diff --git a/docs/conf.py b/docs/conf.py index 904f5c5..14618d4 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -19,7 +19,8 @@ # import os import sys -sys.path.insert(0, os.path.abspath('..')) + +sys.path.insert(0, os.path.abspath("..")) import ssm_client @@ -33,22 +34,22 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode'] +extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] -source_suffix = '.rst' +source_suffix = ".rst" # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = 'ssm-client' +project = "ssm-client" copyright = "2020, Marshall McDonnell" author = "Marshall McDonnell" @@ -71,10 +72,10 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False @@ -85,7 +86,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -#html_theme = 'alabaster' +# html_theme = 'alabaster' html_theme = "sphinx_rtd_theme" html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] @@ -98,13 +99,13 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] # -- Options for HTMLHelp output --------------------------------------- # Output file base name for HTML help builder. -htmlhelp_basename = 'ssm_clientdoc' +htmlhelp_basename = "ssm_clientdoc" # -- Options for LaTeX output ------------------------------------------ @@ -113,15 +114,12 @@ # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. # # 'preamble': '', - # Latex figure (float) alignment # # 'figure_align': 'htbp', @@ -131,9 +129,13 @@ # (source start file, target name, title, author, documentclass # [howto, manual, or own class]). latex_documents = [ - (master_doc, 'ssm_client.tex', - 'ssm-client Documentation', - 'Marshall McDonnell', 'manual'), + ( + master_doc, + "ssm_client.tex", + "ssm-client Documentation", + "Marshall McDonnell", + "manual", + ), ] @@ -141,11 +143,7 @@ # One entry per manual page. 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167fec4..da60f3f 100644 --- a/src/ssm_client/containers/collection_container.py +++ b/src/ssm_client/containers/collection_container.py @@ -3,8 +3,8 @@ class CollectionContainer: def __init__(self, **kwargs): - self.__title = kwargs.get('title', None) - self.__uri = kwargs.get('uri', None) + self.__title = kwargs.get("title", None) + self.__uri = kwargs.get("uri", None) def __eq__(self, other): """ diff --git a/src/ssm_client/containers/dataset_container.py b/src/ssm_client/containers/dataset_container.py index cd9931b..bf2b203 100644 --- a/src/ssm_client/containers/dataset_container.py +++ b/src/ssm_client/containers/dataset_container.py @@ -3,8 +3,8 @@ class DatasetContainer: def __init__(self, **kwargs): - self.__uuid = kwargs.get('uuid', None) - self.__dataset = kwargs.get('dataset', dict()) + self.__uuid = kwargs.get("uuid", None) + self.__dataset = kwargs.get("dataset", dict()) def __eq__(self, other): """ diff --git a/src/ssm_client/io/__init__.py b/src/ssm_client/io/__init__.py index fef9711..b077dfb 100644 --- a/src/ssm_client/io/__init__.py +++ b/src/ssm_client/io/__init__.py @@ -1,6 +1,3 @@ from .formats import read, write -__all__ = [ - 'read', - 'write' -] +__all__ = ["read", "write"] diff --git a/src/ssm_client/io/formats.py b/src/ssm_client/io/formats.py index 6e20488..0f7094a 100644 --- a/src/ssm_client/io/formats.py +++ b/src/ssm_client/io/formats.py @@ -1,7 +1,7 @@ from importlib import import_module -_MODULE_BASE = 'ssm_client.io.' +_MODULE_BASE = "ssm_client.io." class UnknownFileTypeError(Exception): @@ -9,10 +9,10 @@ class UnknownFileTypeError(Exception): ioformats = { - 'jcamp': 'jcamp', - 'rruff': 'rruff', - 'scidata-jsonld': 'scidata_jsonld', - 'ssm-json': 'ssm_json', + "jcamp": "jcamp", + "rruff": "rruff", + "scidata-jsonld": "scidata_jsonld", + "ssm-json": "ssm_json", } @@ -25,11 +25,11 @@ def _get_ioformat(name): def _readfunc(module, name): - return getattr(module, 'read_' + name) + return getattr(module, "read_" + name) def _writefunc(module, name): - return getattr(module, 'write_' + name) + return getattr(module, "write_" + name) def read(filename, ioformat=None, **kwargs) -> dict: diff --git a/src/ssm_client/io/jcamp.py b/src/ssm_client/io/jcamp.py index d85f59c..cf0a214 100644 --- a/src/ssm_client/io/jcamp.py +++ b/src/ssm_client/io/jcamp.py @@ -12,7 +12,7 @@ def read_jcamp(filename: str) -> dict: Args: filename (str): Filename to read from for JCAMP-DX files - Returns: + Returns: scidata_dict (dict): SciData JSON-LD dictionary """ scidata_obj = scidatalib.io.read(filename, ioformat="jcamp") diff --git a/src/ssm_client/io/scidata_jsonld.py b/src/ssm_client/io/scidata_jsonld.py index 7487a14..1ee2a40 100644 --- a/src/ssm_client/io/scidata_jsonld.py +++ b/src/ssm_client/io/scidata_jsonld.py @@ -11,7 +11,7 @@ def read_scidata_jsonld(filename): Return: scidata_dict (dict): SciData JSON-LD dictionary """ - with open(filename, 'r') as fileobj: + with open(filename, "r") as fileobj: scidata_dict = json.load(fileobj) return scidata_dict @@ -25,5 +25,5 @@ def write_scidata_jsonld(filename, scidata_dict): filename (str): Filename for SciData JSON-LD scidata_dict (dict): SciData JSON-LD dictionary to write out """ - with