Merge pull request #110 from ENCODE-DCC/PIP-1523_fix_custom_backend_file

Pip 1523 fix custom backend file

caper/__init__.py

@@ -2,4 +2,4 @@
 from .caper_runner import CaperRunner
 
 __all__ = ['CaperClient', 'CaperClientSubmit', 'CaperRunner']
-__version__ = '1.5.0'
+__version__ = '1.5.1'

caper/caper_backend_conf.py

@@ -355,7 +355,7 @@ def create_file(
 
         if custom_backend_conf is not None:
             s = AutoURI(custom_backend_conf).read()
-            hocon_s.merge(s)
+            hocon_s.merge(s, update=True)
 
         final_backend_conf_file = os.path.join(directory, basename)
         AutoURI(final_backend_conf_file).write(str(hocon_s) + '\n')

caper/hocon_string.py

@@ -9,6 +9,9 @@
 logger = logging.getLogger(__name__)
 
 
+NEW_LINE = '\n'
+
+
 class HOCONString:
     RE_INCLUDE_LINE = r'^\s*include\s'
 
@@ -18,14 +21,14 @@ def __init__(self, hocon_str):
         """
         lines_include = []
         lines_wo_include = []
-        for line in hocon_str.split('\n'):
+        for line in hocon_str.splitlines():
             if re.findall(HOCONString.RE_INCLUDE_LINE, line):
                 lines_include.append(line)
             else:
                 lines_wo_include.append(line)
 
-        self._include = '\n'.join(lines_include)
-        self._contents_wo_include = '\n'.join(lines_wo_include)
+        self._include = NEW_LINE.join(lines_include)
+        self._contents_wo_include = NEW_LINE.join(lines_wo_include)
 
     def __str__(self):
         return self.get_contents()
@@ -35,7 +38,7 @@ def from_dict(cls, d, include=''):
         hocon = ConfigFactory.from_dict(d)
         hocon_str = HOCONConverter.to_hocon(hocon)
         if include:
-            hocon_str = include + '\n' + hocon_str
+            hocon_str = NEW_LINE.join([include, hocon_str])
         return cls(hocon_str=hocon_str)
 
     def to_dict(self):
@@ -45,7 +48,17 @@ def to_dict(self):
         j = HOCONConverter.to_json(c)
         return json.loads(j)
 
-    def merge(self, b):
+    def merge(self, b, update=False):
+        """Merge self with b and then returns a plain string of merged.
+        Args:
+            b:
+                HOCONString, dict, str to be merged.
+                b's `include` statement will always be ignored.
+            update:
+                If `update` then replace self with a merged one.
+        Returns:
+            String of merged HOCONs.
+        """
         if isinstance(b, HOCONString):
             d = b.to_dict()
         elif isinstance(b, str):
@@ -59,7 +72,12 @@ def merge(self, b):
         merge_dict(self_d, d)
 
         hocon = ConfigFactory.from_dict(self_d)
-        return self._include + '\n' + HOCONConverter.to_hocon(hocon)
+
+        contents_wo_include = HOCONConverter.to_hocon(hocon)
+        if update:
+            self._contents_wo_include = contents_wo_include
+
+        return NEW_LINE.join([self._include, contents_wo_include])
 
     def get_include(self):
         return self._include
@@ -68,4 +86,4 @@ def get_contents(self, without_include=False):
         if without_include:
             return self._contents_wo_include
         else:
-            return self._include + '\n' + self._contents_wo_include
+            return NEW_LINE.join([self._include, self._contents_wo_include])

setup.py

@@ -1,11 +1,43 @@
+import os
+import re
+from pathlib import Path
+
 import setuptools
 
+META_PATH = Path('caper', '__init__.py')
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+
+def read(*parts):
+    """
+    Build an absolute path from *parts* and and return the contents of the
+    resulting file.  Assume UTF-8 encoding.
+    """
+    with Path(HERE, *parts).open(encoding='utf-8') as f:
+        return f.read()
+
+
+META_FILE = read(META_PATH)
+
+
+def find_meta(meta):
+    """
+    Extract __*meta*__ from META_FILE.
+    """
+    meta_match = re.search(
+        r"^__{meta}__ = ['\"]([^'\"]*)['\"]".format(meta=meta), META_FILE, re.M
+    )
+    if meta_match:
+        return meta_match.group(1)
+    raise
+
+
 with open('README.md', 'r') as fh:
     long_description = fh.read()
 
 setuptools.setup(
     name='caper',
-    version='1.5.0',
+    version=find_meta('version'),
     python_requires='>=3.6',
     scripts=[
         'bin/caper',

tests/test_hocon_string.py

@@ -99,6 +99,13 @@ def test_merge():
     assert str(hsm) == hs1.merge(d2)
     assert str(hsm) == hs1.merge(s2)
 
+    # merge with update
+    # item 1 should be updated with merged
+    hs1_original_str = str(hs1)
+    assert str(hsm) == hs1.merge(hs2, update=True)
+    assert str(hs1) == str(hsm)
+    assert hs1_original_str != str(hs1)
+
 
 def test_get_include():
     s2 = get_test_hocon_str2()