Revert earlier changes (#3689)

### Fixed

- Reverted changes from earlier PRs.

cg/services/illumina/post_processing/housekeeper_storage.py

@@ -15,7 +15,6 @@
     get_undetermined_fastqs,
     rename_fastq_file_if_needed,
 )
-from cg.store.models import Sample
 from cg.store.store import Store
 from cg.utils.files import get_files_matching_pattern
 
@@ -33,10 +32,6 @@ def _should_fastq_path_be_stored_in_housekeeper(
     Check if a sample fastq file should be tracked in Housekeeper.
     Only fastq files that pass the q30 threshold should be tracked.
     """
-    sample: Sample = store.get_sample_by_internal_id(internal_id=sample_id)
-
-    if sample.is_negative_control:
-        return True
 
     lane = get_lane_from_sample_fastq(sample_fastq_path)
     q30_threshold: int = get_q30_threshold(sequencer_type)

cg/store/crud/update.py

@@ -68,10 +68,7 @@ def update_sample_reads_illumina(self, internal_id: str, sequencer_type: Sequenc
         q30_threshold: int = get_q30_threshold(sequencer_type)
 
         for sample_metric in sample_metrics:
-            if (
-                sample_metric.base_passing_q30_percent >= q30_threshold
-                or sample.is_negative_control
-            ):
+            if sample_metric.base_passing_q30_percent >= q30_threshold:
                 total_reads_for_sample += sample_metric.total_reads_in_lane
 
         sample.reads = total_reads_for_sample

tests/store/crud/update/test_update.py

@@ -1,7 +1,6 @@
 from datetime import datetime
 
 from cg.constants import SequencingRunDataAvailability
-from cg.constants.constants import ControlOptions
 from cg.constants.sequencing import Sequencers
 from cg.store.models import (
     IlluminaSampleSequencingMetrics,
@@ -87,30 +86,6 @@ def test_update_sample_reads_illumina_fail_q30(
     assert sample.reads == 0
 
 
-def test_update_sample_reads_illumina_negative_control(
-    store_with_illumina_sequencing_data: Store, selected_novaseq_x_sample_ids: list[str]
-):
-    # GIVEN a store with Illumina Sequencing Runs and a sample id
-    sample: Sample = store_with_illumina_sequencing_data.get_sample_by_internal_id(
-        selected_novaseq_x_sample_ids[0]
-    )
-    assert sample.reads == 0
-    # GIVEN that the sample is a negative control sample
-    sample.control = ControlOptions.NEGATIVE
-
-    # WHEN updating the sample reads for a sequencing run
-    store_with_illumina_sequencing_data.update_sample_reads_illumina(
-        internal_id=selected_novaseq_x_sample_ids[0], sequencer_type=Sequencers.NOVASEQX
-    )
-
-    # THEN the total reads for the sample is updated
-    total_reads_for_sample: int = 0
-    sample_metrics: list[IlluminaSampleSequencingMetrics] = sample.sample_run_metrics
-    for sample_metric in sample_metrics:
-        total_reads_for_sample += sample_metric.total_reads_in_lane
-    assert sample.reads == total_reads_for_sample
-
-
 def test_update_sample_last_sequenced_at(
     store_with_illumina_sequencing_data: Store,
     selected_novaseq_x_sample_ids: list[str],