test(cpg_flow_test/): add sg.id to all jobs

populationgenomics · Dec 13, 2024 · 454b2a3 · 454b2a3
1 parent 9256c68
commit 454b2a3
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Showing 4 changed files with 9 additions and 6 deletions.
diff --git a/cpg_flow_test/jobs/cumulative_calc.py b/cpg_flow_test/jobs/cumulative_calc.py
@@ -5,10 +5,11 @@
 
 def cumulative_calc(
     b: Batch,
+    sequencing_group: SequencingGroup,
     input_file_path: str,
     output_file_path: str,
 ) -> list[Job]:
-    title = 'Cumulative Calc'
+    title = f'Cumulative Calc: {sequencing_group.id}'
     job = b.new_job(name=title)
     primes_path = b.read_input(input_file_path)
 

diff --git a/cpg_flow_test/jobs/first_n_primes.py b/cpg_flow_test/jobs/first_n_primes.py
@@ -3,8 +3,10 @@
 from hailtop.batch.job import Job
 
 
-def first_n_primes(b: Batch, input_file_path: str, output_file_path: str, depends_on: Job) -> list[Job]:
-    title = 'First N Primes'
+def first_n_primes(
+    b: Batch, sequencing_group: SequencingGroup, input_file_path: str, output_file_path: str, depends_on: Job,
+) -> list[Job]:
+    title = f'First N Primes: {sequencing_group.id}'
     job = b.new_job(name=title)
     id_sum_path = b.read_input(input_file_path)
 

diff --git a/cpg_flow_test/jobs/iterative_digit_sum.py b/cpg_flow_test/jobs/iterative_digit_sum.py
@@ -8,7 +8,7 @@ def iterative_digit_sum(
     sequencing_group: SequencingGroup,
     output_file_path: str,
 ) -> list[Job]:
-    title = 'Iterative Digit Sum'
+    title = f'Iterative Digit Sum: {sequencing_group.id}'
     job = b.new_job(name=title)
 
     cmd = f"""\

diff --git a/cpg_flow_test/stages.py b/cpg_flow_test/stages.py
@@ -71,7 +71,7 @@ def queue_jobs(self, sequencing_group: SequencingGroup, inputs: StageInput) -> S
 
         # Generate first N primes
         primes_output_path = str(self.expected_outputs(sequencing_group).get('primes', ''))
-        job_primes = first_n_primes(b, id_sum_output_path, primes_output_path, depends_on=job_id_sum)
+        job_primes = first_n_primes(b, sequencing_group, id_sum_output_path, primes_output_path, depends_on=job_id_sum)
 
         jobs = [job_id_sum, job_primes]
 
@@ -92,7 +92,7 @@ def queue_jobs(self, sequencing_group: SequencingGroup, inputs: StageInput) -> S
         b = get_batch()
 
         cumulative_calc_output_path = str(self.expected_outputs(sequencing_group).get('cumulative', ''))
-        job_cumulative_calc = cumulative_calc(b, input_json, cumulative_calc_output_path)
+        job_cumulative_calc = cumulative_calc(b, sequencing_group, input_json, cumulative_calc_output_path)
 
         jobs = [job_cumulative_calc]