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Support Dataverse files without a persistentID #355

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merged 6 commits into from
Feb 19, 2024
Merged

Support Dataverse files without a persistentID #355

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0321a08
Support Dataverse files without a persistentID
santisoler Mar 13, 2023
7ad5073
Don't assume that persistentId is always present
santisoler Mar 20, 2023
1e670cf
Simplify the if statement
santisoler Mar 21, 2023
23d2d02
Merge branch 'main' into dataverse-without-persistentid
santisoler Apr 13, 2023
93d9835
Merge branch 'main' into dataverse-without-persistentid
leouieda Feb 19, 2024
15f7536
Only rely on the file ID, not PID
leouieda Feb 19, 2024
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37 changes: 24 additions & 13 deletions pooch/downloaders.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1034,20 +1034,31 @@ def download_url(self, file_name):
download_url : str
The HTTP URL that can be used to download the file.
"""

parsed = parse_url(self.archive_url)

# Iterate over the given files until we find one of the requested name
for filedata in self.api_response.json()["data"]["latestVersion"]["files"]:
if file_name == filedata["dataFile"]["filename"]:
return (
f"{parsed['protocol']}://{parsed['netloc']}/api/access/datafile/"
f":persistentId?persistentId={filedata['dataFile']['persistentId']}"
)

raise ValueError(
f"File '{file_name}' not found in data archive {self.archive_url} (doi:{self.doi})."
)
response = self.api_response.json()
files = {
file["dataFile"]["filename"]: file["dataFile"]
for file in response["data"]["latestVersion"]["files"]
}
if file_name not in files:
raise ValueError(
f"File '{file_name}' not found in data archive "
f"{self.archive_url} (doi:{self.doi})."
)
# Generate download_url using persistentId or file id
persistent_id = files[file_name]["persistentId"]
if persistent_id:
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The file ID will always be there. It's the primary key in the database.

The persistent ID (DOI or Handle) is optional so you can't rely on it being there. I would simply avoid even checking for it if all you want to do is download the file.

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I see. I thought the persistentId is always there, but it's empty if the files doesn't have one. Sorry for the misunderstanding.

If that's the case, you're right, we shouldn't assume that persistentId will always be there. I'll change the if statement then.

BTW, do you have any example where the persistentId is not even included in the response (I'm thinking for testing purposes)?

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Well, from a quick test it looks like persistentId is always present but can be an empty string. I'll put an example below.

I think we're saying the same thing. Always there. Sometimes an empty string. So I'd suggest checking for id instead which will always be there and always be a number. I hope this helps! 😄

curl -s 'https://dataverse.unc.edu/api/datasets/:persistentId?persistentId=doi:10.15139/S3/TRSZ3X' | jq '.data.latestVersion.files[0]'

{
  "description": "summary data file",
  "label": "CureTB data summary and statistics.tab",
  "restricted": false,
  "version": 3,
  "datasetVersionId": 32878,
  "dataFile": {
    "id": 7527010,
    "persistentId": "",
    "pidURL": "",
    "filename": "CureTB data summary and statistics.tab",
    "contentType": "text/tab-separated-values",
    "filesize": 3660,
    "description": "summary data file",
    "storageIdentifier": "s3://unc-dataverse-prod:18704bbebb7-8e1788510d33",
    "originalFileFormat": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "originalFormatLabel": "MS Excel Spreadsheet",
    "originalFileSize": 335887,
    "originalFileName": "CureTB data summary and statistics.xlsx",
    "UNF": "UNF:6:P0vi0QJZpFxCwM3pcX9YJw==",
    "rootDataFileId": -1,
    "md5": "4804fa6347742d850b0e1753c1668882",
    "checksum": {
      "type": "MD5",
      "value": "4804fa6347742d850b0e1753c1668882"
    },
    "creationDate": "2023-03-21"
  }
}

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Well, from a quick test it looks like persistentId is always present but can be an empty string.

Great then! The following two lines actually work both with non-existing persistentId and if persistentId is an empty string. So I think we could leave them as they are, just in case in the future persistentId is dropped from any Dataverse API.

pooch/pooch/downloaders.py

Lines 1049 to 1050 in 1e670cf

persistent_id = files[file_name].get("persistentId")
if persistent_id:

I think we're saying the same thing. Always there. Sometimes an empty string. So I'd suggest checking for id instead which will always be there and always be a number.

My strategy is to check for the id only if the persistentId is missing. This is due to what I commented above regarding defaulting to persistentId, being it the first option offered in Dataverse docs.

Maybe I'm being too conservative about it... I'm trying to keep the chances of breaking backward compatibility as low as possible, while still supporting the cases where persistentId is missing.

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I would suggest changing your strategy to this:

  • Only check for id

Simple! 😄

download_url = (
f"{parsed['protocol']}://{parsed['netloc']}/api/access/datafile/"
f":persistentId?persistentId={persistent_id}"
)
else:
file_id = files[file_name]["id"]
download_url = (
f"{parsed['protocol']}://{parsed['netloc']}/api/access/datafile/"
f"{file_id}"
)
return download_url

def populate_registry(self, pooch):
"""
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