From f4bf821567cf1a50ec1977988a795f1363898aa3 Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Wed, 6 Apr 2016 15:29:04 -0500
Subject: [PATCH] Fixed stdout & stderr type handling. Fixed incorrect type in
align.yaml. Fixed typo in config.
---
chipathlon/conf.py | 2 +-
chipathlon/jobs/modules/align.yaml | 4 ++--
chipathlon/workflow_job.py | 24 +++++++++++++++++++-----
chipathlon/workflow_module.py | 8 ++++----
4 files changed, 26 insertions(+), 12 deletions(-)
diff --git a/chipathlon/conf.py b/chipathlon/conf.py
index c185faa..38c2691 100644
--- a/chipathlon/conf.py
+++ b/chipathlon/conf.py
@@ -51,7 +51,7 @@ resources = {
argument_types = {
"argument": ["argument"],
"file": ["file", "stdout", "stderr"]
-]
+}
# param keys
param_keys = {
diff --git a/chipathlon/jobs/modules/align.yaml b/chipathlon/jobs/modules/align.yaml
index af41ae9..50157d4 100644
--- a/chipathlon/jobs/modules/align.yaml
+++ b/chipathlon/jobs/modules/align.yaml
@@ -91,7 +91,7 @@ align:
type: file
outputs:
- align.sam:
- type: stdout
+ type: file
- align.quality:
type: stderr
paired[read_end]:
@@ -120,7 +120,7 @@ align:
type: file
outputs:
- align.sam:
- type: stdout
+ type: file
- align.quality:
type: stderr
- samtools_sam_to_bam:
diff --git a/chipathlon/workflow_job.py b/chipathlon/workflow_job.py
index c1e4242..bcf47da 100644
--- a/chipathlon/workflow_job.py
+++ b/chipathlon/workflow_job.py
@@ -197,16 +197,30 @@ class WorkflowJob(object):
key, index = arg_info["default"].split(".")
arg_list.append(arg)
# We only add the file object if the passed argument is
- # has type == file
- arg_list.append(argument_map[key][int(index)]["file"] if argument_map[key][int(index)]["type"] == "file" else argument_map[key][int(index)]["value"])
+ # has type == file. We don't want to process
+ # stdout / stderr arguments here.
+ if argument_map[key][int(index)]["type"] == "file":
+ arg_list.append(argument_map[key][int(index)]["file"])
+ elif argument_map[key][int(index)]["type"] == "argument":
+ arg_list.append(argument_map[key][int(index)]["value"])
+ else:
+ print "Error with argument '%s' for file %s. Check the yaml file." % (arg, self.jobname)
+ sys.exit(1)
else:
arg_list.append("%s %s" % (arg, arg_info["default"]))
else:
if not isinstance(arg, bool) and arg[:1] == "$":
key, index = arg.split(".")
- # We only add the file object if the passed argument is
- # has type == file
- arg_list.append(argument_map[key][int(index)]["file"] if argument_map[key][int(index)]["type"] == "file" else argument_map[key][int(index)]["value"])
+ # We only add the file object if the passed argument
+ # has type == file. We don't want to process
+ # stdout / stderr arguments here.
+ if argument_map[key][int(index)]["type"] == "file":
+ arg_list.append(argument_map[key][int(index)]["file"])
+ elif argument_map[key][int(index)]["type"] == "argument":
+ arg_list.append(argument_map[key][int(index)]["value"])
+ else:
+ print "Error with argument '%s' for file %s. Check the yaml file." % (arg, self.jobname)
+ sys.exit(1)
else:
arg_list.append(arg)
return arg_list
diff --git a/chipathlon/workflow_module.py b/chipathlon/workflow_module.py
index 90afc7c..8e2c01f 100644
--- a/chipathlon/workflow_module.py
+++ b/chipathlon/workflow_module.py
@@ -131,7 +131,7 @@ class WorkflowModule(object):
param_name = param_dict.keys()[0]
param = param_dict[param_name]
# Make sure param is one of the file types
- if param["type"] in conf.argument_types["file"]:
+ if param["type"] in chipathlon.conf.argument_types["file"]:
if param_name not in [x["name"] for x in param_list] and param_name not in [x["name"] for x in output_files]:
if prefix is None or self._get_full_name(prefix, markers, param_name) not in master_files:
param_list.append({"name": param_name, "type": "file"})
@@ -172,7 +172,7 @@ class WorkflowModule(object):
for job_dict in job_info[param_type]:
param_name = job_dict.keys()[0]
param = job_dict[param_name]
- if param["type"] in conf.argument_types["file"]:
+ if param["type"] in chipathlon.conf.argument_types["file"]:
full_name = self._get_full_name(prefix, markers, param_name)
# If file is an output file, add to master_files
if param_type == "outputs":
@@ -233,7 +233,7 @@ class WorkflowModule(object):
}
data = module_params
for arg_params, param_key in zip([inputs, additional_files], ["inputs", "additional_files"]):
- for file_dict in [file_param for file_param in module_params[param_key] if file_param["type"] in conf.argument_types["file"]]:
+ for file_dict in [file_param for file_param in module_params[param_key] if file_param["type"] in chipathlon.conf.argument_types["file"]]:
file_name = file_dict["name"]
if file_name not in module_params[param_key]:
valid_params = False
@@ -242,7 +242,7 @@ class WorkflowModule(object):
valid_params = False
msg += "Error loading '%s' jobs. File with name '%s', value '%s', does not exist in master_files.\n" % (self.name, file_name, arg_params[file_name])
for param_dict in module_params[param_key]:
- if param_dict["type"] in conf.argument_types["file"]:
+ if param_dict["type"] in chipathlon.conf.argument_types["file"]:
file_name = param_dict["name"]
if file_name not in arg_params:
valid_params = False
--
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