Generate settings dict from supplied json, with defaults from schema

prinia/primer3.py

+"""
+prinia.primer3
+~~~~~~~~~~~~~~
+
+:copyright: (c) 2017-2018 Sander Bollen
+:copyright: (c) 2017-2018 Leiden University Medical Center
+:license: MIT
+"""
+from pathlib import Path
 from tempfile import NamedTemporaryFile
 from subprocess import check_call
+from typing import Optional
 import os
+import json
 
 import re
 
+from jsonschema import validate
+
 from .models import Primer
 
 
+SETTINGS_SCHEMA = (Path(__file__).parent / Path("static") /
+                   Path("primer3_settings_schema.json"))
+
+
+def parse_settings(settings_file: Optional[Path] = None) -> dict:
+    """
+    Parse settings file to settings dictionary.
+
+    Parameters not specified in settings_file will be taken from default values
+    in schema. If settings_file is None, all values will be the default values
+    in schema
+    :param settings_file: Optional path to settings file
+    :return: dict with settings
+    :raises: ValidationError if settings_file does not conform to schema
+    """
+    with SETTINGS_SCHEMA.open("r") as schema_handle:
+        schema_dict = json.load(schema_handle)
+
+    defaults = {k: v['default'] for k, v in schema_dict['properties'].items()}
+
+    if settings_file is None:
+        return defaults
+
+    with settings_file.open("r") as settings_handle:
+        settings_dict = json.load(settings_handle)
+
+    validate(settings_dict, schema_dict)  # raises ValidationError if failure
+
+    default_keys = defaults.keys() - settings_dict.keys()
+    default_dict = {k: defaults[k] for k in default_keys}
+    generated_dict = {**settings_dict, **default_dict}
+
+    # if range is set, but optimum size is not, calculate opt size
+    if ('primer_product_opt_size' in default_dict and
+            "primer_product_size_range" in settings_dict):
+        product_range = settings_dict['primer_product_size_range']
+        min_size, max_size = product_range.split("-")
+        opt_size = int((int(min_size) + (int(max_size) - int(min_size))) // 2)
+        generated_dict['primer_product_opt_size'] = opt_size
+
+    return generated_dict
+
+
 class Primer3(object):
 
     def __init__(self, primer3_exe, template, target, excluded_region,

prinia/static/primer3_conf.j2

+SEQUENCE_ID=prinia_template
+SEQUENCE_TEMPLATE={{ seq }}
+SEQUENCE_TARGET={{ target }}
+SEQUENCE_EXCLUDED_REGION={{ excluded_region }}
+PRIMER_TASK=pick_detection_primers
+PRIMER_PICK_LEFT_PRIMER=1
+PRIMER_PICK_INTERNAL_OLIGO=0
+PRIMER_PICK_RIGHT_PRIMER=1
+PRIMER_MIN_GC={{ settings.primer_min_gc }}
+PRIMER_INTERNAL_MIN_GC={{ settings.primer_internal_min_gc }}
+PRIMER_OPT_GC_PERCENT={{ settings.primer_opt_gc_percent }}
+PRIMER_MAX_GC={{ settings.primer_max_gc }}
+PRIMER_INTERNAL_MAX_GC={{ settings.primer_internal_max_gc }}
+PRIMER_WT_GC_PERCENT_LT={{ settings.primer_wt_gc_percent_lt }}
+PRIMER_INTERNAL_WT_GC_PERCENT_LT={{ settings.primer_internal_wt_gc_percent_lt }}
+PRIMER_WT_GC_PERCENT_GT={{ settings.primer_wt_gc_percent_gt }}
+PRIMER_INTERNAL_WT_GC_PERCENT_GT={{ settings.primer_internal_wc_gc_percent_gt }}
+PRIMER_GC_CLAMP={{ settings.primer_gc_clamp }}
+PRIMER_MAX_END_GC={{ settings.primer_max_end_gc }}
+PRIMER_OPT_SIZE={{ settings.primer_opt_size }}
+PRIMER_MIN_SIZE={{ settings.primer_min_size }}
+PRIMER_MAX_SIZE={{ settings.primer_max_size }}
+PRIMER_MAX_NS_ACCEPTED={{ settings.primer_max_ns_accepted }}
+PRIMER_PRODUCT_SIZE_RANGE={{ settings.primer_product_size_range }}
+PRIMER_PRODUCT_OPT_SIZE={{ settings.primer_product_opt_size }}
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT={{ settings.primer_pair_wt_product_size_gt }}
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT={{ settings.primer_pair_wt_product_size_gt }}
+P3_FILE_FLAG=1
+SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_MIN_TM={{ settings.primer_min_tm }}
+PRIMER_MAX_TM={{ settings.primer_max_tm }}
+PRIMER_NUM_RETURN={{ settings.primer_num_return }}
\ No newline at end of file

