Version 3.6.0

New in '3.6.0'

• CHG: Simplified dataset service call, by moving an extra (optional) parameter into the filter object.
• CHG: Changed the name of the Equal operator to Like, because that's what it was doing in the first place, then added a new class Equal that actually checks for equality.
• ADD: Added Germinate, James Hutton Institute and ICS logo to the bottom of the about Germinate page.
• CHG: Converted the about Germinate page into the UiBinder framework.
• CHG: Slightly changed the trials template to have a dropdown box for the unit type. This change is backwards compatible, i.e. the importer code will still work with the old templates.
• ADD: Added horizontal version of the side menu logo to the login page to have the branding there as well.
• ADD: Added tooltips to points in the scatter matrix while maintaining the ability to select points with the rectangle.
• CHG: Slightly changed the way chart legends work. They now don't react to hover events anymore (other than showing a tooltip with the full name of the legend item), but rather work by clicking on them. Clicking on a legend item will toggle the item's visibility, i.e. making it easy to hide and show certain categories.
• ADD: Added two buttons to the legend that can be used to hide and show all categories. This is particularly useful if you want to look at a specific category. In that case you would hide them all first, then show the one you're interested in by clicking on it.
• CHG: Changed automatic scrolling on the groups page to only scroll if the user selected a group or if a new group is created. It won't automatically scroll to the details anymore when the page is revisited after having selected a group earlier.
• CHG: Changed icons and opacity levels on the new legend.
• FIX: Fixed an issue where the selection within the scatter matrix interfered with the show/hide functionality of the legend.
• CHG: Updated MySQL JDBC driver to version 8.0.12.
• CHG: Removed redundant lines from web.template.xml as they're already taken care of with annotations.
• CHG: Moved bootstrap-xxs.css further down the file to give it higher proprity.
• FIX: Fixed missing MlsStatus from MCPD import.
• DEL: Removed no longer required SQLServer JDBC driver.
• CHG: Changed table filter operators to now accurately reflect "equal" and "like" with the first looking for exact matches and the second searching for wildcard matches.
• ADD: Added like/equal selector to main search page.
• CHG: The Excel data importer now supports linking accessions to their countries of origin even if no specific location information is available. A location without lat/lng will be created to link the country and the accession.
• ADD: Added example files for a scatter plot.
• ADD: Added onClick behaviour to matrix charts.
• ADD: Added Passport page popup to scatter and matrix charts instead of redirecting to the page. This allows users to explore the passport data of a specific item without having to leave the page.
• ADD: Added click behaviour to PDCI chart. It'll redirect to the accession overview page and filter the table down to only the items within the range of the bar the user clicked on.
• FIX: Fixed a bug in the Hutton banner icon display. It wasn't showing the icons in the correct aspect ratio on some browsers.
• CHG: Added non-numeric phenotypes to phenotype overview table. Min, max, avg and stddev will be empty for them, but at least they are shown.
• ADD: Added user groups and dataset permissions page so that admins can configure these through the web interface rather than the database directly.
• ADD: Added local pedigree chart to the passport page. This shows the accession with its children, parents and grandparents.
• DEL: Removed the compound data chart as it was only ever showing 500 accessions which isn't very useful.
• ADD: Added the option to download or print the license that accompanies a dataset.
• ADD: Added name column to maps.
• ADD: Added download button to groups page to download the information about all items in the current group.
• ADD: Added the option to filter tables by inSet, i.e. by providing a comma separated list of items.
• ADD: Added the inSet option to the search page as well.
• CHG: Simplified internal query building functionality.
• CHG: Unified taxonomies and subtaxa table.
• ADD: Added initial support for template files in the external data directory.
• CHG: Changed image page so that it's always able to link straight to the details page of any kind (accession, compound, etc.).
• ADD: Added the functionality to have a config.properties file located in the external data directory. The internal one has to be read first to detect the location of the external directory, then Germinate will use the external file to read and write properties.
• ADD: Added dataset version column to all exported data that also contains the dataset name.
• CHG: Changed equal-width and split-point binning bins to be generated solely on the client. There's no need to communicate with the server to generate the bins only for the actual data extraction.
• FIX: Fixed Gradient code. Up till now it wasn't adding the last colour to the gradient at all.
• CHG: Unified two binning charts into a single class.
• ADD: Added initial version of a trait details page and trait overview page. These are analogue to the compound details and compound overview page. It's now possible to define synonyms, images and links for traits.
• CHG: Backticked all table and column names in all the queries. This is to make Germinate future-proof, i.e. if table or column names become reserved words by MySQL in the future, we don't have to worry about this.
• ADD: Added Flapjack's HDF5 interaction files to Germinate.
• CHG: Changed d3.js scatter matrix chart to not show the redundant cells, i.e. the ones that are just mirrored from the other half of the matrix.
• ADD: Added map (genetic/physical) visualization that shows the the markers at their position on the chromosomes. By default tiny chromosomes/scaffolds/etc are excluded if they're less than 1% of the maximal length.
• ADD: Added dataset download functionality to both the compound dataset table and the generic dataset table to allow datasets to be downloaded in one go from more places.
• ADD: Added "Forgot password" link to the login form in addition to the information on the help page.
• ADD: Added climate data selection dropdown to geographic search page.
• CHG: Changed group page headings to highlight the current group name.
• ADD: Added link from home page to news page.
