Merge pull request #215 from pbashyal-nmdp/refactor_to_1.0

Refactor to 1.0 (Release Candidate Version)

Author: mmaiers-nmdp

README.md

@@ -48,21 +48,30 @@ Import `pyard` package.
 import pyard
 ```
 
-The cache size of pre-computed reductions can be changed from the default of 1000 (_not working_: will be fixed in a later release.)
-```python
-pyard.max_cache_size = 1_000_000
-```
 
 Initialize `ARD` object with a version of IMGT HLA database
 
 ```python
-ard = pyard.ARD(3290)
+import pyard
+
+ard = pyard.init('3510')
+```
+
+The cache size of pre-computed reductions can be changed from the default of 1000
+```python
+import pyard
+
+max_cache_size = 1_000_000
+ard = pyard.init('3510', cache_size=max_cache_size)
+
 ```
 
 You can specify a different directory for the cached data.
 
 ```python
-ard = pyard.ARD('3290', data_dir='/tmp/py-ard')
+import pyard.ard
+
+ard = pyard.init('3510', data_dir='/tmp/py-ard')
 ```
 
 You can choose to refresh the MAC code for current IMGT HLA database version
@@ -74,7 +83,9 @@ ard.refresh_mac_codes()
 The default initialization is to use the latest IMGT HLA database
 
 ```python
-ard = pyard.ARD()
+import pyard
+
+ard = pyard.init()
 ```
 
 ### Reduce Typings
@@ -84,13 +95,13 @@ Reduce a single locus HLA Typing.
 ```python
 allele = "A*01:01:01"
 
-ard.redux_gl(allele, 'G')
+ard.redux(allele, 'G')
 # >>> 'A*01:01:01G'
 
-ard.redux_gl(allele, 'lg')
+ard.redux(allele, 'lg')
 # >>> 'A*01:01g'
 
-ard.redux_gl(allele, 'lgx')
+ard.redux(allele, 'lgx')
 # >>> 'A*01:01'
 ```
 
@@ -99,14 +110,14 @@ Reduce an ambiguous GL String
 ```python
 # Reduce GL String
 #
-ard.redux_gl("A*01:01/A*01:01N+A*02:AB^B*07:02+B*07:AB", "G")
+ard.redux("A*01:01/A*01:01N+A*02:AB^B*07:02+B*07:AB", "G")
 # 'B*07:02:01G+B*07:02:01G^A*01:01:01G+A*02:01:01G/A*02:02'
 ```
 
 You can also reduce serology based typings.
 
 ```python
-ard.redux_gl('B14', 'lg')
+ard.redux('B14', 'lg')
 # >>> 'B*14:01g/B*14:02g/B*14:03g/B*14:04g/B*14:05g/B*14:06g/B*14:08g/B*14:09g/B*14:10g/B*14:11g/B*14:12g/B*14:13g/B*14:14g/B*14:15g/B*14:16g/B*14:17g/B*14:18g/B*14:19g/B*14:20g/B*14:21g/B*14:22g/B*14:23g/B*14:24g/B*14:25g/B*14:26g/B*14:27g/B*14:28g/B*14:29g/B*14:30g/B*14:31g/B*14:32g/B*14:33g/B*14:34g/B*14:35g/B*14:36g/B*14:37g/B*14:38g/B*14:39g/B*14:40g/B*14:42g/B*14:43g/B*14:44g/B*14:45g/B*14:46g/B*14:47g/B*14:48g/B*14:49g/B*14:50g/B*14:51g/B*14:52g/B*14:53g/B*14:54g/B*14:55g/B*14:56g/B*14:57g/B*14:58g/B*14:59g/B*14:60g/B*14:62g/B*14:63g/B*14:65g/B*14:66g/B*14:68g/B*14:70Qg/B*14:71g/B*14:73g/B*14:74g/B*14:75g/B*14:77g/B*14:82g/B*14:83g/B*14:86g/B*14:87g/B*14:88g/B*14:90g/B*14:93g/B*14:94g/B*14:95g/B*14:96g/B*14:97g/B*14:99g/B*14:102g'
 ```
 

api-spec.yaml

@@ -2,7 +2,7 @@ openapi: 3.0.3
 info:
   title: ARD Reduction
   description: Reduce to ARD Level
-  version: "0.9.1"
+  version: "1.0.0rc1"
 servers:
   - url: 'http://localhost:8080'
 tags:
@@ -14,6 +14,8 @@ tags:
     description: Expand MAC to alleles
   - name: DRBX Blender
     description: Blend DRBX based on DRB1 and DRB3/4/5
+  - name: Validation
+    description: Validate a GL String or Allele
 paths:
   /version:
     get:
@@ -134,7 +136,7 @@ paths:
   /validate:
     post:
       tags:
-        - ARD Reduction
+        - Validation
       operationId: api.validate_controller
       summary: Validate GL String
       description: |

api.py

@@ -1,12 +1,11 @@
 from flask import request
 
 import pyard
-from pyard import ARD
 from pyard.blender import DRBXBlenderError
 from pyard.exceptions import PyArdError, InvalidAlleleError
 
 # Globally accessible for all endpoints
-ard = ARD()
+ard = pyard.init()
 
 
 def validate_controller():
@@ -40,8 +39,8 @@ def redux_controller():
             return {"message": "gl_string and reduction_method not provided"}, 404
         # Perform redux
         try:
-            redux_gl_string = ard.redux_gl(gl_string, reduction_method)
-            return {"ard": redux_gl_string}, 200
+            redux_string = ard.redux(gl_string, reduction_method)
+            return {"ard": redux_string}, 200
         except PyArdError as e:
             return {"message": e.message}, 400
 

pyard/__init__.py

@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+from functools import lru_cache
 
 #
 #    pyard pyARD.
@@ -21,10 +22,29 @@
 #    > http://www.fsf.org/licensing/licenses/lgpl.html
 #    > http://www.opensource.org/licenses/lgpl-license.php
 #
-from .pyard import ARD
 from .blender import blender as dr_blender
 from .broad_splits import find_splits as find_broad_splits
 from .misc import get_imgt_db_versions as db_versions
+from .misc import DEFAULT_CACHE_SIZE
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = "0.9.1"
+__version__ = "1.0.0rc1"
+
+
+def init(
+    imgt_version: str = "Latest",
+    data_dir: str = None,
+    load_mac: bool = True,
+    cache_size: int = DEFAULT_CACHE_SIZE,
+    config: dict = None,
+):
+    from .ard import ARD
+
+    ard = ARD(
+        imgt_version=imgt_version,
+        data_dir=data_dir,
+        load_mac=load_mac,
+        max_cache_size=cache_size,
+        config=config,
+    )
+    return ard