Merge pull request #1020 from oesteban/enh/JSONFileInterface

ENH: IO interfaces to JSON files

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
 * ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
 * BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
 * FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)

nipype/interfaces/io.py

@@ -1801,3 +1801,118 @@ def _get_ssh_client(self):
         client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
         client.connect(host['hostname'], username=host['user'], sock=proxy)
         return client
+
+
+class JSONFileGrabberInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True,
+                   desc='JSON source file')
+
+
+class JSONFileGrabber(IOBase):
+
+    """
+    Datagrabber interface that loads a json file and generates an output for
+    every first-level object
+
+    Example
+    -------
+
+    >>> from nipype.interfaces.io import JSONFileGrabber
+    >>> jsonSource = JSONFileGrabber()
+    >>> jsonSource.inputs.in_file = 'jsongrabber.txt'
+    >>> res = jsonSource.run()
+    >>> print res.outputs.param1
+    exampleStr
+    >>> print res.outputs.param2
+    4
+
+    """
+    input_spec = JSONFileGrabberInputSpec
+    output_spec = DynamicTraitedSpec
+    _always_run = True
+
+    def _list_outputs(self):
+        import json
+
+        with open(self.inputs.in_file, 'r') as f:
+            data = json.load(f)
+
+        if not isinstance(data, dict):
+            raise RuntimeError('JSON input has no dictionary structure')
+
+        outputs = {}
+        for key, value in data.iteritems():
+            outputs[key] = value
+
+        return outputs
+
+
+class JSONFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
+    out_file = File(desc='JSON sink file')
+    in_dict = traits.Dict(desc='input JSON dictionary')
+
+
+class JSONFileSinkOutputSpec(TraitedSpec):
+    out_file = File(desc='JSON sink file')
+
+
+class JSONFileSink(IOBase):
+
+    """ Very simple frontend for storing values into a JSON file.
+
+        .. warning::
+
+            This is not a thread-safe node because it can write to a common
+            shared location. It will not complain when it overwrites a file.
+
+        Examples
+        --------
+
+        >>> jsonsink = JSONFileSink(input_names=['subject_id',
+        ...                         'some_measurement'])
+        >>> jsonsink.inputs.subject_id = 's1'
+        >>> jsonsink.inputs.some_measurement = 11.4
+        >>> jsonsink.run() # doctest: +SKIP
+
+        Using a dictionary as input:
+
+        >>> dictsink = JSONFileSink()
+        >>> dictsink.inputs.in_dict = {'subject_id': 's1',
+        ...                            'some_measurement': 11.4}
+        >>> dictsink.run() # doctest: +SKIP
+
+    """
+    input_spec = JSONFileSinkInputSpec
+    output_spec = JSONFileSinkOutputSpec
+
+    def __init__(self, input_names=[], **inputs):
+        super(JSONFileSink, self).__init__(**inputs)
+        self._input_names = filename_to_list(input_names)
+        add_traits(self.inputs, [name for name in self._input_names])
+
+    def _list_outputs(self):
+        import json
+        import os.path as op
+        if not isdefined(self.inputs.out_file):
+            out_file = op.abspath('datasink.json')
+        else:
+            out_file = self.inputs.out_file
+
+        out_dict = dict()
+
+        if isdefined(self.inputs.in_dict):
+            if isinstance(self.inputs.in_dict, dict):
+                out_dict = self.inputs.in_dict
+        else:
+            for name in self._input_names:
+                val = getattr(self.inputs, name)
+                val = val if isdefined(val) else 'undefined'
+                out_dict[name] = val
+
+        with open(out_file, 'w') as f:
+            json.dump(out_dict, f)
+        outputs = self.output_spec().get()
+        outputs['out_file'] = out_file
+        return outputs
+
+

nipype/interfaces/tests/test_auto_JSONFileGrabber.py

@@ -0,0 +1,25 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.io import JSONFileGrabber
+
+def test_JSONFileGrabber_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    )
+    inputs = JSONFileGrabber.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_JSONFileGrabber_outputs():
+    output_map = dict()
+    outputs = JSONFileGrabber.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/tests/test_auto_JSONFileSink.py

@@ -0,0 +1,26 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.io import JSONFileSink
+
+def test_JSONFileSink_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_dict=dict(),
+    out_file=dict(),
+    )
+    inputs = JSONFileSink.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_JSONFileSink_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = JSONFileSink.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/testing/data/jsongrabber.txt

@@ -0,0 +1 @@
+{"param2": 4, "param1": "exampleStr"}