[pull] develop from solgenomics:master - #29

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solgenomics:master

Commits on Dec 12, 2023

update to sgn-377.0 with fix of fieldmap display issue.
lukasmueller
committed
44bfd82

Commits on Dec 13, 2023

Fix for broken phenotype overlay on fieldmap; issue with geo fieldmap persists.
lukasmueller
committed
34192e4

Commits on Jan 9, 2024

update to sgn-378.0. Add Rosner test and IQR metric to dataset outlier detection tool; upgrade fieldmap to d3 v4; add back missing generic message function; show non-numeric traits and raw trait da…
lukasmueller
committed
7a8929f

Commits on Jan 26, 2024

fix locus owner association; add bulk and buk_open cross types; change BTI logo in footer.
lukasmueller
committed
4bd80d8

Commits on Jan 30, 2024

updating to sgn-380.0. Includes improvements to advanced vector search, the genotyping plate loading script, seed transaction loading and management, and new reporting pages.
lukasmueller
committed
87914ed

Commits on Feb 2, 2024

fix entrypoint check that loaded database in spite of there already being one present.
lukasmueller
committed
a381410

Commits on Feb 9, 2024

Commits on Feb 15, 2024

Update to sgn-381.2. Add brapi logo.
lukasmueller
committed
9de7a03

Commits on Feb 27, 2024

change Bio Chado Schema to sgn copy (from GMOD).
lukasmueller
committed
618d1b5

Commits on Mar 8, 2024

bringing system up to date with sgn-382.0 and bio chado schema from solgenomics repo (not GMOD).
lukasmueller
committed
af64304

Commits on Mar 9, 2024

fix categorical trait formats for Fieldbook; fix BrAPI call AdditionalInfo for germplasm; require genotype protocol and warn of too large datasets for wizard genotype download; add script that down…
lukasmueller
committed
45a8f78

Commits on Mar 14, 2024

Fix Geofieldmap tool; Improve merge stock script; Create seedlots from trial using plot names; add new R libraries.
lukasmueller
committed
95755c3

Commits on Mar 22, 2024

allow download of archived vcf files; add transformation management tool; add dihaploid_induction as a new cross_type; fix issue with BrAPI observation values of 0; fix genotype download issue with…
lukasmueller
committed
3e46b98

Commits on Mar 30, 2024

Commits on Apr 17, 2024

add rtb logo to rtb sites. Fix studies sort order; fix bug if no trait data when creating seedlots from trial; add related stocks to vector page to see transformed accessions.
lukasmueller
committed
c2a2220

Commits on Apr 26, 2024

fix seedlot description in upload; direct phenotyping fixes; remove debugging alert in fieldbook file generator; improve related stocks section for vectors; add dumping script for ontologies to .ob…
lukasmueller
committed
b1037fd

Commits on May 11, 2024

fix mixed model tool results page for lme4 and sommer; fix direct phenotyping page issues; additions to annotation page from file; allow protocol edits; show empty plots on geofieldmap and view onl…
lukasmueller
committed
b1f4329

Commits on May 16, 2024

add genefamily table.
lukasmueller
committed
1853c49

Commits on May 17, 2024

upgrade R to version 4.4
lukasmueller
committed
8c5c837

Commits on May 23, 2024

Fix ANOVA analysis; fix issue with Fieldmap viewer; GCPC tool fixes.
lukasmueller
committed
29a2063

Commits on Jun 4, 2024

remove spaces from scale datatype in BrAPI (enables type specific trait input on Fieldbook); include entry number in trial download; add entry numbers to label designer; improve population related …
lukasmueller
committed
314b9a4

Commits on Jun 18, 2024

fix BrAPI observation call (remove repetition, keep rep); Add ability to select synonyms to be printed in Label Designer; add search by cross ID to BrAPI seedlot search; make marker search case ins…
lukasmueller
committed
7b19687

Commits on Jul 9, 2024

fix phenotype upload; ensure timestamp use most common time zone format; add genetic file parser for accessions and locations; fix missing values and empty traits; display wait message while queryi…
lukasmueller
committed
b3c3def

