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[WIP] updating life cycle of dandiset #275
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Original file line number | Diff line number | Diff line change | ||||||||||
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@@ -1,3 +1,4 @@ | ||||||||||||
from copy import deepcopy | ||||||||||||
import json | ||||||||||||
import os | ||||||||||||
from pathlib import Path | ||||||||||||
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@@ -9,6 +10,7 @@ | |||||||||||
import requests | ||||||||||||
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from dandischema.models import ( | ||||||||||||
Dandiset, | ||||||||||||
LicenseType, | ||||||||||||
PublishedDandiset, | ||||||||||||
RelationType, | ||||||||||||
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@@ -21,7 +23,7 @@ | |||||||||||
from .. import _get_datacite_schema, to_datacite | ||||||||||||
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def datacite_post(datacite: dict, doi: str) -> None: | ||||||||||||
def datacite_post(datacite: dict, doi: str, clean: bool = True) -> None: | ||||||||||||
"""Post the datacite object and check the status of the request""" | ||||||||||||
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||||||||||||
# removing doi in case it exists | ||||||||||||
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@@ -35,21 +37,178 @@ | |||||||||||
auth=("DARTLIB.DANDI", os.environ["DATACITE_DEV_PASSWORD"]), | ||||||||||||
) | ||||||||||||
rp.raise_for_status() | ||||||||||||
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print("\n in datacite_post, after posting", doi, rp.status_code) | ||||||||||||
# checking if i'm able to get the url | ||||||||||||
rg = requests.get(url=f"https://api.test.datacite.org/dois/{doi}/activities") | ||||||||||||
rg.raise_for_status() | ||||||||||||
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||||||||||||
# cleaning url | ||||||||||||
_clean_doi(doi) | ||||||||||||
if clean: | ||||||||||||
# cleaning url | ||||||||||||
_clean_doi(doi) | ||||||||||||
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def datacite_update(datacite: dict, doi: str) -> None: | ||||||||||||
"""Update the datacite object and check the status of the request""" | ||||||||||||
rp = requests.put( | ||||||||||||
url=f"https://api.test.datacite.org/dois/{doi}", | ||||||||||||
json=datacite, | ||||||||||||
headers={"Content-Type": "application/vnd.api+json"}, | ||||||||||||
auth=("DARTLIB.DANDI", os.environ["DATACITE_DEV_PASSWORD"]), | ||||||||||||
) | ||||||||||||
rp.raise_for_status() | ||||||||||||
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# checking if i'm able to get the url | ||||||||||||
rg = requests.get(url=f"https://api.test.datacite.org/dois/{doi}/activities") | ||||||||||||
rg.raise_for_status() | ||||||||||||
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def _clean_doi(doi: str) -> None: | ||||||||||||
"""Remove doi. Status code is ignored""" | ||||||||||||
requests.delete( | ||||||||||||
rq = requests.delete( | ||||||||||||
f"https://api.test.datacite.org/dois/{doi}", | ||||||||||||
auth=("DARTLIB.DANDI", os.environ["DATACITE_DEV_PASSWORD"]), | ||||||||||||
) | ||||||||||||
print("\n in _clean_doi", doi, rq.status_code) | ||||||||||||
return rq.status_code | ||||||||||||
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@pytest.mark.skip( | ||||||||||||
reason="to not produced too many dois, not sure if we want to keep it as a test" | ||||||||||||
) | ||||||||||||
def test_datacite_lifecycle() -> None: | ||||||||||||
"""testing the lifecycle of a public dandiset and doi (from draft to published)""" | ||||||||||||
|
||||||||||||
# checking which doi is available | ||||||||||||
doi_available = False | ||||||||||||
while not doi_available: | ||||||||||||
dandi_id = f"000{random.randrange(500, 999)}" | ||||||||||||
