From cb37516c77d7ca838ebd3218c732b654f0d0f628 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Thu, 16 Nov 2017 16:32:45 -0500
Subject: [PATCH] bubble models up to package level

---
 pep/__init__.py                          | 5 ++---
 pep/models.py                            | 4 ++--
 tests/models/independent/test_Project.py | 5 ++---
 tests/test_utils.py                      | 6 ++----
 4 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/pep/__init__.py b/pep/__init__.py
index 69836397..30d67d2f 100644
--- a/pep/__init__.py
+++ b/pep/__init__.py
@@ -11,15 +11,14 @@
 import os
 from sys import stdout
 from ._version import __version__
+from .models import *
 
 
 FLAGS = ["completed", "running", "failed", "waiting", "partial"]
 
 GENERIC_PROTOCOL_KEY = "*"
-IMPLICATIONS_DECLARATION = "implied_columns"
 SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \
-        ["metadata", "derived_columns", IMPLICATIONS_DECLARATION, "trackhubs"]
-SAMPLE_NAME_COLNAME = "sample_name"
+        ["metadata", "derived_columns", "implied_columns", "trackhubs"]
 LOGGING_LEVEL = "INFO"
 LOGGING_LOCATIONS = (stdout, )
 
diff --git a/pep/models.py b/pep/models.py
index b9f6c63f..a2d6c7f0 100644
--- a/pep/models.py
+++ b/pep/models.py
@@ -68,7 +68,6 @@
 import pandas as _pd
 import yaml
 
-from . import IMPLICATIONS_DECLARATION, SAMPLE_NAME_COLNAME
 from .utils import \
     add_project_sample_constants, alpha_cased, check_bam, check_fastq, \
     expandpath, get_file_size, grab_project_data, import_from_source, \
@@ -85,6 +84,7 @@
 
 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"
@@ -2028,7 +2028,7 @@ def set_file_paths(self, project=None):
 
         project = project or self.prj
 
-        self.infer_columns(implications=project.get(IMPLICATIONS_DECLARATION))
+        self.infer_columns(implications=project.get("implied_columns"))
 
         for col in project.get("derived_columns", []):
             # Only proceed if the specified column exists
diff --git a/tests/models/independent/test_Project.py b/tests/models/independent/test_Project.py
index 2ab94fc5..52854f51 100644
--- a/tests/models/independent/test_Project.py
+++ b/tests/models/independent/test_Project.py
@@ -7,10 +7,9 @@
 import pytest
 import yaml
 import pep
-from pep import SAMPLE_NAME_COLNAME
 from pep.models import \
-        AttributeDict, Project, Sample, \
-        _MissingMetadataException, SAMPLE_ANNOTATIONS_KEY
+        AttributeDict, Project, Sample, _MissingMetadataException, \
+        SAMPLE_ANNOTATIONS_KEY, SAMPLE_NAME_COLNAME
 
 
 __author__ = "Vince Reuter"
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 7dfd1a22..247ccf8c 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -3,9 +3,7 @@
 import copy
 import mock
 import pytest
-from pep import \
-    IMPLICATIONS_DECLARATION, SAMPLE_INDEPENDENT_PROJECT_SECTIONS, \
-    SAMPLE_NAME_COLNAME
+from pep 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
@@ -38,7 +36,7 @@ def basic_project_data():
             "results_subdir": "results_pipeline",
             "submission_subdir": "submission"},
         "derived_columns": ["data_source"],
-        IMPLICATIONS_DECLARATION: {"organism": {"genomes": {
+        "implied_columns": {"organism": {"genomes": {
             "mouse": "mm10", "rat": "rn6", "human": "hg38"}}},
         "trackhubs": []
     }