qc: Removed job id as input parameter #TASK-6766

opencga-app/app/analysis/qc/family_qc/family_qc.py

@@ -12,7 +12,7 @@
 LOGGER = logging.getLogger('variant_qc_logger')
 
 class FamilyQCExecutor:
-    def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job_id, sample_ids, id_):
+    def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, sample_ids, id_):
         """Create output dir
 
         :param str vcf_file: VCF input file path
@@ -21,15 +21,13 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job
         :param str config: Configuration file path
         :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1)
         :param list sample_ids: Sample IDs from the VCF file
-        :param str job_id: ID from the executed job
         :param str id_: ID from the info JSON file
         """
         self.vcf_file = vcf_file
         self.info_file = info_file
         self.bam_file = bam_file
         self.config = config
         self.output_parent_dir = output_parent_dir
-        self.job_id = job_id
         self.sample_ids = sample_ids
         self.id_ = id_
 

opencga-app/app/analysis/qc/individual_qc/individual_qc.py

@@ -11,7 +11,7 @@
 LOGGER = logging.getLogger('variant_qc_logger')
 
 class IndividualQCExecutor:
-    def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job_id, sample_ids, id_):
+    def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, sample_ids, id_):
         """Create output dir
 
         :param str vcf_file: VCF input file path
@@ -20,15 +20,13 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job
         :param str config: Configuration file path
         :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1)
         :param list sample_ids: Sample IDs from the VCF file
-        :param str job_id: ID from the executed job
         :param str id_: ID from the info JSON file
         """
         self.vcf_file = vcf_file
         self.info_file = info_file
         self.bam_file = bam_file
         self.config = config
         self.output_parent_dir = output_parent_dir
-        self.job_id = job_id
         self.sample_ids = sample_ids
         self.id_ = id_
 

opencga-app/app/analysis/qc/sample_qc/sample_qc.py

@@ -19,15 +19,13 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job
         :param str config: Configuration file path
         :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1)
         :param list sample_ids: Sample IDs from the VCF file
-        :param str job_id: ID from the executed job
         :param str id_: ID from the info JSON file
         """
         self.vcf_file = vcf_file
         self.info_file = info_file
         self.bam_file = bam_file
         self.config = config
         self.output_parent_dir = output_parent_dir
-        self.job_id = job_id
         self.sample_ids = sample_ids
         self.id_ = id_
 
@@ -81,9 +79,8 @@ def bcftools_stats(self, vcf_file):
     bam_file = ""
     config = ""
     output_parent_dir = "/tmp/qc_tests/"
-    job_id = ""
     sample_ids = []
     id_ = ""
     se = SampleQCExecutor(vcf_file=vcf_file, info_file=info_file, bam_file=bam_file, config=config,
-                          output_parent_dir=output_parent_dir, job_id=job_id, sample_ids=sample_ids, id_=id_)
+                          output_parent_dir=output_parent_dir, sample_ids=sample_ids, id_=id_)
     sys.exit(se.run())

opencga-app/app/analysis/qc/variant_qc.main.py

@@ -39,8 +39,6 @@ def get_parser():
                         help='configuration file path')
     parser.add_argument('-o', '--output-dir', dest='output_dir',
                         help='output directory path')
-    parser.add_argument('--job-id', dest='job_id',
-                        help='job ID')
 
     parser.add_argument('-l', '--log-level', dest='log_level',
                         default='INFO', choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'],
@@ -196,7 +194,6 @@ def main():
     qc_type = args.qc_type
     config = args.config
     output_dir = os.path.realpath(os.path.expanduser(args.output_dir))
-    job_id = args.job_id
 
     # Setting up logger
     logger = create_logger(args.log_level, output_dir)
@@ -228,7 +225,6 @@ def main():
             bam_file=bam_files[i],
             config=config,
             output_parent_dir=qc_outdir_fpath,
-            job_id=job_id,
             sample_ids=sample_ids,
             id_=id_
         ).run()