deprecate Helper classes and add wait_for_job_completion functionalit…

.github/workflows/NewUpdate.yml

@@ -101,6 +101,9 @@ jobs:
 
         chmod +x ./client-api_r/patches/list_syntax_fix.sh
         ./client-api_r/patches/list_syntax_fix.sh
+
+        chmod +x ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
+        ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
     - name: Remove Sirius Rest Api
       run: |
         cd .updater/api

.updater/clientTests/CondaFeedstockMinimalTests/PythonFeedstockTest.py

@@ -19,7 +19,7 @@
 jobSub.ms_novelist_params.enabled = False
 
 job = api.jobs().start_job(project_id=ps_info.project_id, job_submission=jobSub)
-Helper.wait_for_job_completion(ps_info.project_id, job.id, api.jobs())
+api.wait_for_job_completion(ps_info.project_id, job.id, 60)
 
 formula_id = api.features().get_aligned_feature(ps_info.project_id, featureId, [AlignedFeatureOptField.TOPANNOTATIONS]
                                                 ).top_annotations.formula_annotation.formula_id

.updater/clientTests/CondaFeedstockMinimalTests/RFeedstockTest.R

@@ -21,8 +21,7 @@ job_submission$canopusParams$enabled <- FALSE
 job_submission$msNovelistParams$enabled <- FALSE
 
 job <- sirius_api$jobs_api$StartJob(project_id, job_submission)
-Helper$new()$wait_for_job_completion(project_id, job$id, sirius_api$jobs_api)
-
+api$wait_for_job_completion(project_id, job$id, 60)
 aligned_feature_id <- sirius_api$features_api$GetAlignedFeatures(project_id)[[1]]$alignedFeatureId
 formula_id <- sirius_api$features_api$GetAlignedFeature(project_id, aligned_feature_id, opt_fields = list("topAnnotations"))$topAnnotations$formulaAnnotation$formulaId
 tree <- sirius_api$features_api$GetFragTree(project_id, aligned_feature_id, formula_id)

client-api_python/generated/PySirius/pysirius_api.py

@@ -1,6 +1,10 @@
 # THIS FILE IS NOT AUTO GENERATED AND MIGHT NEED TO BE CHANGED WHEN API ENDPOINTS CHANGE
 
 import PySirius
+import logging
+import traceback
+import time
+from PySirius import Job, ProjectInfo
 
 
 class PySiriusAPI:
@@ -62,4 +66,18 @@ def tags(self):
 
     def models(self):
         """returns the Superclass of all models"""
-        return PySirius.models
+        return PySirius.models
+
+    def wait_for_job_completion(self, project_id, job_id, timeout_in_sec=None):
+        if isinstance(project_id, ProjectInfo):
+            project_id = project_id.project_id
+        if isinstance(job_id, Job):
+            job_id = job_id.id
+        try:
+            while PySirius.JobsApi(self.api_client).get_job(project_id, job_id).progress.state not in ["CANCELED", "FAILED", "DONE"]:
+                time.sleep(1)
+                if isinstance(timeout_in_sec, int):
+                    timeout_in_sec = timeout_in_sec - 1
+                    if timeout_in_sec == 0: return
+        except Exception as e:
+            logging.error(traceback.format_exc())

client-api_python/generated/PySirius/pysirius_helper.py

@@ -2,14 +2,19 @@
 
 import time
 import PySirius
+from warnings import warn
 from PySirius import PySiriusAPI, ProjectInfo, Job
 
-
 class Helper:
     """helper methods for ease of use of the SDK"""
 
+    def __init__(self, *args, **kwargs):
+        warn(f'{self.__class__.__name__} will be deprecated.', DeprecationWarning, stacklevel=2)
+        super().__init__(*args, **kwargs)
+
     @staticmethod
     def wait_for_job_completion(project_id, job_id, jobs_api):
+        warn("This function will be deprecated. Use PySiriusAPI.wait_for_job_completion instead!", DeprecationWarning, stacklevel=2)
         if isinstance(jobs_api, PySiriusAPI):
             jobs_api = jobs_api.jobs()
         if isinstance(project_id, ProjectInfo):

client-api_python/generated/test/test_acceptance.py

@@ -33,7 +33,7 @@ def test_simple_computation(self):
             job_sub.ms_novelist_params.enabled = False
 
