From d0e38a435b6b99e11a313cc47d93ded18ce8e2bb Mon Sep 17 00:00:00 2001 From: joXemMx Date: Mon, 15 Dec 2025 10:54:38 +0100 Subject: [PATCH 1/4] cleanup --- .updater/clientTests/README.md | 3 - .updater/example_scripts/SDK_Example.R | 62 ------ .updater/example_scripts/SDK_example.py | 78 -------- .updater/examples/mgf/laudanosine.mgf | 164 ---------------- .updater/examples/ms/Bicuculline.ms | 97 ---------- .updater/examples/ms/Kaempferol.ms | 204 -------------------- .updater/examples/txt/chelidonine_ms.txt | 3 - .updater/examples/txt/chelidonine_msms1.txt | 59 ------ .updater/examples/txt/chelidonine_msms2.txt | 63 ------ 9 files changed, 733 deletions(-) delete mode 100644 .updater/clientTests/README.md delete mode 100644 .updater/example_scripts/SDK_Example.R delete mode 100644 .updater/example_scripts/SDK_example.py delete mode 100644 .updater/examples/mgf/laudanosine.mgf delete mode 100644 .updater/examples/ms/Bicuculline.ms delete mode 100644 .updater/examples/ms/Kaempferol.ms delete mode 100644 .updater/examples/txt/chelidonine_ms.txt delete mode 100644 .updater/examples/txt/chelidonine_msms1.txt delete mode 100644 .updater/examples/txt/chelidonine_msms2.txt diff --git a/.updater/clientTests/README.md b/.updater/clientTests/README.md deleted file mode 100644 index 8141f70c..00000000 --- a/.updater/clientTests/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# clientTests - -Tests libraries for functionality in different programming languages \ No newline at end of file diff --git a/.updater/example_scripts/SDK_Example.R b/.updater/example_scripts/SDK_Example.R deleted file mode 100644 index 72ca5e62..00000000 --- a/.updater/example_scripts/SDK_Example.R +++ /dev/null @@ -1,62 +0,0 @@ -# load Rsirius -library(Rsirius) - -# create your SiriusSDK instance; keep this -sdk <- SiriusSDK$new() - -# start SIRIUS and get your API client instance -# note: sdk class parameters will change and save the port, process ID and more -api_client <- sdk$start(sirius_path="/your/path/to/sirius", port=8080) - -# create an API instance using your client -api_instance <- rsirius_api$new(api_client) - -# login (if needed) -account_credentials <- AccountCredentials$new("USERNAME", "PASSWORD") -api_instance$login_and_account_api$Login(accept_terms=TRUE, account_credentials) - -# open a project space -project_id <- "my_project_id" -api_instance$projects_api$CreateProjectSpace(project_id, "my/project/path") - -# import preprocessed (.mgf file) data -my_compound <- "path/to/compound.mgf" -api_instance$projects_api$ImportPreprocessedData(project_id, input_files=my_compound) - -# get ID of imported feature -aligned_feature_id <- api_instance$features_api$GetAlignedFeatures(project_id)[[1]]$alignedFeatureId - -# build job submission for SIRIUS formula generation (in this example, from ground up) -alignedFeatureIds <- c(aligned_feature_id) -profile <- Instrument$new("QTOF") -formulaIdParams <- Sirius$new(enabled = TRUE, profile = profile) -job_submission <- JobSubmission$new(alignedFeatureIds = alignedFeatureIds, formulaIdParams = formulaIdParams) - -# start job for calculation -job <- api_instance$jobs_api$StartJob(project_id, job_submission) - -# use job$id to get updates on the job; will say "DONE" when succeeded -while (api_instance$jobs_api$GetJob(project_id, job$id)$progress$state == "RUNNING") { - Sys.sleep(1) -} - -# reap your rewards -formula_candidates <- api_instance$features_api$GetFormulaCandidates(project_id, aligned_feature_id) - -print(formula_candidates[[1]]) -# result of laudanosine.mgf example file -# { -# "formulaId": "598888667212985823", -# "molecularFormula": "C21H27NO4", -# "adduct": "[M + H]+", -# "rank": 1.000000, -# "siriusScore": 23.762199, -# "isotopeScore": 6.088375, -# "treeScore": 17.673823 -# } - -# close project space -api_instance$projects_api$CloseProjectSpace(project_id) - -# shutdown sirius; here is why you should keep your SiriusSDK instance -sdk$shutdown() diff --git a/.updater/example_scripts/SDK_example.py