From 9b63e31b389985696a7178ebe3e89548b6dc2ff2 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Wed, 11 May 2016 17:18:38 +0100
Subject: [PATCH] Working JSON config reader with includes
---
pycgtool/parsers/json.py | 42 +++++++++----------
test/data/martini.json | 4 ++
test/data/martini_aminoacids.json | 9 +++++
test/data/martini_lipids.json | 9 +++++
test/data/twice.json | 15 -------
test/data/water.json | 18 +++++----
test/test_parsers_json.py | 67 ++++++++++++++++++++-----------
7 files changed, 98 insertions(+), 66 deletions(-)
create mode 100644 test/data/martini.json
create mode 100644 test/data/martini_aminoacids.json
create mode 100644 test/data/martini_lipids.json
delete mode 100644 test/data/twice.json
diff --git a/pycgtool/parsers/json.py b/pycgtool/parsers/json.py
index ca6efe8..bbfe9ae 100644
--- a/pycgtool/parsers/json.py
+++ b/pycgtool/parsers/json.py
@@ -1,12 +1,5 @@
import json
-
-
-class DuplicateSectionError(Exception):
- """
- Exception used to indicate that a section has appeared twice in a file.
- """
- def __repr__(self):
- return "Section {0} appears twice in file {1}.".format(*self.args)
+import os
class Record(dict):
@@ -18,21 +11,28 @@ class Record(dict):
class CFG:
- def __init__(self, filename):
+ def __init__(self, filename, from_section=None):
with open(filename) as f:
- try:
- self._json = json.load(f, object_hook=Record)
- except ValueError:
- raise DuplicateSectionError()
+ self._json = json.load(f, object_hook=Record)
- def __getitem__(self, item):
- return Record(self._json[item])
+ while self._json.include:
+ include_file = os.path.join(os.path.dirname(filename), self._json.include.pop())
+ with open(include_file) as include_file:
+ include_json = json.load(include_file, object_hook=Record)
- def __contains__(self, item):
- return item in self._json
+ for curr, incl in zip(self._json.values(), include_json.values()):
+ try:
+ curr += incl
+ except TypeError:
+ curr.update(incl)
- def __enter__(self):
- return self
+ if from_section is not None:
+ self._records = self._json[from_section]
+ else:
+ self._records = self._json
- def __exit__(self, type, value, traceback):
- pass
+ def __getitem__(self, item):
+ return self._records[item]
+
+ def __contains__(self, item):
+ return item in self._records
diff --git a/test/data/martini.json b/test/data/martini.json
new file mode 100644
index 0000000..5bd7733
--- /dev/null
+++ b/test/data/martini.json
@@ -0,0 +1,4 @@
+{
+ "include":["martini_lipids.json", "martini_aminoacids.json"],
+ "molecules":{}
+}
diff --git a/test/data/martini_aminoacids.json b/test/data/martini_aminoacids.json
new file mode 100644
index 0000000..b5d7f37
--- /dev/null
+++ b/test/data/martini_aminoacids.json
@@ -0,0 +1,9 @@
+{
+ "include":[],
+ "molecules":{
+ "GLY":{
+ "beads":[],
+ "bonds":[]
+ }
+ }
+}
diff --git a/test/data/martini_lipids.json b/test/data/martini_lipids.json
new file mode 100644
index 0000000..b9c64f7
--- /dev/null
+++ b/test/data/martini_lipids.json
@@ -0,0 +1,9 @@
+{
+ "include":[],
+ "molecules":{
+ "DOPC":{
+ "beads":[],
+ "bonds":[]
+ }
+ }
+}
diff --git a/test/data/twice.json b/test/data/twice.json
