Information & Computational Sciences

New in Germinate 3.3.1

By on 15/04/2016 in News

Germinate has just been updated to version 3.3.1.

  • CHG: Disabled mouse-wheel scrolling on locator map.
  • ADD: Added option to filter datasets table by count and datapoints.
  • FIX: Fixed issue with Maintenance-Mode.
  • FIX: Fixed issue with spaces in file paths.
  • CHG: Improved performance of ‘germinatebase’ export of whole dataset.
  • FIX: Fixed issue with y-axis tick formats in d3.js multi-line chart.
  • FIX: Fixed issue on admin-config page where the available pages weren’t updated as expected.
  • ADD: Added checkbox column header for item marking columns to easily mark all items.
  • CHG: Updated FontAwesome to version 4.5.0.
  • CHG: Major code-cleanup.
  • ADD: Major Javadoc additions.
  • ADD: Added pedigree information to passport page. Now uses the database tables ‘pedigree’, ‘pedigreedefinitions’, ‘pedigreenotations’ and ‘pedigreedescriptions’.
  • ADD: Added color picker widget to administrator configuration page to make customization of the page easier.
  • ADD: Added “Technologies” section to the documentation. This section explains which third-party libraries (Java, JavaScript, Fonts) we use and how we use them.
  • ADD: Added property that decides if the main website logo (top-left) contains links itself. Usually clicking the whole logo will redirect to “home”, however, since we switched to SVG files, these can contain links on their own (for either the whole logo or even sections of it), so we allow to prioritize the internal links and disable the link to “home” by setting ‘Germinate.Template.Logo.Contains.Link’ to ‘true’.
  • CHG: The search page will now show all tabs regardless of page availability, whereas before it would only show the tabs of those types that have their details page enabled, e.g. the ‘marker-details’ page had to be enabled for the ‘marker’ search tab to show up. Now all tabs show and the table that shows the search results will only contain links to the details page if available.
  • CHG: Changes to the admin configuration page (‘#admin-config’) are now persistent changes to the file. Restarting Tomcat or restarting the web-application will not erase changes made to the configuration anymore.
  • CHG: ‘#news’ and ‘#about’ are now publicly visible, no matter what.
  • ADD: Added ‘Germinate.Gallery.Images.Per.Page’ property to that determines how many images per page each gallery will show (default: 4).
  • FIX: Fixed session persistency bug.
  • CHG: The external data directory can now be used to not only externalize the actual ‘data’ folder, but also ‘download’, ‘res’ and ‘apps’. Germinate will prefer the files found in that location, but fall back to the files bundled with Germinate itself. To use this feature, set the ‘Germinate.ExternalDataFolder’ property to the directory containing the previously mentioned folders (e.g. ‘/srv/data/germinate/germinate-template’ which then contains ‘data’, etc.).
  • CHG: The automatic image scaler will now work with the external data directory image folder as well.
  • CHG: Restyled passport page. Moved information representation to list format when a table didn’t add any functionality to it.
  • DEL: Removed legacy classes related to old table structure.
  • DEL: Removed Apache POI library dependencies.
  • CHG: D3.js chart download context menu is now available on IE as well. However, it only shows the “download data file” option, as IE doesn’t support the required functionality (or rather prohibits it).
  • FIX: Client settings are no longer shared between user logins. Each user has its own settings even when the second user logs in after the first has logged out (in the same browser).
  • CHG: Moved cookie creation to server.
  • CHG: Removed checkbox column from datasets table if the continue button isn’t available, as there is no point in selecting datasets in this case.
  • FIX: Fixed group permission issue where admins weren’t able to see all groups.
  • CHG: Added new property ‘Germinate.Template.GradientColors’ that allows customization of the gradients shown on the website.
  • ADD: Added parallax scrolling banners to selected pages.
  • ADD: Added new property ‘Germinate.Template.Show.Parallax.Banner’ that determines if the parallax banner is shown or not.
  • CHG: ‘’ is now a required field and will be used for genotypic data export. It represents the BRAPI ‘defaultDisplayName’, a human-readable and meaningful name for the accession.
  • ADD: Added data statistics page (#data-stats) with basic statistics.
  • CHG: Applied some changes to the template.
  • FIX: Fixed rare issue with “select” element selection where elements weren’t selected if the number of items matched the visible rows and the selection happened by dragging from inside the select element to outside the select element.
  • CHG: Improved performance of dataset related queries by about 33%!
  • ADD: Added page size selection widget to paginated tables.
  • CHG: Further improved the performance of dataset related queries by pre-calculating dataset sizes and storing the result in the ‘datasetmeta’ table. This is re-calculated every hour to ensure it’s reasonably up-to-date.
  • CHG: Initial adaptation of the Java 8 Streams API on the server.
  • CHG: Improved performance of trials/phenotype export page (phenotypes only retrieved once in total instead of once per “tab”).
  • NEW: Added HDF5 functionalities for genotypic data export.
  • CHG: Switched genotypic data export over to HDF5 by default.
  • NEW: Added “Select all” buttons to multi-select boxes.
  • NEW: Added operator selector to table filter. Users can now switch between logical “AND” and “OR” combination of query fields.
  • NEW: Added column filtering to marker table on map-details page.
  • DEL: Removed phenotype data export preview as it serves no good purpose. The data is already exported, so why not just download it?
  • DEL: Removed two of the four maps (the weighted ones) on #geography as they don’t really provide much new information.
  • ADD: Added country flags to more tables containing country information.

Tags: , , , ,


If you enjoyed this article, subscribe now to receive more just like it.

Comments are closed.