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.
• CHG: Changed the way genotypic data downloads are handled. The export process for genotypic data consists of two steps. Extracting the requested data from HDF5 to flat txt file (plus the map), then converting it to Flapjack. This was always done in one go, even if the user didn't want the data in Flapjack format. The Flapjack project creation can, however, take quite a bit of time and, hence, slow down the whole process. We changed it so that it will give you access to the flat files as soon as they're ready and if you actually want the Flapjack file, it'll export it on demand. This will only very slightly increase the wait for Flapjack users while significantly reducing the wait for all other users.
• CHG: Unified code for regular file download and on demand file download into a single code base.
• FIX: Fixed a bug related to climate data. Min, max and avg were selected across all the data, not just the selected dataset.
• ADD: Added the option to toggle the side menu even on larger screens to make the main page full-width.
• CHG: Changed the naming convention for files downloaded from Germinate. So far, they received a name representing the timestamp at which they were downloaded. However, this didn't give any indication about what kind of data it contains and which dataset is part of it. This has now been changed, such that the file has a prefix that describes the type of data it contains as well as an infix that shows the datasets that have been used to generate the file. To guarantee uniqueness of filenames, a UUID is attached as the postfix.
• ADD: Added data importer for Compound and CompoundData files.
• FIX: Fixed a few synonym related bugs.
• CHG: Introduced a new error page design.
• ADD: Added dataset ids to the filenames of all temporary files. The filename now contains the category of data type and the included datasets.
• ADD: Added optional dataset access log. This keeps track of which user accessed which dataset when. If Germinate operates in public mode, it'll ask the user for their details before they can use the dataset.
• ADD: Added a section titled "Selected datasets" on all the data export pages to make it clear which datasets have been selected on the previous screen.
• FIX: Fixed a bug where multiple login attempts were send in short succession even if the user only tried to log in once. This didn't have any implications on general operation, but wasn't necessary and could make debugging of the login procedure a bit cumbersome.
• CHG: Significantly improved performance of genotypic data export. Before, it was slowed down by parts of the code that generates the genetic map.
• ADD: Added code to the Germinate data import package to easily import genetic data from tab-delimited files instead of just Excel. This was necessary due to the Excel's limitations to the number of columns (16384). The tab-delimited file should be in the same format as the DATA sheet of the Excel template.
• ADD: Re-introduced the static link feature for datasets. Germinate now providing static links to the dataset selection page instead of the actual export page, but then shows the dataset table filtered down to only show the datasets with ids that are provided in the URL. The user can then decide if they want to use this dataset (and accept the license, if any) or if they just want to remove the filter to see all datasets. Closes #19.

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
menu.settings=Settings
widget.dataset.user.tracking.name=Full name
widget.dataset.user.tracking.email=Email address
widget.dataset.user.tracking.institution=Institution
widget.dataset.user.tracking.explanation=Can you let us know what you intend to use this data for in your research?
widget.dataset.selected=Selected datasets
page.allelefreq.title=Allele frequency data
operators.in.set=In set
widget.dataset.user.tracking.explanation.option.basic.research=Basic research (molecular biology, QTL studies, GWAS, phylogenetics, molecular ecology, etc.)
widget.dataset.user.tracking.explanation.option.prebreeding=Pre-breeding (introgression line development, germplasm evaluation etc.)
widget.dataset.user.tracking.explanation.option.breeding.cultivar=Breeding and cultivar development
widget.dataset.user.tracking.explanation.option.education=Education
widget.dataset.user.tracking.explanation.option.direct.use=Direct use of germplasm for production
widget.dataset.user.tracking.explanation.option.other=Other (please specify)
column.passport.pdci=PDCI
page.passport.pdci.title=Passport Data Completeness Index
page.passport.pdci.score=<b>The score of this item is: {0}/10</b>
page.passport.pdci.explanation=<p>This passport data completeness index (PDCI) uses the presence or absence of data points in the documentation of a genebank accession, taking into account the presence or value of other data points. For example, a wild accession should have a well-defined collection site but no variety name. Any type of accession, wild, landrace, breeding material or modern variety, can attain a maximal score of ten for this index.</p><p>Theo van Hintum, Frank Menting and Elisabeth van Strien (2011). <b>Quality indicators for passport data in ex situ genebanks.</b> Plant Genetic Resources, 9, pp 478-485. doi: <a href='https://dx.doi.org/10.1017/S1479262111000682' target='_blank'>10.1017/S1479262111000682</a></p>

• Some translatable text has been changed. The following properties should be changed in your Text.properties file and the according translation files:

# These have been split into title and text now. The title is simple text, no HTML and is shown as the page title,
# whereas the text supports HTML and is shown below.
widget.dataset.title.allelefreq=Allele Frequency Data Export
widget.dataset.text.allelefreq=<p>Please select a dataset for the export process.</p>
widget.dataset.title.genotypes=Genotypic Data Export
widget.dataset.text.genotypes=<p>Please select a dataset for the export process.</p>
widget.dataset.title.trials=Trials Data Export
widget.dataset.text.trials=<p>Please select a dataset for the export process.</p>
widget.dataset.title.compound=Compound Data Export
widget.dataset.text.compound=<p>Please select a dataset for the export process.</p>
widget.dataset.title.climate=Climate Data Export
widget.dataset.text.climate=<p>Please select a dataset for the export process.</p>

# Other changes
tour.introduction.share.text=Click on this to reveal the supported ways of sharing this page with your colleagues/friends/...