b/.updater/example_scripts/SDK_example.py deleted file mode 100644 index 19ed6de9..00000000 --- a/.updater/example_scripts/SDK_example.py +++ /dev/null @@ -1,78 +0,0 @@ -# load PySirius and other libraries -from PySirius import * -import json -import time - -# create your SiriusSDK instance; keep this -sdk = SiriusSDK() - -# start SIRIUS and get your API instance -# note: sdk class parameters will change and save the port, process ID and more -api_instance = sdk.start(sirius_path="/your/path/to/sirius", port=8080) - -# login (if needed) -account_credentials = AccountCredentials(username="USERNAME", password="PASSWORD") -api_instance.get_LoginAndAccountApi().login(accept_terms=True, account_credentials=account_credentials) - -# open a project space -project_id = "my_project_id" -api_instance.get_ProjectsApi().create_project_space(project_id, "my/project/path") - -# import preprocessed (.mgf file) data -my_compound = ["path/to/compound.mgf"] -api_instance.get_ProjectsApi().import_preprocessed_data(project_id, input_files=my_compound) - -# get ID of imported feature -aligned_feature_id = api_instance.get_FeaturesApi().get_aligned_features(project_id)[0].aligned_feature_id - -# build job submission for SIRIUS formula generation (in this example, from ground up) -sirius_json = { - "enabled": True, - "profile": "QTOF" -} -job_submission_json = { - "alignedFeatureIds": [ - aligned_feature_id - ], - "formulaIdParams": - sirius_json -} -job_submission = JobSubmission.from_json(json.dumps(job_submission_json)) - -# start job for calculation -job = api_instance.get_JobsApi().start_job(project_id, job_submission) - -# use job$id to get updates on the job; will say "DONE" when succeeded -while api_instance.get_JobsApi().get_job(project_id, job.id).progress.state == "RUNNING": - time.sleep(1) - -# reap your rewards -formula_candidates = api_instance.get_FeaturesApi().get_formula_candidates(project_id, aligned_feature_id) - -print(formula_candidates[0].to_str()) -# result of laudanosine.mgf example file -# {'adduct': '[M + H]+', -# 'annotatedSpectrum': None, -# 'canopusPrediction': None, -# 'compoundClasses': None, -# 'formulaId': '599279362621783910', -# 'fragmentationTree': None, -# 'isotopePatternAnnotation': None, -# 'isotopeScore': 6.088375197269453, -# 'lipidAnnotation': None, -# 'medianMassDeviation': None, -# 'molecularFormula': 'C21H27NO4', -# 'numOfExplainablePeaks': None, -# 'numOfExplainedPeaks': None, -# 'predictedFingerprint': None, -# 'rank': 1, -# 'siriusScore': 23.762198504770673, -# 'totalExplainedIntensity': None, -# 'treeScore': 17.67382330750122, -# 'zodiacScore': None} - -# close project space -api_instance.get_ProjectsApi().close_project_space(project_id) - -# shutdown sirius; here is why you should keep your SiriusSDK instance -sdk.shutdown() diff --git a/.updater/examples/mgf/laudanosine.mgf b/.updater/examples/mgf/laudanosine.mgf deleted file mode 100644 index 761913e8..00000000 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2.5158826E7 -356.139862060547 3678364.25 \ No newline at end of file diff --git a/.updater/examples/txt/chelidonine_msms1.txt b/.updater/examples/txt/chelidonine_msms1.txt deleted file mode 100644 index 1a495039..00000000 --- a/.updater/examples/txt/chelidonine_msms1.txt +++ /dev/null @@ -1,59 +0,0 @@ -97.12206268310547 12263.9248046875 -100.99124145507812 14292.5673828125 -110.13077545166016 14409.1328125 -119.8829345703125 15182.294921875 -123.09564971923828 13442.43359375 -123.35272979736328 14380.697265625 -131.52880859375 12785.7333984375 -135.04391479492188 221480.078125 -140.47174072265625 13793.8515625 -143.048583984375 25393.037109375 -149.02264404296875 45562.828125 -161.05979919433594 130821.078125 -163.03909301757812 98632.671875 -170.33750915527344 15445.8837890625 -173.05960083007812 161833.6875 -176.07041931152344 38333.31640625 -188.07192993164062 20834.064453125 -188.45452880859375 15425.666015625 -189.65896606445312 12847.6435546875 -228.24488830566406 