Version 3.5.0

New in 3.5.0

VERSION 3.5.0 IS STILL IN DEVELOPMENT, PLEASE CONSULT Version 3.4.0 FOR THE CURRENT RELEASE.

• ADD: SAMPLES! Yes, you read that right, Germinate now supports different levels of entities: Accessions, Plants/Plots and samples. This change has some major implications which will be highlighted in the migration section below.
• CHG: The allelefrequencydata table has finally been dropped.
• CHG: Updated MySQL JDBC driver to fix a bug that would display some special characters wrongly because it was using the wrong encoding.
• FIX: Fixed a bug where the genotype export wasn't working if no accession/marker group is available.
• CHG: Updated the data templates and the associated code for the automated data import.
• CHG: Updated data templates to uniformly support the dataset attributes (Dublin Core, Collaborators, etc).
• CHG: Restructured data templates and unified the genetic-maps into the allele-calls file.
• FIX: Fixed a bug where trying to upload thousands of new group members via the copy/paste field failed.
• CHG: Added tables datasetmembers and datasetmembertypes that indicate which accessions/markers are part of which datasets. This is necessary, since these data types are stored externally and we need to be able to figure out which items are in which datasets.
• FIX: Fixed rare bug where deleting the only group would throw an exception due to edge case in AUTO_INCREMENT reset procedure.
• FIX: Fixed an issue where the dataset table wasn't shown when Germinate was public, but Licenses were available for the datasets in the table.
• FIX: Fixed an issue where the dataset table would show duplicates of datasets if special permissions were given to individual users. The issue was caused by a bug in the dataset metadata task that runs periodically.
• CHG: The genotype export page now only shows those maps that actually share markers with the dataset. Before it showed all the maps even if they had no markers in common with the dataset.

Migrating from 3.4.0 to 3.5.0:

• The allelefrequencydata table is no longer available. If you are storing allele frequency data, please follow these steps:
  • The automatic update process of Germinate will create new entries in germinatebase for each distinct sample_id in allelefrequencydata. These are automatically mapped to their entity parent via the entityparent_id column.
  • These new items in germinatebase will have the following naming convention: germinatebase.name + "-" + allelefrequencydata.sample_id, e.g. if the accession is called "Cactuar-1" and the sample "SAMPLE1" then the new item in germinatebase is called "Cactuar-1-SAMPLE1".
  • We try to make the update process as automatic as possible, but in this case you need to update your raw data files in order for things to match up. Please identify all datasets.source_file values and locate the appropriate data files. Then replace the sample name in the first column with the newly created name from germinatebase, then save.
  • If these files are located in Germinate's external data folder, then this is all that's required, if they are bundled with Germinate, then a re-deploy of the app is necessary.
• Make sure the datasetmembers table is populated with information about which accessions/markers are in which datasets.
• New translatable text has been added. The following properties can be changed in your Text.properties file and the according translation files:

column.accessions.entity.type=Entity type
page.passport.entity.title=Entity data
column.markers.type.description=Marker Type