             job = api.jobs().start_job(project_id=ps_info.project_id, job_submission=job_sub)
-            Helper.wait_for_job_completion(ps_info, job, api)
+            api.wait_for_job_completion(ps_info, job, 60)
 
             formula_candidate = api.features().get_aligned_feature(ps_info.project_id, feature_id, opt_fields=["topAnnotations"]).top_annotations.formula_annotation
             tree = api.features().get_frag_tree(ps_info.project_id, feature_id, formula_candidate.formula_id)

client-api_python/generated/test/test_jobs_api.py

@@ -205,7 +205,7 @@ def test_start_job(self) -> None:
         job_submission = JobSubmission.from_json(json.dumps(job_submission_json))
         response = self.api.jobs().start_job(self.project_id, job_submission)
 
-        Helper.wait_for_job_completion(self.project_id, response.id, self.api.jobs())
+        self.api.wait_for_job_completion(self.project_id, response.id)
 
         self.assertIsInstance(response, Job)
 
@@ -232,7 +232,7 @@ def test_start_job_from_config(self) -> None:
         self.api.jobs().save_job_config(config_name, job_submission, True)
         response = self.api.jobs().start_job_from_config(self.project_id, config_name, [aligned_feature_id])
 
-        Helper.wait_for_job_completion(self.project_id, response.id, self.api.jobs())
+        self.api.wait_for_job_completion(self.project_id, response.id)
 
         self.api.jobs().delete_job_config(config_name)
         self.assertIsInstance(response, Job)

client-api_python/pysirius_api.py

@@ -1,6 +1,10 @@
 # THIS FILE IS NOT AUTO GENERATED AND MIGHT NEED TO BE CHANGED WHEN API ENDPOINTS CHANGE
 
 import PySirius
+import logging
+import traceback
+import time
+from PySirius import Job, ProjectInfo
 
 
 class PySiriusAPI:
@@ -62,4 +66,18 @@ def tags(self):
 
     def models(self):
         """returns the Superclass of all models"""
-        return PySirius.models
+        return PySirius.models
+
+    def wait_for_job_completion(self, project_id, job_id, timeout_in_sec=None):
+        if isinstance(project_id, ProjectInfo):
+            project_id = project_id.project_id
+        if isinstance(job_id, Job):
+            job_id = job_id.id
+        try:
+            while PySirius.JobsApi(self.api_client).get_job(project_id, job_id).progress.state not in ["CANCELED", "FAILED", "DONE"]:
+                time.sleep(1)
+                if isinstance(timeout_in_sec, int):
+                    timeout_in_sec = timeout_in_sec - 1
+                    if timeout_in_sec == 0: return
+        except Exception as e:
+            logging.error(traceback.format_exc())

client-api_python/pysirius_helper.py

@@ -2,14 +2,19 @@
 
 import time
 import PySirius
+from warnings import warn
 from PySirius import PySiriusAPI, ProjectInfo, Job
 
-
 class Helper:
     """helper methods for ease of use of the SDK"""
 
+    def __init__(self, *args, **kwargs):
+        warn(f'{self.__class__.__name__} will be deprecated.', DeprecationWarning, stacklevel=2)
+        super().__init__(*args, **kwargs)
+
     @staticmethod
     def wait_for_job_completion(project_id, job_id, jobs_api):
+        warn("This function will be deprecated. Use PySiriusAPI.wait_for_job_completion instead!", DeprecationWarning, stacklevel=2)
         if isinstance(jobs_api, PySiriusAPI):
             jobs_api = jobs_api.jobs()
         if isinstance(project_id, ProjectInfo):

client-api_r/generated/R/rsirius_api.R

@@ -85,6 +85,32 @@ rsirius_api <- R6::R6Class(
 
       self$tags_api <- TagsApi$new(self$api_client)
 