open(filename, 'w') as fileobj: + with open(filename, "w") as fileobj: json.dump(scidata_dict, fileobj, indent=2) diff --git a/src/ssm_client/io/ssm_json.py b/src/ssm_client/io/ssm_json.py index 9bb65ad..2929291 100644 --- a/src/ssm_client/io/ssm_json.py +++ b/src/ssm_client/io/ssm_json.py @@ -1,3 +1,5 @@ +import json + from scidatalib.scidata import SciData @@ -10,7 +12,7 @@ def read_ssm_json(filename: str) -> dict: Return: scidata_dict (dict): SciData JSON-LD dictionary """ - with open(filename, 'r') as fileobj: + with open(filename, "r") as fileobj: ssm_json_dict = json.load(fileobj) scidata_obj = _ssm_json_to_scidata(ssm_json_dict) return scidata_obj.output @@ -64,7 +66,7 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict: # property properties = sd.get("property", None) if properties: - properties = ','.join(properties) + properties = ",".join(properties) output["scidata"]["property"] = properties # methodology @@ -115,7 +117,6 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict: # dataset dataset = sd.get("dataset", None) if dataset: - dataseries_list = dataset.get("dataseries", list()) if dataseries_list: output_dataseries_list = list() @@ -165,10 +166,12 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict: ] axis = parameter.get("axis", f"axis-{i}") - output_dataseries_list.append({ - f'{axis}': {"parameter": output_parameter}, - "hasAxisType": axis - }) + output_dataseries_list.append( + { + f"{axis}": {"parameter": output_parameter}, + "hasAxisType": axis, + } + ) output_dataseries = output_dataseries_list output["scidata"]["dataseries"] = output_dataseries @@ -188,7 +191,7 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData: """ # Construct UID for SciData document from title title = ssm_json.get("title", "ssm:dataset") - uid = ssm_json.get("uid", f'scidata:jsonld:{title}') + uid = ssm_json.get("uid", f"scidata:jsonld:{title}") # Setup SciData object sd = SciData(uid) @@ -204,7 +207,7 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData: sd.sources(sources) properties = ssm_json.get("scidata").get("property", "").split(",") - sd.meta['@graph']['scidata']['property'] = properties + sd.meta["@graph"]["scidata"]["property"] = properties description = ssm_json.get("description", "") sd.description(description) @@ -294,4 +297,3 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData: sd.dataseries(output_dataseries_list) return sd - diff --git a/src/ssm_client/services/collection_service.py b/src/ssm_client/services/collection_service.py index 7fe4e08..eb2f1b2 100644 --- a/src/ssm_client/services/collection_service.py +++ b/src/ssm_client/services/collection_service.py @@ -25,9 +25,9 @@ def _endpoint(self, collection: str = "") -> str: Returns: endpoint (str): Collection endpoint to use """ - endpoint = f'{self.uri}/{_COLLECTION_ENDPOINT}' + endpoint = f"{self.uri}/{_COLLECTION_ENDPOINT}" if collection: - endpoint += f'/{collection}' + endpoint += f"/{collection}" return endpoint @property @@ -35,7 +35,7 @@ def uri(self): """ URI property for CollectionContainer """ - return f'{self.hostname}' + return f"{self.hostname}" def create(self, title: str) -> CollectionContainer: """ @@ -50,7 +50,7 @@ def create(self, title: str) -> CollectionContainer: response = requests.post(self._endpoint(), json=json) response.raise_for_status() return CollectionContainer(**response.json()) - + def get_collections(self) -> list[CollectionContainer]: response = requests.get(self._endpoint()) response.raise_for_status() diff --git a/src/ssm_client/services/dataset_service.py b/src/ssm_client/services/dataset_service.py index fd55211..4f3b401 100644 --- a/src/ssm_client/services/dataset_service.py +++ b/src/ssm_client/services/dataset_service.py @@ -21,10 +21,8 @@ class UnsupportedDatasetFormatException(Exception): class DatasetService: def __init__( - self, - hostname="http://localhost", - collection=None, - collection_title=None): + self, hostname="http://localhost", collection=None, collection_title=None + ): """ Initialize a DatasetService object @@ -46,8 +44,7 @@ def __init__( "Trying using one method, either the collection OR the title" ) msg = msg.format( - collection_title=collection.title, - title=collection_title + collection_title=collection.title, title=collection_title ) raise MismatchedCollectionException(msg) @@ -66,18 +63,18 @@ def _endpoint(self, dataset=None): endpoint (str): Datasets endpoint to use """ endpoint = [] - endpoint.append(f'{self.uri}/{_COLLECTION_ENDPOINT}') - endpoint.append(f'{self.collection_title}/{_DATASETS_ENDPOINT}') + endpoint.append(f"{self.uri}/{_COLLECTION_ENDPOINT}") + endpoint.append(f"{self.collection_title}/{_DATASETS_ENDPOINT}") if dataset: - endpoint.append(f'{dataset}') - return '/'.join(endpoint) + endpoint.append(f"{dataset}") + return "/".join(endpoint) @property def uri(self): """ URI property for SSM Catalog API """ - return f'{self.hostname}' + return f"{self.hostname}" def create(self, dataset): """ @@ -122,15 +119,15 @@ def get_by_uuid(self, uuid, format: str = _FORMAT_JSONLD): dataset (DatasetContainer): DatasetContainer object with given UUID """ if format not in _DATASET_FORMAT_CHOICES: - msg = ( - "format: {format} not supported\n" - "Supported dataset formats are {choices}" - ) - msg = msg.format( - format=format, - choices=_DATASET_FORMAT_CHOICES, - ) - raise UnsupportedDatasetFormatException(msg) + msg = ( + "format: {format} not supported\n" + "Supported dataset formats are {choices}" + ) + msg = msg.format( + format=format, + choices=_DATASET_FORMAT_CHOICES, + ) + raise UnsupportedDatasetFormatException(msg) params = {"format": format} response = requests.get(self._endpoint(uuid), params=params) response.raise_for_status() diff --git a/tests/__init__.py b/tests/__init__.py index c69554f..e736f8a 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,5 +1,6 @@ """Testing for SSM Python Client.""" + import pathlib TEST_DIR = pathlib.Path(__file__).parent.absolute() -TEST_DATA_DIR = pathlib.Path(TEST_DIR, 'data') +TEST_DATA_DIR = pathlib.Path(TEST_DIR, "data") diff --git a/tests/conftest.py b/tests/conftest.py index afda610..073dbbe 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,6 +5,7 @@ from . import TEST_DATA_DIR + @pytest.fixture def hnmr_ethanol_jcamp(): """ @@ -141,4 +142,4 @@ def metazeunerite_ssm_json(): Metazeunerite SSM JSON file from CURIES """ p = pathlib.Path(TEST_DATA_DIR, "ssm_json", "metazeunerite.json") - return json.loads(p.read_text()) \ No newline at end of file + return json.loads(p.read_text()) diff --git a/tests/e2e/conftest.py b/tests/e2e/conftest.py index 6f84b9b..82cd610 100644 --- a/tests/e2e/conftest.py +++ b/tests/e2e/conftest.py @@ -6,9 +6,7 @@ def pytest_addoption(parser): parser.addoption( - "--base-url", - default="http://localhost", - help="Base url for Calatog API" + "--base-url", default="http://localhost", help="Base url for Calatog API" ) diff --git a/tests/e2e/services/test_collection_service.py b/tests/e2e/services/test_collection_service.py index 29d85a3..0ffc2cd 100644 --- a/tests/e2e/services/test_collection_service.py +++ b/tests/e2e/services/test_collection_service.py @@ -5,14 +5,10 @@ import pytest import requests -from ssm_client.services import CollectionService - - - def test_create(collection_service): """Test creating collection""" - title = 64*"X" + title = 64 * "X" collection = collection_service.create(title) assert len(collection.title) == 64 @@ -31,8 +27,6 @@ def test_read(collection_service): def test_delete(collection_service): # noqa: F811 """Test deleting collection""" title = "foo" - uri = "bar" - json = {'title': title, 'uri': uri} collection = collection_service.create(title) grabbed_collection = collection_service.get_by_title(collection.title) diff --git a/tests/e2e/test_ssm_rester.py b/tests/e2e/test_ssm_rester.py index 82d9485..b6befd9 100644 --- a/tests/e2e/test_ssm_rester.py +++ b/tests/e2e/test_ssm_rester.py @@ -1,13 +1,14 @@ #!/usr/bin/env python """Tests for `ssm_client` package.""" + import json -import tempfile import requests import pytest import ssm_client + def test_collection_create(ssm_rester): """Test creating collection w/ client""" title = 64 * "X" @@ -48,8 +49,7 @@ def test_initialize_dataset_for_collection(ssm_rester): collection_title = 64 * "X" uri = "http://localhost/{}".format(collection_title) collection = ssm_client.containers.CollectionContainer( - title=collection_title, - uri=uri + title=collection_title, uri=uri ) ssm_rester.initialize_dataset_for_collection(collection) assert ssm_rester.dataset.hostname == ssm_rester.hostname @@ -61,18 +61,26 @@ def test_metazeunerite_dataset_jsonld_create(ssm_rester, metazeunerite_jsonld): ssm_rester.initialize_dataset_for_collection(collection) dataset = ssm_rester.dataset.create(metazeunerite_jsonld) assert dataset.uuid is not None - assert dataset.dataset.get("@graph")[0].get("description") == metazeunerite_jsonld.get("@graph").get("description") + assert dataset.dataset.get("@graph")[0].get( + "description" + ) == metazeunerite_jsonld.get("@graph").get("description") -def test_metazeunerite_dataset_ssm_json_create(ssm_rester, metazeunerite_jsonld, metazeunerite_ssm_json): +def test_metazeunerite_dataset_ssm_json_create( + ssm_rester, metazeunerite_jsonld, metazeunerite_ssm_json +): collection = ssm_rester.collection.create("foo-collection-ssm-json") ssm_rester.initialize_dataset_for_collection(collection) dataset = ssm_rester.dataset.create(metazeunerite_jsonld) dataset_ssm_json = ssm_rester.dataset.get_by_uuid(dataset.uuid, format="json") print(dataset.dataset.keys()) - assert dataset.dataset.get("@graph")[0].get("title") == dataset_ssm_json.dataset.get("title") - assert dataset.dataset.get("@graph")[0].get("description") == metazeunerite_ssm_json.get("description") - + assert dataset.dataset.get("@graph")[0].get( + "title" + ) == dataset_ssm_json.dataset.get("title") + assert dataset.dataset.get("@graph")[0].get( + "description" + ) == metazeunerite_ssm_json.get("description") + def test_metazeunerite_dataset_ssm_json_update(ssm_rester, metazeunerite_jsonld): # Create collection and upload metazeunerite