessibility of headings and lists throughout the site.
• Enhanced handling of manuscript numbers. When manuscript numbers are saved in the system, they are parsed against a regular expression specific to the associated journal. This allows minor variations in manuscript numbers to be ignored (e.g., version numbers) when making automatic updates to datasets based on notifications from the journals.
• Adminlisting enhancements for partner admins.
  • Removing irrelevant curation actions that apply to curators and not partners viewing states.
  • Defining possible multiple related ROR identifiers per partner (since some organizations have multiple).
  • Refined admin display query to show both things submitted by a qualified login (shibboleth and tenant) for their institution AND datasets with authors who claim an association with the partner through a ROR id for the institution.

End-of-Sprint 2020-01-28

• Changed the default type of associated publication to “Manuscript in progress”. This encourages submitters to include journal and manuscript information.
• Updated processing for autocomplete values associated with journal names and institutional affiliations. When the name is typed but not selected from the autocomplete list, an asterisk is appended, so the name can be verified by curators.
• New tenants added: Ohio State and UNSW (mostly not part of this codebase except for banner icons)
• Curation search fixes and enhancements
  • Sort into relevance order with initial queries.
  • Fix clear search, journal name filtering
  • Allow All terms boolean search that requires all terms, allow pass through of advanced boolean search
• Curation reporting enhancements
  • Lightbox for views, downloads and citations
  • Scheduled scripting to pre-retrieve citations and cache them for getting fast counts and quick display
  • Views, downloads, citation numbers included in CSV output
  • CSV output no longer limited to 2,000 lines
• Allow waiving of payment based on funder and tracking of payment status when waived

End of sprint 2020-01-14

• Updated internal storage to retain information about the type of payment that was provided for each dataset.
• Added a report of published datasets and their associated payment information.
• Updated the list of countries that are eligible for fee waivers, based on the 2020 listing from the World Bank.
• Set up COUNTER processing to run weekly and update our database for pulling stats
• Updated gems to latest versions that work with the application