Fix/OpenAlex "abstract_inverted_index" field is sometimes a string, not a dictionary #173
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## develop #173 +/- ##
===========================================
- Coverage 95.79% 95.78% -0.02%
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Files 19 19
Lines 4642 4649 +7
Branches 622 624 +2
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+ Hits 4447 4453 +6
Misses 122 122
- Partials 73 74 +1
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jdddog
requested changes
Jul 26, 2023
Comment on lines
1019
to
1042
| 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} |
There was a problem hiding this comment.
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
jdddog
approved these changes
Jul 27, 2023
alexmassen-hane
added a commit
that referenced
this pull request
Jul 28, 2023
…ot a dictionary (#173)
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For the recent 'works' output for the OpenAlex data dump, the "abstract_inverted_index" field can sometimes be json string dump. This PR adds the ability to decode the string dump and pull out the keys and values as needed. The resulting data should still be in the same format as before and it will not require a re-run of the entire workflow.
Please see the post on the Google forum for OpenAlex:
https://groups.google.com/g/openalex-users/c/TsVgxd_GEuw