• ADD: Added dataset metadata download widget to phenotype/compound export page as well as experiment details page.
• ADD: Added AdditionalDataWidget to trait/compound details page so that the user can accept additional licenses to see more data.
• CHG: Renamed description field of Datasets to name and added a new description field.
• FIX: Fixed font size being too big on downloaded pedigree charts.
• FIX: Fixed an issue with locale formatted text fields and their get methods not being able to parse numbers with different decimal separators in other locales.
• CHG: SIGNIFICANTLY simplified the set of stored procedures. For germplasm, phenotype and compound export each, three stored procedures could be unified into a single one per type.
• CHG: Replaced Crowdin logo with Lokalise logo.
• ADD: Added lots of new Google Analytics tracking.
• ADD: Added links from locations table to details pages.
• ADD: Added links from data statistics page to filtered dataset table.
• CHG: Update database template to reflect the recent changes.
• CHG: Completely rewrote the data template importer code to make it a lot simpler and easier to use. This also reduces code duplication/redundancy.
• ADD: Added a larger example file for each data template.
• ADD: Added a very simple user interface on top of the command line importer code.
• ADD: Added JUnit tests for the data importer code!
• ADD: Added value histogram chart to trait and compound details pages. They show the distribution of values for the currently selected trait/compound and dataset. Click the histogram icon in the dataset table to get the histogram per dataset.
• CHG: Rewrote trait and compound data importer to pre-fetch data for duplicate check and also to import the data in a batched fashion of 10k rows at a time instead of each one individually to improve performance.
• CHG: Changed tests to run twice each. The first run imports the data, the second one makes sure that the duplicate checks work as expected, i.e. no data is imported if it already exists.
• CHG: Changed PDCIRunnable to be more efficient. It'll now get the extra data separately instead of joining everything in a huge query. May be slightly slower for small databases, but a lot faster for larger databases.
• ADD: Added accession item marking button to the top of the page. Click the checkbox next to the accession header to mark/unmark an item.
• ADD: Added image icon to accession table to show if an accession has at least one image associated with it.
• CHG: Changed table filter to use more appropriate operators based on the type of column selected.
• CHG: Changed pedigree chart to only activate zooming once it has focus. This keeps it from zooming if the user scrolls over it.
• ADD: Added the option to export the list of marked accessions to an external page. This happens by using the new property Germinate.Template.Marked.Accessions.Url (needs to contain {{IDS}}) and the text property widget.marked.item.list.accession.export. A new link will be added to the marked accessions page and clicking it will redirect the user to the given URL where {{IDS}} has been replaced with a comma-separated list of the marked ids. This may come in handy if you want to send the ids to a seed store or similar tool.
• ADD: Added the option to mark "entity children" and "entity parents" from any accession table. This means that you can either filter the table down to get the accessions/plant/sample you're interested in and then mark its parents/children, or you can right-click individuals and only mark parents/children of this individual.
• CHG: To declutter the item marking menu, some options have been removed. It's no longer possible to mark/unmark items on a page basis (rather than individually or the whole table). Furthermore, actions that relate to the whole table are only available through the header checkbox (mark/unmark whole table, create group), whereas the context-menu of an individual row shows options related to the individual.
• CHG: Changed the way synonyms are stored. They are now stored as a JSON array rather than individual rows in the synonyms table. To make searching and filtering possible, the search functionalities have been adjusted to work with the new data type.
• CHG: Changed the layout of the passport page if a non-accession is selected. In which case, the entity that's selected as well as its parent entity will be shown. To save space, empty sections of the passport page are now not shown.
• ADD: Added the option to define multiple polygons on the location search page.
• CHG: Updated GWT to 2.8.2.
• FIX: Fixed an issue where it was possible to query e.g. dataset A from the trials/compound data table of dataset B. It would still only return data if the user is allowed to use the dataset, but it may be confusing to return data at all.
• FIX: Fixed an issue where dataset dublin core downloads were not working due to Internet Explorer not supporting the way it was done. To make this work on IE, an actual call to the server had to be implemented rather than just downloading it directly on the client.
• ADD: Added the number of photos to the accessions table rather than just an indication of there being at least one photo.
• FIX: Fixed synonym search for markers.
• DEL: Removed duplicate query printing in debug mode when a parallel callback is used.
• ADD: Added more indices to improve the performance of multiple queries significantly.
• DEL: Removed default column sorting on some tables to improve performance, because unnecessary sorting is slow.
• FIX: Increased column limit for dataset metadata fields.
• CHG: Improved performance of scatter matrix plot by removing the live preview of the selection mode. Selection happens at the end.
• ADD: Added table column help icons. References #24. Closes #29.
• ADD: Added code for the import of germplasm entity level information. Closes #30.
• CHG: Added PUID and biological status columns to accession table, removed latitude and longitude columns (filtering on these is better done on the maps anyway).
• ADD: Added the ability to export genotypic/phenotypic/compound data against the list of currently selected accessions/markers. Closes #31.
• ADD: Added image preview to accessions table if an accession has an image.
• ADD: Added biological status pie chart to statistics page to show the distribution of SAMPSTAT (MCPD) values.
• CHG: Changed phenotype importer to be case-insensitive.
• ADD: Added Plotly.js as a dependency. Refs #32.
• CHG: Changed a lot of charts over to Plotly.js. including the scatter plots, scatter matrices, everything except the taxonomy pie chart on the statistics page, etc. Refs #32.

