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Always fetch entire dataset for dataverse
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@yuvipanda
yuvipanda committed Dec 17, 2024
1 parent 1260a5a commit b7050ba
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Showing 2 changed files with 103 additions and 63 deletions.
94 changes: 49 additions & 45 deletions repo2docker/contentproviders/dataverse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,26 @@ def detect(self, spec, ref=None, extra_args=None):
# that can be figured out during fetch as needed
return {"host": host, "url": url}

def get_dataset_id_from_file_id(self, host: str, file_id: str) -> str:
"""
Return the persistent_id (DOI) that a given file_id (int or doi) belongs to
"""
if file_id.isdigit():
# the file_id is an integer, rather than a persistent id (DOI)
api_url = f"{host}/api/files/{file_id}?returnDatasetVersion=true"
else:
# the file_id is a doi itself
api_url = f"{host}/api/files/:persistentId?persistentId={file_id}&returnDatasetVersion=true"

resp = self._request(api_url)
if resp.status_code == 404:
raise ValueError(f"File with id {file_id} not found in {host}")

resp.raise_for_status()

data = resp.json()["data"]
return data["datasetVersion"]["datasetPersistentId"]

def get_persistent_id_from_url(self, url: str) -> str:
"""
Return the persistentId for given dataverse URL.
Expand All @@ -80,72 +100,56 @@ def get_persistent_id_from_url(self, url: str) -> str:
If a URL can not be parsed, throw an exception
"""

def get_datafiles(self, dataverse_host: str, url: str) -> list[dict]:
"""
Return a list of dataFiles for given persistent_id
"""

parsed_url = urlparse(url)
path = parsed_url.path
qs = parse_qs(parsed_url.query)
dataverse_host = f"{parsed_url.scheme}://{parsed_url.netloc}"
url_kind = None
persistent_id = None
is_ambiguous = False

# https://dataverse.harvard.edu/citation?persistentId=doi:10.7910/DVN/TJCLKP
if path.startswith("/citation"):
is_ambiguous = True
persistent_id = qs["persistentId"][0]
# https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/TJCLKP
if path.startswith("/citation") or path.startswith("/dataset.xhtml"):
return qs["persistentId"][0]
elif path.startswith("/dataset.xhtml"):
# https://dataverse.harvard.edu/api/access/datafile/3323458
persistent_id = qs["persistentId"][0]
elif path.startswith("/api/access/datafile"):
# What we have here is an entity id, which we can use to get a persistentId
entity_id = os.path.basename(parsed_url.path)
# FIXME: Should we be URL Encoding something here to protect from path traversal
# or similar attacks?
search_query = f"q=entityId:{entity_id}&type=file"
search_api_url = urlunparse(
parsed_url._replace(path="/api/search", query=search_query)
)
self.log.debug("Querying Dataverse: " + search_api_url)
data = self.urlopen(search_api_url).json()["data"]
if data["count_in_response"] != 1:
raise ValueError(
f"Dataverse search query failed!\n - url: {url}\n - resp: {json.dumps(data)}\n"
)
return data["items"][0]["dataset_persistent_id"]
file_id = os.path.basename(parsed_url.path)
persistent_id = self.get_dataset_id_from_file_id(dataverse_host, file_id)
elif parsed_url.path.startswith("/file.xhtml"):
file_persistent_id = qs["persistentId"][0]
dataset_persistent_id = file_persistent_id.rsplit("/", 1)[0]
if file_persistent_id == dataset_persistent_id:
# We can't figure this one out, throw an error
raise ValueError(f"Could not find dataset id for {url}")
return dataset_persistent_id

raise ValueError(f"Could not determine persistent id for dataverse URL {url}")

def get_datafiles(self, host: str, persistent_id: str) -> list[dict]:
"""
Return a list of dataFiles for given persistent_id
"""
dataset_url = f"{host}/api/datasets/:persistentId?persistentId={persistent_id}"
persistent_id = self.get_dataset_id_from_file_id(dataverse_host, file_persistent_id)
else:
raise ValueError(f"Could not determine persistent id for dataverse URL {url}")