Commits on Jul 12, 2024

update to tag sgn-393.0.
lukasmueller
committed
f7dfdbc

Commits on Jul 13, 2024

fix an issue with the generic file parser module.
lukasmueller
committed
5b1ccd0

Commits on Aug 4, 2024

Commits on Aug 9, 2024

bring sgn to sgn-395.0. Includes longer timeout for label designer; add dataset functions.
lukasmueller
committed
15f49fa

Commits on Aug 14, 2024

remove the synonym option from the label designer as it causes issues with the label generation process.
lukasmueller
committed
eee3541

Commits on Sep 10, 2024

add vector search to quicksearch; fix a multiple submission issue with the multiple trial upload; quote params in multiple trial upload script; improve multiple trial upload error reporting; improv…
lukasmueller
committed
4562c9a

Commits on Sep 20, 2024

tweak clustering tool; add links from list items to their detail pages; add season time events; fix plants being allocated incorrectly in greenhouse/nursery trial design; make cluster plots interac…
lukasmueller
committed
8507bc5

Commits on Oct 2, 2024

fix observationUnitPUI in brapi call; parse and validate Fieldbook multicat traits correctly; fix some curious issues that newly installed lint raised; fix kinship and cluster result load from resu…
lukasmueller
committed
0caa038

Commits on Oct 5, 2024

add an improved empty_fixture (for breedbase_site).
lukasmueller
committed
873c5e8

Commits on Oct 24, 2024

add capability to transfer photos from fieldbook using brapi; hide Trait Properties section on cvterm pages for traits and rename to Variable Properties on varaible detail pages; display hierarchic…
lukasmueller
committed
3db66a2

Commits on Oct 28, 2024

Fix an issue with the pedigree upload; fix a javascript issue with the audit tables.
lukasmueller
committed
5626341

Commits on Nov 6, 2024

Commits on Nov 20, 2024

update to sgn-403.0. Includes transformation workflow with overall unique numeric IDs; fix issue with stored analysis page; add bulk download of seedlots with list; add trial usage filter for seedl…
lukasmueller
committed
dbd9003

Commits on Dec 7, 2024

Commits on Dec 9, 2024

change the git submodule for bio chado schema.
lukasmueller
committed
501b05a

Commits on Jan 10, 2025

Bringing repo up to tag sgn-4.05.0. Changes include improvements to the List Manager, which now includes the ability to merge lists and perform union and intersection operation between lists as wel…
lukasmueller
committed
7626a0e

Commits on Jan 25, 2025

Add phenotype QC module; Ability to batch update trial metadata; List manager improvements; improve tracking workflows.
lukasmueller
committed
3f6e14b

Commits on Feb 2, 2025

add more accessors for create_date for time-based queries.
lukasmueller
committed
1bbef9f

Commits on Feb 7, 2025

update to sgn-408.0. Add dataset compatibility tool; improve accession photo display; fix notes in phenotyping spreadsheet upload; remove fuzzy search requirement for submitters in accession upload…
lukasmueller
committed
034d89d

Commits on Feb 10, 2025

allow curators to set the representative accession image; add a new nirs analyzer; show acquisitionDate in BrAPI; refactor create seedlots from trial feature to address issues encountered by some u…
lukasmueller
committed
c58380a

Commits on Feb 11, 2025

update to sgn-410.0. Fix an issue with a missing default configuration parameter that caused some tools to crash.
lukasmueller
committed
0a6c744

Commits on Feb 19, 2025

allow transformation ids to be deleted; tweak sgn.conf for outlier filtering tool; fix field management factors in BrAPI so that they are not listed as traits; add deletion of entry numbers and fix…
lukasmueller
committed
ef68b80

Commits on Feb 24, 2025

Commits on Mar 3, 2025

Commits on Mar 14, 2025

update to sgn-414.0. Includes new ability to set the type of a seedlot (such as seed or root, etc); fix an issue in a brapi call where the date format was not ISO; fix download for permanent outlie…
lukasmueller
committed
d3ce529