Migrating from 3.5.0 to 3.6.0:

• Create a horizontal version version of the logo.svg in the instance-stuff/<your-instance>/template folder and save it as logo-horizontal.svg in the same folder.
• The following new pages are available. If you want to use them, please add them to your config.properties property Germinate.AvailablePages: traits, trait-details, trial-site-details, user-permissions
• New translatable text has been added. The following properties can be changed in your Text.properties file and the according translation files:

operators.like=Like
column.maps.description=Map Description
menu.user.permissions=User permissions
page.user.groups.title=User groups
page.user.groups.text=<p>The table below shows the groups of users that are currently defined. You can add new groups, delete existing groups and add users to or remove users from groups.</p>
page.dataset.permissions.title=Dataset permissions
page.dataset.permissions.text=<p>The table below shows all available datasets. After selecting a dataset, you can define which user groups or individual users should have access to this dataset.</p>
column.user.username=Username
column.user.fullname=Full name
column.user.email=Email
column.user.institution=Institution
page.user.groups.add.user=Add user
page.dataset.permissions.dataset=Dataset
page.groups.current.members=Current group members
page.dataset.permissions.users.title=User permissions
page.dataset.permissions.groups.title=Group permissions
page.dataset.permissions.current.user.permissions=Current user permissions
page.dataset.permissions.current.group.permissions=Current group permissions
page.dataset.permissions.add.group=Add group
general.print=Print
general.save=Save
download.format.html=HTML
column.dataset.site.name=Location
column.dataset.country=Country
operator.in.set=In set
search.box.tooltip.in.set=Separate items with commas.
general.remove=Remove
column.phenotype.unit.name=Unit
menu.traits=Traits
page.traits.title=Traits
page.trait.details.image.title=Images
page.trait.details.for.trait=Details for trait: {0}
page.maps.histogram.title=Histogram
page.maps.histogram.text=<p>The diagram below shows the density of markers on each chromosome. Selecting in the diagram by dragging will add the selection to the export options.</p>will show the closest marker to the mouse position.</p>
page.login.password.reset.link=Forgot your password?
page.passport.pedigree.chart=Pedigree local view
page.passport.pedigree.chart.sub=Shows grandparents, parents and children only. Red edges represent female parents and blue edges male parents.
column.dataset.name=Dataset Name
page.trait.details.datasets.title=Datasets
page.trait.details.dataset.text=This table shows all datasets containing the selected trait. Additionally, the number of germplasm for which there is a value for this trait within the current dataset is shown alongside the total number of phenotype values per dataset.
page.compound.details.dataset.title=Dataset
page.compound.details.dataset.text=This table shows all datasets containing the selected compound. Additionally, the number of germplasm for which there is a value for this compound within the current dataset is shown alongside the total number of compound values per dataset.
widget.dataset.download.attributes=Attributes
widget.dataset.download.dublin.core=Dublin Core
widget.dataset.metadata.download.title=Download Metadata
widget.dataset.metadata.download.text=Please select at least one attribute for which to export the attribute data. Then click on the download button below the list.
notification.attribute.selection.empty=Please select at least one attribute.
page.trialsites.title=Trial Site Details
page.geography.locations.table.title=Location Table
column.location.type=Type
help.maps=<p>This page shows a table with information about all the genetic/physical maps that are stored in Germinate. Selecting a map in the table will show all markers on this map. Clicking on a marker in the table redirects to a page with detailed information about the selected marker.</p><p>For smaller maps, a heatmap marker distribution map is shown below the table that illustrates where the markers are located on each chromosome/linkage group.</p><p>The final section of this page allows you to download the selected map in a number of formats. You can also filter the markers on the map down by using the export options. As long as the export options are open (not collapsed), the downloads will be restricted to the selection in the options.</p>
help.markers=<p>The marker details page shows all the information associated with the selected marker. This includes which datasets the marker has been used in, which genetic/physical maps it''s part of, etc.</p>
help.genotypic.export=<p>Genotypic data is exported for either the whole dataset or a subselection of accessions or markers. This page allows you to select which accession and marker groups should be included in the output and which genetic/physical map they should be exported against. To export the data for all accessions/markers, simply select the first item in the lists.</p><p>If you have items in your marked item list, a button below the selection box can be used to create a group from the list and then use that new group for the export.</p>
page.datasets.histogram.title=Value histogram
column.accessions.has.image=Has image
page.trials.data.table.title=Data table
page.compounds.data.table.title=Data table
widget.marked.item.list.accession.export=Export accessions
page.cart.button.add.entity.parents=Mark entity parents
page.cart.button.remove.entity.parents=Unmark entity parents
page.cart.button.add.entity.children=Mark entity children
page.cart.button.remove.entity.children=Unmark entity children
column.phenotype.synonyms=Synonyms
column.help.passport.pdci=Passport Data Completeness Index
column.help.accessions.entityp.type=This can be "Accession", "Plant/Plot" or "Sample"
column.help.pedigree.relationship.type=This can be "F" (female), "M" (male) or "OTHER"
column.help.dataset.datapoints=Number of individual data points
column.help.dataset.size=Number of database objects
column.location.country=Country
column.accession.puid=PUID
column.help.accession.puid=Permanent Unique Identifier
column.accession.biological.status=Biological status
widget.table.multi.select.text=Use the checkboxes to select one or more rows.
widget.list.group.marked.items=Marked items
page.data.statistics.biological.status.title=Accessions grouped by biological status
page.data.statistics.biological.status.text=Below you can see the percentage of accessions for each biological status (SAMPSTAT) defined in the Multi-Crop Passport Descriptors (MCPD v2.1). Hovering over a bar will show the actual number of accessions. Clicking on a bar will take you to the accession overview page which will then just show the accessions with this biological status.
widget.chart.options=Options