resp = self._request(dataset_url, headers={"accept": "application/json"})
# Assume it's a dataset
is_dataset = True
if resp.status_code == 404:
dataset_api_url = f"{dataverse_host}/api/datasets/:persistentId?persistentId={persistent_id}"
resp = self._request(dataset_api_url, headers={"accept": "application/json"})
if resp.status_code == 404 and is_ambiguous:
# It's possible this is a *file* persistent_id, not a dataset one
file_url = f"{host}/api/files/:persistentId?persistentId={persistent_id}"
resp = self._request(file_url, headers={"accept": "application/json"})
persistent_id = self.get_dataset_id_from_file_id(dataverse_host, persistent_id)
dataset_api_url = f"{dataverse_host}/api/datasets/:persistentId?persistentId={persistent_id}"
resp = self._request(dataset_api_url, headers={"accept": "application/json"})

if resp.status_code == 404:
# This persistent id is just not here
raise ValueError(f"{persistent_id} on {host} is not found")

# It's not a dataset, it's a file!
is_dataset = False
raise ValueError(f"{persistent_id} on {dataverse_host} is not found")

# We already handled 404, raise error for everything else
resp.raise_for_status()

data = resp.json()["data"]

if is_dataset:
return data["latestVersion"]["files"]
else:
# Only one file object
return [data]
return data["latestVersion"]["files"]

def fetch(self, spec, output_dir, yield_output=False):
"""Fetch and unpack a Dataverse dataset."""
Expand All @@ -156,7 +160,7 @@ def fetch(self, spec, output_dir, yield_output=False):

yield f"Fetching Dataverse record {persistent_id}.\n"

for fobj in self.get_datafiles(host["url"], persistent_id):
for fobj in self.get_datafiles(host["url"], url):
file_url = (
# without format=original you get the preservation format (plain text, tab separated)
f'{host["url"]}/api/access/datafile/{deep_get(fobj, "dataFile.id")}?format=original'
Expand Down
72 changes: 54 additions & 18 deletions tests/contentproviders/test_dataverse.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -85,38 +85,74 @@ def test_get_persistent_id(url, persistent_id):


