diff --git a/pep/__init__.py b/pep/__init__.py index 30d67d2f..b04d2cfe 100644 --- a/pep/__init__.py +++ b/pep/__init__.py @@ -14,11 +14,6 @@ from .models import * -FLAGS = ["completed", "running", "failed", "waiting", "partial"] - -GENERIC_PROTOCOL_KEY = "*" -SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \ - ["metadata", "derived_columns", "implied_columns", "trackhubs"] LOGGING_LEVEL = "INFO" LOGGING_LOCATIONS = (stdout, ) diff --git a/pep/const.py b/pep/const.py new file mode 100644 index 00000000..c424ad1c --- /dev/null +++ b/pep/const.py @@ -0,0 +1,30 @@ +""" Package constants """ + +__author__ = "Vince Reuter" +__email__ = "vreuter@virginia.edu" + +__all__ = ["ALL_INPUTS_ATTR_NAME", "COL_KEY_SUFFIX", "COMPUTE_SETTINGS_VARNAME", + "DATA_SOURCE_COLNAME", "DATA_SOURCES_SECTION", + "DEFAULT_COMPUTE_RESOURCES_NAME", "FLAGS", + "GENERIC_PROTOCOL_KEY", "REQUIRED_INPUTS_ATTR_NAME", + "SAMPLE_ANNOTATIONS_KEY", "SAMPLE_EXECUTION_TOGGLE", + "SAMPLE_NAME_COLNAME", "SAMPLE_INDEPENDENT_PROJECT_SECTIONS", + "VALID_READ_TYPES"] + + +COMPUTE_SETTINGS_VARNAME = "PEPENV" +DEFAULT_COMPUTE_RESOURCES_NAME = "default" +SAMPLE_NAME_COLNAME = "sample_name" +DATA_SOURCE_COLNAME = "data_source" +SAMPLE_ANNOTATIONS_KEY = "sample_annotation" +DATA_SOURCES_SECTION = "data_sources" +SAMPLE_EXECUTION_TOGGLE = "toggle" +COL_KEY_SUFFIX = "_key" +VALID_READ_TYPES = ["single", "paired"] +REQUIRED_INPUTS_ATTR_NAME = "required_inputs_attr" +ALL_INPUTS_ATTR_NAME = "all_inputs_attr" +FLAGS = ["completed", "running", "failed", "waiting", "partial"] +GENERIC_PROTOCOL_KEY = "*" +SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \ + ["metadata", "derived_columns", "implied_columns", "trackhubs"] + diff --git a/pep/models.py b/pep/models.py index a2d6c7f0..01d005e9 100644 --- a/pep/models.py +++ b/pep/models.py @@ -68,6 +68,7 @@ import pandas as _pd import yaml +from .const import * from .utils import \ add_project_sample_constants, alpha_cased, check_bam, check_fastq, \ expandpath, get_file_size, grab_project_data, import_from_source, \ @@ -82,18 +83,6 @@ __all__ = __functions__ + __classes__ -COMPUTE_SETTINGS_VARNAME = "PEPENV" -DEFAULT_COMPUTE_RESOURCES_NAME = "default" -SAMPLE_NAME_COLNAME = "sample_name" -DATA_SOURCE_COLNAME = "data_source" -SAMPLE_ANNOTATIONS_KEY = "sample_annotation" -DATA_SOURCES_SECTION = "data_sources" -SAMPLE_EXECUTION_TOGGLE = "toggle" -COL_KEY_SUFFIX = "_key" -VALID_READ_TYPES = ["single", "paired"] -REQUIRED_INPUTS_ATTR_NAME = "required_inputs_attr" -ALL_INPUTS_ATTR_NAME = "all_inputs_attr" - ATTRDICT_METADATA = {"_force_nulls": False, "_attribute_identity": False} _LOGGER = logging.getLogger(__name__) diff --git a/pep/utils.py b/pep/utils.py index cf108987..4067229d 100644 --- a/pep/utils.py +++ b/pep/utils.py @@ -1,7 +1,6 @@ """ Helpers without an obvious logical home. """ from collections import defaultdict, Iterable -import copy import contextlib import logging import os @@ -11,9 +10,7 @@ import yaml -from . import \ - GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS, \ - SAMPLE_NAME_COLNAME +from .const import GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS _LOGGER = logging.getLogger(__name__) @@ -299,7 +296,7 @@ def sample_folder(prj, sample): :return str: this Project's root folder for the given Sample """ return os.path.join(prj.metadata.results_subdir, - sample[SAMPLE_NAME_COLNAME]) + sample["sample_name"]) diff --git a/tests/test_utils.py b/tests/test_utils.py index 247ccf8c..b5e2a325 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -3,7 +3,7 @@ import copy import mock import pytest -from pep import SAMPLE_INDEPENDENT_PROJECT_SECTIONS, SAMPLE_NAME_COLNAME +from pep.const import SAMPLE_INDEPENDENT_PROJECT_SECTIONS, SAMPLE_NAME_COLNAME from pep.models import AttributeDict, Project, Sample from pep.utils import add_project_sample_constants, grab_project_data from tests.helpers import named_param, nonempty_powerset