Commits on Mar 24, 2025

Commits on Apr 3, 2025

update to sgn-416.0. Fix an issue with the trial image section when there are a lot of images; add a generic analysis_result stock type for analyses that are not accession, plot, or tissue_sample s…
lukasmueller
committed
56814c7

Commits on Apr 10, 2025

add FielDHub R package for new diagonal design; fix a missing constructor that broke certain password resets; improve phenotype heatmap loading speed; add custom reports feature; fix genotype downl…
lukasmueller
committed
185e07b

Commits on Apr 15, 2025

Updating to sgn-418.0. Include spatial model in mixed model tool; make image analysis pipeline configurable in sgn_local.conf; fix analysis download; add organisms to wizard; fix indentation in CXG…
lukasmueller
committed
f59a346

Commits on Apr 18, 2025

Commits on May 5, 2025

Fix breeding program validation for cross upload on experiment details page; make sampling trial tissue types configurable; set brapi_require_login to 1 by default; make the trait search word speci…
lukasmueller
committed
a6f571b

Commits on May 15, 2025

update javascript minify package; add the ability to link a transformation with its negative control; add histogram download links to solgs; refactor the backend image loading script; fix an issue …
lukasmueller
committed
15226fc

Commits on May 28, 2025

Commits on Jun 2, 2025

add libimage-exiftool-perl to Dockerfile.
lukasmueller
committed
2a95572

Commits on Jun 4, 2025

Commits on Jun 5, 2025

try wiggly bracket notation in assignment for VERSION etc.
lukasmueller
committed
dd6ba80

Commits on Jun 19, 2025

add new NIRS device InnoSpectraNIRS-S-G1; add optional trial_stock_type column for multi trial upload; fix sorting of ontologies in post composing tool; in list dialog, check whether list items hav…
lukasmueller
committed
03bff86

Commits on Jun 26, 2025

update to tag sgn-424.0. Fix linkage between crossing experiment and field trial section; fix add accessions from a list; add show password check box to login page.
lukasmueller
committed
fb69253

Commits on Jul 3, 2025

Allow plots to have structured plant and subplot entries with their own coordinates and arrangement within the plot; make headers in the fieldbook file upload more flexible which should allow for e…
lukasmueller
committed
d7c661e

Commits on Jul 10, 2025

Update to sgn-426.0. Fixes an important issue with CXGN::Job to correclty retrieve error conditions. When replacing accessions in plots, accession assignments are changed for all objects inheriting…
lukasmueller
committed
09f0ac4

Commits on Jul 28, 2025

Fixes and important bug by which pedigree data could be accidentally deleted when updating stock attributes; allow both point and polygon coordinates for plot geolocation information; remove a link…
lukasmueller
committed
6c15e28

Commits on Aug 15, 2025

Allow obsoleted accessions to be included in transgenic historical data upload; fix polygon created when there are more than three points on geo field map; obsolete multiple transformants at once; …
lukasmueller
committed
217d337

Commits on Aug 22, 2025

in load images script, also add ability to link with cvterms; Download cross and family name info using progeny list; add dbpatch to add missing cvterms in materialized_stockprop to fix vector search.
lukasmueller
committed
b00e16e

Commits on Aug 27, 2025

Update R apt source
dwaring87
committed
9230728

Commits on Aug 28, 2025

Merge pull request #54 from solgenomics/fix_R_apt_source
lukasmueller
authored
a724ec5

Commits on Aug 29, 2025

add EXIF parsing function to image object.
lukasmueller
committed
1b1b9fa

Commits on Sep 5, 2025

Commits on Sep 10, 2025

update to sgn-431.0. Includes new functionality to record number of insertions in transformants; edits to the manual; fix in the GCPC tool link to the selection index tool.
lukasmueller
committed
655361e

Commits on Sep 15, 2025

add important fix for spatial correction in field map.
lukasmueller
committed
a020763

Commits on Sep 18, 2025

Commits on Oct 3, 2025

Include option to parse barcodes contained in images for association with observation units; tweak phenotype upload - do not apply checks to values that are undef, emtpy string, . or NA; fix tissue…
lukasmueller
committed
8654198