prinia/static/primer3_settings_schema.json

@@ -95,7 +95,7 @@
     "primer_max_ns_accepted": {
       "description": "Maximum number of unknown bases (N) accepted in a primer",
       "type": "integer",
-      "default:": 0,
+      "default": 0,
       "minimum": 0
     },
     "primer_product_size_range": {

tests/data/valid_partial_settings.json

+{
+  "primer_gc_clamp": 1,
+  "primer_max_end_gc": 0,
+  "primer_opt_size": 21,
+  "primer_min_size": 19,
+  "primer_max_size": 29,
+  "primer_max_ns_accepted": 1,
+  "primer_product_size_range": "300-500",
+  "primer_pair_wt_product_size_gt": 0.12,
+  "primer_pair_wt_product_size_lt": 0.12,
+  "primer_min_tm": 55,
+  "primer_max_tm": 75,
+  "primer_num_return": 100
+}
\ No newline at end of file

tests/test_primer3.py

+"""
+test_primer3.py
+~~~~~~~~~~~~~~~
+
+:copyright: (c) 2018 Sander Bollen
+:copyright: (c) 2018 Leiden University Medical Center
+:license: MIT
+"""
+from pathlib import Path
+from pytest import fixture
+
+from prinia.primer3 import parse_settings
+
+
+data_dir = Path(__file__).parent / Path("data")
+
+@fixture
+def valid_settings():
+    return data_dir / Path("valid_settings.json")
+
+
+@fixture
+def valid_partial_settings():
+    return data_dir / Path("valid_partial_settings.json")
+
+
+def test_none_settings():
+    parsed = parse_settings()
+    assert parsed == {
+        "primer_min_gc": 20,
+        "primer_internal_min_gc": 20,
+        "primer_opt_gc_percent": 50,
+        "primer_max_gc": 80,
+        "primer_internal_max_gc": 80,
+        "primer_wt_gc_percent_lt": 0,
+        "primer_internal_wt_gc_percent_lt": 0,
+        "primer_wt_gc_percent_gt": 0,
+        "primer_internal_wt_gc_percent_gt": 0,
+        "primer_gc_clamp": 0,
+        "primer_max_end_gc": 5,
+        "primer_opt_size": 25,
+        "primer_min_size": 20,
+        "primer_max_size": 30,
+        "primer_max_ns_accepted": 0,
+        "primer_product_size_range": "200-450",
+        "primer_product_opt_size": 325,
+        "primer_pair_wt_product_size_gt": 0.1,
+        "primer_pair_wt_product_size_lt": 0.1,
+        "primer_min_tm": 58,
+        "primer_max_tm": 62,
+        "primer_num_return": 200
+    }
+
+
+def test_complete_settings(valid_settings):
+    parsed = parse_settings(valid_settings)
+
+    # TODO: work out
+
+
+def test_partial_settings(valid_partial_settings):
+    parsed = parse_settings(valid_partial_settings)
+
+    # TODO: work out

tests/test_schemas.py

@@ -25,6 +25,7 @@ data_dir = Path(__file__).parent / Path("data")
 
 setting_jsons_data = [
     (data_dir / Path("valid_settings.json"), True),
+    (data_dir / Path("valid_partial_settings.json"), True),
     (data_dir / Path("settings_wrong_types.json"), False),
     (data_dir / Path("settings_invalid_values.json"), False)
 ]

tox.ini

 [tox]
-envlist = py27, py34
+envlist = py35
 
 [testenv]
 usedevelop = True