adapt python sdk tests to new version

.updater/clientTests/PythonTests/test/test_compounds_api.py

@@ -18,7 +18,7 @@
 import unittest
 
 import PySirius
-from PySirius import PySiriusAPI, SiriusSDK
+from PySirius import PySiriusAPI, SiriusSDK, PagedModelCompound
 from PySirius.models.compound import Compound
 from PySirius.models.trace_set import TraceSet
 from PySirius.models.page_compound import PageCompound
@@ -121,7 +121,7 @@ def test_get_compounds_paged(self) -> None:
         Page of available compounds (group of ion identities) in the given project-space.
         """
         response = self.api.compounds().get_compounds_paged(self.project_id)
-        self.assertIsInstance(response, PageCompound)
+        self.assertIsInstance(response, PagedModelCompound)
 
     def test_get_traces(self) -> None:
         """Test case for get_traces

.updater/clientTests/PythonTests/test/test_features_api.py

@@ -12,34 +12,23 @@
 """  # noqa: E501
 
 import os
-import json
 import unittest
 
-import PySirius
-from PySirius import PySiriusAPI, SiriusSDK
-from PySirius.models.ms_data import MsData
-from PySirius.models.feature_import import FeatureImport
+from PySirius import SiriusSDK, PagedModelAlignedFeature, PagedModelStructureCandidateScored, \
+    PagedModelStructureCandidateFormula, PagedModelFormulaCandidate, QuantificationTableExperimental, \
+    PagedModelSpectralLibraryMatch, TraceSetExperimental
 from PySirius.models.aligned_feature import AlignedFeature
-from PySirius.models.aligned_feature_quality import AlignedFeatureQuality
-from PySirius.models.compound_classes import CompoundClasses
-from PySirius.models.quantification_table import QuantificationTable
-from PySirius.models.canopus_prediction import CanopusPrediction
 from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData
-from PySirius.models.page_aligned_feature import PageAlignedFeature
 from PySirius.models.annotated_spectrum import AnnotatedSpectrum
+from PySirius.models.canopus_prediction import CanopusPrediction
+from PySirius.models.compound_classes import CompoundClasses
 from PySirius.models.formula_candidate import FormulaCandidate
-from PySirius.models.page_formula_candidate import PageFormulaCandidate
 from PySirius.models.fragmentation_tree import FragmentationTree
 from PySirius.models.isotope_pattern_annotation import IsotopePatternAnnotation
 from PySirius.models.lipid_annotation import LipidAnnotation
-# from PySirius.models.spectral_library_match import SpectralLibraryMatch
-from PySirius.models.page_spectral_library_match import PageSpectralLibraryMatch
 from PySirius.models.spectral_library_match_summary import SpectralLibraryMatchSummary
 from PySirius.models.structure_candidate_formula import StructureCandidateFormula
 from PySirius.models.structure_candidate_scored import StructureCandidateScored
-from PySirius.models.page_structure_candidate_formula import PageStructureCandidateFormula
-from PySirius.models.page_structure_candidate_scored import PageStructureCandidateScored
-from PySirius.models.trace_set import TraceSet
 
 
 class TestFeaturesApi(unittest.TestCase):
@@ -49,7 +38,9 @@ def setUp(self) -> None:
         self.api = SiriusSDK().attach_or_start_sirius()
         self.project_id = "test_features_api"
         self.path_to_project = f"{os.environ.get('HOME')}/tomato_small.sirius"
-        self.api.projects().open_project_space(self.project_id, self.path_to_project)
+        # check if test project already open -> allows to run tests in independent calls.
+        if self.api.projects().get_project_space_without_preload_content(self.project_id).status == 404:
+            self.api.projects().open_project_space(self.project_id, self.path_to_project)
         # the single one ID with MSNovelist results computed
         self.aligned_feature_id = "586487307819356741"
 
@@ -103,32 +94,31 @@ def test_delete_aligned_feature(self) -> None:
 
         Delete feature (aligned over runs) with the given identifier from the specified project-space.
         """
-        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]
-        import_result = self.api.projects().import_preprocessed_data(self.project_id, input_files=input_files)
-        feature_ids = import_result.affected_aligned_feature_ids
-
-        response_before = self.api.features().get_aligned_features(self.project_id)
-        self.api.features().delete_aligned_feature(self.project_id, feature_ids[0])
-        self.api.features().delete_aligned_feature(self.project_id, feature_ids[1])
-        response_after = self.api.features().get_aligned_features(self.project_id)
+        project_info = self.api.projects().create_project_space(project_id="delete-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]
+            import_result = self.api.projects().import_preprocessed_data(project_id, input_files=input_files)
+            feature_ids = import_result.affected_aligned_feature_ids
 