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247210.5625 -307.0962829589844 92225.703125 -322.0029602050781 21654.107421875 -322.13299560546875 19328.5859375 -323.0909729003906 2.2080202E7 -323.3393859863281 75778.2890625 -323.5143127441406 37334.8359375 -323.7469482421875 66438.7890625 -324.09478759765625 464599.0 -329.4949645996094 15130.5673828125 -336.1220703125 1769652.0 -337.1259765625 51037.75 -338.13946533203125 50472.62890625 -339.15869140625 17019.75390625 -354.1330261230469 1293757.25 -354.3833923339844 30273.107421875 -354.8420715332031 37017.93359375 -355.1363525390625 6154083.0 -355.4226989746094 21227.328125 -355.8882141113281 26202.85546875 \ No newline at end of file From 091bd208f8cbd8b8df5a550f3f95da516e306207 Mon Sep 17 00:00:00 2001 From: joXemMx Date: Mon, 15 Dec 2025 10:55:31 +0100 Subject: [PATCH 2/4] add tomato project as LFS file --- .gitattributes | 1 + .updater/clientTests/Data/tomato_small.sirius | 3 +++ 2 files changed, 4 insertions(+) create mode 100644 .gitattributes create mode 100644 .updater/clientTests/Data/tomato_small.sirius diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..c4404055 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.sirius filter=lfs diff=lfs merge=lfs -text diff --git a/.updater/clientTests/Data/tomato_small.sirius b/.updater/clientTests/Data/tomato_small.sirius new file mode 100644 index 00000000..74582170 --- /dev/null +++ b/.updater/clientTests/Data/tomato_small.sirius @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:883cad67e5afa4b84ff427c6950270393a02c7d2ce16f77ca533e405fac2e057 +size 491077632 From 75bb2848820de162e5919853641282b3c133d90a Mon Sep 17 00:00:00 2001 From: joXemMx Date: Mon, 15 Dec 2025 11:25:22 +0100 Subject: [PATCH 3/4] adapt to tomato project being moved to LFS --- .github/workflows/PythonTest.yml | 4 ---- .github/workflows/RTest.yml | 4 ---- .../generated/test/test_features_api.py | 16 +++++++--------- .../generated/test/test_projects_api.py | 11 ++++++----- .../generated/tests/testthat/test_features_api.R | 2 +- .../generated/tests/testthat/test_projects_api.R | 13 +++++-------- 6 files changed, 19 insertions(+), 31 deletions(-) diff --git a/.github/workflows/PythonTest.yml b/.github/workflows/PythonTest.yml index 185eb03a..0f9934d2 100644 --- a/.github/workflows/PythonTest.yml +++ b/.github/workflows/PythonTest.yml @@ -70,10 +70,6 @@ jobs: unzip -q sirius-${version}-linux-x64.zip - 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 $HOME/tomato_small.sirius - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml index 2f5c0d1e..86fdded9 100644 --- a/.github/workflows/RTest.yml +++ b/.github/workflows/RTest.yml @@ -73,10 +73,6 @@ jobs: unzip -q sirius-${version}-linux-x64.zip - 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/)" diff --git a/client-api_python/generated/test/test_features_api.py b/client-api_python/generated/test/test_features_api.py index 5b3eafc2..54e0e2ca 100644 --- a/client-api_python/generated/test/test_features_api.py +++ b/client-api_python/generated/test/test_features_api.py @@ -20,7 +20,11 @@ class TestFeaturesApi(unittest.TestCase): def setUp(self) -> None: self.api = SiriusSDK().attach_to_sirius(sirius_port=8080) self.project_id = "test_features_api" - self.path_to_project = f"{os.environ.get('HOME')}/tomato_small.sirius" + path_to_demo_data = os.environ.get('HOME') + "/sirius-client-openAPI/.updater/clientTests/Data" + self.preproc_ms2_file_1 = path_to_demo_data + "/Kaempferol.ms" + self.preproc_ms2_file_2 = path_to_demo_data + "/laudanosine.mgf" + self.path_to_project = path_to_demo_data + "/tomato_small.sirius" + # check if test project already open -> allows to run tests in independent calls. if self.api.projects().get_project_without_preload_content(self.project_id).status == 404: self.project_info = self.api.projects().open_project(self.project_id, self.path_to_project) @@ -86,10 +90,7 @@ def test_delete_aligned_feature(self) -> None: project_info = self.api.projects().create_project(project_id="delete-feature-project") project_id = project_info.project_id try: - path_to_demo_data = f"{os.environ.get('HOME')}/sirius-client-openAPI/.updater/clientTests/Data" - preproc_ms2_file_1 = path_to_demo_data + "/Kaempferol.ms" - preproc_ms2_file_2 = path_to_demo_data + "/laudanosine.mgf" - input_files = [preproc_ms2_file_1, preproc_ms2_file_2] + input_files = [self.preproc_ms2_file_1, self.preproc_ms2_file_2] import_result = self.api.projects().import_preprocessed_data(project_id, input_files=input_files) feature_ids = import_result.affected_aligned_feature_ids @@ -117,10 +118,7 @@ def test_delete_aligned_features(self) -> None: project_info = self.api.projects().create_project(project_id="delete-features-project") project_id = project_info.project_id try: - path_to_demo_data = f"{os.environ.get('HOME')}/sirius-client-openAPI/.updater/clientTests/Data" - preproc_ms2_file_1 = path_to_demo_data + "/Kaempferol.ms" - preproc_ms2_file_2 = path_to_demo_data + "/laudanosine.mgf" - input_files = [preproc_ms2_file_1, preproc_ms2_file_2] + input_files = [self.preproc_ms2_file_1, self.preproc_ms2_file_2] import_result = self.api.projects().import_preprocessed_data(project_id, input_files=input_files) feature_ids = import_result.affected_aligned_feature_ids diff --git a/client-api_python/generated/test/test_projects_api.py b/client-api_python/generated/test/test_projects_api.py index ee189548..c078a7fa 100644 --- a/client-api_python/generated/test/test_projects_api.py +++ b/client-api_python/generated/test/test_projects_api.py @@ -19,10 +19,11 @@ class TestProjectsApi(unittest.TestCase): def setUp(self) -> None: self.api = SiriusSDK().attach_to_sirius(sirius_port=8080) self.projects = self.api.projects() - path_to_demo_data = f"{os.environ.get('HOME')}/sirius-client-openAPI/.updater/clientTests/Data" + path_to_demo_data = os.environ.get('HOME') + "/sirius-client-openAPI/.updater/clientTests/Data" self.preproc_ms2_file_1 = path_to_demo_data + "/Kaempferol.ms" self.preproc_ms2_file_2 = path_to_demo_data + "/laudanosine.mgf" self.full_ms_file = path_to_demo_data + "/SPF4_Eso3_GH6_01_22643.mzXML" + self.tomato_project = path_to_demo_data + "/tomato_small.sirius" # equals test_create_project self.project_id = "test_projects_api" @@ -65,7 +66,7 @@ def test_get_canopus_classy_fire_data(self) -> None: Get CANOPUS prediction vector definition for ClassyFire classes """ try: - self.projects.open_project("tomato", f"{os.environ.get('HOME')}/tomato_small.sirius") + self.projects.open_project("tomato", self.tomato_project) response = self.projects.get_canopus_classy_fire_data("tomato", 1) finally: self.projects.close_project("tomato") @@ -77,7 +78,7 @@ def test_get_canopus_npc_data(self) -> None: Get CANOPUS prediction vector definition for NPC classes """ try: - self.projects.open_project("tomato", f"{os.environ.get('HOME')}/tomato_small.sirius") + self.projects.open_project("tomato", self.tomato_project) response = self.projects.get_canopus_npc_data("tomato", 1) finally: self.projects.close_project("tomato") @@ -89,7 +90,7 @@ def test_get_finger_id_data(self) -> None: Get CSI:FingerID fingerprint (prediction vector) definition """ try: - self.projects.open_project("tomato", f"{os.environ.get('HOME')}/tomato_small.sirius") + self.projects.open_project("tomato", self.tomato_project) response = self.projects.get_finger_id_data("tomato", 1) finally: self.projects.close_project("tomato") @@ -156,7 +157,7 @@ def test_open_project(self) -> None: Open an existing project-space and make it accessible via the given projectId. """ try: - response = self.projects.open_project("tomato", f"{os.environ.get('HOME')}/tomato_small.sirius") + response = self.projects.open_project("tomato", self.tomato_project) finally: self.projects.close_project("tomato") self.assertIsInstance(response, ProjectInfo) 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 4b1071c0..ba3f321a 100644 --- a/client-api_r/generated/tests/testthat/test_features_api.R +++ b/client-api_r/generated/tests/testthat/test_features_api.R @@ -15,7 +15,7 @@ preproc_ms2_file_2 <- paste(path_to_demo_data, "laudanosine.mgf", sep = "/") # the single ID with MSNovelist AND spectral library search results computed aligned_feature_id <- "586487310566638367" -tomato_project <- paste(Sys.getenv("HOME"), "tomato_small.sirius", sep = "/") +tomato_project <- paste(path_to_demo_data, "tomato_small.sirius", sep = "/") basic_spectrum <- c(BasicSpectrum$new(peaks = c(SimplePeak$new(1.23, 4.56)), precursorMz = 1.23)) feature_import <- c(FeatureImport$new(name = "testfeature", feature_id = "testfeature", ionMass = 1.23, adduct = "[M+?]+", ms1Spectra = basic_spectrum, ms2Spectra = basic_spectrum)) 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 b03e16a5..8b474d88 100644 --- a/client-api_r/generated/tests/testthat/test_projects_api.R +++ b/client-api_r/generated/tests/testthat/test_projects_api.R @@ -7,6 +7,7 @@ sdk <- SiriusSDK$new() api <- sdk$attach_to_sirius(sirius_port=8080) api_instance <- api$projects_api path_to_demo_data <- paste(Sys.getenv("HOME"), "sirius-client-openAPI/.updater/clientTests/Data", sep = "/") +tomato_project <- paste(path_to_demo_data, "tomato_small.sirius", sep = "/") preproc_ms2_file_1 <- paste(path_to_demo_data, "Kaempferol.ms", sep = "/") preproc_ms2_file_2 <- paste(path_to_demo_data, "laudanosine.mgf", sep = "/") full_ms_file <- paste(path_to_demo_data, "SPF4_Eso3_GH6_01_22643.mzXML", sep = "/") @@ -75,8 +76,7 @@ test_that("GetCanopusClassyFireData", { tryCatch({ project_id <- "GetCanopusClassyFireData" - project_dir <- paste(Sys.getenv("HOME"), "tomato_small.sirius", sep = "/") - api_instance$OpenProject(project_id, project_dir) + api_instance$OpenProject(project_id, tomato_project) response <- api_instance$GetCanopusClassyFireData(project_id, 1) expect_true(inherits(response, "data.frame")) @@ -99,8 +99,7 @@ test_that("GetCanopusNpcData", { tryCatch({ project_id <- "GetCanopusNpcData" - project_dir <- paste(Sys.getenv("HOME"), "tomato_small.sirius", sep = "/") - api_instance$OpenProject(project_id, project_dir) + api_instance$OpenProject(project_id, tomato_project) response <- api_instance$GetCanopusNpcData(project_id, 1) expect_true(inherits(response, "data.frame")) @@ -123,8 +122,7 @@ test_that("GetFingerIdData", { tryCatch({ project_id <- "GetFingerIdData" - project_dir <- paste(Sys.getenv("HOME"), "tomato_small.sirius", sep = "/") - api_instance$OpenProject(project_id, project_dir) + api_instance$OpenProject(project_id, tomato_project) response <- api_instance$GetFingerIdData(project_id, 1) expect_true(inherits(response, "data.frame")) @@ -478,9 +476,8 @@ test_that("OpenProject", { tryCatch({ project_id <- "OpenProject" - project_dir <- paste(Sys.getenv("HOME"), "tomato_small.sirius", sep = "/") - response <- api_instance$OpenProject(project_id, project_dir) + response <- api_instance$OpenProject(project_id, tomato_project) expect_true(inherits(response, "ProjectInfo")) }, finally = { From 5f1ea1202fbfea9badb66ea1c9ac7878de10f563 Mon Sep 17 00:00:00 2001 From: joXemMx Date: Mon, 15 Dec 2025 11:36:26 +0100 Subject: [PATCH 4/4] enable lfs in checkout actions --- .github/workflows/PythonTest.yml | 2 ++ .github/workflows/RTest.yml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/.github/workflows/PythonTest.yml b/.github/workflows/PythonTest.yml index 0f9934d2..cd159f3d 100644 --- a/.github/workflows/PythonTest.yml +++ b/.github/workflows/PythonTest.yml @@ -33,6 +33,8 @@ jobs: SIRIUS_PW: ${{ secrets.SIRIUS_PW }} steps: - uses: actions/checkout@v3 + with: + lfs: true - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v3 with: diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml index 86fdded9..962c6c68 100644 --- a/.github/workflows/RTest.yml +++ b/.github/workflows/RTest.yml @@ -33,6 +33,8 @@ jobs: SIRIUS_PW: ${{ secrets.SIRIUS_PW }} steps: - uses: actions/checkout@v3 + with: + lfs: true - name: Set up R ${{ matrix.r-version }} uses: r-lib/actions/setup-r@v2 with: