From 44bfd82cd626549f70f1ebdf2bda8c675341a42b Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 12 Dec 2023 15:47:52 -0500 Subject: [PATCH 001/103] update to sgn-377.0 with fix of fieldmap display issue. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index d94ab31..5dc670e 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit d94ab31bad8b7cd63ccf6e98aedeec31e609b9d6 +Subproject commit 5dc670ede44e30dfa5f9cb0727085b6c85226b18 From 34192e45e4f05a3a410e32086977d49c72be1f73 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 13 Dec 2023 12:59:16 -0500 Subject: [PATCH 002/103] Fix for broken phenotype overlay on fieldmap; issue with geo fieldmap persists. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 5dc670e..161d9e1 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 5dc670ede44e30dfa5f9cb0727085b6c85226b18 +Subproject commit 161d9e14fc8177f5ac02603aa33868d963ab812e From 7a8929fd88b8a6d6774e68a6068b15a3bb675d96 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 8 Jan 2024 23:32:39 -0500 Subject: [PATCH 003/103] 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 data on trait detail page; other improvements. --- cxgn/R_libs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index 1df4101..96124ba 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit 1df41016dbaa8d9fac5e22c84a8e40e227b007a4 +Subproject commit 96124bac4e702d9c4960354846ece2911c5aec8e diff --git a/cxgn/sgn b/cxgn/sgn index 161d9e1..5b89ae5 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 161d9e14fc8177f5ac02603aa33868d963ab812e +Subproject commit 5b89ae5077da47eb38a634f43b53ec4ce090e06c From 4bd80d86e35c2ea93d9b7eb086b0a6781e2c5314 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 26 Jan 2024 00:19:22 -0500 Subject: [PATCH 004/103] fix locus owner association; add bulk and buk_open cross types; change BTI logo in footer. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 5b89ae5..1d40582 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 5b89ae5077da47eb38a634f43b53ec4ce090e06c +Subproject commit 1d40582fd618710ff7cd64d74ad432384783c022 From 87914ed297d537fe85a62bb9e5e5e072156ed096 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 30 Jan 2024 14:19:50 -0500 Subject: [PATCH 005/103] 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. --- cxgn/cassava | 2 +- cxgn/cassbase | 2 +- cxgn/musabase | 2 +- cxgn/sgn | 2 +- cxgn/sweetpotatobase | 2 +- cxgn/yambase | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cxgn/cassava b/cxgn/cassava index 1d9687d..c1dcdac 160000 --- a/cxgn/cassava +++ b/cxgn/cassava @@ -1 +1 @@ -Subproject commit 1d9687d3f69c84288449743dcf6b9cb7269e9a9a +Subproject commit c1dcdac27a0481ddcb484f60c7d5db6a02ff853b diff --git a/cxgn/cassbase b/cxgn/cassbase index 3583ef1..539c0b1 160000 --- a/cxgn/cassbase +++ b/cxgn/cassbase @@ -1 +1 @@ -Subproject commit 3583ef12be9eaefe55ae0f470578b41b750f8b48 +Subproject commit 539c0b18be07972c90a418d44b18b906e5d607e6 diff --git a/cxgn/musabase b/cxgn/musabase index 6a91a48..a9499b4 160000 --- a/cxgn/musabase +++ b/cxgn/musabase @@ -1 +1 @@ -Subproject commit 6a91a485ed3b6ba8733ad36ba2096fd8935592fe +Subproject commit a9499b4ba39755f313872ebe44caf3ff5ee096f2 diff --git a/cxgn/sgn b/cxgn/sgn index 1d40582..704bdc8 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 1d40582fd618710ff7cd64d74ad432384783c022 +Subproject commit 704bdc82f04262e6df689163665341213c43dfec diff --git a/cxgn/sweetpotatobase b/cxgn/sweetpotatobase index f5e5e24..0d799ec 160000 --- a/cxgn/sweetpotatobase +++ b/cxgn/sweetpotatobase @@ -1 +1 @@ -Subproject commit f5e5e24e3741f8b291fbefc82aa46fce82eb992e +Subproject commit 0d799ec74bc66142dcd87dd7790e344b5e9bcaba diff --git a/cxgn/yambase b/cxgn/yambase index 5e6376d..f9d96e6 160000 --- a/cxgn/yambase +++ b/cxgn/yambase @@ -1 +1 @@ -Subproject commit 5e6376d429bad2741e359940365ddb1b169588ec +Subproject commit f9d96e6fefb09857a9d6a74668e96238bc6a15fe From a3814107d384f3f071585d79e733c47a3e8ebd4f Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 2 Feb 2024 10:30:52 -0500 Subject: [PATCH 006/103] fix entrypoint check that loaded database in spite of there already being one present. --- entrypoint.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/entrypoint.sh b/entrypoint.sh index 92b3b87..76b66b5 100644 --- a/entrypoint.sh +++ b/entrypoint.sh @@ -18,7 +18,7 @@ umask 002 echo "CHECKING IF A DATABASE NEEDS TO BE INSTALLED..."; -if [ $(psql -h ${PGHOST} -U postgres -d postgres -Atc 'select count(distinct table_schema) from information_schema.tables;') == "2" ]; then +if [ $(psql -h ${PGHOST} -U postgres -Atc 'select count(distinct table_schema) from information_schema.tables;') == "2" ]; then echo "INSTALLING DATABASE..."; echo "CREATING web_usr..."; psql -d postgres -c "CREATE USER web_usr PASSWORD 'postgres';" From 166b0848f3c090c27be02856817996cffbe56c78 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 8 Feb 2024 19:47:08 -0500 Subject: [PATCH 007/103] Updating to sgn-381.0. In trial create workflow, trial type is now listed in alphabetical order, and planting date has been made optional again. The multiple trial fieldmap view now overlays phenotypic data correctly on all the trials. Fixed population requirement for stock loading script. BrAPI observations query fixed to not use materialized views. In the Cview repo, includes fixes for Cview IL map. --- cxgn/Cview | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/Cview b/cxgn/Cview index d1ade92..478fd8e 160000 --- a/cxgn/Cview +++ b/cxgn/Cview @@ -1 +1 @@ -Subproject commit d1ade9233cc390c5f22957a9f2e0378c3767201a +Subproject commit 478fd8e003d68ca8ef3b447543f45ec11727984e diff --git a/cxgn/sgn b/cxgn/sgn index 704bdc8..9f67885 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 704bdc82f04262e6df689163665341213c43dfec +Subproject commit 9f67885be0acae9a6d7b2906b25290cf146ccba9 From 0cdba5c671b836fa6be2dc05df43f3068ab2d82f Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 8 Feb 2024 21:07:31 -0500 Subject: [PATCH 008/103] if breedbase database does not exist, create it, otherwise do not. --- entrypoint.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/entrypoint.sh b/entrypoint.sh index 76b66b5..a9e615f 100644 --- a/entrypoint.sh +++ b/entrypoint.sh @@ -18,7 +18,7 @@ umask 002 echo "CHECKING IF A DATABASE NEEDS TO BE INSTALLED..."; -if [ $(psql -h ${PGHOST} -U postgres -Atc 'select count(distinct table_schema) from information_schema.tables;') == "2" ]; then +if [[ $(psql -lqt -h ${PGHOST} -U ${PGUSER} | cut -d '|' -f1 | sed 's/^[[:blank:]]*//;s/[[:blank:]]*$//;' | grep -w breedbase ) = '' ]]; then echo "INSTALLING DATABASE..."; echo "CREATING web_usr..."; psql -d postgres -c "CREATE USER web_usr PASSWORD 'postgres';" From 6e43febb4fd0573c4122f61dd667d24776571388 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 8 Feb 2024 22:11:48 -0500 Subject: [PATCH 009/103] update to release sgn-381.1. Includes fixes to the pedigree section in the accession detail page. Fixes issue with entrypoint.sh and how database are loaded automatically. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 9f67885..856907d 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 9f67885be0acae9a6d7b2906b25290cf146ccba9 +Subproject commit 856907d9bb564f74d6e6c35ea2f6209553d70674 From 9de7a035c57a1ccd9725120c0087d7e160fdc4be Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 15 Feb 2024 16:19:08 -0500 Subject: [PATCH 010/103] Update to sgn-381.2. Add brapi logo. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 856907d..6519557 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 856907d9bb564f74d6e6c35ea2f6209553d70674 +Subproject commit 6519557723f8944d7ca8a98de7f1fcdea3de85df From 618d1b577eace9866e56ae1ceaee3e150ffab5f7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 27 Feb 2024 10:17:23 -0500 Subject: [PATCH 011/103] change Bio Chado Schema to sgn copy (from GMOD). --- cxgn/Bio-Chado-Schema | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema index c86838f..ac0ef31 160000 --- a/cxgn/Bio-Chado-Schema +++ b/cxgn/Bio-Chado-Schema @@ -1 +1 @@ -Subproject commit c86838f9fdcf74c932bd6d3ac57b6fc5ce086d47 +Subproject commit ac0ef31606a7c82a786d9c88c86bd249923c8393 diff --git a/cxgn/sgn b/cxgn/sgn index 6519557..86aa110 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6519557723f8944d7ca8a98de7f1fcdea3de85df +Subproject commit 86aa1104139bd3966a7c7a5e19ef5aa58cc87607 From af64304ed720ef104141ec4487e10fa773f0e26e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 8 Mar 2024 15:57:07 -0500 Subject: [PATCH 012/103] bringing system up to date with sgn-382.0 and bio chado schema from solgenomics repo (not GMOD). --- cxgn/Bio-Chado-Schema | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema index ac0ef31..a268fe0 160000 --- a/cxgn/Bio-Chado-Schema +++ b/cxgn/Bio-Chado-Schema @@ -1 +1 @@ -Subproject commit ac0ef31606a7c82a786d9c88c86bd249923c8393 +Subproject commit a268fe08f356084389aa921b3be23443ef5b3467 diff --git a/cxgn/sgn b/cxgn/sgn index 86aa110..0dfa595 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 86aa1104139bd3966a7c7a5e19ef5aa58cc87607 +Subproject commit 0dfa5955ec3e17397718683f9b9454e30f76698a From 45a8f78945e39899881c41ad3c46e5ca8c676694 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 9 Mar 2024 18:19:22 -0500 Subject: [PATCH 013/103] 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 downloads accessions for seedlot names. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 0dfa595..6610c45 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 0dfa5955ec3e17397718683f9b9454e30f76698a +Subproject commit 6610c45d1ef4137e8e87aa2c40003d5b9d6ab94c From 95755c37bb4741dd00df594dfdcd56abb6c5cf00 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 14 Mar 2024 16:15:14 -0400 Subject: [PATCH 014/103] Fix Geofieldmap tool; Improve merge stock script; Create seedlots from trial using plot names; add new R libraries. --- cxgn/R_libs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index 96124ba..bad50ce 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit 96124bac4e702d9c4960354846ece2911c5aec8e +Subproject commit bad50ce001c2c1feafdb9ca198fcf6dc7c1c568f diff --git a/cxgn/sgn b/cxgn/sgn index 6610c45..3308724 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6610c45d1ef4137e8e87aa2c40003d5b9d6ab94c +Subproject commit 330872458b44691a473cf954726dbfa186d15f01 From 3e46b98e59d19f4b88efaa47d0f05a2af71106b9 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 21 Mar 2024 22:46:23 -0400 Subject: [PATCH 015/103] 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 without protocol; fix download from project detail page; other improvements. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 3308724..3352df8 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 330872458b44691a473cf954726dbfa186d15f01 +Subproject commit 3352df84e31aafd7290c89a9bd8a0078fd3528b9 From e3c0f745a24eaed786e274f569ef1ae90a26330c Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 29 Mar 2024 23:12:18 -0400 Subject: [PATCH 016/103] Add transformation and tracking experiment features; add new cross_type dihaploid_induction; fix blast db related script; allow synonyms in accession upload to be replaced or appended; add new rtb logo; allow download of cached vcf files that were uploaded; other improvements. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 3352df8..1744d12 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 3352df84e31aafd7290c89a9bd8a0078fd3528b9 +Subproject commit 1744d12176bf6908cb929a31bb5d962264e4415b From f3df869247cd4671b848c669af6c8ec1e38293c6 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 29 Mar 2024 23:39:02 -0400 Subject: [PATCH 017/103] change version of Selenium to version 1.49. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e7f7111..16dc73e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -92,7 +92,7 @@ RUN apt-get install libmoosex-runnable-perl -y RUN apt-get install libgdbm6 libgdm-dev -y RUN apt-get install nodejs -y -RUN cpanm Selenium::Remote::Driver@1.44 +RUN cpanm Selenium::Remote::Driver@1.49 #INSTALL OPENCV IMAGING LIBRARY From c2a222002762a0edcfa1f14b2b4b7addc0cc4fc8 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 17 Apr 2024 09:06:35 -0400 Subject: [PATCH 018/103] 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. --- cxgn/cassava | 2 +- cxgn/sgn | 2 +- cxgn/sweetpotatobase | 2 +- cxgn/yambase | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cxgn/cassava b/cxgn/cassava index c1dcdac..bbf7328 160000 --- a/cxgn/cassava +++ b/cxgn/cassava @@ -1 +1 @@ -Subproject commit c1dcdac27a0481ddcb484f60c7d5db6a02ff853b +Subproject commit bbf73281b57a04a231e0c5d47521fbe09b683320 diff --git a/cxgn/sgn b/cxgn/sgn index 1744d12..454f822 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 1744d12176bf6908cb929a31bb5d962264e4415b +Subproject commit 454f8228d1a42d913eef56549591bf42a972d89c diff --git a/cxgn/sweetpotatobase b/cxgn/sweetpotatobase index 0d799ec..1e1d1eb 160000 --- a/cxgn/sweetpotatobase +++ b/cxgn/sweetpotatobase @@ -1 +1 @@ -Subproject commit 0d799ec74bc66142dcd87dd7790e344b5e9bcaba +Subproject commit 1e1d1eb8898988471ebe4230262c46b10df6e09c diff --git a/cxgn/yambase b/cxgn/yambase index f9d96e6..6b5313d 160000 --- a/cxgn/yambase +++ b/cxgn/yambase @@ -1 +1 @@ -Subproject commit f9d96e6fefb09857a9d6a74668e96238bc6a15fe +Subproject commit 6b5313d0bd12a37f4cf5642e465cb544dd2b9bc5 From b1037fddb1c099ee95ad36b8647c5c62fc3feb87 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 26 Apr 2024 09:15:27 -0400 Subject: [PATCH 019/103] 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 .obo files; fix issue with raw data phenotype section; plot order download: include correct name (harvest or planting order); create a file-based annotation search page. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 454f822..5f297b7 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 454f8228d1a42d913eef56549591bf42a972d89c +Subproject commit 5f297b724eb8b8ff6475670e268d2340057cdbb6 From b1f432932e0e49790b96190fcced8f5f21fa7169 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 11 May 2024 11:48:46 -0400 Subject: [PATCH 020/103] 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 only mode; implement marker validation for markersets; update certain brapi calls to 2.1 version; add new stability tool; add breeding_program type for breeding program folder. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 5f297b7..2f9f0fb 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 5f297b724eb8b8ff6475670e268d2340057cdbb6 +Subproject commit 2f9f0fbff645f787cc02b2629a7d618a79fb24b4 From 1853c491ea70ae524aaccfde7e59ef9cb91754bf Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 15 May 2024 23:21:38 -0400 Subject: [PATCH 021/103] add genefamily table. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 2f9f0fb..669a8ef 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 2f9f0fbff645f787cc02b2629a7d618a79fb24b4 +Subproject commit 669a8ef5f14de7b6ac097bd6be9c6a2741d44ba3 From 8c5c837a643984caa95ae6fa36d7e99aea49d820 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 16 May 2024 22:28:01 -0400 Subject: [PATCH 022/103] upgrade R to version 4.4 --- cxgn/R_libs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index bad50ce..608ac33 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit bad50ce001c2c1feafdb9ca198fcf6dc7c1c568f +Subproject commit 608ac331495d40f1c282d6e8a2ba1babfdb740ab From 29a2063881dcc126f97eddc609bcb67995bbc409 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 22 May 2024 22:23:26 -0400 Subject: [PATCH 023/103] Fix ANOVA analysis; fix issue with Fieldmap viewer; GCPC tool fixes. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 669a8ef..cb67980 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 669a8ef5f14de7b6ac097bd6be9c6a2741d44ba3 +Subproject commit cb679804d517aed0dd3b9a0a7194f6c9109e59dd From 314b9a4ef4e87d1e8485237038177ab9b3905d58 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 3 Jun 2024 21:51:39 -0400 Subject: [PATCH 024/103] 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 function on accession detail page; limit stock property autocomplete to 100 in stock search to prevent page crashes in large databases; flexible headers and entry numbers in single and multi trial upload; tweak GPCP tool for non-dioecious plants; run test on ubuntu-latest. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index cb67980..2758acd 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit cb679804d517aed0dd3b9a0a7194f6c9109e59dd +Subproject commit 2758acd6de2f3151eb00cd653b11229994a99309 From 7b19687036868219fdabcce1f8c90524b1098255 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 17 Jun 2024 21:33:53 -0400 Subject: [PATCH 025/103] 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 insensitive; trial upload: make the plot_name optional - will be added automatically; implement an improved dataset selection tool based on a datatable for major analysis tools; limit autocomplete for stock search to prevent page crashes in large databases. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 2758acd..b296c59 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 2758acd6de2f3151eb00cd653b11229994a99309 +Subproject commit b296c5982234a4a9bf856d0e42e028395095d917 From b3c3def8154963a3aaf1052066e30b5bd90101e4 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 8 Jul 2024 22:57:13 -0400 Subject: [PATCH 026/103] 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 querying for geno protocols; add doubly resolvable row - column design; fix field layout view when using cross unique ids or family names in trial; update _BrAPIv2_phenotyping.t timestamps; fix csv file extension for kasp data download; other improvements. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index b296c59..8bb9ffe 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit b296c5982234a4a9bf856d0e42e028395095d917 +Subproject commit 8bb9ffe4b8a109863296bb83863c6c2c599bcbc2 From f7dfdbce3dc604c094224aa5cf37152edd231d89 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 12 Jul 2024 13:58:25 -0400 Subject: [PATCH 027/103] update to tag sgn-393.0. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 8bb9ffe..a1fe514 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 8bb9ffe4b8a109863296bb83863c6c2c599bcbc2 +Subproject commit a1fe514d1f21ee1f5b425747cc523c75477e8aff From 5b1ccd0af560978d53289bbc1ab1603b29f4ca16 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 12 Jul 2024 21:35:08 -0400 Subject: [PATCH 028/103] fix an issue with the generic file parser module. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index a1fe514..5e02445 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit a1fe514d1f21ee1f5b425747cc523c75477e8aff +Subproject commit 5e02445dd85a02363d5f1e429a736956b27c0907 From 0066a97c6eda1c93ad23f9f5ba92fe495d304d9e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sun, 4 Aug 2024 13:42:44 -0400 Subject: [PATCH 029/103] fix PERL5LIB path to use locally managed Bio-Chado-Schema repo. --- starmachine.