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Nicolas Morales edited this page Feb 23, 2023 · 107 revisions

V10.1

Major code changes

  • Fixes testing

Persistent Database Requirements for upgrading from V10.0

  • None

V10.0

Major code changes

  • Upload and processing of EarthSense ground rover Lidar point clouds
  • Extraction of plot level point cloud phenotypes

Persistent Database Requirements for upgrading from V9.7

  • Database patch: sgn/db/00164/AddEarthSenseCollectionsCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00165/UpdateMaterializedViewTrialDesigns.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database ISOL ontology update: sgn/ontology/imagesol.obo. To apply this change, make sure to set RUN_DB_ONTOLOGY_ISOL_UPDATES=TRUE in the docker-compose.yml before starting the service.
  • Database G2F ontology update: sgn/ontology/G2F.obo. To apply this change, make sure to set RUN_DB_ONTOLOGY_G2F_UPDATES=TRUE in the docker-compose.yml before starting the service.

V9.7

Major code changes

  • Upload of 10-channel aerial imagery, such as from MicaSense dual camera setup.
  • Upload of stitched orthomosaics (10-channel or 5-channel) as multi-band stacks from Agisoft.

Persistent Database Requirements for upgrading from V9.6

  • Database patch: sgn/db/00164/AddMicaSenseDoubleCameraProjectMdImageCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00164/AddRoverVehicleCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database ISOL ontology update: sgn/ontology/imagesol.obo. To apply this change, make sure to set RUN_DB_ONTOLOGY_ISOL_UPDATES=TRUE in the docker-compose.yml before starting the service.

V9.6

Major code changes

  • Move genotyping plates into genotyping projects
  • Can change dates of an imaging event

Persistent Database Requirements for upgrading from V9.5

  • Database patch: sgn/db/00164/UpdatePhenotypeMaterializedViewFixTimeTerms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V9.5

Major code changes

  • Changes to genotyping project interface.
  • Can associate field trials to imaging event afterwards.

Persistent Database Requirements for upgrading from V9.4

  • Database patch: sgn/db/00162/AddGenotypingProjectCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V9.4

Major code changes

  • Include facility indentifiers for genotyping plates.
  • Better metabolomics data upload

Persistent Database Requirements for upgrading from V9.3

  • Database patch: sgn/db/00161/AddFacilityIdentifierCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00163/UpdateSpPersonAdminField.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V9.3

Major code changes

  • Better georeferenced plot-polygons from aerial imagery.

Persistent Database Requirements for upgrading from V9.2

  • Database patch: sgn/db/00160/AddTrialSoilDataCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00162/AddOriginallyUploadedGeoTIFFCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00162/AddSensoryTrialType.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V9.2

Major code changes

  • Better georeferenced plot-polygons from aerial imagery.
  • Showing georeferenced plot-polygons on trial detail page.

Persistent Database Requirements for upgrading from V9.1

  • Database patch: sgn/db/00162/AddGeoParamsGPSCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V9.1

Major code changes

  • Better drone image analytics

Persistent Database Requirements for upgrading from V9.0

  • None

V9.0

Major code changes

  • Starting work on ground rover lidar data upload
  • Debian Bullseye, R4.2.0, PostgreSQL 14 environment (REQUIRES RELOAD OF DATABASE. GOING FROM PostgreSQL 12 to 14.)

Persistent Database Requirements for upgrading from V8.9

  • Database patch: sgn/db/00161/AddDroneRunGroundRoverCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V8.9

Major code changes

  • Save aerial imaging orthophoto type (OpenDroneMap, Pix4D, etc.)
  • Upload OpenDroneMap stacked image (.tif) for 5 bands

Persistent Database Requirements for upgrading from V8.8

  • Database patch: sgn/db/00161/AddDroneRunOrthophotoTypeCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V8.8

Major code changes

  • Better field trial analyse for spatial 2DSpl corrections and random regression permanent environment (PE)

Persistent Database Requirements for upgrading from V8.7

  • None

V8.7

Major code changes

  • Save and share raw image captures for imaging event, alongside stitched orthophoto images.

Persistent Database Requirements for upgrading from V8.6

  • Database patch: sgn/db/00160/AddProjectTableTypeCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V8.6

Major code changes

  • Drone imagery analytics with better GRM support.
  • Change in genotype data dosage (DS) storage.