print(f"searching for available doi, trying dandi_id: {dandi_id}") | ||||||||||||
doi_root = f"10.80507/dandi.{dandi_id}" | ||||||||||||
if _clean_doi(doi_root) != 405: | ||||||||||||
doi_available = True | ||||||||||||
print(f"found available doi, dandi_id: {dandi_id}") | ||||||||||||
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dandi_id_prefix = f"DANDI:{dandi_id}" | ||||||||||||
# creating the main/root doi and url | ||||||||||||
doi_root = f"10.80507/dandi.{dandi_id}" | ||||||||||||
url_root = f"https://dandiarchive.org/dandiset/{dandi_id}" | ||||||||||||
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||||||||||||
# creating draft dandiset with minimal metadata | ||||||||||||
version = "draft" | ||||||||||||
meta_dict = { | ||||||||||||
"identifier": dandi_id_prefix, | ||||||||||||
"id": f"{dandi_id_prefix}/{version}", | ||||||||||||
"name": "Testing Dataset: lifecycle", | ||||||||||||
"description": "testing lifecycle of a dataset and doi: draft", | ||||||||||||
"version": version, | ||||||||||||
"contributor": [ | ||||||||||||
{ | ||||||||||||
"name": "A_last, A_first", | ||||||||||||
"email": "[email protected]", | ||||||||||||
"roleName": [RoleType("dcite:ContactPerson")], | ||||||||||||
"schemaKey": "Person", | ||||||||||||
} | ||||||||||||
], | ||||||||||||
"license": [LicenseType("spdx:CC-BY-4.0")], | ||||||||||||
"citation": "A_last, A_first 2021", | ||||||||||||
"manifestLocation": [ | ||||||||||||
f"https://api.dandiarchive.org/api/dandisets/{dandi_id}/versions/{version}/assets/" | ||||||||||||
], | ||||||||||||
"assetsSummary": { | ||||||||||||
"schemaKey": "AssetsSummary", | ||||||||||||
"numberOfBytes": 10, | ||||||||||||
"numberOfFiles": 1, | ||||||||||||
}, | ||||||||||||
Comment on lines
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. hopefully does not matter but whenever dandiset is created, there is no assets summary yet -- it is done async IIRC, hence
Suggested change
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} | ||||||||||||
# in addition to minimal metadata, we need to add doi and url if we want to create draft doi | ||||||||||||
meta_dict["doi"] = doi_root | ||||||||||||
meta_dict["url"] = url_root | ||||||||||||
# creating draft dandiset | ||||||||||||
dset = Dandiset(**meta_dict) | ||||||||||||
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# creating datacite object and posting the main doi entry (should be draft) | ||||||||||||
datacite = to_datacite(dset) | ||||||||||||
datacite_post(datacite, doi_root, clean=False) | ||||||||||||
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# updating the draft but not enough to create PublishDandiset | ||||||||||||
meta_dict["description"] = "testing lifecycle of a dataset and doi: new draft" | ||||||||||||
# the dandi workflow should check if we cna create a datacite that can be validated and published | ||||||||||||
# try: datacite_new = to_datacite(meta_dict, validate=True, publish=True) | ||||||||||||
# if the metadata is not enough to create a valid datacite, we should update the draft doi | ||||||||||||
datacite_new = to_datacite(meta_dict) | ||||||||||||
datacite_update(datacite_new, doi_root) | ||||||||||||
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# creating v1.0.0 | ||||||||||||
version = "1.0.0" | ||||||||||||
# adding contributors and updating description | ||||||||||||
meta_dict["contributor"].append( | ||||||||||||
{ | ||||||||||||
"name": "B_last, B_first", | ||||||||||||
"email": "[email protected]", | ||||||||||||
"roleName": [RoleType("dcite:DataCurator")], | ||||||||||||
"schemaKey": "Person", | ||||||||||||
} | ||||||||||||
) | ||||||||||||
meta_dict["description"] = "testing lifecycle of a dataset and doi: v1.0.0" | ||||||||||||
# adding mandatory metadata for PublishDandiset | ||||||||||||
publish_meta = { | ||||||||||||
"datePublished": "2020", | ||||||||||||
"publishedBy": { | ||||||||||||