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/starmachine.conf b/starmachine.conf index e8db461..933c018 100644 --- a/starmachine.conf +++ b/starmachine.conf @@ -2,7 +2,7 @@ root_dir = /home/production/cxgn/starmachine env[CATALYST_CONFIG] = /etc/starmachine -env[PERL5LIB] = /home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin +env[PERL5LIB] = /home/production/cxgn/Bio-Chado-Schema/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin sgn[env][CATALYST_CONFIG] = /home/production/cxgn/sgn/sgn.conf sgn[app_dir] = /home/production/cxgn/sgn sgn[psgi_file] = bin/sgn.psgi From d68283bbf1cdd599d515f92a59d739a84fcf0348 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sun, 4 Aug 2024 13:47:25 -0400 Subject: [PATCH 030/103] update to sgn-394.0. Improves genotype metadata display; move seedlot upload to new upload backend; fix dataset detail page functions; move pedigree upload to new upload backend; change brapi observation_table call to the native backend from matview; add option for email notification for async accession and multi trial upload; add improved dataset interface to solGS; other code cleaning and improvements. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 5e02445..a5307b0 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 5e02445dd85a02363d5f1e429a736956b27c0907 +Subproject commit a5307b062103f2410a77cacd0eb190793412a3a3 From 15f49fa438e1ae6512b8ce7c540141b85112ee3a Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 9 Aug 2024 15:17:57 -0400 Subject: [PATCH 031/103] bring sgn to sgn-395.0. Includes longer timeout for label designer; add dataset functions. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index a5307b0..bd5a2d4 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit a5307b062103f2410a77cacd0eb190793412a3a3 +Subproject commit bd5a2d4a028bd14dcbd2c5900fd17ff1cd22ba65 From eee3541142e5b3dfd0df1373a568b780ceb64073 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 14 Aug 2024 17:54:53 -0400 Subject: [PATCH 032/103] remove the synonym option from the label designer as it causes issues with the label generation process. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index bd5a2d4..af91946 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit bd5a2d4a028bd14dcbd2c5900fd17ff1cd22ba65 +Subproject commit af919465812ceb7dddf56618a742557561fdae9e From 4562c9a737ccc0b67d94609d7dcda1e701f46a78 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 10 Sep 2024 16:40:40 -0400 Subject: [PATCH 033/103] 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; improve dataset and list display speed. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index af91946..dd3a55d 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit af919465812ceb7dddf56618a742557561fdae9e +Subproject commit dd3a55d24e7839ce625c1337070d328c4a6794b5 From 8507bc5044f49eb945aac23ef63a91aa82c3c804 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 20 Sep 2024 14:36:37 -0400 Subject: [PATCH 034/103] 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 interactive; tweak image loading script. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index dd3a55d..a3002c4 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit dd3a55d24e7839ce625c1337070d328c4a6794b5 +Subproject commit a3002c4bba80fca98db8cb73deefc14620e2f50d From 0caa03835354592f78e0e52c28f84fc3619ba3e7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 1 Oct 2024 22:09:46 -0400 Subject: [PATCH 035/103] 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 result url; fix an issue with the btract parsing from Sendusu; add super-linter to check the code upon PR generation; fix an issue with stock merging when the same dbxrefs are present for both stocks; fix solGS job submisson info feedback; interactive graphs for more breeding tools. --- cxgn/local-lib | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/local-lib b/cxgn/local-lib index 540344a..16a3711 160000 --- a/cxgn/local-lib +++ b/cxgn/local-lib @@ -1 +1 @@ -Subproject commit 540344aa887d1048d497f9aa6c966916a9ffe3ad +Subproject commit 16a3711e9e900ef5c45fac325ead892ba2638148 diff --git a/cxgn/sgn b/cxgn/sgn index a3002c4..be9c4ba 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit a3002c4bba80fca98db8cb73deefc14620e2f50d +Subproject commit be9c4ba79a8cecc515e83c0e3610d1c6682b1239 From 873c5e81502ed45e9652e5d00de62ddef97d872c Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 5 Oct 2024 04:43:24 -0400 Subject: [PATCH 036/103] add an improved empty_fixture (for breedbase_site). --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index be9c4ba..689ec71 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit be9c4ba79a8cecc515e83c0e3610d1c6682b1239 +Subproject commit 689ec712cb148d280f7a10e5dba7b3efb4c2e079 From 3db66a2bf31ddc7a3576baf5980c4d5c93e623b9 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 24 Oct 2024 17:58:25 -0400 Subject: [PATCH 037/103] 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 hierarchical clustering plot; allow upload of description field for stocks in UI and in the back end script; tweak load_people.pl script; tweak linter; add protocol checks for vcf upload using scripts; add extra checks for numeric values in weight and count fields for seedlotsshow error message if no trait list is selected when creating a phenotyping file; fix filter by count or weight in seedlot search; add capability to delete seedlot transactions. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 689ec71..a463399 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 689ec712cb148d280f7a10e5dba7b3efb4c2e079 +Subproject commit a463399e1083ae62e6f9b25f9324e18a400b25ae From 56263416f18eb72e57d248ba826479a52d763c15 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 28 Oct 2024 14:33:46 -0400 Subject: [PATCH 038/103] Fix an issue with the pedigree upload; fix a javascript issue with the audit tables. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index a463399..9307e5f 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit a463399e1083ae62e6f9b25f9324e18a400b25ae +Subproject commit 9307e5f16b733c18704fbfa6a29ee98374f37d53 From 687ff1542a92369b8a94b34fac2d29542cec36d0 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 5 Nov 2024 21:57:12 -0500 Subject: [PATCH 039/103] make sure /etc/crontab is owned by root. --- entrypoint.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/entrypoint.sh b/entrypoint.sh index a9e615f..29b385b 100644 --- a/entrypoint.sh +++ b/entrypoint.sh @@ -8,6 +8,8 @@ chown 106 /etc/munge/munge.key /etc/init.d/slurmd start #/etc/init.d/postgres start +chown root /etc/crontab # in case it was mounted from local dir + if [ "${MODE}" = 'TESTING' ]; then exec perl t/test_fixture.pl --carpalways -v "${@}" fi From 73d6af3754e1fd9a8a976bcc47dfb579a6150ff7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 5 Nov 2024 22:02:37 -0500 Subject: [PATCH 040/103] update to sgn-402.0 tag. Fix BrAPI logins; fix a typo in Synonyms on the cvterm detail page; add script to rename locations in bulk; Enable select all seedlots in available seedlots dialog; add strip plot trial design as an upload option. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 9307e5f..0c3c18c 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 9307e5f16b733c18704fbfa6a29ee98374f37d53 +Subproject commit 0c3c18ccbbff98b147104d6e51deaa559862f589 From dbd90033bfd4c54a12d0fe0566e3b7ea15d3620c Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 20 Nov 2024 09:34:50 -0500 Subject: [PATCH 041/103] 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 seedlots; fix an issue with missing genotype data warning; fix issue with duplicate plots in brapi call related to management factors. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 0c3c18c..e7f8435 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 0c3c18ccbbff98b147104d6e51deaa559862f589 +Subproject commit e7f843531b6e60bcfabe0efadbb70a2a141505bd From 6b80ab35fa3e910548127a21a6f001110f05832d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 7 Dec 2024 15:38:11 -0500 Subject: [PATCH 042/103] Fix VCF loading issue when there is no header in the vcf file; enable creation of empty seedlots and fix issues when space instead of 0 is provided; fix seedlot trial filter; move single trial upload to generic upload module; tweak load_people.pl script; fix some trial deletion edge cases. --- cxgn/Bio-Chado-Schema | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema index a268fe0..a2d122e 160000 --- a/cxgn/Bio-Chado-Schema +++ b/cxgn/Bio-Chado-Schema @@ -1 +1 @@ -Subproject commit a268fe08f356084389aa921b3be23443ef5b3467 +Subproject commit a2d122e567c44c831cb1c95ebf06b82323e838a2 diff --git a/cxgn/sgn b/cxgn/sgn index e7f8435..51b6389 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit e7f843531b6e60bcfabe0efadbb70a2a141505bd +Subproject commit 51b6389a9cb431e905ab28b538d5d45546dea951 From 2e971fe0252df06a18f9d655974cf78fdacc8a75 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 7 Dec 2024 15:44:16 -0500 Subject: [PATCH 043/103] add merged master for bio chado schema. --- cxgn/Bio-Chado-Schema | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema index a2d122e..d9ef0f3 160000 --- a/cxgn/Bio-Chado-Schema +++ b/cxgn/Bio-Chado-Schema @@ -1 +1 @@ -Subproject commit a2d122e567c44c831cb1c95ebf06b82323e838a2 +Subproject commit d9ef0f376b7c94b6628c5ca981cbe18a84f08754 From 501b05af4b122d8fccfad05de8e771f6d808541d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 9 Dec 2024 10:34:35 -0500 Subject: [PATCH 044/103] change the git submodule for bio chado schema. --- .gitmodules | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.gitmodules b/.gitmodules index 257619f..6064255 100644 --- a/.gitmodules +++ b/.gitmodules @@ -99,13 +99,10 @@ url = https://github.com/GMOD/chado_tools [submodule "cxgn/cxgn/Bio-Chado-Schema"] path = cxgn/Bio-Chado-Schema - url = https://github.com/GMOD/Bio-Chado-Schema + url = https://github.com/solgenomics/bio-chado-schema [submodule "cxgn/chado_tools"] path = cxgn/chado_tools url = https://github.com/GMOD/chado_tools -[submodule "cxgn/Bio-Chado-Schema"] - path = cxgn/Bio-Chado-Schema - url = https://github.com/GMOD/Bio-Chado-Schema [submodule "cxgn/QuantGenResources"] path = cxgn/QuantGenResources url = https://github.com/solgenomics/QuantGenResources.git @@ -117,3 +114,6 @@ url = https://github.com/solgenomics/sgn-biotools.git +[submodule "cxgn/Bio-Chado-Schema"] + path = cxgn/Bio-Chado-Schema + url = git@github.com:solgenomics/bio-chado-schema From 7626a0ed8a80e6afa7ef1b38d74fb6632ec2569b Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 9 Jan 2025 22:54:54 -0500 Subject: [PATCH 045/103] 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 well as list UI improvements such as filter by list type and hide auto created lists by default; a new upload for bulk trial metadata such as planting data and harvest date for many trials from an Excel file; allow counter and boolean trait formats for Fieldbook compatibility; Fix a bug in the analysis overview display; Allow copy of all the search results in accession search by enabling all results to be shown without pagination; Allow a comment to be added to the obsolete function for accessions and transformants; add an image of the accession to the accession detail page header; updated documentation and other bug fixes. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 51b6389..8518f7a 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 51b6389a9cb431e905ab28b538d5d45546dea951 +Subproject commit 8518f7a2fcf3a36676d76e55810447bf9a0227a0 From 3f6e14ba40ddbd870c1c0f7046d7b6926f333ca3 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 25 Jan 2025 09:48:22 -0500 Subject: [PATCH 046/103] Add phenotype QC module; Ability to batch update trial metadata; List manager improvements; improve tracking workflows. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 8518f7a..f59ba6e 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 8518f7a2fcf3a36676d76e55810447bf9a0227a0 +Subproject commit f59ba6ed7443c53a358f1c9f25089c4ea7eb8a24 From 1bbef9f27eb93ed1ce19cf3b56ebcec75b1d0e2d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sun, 2 Feb 2025 18:31:00 -0500 Subject: [PATCH 047/103] add more accessors for create_date for time-based queries. --- cxgn/Bio-Chado-Schema | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema index d9ef0f3..b9514e5 160000 --- a/cxgn/Bio-Chado-Schema +++ b/cxgn/Bio-Chado-Schema @@ -1 +1 @@ -Subproject commit d9ef0f376b7c94b6628c5ca981cbe18a84f08754 +Subproject commit b9514e572ae9bef225856521b3949eeb578fa91b From 034d89d108590d4de0bb20008d798f911938d9b7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 6 Feb 2025 20:51:07 -0500 Subject: [PATCH 048/103] 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; fix related stock section on vector detail page; clearly define relationship between observation unit and germplasm for phenotyping download. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index f59ba6e..597e8d8 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit f59ba6ed7443c53a358f1c9f25089c4ea7eb8a24 +Subproject commit 597e8d816b9eca0d481780c7e4ae1f1cbe22fbc0 From c58380a4ea7f4466fb29839ea250dddbd66c094d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 10 Feb 2025 16:31:06 -0500 Subject: [PATCH 049/103] 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 users; allow subplot or plant as source when uploading seedlots. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 597e8d8..390e8c9 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 597e8d816b9eca0d481780c7e4ae1f1cbe22fbc0 +Subproject commit 390e8c9531dc343bab20f6a07f2c5922e85fa501 From 0a6c7444547d2628b9910e0d21ff07c353d82358 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 11 Feb 2025 16:03:41 -0500 Subject: [PATCH 050/103] update to sgn-410.0. Fix an issue with a missing default configuration parameter that caused some tools to crash. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 390e8c9..9438e32 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 390e8c9531dc343bab20f6a07f2c5922e85fa501 +Subproject commit 9438e32f53ab6c737b27f532a106d641b7b3f63b From ef68b80bc31fe922f0f10d5e7041af5de394bd5d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 19 Feb 2025 17:18:29 -0500 Subject: [PATCH 051/103] 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 a formatting issue of the entry numbers downloaded file; fix storage of phenotypic values of 0; fix deletion of phenotypic values under certain conditions. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 9438e32..71506b8 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 9438e32f53ab6c737b27f532a106d641b7b3f63b +Subproject commit 71506b80ac7e77a576a41a2ccf94435cffc8b2f1 From 9b3856e10f57071a8ef6ec48ce16dddc31fc6ca3 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sun, 23 Feb 2025 20:58:49 -0500 Subject: [PATCH 052/103] Update to sgn-412.0. Includes support for tissue_samples in wizard; improvements to the file parser; fixes an issue with the analysis section on the accession detail page and a stray popup. --- cxgn/cxgn-corelibs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/cxgn-corelibs b/cxgn/cxgn-corelibs index ab18307..fa93619 160000 --- a/cxgn/cxgn-corelibs +++ b/cxgn/cxgn-corelibs @@ -1 +1 @@ -Subproject commit ab1830753dfb1f577028b2103c7e432d385112b1 +Subproject commit fa93619d8c0e2eeb38f7826e041a68fb1b275974 diff --git a/cxgn/sgn b/cxgn/sgn index 71506b8..c3440d5 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 71506b80ac7e77a576a41a2ccf94435cffc8b2f1 +Subproject commit c3440d500f459f5c391eed2c2e6f0d2500a48d72 From 05528e49b14055b3806eefbf249f704fbc06a581 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 24 Feb 2025 10:18:42 -0500 Subject: [PATCH 053/103] remove Bio::Chado::Schema from local-lib, need to use Bio::Chado::Schema git repo. --- cxgn/local-lib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/local-lib b/cxgn/local-lib index 16a3711..0f68839 160000 --- a/cxgn/local-lib +++ b/cxgn/local-lib @@ -1 +1 @@ -Subproject commit 16a3711e9e900ef5c45fac325ead892ba2638148 +Subproject commit 0f6883914b11698eedca510274271d37ee2c442a From 19a516385fdaadab90dd1da919dd248a4c470f06 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 3 Mar 2025 13:35:54 -0500 Subject: [PATCH 054/103] move cxgn/Bio-Chado-Schema to cxgn/bio-chado-schema --- .gitmodules | 2 +- cxgn/{Bio-Chado-Schema => bio-chado-schema} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename cxgn/{Bio-Chado-Schema => bio-chado-schema} (100%) diff --git a/.gitmodules b/.gitmodules index 6064255..53ffdc9 100644 --- a/.gitmodules +++ b/.gitmodules @@ -115,5 +115,5 @@ [submodule "cxgn/Bio-Chado-Schema"] - path = cxgn/Bio-Chado-Schema + path = cxgn/bio-chado-schema url = git@github.com:solgenomics/bio-chado-schema diff --git a/cxgn/Bio-Chado-Schema b/cxgn/bio-chado-schema similarity index 100% rename from cxgn/Bio-Chado-Schema rename to cxgn/bio-chado-schema From 5501fae3017a65c6f03ebd77abdeea674d32655e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 3 Mar 2025 13:39:07 -0500 Subject: [PATCH 055/103] Update to sgn-413.0. Includes a fix for pop menus that only had XLS downloads instead of XLSX; tweak html in personalized homepage; fix decoding of latin character sets into UTF-8. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index c3440d5..5d075b7 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit c3440d500f459f5c391eed2c2e6f0d2500a48d72 +Subproject commit 5d075b7db2d8e390a1a60d645fc9fd238f1e6620 From df923c8f8b53584b71481619bcceaae3a5187ac5 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 3 Mar 2025 13:50:38 -0500 Subject: [PATCH 056/103] fix Perl library paths for new bio-chado-schema spelling (case). --- Dockerfile | 2 +- starmachine.conf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 16dc73e..3baf805 100644 --- a/Dockerfile +++ b/Dockerfile @@ -134,7 +134,7 @@ RUN adduser --disabled-password --gecos "" -u 1250 production && chown -R produc WORKDIR /home/production/cxgn/sgn -ENV PERL5LIB=/home/production/cxgn/Bio-Chado-Schema/lib:/home/production/cxgn/local-lib/:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/chado_tools/chado/lib:. +ENV PERL5LIB=/home/production/cxgn/bio-chado-schema/lib:/home/production/cxgn/local-lib/:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/chado_tools/chado/lib:. ENV HOME=/home/production ENV PGPASSFILE=/home/production/.pgpass diff --git a/starmachine.conf b/starmachine.conf index 933c018..c598505 100644 --- a/starmachine.conf +++ b/starmachine.conf @@ -2,7 +2,7 @@ root_dir = /home/production/cxgn/starmachine env[CATALYST_CONFIG] = /etc/starmachine -env[PERL5LIB] = /home/production/cxgn/Bio-Chado-Schema/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin +env[PERL5LIB] = /home/production/cxgn/bio-chado-schema/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin sgn[env][CATALYST_CONFIG] = /home/production/cxgn/sgn/sgn.conf sgn[app_dir] = /home/production/cxgn/sgn sgn[psgi_file] = bin/sgn.psgi From d3ce5291b799a64a684ad1793406ac5c0b739ba0 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 14 Mar 2025 19:40:48 -0400 Subject: [PATCH 057/103] 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 outliers; fix an issue with the NIRS code that could generate an out of memory condition; update jquery library (minor version) to address some issues in the wizard. --- cxgn/cassava | 2 +- cxgn/cxgn-corelibs | 2 +- cxgn/musabase | 2 +- cxgn/sgn | 2 +- cxgn/solgenomics | 2 +- cxgn/sweetpotatobase | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cxgn/cassava b/cxgn/cassava index bbf7328..55e5ca6 160000 --- a/cxgn/cassava +++ b/cxgn/cassava @@ -1 +1 @@ -Subproject commit bbf73281b57a04a231e0c5d47521fbe09b683320 +Subproject commit 55e5ca68ed6d236d2494d7d445dc95982f2c7b62 diff --git a/cxgn/cxgn-corelibs b/cxgn/cxgn-corelibs index fa93619..a8526aa 160000 --- a/cxgn/cxgn-corelibs +++ b/cxgn/cxgn-corelibs @@ -1 +1 @@ -Subproject commit fa93619d8c0e2eeb38f7826e041a68fb1b275974 +Subproject commit a8526aabb1140ecb887f22ea75575222e7d83853 diff --git a/cxgn/musabase b/cxgn/musabase index a9499b4..cdbca93 160000 --- a/cxgn/musabase +++ b/cxgn/musabase @@ -1 +1 @@ -Subproject commit a9499b4ba39755f313872ebe44caf3ff5ee096f2 +Subproject commit cdbca9332d2da74c2764aeb32c3ae3b33cad8421 diff --git a/cxgn/sgn b/cxgn/sgn index 5d075b7..135b300 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 5d075b7db2d8e390a1a60d645fc9fd238f1e6620 +Subproject commit 135b300a7fa048e0d7a8928b7e00a06e1134240e diff --git a/cxgn/solgenomics b/cxgn/solgenomics index 30e674e..387b208 160000 --- a/cxgn/solgenomics +++ b/cxgn/solgenomics @@ -1 +1 @@ -Subproject commit 30e674e052a5c61bce16fb83517c2904a96c5be6 +Subproject commit 387b2088472e1f96f1f119625ab03a2c22a98bfd diff --git a/cxgn/sweetpotatobase b/cxgn/sweetpotatobase index 1e1d1eb..0d56f92 160000 --- a/cxgn/sweetpotatobase +++ b/cxgn/sweetpotatobase @@ -1 +1 @@ -Subproject commit 1e1d1eb8898988471ebe4230262c46b10df6e09c +Subproject commit 0d56f9298500eb24ab0a9bbb8d9c060a40321405 From 6533484f82e5eefc2499a58e7f81bc552226cf75 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 24 Mar 2025 16:20:11 -0400 Subject: [PATCH 058/103] tweak accession upload to prevent duplicate names across different stock types; implement storage for pca results; detect failed slurm jobs and display accordingly. --- cxgn/cxgn-corelibs | 2 +- cxgn/sgn | 2 +- docker-compose.yml | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/cxgn/cxgn-corelibs b/cxgn/cxgn-corelibs index a8526aa..556f59e 160000 --- a/cxgn/cxgn-corelibs +++ b/cxgn/cxgn-corelibs @@ -1 +1 @@ -Subproject commit a8526aabb1140ecb887f22ea75575222e7d83853 +Subproject commit 556f59e0dd04fbc62f2b1208a9ab9a346a127a62 diff --git a/cxgn/sgn b/cxgn/sgn index 135b300..6b7fa62 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 135b300a7fa048e0d7a8928b7e00a06e1134240e +Subproject commit 6b7fa62baf66eab9804c8f95dbe4ab5222504482 diff --git a/docker-compose.yml b/docker-compose.yml index 8cfb5ff..3802c97 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -4,7 +4,6 @@ services: - webdata:/home/production/volume ports: - 8080:8080 - - 25:25 image: breedbase/breedbase:latest depends_on: - breedbase_db From 74fc36f003d28e0f46bc08ba7e65efa263afe108 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 24 Mar 2025 18:51:29 -0400 Subject: [PATCH 059/103] add image section to trial detail page. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 6b7fa62..e7d5209 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6b7fa62baf66eab9804c8f95dbe4ab5222504482 +Subproject commit e7d5209775590b33bef7ef1777321a5a142c1091 From 56814c7fd28e440b7932d9494a2ea73764610903 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 3 Apr 2025 17:59:09 -0400 Subject: [PATCH 060/103] 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 specific; fix an issue with a BrAPI year field; add multi-line filter for wizard; add a script to transform excel-based ontologies to obo files; fix issues with Sankey code library; allow curators to un-obsolete obsoleted stocks; add a separate page for transcriptomics data; fix an issue with the genotype download on the generic download page. --- cxgn/R_libs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index 608ac33..16c3847 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit 608ac331495d40f1c282d6e8a2ba1babfdb740ab +Subproject commit 16c38476ee5ac920898d579157f09e80f9c97545 diff --git a/cxgn/sgn b/cxgn/sgn index e7d5209..2a6dab1 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit e7d5209775590b33bef7ef1777321a5a142c1091 +Subproject commit 2a6dab1e268850453b736dbac51dae67144643c7 From 185e07b3de47cd3389e0aefce700604e4408efc1 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 10 Apr 2025 19:13:59 -0400 Subject: [PATCH 061/103] 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 download on download page; fix a cosmetic issue with the representative accession image. This release is mainly to include additional R_libs so that the new field layout code passes the tests. --- cxgn/R_libs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index 16c3847..150be4c 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit 16c38476ee5ac920898d579157f09e80f9c97545 +Subproject commit 150be4ca0e6f153711a16bea015614c18d3b8a36 diff --git a/cxgn/sgn b/cxgn/sgn index 2a6dab1..219c646 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 2a6dab1e268850453b736dbac51dae67144643c7 +Subproject commit 219c6461b3d3612aca937781184a630261a82850 From f59a3464d7dfc0d2dd2a6f4c8f0589120cfce914 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 14 Apr 2025 22:31:56 -0400 Subject: [PATCH 062/103] 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 CXGN::Trial::FieldMap. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 219c646..e5f6313 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 219c6461b3d3612aca937781184a630261a82850 +Subproject commit e5f63131903d138bc37a397f018f29f1d83974d7 From a3855b5526555bab4d0a94a5d9da2a21a0d8a25e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 18 Apr 2025 15:06:36 -0400 Subject: [PATCH 063/103] add new SpJobs DBIx::Class object --- cxgn/cxgn-corelibs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/cxgn-corelibs b/cxgn/cxgn-corelibs index 556f59e..e58c6d6 160000 --- a/cxgn/cxgn-corelibs +++ b/cxgn/cxgn-corelibs @@ -1 +1 @@ -Subproject commit 556f59e0dd04fbc62f2b1208a9ab9a346a127a62 +Subproject commit e58c6d666b00ecd507983ed08061c618bd469749 From ca913992082926a9d2f32e5e28dc6be9fd0bc112 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 18 Apr 2025 15:09:45 -0400 Subject: [PATCH 064/103] Download obsoleted stocks metadata using a list; improve handling of genotyping data deletion and plates; add a new field layout with diagonal checks. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index e5f6313..ed5b69b 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit e5f63131903d138bc37a397f018f29f1d83974d7 +Subproject commit ed5b69bb8e869a3a2806306728337813a72c954f From a6f571b75a3b72bbc7951bc78dd41f62edf7cbd4 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 5 May 2025 15:54:21 -0400 Subject: [PATCH 065/103] 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 specific; speed up fuzzy search for accession uploads. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index ed5b69b..3111039 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit ed5b69bb8e869a3a2806306728337813a72c954f +Subproject commit 31110397d7c2c55d852301574c49582b3a1250a6 From 15226fcda90ebd052b757297a911d36287eda975 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 15 May 2025 13:34:37 -0400 Subject: [PATCH 066/103] 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 with the display of dbxrefs on stock detail pages; add ability to validate locus-based lists; fix location dropdown in crosses to seedlots tool; tweak analysis upload requirements; calculate and store solgs adjusted means. --- cxgn/R_libs | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index 150be4c..f496b10 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit 150be4ca0e6f153711a16bea015614c18d3b8a36 +Subproject commit f496b1004815a355af7b806f718ef8c927c7b012 diff --git a/cxgn/sgn b/cxgn/sgn index 3111039..20af427 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 31110397d7c2c55d852301574c49582b3a1250a6 +Subproject commit 20af42712726f132217b5d7e52743fd15467870b From b0c5f6521fbadeb003e59bac4cb292d1637dd690 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 27 May 2025 20:45:11 -0400 Subject: [PATCH 067/103] fix an issue with fieldbook upload; tweak CXGN::Fieldbook::TraitProps as used by load_trait_props.pl; add spatial correction and visualization functionality in the trial detail page; fix a typo on the accession usage page. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 20af427..f8f63a4 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 20af42712726f132217b5d7e52743fd15467870b +Subproject commit f8f63a4ad7c66a370bc0535392d5f756452d931e From 30a3c15781652c678b656befcac1735ab8f18b7a Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 28 May 2025 18:03:57 -0400 Subject: [PATCH 068/103] Add environment variables with version info that can be displayed in footer. --- Dockerfile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 3baf805..7f65245 100644 --- a/Dockerfile +++ b/Dockerfile @@ -158,6 +158,10 @@ LABEL org.opencontainers.image.title="breedbase/breedbase" LABEL org.opencontainers.image.description="Breedbase web server" LABEL org.opencontainers.image.documentation="https://solgenomics.github.io/sgn/" +ENV VERSION=$BUILD_VERSION +ENV BUILD_DATE=$CREATED + + # start services when running container... # ENTRYPOINT ["/entrypoint.sh"] From 2a9557229ed697bee5daffb84fd2115018f8be87 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 2 Jun 2025 07:19:17 -0400 Subject: [PATCH 069/103] add libimage-exiftool-perl to Dockerfile. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7f65245..8625546 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ RUN apt-get update --fix-missing -y RUN apt-get install -y aptitude -RUN aptitude install -y npm libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink +RUN aptitude install -y npm libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink # Set the locale correclty to UTF-8 RUN locale-gen en_US.UTF-8 From 89a9e24256cd17a614e4f295b45e22941636693e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 4 Jun 2025 04:05:13 -0400 Subject: [PATCH 070/103] updating to sgn-422.0. Fixes footer version info; display seedlot info on population detail page for each member; unify job tracking info in table on account page; allow crosses for multi-trial upload; add cvprop for chebi traits; create composed traits if cvterm does not exist; store email in all email fields for quick account creation script to avoid issues with password reset; add list validation for locus names; use natural sorting of ontologies and cvs in post composing tool; add search box for trait select on postcomposing page. --- cxgn/R_libs | 2 +- cxgn/local-lib | 2 +- cxgn/sgn | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cxgn/R_libs b/cxgn/R_libs index f496b10..68bba4f 160000 --- a/cxgn/R_libs +++ b/cxgn/R_libs @@ -1 +1 @@ -Subproject commit f496b1004815a355af7b806f718ef8c927c7b012 +Subproject commit 68bba4f303a16951092bc1c1d700d607082405b6 diff --git a/cxgn/local-lib b/cxgn/local-lib index 0f68839..438b265 160000 --- a/cxgn/local-lib +++ b/cxgn/local-lib @@ -1 +1 @@ -Subproject commit 0f6883914b11698eedca510274271d37ee2c442a +Subproject commit 438b265c2cdaa7c1007e186cff0d62cd1f37ef47 diff --git a/cxgn/sgn b/cxgn/sgn index f8f63a4..1b7f011 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit f8f63a4ad7c66a370bc0535392d5f756452d931e +Subproject commit 1b7f0115271578adbef7dadba95a707aa7a2672c From 7ee4bb9ac086e1a514de28bc1cb7689194dd00b0 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 4 Jun 2025 05:23:24 -0400 Subject: [PATCH 071/103] move ENV closer to ARG. --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8625546..5268da9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -147,6 +147,9 @@ ARG CREATED ARG REVISION ARG BUILD_VERSION +ENV VERSION=$BUILD_VERSION +ENV BUILD_DATE=$CREATED + LABEL maintainer="lam87@cornell.edu" LABEL org.opencontainers.image.created=$CREATED LABEL org.opencontainers.image.url="https://breedbase.org/" @@ -158,8 +161,6 @@ LABEL org.opencontainers.image.title="breedbase/breedbase" LABEL org.opencontainers.image.description="Breedbase web server" LABEL org.opencontainers.image.documentation="https://solgenomics.github.io/sgn/" -ENV VERSION=$BUILD_VERSION -ENV BUILD_DATE=$CREATED # start services when running container... From dd6ba80073d6d977ecf385d33f95f2a9230fe7ea Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 5 Jun 2025 04:29:50 -0400 Subject: [PATCH 072/103] try wiggly bracket notation in assignment for VERSION etc. --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5268da9..f4f1a0b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -147,8 +147,8 @@ ARG CREATED ARG REVISION ARG BUILD_VERSION -ENV VERSION=$BUILD_VERSION -ENV BUILD_DATE=$CREATED +ENV VERSION=${BUILD_VERSION} +ENV BUILD_DATE=${CREATED} LABEL maintainer="lam87@cornell.edu" LABEL org.opencontainers.image.created=$CREATED From 03bff864b8b3752a84af53fb7837d6f32960b83e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 19 Jun 2025 10:45:26 -0400 Subject: [PATCH 073/103] 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 have been added to the dialog but not submitted before validating; set all email addresses for quick account creation to avoid issues down the road with password reset; add optional trial_stock_type column for multi trial upload; new cvprop for biochem ChEBI traits; show linkages between accession, plots, and tissue_samples in trial detail page; allow crosses in multi trial upload; add NIRS section to trial detail page; configure fieldbook using QRCode; Display seedlot inventory for each population member with download function; in list manager, change date format to fix sorting. --- cxgn/cassava | 2 +- cxgn/gtsimsrch | 2 +- cxgn/sgn | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cxgn/cassava b/cxgn/cassava index 55e5ca6..55d31ab 160000 --- a/cxgn/cassava +++ b/cxgn/cassava @@ -1 +1 @@ -Subproject commit 55e5ca68ed6d236d2494d7d445dc95982f2c7b62 +Subproject commit 55d31ab04d0b783c602e95090e892d135fe358cf diff --git a/cxgn/gtsimsrch b/cxgn/gtsimsrch index c1379f7..de5469e 160000 --- a/cxgn/gtsimsrch +++ b/cxgn/gtsimsrch @@ -1 +1 @@ -Subproject commit c1379f79e65b0ad070fba7496ff209255db8f0aa +Subproject commit de5469e70d53621dbe7028bd9ddd020ba62aefea diff --git a/cxgn/sgn b/cxgn/sgn index 1b7f011..cecc637 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 1b7f0115271578adbef7dadba95a707aa7a2672c +Subproject commit cecc63729b11375831f5ccfe5b5bc54ac0059e18 From fb6925361fdfdb3f9a16c3b98edef90935bed1a7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 26 Jun 2025 15:41:39 -0400 Subject: [PATCH 074/103] 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. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index cecc637..0e15001 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit cecc63729b11375831f5ccfe5b5bc54ac0059e18 +Subproject commit 0e15001d67f01dd06a5b914d1d20ee4f722ec116 From d7c661ec9527b83edf4752ce56deb0df848b3216 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 2 Jul 2025 23:07:20 -0400 Subject: [PATCH 075/103] 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 easier image upload if other data has been transferred by BrAPI; tool compatibility feature improvements; make sure plants are added to subplots when they are present and not to plots. --- cxgn/cassbase | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/cassbase b/cxgn/cassbase index 539c0b1..76d6dcd 160000 --- a/cxgn/cassbase +++ b/cxgn/cassbase @@ -1 +1 @@ -Subproject commit 539c0b18be07972c90a418d44b18b906e5d607e6 +Subproject commit 76d6dcdd2dab7c7cf95ef3f60cb6eb1bcec6eabe diff --git a/cxgn/sgn b/cxgn/sgn index 0e15001..42a96c4 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 0e15001d67f01dd06a5b914d1d20ee4f722ec116 +Subproject commit 42a96c4f99cf3af8d18eb59b6e961c10c387d82a From 09f0ac4c9277549c64375878624ab9efed9bb959 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 10 Jul 2025 15:40:34 -0400 Subject: [PATCH 076/103] 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 from that plot, such as subplot, plant and tissue_sample; improve tool compatibility checker; rename management factors to treatment factors (management factors to be implemented later); add a script to update stockprops in bulk. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 42a96c4..19c0655 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 42a96c4f99cf3af8d18eb59b6e961c10c387d82a +Subproject commit 19c0655f65370d375eaaacbd4ae17b27c31ebd6d From 6c15e2875595e0243ad471527c4a997d75f26c23 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 28 Jul 2025 14:26:26 -0400 Subject: [PATCH 077/103] 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 to a specific analysis on the image_analysis tool page; improve error messages during the observation upload; improvements for the composed trait submission, including possibility to refresh lists without reloading the page; implement upload for historical tranformation data and sort transformant tables with natural sort; link to the correct label designer tool from the trial detail page; allow images to be searched by associated accessions. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 19c0655..a1a2400 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 19c0655f65370d375eaaacbd4ae17b27c31ebd6d +Subproject commit a1a240041d6484576a8f96c8188c229150943eab From 217d337ffe53c189a2f08bab4b92ed4bf465563b Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 15 Aug 2025 15:31:50 -0400 Subject: [PATCH 078/103] 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; indicate if marker found in multiple protocols; add ontology terms for time ontology; fix a couple of issues with phenotype upload. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index a1a2400..6054702 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit a1a240041d6484576a8f96c8188c229150943eab +Subproject commit 6054702ced5cd01d7dd263bcf4129a5f8a90e952 From b00e16e9f87a707a4feb1d3f1f5480dc1306e92a Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 22 Aug 2025 10:58:49 -0400 Subject: [PATCH 079/103] 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. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 6054702..8331bf0 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6054702ced5cd01d7dd263bcf4129a5f8a90e952 +Subproject commit 8331bf0450bb8b8390e4176fdf272d9e36bf207a From 9230728715b61034640ef6744eb8668a411ef3bb Mon Sep 17 00:00:00 2001 From: David Waring Date: Wed, 27 Aug 2025 13:39:11 -0400 Subject: [PATCH 080/103] Update R apt source --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f4f1a0b..f883250 100644 --- a/Dockerfile +++ b/Dockerfile @@ -31,7 +31,7 @@ RUN bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38D # add cran backports repo and required deps # -RUN echo "deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian bullseye-cran40/" >> /etc/apt/sources.list +RUN echo "deb https://cloud.r-project.org/bin/linux/debian/ bullseye-cran40/" >> /etc/apt/sources.list RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ bullseye-pgdg main" | tee /etc/apt/sources.list.d/pgdg.list From 1b1b9fa6130bc6add7b590d97c41754ce83bc2ca Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 29 Aug 2025 11:42:01 -0400 Subject: [PATCH 081/103] add EXIF parsing function to image object. --- cxgn/cxgn-corelibs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/cxgn-corelibs b/cxgn/cxgn-corelibs index e58c6d6..db6292e 160000 --- a/cxgn/cxgn-corelibs +++ b/cxgn/cxgn-corelibs @@ -1 +1 @@ -Subproject commit e58c6d666b00ecd507983ed08061c618bd469749 +Subproject commit db6292e3219d514beddf50c3a39926041badf10a From 44b0a35172e1cd5427c03c3b9000247df9c5beca Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 5 Sep 2025 19:29:40 -0400 Subject: [PATCH 082/103] modify docker-compose.test.yml --- docker-compose.test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.test.yml b/docker-compose.test.yml index 12b1f78..aafaa6b 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -3,7 +3,7 @@ services: build: context: . cache_from: - - breedbase/breedbase:v0.54 + - breedbase/breedbase:latest environment: HOME: /root MODE: 'TESTING' From d66cea73bc1c3b51f7298b3891805fc278b0a481 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 5 Sep 2025 19:43:39 -0400 Subject: [PATCH 083/103] update to tag sgn-430.0. Includes important fix for list validation issues; fix geoCoordinates to float instead of string to improve BrAPI compatibility; remove ghost image rows in trial detail page image section after images are deleted; add a script to fix tissue sample / plot associations; improve delete stock script; add new functionalities to lists. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 8331bf0..fb7e59f 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 8331bf0450bb8b8390e4176fdf272d9e36bf207a +Subproject commit fb7e59ffdde143d9b0e0d73c93fda401eac9fb34 From 655361ebbb520e568312e08e7d58a17ed67a125d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 10 Sep 2025 14:55:26 -0400 Subject: [PATCH 084/103] 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. --- cxgn/local-lib | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/local-lib b/cxgn/local-lib index 438b265..8296a6e 160000 --- a/cxgn/local-lib +++ b/cxgn/local-lib @@ -1 +1 @@ -Subproject commit 438b265c2cdaa7c1007e186cff0d62cd1f37ef47 +Subproject commit 8296a6e21b9879a72c643ccfc99b8b15c6ab3b8e diff --git a/cxgn/sgn b/cxgn/sgn index fb7e59f..6ca2b29 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit fb7e59ffdde143d9b0e0d73c93fda401eac9fb34 +Subproject commit 6ca2b29c80203c5e6b9c0af1c8eb62045334b1b5 From a0207638f23b4e1b61d36d4d73a7720ea09d20a5 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sun, 14 Sep 2025 20:32:03 -0400 Subject: [PATCH 085/103] add important fix for spatial correction in field map. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 6ca2b29..553329e 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6ca2b29c80203c5e6b9c0af1c8eb62045334b1b5 +Subproject commit 553329ed981e9b23acf97a0a0e6ac611acfabaca From d4798129ec95185ca41d903f1e3d7a940b5f5626 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 18 Sep 2025 07:48:20 -0400 Subject: [PATCH 086/103] add missing library files for exif feature; add ability to upload Fieldbook files based on observation unit ids in addition to observation unit names. --- Dockerfile | 4 ++-- cxgn/sgn | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index f883250..d6b9be6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ RUN apt-get update --fix-missing -y RUN apt-get install -y aptitude -RUN aptitude install -y npm libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink +RUN aptitude install -y npm libimage-magick-perl libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink # Set the locale correclty to UTF-8 RUN locale-gen en_US.UTF-8 @@ -96,7 +96,7 @@ RUN cpanm Selenium::Remote::Driver@1.49 #INSTALL OPENCV IMAGING LIBRARY -RUN apt-get install -y python3-dev python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev cmake +RUN apt-get install -y python3-dev python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev libzbar-tools cmake RUN pip3 install --upgrade pip RUN pip3 install grpcio==1.40.0 imutils numpy matplotlib pillow statistics PyExifTool pytz pysolar scikit-image packaging pyzbar pandas opencv-python \ diff --git a/cxgn/sgn b/cxgn/sgn index 553329e..bb337ea 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 553329ed981e9b23acf97a0a0e6ac611acfabaca +Subproject commit bb337eacdb6f54ff419260437604da3bde9f29b9 From c162b3a4cfd561c18dec893ddf8ed58fafeba2a0 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 18 Sep 2025 10:04:18 -0400 Subject: [PATCH 087/103] this actually includes the merge for the fieldbook numeric ids upload. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index bb337ea..4e8f0b5 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit bb337eacdb6f54ff419260437604da3bde9f29b9 +Subproject commit 4e8f0b5dbf2f5609cfa5eca1831a4d558621144b From d8461f32013bce465cec4baa905377658c75107c Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 18 Sep 2025 12:14:40 -0400 Subject: [PATCH 088/103] fix zbar-tools package name --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d6b9be6..d5f2cf8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -96,7 +96,7 @@ RUN cpanm Selenium::Remote::Driver@1.49 #INSTALL OPENCV IMAGING LIBRARY -RUN apt-get install -y python3-dev python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev libzbar-tools cmake +RUN apt-get install -y python3-dev python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev zbar-tools cmake RUN pip3 install --upgrade pip RUN pip3 install grpcio==1.40.0 imutils numpy matplotlib pillow statistics PyExifTool pytz pysolar scikit-image packaging pyzbar pandas opencv-python \ From 8654198b900279ca0962e50377cbaf96f2f7c9f2 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 2 Oct 2025 21:16:07 -0400 Subject: [PATCH 089/103] 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_sample count; add subplot data dimension to the wizard. --- cxgn/local-lib | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/local-lib b/cxgn/local-lib index 8296a6e..bff49e3 160000 --- a/cxgn/local-lib +++ b/cxgn/local-lib @@ -1 +1 @@ -Subproject commit 8296a6e21b9879a72c643ccfc99b8b15c6ab3b8e +Subproject commit bff49e39724aaf508385c186eb2e9cd22640247a diff --git a/cxgn/sgn b/cxgn/sgn index 4e8f0b5..004fbd1 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 4e8f0b5dbf2f5609cfa5eca1831a4d558621144b +Subproject commit 004fbd1ffb93d1d1bee19cb9a1c1cebf6f9308d3 From 41056f7f598b577370cced277e688813f593c9e5 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 16 Oct 2025 19:23:27 -0400 Subject: [PATCH 090/103] 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 stock_id in stock search and wizard and display stock ids in result pages; adds libreoffice document format support for uploads; fixes an issue with authentication in the brapi observation call; improves loading speed of image section on trial detail pages; adds a list comparison tool. --- cxgn/bio-chado-schema | 2 +- cxgn/sgn | 2 +- cxgn/solgenomics | 2 +- cxgn/sweetpotatobase | 2 +- cxgn/yambase | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/cxgn/bio-chado-schema b/cxgn/bio-chado-schema index b9514e5..c9e3e99 160000 --- a/cxgn/bio-chado-schema +++ b/cxgn/bio-chado-schema @@ -1 +1 @@ -Subproject commit b9514e572ae9bef225856521b3949eeb578fa91b +Subproject commit c9e3e9959ab0a554a54edcc644fc8fa076b89a1b diff --git a/cxgn/sgn b/cxgn/sgn index 004fbd1..cbaecc4 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 004fbd1ffb93d1d1bee19cb9a1c1cebf6f9308d3 +Subproject commit cbaecc4f461a307f7e1eb5c9bb564b786d3773ba diff --git a/cxgn/solgenomics b/cxgn/solgenomics index 387b208..9f6a481 160000 --- a/cxgn/solgenomics +++ b/cxgn/solgenomics @@ -1 +1 @@ -Subproject commit 387b2088472e1f96f1f119625ab03a2c22a98bfd +Subproject commit 9f6a481c3cae45b7bfd1f3f334403851f5d73208 diff --git a/cxgn/sweetpotatobase b/cxgn/sweetpotatobase index 0d56f92..00ec650 160000 --- a/cxgn/sweetpotatobase +++ b/cxgn/sweetpotatobase @@ -1 +1 @@ -Subproject commit 0d56f9298500eb24ab0a9bbb8d9c060a40321405 +Subproject commit 00ec650f8736c436550f24fe113e9e3f3f067b9d diff --git a/cxgn/yambase b/cxgn/yambase index 6b5313d..097acdf 160000 --- a/cxgn/yambase +++ b/cxgn/yambase @@ -1 +1 @@ -Subproject commit 6b5313d0bd12a37f4cf5642e465cb544dd2b9bc5 +Subproject commit 097acdfe337d256e180de87a6d77f9235f9c8c05 From c9b85e46074343caa4d4700381fc711b2c98ed1a Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Tue, 4 Nov 2025 10:10:12 -0500 Subject: [PATCH 091/103] 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 were genotyped with in a table format; adds a list comparison tool with downloadable diffs between lists; fixes an issue with changing accessions in a trial using a file upload; adds the ability to scan barcodes in images containing observation unit information, with options to associate the image automatically with that observation unit; do not check the trait constraints for trait values that are not defined; adds a vector viewer on the vector construct detail pages; improve label writer features - display dimensions in either S.I. units or inches, adds options to left align or center align label texts, fixes an issue with barcode fuzzyness by moving internal barcode image creation from jpg to png; adds .ods file format support for all uploads; fixes an issue with authentication in the observation brapi call; adds ability to run image analysis for analyses that detect mulitple sub-objects and report multiple values, creates a new tissue sample for each sub-image; speeds up image section on trial detail page; adds a feature that stores marker names associated with each marker in a genotyping protocol, can assign specific names for markers in an alias column; adds improved logging for pca tool; fixes how the wizard download handles tempfiles; fixes a bug in the spatial correction tool. --- cxgn/citrusgreening | 2 +- cxgn/erysimum | 2 +- cxgn/fernbase | 2 +- cxgn/sgn | 2 +- cxgn/solgenomics | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/cxgn/citrusgreening b/cxgn/citrusgreening index 74d2b5c..5ea452b 160000 --- a/cxgn/citrusgreening +++ b/cxgn/citrusgreening @@ -1 +1 @@ -Subproject commit 74d2b5c5b08a81dd2b94ea53c1a5dd4c958beafb +Subproject commit 5ea452b4d1a4e7b7c7cc8b245258751932af9d2f diff --git a/cxgn/erysimum b/cxgn/erysimum index 41c2fc0..994e536 160000 --- a/cxgn/erysimum +++ b/cxgn/erysimum @@ -1 +1 @@ -Subproject commit 41c2fc0ab31741b1a167cac77874e11a54457aba +Subproject commit 994e53609c7c60a4127b961643ca9cc287e7ba70 diff --git a/cxgn/fernbase b/cxgn/fernbase index 6b9a93c..a9642b8 160000 --- a/cxgn/fernbase +++ b/cxgn/fernbase @@ -1 +1 @@ -Subproject commit 6b9a93c1dd6a545cf0a02a86945a5b15426b284d +Subproject commit a9642b885f8d8defd45b064e050da96a1b4e8a08 diff --git a/cxgn/sgn b/cxgn/sgn index cbaecc4..cc6f74b 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit cbaecc4f461a307f7e1eb5c9bb564b786d3773ba +Subproject commit cc6f74beac282d451b4354d5f7cf449a51538c09 diff --git a/cxgn/solgenomics b/cxgn/solgenomics index 9f6a481..d68adb8 160000 --- a/cxgn/solgenomics +++ b/cxgn/solgenomics @@ -1 +1 @@ -Subproject commit 9f6a481c3cae45b7bfd1f3f334403851f5d73208 +Subproject commit d68adb894b174852492e245d0963292bc648084b From d2a58d9a7e439593ebc830a05e754c1d9b1695e7 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 10 Nov 2025 16:57:37 -0500 Subject: [PATCH 092/103] adding a download dir to both breedbase_web and selenium dockers to better deal with web downloads. --- docker-compose.override.