From ad5167a4f20ab0725b1bdb39ae82c5ec45faed91 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 00:03:21 +0200
Subject: [PATCH 01/15] error 423 seems tomato_small is locked, may be due to
 rights

---
 .github/workflows/PythonTest.yml | 4 +++-
 .github/workflows/RTest.yml      | 6 ++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/PythonTest.yml b/.github/workflows/PythonTest.yml
index 01e8444b..04db6a18 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 ${{ 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..82f21285 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 ${{ 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/)"

From fd71de4baac15884b3ca934b9d277ad6d26694be Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 00:07:17 +0200
Subject: [PATCH 02/15] add missing tests

---
 .github/workflows/RTest.yml | 40 +++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 82f21285..45cdb689 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -75,8 +75,48 @@ 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: |
+        testthat::test_file("client-api_r/generated/tests/testthat/test_actuator_api.R")
+      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")
+      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: |
+        testthat::test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R")
+      shell: Rscript {0}
+    - name: Test Projects 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_projects_api.R")
+      shell: Rscript {0}
+    - name: Test Compounds 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_compounds_api.R")
+      shell: Rscript {0}
+    - name: Test Databases 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_databases_api.R")
+      shell: Rscript {0}
+    - name: Test Features 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_features_api.R")
+      shell: Rscript {0}
+    - name: Test Jobs 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_jobs_api.R")
+      shell: Rscript {0}
+    - name: Test acceptance
+      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_acceptance.R")
       shell: Rscript {0}
\ No newline at end of file

From b9bb5e4e71650d2e0207f6819a0ec783779ac2d9 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 00:23:38 +0200
Subject: [PATCH 03/15] fix filename

---
 .github/workflows/RTest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 45cdb689..4fd5825e 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -103,7 +103,7 @@ jobs:
     - name: Test Databases 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_databases_api.R")
+        testthat::test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R")
       shell: Rscript {0}
     - name: Test Features API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'

From bd200c8937d77f9c2128e61562963188fb736f74 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 00:30:08 +0200
Subject: [PATCH 04/15] still need to load Rsirius (NOT done automatically by
 testthat)

---
 .github/workflows/RTest.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 4fd5825e..9e6797e3 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -78,45 +78,54 @@ jobs:
     - name: Test Actuator API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
+        library(Rsirius)
         testthat::test_file("client-api_r/generated/tests/testthat/test_actuator_api.R")
       shell: Rscript {0}
     - name: Test Info API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
+        library(Rsirius)
         testthat::test_file("client-api_r/generated/tests/testthat/test_info_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_projects_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_compounds_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_features_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_jobs_api.R")
       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)
         testthat::test_file("client-api_r/generated/tests/testthat/test_acceptance.R")
       shell: Rscript {0}
\ No newline at end of file

From 94b4c0f2a59facaa6f0e9756eeca7ebd9dd9e855 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 11:08:17 +0200
Subject: [PATCH 05/15] remove debug prints

---
 client-api_python/generated/test/test_features_api.py | 7 -------
 1 file changed, 7 deletions(-)

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:

From 4c30f98b85846e0b745d37a6434ee5d1b61c397d Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 12:00:25 +0200
Subject: [PATCH 06/15] explicitly set sirius_port

---
 client-api_r/generated/tests/testthat/test_acceptance.R       | 2 +-
 client-api_r/generated/tests/testthat/test_actuator_api.R     | 2 +-
 client-api_r/generated/tests/testthat/test_compounds_api.R    | 4 ++--
 client-api_r/generated/tests/testthat/test_features_api.R     | 2 +-
 client-api_r/generated/tests/testthat/test_info_api.R         | 2 +-
 client-api_r/generated/tests/testthat/test_jobs_api.R         | 2 +-
 .../generated/tests/testthat/test_login_and_account_api.R     | 2 +-
 client-api_r/generated/tests/testthat/test_projects_api.R     | 2 +-
 .../generated/tests/testthat/test_searchable_databases_api.R  | 2 +-
 9 files changed, 10 insertions(+), 10 deletions(-)

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..500fcd17 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
 