scidata JSON-LD @@ -85,7 +93,13 @@ def test_metazeunerite_dataset_ssm_json_update(ssm_rester, metazeunerite_jsonld) # Modify the 51st data entry for y-axis dataseries = dataset_ssm_json.dataset.get("scidata").get("dataseries") - y = dataseries[1].get("y-axis").get("parameter").get("numericValueArray")[0].get("numberArray") + y = ( + dataseries[1] + .get("y-axis") + .get("parameter") + .get("numericValueArray")[0] + .get("numberArray") + ) y[50] -= 100.0 # Write out the modified SSM JSON metazeunerite data to file @@ -96,6 +110,8 @@ def test_metazeunerite_dataset_ssm_json_update(ssm_rester, metazeunerite_jsonld) # Upload the modified metazeunerite SSM JSON file to converter for SciData JSON-LD format output with open(ssm_json_filename, "r") as f: file_args = {"upload_file": (ssm_json_filename, f)} - response = requests.post("http://localhost:8000/convert/jsonld", files=file_args) + response = requests.post( + "http://localhost:8000/convert/jsonld", files=file_args + ) print(response.content) assert response.status_code == 200 diff --git a/tests/unit/containers/test_collection_container.py b/tests/unit/containers/test_collection_container.py index 507c83c..8a95f5b 100644 --- a/tests/unit/containers/test_collection_container.py +++ b/tests/unit/containers/test_collection_container.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """Tests for CollectionContainer.""" + import json from ssm_client.containers import CollectionContainer @@ -16,19 +17,21 @@ def test_construction_default(): def test_construction_just_title(): """Test creating default collection""" kwargs = { - "title": "5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988"} # noqa: E501 + "title": "5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988" + } # noqa: E501 collection = CollectionContainer(**kwargs) - assert collection.title == kwargs['title'] + assert collection.title == kwargs["title"] assert collection.uri is None def test_construction_just_uri(): """Test creating default collection""" kwargs = { - "uri": "http://fuseki:3030/5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988"} # noqa: E501 + "uri": "http://fuseki:3030/5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988" + } # noqa: E501 collection = CollectionContainer(**kwargs) assert collection.title is None - assert collection.uri == kwargs['uri'] + assert collection.uri == kwargs["uri"] def test_collection_str(): diff --git a/tests/unit/containers/test_dataset_container.py b/tests/unit/containers/test_dataset_container.py index b9b77fd..1dc0896 100644 --- a/tests/unit/containers/test_dataset_container.py +++ b/tests/unit/containers/test_dataset_container.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """Tests for DatasetContainer.""" + import json import pytest @@ -14,7 +15,7 @@ def dataset(): "@id": "http://dbpedia.org/resource/John_Lennon", "name": "John Lennon", "born": "1940-10-09", - "spouse": "http://dbpedia.org/resource/Cynthia_Lennon" + "spouse": "http://dbpedia.org/resource/Cynthia_Lennon", } return dataset @@ -29,9 +30,10 @@ def test_construction_default(): def test_construction_just_uuid(): """Test creating default dataset""" kwargs = { - "uuid": "5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988"} # noqa: E501 + "uuid": "5D0DC5589FA2C1F5DE2AB19B47F3923E65B261FABD8ED0F9A9B57CBBE3799988" + } # noqa: E501 dataset = DatasetContainer(**kwargs) - assert dataset.uuid == kwargs['uuid'] + assert dataset.uuid == kwargs["uuid"] assert dataset.dataset == dict() @@ -40,7 +42,7 @@ def test_construction_just_uri(dataset): kwargs = {"dataset": dataset} dataset = DatasetContainer(**kwargs) assert dataset.uuid is None - assert dataset.dataset == kwargs['dataset'] + assert dataset.dataset == kwargs["dataset"] def test_dataset_str(dataset): @@ -52,7 +54,9 @@ def test_dataset_str(dataset): uuid = "foo" dataset_container = DatasetContainer(uuid=uuid, dataset=dataset) pretty_dataset = json.dumps(dataset_container.dataset, sort_keys=True, indent=4) - assert target.format(uuid=uuid, dataset=pretty_dataset) == dataset_container.__str__() + assert ( + target.format(uuid=uuid, dataset=pretty_dataset) == dataset_container.__str__() + ) def test_dataset_repr(): diff --git a/tests/unit/io/test_formats.py b/tests/unit/io/test_formats.py index 0f9920f..6ac7df0 100644 --- a/tests/unit/io/test_formats.py +++ b/tests/unit/io/test_formats.py @@ -1,18 +1,19 @@ """Tests for io.formats""" + import pytest from ssm_client import io def test_get_ioformat_scidata_jsonld(): - fmt = io.formats._get_ioformat('scidata-jsonld') - assert fmt.__name__ == 'ssm_client.io.scidata_jsonld' + fmt = io.formats._get_ioformat("scidata-jsonld") + assert fmt.__name__ == "ssm_client.io.scidata_jsonld" def test_get_ioformat_jcamp(): - fmt = io.formats._get_ioformat('jcamp') - assert fmt.__name__ == 'ssm_client.io.jcamp' + fmt = io.formats._get_ioformat("jcamp") + assert fmt.