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

column.maps.name=Map Name
widget.table.filter.info=<b>Table filtering supports many different comparisons. ''Equal'' searches for exact matches, while ''Like'', by default, looks for matches starting or ending with the query, but also support the wildcard character ''%''.</b>
column.locations.site.name=Site name
column.compound.name=Compound Name
column.phenotype.name=Trait Name

• Some translatable text has been removed. The following properties can be removed from your Text.properties file as they are no longer used:

column.climate.id=
column.climate.location=
column.locations.accession.count=
column.markers.allele.one=
column.markers.allele.two=
column.phenotype.data.treatment.description=
contact.us.message=
general.by=
general.copy=
general.date.format.long=
general.error=
general.help=
general.info=
general.link.get.text=
general.month=
general.range.from=
general.range.to=
general.success=
general.warning=
help.climate=
help.genotype=
help.genotype.result=
help.geography=
help.megaenvironment=
help.phenotypes=
menu.menu=
notification.annotations.deleted=
notification.climate.group.selection.empty=
notification.climate.selection.empty=
notification.compound.dataset.no.compound=
notification.genotype.groups.accessions.no.data=
notification.genotype.groups.markers.no.data=
notification.geography.accessions.no.data=
notification.groups.group.election.empty=
notification.groups.types.no.data=
notification.login.password.invalid=
notification.login.prompt=
notification.login.successful=
notification.login.username.invalid=
notification.phenotype.dataset.no.phenotypes=
notification.query.invalid=
notification.upload.file.select=
operators.in.set=
page.about.button.search.members=
page.accessions.browse.download.dataset=
page.accessions.browse.download.dataset.complete=
page.climate.download.table.excel=
page.compound.details.compound.data.chart=
page.dataset.title=
page.genotype.cdf.hetero.text=
page.genotype.cdf.hetero.title=
page.genotype.result.text.one=
page.genotype.result.text.rwo=
page.geography.locations.elevation.inverse.text=
page.geography.locations.elevation.inverse.title=
page.geography.locations.elevation.text=
page.geography.locations.elevation.title=
page.groups.filter.title=
page.markers.details.title=
page.markers.genotypes.count=
page.phenotypes.dataset.title=
page.phenotypes.geochart.all.phenotypes=
page.phenotypes.geochart.title=
page.phenotypes.result.title=
page.phenotypes.table.show.switch=
page.phenotypes.table.show.title=
tooltip.table.header.filter.cell=
widget.d3.chart.compound.data.limit.warning=
widget.d3.chart.compound.y.axis.title=