Merge pull request #387 from 4dn-dcic/drr_add_kwargs

Accept kwargs

CHANGELOG.rst

@@ -3,6 +3,13 @@
 Change Log
 ==========
 
+3.2.2
+=====
+`PR 387: Add kwargs <https://github.com/4dn-dcic/tibanna/pull/387>`_
+
+* Add kwargs to various class' init methods
+
+
 3.2.1
 =====
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "3.2.1"
+version = "3.2.2"
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

tibanna/ami.py

@@ -20,7 +20,7 @@ class AMI(object):
     AMI_NAME = 'tibanna-ami-' + datetime.strftime(datetime.today(), '%Y%m%d')  # e.g tibanna-ami-20201113
     ARCHITECTURE = 'x86'
 
-    def __init__(self, base_ami=None, base_region=None, userdata_file=None, ami_name=None, architecture=None):
+    def __init__(self, base_ami=None, base_region=None, userdata_file=None, ami_name=None, architecture=None, **kwargs):
         if base_ami:
             self.BASE_AMI = base_ami
         elif architecture == 'x86':

tibanna/awsem.py

@@ -9,7 +9,7 @@
 
 
 class AwsemRunJson(SerializableObject):
-    def __init__(self, Job=None, config=None, strict=True):
+    def __init__(self, Job=None, config=None, strict=True, **kwargs):
         if strict:
             if not Job or not config:
                 raise MalFormattedPostRunJsonException("Job and config are required fields.")
@@ -24,7 +24,7 @@ def create_Job(self, Job, strict=True):
 
 class AwsemRunJsonJob(SerializableObject):
     def __init__(self, App=None, Input=None, Output=None, JOBID='',
-                 start_time=None, Log=None, strict=True):
+                 start_time=None, Log=None, strict=True, **kwargs):
         if strict:
             if App is None or Input is None or Output is None or not JOBID:
                 raise MalFormattedRunJsonException
@@ -63,7 +63,7 @@ def start_time_as_datetime(self):
 
 
 class AwsemRunJsonLog(SerializableObject):
-    def __init__(self, log_bucket_directory=None):
+    def __init__(self, log_bucket_directory=None, **kwargs):
         self.log_bucket_directory = log_bucket_directory
 
 
@@ -72,7 +72,8 @@ def __init__(self, App_name=None, App_version=None, language=None,
                  cwl_url=None, main_cwl=None, other_cwl_files=None,
                  wdl_url=None, main_wdl=None, other_wdl_files=None, workflow_engine=None, run_args=None,
                  container_image=None, command=None,
-                 snakemake_url=None, main_snakemake=None, other_snakemake_files=None):
+                 snakemake_url=None, main_snakemake=None, other_snakemake_files=None,
+                 **kwargs):
         self.App_name = App_name
         self.App_version = App_version
         self.language = language
@@ -90,11 +91,12 @@ def __init__(self, App_name=None, App_version=None, language=None,
         self.main_snakemake = main_snakemake
         self.other_snakemake_files = other_snakemake_files
 
+
 class AwsemRunJsonInput(SerializableObject):
     def __init__(self, Input_files_data=None, Input_parameters=None, Secondary_files_data=None,
                  # Input_files_reference is for older postrunjson
                  # Env is missing in older postrunjson
-                 Input_files_reference=None, Env=None):
+                 Input_files_reference=None, Env=None, **kwargs):
         if not Input_files_data:
             Input_files_data = {}
         if not Input_parameters:
@@ -223,7 +225,7 @@ def as_dict_as_wdl_input(self, input_dir='', input_mount_dir_prefix=''):
 
 class AwsemRunJsonOutput(SerializableObject):
     def __init__(self, output_bucket_directory=None, output_target=None,
-                 secondary_output_target=None, alt_cond_output_argnames=None):
+                 secondary_output_target=None, alt_cond_output_argnames=None, **kwargs):
         self.output_bucket_directory = output_bucket_directory or {}
         self.output_target = output_target or {}
         self.secondary_output_target = secondary_output_target or {}
@@ -269,7 +271,7 @@ def alt_output_target(self, argname_list):
 
 
 class AwsemPostRunJson(AwsemRunJson):
-    def __init__(self, Job=None, config=None, commands=None,log=None, strict=True):
+    def __init__(self, Job=None, config=None, commands=None, log=None, strict=True, **kwargs):
         if strict:
             if not Job or not config:
                 raise MalFormattedPostRunJsonException("Job and config are required fields.")
@@ -292,7 +294,7 @@ def __init__(self, App=None, Input=None, Output=None, JOBID='',
                  total_input_size=None, total_output_size=None, total_tmp_size=None,
                  # older postrunjsons don't have these fields
                  filesystem='', instance_id='', instance_availablity_zone='', instance_type='',
-                 Metrics=None, strict=True):
+                 Metrics=None, strict=True, **kwargs):
         if strict:
             if App is None or Input is None or Output is None or not JOBID or start_time is None:
                 errmsg = "App, Input, Output, JOBID and start_time are required fields"

tibanna/job.py

@@ -35,7 +35,7 @@ def status(job_ids=None, exec_arns=None):
 
 class Job(object):
 
-    def __init__(self, job_id=None, exec_arn=None, sfn=None):
+    def __init__(self, job_id=None, exec_arn=None, sfn=None, **kwargs):
         """A job can be identified with either a job_id or an exec_arn.
         For old tibanna versions (with no dynamoDB deployed),
         a job can be identified with a job_id and sfn.