@pytest.mark.parametrize(
("spec", "md5tree"),
("specs", "md5tree"),
[
(
"doi:10.7910/DVN/TJCLKP",
(
"doi:10.7910/DVN/TJCLKP",
"https://dataverse.harvard.edu/citation?persistentId=doi:10.7910/DVN/TJCLKP",
),
{
"data/primary/primary-data.zip": "a8f6fc3fc58f503cd48e23fa8b088694",
"data/2023-01-03.tsv": "6fd497bf13dab9a06fe737ebc22f1917",
"code/language.py": "9d61582bcf497c83bbd1ed0eed3c772e",
},
),
(
# A citation targeting a single file
"https://dataverse.harvard.edu/citation?persistentId=doi:10.7910/DVN/6ZXAGT/3YRRYJ",
(
"https://dataverse.harvard.edu/file.xhtml?persistentId=doi:10.7910/DVN/6ZXAGT/3YRRYJ",
"https://dataverse.harvard.edu/citation?persistentId=doi:10.7910/DVN/6ZXAGT/3YRRYJ",
"doi:10.7910/DVN/6ZXAGT/3YRRYJ"
),
{
"ARCHAEOGLOBE_CONSENSUS_ASSESSMENT.tab": "17a91888ed8e91dfb63acbbab6127ac5"
'ArchaeoGLOBE-master/analysis/figures/1_response_distribution.png': '243c6a3dd66bc3c84102829b277ef333',
'ArchaeoGLOBE-master/analysis/figures/2_trends_map_knowledge.png': '2ace6ae9d470dda6cf2f9f9a6588171a',
'ArchaeoGLOBE-master/analysis/figures/3_trends_global.png': '63ccd0a7b2d20440cd8f418d4ee88c4d',
'ArchaeoGLOBE-master/analysis/figures/4_consensus_transitions.png': 'facfaedabeac77c4496d4b9e962a917f',
'ArchaeoGLOBE-master/analysis/figures/5_ArchaeoGLOBE_HYDE_comparison.png': '8e002e4d50f179fc1808f562b1353588',
'ArchaeoGLOBE-master/apt.txt': 'b4224032da6c71d48f46c9b78fc6ed77',
'ArchaeoGLOBE-master/analysis/archaeoglobe.pdf': 'f575be4790efc963ef1bd40d097cc06d',
'ArchaeoGLOBE-master/analysis/archaeoglobe.Rmd': 'f37d5f7993fde9ebd64d16b20fc22905',
'ArchaeoGLOBE-master/ArchaeoGLOBE.Rproj': 'd0250e7918993bab1e707358fe5633e0',
'ArchaeoGLOBE-master/CONDUCT.md': 'f87ef290340322089c32b4e573d8f1e8',
'ArchaeoGLOBE-master/.circleci/config.yml': '6eaa54073a682b3195d8fab3a9dd8344',
'ArchaeoGLOBE-master/CONTRIBUTING.md': 'b3a6abfc749dd155a3049f94a855bf9f',
'ArchaeoGLOBE-master/DESCRIPTION': '745ef979494999e483987de72c0adfbd',
'ArchaeoGLOBE-master/dockerfile': 'aedce68e5a7d6e79cbb24c9cffeae593',
'ArchaeoGLOBE-master/.binder/Dockerfile': '7564a41246ba99b60144afb1d3b6d7de',
'ArchaeoGLOBE-master/.gitignore': '62c1482e4febbd35dc02fb7e2a31246b',
'ArchaeoGLOBE-master/analysis/data/derived-data/hyde_crop_prop.RDS': '2aea7748b5586923b0de9d13af58e59d',
'ArchaeoGLOBE-master/analysis/data/derived-data/kk_anthro_prop.RDS': '145a9e5dd2c95625626a720b52178b70',
'ArchaeoGLOBE-master/LICENSE.md': '3aa9d41a92a57944bd4590e004898445',
'ArchaeoGLOBE-master/analysis/data/derived-data/placeholder': 'd41d8cd98f00b204e9800998ecf8427e',
'ArchaeoGLOBE-master/.Rbuildignore': 'df15e4fed49abd685b536fef4472b01f',
'ArchaeoGLOBE-master/README.md': '0b0faabe580c4d76a0e0d64a4f54bca4',
'ArchaeoGLOBE-master/analysis/data/derived-data/README.md': '547fd1a6e874f6178b1cf525b5b9ae72',
'ArchaeoGLOBE-master/analysis/figures/S1_FHG_consensus.png': 'd2584352e5442b33e4b23e361ca70fe1',
'ArchaeoGLOBE-master/analysis/figures/S2_EXAG_consensus.png': '513eddfdad01fd01a20263a55ca6dbe3',
'ArchaeoGLOBE-master/analysis/figures/S3_INAG_consensus.png': 'b16ba0ecd21b326f873209a7e55a8deb',
'ArchaeoGLOBE-master/analysis/figures/S4_PAS_consensus.png': '05695f9412337a00c1cb6d1757d0ec5c',
'ArchaeoGLOBE-master/analysis/figures/S5_URBAN_consensus.png': '10119f7495d3b8e7ad7f8a0770574f15',
'ArchaeoGLOBE-master/analysis/figures/S6_trends_map_landuse.png': 'b1db7c97f39ccfc3a9e094c3e6307af0',
'ArchaeoGLOBE-master/analysis/figures/S7_ArchaeoGLOBE_KK10_comparison.png': '30341748324f5f66acadb34c114c3e9d',
}
)
],
)
def test_fetch(spec, md5tree):
def test_fetch(specs: list[str], md5tree):
dv = Dataverse()

with TemporaryDirectory() as d:
output = []
for l in dv.fetch(dv.detect(spec), d):
output.append(l)
for spec in specs:
with TemporaryDirectory() as d:
output = []
for l in dv.fetch(dv.detect(spec), d):
output.append(l)

# Verify md5 sum of the files we expect to find
# We are using md5 instead of something more secure because that is what
# dataverse itself uses
for subpath, expected_sha in md5tree.items():
with open(os.path.join(d, subpath), "rb") as f:
h = hashlib.md5()
h.update(f.read())
assert h.hexdigest() == expected_sha
# Verify md5 sum of the files we expect to find
# We are using md5 instead of something more secure because that is what
# dataverse itself uses
for subpath, expected_sha in md5tree.items():
with open(os.path.join(d, subpath), "rb") as f:
h = hashlib.md5()
h.update(f.read())
assert h.hexdigest() == expected_sha

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