Commits on Oct 16, 2025

update to sgn-435.0. Adds a section with a graphical vector view to vector detail pages; adds ability to run multiple image analyses on one image with the Image Analysis tool; allows searching with…
lukasmueller
committed
41056f7

Commits on Nov 4, 2025

update to sgn-436.0. Adds the ability to add plots and plants to a greenhouse design even after the trial has been created; adds a tool to view all the accessions and the genotyping protocols they …
lukasmueller
committed
c9b85e4

Commits on Nov 10, 2025

adding a download dir to both breedbase_web and selenium dockers to better deal with web downloads.
lukasmueller
committed
d2a58d9

Commits on Nov 14, 2025

Commits on Nov 16, 2025

bring up to date with sgn-437.0. Includes fixes for primer3 tool; fixes in-silico PCR tool; fix an issue with the vector viewer css import; return ids in the same order as the names in the accessio…
lukasmueller
committed
1fb7c05

Commits on Nov 19, 2025

add a new page and menu item about NARITA pathogen analysis.
lukasmueller
committed
28cdbdf

Commits on Dec 6, 2025

compile unigene contigalign program.
lukasmueller
committed
be2ce53

Commits on Dec 11, 2025

remove make statement from entrypoint.
lukasmueller
committed
a322504

Commits on Dec 19, 2025

update to sgn-438.0. Includes a fix for slow experimental design tables on trial detail page; adds a trend line to repetitive measurement graph with linear regression; fixes an issue with genotypin…
lukasmueller
committed
710cf39

Commits on Jan 8, 2026

Finally updates the manual for fieldbook interfacing; fixes the seedlot information on the accession detail page; fixes issues with the motif finder tool.
lukasmueller
committed
60077ff

Commits on Jan 23, 2026

updating to sgn-440.0. Adds a transcriptomics section to the manual; adds support for Synonym Search Tool auth client; fixes aspects of the find genotypes by accession feature and allow filtering b…
lukasmueller
committed
43ca35e

Commits on Jan 26, 2026

add clustalw from apt repo as it is used by CAPS designer.
lukasmueller
committed
c7cf5e8

Commits on Jan 30, 2026

fixes and issue with datasets when names are duplicated; fixes an issue with trial downloads when crosses are used in the trial instead of accessions; fixes an issue with coordinates of plants with…
lukasmueller
committed
edaf52f

Commits on Feb 6, 2026

fixes an issue with the db patch for the new treatment backend; adds new Perl modules to local-lib for the upcoming SSO feature; tweaks dbpatch system for improved script integration.
lukasmueller
committed
e593c42

Commits on Feb 8, 2026

add new solgenomics content.
lukasmueller
committed
37e2676

Commits on Feb 9, 2026

Syncs plant per plot with first page in greenhouse trial; fixes an issue with the new treatment backend dbpatch; revises a section about images to the manual; removes the requirement for an organis…
lukasmueller
committed
8377e69

Commits on Feb 16, 2026

Commits on Feb 17, 2026

add libtext-multimarkdown-perl to Dockerfile.
lukasmueller
committed
ee9a364

Commits on Feb 23, 2026

Update sgn to sgn-444.0. Adds a wiki system.
lukasmueller
committed
8726011

Commits on Feb 24, 2026

add package for save evaluation of math expressions.
lukasmueller
committed
7b58337

Commits on Feb 25, 2026

Update to sgn-445.0. Fixes a matview definition for traits to show only trait_ontology type traits in the wizard; adds subplots as a source observation unit type for creating genotyping plates.
lukasmueller
committed
7405c53

Commits on Mar 6, 2026

Commits on Mar 14, 2026

Update to sgn-447.0. Adds support for Single Sign-On Logins (SSO) with Google and other OAuth providers; adds back a link to compose traits page; adds a message to LabelDesigner that labels have to…
lukasmueller
committed
0a6fec3

Commits on Mar 27, 2026

Update to sgn-448.Provide option to store accession list after accession upload permanently; Fix an issue with the wiki home page; add option for plant date info for label designer; retrieve create…
lukasmueller
committed
4363228