-        self.assertIsInstance(response_before, list)
-        self.assertIsInstance(response_before[0], AlignedFeature)
+            response_before = self.api.features().get_aligned_features(project_id)
+            self.api.features().delete_aligned_feature(project_id, feature_ids[0])
+            self.api.features().delete_aligned_feature(project_id, feature_ids[1])
+            response_after = self.api.features().get_aligned_features(project_id)
 
-        self.assertIsInstance(response_after, list)
-        self.assertIsInstance(response_after[0], AlignedFeature)
+            self.assertIsInstance(response_before, list)
+            self.assertIsInstance(response_before[0], AlignedFeature)
 
-        self.assertEqual(len(response_before) - len(response_after), 2)
+            self.assertIsInstance(response_after, list)
+            self.assertEqual(len(response_after), 0)
 
-    def test_delete_aligned_features(self) -> None:
-        """Test case for delete_aligned_features
-
-        Delete feature (aligned over runs) with the given identifier from the specified project-space.
-        """
-        pass
+            self.assertEqual(len(response_before) - len(response_after), 2)
+        finally:
+            self.api.projects().close_project_space(project_id)
+            os.remove(project_info.location)
 
     def test_get_aligned_feature(self) -> None:
         """Test case for get_aligned_feature
@@ -153,7 +143,7 @@ def test_get_aligned_features_paged(self) -> None:
         Get all available features (aligned over runs) in the given project-space.
         """
         response = self.api.features().get_aligned_features_paged(self.project_id)
-        self.assertIsInstance(response, PageAlignedFeature)
+        self.assertIsInstance(response, PagedModelAlignedFeature)
 
     def test_get_best_matching_compound_classes(self) -> None:
         """Test case for get_best_matching_compound_classes
@@ -200,15 +190,15 @@ def test_get_de_novo_structure_candidates_by_formula_paged(self) -> None:
         response = self.api.features().get_de_novo_structure_candidates_by_formula_paged(self.project_id,
                                                                                          self.aligned_feature_id,
                                                                                          self.formula_id)
-        self.assertIsInstance(response, PageStructureCandidateScored)
+        self.assertIsInstance(response, PagedModelStructureCandidateScored)
 
     def test_get_de_novo_structure_candidates_paged(self) -> None:
         """Test case for get_de_novo_structure_candidates_paged
 
         Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.  StructureCandidates can be enriched with molecular fingerprint.
         """
         response = self.api.features().get_de_novo_structure_candidates_paged(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, PageStructureCandidateFormula)
+        self.assertIsInstance(response, PagedModelStructureCandidateFormula)
 
     def test_get_fingerprint_prediction(self) -> None:
         """Test case for get_fingerprint_prediction
@@ -259,7 +249,7 @@ def test_get_formula_candidates_paged(self) -> None:
         Page of FormulaResultContainers available for this feature with minimal information.
         """
         response = self.api.features().get_formula_candidates_paged(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, PageFormulaCandidate)
+        self.assertIsInstance(response, PagedModelFormulaCandidate)
 
     def test_get_frag_tree(self) -> None:
         """Test case for get_frag_tree
@@ -301,8 +291,8 @@ def test_get_quantification(self) -> None:
         """Test case for get_quantification
 
         """
-        response = self.api.features().get_quantification(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, QuantificationTable)
+        response = self.api.features().get_quantification_experimental(self.project_id, self.aligned_feature_id)
+        self.assertIsInstance(response, QuantificationTableExperimental)
 
     def test_get_spectral_library_match(self) -> None:
         """Test case for get_spectral_library_match
@@ -326,7 +316,7 @@ def test_get_spectral_library_matches_paged(self) -> None:
         Page of spectral library matches for the given 'alignedFeatureId'.
         """
         response = self.api.features().get_spectral_library_matches_paged(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, PageSpectralLibraryMatch)
+        self.assertIsInstance(response, PagedModelSpectralLibraryMatch)
 
     def test_get_spectral_library_matches_summary(self) -> None:
         """Test case for get_spectral_library_matches_summary
@@ -377,22 +367,22 @@ def test_get_structure_candidates_by_formula_paged(self) -> None:
         response = self.api.features().get_structure_candidates_by_formula_paged(self.project_id,
                                                                                  self.aligned_feature_id,
                                                                                  self.formula_id)
-        self.assertIsInstance(response, PageStructureCandidateScored)
+        self.assertIsInstance(response, PagedModelStructureCandidateScored)
 
     def test_get_structure_candidates_paged(self) -> None:
         """Test case for get_structure_candidates_paged
 
         Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
         """
         response = self.api.features().get_structure_candidates_paged(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, PageStructureCandidateFormula)
+        self.assertIsInstance(response, PagedModelStructureCandidateFormula)
 
     def test_get_traces1(self) -> None:
         """Test case for get_traces1
 
         """
-        response = self.api.features().get_traces1(self.project_id, self.aligned_feature_id)
-        self.assertIsInstance(response, TraceSet)
+        response = self.api.features().get_traces_experimental(self.project_id, self.aligned_feature_id)
+        self.assertIsInstance(response, TraceSetExperimental)
 
 
 if __name__ == '__main__':