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 6a74f6d..c195353 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -11,6 +11,9 @@ services: - type: bind source: .git target: /home/production/.git + - type: bind + source: /tmp/downloads + target: /downloads environment: MODE: 'DEVELOPMENT' PGDATABASE: breedbase @@ -19,7 +22,7 @@ services: PGUSER: postgres SGN_TEST_SERVER: http://breedbase:3010 SGN_REMOTE_SERVER_ADDR: selenium - + DBIC_TRACE: 0 selenium: container_name: selenium image: selenium/standalone-firefox-debug @@ -27,6 +30,9 @@ services: - type: bind source: ./cxgn/sgn/t/data target: /home/production/cxgn/sgn/t/data + - type: bind + source: /tmp/downloads + target: /downloads ports: - 5900:5900 - 4444:4444 From dd823c686b3bb75ca5c8795e50b770e6e648eaae Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 14 Nov 2025 14:16:16 -0500 Subject: [PATCH 093/103] mount downloads dirs from a docker volume for improved compatibility. --- docker-compose.override.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docker-compose.override.yml b/docker-compose.override.yml index c195353..80264b7 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -11,9 +11,7 @@ services: - type: bind source: .git target: /home/production/.git - - type: bind - source: /tmp/downloads - target: /downloads + - shared_data:/downloads environment: MODE: 'DEVELOPMENT' PGDATABASE: breedbase @@ -30,9 +28,7 @@ services: - type: bind source: ./cxgn/sgn/t/data target: /home/production/cxgn/sgn/t/data - - type: bind - source: /tmp/downloads - target: /downloads + - shared_data:/downloads ports: - 5900:5900 - 4444:4444 @@ -41,3 +37,6 @@ services: environment: POSTGRES_DB: breedbase POSTGRES_PASSWORD: postgres + +volumes: + shared_data: From dca92756f0dcf83b456a615a2e3972493369239f Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 14 Nov 2025 14:32:59 -0500 Subject: [PATCH 094/103] add downloads dirs to docker-compose.test.yml. --- docker-compose.test.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docker-compose.test.yml b/docker-compose.test.yml index aafaa6b..647f4c6 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -19,6 +19,7 @@ services: - ./cxgn:/home/production/cxgn # repos/sgn/sgn_test.conf assumes /home/vagrant - ./.git:/home/production/.git + - shared_data:/downloads command: ["t/unit", "t/unit_fixture", "t/unit_mech"] networks: - test-breedbase @@ -34,6 +35,7 @@ services: - type: bind source: ./cxgn/sgn/t/data target: /home/production/cxgn/sgn/t/data + - shared_data:/downloads ports: - 5900:5900 - 4444:4444 @@ -49,5 +51,8 @@ services: networks: - test-breedbase +volumes: + shared_data: + networks: test-breedbase: From 1fb7c050aeaf9da3d077c774c26a9819241b5c44 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Sat, 15 Nov 2025 23:49:21 -0500 Subject: [PATCH 095/103] 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 accession transform utility; add the new CASS logo; fix an issue with start and end date in the phenotype download; enable COMP trait variable uploads; fix an issue with CXGN::Jobs; in label designer tool, store the selected units (cm or inches) so that it is retrieved correctly when it is opened later; other improvements to label designer. --- cxgn/cassbase | 2 +- cxgn/sgn | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cxgn/cassbase b/cxgn/cassbase index 76d6dcd..b2fe3f9 160000 --- a/cxgn/cassbase +++ b/cxgn/cassbase @@ -1 +1 @@ -Subproject commit 76d6dcdd2dab7c7cf95ef3f60cb6eb1bcec6eabe +Subproject commit b2fe3f92307634a27850006fa67dd48016bd9ad8 diff --git a/cxgn/sgn b/cxgn/sgn index cc6f74b..62593f5 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit cc6f74beac282d451b4354d5f7cf449a51538c09 +Subproject commit 62593f5470d9d05ca319e6259439d34cd235604d From 28cdbdf02adc10518b4f4f4674aeb4c772aaa7c4 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Wed, 19 Nov 2025 18:13:48 -0500 Subject: [PATCH 096/103] add a new page and menu item about NARITA pathogen analysis. --- cxgn/musabase | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/musabase b/cxgn/musabase index cdbca93..e9e9941 160000 --- a/cxgn/musabase +++ b/cxgn/musabase @@ -1 +1 @@ -Subproject commit cdbca9332d2da74c2764aeb32c3ae3b33cad8421 +Subproject commit e9e9941c634d290c11b6695890f1c01aa5591722 From be2ce53359f98b9dd268291ceb22b804d86eb00d Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 5 Dec 2025 21:26:31 -0500 Subject: [PATCH 097/103] compile unigene contigalign program. --- entrypoint.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/entrypoint.sh b/entrypoint.sh index 29b385b..e7f4801 100644 --- a/entrypoint.sh +++ b/entrypoint.sh @@ -118,3 +118,8 @@ else chmod 777 /var/log/sgn/error.log tail -f /var/log/sgn/error.log fi + +# for unigene page, compile drawcontig align program +cd /home/production/cxgn/sgn/programs +make +cd /home/production/cxgn/sgn From a32250431e11aa7cb39830b5190cb35fffa7f67e Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 11 Dec 2025 17:37:48 -0500 Subject: [PATCH 098/103] remove make statement from entrypoint. --- entrypoint.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/entrypoint.sh b/entrypoint.sh index e7f4801..0329234 100644 --- a/entrypoint.sh +++ b/entrypoint.sh @@ -120,6 +120,6 @@ else fi # for unigene page, compile drawcontig align program -cd /home/production/cxgn/sgn/programs -make -cd /home/production/cxgn/sgn +#cd /home/production/cxgn/sgn/programs +#make +#cd /home/production/cxgn/sgn From 710cf398d69adc7e1704e0a8eae0b664d17d96ef Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 19 Dec 2025 11:29:05 -0500 Subject: [PATCH 099/103] 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 genotyping download; adds the ability to create new accessions from other accessions, plots, plants or tissue_samples; adds BrAPI NIRS endpoints. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 62593f5..98cc69b 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 62593f5470d9d05ca319e6259439d34cd235604d +Subproject commit 98cc69be5989911b795a6d31241289ac246a0aba From 60077ff8160395e828cd44b1850f503a8897fa45 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 8 Jan 2026 13:52:45 -0500 Subject: [PATCH 100/103] Finally updates the manual for fieldbook interfacing; fixes the seedlot information on the accession detail page; fixes issues with the motif finder tool. --- cxgn/cassbase | 2 +- cxgn/sgn | 2 +- cxgn/solgenomics | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cxgn/cassbase b/cxgn/cassbase index b2fe3f9..dba76f1 160000 --- a/cxgn/cassbase +++ b/cxgn/cassbase @@ -1 +1 @@ -Subproject commit b2fe3f92307634a27850006fa67dd48016bd9ad8 +Subproject commit dba76f1924990c22ea2512572dfd5c0e8bf3c0b6 diff --git a/cxgn/sgn b/cxgn/sgn index 98cc69b..b675ecc 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 98cc69be5989911b795a6d31241289ac246a0aba +Subproject commit b675ecc9db4f1417913587250d3778138f050cad diff --git a/cxgn/solgenomics b/cxgn/solgenomics index d68adb8..418f9eb 160000 --- a/cxgn/solgenomics +++ b/cxgn/solgenomics @@ -1 +1 @@ -Subproject commit d68adb894b174852492e245d0963292bc648084b +Subproject commit 418f9eb0f221c354ff1ac7fcc912ca12deb3df85 From 43ca35ee6f4efc64e132cf0224ca835f6802cf00 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Thu, 22 Jan 2026 20:51:55 -0500 Subject: [PATCH 101/103] 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 by genotyping projects; adds study create date to additional info for BrAPI call (needs to be added to the spec!). --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index b675ecc..6c69ea9 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit b675ecc9db4f1417913587250d3778138f050cad +Subproject commit 6c69ea99183455203921b02883511c83f580f144 From c7cf5e89fcabfae33da3decd0794f8cf7e8b1465 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Mon, 26 Jan 2026 17:31:13 -0500 Subject: [PATCH 102/103] add clustalw from apt repo as it is used by CAPS designer. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d5f2cf8..f715acf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ RUN apt-get update --fix-missing -y RUN apt-get install -y aptitude -RUN aptitude install -y npm libimage-magick-perl libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink +RUN aptitude install -y npm libimage-magick-perl libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle clustalw bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink # Set the locale correclty to UTF-8 RUN locale-gen en_US.UTF-8 From edaf52f3d74d5870508fb3329f1782bdc4a57852 Mon Sep 17 00:00:00 2001 From: Lukas Mueller Date: Fri, 30 Jan 2026 13:27:39 -0500 Subject: [PATCH 103/103] 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 within a plot in the greenhouse trial type; optimizes the loading of the field view on the trial detail page by speeding up the respective brapi call; adds more options to the trial layout download; prepare breedbase for compatibility with snpsnapp app. --- cxgn/sgn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cxgn/sgn b/cxgn/sgn index 6c69ea9..c5ddc4a 160000 --- a/cxgn/sgn +++ b/cxgn/sgn @@ -1 +1 @@ -Subproject commit 6c69ea99183455203921b02883511c83f580f144 +Subproject commit c5ddc4ac1cbcde8d8dfcf3cf22a768c3f95b6f2c