Commits on Apr 10, 2026

Bring up to version sgn-449.0. Includes support for intercropping; use of obsoleted stocks in trials; fixes to the trait search so that treatments will not be shown; a cosmetic tweak to the cvterm …
lukasmueller
committed
04b364d

Commits on Apr 15, 2026

update to sgn-450.0. Implements multi-image analysis; fix stuck wizard issues; fixes and issue with the phenotype download based on datasets; adds multi measurement phenotype upload support; fixes …
lukasmueller
committed
0bc68ec

Commits on Apr 16, 2026

Update to sgn-451.0. Fixes an issue with repetitive measurements multi-line download; fixes an issue when adding accessions using lists; sets the default for allow_trait_edits to 1 similar to previ…
lukasmueller
committed
244f6b8

Commits on Apr 27, 2026

Update to sgn-452.0. Fixes an issue with a repetitive measurement download; improve the dialog that adds attributes to trait variables, including preset pull down menus for certain variable attribu…
lukasmueller
committed
9ac5f18

Commits on May 13, 2026

Updating to sgn-453.0. Fixes an issue with a package name in a dbpatch; outputs a pedigree on labeldesigner with only the maternal parent; correctly outputs values of 0; correctly downloads values …

mueller
authored and
mueller
committed
66fc213

Commits on May 18, 2026

fix an issue with exif verification in the image upload (adapt to a change on the fieldbook side); and code cleanups such as replacing evals with try catch blocks; makes autogenerated names tool mo…
lukasmueller
committed
54ab350

Commits on Jun 4, 2026

bring up to sgn-455.0 with changes to npm management.
lukasmueller
committed
e818d11

Commits on Jun 6, 2026

Add installation of recent npm and node versions to Dockerfile.
lukasmueller
committed
a734e8c
update checkout
lukasmueller
committed
6bec45c
move npm version install to after we have a production user.
lukasmueller
committed
040956d

Commits on Jun 10, 2026

updating to version sgn-456.0. Fixes an issue with a brapi call that mixed up trial names and descriptions; handles breeding program links correctly from the folder pages; adds years to the cxgn ti…
lukasmueller
committed
95da289

Commits on Jun 22, 2026

remove npm from apt command.
lukasmueller
committed
94aada7

Commits on Jun 30, 2026

Bring Breedbase up to sgn-457.0. Adds synonym and parent UI to cvterm detail page; adds observationUnitDbId as valid input for phenotype spreadsheet upload; fixes trial description in brapi calls v…
lukasmueller
committed
7a11f45

Commits on Jul 15, 2026

fixes the stock merge function for stocks with large pedigrees by not parsing the entire pedigree, just retrieving the parents; fixes a bug in the stock merge that resulted in duplicate attributes …
lukasmueller
committed
ee5de68

Commits on Jul 23, 2026

Pin opencv-python to v4
dwaring87
committed
1ef79fa

Commits on Jul 24, 2026

Merge pull request #56 from solgenomics/pin_opencv_v4
lukasmueller
authored
b7cb1e8

Commits on Jul 29, 2026

adds support for exporting datasets to figshare. Pins python libraries to version 4 in Dockerfile.
lukasmueller
committed
1363fca

Commits on Jul 31, 2026

Updating to tag sgn-460.0. Fixes and issue with text formats and download in the full grid trial view; adds a date picker for the date input on the tracking record page; allows unicode characters i…
lukasmueller
committed
dd178b0

Commits on Aug 3, 2026

Fixes plot-associated images in trial image section; slightly refactors CXGN::Job object and modify Blast function to use it; improves LabelDesigner speed so that it can be used again for larger tr…
lukasmueller
committed
fa1bab6

Commits on Aug 17, 2026

update to tag sgn-463.0. Fixes an issue with the accession properties download; improves error messaging for missing accessions when swapping accessions in a field layout; upgrades drone python scr…
lukasmueller
committed
9ddf402

Commits on Aug 21, 2026

remove opencv version lockdown.
lukasmueller
committed
6970467

Commits on Aug 25, 2026

Commits on Aug 27, 2026

update to version 5 of opencv
lukasmueller
committed
4f1d90f