__name__ == "ssm_client.io.jcamp" def test_get_ioformat_raise_exception(): with pytest.raises(io.formats.UnknownFileTypeError): - io.formats._get_ioformat('cat') + io.formats._get_ioformat("cat") diff --git a/tests/unit/io/test_jcamp.py b/tests/unit/io/test_jcamp.py index 1247024..61ed4fa 100644 --- a/tests/unit/io/test_jcamp.py +++ b/tests/unit/io/test_jcamp.py @@ -2,12 +2,10 @@ from typing import List from ssm_client.io import jcamp -from tests import TEST_DATA_DIR def _remove_elements_from_list( - old_list: List[str], - skip_elements: List[str] + old_list: List[str], skip_elements: List[str] ) -> List[str]: """ Utility function for removing elements from a list @@ -19,7 +17,7 @@ def _remove_elements_from_list( new_list = [] for element in old_list: keep = True - element_list = [x.strip() for x in element.split(',')] + element_list = [x.strip() for x in element.split(",")] for key in skip_elements: for x in element_list: if key in x: @@ -33,17 +31,19 @@ def _remove_elements_from_list( # Tests + @pytest.mark.skip("Broken test due to SciDataLib not handling jcamp 'children'") def test_read_hnmr(hnmr_ethanol_jcamp): scidata_dict = jcamp.read_jcamp(hnmr_ethanol_jcamp.resolve()) + assert scidata_dict == 0 def test_read_infrared(infrared_ethanol_jcamp): scidata_dict = jcamp.read_jcamp(infrared_ethanol_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == 'ETHANOL' - assert graph['publisher'] == 'DOW CHEMICAL COMPANY' + graph = scidata_dict.get("@graph") + assert graph["title"] == "ETHANOL" + assert graph["publisher"] == "DOW CHEMICAL COMPANY" description = graph.get("description") for jcamp_keyword in ["JCAMP-DX", "COBLENTZ"]: assert jcamp_keyword in description @@ -83,22 +83,22 @@ def test_read_infrared(infrared_ethanol_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 3570 + assert len(parameter_0.get("dataarray")) == 3570 def test_read_infrared_compressed(infrared_ethanol_compressed_jcamp): scidata_dict = jcamp.read_jcamp(infrared_ethanol_compressed_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == '$$ Begin of the data block' + graph = scidata_dict.get("@graph") + assert graph["title"] == "$$ Begin of the data block" description = graph.get("description") assert "JCAMP-DX" in description methodology = scidata_dict["@graph"]["scidata"]["methodology"] - assert len(methodology["aspects"]) == 0 + assert len(methodology["aspects"]) == 0 system = scidata_dict["@graph"]["scidata"]["system"] - assert len(system["facets"]) == 0 + assert len(system["facets"]) == 0 dataset = scidata_dict.get("@graph").get("scidata").get("dataset") assert len(dataset) == 5 @@ -112,31 +112,32 @@ def test_read_infrared_compressed(infrared_ethanol_compressed_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 1970 + assert len(parameter_0.get("dataarray")) == 1970 @pytest.mark.skip("Broken test due to SciDataLib not handling jcamp 'children'") def test_read_infrared_compound(infrared_compound_jcamp): scidata_dict = jcamp.read_jcamp(infrared_compound_jcamp.resolve()) + assert scidata_dict == 0 def test_read_infrared_multiline(infrared_multiline_jcamp): scidata_dict = jcamp.read_jcamp(infrared_multiline_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == 'multiline datasets test' - assert graph['publisher'] == 'Origin test' + graph = scidata_dict.get("@graph") + assert graph["title"] == "multiline datasets test" + assert graph["publisher"] == "Origin test" description = graph.get("description") assert "JCAMP-DX" in description methodology = scidata_dict["@graph"]["scidata"]["methodology"] - assert len(methodology["aspects"]) == 2 + assert len(methodology["aspects"]) == 2 aspects = methodology["aspects"] - assert len(aspects[0]["settings"]) == 1 + assert len(aspects[0]["settings"]) == 1 assert aspects[0]["settings"][0]["value"]["number"] == 32.0 system = scidata_dict["@graph"]["scidata"]["system"] - assert len(system["facets"]) == 0 + assert len(system["facets"]) == 0 dataset = scidata_dict.get("@graph").get("scidata").get("dataset") assert len(dataset) == 5 @@ -150,25 +151,25 @@ def test_read_infrared_multiline(infrared_multiline_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 1919 + assert len(parameter_0.get("dataarray")) == 1919 def test_read_mass(mass_ethanol_jcamp): scidata_dict = jcamp.read_jcamp(mass_ethanol_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == 'ethanol' - assert graph['publisher'] == 'Widener University' + graph = scidata_dict.get("@graph") + assert graph["title"] == "ethanol" + assert graph["publisher"] == "Widener University" description = graph.get("description") assert "JCAMP-DX" in description methodology = scidata_dict["@graph"]["scidata"]["methodology"] - assert len(methodology["aspects"]) == 1 + assert len(methodology["aspects"]) == 1 aspects = methodology["aspects"] assert aspects[0]["instrument"] == "NIST Database" system = scidata_dict["@graph"]["scidata"]["system"] - assert len(system["facets"]) == 0 + assert len(system["facets"]) == 0 dataset = scidata_dict.get("@graph").get("scidata").get("dataset") assert len(dataset) == 5 @@ -182,23 +183,23 @@ def test_read_mass(mass_ethanol_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 12 + assert len(parameter_0.get("dataarray")) == 12 def