kopia lustrzana https://github.com/jupyterhub/repo2docker
126 wiersze
4.8 KiB
Python
126 wiersze
4.8 KiB
Python
import json
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import os
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import shutil
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from urllib.parse import parse_qs, urlparse, urlunparse
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from ..utils import copytree, deep_get
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from .doi import DoiProvider
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class Dataverse(DoiProvider):
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"""
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Provide contents of a Dataverse dataset.
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This class loads a a list of existing Dataverse installations from the internal
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file dataverse.json. This file is manually updated with the following command:
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python setup.py generate_dataverse_file
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"""
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def __init__(self):
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data_file = os.path.join(os.path.dirname(__file__), "dataverse.json")
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with open(data_file) as fp:
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self.hosts = json.load(fp)["installations"]
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super().__init__()
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def detect(self, doi, ref=None, extra_args=None):
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"""Trigger this provider for things that resolve to a Dataverse dataset.
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Handles:
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- DOI pointing to {siteURL}/dataset.xhtml?persistentId={persistentId}
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- DOI pointing to {siteURL}/file.xhtml?persistentId={persistentId}&...
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- URL {siteURL}/api/access/datafile/{fileId}
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Examples:
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- https://dataverse.harvard.edu/api/access/datafile/3323458
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- doi:10.7910/DVN/6ZXAGT
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- doi:10.7910/DVN/6ZXAGT/3YRRYJ
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"""
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url = self.doi2url(doi)
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# Parse the url, to get the base for later API calls
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parsed_url = urlparse(url)
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# Check if the url matches any known Dataverse installation, bail if not.
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host = next(
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(
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host
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for host in self.hosts
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if urlparse(host["url"]).netloc == parsed_url.netloc
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),
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None,
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)
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if host is None:
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return
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query_args = parse_qs(parsed_url.query)
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# Corner case handling
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if parsed_url.path.startswith("/file.xhtml"):
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# There's no way of getting file information using its persistentId, the only thing we can do is assume that doi
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# is structured as "doi:<dataset_doi>/<file_doi>" and try to handle dataset that way.
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new_doi = doi.rsplit("/", 1)[0]
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if new_doi == doi:
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# tough luck :( Avoid inifite recursion and exit.
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return
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return self.detect(new_doi)
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elif parsed_url.path.startswith("/api/access/datafile"):
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# Raw url pointing to a datafile is a typical output from an External Tool integration
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entity_id = os.path.basename(parsed_url.path)
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search_query = "q=entityId:" + entity_id + "&type=file"
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# Knowing the file identifier query search api to get parent dataset
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search_url = urlunparse(
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parsed_url._replace(path="/api/search", query=search_query)
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)
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self.log.debug("Querying Dataverse: " + search_url)
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data = self.urlopen(search_url).json()["data"]
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if data["count_in_response"] != 1:
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self.log.debug(
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f"Dataverse search query failed!\n - doi: {doi}\n - url: {url}\n - resp: {json.dump(data)}\n"
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)
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return
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self.record_id = deep_get(data, "items.0.dataset_persistent_id")
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elif (
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parsed_url.path.startswith("/dataset.xhtml")
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and "persistentId" in query_args
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):
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self.record_id = deep_get(query_args, "persistentId.0")
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if hasattr(self, "record_id"):
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return {"record": self.record_id, "host": host}
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def fetch(self, spec, output_dir, yield_output=False):
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"""Fetch and unpack a Dataverse dataset."""
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record_id = spec["record"]
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host = spec["host"]
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yield f"Fetching Dataverse record {record_id}.\n"
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url = f'{host["url"]}/api/datasets/:persistentId?persistentId={record_id}'
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resp = self.urlopen(url, headers={"accept": "application/json"})
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record = resp.json()["data"]
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for fobj in deep_get(record, "latestVersion.files"):
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file_url = (
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f'{host["url"]}/api/access/datafile/{deep_get(fobj, "dataFile.id")}'
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)
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filename = os.path.join(fobj.get("directoryLabel", ""), fobj["label"])
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file_ref = {"download": file_url, "filename": filename}
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fetch_map = {key: key for key in file_ref.keys()}
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yield from self.fetch_file(file_ref, fetch_map, output_dir)
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new_subdirs = os.listdir(output_dir)
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# if there is only one new subdirectory move its contents
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# to the top level directory
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if len(new_subdirs) == 1 and os.path.isdir(new_subdirs[0]):
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d = new_subdirs[0]
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copytree(os.path.join(output_dir, d), output_dir)
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shutil.rmtree(os.path.join(output_dir, d))
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@property
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def content_id(self):
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"""The Dataverse persistent identifier."""
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return self.record_id
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