Persistent Database Requirements for upgrading from V8.5

  • Database patch: sgn/db/00157/AddTrialStatusCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00160/GenotypeDosageChange.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00160/AddGRMGenotypingProtocolCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V8.5

Major code changes

  • Fixes JS error on startup.
  • Faster GRM creation.

Persistent Database Requirements for upgrading from V8.4

  • None

V8.4

Major code changes

  • Use GRM protocol in drone image analytics, with better GRM caching.
  • Better timing for running drone image standard processes.

Persistent Database Requirements for upgrading from V8.3

  • If you have a sgn_local.conf mounted in the docker-compose.yml, add the following key value line into your sgn_local.conf:
    image_analysis_log /home/production/archive/breedbase/image_analysis.log

V8.3

Major code changes

  • Fall back onto Debian 10, R 3.6.3, Sommer 4.1.3 because better Sommer 2DSpl results.
  • Parallelized GRM construction for speed.

Persistent Database Requirements for upgrading from V8.2

  • None

V8.2

Major code changes

  • Downgraded R Sommer to 4.1.3 from 4.1.5 because spl2D differences.
  • Fixes bug with matview refreshing.

Persistent Database Requirements for upgrading from V8.1

  • None

V8.1

Major code changes

  • Fixes bug loading imaging vehicles.
  • Fixes bug with JS.

Persistent Database Requirements for upgrading from V8.0

  • None

V8.0

Major code changes

  • Data privacy settings for separating companies and users.
  • Point cloud support.

Persistent Database Requirements for upgrading from V7.9

  • Database patch: sgn/db/00158/AddCompanyPrivateAccessCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00158/AddMoreStitchingReportandODMCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00159/AddCamelinaSativaOrganism.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00159/SaveDefaultCompanyUserAccess.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.9

Major code changes

  • Fixes bug on trial detail page.

Persistent Database Requirements for upgrading from V7.8

  • None

V7.8

Major code changes

  • Save OpenDroneMap report and point cloud (.ply).
  • Upload stock relatedness (e.g. genomic relationships) data.

Persistent Database Requirements for upgrading from V7.7

  • Database patch: sgn/db/00157/CreateStockRelatednessTable.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00157/UpdateCompanyCity.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00158/AddStitchingReportandODMCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00158/UpdateStockRelatednessProject.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.7

Major code changes

  • Drag GCP generated template. Fixed scaling issue of template and GCPs.

Persistent Database Requirements for upgrading from V7.6

  • Database patch: sgn/db/00155/AddFileMetadataJsonCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00156/AddPolygonTemplateMetadataCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00156/AddProjectTypeId.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.6

Major code changes

  • Allow brightening of image during standard process.

Persistent Database Requirements for upgrading from V7.5

  • None

V7.5

Major code changes

  • Ground control points (GCPs) allow templating of many imaging events at once (e.g. the orthophoto image contains many field trials in it).
  • Drag GCP generated template. Fixed scaling issue of template and GCPs.
  • Data separation database patches.

Persistent Database Requirements for upgrading from V7.4

  • Database patch: sgn/db/00155/CreatePrivateCompanyTable.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00155/UpdatePhenotypeMaterializedViewPrivateCompany.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00156/AddPrivateCompanyMdImage.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.4

Major code changes

  • Fix dragging plot-polygon template with margins.
  • Prevent adding ontology terms to protected ontologies.

Persistent Database Requirements for upgrading from V7.3

  • None

V7.3

Major code changes

  • Upload an imaging event to many field trials at once (e.g. the orthophoto image contains many field trials in it).
  • Template an imaging event in the Standard Process for many field trials at once. During templating, upload a spreadsheet to assign polygon numbers to plot numbers of many field trials.
  • Visualize plot-image phenotype margins during Standard Process, and afterward can regenerate phenotypes for different margins.

Persistent Database Requirements for upgrading from V7.2

  • Database patch: sgn/db/00154/AddFamilyTypeCvterm.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database patch: sgn/db/00154/AddLinkedImagingEventCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.2

Major code changes

Persistent Database Requirements for upgrading from V7.1

  • None

V7.1

Major code changes

  • BrAPI v2 Observations call is faster

Persistent Database Requirements for upgrading from V7.0

  • Database patch: sgn/db/00154/UpdatePhenotypeMaterializedViewAdditionalPhenotypeProps.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.

