Sanitizing ArrayData for REST-API

aiida/orm/nodes/data/array/array.py

@@ -201,9 +201,11 @@ def _get_array_entries(self):
         the value is the numpy array transformed into a list. This is so that
         it can be transformed into a json object.
         """
+
         array_dict = {}
         for key, val in self.get_iterarrays():
-            array_dict[key] = val.tolist()
+
+            array_dict[key] = clean_array(val)
         return array_dict
 
     def _prepare_json(self, main_file_name='', comments=True):  # pylint: disable=unused-argument
@@ -222,3 +224,28 @@ def _prepare_json(self, main_file_name='', comments=True):  # pylint: disable=un
             json_dict['comments'] = get_file_header(comment_char='')
 
         return json.dumps(json_dict).encode('utf-8'), {}
+
+
+def clean_array(array):
+    """
+    Replacing np.nan and np.inf/-np.inf for Nones.
+
+    The function will also sanitize the array removing ``np.nan`` and ``np.inf``
+    for ``None`` of this way the resulting JSON is always valid.
+    Both ``np.nan`` and ``np.inf``/``-np.inf`` are set to None to be in
+    accordance with the
+    `ECMA-262 standard <https://www.ecma-international.org/publications-and-standards/standards/ecma-262/>`_.
+
+    :param array: input array to be cleaned
+    :return: cleaned list to be serialized
+    :rtype: list
+    """
+    import numpy as np
+
+    output = np.reshape(
+        np.asarray([
+            entry if not np.isnan(entry) and not np.isinf(entry) else None for entry in array.flatten().tolist()
+        ]), array.shape
+    )
+
+    return output.tolist()

docs/source/howto/share_data.rst

@@ -183,6 +183,11 @@ The AiiDA REST API allows to query your AiiDA database over HTTP(S) and returns
     As of October 2020, the AiiDA REST API only supports ``GET`` methods (reading); in particular, it does *not* yet support workflow management.
     This feature is, however, part of the `AiiDA roadmap <https://github.com/aiidateam/aiida-core/wiki/AiiDA-release-roadmap>`_.
 
+
+.. note::
+    To ensure that when serving ``orm.ArrayData`` one always obtains a valid JSON compliant with the `ECMA-262 standard <https://www.ecma-international.org/publications-and-standards/standards/ecma-262/>`_, any ``np.nan``, ``np.inf`` and/or ``-np.inf`` entries will be replaced by ``None`` which will be rendered as ``null`` when getting the array via the API call.
+
+
 .. _how-to:share:serve:launch:
 
 Launching the REST API

docs/source/reference/rest_api.rst

@@ -946,7 +946,7 @@ Querybuilder
         Posts a query to the database. The content of the query is passed in a attached JSON file.
 
 To use this endpoint, you need a http operator that allows to pass attachments.
-We will demonstrate two options, the `HTTPie <https://httpie.io/>`_ (to use in the terminal) and the python library `Requests <https://docs.python-requests.org/en/latest/#>`_ (to use in python).
+We will demonstrate two options, the `HTTPie <https://httpie.io/>`_ (to use in the terminal) and the python library `Requests <https://requests.readthedocs.io/en/latest/>`_ (to use in python).
 
 Option 1: HTTPie
 

tests/restapi/test_routes.py

@@ -14,11 +14,13 @@
 import json
 
 from flask_cors.core import ACL_ORIGIN
+import numpy as np
 import pytest
 
 from aiida import orm
 from aiida.common.links import LinkType
 from aiida.manage import get_manager
+from aiida.orm.nodes.data.array.array import clean_array
 from aiida.restapi.run_api import configure_api
 
 
@@ -141,6 +143,12 @@ def init_profile(self, aiida_profile_clean, aiida_localhost):  # pylint: disable
             computer = orm.Computer(**dummy_computer)
             computer.store()
 
+        # Setting array data for the tests
+        array = orm.ArrayData()
+        array.set_array('array_clean', np.asarray([[4, 5, 7], [9, 5, 1], [3, 4, 4]]))
+        array.set_array('array_dirty', np.asarray([[4, 5, np.nan], [9, np.inf, -1 * np.inf], [np.nan, 4, 4]]))
+        array.store()
+
         # Prepare typical REST responses
         self.process_dummy_data()
 
@@ -205,6 +213,7 @@ def process_dummy_data(self):
             'parameterdata': orm.Dict,
             'structuredata': orm.StructureData,
             'data': orm.Data,
+            'arraydata': orm.ArrayData,
         }
         for label, dataclass in data_types.items():
             data = orm.QueryBuilder().append(dataclass, tag='data', project=data_projections).order_by({
@@ -300,7 +309,6 @@ def process_test(
         if result_node_type is None and result_name is None:
             result_node_type = entity_type
             result_name = entity_type
-
         url = self._url_prefix + url
 
         with self.app.test_client() as client:
@@ -321,7 +329,6 @@ def process_test(
                 else:
                     from aiida.common.exceptions import InputValidationError
                     raise InputValidationError('Pass the expected range of the dummydata')
-
                 expected_node_uuids = [node['uuid'] for node in expected_data]
                 result_node_uuids = [node['uuid'] for node in response['data'][result_name]]
                 assert expected_node_uuids == result_node_uuids
@@ -745,7 +752,7 @@ def test_calculation_inputs(self):
         self.process_test(
             'nodes',
             f'/nodes/{str(node_uuid)}/links/incoming?orderby=id',
-            expected_list_ids=[5, 3],
+            expected_list_ids=[6, 4],
             uuid=node_uuid,
             result_node_type='data',
             result_name='incoming'
@@ -759,7 +766,7 @@ def test_calculation_input_filters(self):
         self.process_test(
             'nodes',
             f"/nodes/{str(node_uuid)}/links/incoming?node_type=\"data.core.dict.Dict.\"",
-            expected_list_ids=[3],
+            expected_list_ids=[4],
             uuid=node_uuid,
             result_node_type='data',
             result_name='incoming'
@@ -1347,3 +1354,26 @@ def test_querybuilder_project_implicit(self):
                 # All are Nodes, and all properties are projected, full_type should be present
                 assert 'full_type' in entity
                 assert 'attributes' in entity
+
+    def test_array_download(self):
+        """
+        Test download of arraydata as a json file
+        """
+        from aiida.orm import load_node
+
+        node_uuid = self.get_dummy_data()['arraydata'][0]['uuid']
+        url = f'{self.get_url_prefix()}/nodes/{node_uuid}/download?download_format=json&download=False'
+        with self.app.test_client() as client:
+            rv_obj = client.get(url)
+
+        data_json = json.loads(rv_obj.json['data']['download']['data'])
+
+        assert json.dumps(data_json, allow_nan=False)
+
+        data_array = load_node(node_uuid)
+        array_names = data_array.get_arraynames()
+        for name in array_names:
+            if not np.isnan(data_array.get_array(name)).any():
+                assert np.allclose(data_array.get_array(name), data_json[name])
+            else:
+                assert clean_array(data_array.get_array(name)) == data_json[name]