diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml index 73acd205..1e2b2d21 100644 --- a/.github/workflows/NewUpdate.yml +++ b/.github/workflows/NewUpdate.yml @@ -20,7 +20,7 @@ jobs: - name: Download latest generators run: | cd .updater/openapi_generator - wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.10.0/openapi-generator-cli-7.10.0.jar -O openapi-generator-cli.jar + wget -nv https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.10.0/openapi-generator-cli-7.10.0.jar -O openapi-generator-cli.jar java -jar openapi-generator-cli.jar version > version - name: Download latest Sirius Release uses: nick-fields/retry@v2 @@ -34,7 +34,7 @@ jobs: echo "Writing Version files: $packageVersion" echo $packageVersion > ./packageVersion.txt echo "Downloading Version: $packageVersion" - cat ./releases.json | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i - + cat ./releases.json | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i - echo "Download Complete" unzip *.zip echo "Api Ready" @@ -45,7 +45,7 @@ jobs: run: | while ! nc -z localhost 8080; do sleep 0.1; done cd .updater/api - wget http://localhost:8080/v3/api-docs -O api-docs-strings.json + wget -nv http://localhost:8080/v3/api-docs -O api-docs-strings.json - name: Shutdown SIRIUS run: curl -X POST http://localhost:8080/actuator/shutdown - name: Run Rest Api with enums @@ -55,7 +55,7 @@ jobs: run: | while ! nc -z localhost 8080; do sleep 0.1; done cd .updater/api - wget http://localhost:8080/v3/api-docs -O api-docs-enums.json + wget -nv http://localhost:8080/v3/api-docs -O api-docs-enums.json - name: Shutdown SIRIUS run: curl -X POST http://localhost:8080/actuator/shutdown - name: Update Clients diff --git a/.github/workflows/PythonTest.yml b/.github/workflows/PythonTest.yml index 01e8444b..d37b5e2d 100644 --- a/.github/workflows/PythonTest.yml +++ b/.github/workflows/PythonTest.yml @@ -45,7 +45,9 @@ jobs: - name: Change HOME to working directory of runner run: echo "HOME=/home/runner/work/sirius-client-openAPI" >> $GITHUB_ENV - name: Download tomato_small project space - run: wget ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius + run: | + wget -nv ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius + chmod 666 $HOME/tomato_small.sirius - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml index 677bc7f1..a8016185 100644 --- a/.github/workflows/RTest.yml +++ b/.github/workflows/RTest.yml @@ -40,10 +40,12 @@ jobs: path: .updater/api/sirius key: sirius fail-on-cache-miss: true - - name: Download tomato_small project space - run: wget ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O tomato_small.sirius - name: Change HOME to working directory of runner run: echo "HOME=/home/runner/work/sirius-client-openAPI" >> $GITHUB_ENV + - name: Download tomato_small project space + run: | + wget -nv ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius + chmod 666 $HOME/tomato_small.sirius - name: Check SIRIUS download run: | echo "Show content of cache download (.updater/api/)" @@ -73,8 +75,75 @@ jobs: quit(status=1) } shell: Rscript {0} + - name: Test Actuator API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_actuator_api.R", reporter=multi_reporter) + shell: Rscript {0} - name: Test Info API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - testthat::test_file("client-api_r/generated/tests/testthat/test_info_api.R") + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_info_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Login and Account API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Projects API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_projects_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Compounds API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_compounds_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Databases API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Features API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_features_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test Jobs API + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_jobs_api.R", reporter=multi_reporter) + shell: Rscript {0} + - name: Test acceptance + if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' + run: | + library(Rsirius) + library(testthat) + multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) + test_file("client-api_r/generated/tests/testthat/test_acceptance.R", reporter=multi_reporter) shell: Rscript {0} \ No newline at end of file diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml index 69e4d5ab..37293bb0 100644 --- a/.github/workflows/update-api.yml +++ b/.github/workflows/update-api.yml @@ -20,7 +20,7 @@ jobs: timeout_minutes: 2 command: | cd .updater/api - curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i - echo "Download Complete" + curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i - echo "Download Complete" unzip -o *.zip echo "Api Ready" - name: Check cached version @@ -31,11 +31,11 @@ jobs: command: | cd .updater/api currVersion=$(cat ./sirius/HashCode) - curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i - newVersion=$(cat *.sha256 | cut -d " " -f 1) + curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i - newVersion=$(cat *.sha256 | cut -d " " -f 1) echo New Version is $newVersion if [ "$currVersion" != "$newVersion" ]; then sleep 1 - curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i - + curl -s https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i - unzip -o *.zip echo $newVersion > ./sirius/HashCode - fi + fi \ No newline at end of file diff --git a/client-api_python/generated/test/test_features_api.py b/client-api_python/generated/test/test_features_api.py index 864827cd..ef3721b7 100644 --- a/client-api_python/generated/test/test_features_api.py +++ b/client-api_python/generated/test/test_features_api.py @@ -45,13 +45,6 @@ def setUp(self) -> None: self.aligned_feature_id = "586487307819356741" self.formula_candidates = self.api.features().get_formula_candidates(self.project_id, self.aligned_feature_id) - print("########### DEBUG ###########") - print("Project info:") - print(self.project_info) - print("Candidates for MSNovelist feature:") - print(self.formula_candidates) - print("All Features:") - print(self.api.features().get_aligned_features(self.project_id)) self.formula_id = self.formula_candidates[0].formula_id def tearDown(self) -> None: diff --git a/client-api_r/generated/R/api_client.R b/client-api_r/generated/R/api_client.R index 75b12a32..4257ae14 100644 --- a/client-api_r/generated/R/api_client.R +++ b/client-api_r/generated/R/api_client.R @@ -414,7 +414,7 @@ ApiClient <- R6::R6Class( } # not json mime type, simply return the first one - return(headers[1]) + return(headers[[1]]) } } ) diff --git a/client-api_r/generated/tests/testthat/test_acceptance.R b/client-api_r/generated/tests/testthat/test_acceptance.R index f6fbb152..dc829492 100644 --- a/client-api_r/generated/tests/testthat/test_acceptance.R +++ b/client-api_r/generated/tests/testthat/test_acceptance.R @@ -5,7 +5,7 @@ context("Test Acceptance") options(warn = -1) sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$jobs_api features_api <- api$features_api projects_api <- api$projects_api diff --git a/client-api_r/generated/tests/testthat/test_actuator_api.R b/client-api_r/generated/tests/testthat/test_actuator_api.R index e1f968ff..8fe91be9 100644 --- a/client-api_r/generated/tests/testthat/test_actuator_api.R +++ b/client-api_r/generated/tests/testthat/test_actuator_api.R @@ -4,7 +4,7 @@ context("Test ActuatorApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$actuator_api test_that("Health", { diff --git a/client-api_r/generated/tests/testthat/test_compounds_api.R b/client-api_r/generated/tests/testthat/test_compounds_api.R index 76bf1224..c991ca67 100644 --- a/client-api_r/generated/tests/testthat/test_compounds_api.R +++ b/client-api_r/generated/tests/testthat/test_compounds_api.R @@ -4,7 +4,7 @@ context("Test CompoundsApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$compounds_api projects_api <- api$projects_api diff --git a/client-api_r/generated/tests/testthat/test_features_api.R b/client-api_r/generated/tests/testthat/test_features_api.R index 6112cf7d..4cdb7910 100644 --- a/client-api_r/generated/tests/testthat/test_features_api.R +++ b/client-api_r/generated/tests/testthat/test_features_api.R @@ -5,7 +5,7 @@ context("Test FeaturesApi") options(warn = -1) sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$features_api projects_api <- api$projects_api diff --git a/client-api_r/generated/tests/testthat/test_info_api.R b/client-api_r/generated/tests/testthat/test_info_api.R index bd15022f..2175ef63 100644 --- a/client-api_r/generated/tests/testthat/test_info_api.R +++ b/client-api_r/generated/tests/testthat/test_info_api.R @@ -4,7 +4,7 @@ context("Test InfoApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$info_api test_that("GetConnectionCheck", { diff --git a/client-api_r/generated/tests/testthat/test_jobs_api.R b/client-api_r/generated/tests/testthat/test_jobs_api.R index 619702da..b48a97d4 100644 --- a/client-api_r/generated/tests/testthat/test_jobs_api.R +++ b/client-api_r/generated/tests/testthat/test_jobs_api.R @@ -5,7 +5,7 @@ context("Test JobsApi") options(warn=-1) sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$jobs_api features_api <- api$features_api projects_api <- api$projects_api @@ -32,7 +32,7 @@ test_that("DeleteJob", { projects_api$ImportPreprocessedDataAsJob(project_id, input_files=input_file) response_before <- api_instance$GetJobs(project_id) - api_instance$DeleteJob(project_id, response_before[[1]]$id) + api_instance$DeleteJob(project_id, response_before[[1]]$id, await_deletion=TRUE) response_after <- api_instance$GetJobs(project_id) expect_equal(length(response_before), length(response_after)+1) @@ -92,7 +92,7 @@ test_that("DeleteJobs", { projects_api$ImportPreprocessedDataAsJob(project_id, input_files=input_file) response_before <- api_instance$GetJobs(project_id) - api_instance$DeleteJobs(project_id) + api_instance$DeleteJobs(project_id, await_deletion=TRUE) response_after <- api_instance$GetJobs(project_id) expect_equal(length(response_before), length(response_after)+1) diff --git a/client-api_r/generated/tests/testthat/test_login_and_account_api.R b/client-api_r/generated/tests/testthat/test_login_and_account_api.R index 2cc778e0..57c54c73 100644 --- a/client-api_r/generated/tests/testthat/test_login_and_account_api.R +++ b/client-api_r/generated/tests/testthat/test_login_and_account_api.R @@ -4,7 +4,7 @@ context("Test LoginAndAccountApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$login_and_account_api test_that("GetAccountInfo", { @@ -26,7 +26,6 @@ test_that("GetSignUpURL", { # Get SignUp URL (For signUp via web browser) # @return [character] - # TODO deserialize error response <- api_instance$GetSignUpURL() expect_true(inherits(response, "character")) }) diff --git a/client-api_r/generated/tests/testthat/test_projects_api.R b/client-api_r/generated/tests/testthat/test_projects_api.R index 0a8dcbc6..b03e16a5 100644 --- a/client-api_r/generated/tests/testthat/test_projects_api.R +++ b/client-api_r/generated/tests/testthat/test_projects_api.R @@ -4,7 +4,7 @@ context("Test ProjectsApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$projects_api path_to_demo_data <- paste(Sys.getenv("HOME"), "sirius-client-openAPI/.updater/clientTests/Data", sep = "/") preproc_ms2_file_1 <- paste(path_to_demo_data, "Kaempferol.ms", sep = "/") diff --git a/client-api_r/generated/tests/testthat/test_searchable_databases_api.R b/client-api_r/generated/tests/testthat/test_searchable_databases_api.R index df343110..f2759e9a 100644 --- a/client-api_r/generated/tests/testthat/test_searchable_databases_api.R +++ b/client-api_r/generated/tests/testthat/test_searchable_databases_api.R @@ -4,7 +4,7 @@ context("Test SearchableDatabasesApi") sdk <- SiriusSDK$new() -api <- sdk$attach_to_sirius() +api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$searchable_databases_api home_dir <- Sys.getenv("HOME") path_to_demo_data <- paste(home_dir, "sirius-client-openAPI/.updater/clientTests/Data", sep = "/") diff --git a/client-api_r/templates/r/api_client.mustache b/client-api_r/templates/r/api_client.mustache index cb2fa4af..34458ad0 100644 --- a/client-api_r/templates/r/api_client.mustache +++ b/client-api_r/templates/r/api_client.mustache @@ -477,7 +477,7 @@ ApiClient <- R6::R6Class( } # not json mime type, simply return the first one - return(headers[1]) + return(headers[[1]]) } } )