V7.0

Major code changes

  • Includes Canopy Cover Canopeo algorithm (CCC) vegetation index.
  • Docker can run database patches or ontology updates on docker-compose up -d when RUN_DB_PATCHES=TRUE or RUN_DB_ONTOLOGY_XXX_UPDATES=TRUE, respectively, is set in the docker-compose.yml.
  • High-dimensional phenotypes store additional "device_id" and "comments" for each recording.

Persistent Database Requirements for upgrading from V6.3

  • Database patch: sgn/db/00154/AddCCCVegetationIndexCvterms.pm. To apply this change, make sure to set RUN_DB_PATCHES=TRUE in the docker-compose.yml before starting the service.
  • Database ISOL ontology update: sgn/ontology/imagesol.obo. To apply this change, make sure to set RUN_DB_ONTOLOGY_ISOL_UPDATES=TRUE in the docker-compose.yml before starting the service.

V6.3

Major code changes

  • Restrict maximum number of standard processes running at once.

Persistent Database Requirements for upgrading from V6.2

  • None

V6.2

Major code changes

  • More aerial imagery analyses.

Persistent Database Requirements for upgrading from V6.1

  • Database patch: sgn/db/00153/AddEntryNumberCvterm.pm

V6.1

Major code changes

  • Better support for repeated measurements.
  • Interface to edit management factor details.

Persistent Database Requirements for upgrading from V6.0

  • None

V6.0

Major code changes

  • Interactive plot-polygon tool for aerial image processing with polygon margin buffering.
  • More spatial correction analyses.
  • Docker images are faster to update now.

Persistent Database Requirements for upgrading from V5.6

  • Database patch: sgn/db/00153/SaveChromosomeRankInNdProtocolFix.pm

V5.6

Major code changes

  • Interactive plot-polygon tool for aerial image processing with polygon margin buffering.
  • Ability to change upper and lower threshold values.
  • Ability to change polygon margin buffering when extracting zonal statistics.

Persistent Database Requirements for upgrading from V5.5

  • Database patch: sgn/db/00152/AddPlotPolygonMarginsPhenotypeCvterm.pm

V5.5

Major code changes

  • Interactive plot-polygon tool for aerial image processing.
  • Add subplots to a trial from trial detail page. Plants can be added to subplots.

Persistent Database Requirements for upgrading from V5.4

  • Database patch: sgn/db/00150/AddPhenotypeAdditionalInfoCvterm.pm
  • Database patch: sgn/db/00150/CreateMaterializedMarkerviewUpdated2.pm
  • Database patch: sgn/db/00151/SaveChromosomeRankInNdProtocol.pm

V5.4

Major code changes

  • Allow for multiple logins per user across different devices.

Persistent Database Requirements for upgrading from V5.3

  • Database patch: sgn/db/00147/CreateSpTokenTable.pm

V5.3

Major code changes

  • Improved spatial analytics.
  • SSR genotyping data management.

Persistent Database Requirements for upgrading from V5.2

  • Database patch: sgn/db/00148/AddPCRMarkerCvterms.pm
  • Database patch: sgn/db/00148/UpdatePhenotypeMaterializedViewGenotypingProjects.pm

V5.2

Major code changes

  • Sequence metadata and genotype querying system.
  • Various bug fixes

Persistent Database Requirements for upgrading from V5.1

  • Database patch: sgn/db/00147/CreateMaterializedMarkerview.pm
  • Database patch: sgn/db/00147/CreateMaterializedMarkerviewUpdated.pm

V5.1

Major code changes

  • Fixes OpenDroneMap orthophoto saving.

Persistent Database Requirements for upgrading from V5.0

  • None

V5.0

Major code changes

  • Georeferencing aerial-image derived plot-polygons.
  • Catalog ordering of accessions.

