diff --git a/conftest.py b/conftest.py index 9cc6eb630f..a0e4fa49bd 100644 --- a/conftest.py +++ b/conftest.py @@ -25,9 +25,11 @@ import tempfile import time import urllib +from pathlib import Path import pytest import responses +import yaml from click.testing import CliRunner @@ -452,17 +454,24 @@ def renku_cli(*args): return renku_cli -@pytest.fixture -def doi_dataset(): - """Return a yaml of dataset using DOI for its id.""" - from pathlib import Path - dataset_path = Path( - __file__ - ).parent / 'tests' / 'fixtures' / 'doi-dataset.yml' - with open(dataset_path.as_posix()) as f: - dataset_yaml = f.read() +@pytest.fixture( + params=[{ + 'path': + Path(__file__).parent / 'tests' / 'fixtures' / 'doi-dataset.yml', + }, { + 'path': + Path(__file__).parent / 'tests' / 'fixtures' / + 'broken-dataset-v0.5.2.yml', + }] +) +def dataset_metadata(request): + """Return dataset metadata fixture.""" + from renku.core.models.jsonld import NoDatesSafeLoader + + file_path = request.param['path'] - return dataset_yaml + data = yaml.load(file_path.read_text(), Loader=NoDatesSafeLoader) + yield data @pytest.fixture() diff --git a/renku/core/commands/checks/migration.py b/renku/core/commands/checks/migration.py index 89998f3bb5..f1583b3f06 100644 --- a/renku/core/commands/checks/migration.py +++ b/renku/core/commands/checks/migration.py @@ -26,6 +26,7 @@ from renku.core.models.datasets import Dataset from renku.core.models.refs import LinkReference +from renku.core.utils.urls import url_to_string from ..echo import WARNING @@ -235,9 +236,19 @@ def fix_uncommitted_labels(client): dataset.to_yaml() +def fix_dataset_files_urls(client): + """Ensure dataset files have correct url format.""" + for dataset in client.datasets.values(): + for file_ in dataset.files: + file_.url = url_to_string(file_.url) + + dataset.to_yaml() + + STRUCTURE_MIGRATIONS = [ ensure_clean_lock, migrate_datasets_pre_v0_3, migrate_broken_dataset_paths, fix_uncommitted_labels, + fix_dataset_files_urls, ] diff --git a/renku/core/models/datasets.py b/renku/core/models/datasets.py index 5345577ea9..19e17d0099 100644 --- a/renku/core/models/datasets.py +++ b/renku/core/models/datasets.py @@ -128,6 +128,12 @@ def _convert_dataset_files_creators(value): return [Creator.from_jsonld(c) for c in coll] +def convert_filename_path(p): + """Return name of the file.""" + if p: + return Path(p).name + + @jsonld.s( type='schema:DigitalDocument', slots=True, @@ -153,7 +159,7 @@ class DatasetFile(Entity, CreatorsMixin): dataset = jsonld.ib(context='schema:isPartOf', default=None, kw_only=True) - filename = attr.ib(kw_only=True, converter=lambda x: Path(x).name) + filename = attr.ib(kw_only=True, converter=convert_filename_path) name = jsonld.ib(context='schema:name', kw_only=True, default=None) diff --git a/renku/core/utils/urls.py b/renku/core/utils/urls.py new file mode 100644 index 0000000000..2a214352ba --- /dev/null +++ b/renku/core/utils/urls.py @@ -0,0 +1,41 @@ +# -*- coding: utf-8 -*- +# +# Copyright 2019 - Swiss Data Science Center (SDSC) +# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and +# Eidgenössische Technische Hochschule Zürich (ETHZ). +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Helpers utils for handling URLs.""" + +from urllib.parse import ParseResult + + +def url_to_string(url): + """Convert url from ``list`` or ``ParseResult`` to string.""" + if isinstance(url, list): + return ParseResult( + scheme=url[0], + netloc=url[1], + path=url[2], + params=None, + query=None, + fragment=None, + ).geturl() + + if isinstance(url, ParseResult): + return url.geturl() + + if isinstance(url, str): + return url + + raise ValueError('url value not recognized') diff --git a/tests/cli/test_migrate.py b/tests/cli/test_migrate.py index 59c597bdca..f5d84c9a56 100644 --- a/tests/cli/test_migrate.py +++ b/tests/cli/test_migrate.py @@ -23,6 +23,8 @@ from renku import LocalClient from renku.cli import cli from renku.core.management.config import RENKU_HOME +from renku.core.models.datasets import Dataset +from renku.core.utils.urls import url_to_string @pytest.mark.migration @@ -161,3 +163,15 @@ def test_migrations_run_once(isolated_runner, old_project): result = isolated_runner.invoke(cli, ['migrate', 'datasets']) assert 