@@ -62,7 +62,7 @@ test_that("DeleteCompound", {
     api_instance$DeleteCompound(project_id, compound_id)
     response_after <- api_instance$GetCompounds(project_id)
 
-    expect_equal(length(response_before) - length(response_after), 1)
+    expect_equal(length(response_before) - length(response_after), 2)
 
   }, finally = {
 
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..d1e133c1 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
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..19610c52 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", {
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 = "/")

From 9a1b7fca3815fbbb759f065883a5a56151099931 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 12:03:41 +0200
Subject: [PATCH 07/15] use custom multireporter

---
 .github/workflows/RTest.yml | 36 +++++++++++++++++++++++++++---------
 1 file changed, 27 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 9e6797e3..3033d4ff 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -79,53 +79,71 @@ jobs:
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
         library(Rsirius)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_actuator_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+        test_file("client-api_r/generated/tests/testthat/test_actuator_api.R", reporter=multi_reporter)
       shell: Rscript {0}
     - name: Test Info API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
         library(Rsirius)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_info_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$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)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+        test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R", reporter=multi_reporter)
       shell: Rscript {0}
     - name: Test Projects API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
         library(Rsirius)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_projects_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$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)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_compounds_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+        test_file("client-api_r/generated/tests/testthat/test_compounds_api.R", reporter=multi_reporter)
       shell: Rscript {0}
     - name: Test Databases API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
         library(Rsirius)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$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)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_features_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+        test_file("client-api_r/generated/tests/testthat/test_features_api.R", reporter=multi_reporter)
       shell: Rscript {0}
     - name: Test Jobs API
       if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: |
         library(Rsirius)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_jobs_api.R")
+        library(testthat)
+        multi_reporter = MultiReporter$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)
-        testthat::test_file("client-api_r/generated/tests/testthat/test_acceptance.R")
+        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

From a4197b4168fb8f944505abdbc265a58615b66970 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 12:19:42 +0200
Subject: [PATCH 08/15] remove deliberate fail

---
 client-api_r/generated/tests/testthat/test_compounds_api.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 500fcd17..c991ca67 100644
--- a/client-api_r/generated/tests/testthat/test_compounds_api.R
+++ b/client-api_r/generated/tests/testthat/test_compounds_api.R
@@ -62,7 +62,7 @@ test_that("DeleteCompound", {
     api_instance$DeleteCompound(project_id, compound_id)
     response_after <- api_instance$GetCompounds(project_id)
 
-    expect_equal(length(response_before) - length(response_after), 2)
+    expect_equal(length(response_before) - length(response_after), 1)
 
   }, finally = {
 

From 18c92e71b7c4bb1d1c7ae9b4181bda5452e68185 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 12:28:04 +0200
Subject: [PATCH 09/15] remove old TODO

---
 .../generated/tests/testthat/test_login_and_account_api.R        | 1 -
 1 file changed, 1 deletion(-)

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 19610c52..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
@@ -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"))
 })

From 0b6db3403e90d685e9d1ec888acab3d4529e67cf Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 13:32:06 +0200
Subject: [PATCH 10/15] quick change to cache 6.3.3-SNAPSHOT specifically

---
 .github/workflows/update-api.yml | 21 +++------------------
 1 file changed, 3 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml
index 69e4d5ab..7c0ab139 100644
--- a/.github/workflows/update-api.yml
+++ b/.github/workflows/update-api.yml
@@ -20,22 +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://github.com/sirius-ms/sirius/releases/download/v6.3.3-SNAPSHOT/sirius-6.3.3-SNAPSHOT-linux-x64.zip
+            echo "Download Complete"
             unzip -o *.zip
-            echo "Api Ready"
-    - name: Check cached version
-      uses: nick-fields/retry@v2
-      with:
-        max_attempts: 5
-        timeout_minutes: 2
-        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)
-            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 -
-            unzip -o *.zip
-            echo $newVersion > ./sirius/HashCode
-            fi
+            echo "Api Ready"
\ No newline at end of file