Persistent Database Requirements for upgrading from V4.11

  • Database patch: sgn/db/00145/AddCatalogRelatedCvterms.pm
  • Database patch: sgn/db/00145/AddOrderTables.pm
  • Database patch: sgn/db/00145/AddSpOrderPropertyCvAndCvterm.pm
  • Database patch: sgn/db/00145/AddVendorRole.pm
  • Database patch: sgn/db/00146/AddDroneRunResizeRatioCvterm.pm
  • Database patch: sgn/db/00146/AddGeoCoordinateParamPolygonsCvterm.pm
  • Database patch: sgn/db/00146/AddRotateKeepOriginalSizeCvterm.pm
  • Database patch: sgn/db/00146/UpdatePhenotypeMaterializedViewSpeed.pm

V4.11

Major code changes

  • NOAA NCDC weather plotting tool.

Persistent Database Requirements for upgrading from V4.10

  • None

V4.10

Major code changes

  • Drone imagery analytics

Persistent Database Requirements for upgrading from V4.9

  • Database patch: sgn/db/00143/AddAdditionalInfoType.pm
  • Database patch: sgn/db/00144/AddMiscellaneousTrialType.pm

V4.9

Major code changes

  • Drone imagery analytics with cross validation

Persistent Database Requirements for upgrading from V4.8

  • Database patch: sgn/db/00144/FixMatviewsTable.pm

V4.8

Major code changes

  • Fixes bug with OpenDroneMap stitching.
  • Minor cosmetic changes to ImageBreed skin.

Persistent Database Requirements for upgrading from V4.7

  • Database patch: sgn/db/00143/UpdateMetadataMdImageTableCharacterLength.pm

V4.7

Major code changes

  • Minor bug fixes

Persistent Database Requirements for upgrading from V4.6

  • Database patch: sgn/db/00143/UpdatePhenotypeJSONbMaterializedViewTissueSampleFix.pm

V4.6

Major code changes

  • Bulk upload imaging events previously processed using ArcGIS or other GIS software. Allows bulk upload of GeoTiffs and GeoJSON files to define imaging events, define plot-polygons, excise plot-images, and extract plot-phenotypes into the database automatically.

Persistent Database Requirements for upgrading from V4.5

  • Database patch: sgn/db/00142/AddImagingEventGeoParamCoordinatesUTMWGSCvterm.pm
  • Database patch: sgn/db/00141/AddVcfType.pm

V4.5

Major code changes

  • Removed 2GB limit when uploading imaging events either one at a time, in bulk, or in bulk with provided GeoJSON.
  • When uploading imaging events in bulk with GeoJSON files, an angle rotation can be supplied.

Persistent Database Requirements for upgrading from V4.4

  • None

V4.4

Major code changes

  • Bulk download imaging events

Persistent Database Requirements for upgrading from V4.3

  • None

V4.3

Major code changes

  • Bulk upload imaging events previously processed using ArcGIS or other GIS software. Allows bulk upload of GeoTiffs and GeoJSON files to define imaging events, define plot-polygons, excise plot-images, and extract plot-phenotypes into the database automatically.
  • Fixes bug when uploading duplicate genotypes to the same genotyping protocol.

Persistent Database Requirements for upgrading from V4.2

  • Database patch: sgn/db/00142/AddImagingEventGeoParamCoordinatesCvterm.pm

V4.2

Major code changes

  • Bulk upload imaging events

Persistent Database Requirements for upgrading from V4.1

  • None

V4.1

Major code changes

  • Apply the same aerial imagery standard process to other imaging events.

Persistent Database Requirements for upgrading from V4.0

  • None

V4.0

Major code changes

  • Database patches are run automatically on start up, making updating between releases easier (e.g. v4.0 to v4.1). Consult the docker-compose.yml to make sure RUN_DB_PATCHES=TRUE and the database parameters are provided in the environment.

Persistent Database Requirements for upgrading from V3.10

  • Database patch: sgn/db/00140/AddVendorSubmissionIDProjectProp.pm

V3.10

Major code changes

  • Better OpenDroneMap integration.
  • Bulk upload of imaging events.

Persistent Database Requirements for upgrading from V3.9

  • Database patch: sgn/db/00141/AddImagingEventBaseDateCvterm.pm

V3.9

Major code changes

  • Better OpenDroneMap integration.
  • Environmental simulation analytics improvements.

Persistent Database Requirements for upgrading from V3.8

  • Database patch: sgn/db/00140/AddAnalysisSingleMultiTrialCvterm.pm
  • Database patch: sgn/db/00140/AddDroneImageryODMRunningCvterm.pm
  • Database patch: sgn/db/00140/CreateProjectOwnerTable.pm

V3.8

Major code changes

  • Tools to store genomic sequence metadata.
  • Environmental simulation analytics improvements.

Persistent Database Requirements for upgrading from V3.7

  • Database patch: sgn/db/00139/AddNdProtocolTerms.pm
  • Database patch: sgn/db/00139/AddSequenceMetadataTypes.pm
  • Database patch: sgn/db/00139/CreateFeaturepropJSONTable.pm

V3.7

Major code changes

  • OpenDroneMap orthophotomosaic support for MicaSense 5-channel images and color camera images.
  • Download relationship matrix from high-dimensional phenotype data (NIRS, Transcriptomics, Metabolomics).

Persistent Database Requirements for upgrading from V3.6

  • None

V3.6

Major code changes

  • OpenDroneMap orthophotomosaic support for MicaSense 5-channel images.

Persistent Database Requirements for upgrading from V3.5

  • None

V3.5

Major code changes

  • OpenDroneMap orthophotomosaic support in progress.
  • Upload of additional cross properties.
  • Interactive mapping tool for specifying geo-coordinates of plots in the field.

Persistent Database Requirements for upgrading from V3.4

  • Database patch: sgn/db/00138/AddCrossAdditionalInfoCvterm.pm

V3.4

Major code changes

  • Greatly reduced size of Docker image.
  • Drone imagery statistics/analytics for minimizing and simulating spatial environmental effects.

Persistent Database Requirements for upgrading from V3.3

  • Database patch: sgn/db/00137/FixFieldbookImageCvterm.pm
  • Database TREAT ontology update: sgn/ontology/cxgn_plant_treatment.obo
  • Database ALF new ontology (trait ontology): sgn/ontology/Alfalfa.obo

V3.3

Major code changes

  • Improvements to Analytics protocols for Environment Simulation studies of Drone Imagery analyses.

Persistent Database Requirements for upgrading from V3.2

  • None

V3.2

Major code changes

  • Genotypes can be uploaded (e.g. using VCF file) for mixed stock types (accessions, tissue samples, plots, etc).
  • Analytics protocols can be saved for Environment Simulation studies of Drone Imagery analyses.

Persistent Database Requirements for upgrading from V3.1

  • Database patch: sgn/db/00134/AddIsPublicDataset.pm
  • Database patch: sgn/db/00135/UpdateWizardMaterializedViewsForGenoProtocols.pm
  • Database patch: sgn/db/00136/AddAnalyticsProtocolCvterms.pm

V3.1

Major code changes

  • Traits assayed on stock detail page now working.
  • High-dimensional phenotype (NIRS, Transcriptomics, Metabolomics) download interface.
  • Drone imagery statistics/analytics for minimizing and simulating spatial environmental effects.

Persistent Database Requirements for upgrading from V3.0

  • None

V3.0

Major code changes

  • ImageBreed is now running on Debian 10 instead of Debian 9.
  • Drone imagery statistics/analytics for minimizing and simulating spatial environmental effects.

Persistent Database Requirements for upgrading from V2.4

  • Database patch: sgn/db/00132/AddReleasedVarietyName.pm
  • Database patch: sgn/db/00132/AddTraitCvterms.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V2.4

Major code changes

  • Drone imagery statistics/analytics for minimizing and simulating spatial environmental effects.
  • High-dimensional phenotype upload for NIRS/Transcriptomics/Metabolomics.

Persistent Database Requirements for upgrading from V2.3

  • Database patch: sgn/db/00134/AddCrossTransactionRelatedCvterms.pm

V2.3

Major code changes

  • Drone imagery statistics/analytics for minimizing and simulating spatial environmental effects.

Persistent Database Requirements for upgrading from V2.2

  • None

V2.2

  • V2.2.1

Major code changes

  • Create or upload a sampling trial to define samples with greater flexibility.
  • The NIRS upload is now part of a generic high-dimensional phenotype upload workflow. High-dimensional phenotypes will also work for transcriptomics and metabolomics in the future. High-dimensional phenotypes can be uploaded for samples or other stocks in the database.

