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BUG: catch another situation where invalid manifest lines were not handled #140

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merged 2 commits into from
Nov 25, 2024
Merged

BUG: catch another situation where invalid manifest lines were not handled #140

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BUG: catch another situation where invalid manifest lines were not ha…
fedorov Nov 25, 2024
a2358ad
ENH: remove all manifest rows that do not contain S3 URL
fedorov Nov 25, 2024
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9 changes: 8 additions & 1 deletion idc_index/index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -779,6 +779,11 @@ def _validate_update_manifest_and_get_download_size(
# Rename the column
manifest_df.columns = ["manifest_cp_cmd"]

# remove all rows that do not contain an S3 URL
manifest_df = manifest_df[
manifest_df["manifest_cp_cmd"].str.contains(r"s3://", na=False)
]

# create a copy of the index
index_df_copy = self.index[
[
Expand Down Expand Up @@ -916,7 +921,9 @@ def _validate_update_manifest_and_get_download_size(
REGEXP_EXTRACT(manifest_cp_cmd, '(?:.*?\\/){{3}}([^\\/?#]+)', 1) AS manifest_crdc_series_uuid,
REGEXP_REPLACE(regexp_replace(manifest_cp_cmd, 'cp ', ''), '\\s[^\\s]*$', '') AS s3_url,
FROM
manifest_df )
manifest_df
WHERE
REGEXP_REPLACE(regexp_replace(manifest_cp_cmd, 'cp ', ''), '\\s[^\\s]*$', '') IS NOT NULL)
SELECT
seriesInstanceuid,
index_crdc_series_uuid,
Expand Down
1 change: 1 addition & 0 deletions tests/study_manifest_aws.s5cmd
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# To download the files in this manifest, first install s5cmd (https://github.com/peak/s5cmd),
# then run the following command:
# s5cmd --no-sign-request --endpoint-url https://s3.amazonaws.com run study_manifest_aws.s5cmd
study_manifest_cp_command
cp s3://idc-open-data/28621ba9-1aca-4aab-a2a1-f6d2c3e2ab19/* .
cp s3://idc-open-data/f0b76401-c6d1-4b61-a5fd-3fa596e6cc41/* .
cp s3://idc-open-data/4ea3bbe6-98da-4b92-abe6-2ee18927e3c9/* .
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