1 == result.exit_code + + +@pytest.mark.migration +def test_migration_broken_urls(dataset_metadata): + """Check that migration of broken dataset file URLs is string.""" + dataset = Dataset.from_jsonld( + dataset_metadata, + client=LocalClient('.'), + ) + + for file_ in dataset.files: + assert isinstance(url_to_string(file_.url), str) diff --git a/tests/core/commands/test_serialization.py b/tests/core/commands/test_serialization.py index a6f1ce750c..03df5f9a37 100644 --- a/tests/core/commands/test_serialization.py +++ b/tests/core/commands/test_serialization.py @@ -18,9 +18,13 @@ """Serialization tests for renku models.""" import datetime +from urllib.parse import quote, urljoin import yaml +from renku.core.management.client import LocalClient +from renku.core.models.datasets import Dataset + def test_dataset_serialization(client, dataset, data_file): """Test Dataset serialization.""" @@ -71,20 +75,32 @@ def test_dataset_deserialization(client, dataset): assert type(creator.get(attribute)) is type_ -def test_doi_migration(doi_dataset): - """Test migration of id with doi.""" - import yaml - from urllib.parse import quote, urljoin +def test_dataset_doi_metadata(dataset_metadata): + """Check dataset metadata for correct DOI.""" from renku.core.utils.doi import is_doi - from renku.core.models.datasets import Dataset - from renku.core.models.jsonld import NoDatesSafeLoader + dataset = Dataset.from_jsonld( + dataset_metadata, + client=LocalClient('.'), + ) + + if is_doi(dataset.identifier): + assert urljoin( + 'https://doi.org', dataset.identifier + ) == dataset.same_as + assert dataset._id.endswith( + 'datasets/{}'.format(quote(dataset.identifier, safe='')) + ) + + +def test_dataset_files_empty_metadata(dataset_metadata): + """Check parsing metadata of dataset files with empty filename.""" dataset = Dataset.from_jsonld( - yaml.load(doi_dataset, Loader=NoDatesSafeLoader) + dataset_metadata, + client=LocalClient('.'), ) - assert is_doi(dataset.identifier) - assert urljoin( - 'https://localhost', 'datasets/' + quote(dataset.identifier, safe='') - ) == dataset._id - assert dataset.same_as == urljoin('https://doi.org', dataset.identifier) + files = [file.filename for file in dataset.files if not file.filename] + + if files: + assert None in files diff --git a/tests/fixtures/broken-dataset-v0.5.2.yml b/tests/fixtures/broken-dataset-v0.5.2.yml new file mode 100644 index 0000000000..c98310b78d --- /dev/null +++ b/tests/fixtures/broken-dataset-v0.5.2.yml @@ -0,0 +1,1545 @@ +'@context': + _id: '@id' + _label: rdfs:label + _project: schema:isPartOf + added: schema:dateCreated + affiliation: schema:affiliation + alternate_name: schema:alternateName + created: schema:dateCreated + creator: schema:creator + date_published: schema:datePublished + description: schema:description + email: schema:email + files: schema:hasPart + identifier: schema:identifier + in_language: schema:inLanguage + keywords: schema:keywords + license: schema:license + name: schema:name + path: prov:atLocation + prov: http://www.w3.org/ns/prov# + schema: http://schema.org/ + url: schema:url + version: schema:version + wfprov: http://purl.org/wf4ever/wfprov# +'@type': +- prov:Entity +- schema:Dataset +- wfprov:Artifact +_id: https://doi.org/10.5281/zenodo.3348115 +_label: dd38afca-0e96-4034-a2e5-dc7505c0af30 +_project: + '@context': + _id: '@id' + foaf: http://xmlns.com/foaf/0.1/ + prov: http://www.w3.org/ns/prov# + '@type': + - foaf:Project + - prov:Location + _id: https://dev.renku.ch/virginiafriedrich/zurich-bikes-2 +created: '2019-07-30 09:21:18.054971' +creator: +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. Hemberger +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Patricia Schmidt +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Rory Smith +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Christian D. Ott +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Michael Boyle +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Lawrence E. Kidder +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Harald P. Pfeiffer +- '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Vijay Varma +date_published: + '@type': schema:Date + '@value': '2019-07-24' +description: "