deleted file mode 100644
index 8f67dec..0000000
--- a/test/data/twice.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{"SOL":{
- "beads":[
- {"name":"W", "type":"P4", "atoms":["OW", "HW1", "HW2"]}
- ],
- "bonds":[
- ]
-}}
-
-{"SOL":{
- "beads":[
- {"name":"W", "type":"P4", "atoms":["OW", "HW1", "HW2"]}
- ],
- "bonds":[
- ]
-}}
diff --git a/test/data/water.json b/test/data/water.json
index b9597be..af0c31b 100644
--- a/test/data/water.json
+++ b/test/data/water.json
@@ -1,7 +1,11 @@
-{"SOL":{
- "beads":[
- {"name":"W", "type":"P4", "atoms":["OW", "HW1", "HW2"]}
- ],
- "bonds":[
- ]
-}}
+{
+ "include":[],
+ "molecules":{
+ "SOL":{
+ "beads":[
+ {"name":"W", "type":"P4", "atoms":["OW", "HW1", "HW2"]}
+ ],
+ "bonds":[]
+ }
+ }
+}
diff --git a/test/test_parsers_json.py b/test/test_parsers_json.py
index c7aebaf..c6f6c05 100644
--- a/test/test_parsers_json.py
+++ b/test/test_parsers_json.py
@@ -1,32 +1,53 @@
import unittest
-from pycgtool.parsers.json import CFG, DuplicateSectionError
+from pycgtool.parsers.json import CFG
class TestParsersJson(unittest.TestCase):
- def test_cfg_with(self):
- with CFG("test/data/water.json"):
- pass
-
- def test_cfg_get_section(self):
- with CFG("test/data/water.json") as cfg:
- self.assertTrue("SOL" in cfg)
- self.assertEqual(1, len(cfg["SOL"].beads))
- bead = cfg["SOL"].beads[0]
- self.assertEqual("W", bead.name)
- self.assertEqual("P4", bead.type)
- self.assertEqual(["OW", "HW1", "HW2"], bead.atoms)
- self.assertEqual(0, len(cfg["SOL"].bonds))
-
- def test_cfg_duplicate_error(self):
- with self.assertRaises(DuplicateSectionError):
- CFG("test/data/twice.json")
-
- @unittest.expectedFailure
+ def test_json_water(self):
+ cfg = CFG("test/data/water.json", "molecules")
+
+ self.assertTrue("SOL" in cfg)
+ self.assertEqual(1, len(cfg["SOL"].beads))
+ bead = cfg["SOL"].beads[0]
+ self.assertEqual("W", bead.name)
+ self.assertEqual("P4", bead.type)
+ self.assertEqual(["OW", "HW1", "HW2"], bead.atoms)
+ self.assertEqual(0, len(cfg["SOL"].bonds))
+
+ def test_json_sugar(self):
+ cfg = CFG("test/data/sugar.json", "molecules")
+
+ ref_beads = [["C1", "P3", "C1", "O1"],
+ ["C2", "P3", "C2", "O2"],
+ ["C3", "P3", "C3", "O3"],
+ ["C4", "P3", "C4", "O4"],
+ ["C5", "P2", "C5", "C6", "O6"],
+ ["O5", "P4", "O5"]]
+
+ ref_bonds = [["C1", "C2"],
+ ["C2", "C3"],
+ ["C3", "C4"],
+ ["C4", "C5"],
+ ["C5", "O5"],
+ ["O5", "C1"]]
+
+ self.assertTrue("ALLA" in cfg)
+
+ self.assertEqual(6, len(cfg["ALLA"].beads))
+ for ref_bead, bead in zip(ref_beads, cfg["ALLA"].beads):
+ self.assertEqual(ref_bead[0], bead.name)
+ self.assertEqual(ref_bead[1], bead.type)
+ self.assertEqual(ref_bead[2:], bead.atoms)
+
+ self.assertEqual(6, len(cfg["ALLA"].bonds))
+ for ref_bond, bond in zip(ref_bonds, cfg["ALLA"].bonds):
+ self.assertEqual(ref_bond, bond)
+
def test_include_file(self):
- with CFG("test/data/martini.json") as cfg:
- self.assertTrue("DOPC" in cfg)
- self.assertTrue("GLY" in cfg)
+ cfg = CFG("test/data/martini.json", "molecules")
+ self.assertTrue("DOPC" in cfg)
+ self.assertTrue("GLY" in cfg)
if __name__ == '__main__':
--
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