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.
solgenomics · Dec 7, 2024 · 6b80ab3 · 6b80ab3
1 parent dbd9003
commit 6b80ab3
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/cxgn/Bio-Chado-Schema b/cxgn/Bio-Chado-Schema
diff --git a/cxgn/sgn b/cxgn/sgn
+37 −27		bin/delete_trials.pl
+13 −4		bin/load_people.pl
+192 −461		bin/upload_multiple_trial_design.pl
+7 −3		js/source/legacy/CXGN/BreedersToolbox/UploadPhenotype.js
+147 −160		js/source/legacy/CXGN/BreedersToolbox/UploadTrial.js
+5 −4		js/source/legacy/solGS/pca.js
+7 −15		lib/CXGN/Genotype/ParseUpload/Plugin/transposedVCF.pm
+6 −0		lib/CXGN/Phenotypes/ParseUpload/Plugin/PhenotypeSpreadsheetSimple.pm
+144 −0		lib/CXGN/Phenotypes/ParseUpload/Plugin/PhenotypeSpreadsheetSimpleGeneric.pm
+79 −66		lib/CXGN/Project.pm
+1 −1		lib/CXGN/Stock/Search.pm
+12 −6		lib/CXGN/Stock/Seedlot.pm
+2 −3		lib/CXGN/Stock/Seedlot/Transaction.pm
+1 −1		lib/CXGN/Trial/Folder.pm
+9 −0		lib/CXGN/Trial/ParseUpload.pm
+4 −0		lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignExcelFormat.pm
+650 −0		lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignGeneric.pm
+4 −0		lib/CXGN/Trial/ParseUpload/Plugin/TrialExcelFormat.pm
+444 −0		lib/CXGN/Trial/ParseUpload/Plugin/TrialGeneric.pm
+4 −2		lib/CXGN/Trial/TrialLayout/Genotyping.pm
+1 −1		lib/SGN/Controller/AJAX/PhenotypesUpload.pm
+6 −7		lib/SGN/Controller/AJAX/Seedlot.pm
+1 −8		lib/SGN/Controller/AJAX/Stock.pm
+62 −131		lib/SGN/Controller/AJAX/Trial.pm
+3 −3		mason/breeders_toolbox/add_seedlot_dialogs.mas
+2 −2		mason/breeders_toolbox/seedlot_details.mas
+10 −6		mason/breeders_toolbox/trial/trial_upload_dialogs.mas
+4 −0		mason/breeders_toolbox/upload_phenotype_spreadsheet.mas
+1 −1		mason/stock/trials.mas
+8 −1		t/data/cassava_test.vcf
+21 −0		t/data/trial/demo_multiple_trial_design.csv
+9 −0		t/data/trial/trial_layout_bad_accessions.csv
+9 −0		t/data/trial/trial_layout_example.csv
+9 −0		t/data/trial/trial_layout_example_flexible.csv
+9 −0		t/data/trial/trial_layout_example_with_management_factor.csv
+9 −0		t/data/trial/trial_layout_with_seedlot_example.csv
+22 −22		t/selenium2/breeders/upload_multi_trial_file.t
+13 −7		t/test_fixture.pl
+3 −3		t/unit/CXGN/GenotypeIO.t
+11 −4		t/unit_fixture/CXGN/Trial/ParseUpload.t
+5 −5		t/unit_fixture/CXGN/Uploading/Phenotype.t
+4 −4		t/unit_fixture/CXGN/Uploading/Phenotype_with_multi_categories.t
+132 −129		t/unit_fixture/CXGN/Uploading/TrialUpload.t
+0 −6		t/unit_mech/AJAX/_BrAPIv2_phenotyping.t