Persistent Database Requirements for upgrading from V2.1

  • Database patch: sgn/db/00132/AddHighDimPhenotypeProtocolCvterms.pm
  • Database patch: sgn/db/00135/AddProtocolColumnToNdExperimentPhenotypeBridge.pm
  • Database patch: sgn/db/00136/AddProtocoltoStoredNIRSRetroactively.pm

V2.1

Major code changes

  • High-density genotypic information can now store many millions of markers and genotypes. This was accomplished by separating data by chromosome. It is not necessary to reload or modify previously-stored genotyping data.
  • Compute relationship matrix using high-throughput phenotypes and use in analyses.

Persistent Database Requirements for upgrading from V2.0

  • None

V2.0

  • V2.0.1
  • V2.0.2

Major code changes

  • New storage mechanism for phenotypic values, offering greater speed and scalability across the system.

Persistent Database Requirements for upgrading from V1.11. This will take a long time to run depending on the size of your database, so please use a screen session. Please backup your database prior to upgrading to V2.0.

  • Backup your database first by logging into where the database is running (e.g. docker exec -it breedbase_db bash) then create a backup to a file using pg_dump -U postgres empty_fixture | gzip > YourBreedbase_v1.sql.gz. Keep this backup safe!
  • Database patch: sgn/db/00132/AddNdExperimentPhenotypeBridge.pm
  • Database patch: sgn/db/00133/MigratePhenotypesToNdExperimentPhenotypeBridge.pm
  • Database patch: sgn/db/00134/UpdatePhenotypeJsonbTableMaterializedViewForNdExperimentPhenotypeBridge.pm
  • Database patch: sgn/db/00134/UpdateWizardMaterializedViewsForNdExperimentPhenotypeBridge.pm

V1.11

Major code changes

  • Export genotyping plates to vendors.
  • Fixes aerial imaging event processing for multi-spectral MicaSense when using ground control points.

Persistent Database Requirements for upgrading from V1.10

  • Database patch: sgn/db/00130/AddVendorOrderIDProjectProp.pm
  • Database patch: sgn/db/00131/AddMixedModelProtocol.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V1.10

Major code changes

  • Properties for accessions can be defined in the configuration file and used when uploading accessions in a file.
  • The genotype data upload will check marker information if data is uploaded under the same genotyping protocol (e.g. the reference, alternate, position, info, format, etc. are checked for consistency).

Persistent Database Requirements for upgrading from V1.9

  • None

V1.9

Major code changes

  • Product profiles can be defined for breeding programs
  • Residuals from drone imagery analyses can be saved
  • Seedlot bug was fixed

Persistent Database Requirements for upgrading from V1.8

  • Database patch: sgn/db/00131/AddProductProfileCvterm.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V1.8

Major code changes

  • NIRS upload now uses R waves package to aggregate spectra. NIRS spectra can be trained against phenotypes in the database, and the trained model can be used to predict the phenotype for new samples with spectra.

Persistent Database Requirements for upgrading from V1.7

  • None

V1.7

Major code changes

  • Aerial image models can use pedigree + genomic relationship matrix

Persistent Database Requirements for upgrading from V1.6

  • Database patch: sgn/db/00129/FixPhenomeGenotypingTable.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V1.6

Major code changes

  • Can upload Tassel5 HDF5 genotype data (.h5).
  • Model for GBLUP using Sommer
  • R version now 3.6.3, so all R packages were updated

Persistent Database Requirements for upgrading from V1.5

  • Database patch: sgn/db/00130/AddSommerAnalysisCvterms.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V1.5

Major code changes

  • Fixes models for computing genetic and temporal effects from Legendre polynomial random regressions.
  • Compute and save numerical derivatives of phenotypes across rows and columns
  • Compute and save precipitation sum from planting date to aerial imaging event date. Similar to growing degree day (GDD) calculation.

Persistent Database Requirements for upgrading from V1.4

  • Database patch: sgn/db/00129/AddFamilynameRelatedCvterms.pm
  • Database patch: sgn/db/00130/AddAveragePrecipitationSumCvterms.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

V1.4

Major code changes

  • Adds models for computing genetic and temporal effects from Legendre polynomial random regressions.

Persistent Database Requirements for upgrading from V1.3

  • Database patch: sgn/db/00129/AddAIREMLf90AndSommerModelCvterms.pm
  • Database SGNSTAT ontology update: sgn/ontology/cxgn_statistics.obo

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