+    },
+
+    wait_for_job_completion = function(project_id, job_id, timeout_in_sec=NULL) {
+      if (inherits(project_id, "ProjectInfo")) {
+        project_id <- project_id$projectId
+      }
+      if (inherits(job_id, "Job")) {
+        job_id <- job_id$id
+      }
+      tryCatch({
+        while (!(self$jobs_api$GetJob(project_id, job_id)$progress$state %in% c("CANCELED", "FAILED", "DONE"))) {
+          Sys.sleep(1)
+          if (inherits(timeout_in_sec, "numeric")) {
+            timeout_in_sec <- timeout_in_sec - 1
+            if (timeout_in_sec == 0) {
+              return()
+            }
+          }
+        }
+      }, error = function(e){
+        message('Caught an error!')
+        message(e)
+      }, warning = function(w){
+        message('Caught an warning!')
+        message(w)
+      })
     }
   )
 )

client-api_r/generated/R/rsirius_helper.R

@@ -2,6 +2,7 @@ Helper <- R6::R6Class(
   "Helper",
   public = list(
     wait_for_job_completion = function(project_id, job_id, jobs_api) {
+      .Deprecated("rsirius_api$wait_for_job_completion")
       if (inherits(jobs_api, "rsirius_api")) {
         jobs_api <- jobs_api$jobs_api
       }

client-api_r/generated/tests/testthat.R

@@ -1,4 +1,4 @@
 library(testthat)
-library(Rsirius)
+library(RSirius)
 
-test_check("Rsirius")
+test_check("RSirius")

client-api_r/generated/tests/testthat/test_acceptance.R

@@ -33,7 +33,7 @@ test_that("Test Acceptance", {
     job_submission$alignedFeatureIds <- list(features_api$GetAlignedFeatures(project_id)[[1]]$alignedFeatureId)
 
     response <- api_instance$StartJob(project_id, job_submission)
-    Helper$new()$wait_for_job_completion(project_id, response$id, api_instance)
+    api$wait_for_job_completion(project_id, response$id, 60)
 
     formula_candidate <- features_api$GetAlignedFeature(project_id, job_submission$alignedFeatureIds[[1]], opt_fields = list("topAnnotations"))$
       topAnnotations$

client-api_r/generated/tests/testthat/test_jobs_api.R

@@ -324,7 +324,7 @@ test_that("StartJob", {
     job_submission$alignedFeatureIds <- list(features_api$GetAlignedFeatures(project_id)[[1]]$alignedFeatureId)
 
     response <- api_instance$StartJob(project_id, job_submission)
-    Helper$new()$wait_for_job_completion(project_id, response$id, api_instance)
+    api$wait_for_job_completion(project_id, response$id)
 
     expect_true(inherits(response, "Job"))
 
@@ -366,7 +366,7 @@ test_that("StartJobFromConfig", {
 
     api_instance$SaveJobConfig(project_id, job_submission, TRUE)
     response <- api_instance$StartJobFromConfig(project_id, project_id, job_submission$alignedFeatureIds)
-    Helper$new()$wait_for_job_completion(project_id, response$id, api_instance)
+    api$wait_for_job_completion(project_id, response$id)
 
     expect_true(inherits(response, "Job"))
 

client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+FILE="client-api_r/generated/R/rsirius_api.R"
+
+# Remove the last 3 lines (closing braces)
+head -n -3 "$FILE" > "${FILE}.tmp"
+
+# Append the new function and closing braces
+cat >> "${FILE}.tmp" << 'EOF'
+    },
+
+    wait_for_job_completion = function(project_id, job_id, timeout_in_sec=NULL) {
+      if (inherits(project_id, "ProjectInfo")) {
+        project_id <- project_id$projectId
+      }
+      if (inherits(job_id, "Job")) {
+        job_id <- job_id$id
+      }
+      tryCatch({
+        while (!(self$jobs_api$GetJob(project_id, job_id)$progress$state %in% c("CANCELED", "FAILED", "DONE"))) {
+          Sys.sleep(1)
+          if (inherits(timeout_in_sec, "numeric")) {
+            timeout_in_sec <- timeout_in_sec - 1
+            if (timeout_in_sec == 0) {
+              return()
+            }
+          }
+        }
+      }, error = function(e){
+        message('Caught an error!')
+        message(e)
+      }, warning = function(w){
+        message('Caught an warning!')
+        message(w)
+      })
+    }
+  )
+)
+EOF
+
+mv "${FILE}.tmp" "$FILE"
+
+echo "Function appended successfully"

client-api_r/rsirius_helper.R

@@ -2,6 +2,7 @@ Helper <- R6::R6Class(
   "Helper",
   public = list(
     wait_for_job_completion = function(project_id, job_id, jobs_api) {
+      .Deprecated("rsirius_api$wait_for_job_completion")
       if (inherits(jobs_api, "rsirius_api")) {
         jobs_api <- jobs_api$jobs_api
       }