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adjusted capturer log level and added arguments. #136

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adjusted capturer log level and added arguments. #136

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19 changes: 14 additions & 5 deletions biosimulators_utils/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,25 @@
:License: MIT
"""

from .log.data_model import StandardOutputErrorCapturerLevel
from .omex_meta.data_model import OmexMetadataInputFormat, OmexMetadataOutputFormat, OmexMetadataSchema
from .report.data_model import ReportFormat # noqa: F401
from .viz.data_model import VizFormat # noqa: F401
from kisao import AlgorithmSubstitutionPolicy # noqa: F401
import appdirs
import enum
import os
from typing import List

__all__ = ['Config', 'get_config', 'Colors', 'get_app_dirs']

DEFAULT_STDOUT_CAPTURE_LEVEL = StandardOutputErrorCapturerLevel.python
DEFAULT_OMEX_METADATA_INPUT_FORMAT = OmexMetadataInputFormat.rdfxml
DEFAULT_OMEX_METADATA_OUTPUT_FORMAT = OmexMetadataOutputFormat.rdfxml_abbrev
DEFAULT_OMEX_METADATA_SCHEMA = OmexMetadataSchema.biosimulations
DEFAULT_ALGORITHM_SUBSTITUTION_POLICY = AlgorithmSubstitutionPolicy.SIMILAR_VARIABLES
DEFAULT_H5_REPORTS_PATH = 'reports.h5'
DEFAULT_CSV_REPORTS_PATH = 'reports.csv'
DEFAULT_REPORTS_PATH = 'reports.zip'
DEFAULT_PLOTS_PATH = 'plots.zip'
DEFAULT_LOG_PATH = 'log.yml'
Expand All @@ -30,6 +34,7 @@
DEFAULT_BIOSIMULATIONS_API_AUDIENCE = 'api.biosimulations.org'



class Config(object):
""" Configuration

Expand Down Expand Up @@ -82,7 +87,7 @@ def __init__(self,
COLLECT_COMBINE_ARCHIVE_RESULTS=False,
COLLECT_SED_DOCUMENT_RESULTS=False,
SAVE_PLOT_DATA=True,
REPORT_FORMATS=[ReportFormat.h5],
REPORT_FORMATS=[ReportFormat.csv],
VIZ_FORMATS=[VizFormat.pdf],
H5_REPORTS_PATH=DEFAULT_H5_REPORTS_PATH,
REPORTS_PATH=DEFAULT_REPORTS_PATH,
Expand All @@ -96,7 +101,8 @@ def __init__(self,
BIOSIMULATIONS_API_AUTH_ENDPOINT=DEFAULT_BIOSIMULATIONS_API_AUTH_ENDPOINT,
BIOSIMULATIONS_API_AUDIENCE=DEFAULT_BIOSIMULATIONS_API_AUDIENCE,
VERBOSE=False,
DEBUG=False):
DEBUG=False,
STDOUT_CAPTURE_LEVEL=DEFAULT_STDOUT_CAPTURE_LEVEL):
"""
Args:
OMEX_METADATA_INPUT_FORMAT (:obj:`OmexMetadataInputFormat`, optional): format to validate OMEX Metadata files against
Expand Down Expand Up @@ -162,21 +168,23 @@ def __init__(self,
self.BIOSIMULATIONS_API_AUDIENCE = BIOSIMULATIONS_API_AUDIENCE
self.VERBOSE = VERBOSE
self.DEBUG = DEBUG
self.STDOUT_CAPTURE_LEVEL = STDOUT_CAPTURE_LEVEL



def get_config():
def get_config(report_format: str = 'csv', viz_format: str = 'pdf'):
""" Get the configuration

Returns:
:obj:`Config`: configuration
"""
report_formats = os.environ.get('REPORT_FORMATS', 'h5').strip()
report_formats = os.environ.get('REPORT_FORMATS', report_format).strip()
if report_formats:
report_formats = [ReportFormat(format.strip().lower()) for format in report_formats.split(',')]
else:
report_formats = []

viz_formats = os.environ.get('VIZ_FORMATS', 'pdf').strip()
viz_formats = os.environ.get('VIZ_FORMATS', viz_format).strip()
if viz_formats:
viz_formats = [VizFormat(format.strip().lower()) for format in viz_formats.split(',')]
else:
Expand Down Expand Up @@ -216,6 +224,7 @@ def get_config():
BIOSIMULATIONS_API_AUDIENCE=os.environ.get('BIOSIMULATIONS_API_AUDIENCE', DEFAULT_BIOSIMULATIONS_API_AUDIENCE),
VERBOSE=os.environ.get('VERBOSE', '1').lower() in ['1', 'true'],
DEBUG=os.environ.get('DEBUG', '0').lower() in ['1', 'true'],
STDOUT_CAPTURE_LEVEL=os.environ.get('STDOUT_CAPTURE_LEVEL', DEFAULT_STDOUT_CAPTURE_LEVEL),
)


Expand Down
15 changes: 10 additions & 5 deletions biosimulators_utils/sedml/exec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
import tempfile
import termcolor
import types # noqa: F401
from typing import Union, Tuple


__all__ = [
Expand All @@ -47,11 +48,12 @@
]


def exec_sed_doc(task_executer, doc, working_dir, base_out_path, rel_out_path=None,
apply_xml_model_changes=False,
log=None, indent=0, pretty_print_modified_xml_models=False,
log_level=StandardOutputErrorCapturerLevel.c,
config=None):
def exec_sed_doc(task_executer: types.FunctionType, doc: Union[SedDocument, str],
working_dir: str, base_out_path: str, rel_out_path: str = None,
apply_xml_model_changes: bool = False, log: SedDocumentLog = None,
indent: int = 0, pretty_print_modified_xml_models: bool = False,
log_level: StandardOutputErrorCapturerLevel = None,
config: Config = None) -> Tuple[ReportResults, SedDocumentLog]:
""" Execute the tasks specified in a SED document and generate the specified outputs

Args:
Expand Down Expand Up @@ -103,6 +105,9 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
"""
if not config:
config = get_config()

if not log_level:
log_level = config.STDOUT_CAPTURE_LEVEL

# process arguments
if not isinstance(doc, SedDocument):
Expand Down