test_read_neutron(neutron_emodine_jcamp): scidata_dict = jcamp.read_jcamp(neutron_emodine_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == "Emodine, C15H10O4" - assert graph['publisher'] == 'TFXA, ISIS' + graph = scidata_dict.get("@graph") + assert graph["title"] == "Emodine, C15H10O4" + assert graph["publisher"] == "TFXA, ISIS" description = graph.get("description") assert "JCAMP-DX" in description methodology = scidata_dict["@graph"]["scidata"]["methodology"] - assert len(methodology["aspects"]) == 1 + assert len(methodology["aspects"]) == 1 system = scidata_dict["@graph"]["scidata"]["system"] - assert len(system["facets"]) == 0 + assert len(system["facets"]) == 0 dataset = scidata_dict.get("@graph").get("scidata").get("dataset") assert len(dataset) == 5 @@ -212,20 +213,20 @@ def test_read_neutron(neutron_emodine_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 1992 + assert len(parameter_0.get("dataarray")) == 1992 def test_read_uvvis(uvvis_toluene_jcamp): scidata_dict = jcamp.read_jcamp(uvvis_toluene_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == "Toluene" - assert graph['publisher'] == 'INSTITUTE OF ENERGY PROBLEMS OF CHEMICAL PHYSICS, RAS' + graph = scidata_dict.get("@graph") + assert graph["title"] == "Toluene" + assert graph["publisher"] == "INSTITUTE OF ENERGY PROBLEMS OF CHEMICAL PHYSICS, RAS" description = graph.get("description") assert "JCAMP-DX" in description methodology = scidata_dict["@graph"]["scidata"]["methodology"] - assert len(methodology["aspects"]) == 1 + assert len(methodology["aspects"]) == 1 system = scidata_dict["@graph"]["scidata"]["system"] assert len(system["facets"]) == 1 @@ -242,15 +243,15 @@ def test_read_uvvis(uvvis_toluene_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 335 + assert len(parameter_0.get("dataarray")) == 335 def test_read_raman(raman_tannic_acid_jcamp): scidata_dict = jcamp.read_jcamp(raman_tannic_acid_jcamp.resolve()) - graph = scidata_dict.get('@graph') - assert graph['title'] == 'tannic acid' - assert graph['publisher'] == 'Ocean Optics R2000' + graph = scidata_dict.get("@graph") + assert graph["title"] == "tannic acid" + assert graph["publisher"] == "Ocean Optics R2000" methodology = scidata_dict["@graph"]["scidata"]["methodology"] assert len(methodology["aspects"]) == 1 @@ -272,7 +273,7 @@ def test_read_raman(raman_tannic_acid_jcamp): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 1949 + assert len(parameter_0.get("dataarray")) == 1949 def test_write_raman(tmp_path, raman_tannic_acid_jcamp): @@ -293,6 +294,6 @@ def test_write_raman(tmp_path, raman_tannic_acid_jcamp): target = _remove_elements_from_list(target, skip_keys) for result_element, target_element in zip(result, target): - result_list = [x.strip() for x in result_element.split(',')] - target_list = [x.strip() for x in target_element.split(',')] + result_list = [x.strip() for x in result_element.split(",")] + target_list = [x.strip() for x in target_element.split(",")] assert result_list == target_list diff --git a/tests/unit/io/test_rruff.py b/tests/unit/io/test_rruff.py index 6b39ec9..ac3a2af 100644 --- a/tests/unit/io/test_rruff.py +++ b/tests/unit/io/test_rruff.py @@ -1,13 +1,12 @@ from ssm_client.io import rruff -from tests import TEST_DATA_DIR def test_read_rruff(raman_soddyite_rruff): scidata_dict = rruff.read_rruff(raman_soddyite_rruff.absolute()) - graph = scidata_dict.get('@graph') - assert graph['title'] == 'Soddyite' - assert graph['publisher'] == 'RRUFF' + graph = scidata_dict.get("@graph") + assert graph["title"] == "Soddyite" + assert graph["publisher"] == "RRUFF" assert graph["uid"] == "rruff:R060361" assert "sources" in graph sources = graph["sources"] @@ -32,16 +31,16 @@ def test_read_rruff(raman_soddyite_rruff): methodology = graph.get("scidata").get("methodology") assert "aspects" in methodology aspects = methodology.get("aspects") - assert len(aspects) == 1 + assert len(aspects) == 1 assert "settings" in aspects[0] settings = aspects[0].get("settings") - assert len(settings) == 1 + assert len(settings) == 1 wavelength = settings[0].get("value").get("number") assert wavelength == 780 system = scidata_dict.get("@graph").get("scidata").get("system") assert "facets" in system - assert len(system.get("facets")) == 1 + assert len(system.get("facets")) == 1 material_facet = system["facets"][0] assert material_facet["@id"] == "material/1/" assert len(material_facet["@type"]) == 12 @@ -60,7 +59,7 @@ def test_read_rruff(raman_soddyite_rruff): parameter_0 = dataseries_0.get("parameter")[0] assert len(parameter_0) == 9 assert "dataarray" in parameter_0 - assert len(parameter_0.get("dataarray")) == 2444 + assert len(parameter_0.get("dataarray")) == 2444 def test_write_rruff(tmp_path, raman_soddyite_rruff): @@ -73,6 +72,6 @@ def test_write_rruff(tmp_path, raman_soddyite_rruff): target = raman_soddyite_rruff.read_text().splitlines() for result_element, target_element in zip(result, target): - result_list = [x.strip() for x in result_element.split(',')] - target_list = [x.strip() for x in target_element.split(',')] + result_list = [x.strip() for x in result_element.split(",")] + target_list = [x.strip() for x in target_element.split(",")] assert result_list == target_list diff --git a/tests/unit/io/test_scidata_jsonld.py b/tests/unit/io/test_scidata_jsonld.py index f577a89..ac81060 100644 --- a/tests/unit/io/test_scidata_jsonld.py +++ b/tests/unit/io/test_scidata_jsonld.py @@ -1,4 +1,5 @@ """Tests for io.scidata""" + import pathlib import pytest @@ -7,22 +8,22 @@ @pytest.fixture def outfile(): - outfile = pathlib.Path('output.jsonld') + outfile = pathlib.Path("output.jsonld") yield outfile outfile.unlink() def test_write(scidata_nmr_jsonld, outfile): - io.write(outfile.name, scidata_nmr_jsonld, ioformat='scidata-jsonld') + io.write(outfile.name, scidata_nmr_jsonld, ioformat="scidata-jsonld") assert outfile.is_file() def test_read(scidata_nmr_jsonld, outfile): - io.write(outfile.name, scidata_nmr_jsonld, ioformat='scidata-jsonld') - output = io.read(outfile.name, ioformat='scidata-jsonld') - assert '@context' in output - assert '@id' in output - assert 'version' in output - assert 'generatedAt' in output - assert output.get('version') == 2 - assert output.get('@id') == "https://stuchalk.github.io/scidata/examples/nmr/" # noqa: E501 + io.write(outfile.name, scidata_nmr_jsonld, ioformat="scidata-jsonld") + output = io.read(outfile.name, ioformat="scidata-jsonld") + assert "@context" in output + assert "@id" in output + assert "version" in output + assert "generatedAt" in output + assert output.get("version") == 2 + assert output.get("@id") == "https://stuchalk.github.io/scidata/examples/nmr/" # noqa: E501 diff --git a/tests/unit/services/test_collection_service.py b/tests/unit/services/test_collection_service.py index 9a4b2dd..cefa682 100644 --- a/tests/unit/services/test_collection_service.py +++ b/tests/unit/services/test_collection_service.py @@ -16,9 +16,9 @@ def collection_service(): def test_create(collection_service, requests_mock): # noqa: F811 """Test creating collection""" - title = 64*"X" + title = 64 * "X" uri = "http://localhost/{}".format(title) - json = {'title': title, 'uri': uri} + json = {"title": title, "uri": uri} requests_mock.post(collection_service._endpoint(), json=json) collection = collection_service.create(title) @@ -30,7 +30,7 @@ def test_read(collection_service, requests_mock): # noqa: F811 """Test read collection""" title = "foo" uri = "bar" - json = {'title': title, 'uri': uri} + json = {"title": title, "uri": uri} requests_mock.post(collection_service._endpoint(), json=json) collection = collection_service.create(title) @@ -44,7 +44,7 @@ def test_delete(collection_service, requests_mock): # noqa: F811 """Test deleting collection""" title = "foo" uri = "bar" - json = {'title': title, 'uri': uri} + json = {"title": title, "uri": uri} requests_mock.post(collection_service._endpoint(), json=json) collection = collection_service.create(title) diff --git a/tests/unit/services/test_dataset_service.py b/tests/unit/services/test_dataset_service.py index e5b3237..32eaf38 100644 --- a/tests/unit/services/test_dataset_service.py +++ b/tests/unit/services/test_dataset_service.py @@ -4,12 +4,10 @@ import pytest import requests -import requests_mock # noqa: F401 from ssm_client.containers import CollectionContainer from ssm_client.services import DatasetService -from ssm_client.services.dataset_service import \ - MismatchedCollectionException +from ssm_client.services.dataset_service import MismatchedCollectionException @pytest.fixture @@ -19,7 +17,7 @@ def dataset_input(): "@id": "http://dbpedia.org/resource/John_Lennon", "name": "John Lennon", "born": "1940-10-09", - "spouse": "http://dbpedia.org/resource/Cynthia_Lennon" + "spouse": "http://dbpedia.org/resource/Cynthia_Lennon", } return dataset_input @@ -30,21 +28,16 @@ def dataset_output(): "@context": { "birthDate": { "@id": "http://schema.org/birthDate", - "@type": "http://www.w3.org/2001/XMLSchema#date" + "@type": "http://www.w3.org/2001/XMLSchema#date", }, - "name": { - "@id": "http://xmlns.com/foaf/0.1/name" - }, - "spouse": { - "@id": "http://schema.org/spouse", - "@type": "@id" - }, - "xsd": "http://www.w3.org/2001/XMLSchema#" + "name": {"@id": "http://xmlns.com/foaf/0.1/name"}, + "spouse": {"@id": "http://schema.org/spouse", "@type": "@id"}, + "xsd": "http://www.w3.org/2001/XMLSchema#", }, "@id": "http://dbpedia.org/resource/John_Lennon", "birthDate": "1940-10-09", "name": "John Lennon", - "spouse": "http://dbpedia.org/resource/Cynthia_Lennon" + "spouse": "http://dbpedia.org/resource/Cynthia_Lennon", } return dataset_output @@ -77,10 +70,12 @@ def test_construction(collection): assert dataset.collection_title == collection.title with pytest.raises(MismatchedCollectionException): - DatasetService(collection=collection, collection_title=64*"Z") + DatasetService(collection=collection, collection_title=64 * "Z") -def test_create(dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock): # noqa: F811, E501 +def test_create( + dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock +): # noqa: F811, E501 """Test creating dataset""" json = {"uuid": dataset_uuid, "dataset": dataset_output} @@ -90,7 +85,9 @@ def test_create(dataset_input, dataset_output, dataset_uuid, dataset_service, re assert dataset.dataset == dataset_output -def test_read(dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock): # noqa: F811, E501 +def test_read( + dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock +): # noqa: F811, E501 """Test read dataset""" json = {"uuid": dataset_uuid, "dataset": dataset_output} @@ -104,7 +101,9 @@ def test_read(dataset_input, dataset_output, dataset_uuid, dataset_service, requ assert dataset == grabbed_dataset -def test_replace_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock): # noqa: F811, E501 +def test_replace_dataset_for_uuid( + dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock +): # noqa: F811, E501 """Test replacing a dataset""" json = {"uuid": dataset_uuid, "dataset": dataset_output} @@ -121,13 +120,11 @@ def test_replace_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, d new_dataset_output = { "@context": { - "name": { - "@id": "http://xmlns.com/foaf/0.1/name" - }, - "xsd": "http://www.w3.org/2001/XMLSchema#" + "name": {"@id": "http://xmlns.com/foaf/0.1/name"}, + "xsd": "http://www.w3.org/2001/XMLSchema#", }, "@id": "http://dbpedia.org/resource/Ringo_Starr", - "name": "Ringo Starr" + "name": "Ringo Starr", } json["dataset"] = new_dataset_output @@ -135,7 +132,8 @@ def test_replace_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, d # Replace the dataset requests_mock.put(dataset_service._endpoint(dataset_uuid), json=json) new_dataset = dataset_service.replace_dataset_for_uuid( - dataset.uuid, new_dataset_input) + dataset.uuid, new_dataset_input + ) # Ensure the dataset we updated and the one we get back match requests_mock.get(dataset_service._endpoint(dataset_uuid), json=json) @@ -144,7 +142,9 @@ def test_replace_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, d assert dataset != grabbed_dataset -def test_update_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock): # noqa: F811, E501 +def test_update_dataset_for_uuid( + dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock +): # noqa: F811, E501 """Test updating a dataset""" json = {"uuid": dataset_uuid, "dataset": dataset_output} @@ -161,7 +161,8 @@ def test_update_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, da # Replace the dataset requests_mock.patch(dataset_service._endpoint(dataset_uuid), json=json) new_dataset = dataset_service.update_dataset_for_uuid( - dataset.uuid, dataset_update_input) + dataset.uuid, dataset_update_input + ) # Ensure the dataset we updated and the one we get back match requests_mock.get(dataset_service._endpoint(dataset_uuid), json=json) @@ -170,7 +171,9 @@ def test_update_dataset_for_uuid(dataset_input, dataset_output, dataset_uuid, da assert dataset != grabbed_dataset -def test_delete(dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock): # noqa: F811, E501 +def test_delete( + dataset_input, dataset_output, dataset_uuid, dataset_service, requests_mock +): # noqa: F811, E501 """Test deleting dataset""" json = {"uuid": dataset_uuid, "dataset": dataset_output} diff --git a/tests/unit/test_ssm_rester.py b/tests/unit/test_ssm_rester.py index a82f1e8..31ca22f 100644 --- a/tests/unit/test_ssm_rester.py +++ b/tests/unit/test_ssm_rester.py @@ -18,7 +18,7 @@ def ssm_rester(): def test_collection_create(ssm_rester, requests_mock): # noqa: F811 """Test creating collection w/ client""" title = 64 * "X" - json = {'title': title.lower()} + json = {"title": title.lower()} requests_mock.post(ssm_rester.collection._endpoint(), json=json) print(ssm_rester.collection) @@ -31,7 +31,7 @@ def test_collection_read(ssm_rester, requests_mock): # noqa: F811 """Test read collection w/ client""" title = "foo" uri = "bar" - json = {'title': title, 'uri': uri} + json = {"title": title, "uri": uri} requests_mock.post(ssm_rester.collection._endpoint(), json=json) collection = ssm_rester.collection.create(title) @@ -45,7 +45,7 @@ def test_collection_delete(ssm_rester, requests_mock): # noqa: F811 """Test deleting collection w/ client""" title = "foo" uri = "bar" - json = {'title': title, 'uri': uri} + json = {"title": title, "uri": uri} requests_mock.post(ssm_rester.collection._endpoint(), json=json) collection = ssm_rester.collection.create(title) diff --git a/tutorials/ssm_rester.ipynb b/tutorials/ssm_rester.ipynb index 943931d..500e271 100644 --- a/tutorials/ssm_rester.ipynb +++ b/tutorials/ssm_rester.ipynb @@ -9,7 +9,8 @@ "source": [ "import os\n", "import sys\n", - "sys.path.insert(0, os.path.abspath('../'))" + "\n", + "sys.path.insert(0, os.path.abspath(\"../\"))" ] }, { @@ -36,7 +37,6 @@ }, "outputs": [], "source": [ - "import json\n", "from ssm_client import SSMRester\n", "\n", "rester = SSMRester(hostname=\"http://ssm-dev.ornl.gov\", port=8080)\n", @@ -64,7 +64,7 @@ "metadata": {}, "outputs": [], "source": [ - "rester.dataset.delete_by_uuid(dataset.uuid)\n" + "rester.dataset.delete_by_uuid(dataset.uuid)" ] } ],