Make the test pipeline run again and pass all current, manually validated tests

.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

.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

.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}

.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

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:

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]])
       }
     }
   )

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

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", {

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
 

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
 

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", {

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)
 

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"))
 })

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 = "/")

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 = "/")

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]])
       }
     }
   )