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ENH: update to IDC v19 #124

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merged 4 commits into from
Sep 11, 2024
Merged

ENH: update to IDC v19 #124

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bdbf99f
ENH: update to IDC v19
fedorov Sep 11, 2024
a455714
ENH: upgrade idc-index-data and use query-based clinical_index
fedorov Sep 11, 2024
32055be
BUG: do not use run_sql() function due to lack of access to local DF
fedorov Sep 11, 2024
879bcea
BUG: reverting prior change and downgrading duckdb
fedorov Sep 11, 2024
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3 changes: 2 additions & 1 deletion idc_index/index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def __init__(self):
"clinical_index": {
"description": "Index of clinical data accompanying the available images.",
"installed": False,
"url": f"https://idc-open-metadata.s3.amazonaws.com/bigquery_export/idc_{idc_version}_clinical/column_metadata/000000000000.parquet",
"url": f"{asset_endpoint_url}/clinical_index.parquet",
},
}

Expand Down Expand Up @@ -1794,6 +1794,7 @@ def sql_query(self, sql_query):
"""

index = self.index
logger.debug("Executing SQL query: " + sql_query)
# TODO: find a more elegant way to automate the following: https://www.perplexity.ai/search/write-python-code-that-iterate-XY9ppywbQFSRnOpgbwx_uQ
if hasattr(self, "sm_index"):
sm_index = self.sm_index
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -33,8 +33,8 @@ classifiers = [
dynamic = ["version"]
dependencies = [
"click",
'duckdb>=0.10.0',
"idc-index-data==18.2.0",
'duckdb>=0.10.0,<1.1.0',
"idc-index-data==19.0.1",
"packaging",
"pandas<2.2",
"psutil",
Expand Down
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