"id": "urn:uuid:08fffc59-9f1b-44d6-8e02-6729d266d1b6", | ||||||||||||
"name": "DANDI publish", | ||||||||||||
"startDate": "2021-05-18T19:58:39.310338-04:00", | ||||||||||||
"endDate": "2021-05-18T19:58:39.310361-04:00", | ||||||||||||
"wasAssociatedWith": [ | ||||||||||||
{ | ||||||||||||
"id": "urn:uuid:9267d2e1-4a37-463b-9b10-dad3c66d8eaa", | ||||||||||||
"identifier": "RRID:SCR_017571", | ||||||||||||
"name": "DANDI API", | ||||||||||||
"version": version, | ||||||||||||
"schemaKey": "Software", | ||||||||||||
} | ||||||||||||
], | ||||||||||||
"schemaKey": "PublishActivity", | ||||||||||||
}, | ||||||||||||
} | ||||||||||||
meta_dict.update(publish_meta) | ||||||||||||
# updating the version, id etc. | ||||||||||||
meta_dict["version"] = version | ||||||||||||
meta_dict["id"] = f"{dandi_id_prefix}/{version}" | ||||||||||||
meta_dict["doi"] = f"{doi_root}/{version}" | ||||||||||||
meta_dict["url"] = f"https://dandiarchive.org/dandiset/{dandi_id}/{version}" | ||||||||||||
# creating new published dandiset | ||||||||||||
dset_v1 = PublishedDandiset(**meta_dict) | ||||||||||||
# creating datacite object and posting (should be findable) | ||||||||||||
datacite_v1 = to_datacite(dset_v1, publish=True, validate=True) | ||||||||||||
datacite_post(datacite_v1, meta_dict["doi"], clean=False) | ||||||||||||
|
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# updating the main doi but keeping the root doi and url | ||||||||||||
datacite = deepcopy(datacite_v1) | ||||||||||||
datacite["data"]["attributes"]["doi"] = doi_root | ||||||||||||
datacite["data"]["attributes"]["url"] = url_root | ||||||||||||
# updating the doi (should change from draft to findable) | ||||||||||||
datacite_update(datacite, doi_root) | ||||||||||||
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||||||||||||
# creating v2.0.0 | ||||||||||||
version = "2.0.0" | ||||||||||||
# updating description | ||||||||||||
meta_dict["description"] = "testing lifecycle of a dataset and doi: v2.0.0" | ||||||||||||
meta_dict["version"] = version | ||||||||||||
meta_dict["id"] = f"{dandi_id_prefix}/{version}" | ||||||||||||
meta_dict["doi"] = f"{doi_root}/{version}" | ||||||||||||
meta_dict["url"] = f"https://dandiarchive.org/dandiset/{dandi_id}/{version}" | ||||||||||||
# creating new published dandiset | ||||||||||||
dset_v2 = PublishedDandiset(**meta_dict) | ||||||||||||
# creating datacite object and posting (should be findable) | ||||||||||||
datacite_v2 = to_datacite(dset_v2, publish=True, validate=True) | ||||||||||||
datacite_post(datacite_v2, meta_dict["doi"], clean=False) | ||||||||||||
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# updating the main doi to v2 but keeping the root doi and url | ||||||||||||
datacite = deepcopy(datacite_v2) | ||||||||||||
datacite["data"]["attributes"]["doi"] = doi_root | ||||||||||||
datacite["data"]["attributes"]["url"] = url_root | ||||||||||||
# updating the findable doi | ||||||||||||
datacite_update(datacite, doi_root) | ||||||||||||
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@pytest.fixture(scope="module") | ||||||||||||
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@@ -59,7 +218,7 @@ | |||||||||||
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@pytest.fixture(scope="function") | ||||||||||||
def metadata_basic() -> Dict[str, Any]: | ||||||||||||
dandi_id_noprefix = f"000{random.randrange(100, 999)}" | ||||||||||||
dandi_id_noprefix = f"000{random.randrange(100, 499)}" | ||||||||||||
dandi_id = f"DANDI:{dandi_id_noprefix}" | ||||||||||||
version = "0.0.0" | ||||||||||||
# meta data without doi, datePublished and publishedBy | ||||||||||||
|
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that is because the issue with DOI deletion was not yet addressed on datacite side, right?
then better be mentioned. in the current skip.
Otherwise -- test should be diligent about removing any DOI it created in its life time.