From 45ea6dda56716c075e117cb125284006b37e68c4 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 13:39:30 +0200
Subject: [PATCH 11/15] use wget

---
 .github/workflows/update-api.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml
index 7c0ab139..caee7db1 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://github.com/sirius-ms/sirius/releases/download/v6.3.3-SNAPSHOT/sirius-6.3.3-SNAPSHOT-linux-x64.zip
+            wget https://github.com/sirius-ms/sirius/releases/download/v6.3.3-SNAPSHOT/sirius-6.3.3-SNAPSHOT-linux-x64.zip
             echo "Download Complete"
             unzip -o *.zip
             echo "Api Ready"
\ No newline at end of file

From ea106ccad42fcbc8667693a3f98100bebdcf5f18 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 15:25:55 +0200
Subject: [PATCH 12/15] fix list indexing in select_header

---
 client-api_r/generated/R/api_client.R        | 2 +-
 client-api_r/templates/r/api_client.mustache | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

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/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]])
       }
     }
   )

From 2578f1bbedb1d1ffbc5c2647f53f74eeea9e84ee Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 15:26:30 +0200
Subject: [PATCH 13/15] set await_deletion for job deletion

---
 client-api_r/generated/tests/testthat/test_jobs_api.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 d1e133c1..b48a97d4 100644
--- a/client-api_r/generated/tests/testthat/test_jobs_api.R
+++ b/client-api_r/generated/tests/testthat/test_jobs_api.R
@@ -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)
 

From 0baf1785892dec6b1fd69a9e2c9c487fec1d067f Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 15:56:33 +0200
Subject: [PATCH 14/15] reset update-api for now

---
 .github/workflows/update-api.yml | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml
index caee7db1..63204ce2 100644
--- a/.github/workflows/update-api.yml
+++ b/.github/workflows/update-api.yml
@@ -20,7 +20,22 @@ jobs:
         timeout_minutes: 2
         command: |
             cd .updater/api
-            wget https://github.com/sirius-ms/sirius/releases/download/v6.3.3-SNAPSHOT/sirius-6.3.3-SNAPSHOT-linux-x64.zip
-            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 -i -            echo "Download Complete"
             unzip -o *.zip
-            echo "Api Ready"
\ No newline at end of file
+            echo "Api Ready"
+    - name: Check cached version
+      uses: nick-fields/retry@v2
+      with:
+        max_attempts: 5
+        timeout_minutes: 2
+        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)
+            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 -
+            unzip -o *.zip
+            echo $newVersion > ./sirius/HashCode
+            fi
\ No newline at end of file

From ef3df9c202c9e755543a256a3166c2313033a79a Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 2 Oct 2025 17:14:31 +0200
Subject: [PATCH 15/15] non-verbose wget

---
 .github/workflows/NewUpdate.yml  | 8 ++++----
 .github/workflows/PythonTest.yml | 2 +-
 .github/workflows/RTest.yml      | 2 +-
 .github/workflows/update-api.yml | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

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 04db6a18..d37b5e2d 100644
--- a/.github/workflows/PythonTest.yml
+++ b/.github/workflows/PythonTest.yml
@@ -46,7 +46,7 @@ jobs:
       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
+        wget -nv ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius
         chmod 666 $HOME/tomato_small.sirius
     - name: Lint with flake8
       run: |
diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 3033d4ff..a8016185 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -44,7 +44,7 @@ jobs:
       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
+        wget -nv ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius
         chmod 666 $HOME/tomato_small.sirius
     - name: Check SIRIUS download
       run: |
diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml
index 63204ce2..37293bb0 100644
--- a/.github/workflows/update-api.yml
+++ b/.github/workflows/update-api.yml
@@ -20,7 +20,7 @@ jobs:
         timeout_minutes: 2
         command: |
             cd .updater/api
-            curl -s  https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i -            echo "Download Complete"
+            curl -s  https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i -            echo "Download Complete"
             unzip -o *.zip
             echo "Api Ready"
     - name: Check cached version
@@ -31,11 +31,11 @@ jobs:
         command: |
             cd .updater/api
             currVersion=$(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
\ No newline at end of file