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mlm483 wants to merge 14 commits into from
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Merge for Release/1.0 #51

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eb8d548
add nginx rule to send LetsEncrypt request to nginx web root
dmeidlin Sep 17, 2024
93971f7
Auto updated submodule references
rob-ouser-bi Sep 19, 2024
6acc748
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rob-ouser-bi Sep 20, 2024
b7fb8b5
Merge pull request #50 from Breeding-Insight/bug/BI-2113
dmeidlin Sep 20, 2024
a2063f1
Auto updated submodule references
rob-ouser-bi Sep 21, 2024
bf392d6
Auto updated submodule references
rob-ouser-bi Sep 24, 2024
1f549b6
Auto updated submodule references
rob-ouser-bi Oct 5, 2024
b34871e
Auto updated submodule references
rob-ouser-bi Oct 8, 2024
bc70feb
Auto updated submodule references
rob-ouser-bi Oct 9, 2024
1e2ab14
Auto updated submodule references
rob-ouser-bi Oct 11, 2024
6d72975
Auto updated submodule references
rob-ouser-bi Oct 25, 2024
a258097
Auto updated submodule references
rob-ouser-bi Oct 30, 2024
de44039
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rob-ouser-bi Oct 31, 2024
522d9a0
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rob-ouser-bi Nov 5, 2024
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2 changes: 1 addition & 1 deletion bi-api
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Submodule bi-api updated 42 files
+2 −0 .env.template
+2 −2 src/main/java/org/breedinginsight/brapi/v2/BrAPICropController.java
+120 −19 src/main/java/org/breedinginsight/brapi/v2/BrAPIGermplasmController.java
+63 −27 src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationsController.java
+8 −7 src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
+23 −1 src/main/java/org/breedinginsight/brapi/v2/BrAPIProgramsController.java
+13 −19 src/main/java/org/breedinginsight/brapi/v2/BrAPIStudiesController.java
+8 −10 src/main/java/org/breedinginsight/brapi/v2/BrAPITrialsController.java
+1 −0 src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java
+0 −80 src/main/java/org/breedinginsight/brapi/v2/ProgramController.java
+0 −1 src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
+16 −0 src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
+16 −14 src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
+70 −0 src/main/java/org/breedinginsight/brapi/v2/model/request/query/ObservationQuery.java
+83 −49 src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
+0 −10 src/main/java/org/breedinginsight/brapps/importer/model/base/Germplasm.java
+6 −2 src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
+14 −0 src/main/java/org/breedinginsight/brapps/importer/services/processors/GermplasmProcessor.java
+7 −1 src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/ExperimentUtilities.java
+2 −1 ...inginsight/brapps/importer/services/processors/experiment/appendoverwrite/factory/data/OverwrittenData.java
+13 −1 ...t/brapps/importer/services/processors/experiment/appendoverwrite/middleware/process/ImportTableProcess.java
+5 −1 .../brapps/importer/services/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java
+2 −1 .../org/breedinginsight/brapps/importer/services/processors/experiment/services/ExperimentValidateService.java
+87 −0 src/main/java/org/breedinginsight/db/migration/V1_31_0__Set_Dev_Admin_Email.java
+7 −10 src/main/java/org/breedinginsight/services/ProgramUserService.java
+5 −0 src/main/java/org/breedinginsight/services/validators/TraitFileValidatorError.java
+4 −0 src/main/java/org/breedinginsight/services/validators/TraitValidatorError.java
+1 −0 src/main/java/org/breedinginsight/services/validators/TraitValidatorErrorInterface.java
+26 −1 src/main/java/org/breedinginsight/services/validators/TraitValidatorService.java
+2 −2 src/main/java/org/breedinginsight/utilities/FileUtil.java
+22 −7 src/main/java/org/breedinginsight/utilities/Utilities.java
+1 −9 src/main/java/org/breedinginsight/utilities/response/mappers/GermplasmQueryMapper.java
+1 −0 src/main/resources/application.yml
+3 −2 src/main/resources/version.properties
+1 −1 src/test/java/org/breedinginsight/api/v1/controller/metadata/MetadataFilterIntegrationTest.java
+3 −5 src/test/java/org/breedinginsight/brapi/v2/BrAPIObservationsControllerIntegrationTest.java
+6 −0 src/test/java/org/breedinginsight/brapi/v2/GermplasmControllerIntegrationTest.java
+144 −45 src/test/java/org/breedinginsight/brapps/importer/GermplasmFileImportTest.java
+23 −0 src/test/java/org/breedinginsight/services/validators/TraitValidatorUnitTest.java
+3 −3 src/test/resources/files/germplasm_import/minimal_germplasm_import.csv
+6 −0 src/test/resources/files/germplasm_import/new_and_existing_list_entries.csv
+5 −0 src/test/resources/files/germplasm_import/valid_duplicate_entries.csv
2 changes: 1 addition & 1 deletion bi-web
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Submodule bi-web updated 17 files
+1 −0 .github/pull_request_template.md
+2 −2 package.json
+1 −2 src/breeding-insight/utils/GermplasmUtils.ts
+3 −3 src/components/admin/AdminProgramsTable.vue
+2 −2 src/components/admin/AdminUsersTable.vue
+2 −0 src/components/experiments/ExperimentsObservationsTable.vue
+2 −3 src/components/germplasm/GermplasmLink.vue
+2 −1 src/components/germplasm/GermplasmListsTable.vue
+4 −2 src/components/germplasm/GermplasmTable.vue
+5 −2 src/components/ontology/OntologyTable.vue
+2 −2 src/components/program/ProgramLocationsTable.vue
+2 −2 src/components/program/ProgramUsersTable.vue
+1 −1 src/components/tables/expandableTable/ExpandableTable.vue
+5 −2 src/components/trait/TraitDetailPanel.vue
+1 −2 src/components/trait/TraitsImportTable.vue
+4 −2 src/components/trait/forms/BaseTraitForm.vue
+11 −1 src/views/import/ImportExperiment.vue
3 changes: 3 additions & 0 deletions proxy/biproxy.docker
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,9 @@ upstream web {\n\
server {\n\
server_name ${REGISTERED_DOMAIN};\n\
\n\
location /.well-known/acme-challenge/ {\n\
root /usr/share/nginx/html;\n\
}\n\
location /v1 {\n\
proxy_pass http://api;\n\
include /etc/nginx/conf.d/proxy-headers.conf;\n\
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