This repository contains all publicly available numerical relativity\ + \ surrogate data for waveforms produced by the Spectral Einstein Code. The base method for building surrogate models can be\ + \ found in Field et al., PRX 4, 031006 (2014).

\n\n

Several numerical relativity\ + \ surrogate models are currently available in this catalog:

\n\n\n\n

 

\n\ + \n

 

\n\n

If you find these surrogate models useful in your own research\ + \ please cite the Field et al., PRX (2014) paper as well as the relevant paper describing\ + \ the specific numerical relativity surrogate model, if available (e.g., the Blackman\ + \ et al. 2015 paper for non-spinning binary black hole coalescences).

\n\n

Caveats:

\n\ + \n
    \n\t
  1. \n\t

    Evaluating surrogate models outside of the ranges they were\ + \ trained upon may give inaccurate results. Please use with caution when extrapolating.

    \n\ + \t
    2. \n\t
  2. \n\t

    The surrogate data available here for non-spinning binary\ + \ black holes produced in Blackman et al. 2015 contains the (2,0) mode. However,\ + \ this mode was not used in the paper. While this surrogate can predict a (2,0)\ + \ mode, current numerical relativity simulations may not yet be able to accumulate\ + \ (non-oscillatory) Christodoulou memory sufficiently. The surrogate (2,0) mode\ + \ is founded upon basis SpEC waveforms that have been hybridized with leading order\ + \ post-Newtonian waveforms. Therefore, the (2,0) mode can be included in the mode’s\ + \ output but should be used with caution. Currently, the default option to evaluate\ + \ this surrogate (using GWSurrogate) is to exclude all m=0 modes.

    \n\t
    3. \n\ +
" +files: +- '@type': + - prov:Entity + - schema:DigitalDocument + - wfprov:Artifact + _id: 5254c9ec-79b2-4db5-9b1d-f06f714deab9 + _label: UNCOMMITTED + _project: null + added: '2019-07-30 09:21:18.055151' + creator: + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. Hemberger + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Patricia Schmidt + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Rory Smith + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Christian D. Ott + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Michael Boyle + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Lawrence E. Kidder + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Harald P. Pfeiffer + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Vijay Varma + dataset: Binary black-hole surrogate waveform catalog + path: data/binary.blackhole.surrog/GWSurrogate_example.html + url: https://zenodo.org/api/files/f6c6c4f3-f63e-43fd-a16b-5629af025bac/GWSurrogate_example.html +- '@type': + - prov:Entity + - schema:DigitalDocument + - wfprov:Artifact + _id: b131abdf-674b-4318-9859-4e5c285562c8 + _label: UNCOMMITTED + _project: null + added: '2019-07-30 09:21:18.055190' + creator: + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. Hemberger + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Patricia Schmidt + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Rory Smith + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Christian D. Ott + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Michael Boyle + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Lawrence E. Kidder + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Harald P. Pfeiffer + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Vijay Varma + dataset: Binary black-hole surrogate waveform catalog + path: data/binary.blackhole.surrog/NRHybSur3dq8.h5 + url: https://zenodo.org/api/files/f6c6c4f3-f63e-43fd-a16b-5629af025bac/NRHybSur3dq8.h5 +- '@type': + - prov:Entity + - schema:DigitalDocument + - wfprov:Artifact + _id: f145dc52-4540-4e21-a4e3-512ff792f463 + _label: UNCOMMITTED + _project: null + added: '2019-07-30 09:21:18.055219' + creator: + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. Hemberger + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Patricia Schmidt + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Rory Smith + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Christian D. Ott + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Michael Boyle + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Lawrence E. Kidder + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Harald P. Pfeiffer + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Vijay Varma + dataset: Binary black-hole surrogate waveform catalog + path: data/binary.blackhole.surrog/NRHybSur3dq8.html + url: https://zenodo.org/api/files/f6c6c4f3-f63e-43fd-a16b-5629af025bac/NRHybSur3dq8.html +- '@type': + - prov:Entity + - schema:DigitalDocument + - wfprov:Artifact + _id: d60f372b-a12c-45fc-a3b4-5423fbe2d165 + _label: UNCOMMITTED + _project: null + added: '2019-07-30 09:21:18.055245' + creator: + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. Hemberger + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Patricia Schmidt + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Rory Smith + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Christian D. Ott + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Michael Boyle + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Lawrence E. Kidder + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Harald P. Pfeiffer + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Vijay Varma + dataset: Binary black-hole surrogate waveform catalog + path: data/binary.blackhole.surrog/NRSur4d2s_FDROM_grid12.h5 + url: https://zenodo.org/api/files/f6c6c4f3-f63e-43fd-a16b-5629af025bac/NRSur4d2s_FDROM_grid12.h5 +- '@type': + - prov:Entity + - schema:DigitalDocument + - wfprov:Artifact + _id: ea6f82cb-b571-4f9e-9bcd-2f6488ccca85 + _label: UNCOMMITTED + _project: null + added: '2019-07-30 09:21:18.055271' + creator: + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Scott E. Field + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Chad R. Galley + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jan S. Hesthaven + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jason Kaye + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Manuel Tiglio + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Jonathan Blackman + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: "B\xE9la Szil\xE1gyi" + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Mark A. Scheel + - '@type': schema:Person + _id: mailto:None + affiliation: null + alternate_name: null + email: null + name: Daniel A. 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