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Fix/OpenAlex "abstract_inverted_index" field is sometimes a string, not a dictionary #173

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Jul 27, 2023
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Fix/OpenAlex "abstract_inverted_index" field is sometimes a string, not a dictionary #173

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40180d0
Fix for if abstract_inverted_index is a string
alexmassen-hane Jul 26, 2023
8777079
Made requested changes
alexmassen-hane Jul 27, 2023
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4 changes: 2 additions & 2 deletions ...y_workflows/fixtures/openalex/2023-04-16/data/works/updated_date=2023-04-16/part_000.json
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26 changes: 22 additions & 4 deletions academic_observatory_workflows/workflows/openalex_telescope.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1016,12 +1016,30 @@ def transform_object(obj: dict):

field = "abstract_inverted_index"
if field in obj:
if not isinstance(obj.get(field), dict):
if not isinstance(obj.get(field), (dict, str)):
return
keys = list(obj[field].keys())
values = [str(value)[1:-1] for value in obj[field].values()]
else:
# If data is held in a string dump, load json string again.
if isinstance(obj.get(field), str):
obj_part = json.loads(obj[field])
field2 = "InvertedIndex"
if isinstance(obj_part.get(field2), dict):
keys = list(obj_part[field2].keys())
values = [str(value)[1:-1] for value in obj_part[field2].values()]

index_sum = sum(len(value.split(", ")) for value in values)
assert (
index_sum == obj_part["IndexLength"]
), f"Calculated IndexLength {index_sum} does not match value from file {obj_part['IndexLength']}."

obj[field] = {"keys": keys, "values": values}
else:
raise TypeError(f"obj_part['InvertedIndex'] is not a dictionary: {obj_part}")
else:
keys = list(obj[field].keys())
values = [str(value)[1:-1] for value in obj[field].values()]

obj[field] = {"keys": keys, "values": values}
obj[field] = {"keys": keys, "values": values}
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I don't think we need to check if the index length matches, as it is a problem for OpenAlex to fix if that is the case. It could be a data quality check that we do in the future (if we re-ran the workflow and updated the field).

You could simplify the code a bit by putting the parsing into a function, like this:

    field = "abstract_inverted_index"
    if field in obj:
        def parse_abstract(dict_: dict):
            keys_ = list(dict_.keys())
            values_ = [str(value_)[1:-1] for value_ in dict_.values()]
            return {"keys": keys_, "values": values_}
        if isinstance(obj.get(field), str):
            data = json.loads(obj[field])
            obj[field] = parse_abstract(data["InvertedIndex"])
        elif isinstance(obj.get(field), dict):
            obj[field] = parse_abstract(obj[field])
        else:
            return


field = "international"
if field in obj:
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21 changes: 18 additions & 3 deletions academic_observatory_workflows/workflows/tests/test_openalex_telescope.py
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Original file line number Diff line number Diff line change
Expand Up @@ -462,10 +462,25 @@ def test_transform_object(self):
obj3,
)

# Test object with nested "abstract_inverted_index" none
obj4 = {"abstract_inverted_index": None}
# Test object when "abstract_inverted_index" is a json string dump
obj4 = {
"abstract_inverted_index": '{"IndexLength": 7, "InvertedIndex": { "Malignant": [0], "hyperthermia": [1], "susceptibility": [2],"(MHS)": [3], "is": [4, 6], "primarily": [5]}}'
}
transform_object(obj4)
self.assertDictEqual({"abstract_inverted_index": None}, obj4)
self.assertDictEqual(
{
"abstract_inverted_index": {
"keys": ["Malignant", "hyperthermia", "susceptibility", "(MHS)", "is", "primarily"],
"values": ["0", "1", "2", "3", "4, 6", "5"],
}
},
obj4,
)

# Test object with nested "abstract_inverted_index" none
obj5 = {"abstract_inverted_index": None}
transform_object(obj5)
self.assertDictEqual({"abstract_inverted_index": None}, obj5)


def upload_folder_to_s3(bucket_name: str, folder_path: str, s3_prefix=None):
Expand Down