.updater/clientTests/PythonTests/test/test_jobs_api.py

@@ -20,7 +20,7 @@
 import PySirius
 from PySirius import PySiriusAPI, SiriusSDK
 from PySirius.models.job import Job
-from PySirius.models.page_job import PageJob
+from PySirius.models.paged_model_job import PagedModelJob
 from PySirius.models.job_submission import JobSubmission
 
 
@@ -31,7 +31,10 @@ def setUp(self) -> None:
         self.api = SiriusSDK().attach_or_start_sirius()
         self.project_id = "test_jobs_api"
         self.path_to_project = f"{os.environ.get('HOME')}/test_jobs_api.sirius"
-        self.api.projects().create_project_space(self.project_id, self.path_to_project)
+        if self.api.projects().get_project_space_without_preload_content(self.project_id).status == 404:
+            if os.path.exists(self.path_to_project):
+                os.remove(self.path_to_project)
+            self.api.projects().create_project_space(self.project_id, self.path_to_project)
 
         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"
@@ -157,7 +160,7 @@ def test_get_jobs_paged(self) -> None:
         Get Page of jobs with information such as current state and progress (if available).
         """
         response = self.api.jobs().get_jobs_paged(self.project_id)
-        self.assertIsInstance(response, PageJob)
+        self.assertIsInstance(response, PagedModelJob)
 
     def test_has_jobs(self) -> None:
         """Test case for has_jobs

.updater/clientTests/PythonTests/test/test_projects_api.py

@@ -14,8 +14,7 @@
 import os
 import unittest
 
-from PySirius import SiriusSDK
-from PySirius.api.projects_api import ProjectsApi
+from PySirius import SiriusSDK, JobOptField
 from PySirius.models.job import Job
 from PySirius.models.project_info import ProjectInfo
 from PySirius.models.import_result import ImportResult
@@ -26,7 +25,8 @@ class TestProjectsApi(unittest.TestCase):
     """ProjectsApi unit test stubs"""
 
     def setUp(self) -> None:
-        self.projects = SiriusSDK().attach_or_start_sirius().projects()
+        self.api = SiriusSDK().attach_or_start_sirius()
+        self.projects = self.api.projects()
         path_to_demo_data = f"{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"
@@ -35,7 +35,11 @@ def setUp(self) -> None:
         # equals test_create_project_space
         self.project_id = "test_projects_api"
         self.path_to_project = f"{os.environ.get('HOME')}/test_projects_api.sirius"
-        self.create_response = self.projects.create_project_space(self.project_id, self.path_to_project)
+
+        if self.api.projects().get_project_space_without_preload_content(self.project_id).status == 404:
+            if os.path.exists(self.path_to_project):
+                os.remove(self.path_to_project)
+            self.create_response = self.projects.create_project_space(self.project_id, self.path_to_project)
 
     def tearDown(self) -> None:
         # equals test_close_project_space
@@ -103,8 +107,8 @@ def test_import_ms_run_data(self) -> None:
         Import and Align full MS-Runs from various formats into the specified project  Possible formats (mzML, mzXML)
         """
         input_files = [self.full_ms_file]
-        parameters = LcmsSubmissionParameters()
-        response = self.projects.import_ms_run_data(self.project_id, parameters, input_files=input_files)
+        parameters = LcmsSubmissionParameters(align_lcms_runs=False)
+        response = self.projects.import_ms_run_data(project_id=self.project_id, parameters=parameters, input_files=input_files)
         self.assertIsInstance(response, ImportResult)
 
     def test_import_ms_run_data_as_job(self) -> None:
@@ -113,8 +117,8 @@ def test_import_ms_run_data_as_job(self) -> None:
         Import and Align full MS-Runs from various formats into the specified project as background job.
         """
         input_files = [self.full_ms_file]
-        parameters = LcmsSubmissionParameters()
-        response = self.projects.import_ms_run_data_as_job(self.project_id, parameters, input_files=input_files)
+        parameters = LcmsSubmissionParameters(align_lcms_runs=False)
+        response = self.projects.import_ms_run_data_as_job(project_id=self.project_id, parameters=parameters, input_files=input_files)
         self.assertIsInstance(response, Job)
 
     def test_import_preprocessed_data(self) -> None:

.updater/clientTests/PythonTests/test/test_searchable_databases_api.py

@@ -83,7 +83,7 @@ def test_import_into_database(self) -> None:
 
         Start import of structure and spectra files into the specified database.
         """
-        response = self.dbs.import_into_database(self.database_id, input_files=[self.test_file])
+        response = self.dbs.import_into_database_e(self.database_id, input_files=[self.test_file])
         self.assertIsInstance(response, SearchableDatabase)
 
     def test_remove_database(self) -> None: